text:
Isolation and Structure Elucidation of Pentahydroxyscirpene, a Trichothecene Fusarium Mycotoxin
Pentahydroxyscirpene, a novel trichothecene-type compound, was isolated from Fusarium-inoculated rice. The structure of pentahydroxyscirpene was elucidated by 1D and 2D NMR spectroscopy and X-ray single-crystal diffraction. The conformation in solution was determined by NOESY experiments supported by quantum chemical calculations. In vitro toxicity tests showed that pentahydroxyscirpene inhibits protein synthesis as do other trichothecenes. PMID:24367932
[Isolation and structure elucidation of three dihydrophenanthrenes from Ephemerantha lonchophylla].
Wang, T; Ma, G; Yang, G; Pan, Y
In this paper, three dihydrophenanthrenes are isolated from the Stems and pseudobulbs of Ephemerantha lonchophylla (Orchidaceae). They are identified as Iusianthridin (1), ephemeranthol-B (2) and erianthridin (3) by spectral data. PMID:12572433
Nature's Anti-Alzheimer's Drug: Isolation and Structure Elucidation of Galantamine from "Leucojum Aestivum"
ERIC Educational Resources Information Center
Halpin, Catherine M.; Reilly, Ciara; Walsh, John J.
The discovery that galantamine penetrates the blood-brain barrier has led to its clinical use in the treatment of choline-deficiency conditions in the brain, such as Alzheimer's disease. This experiment involves the isolation and structure elucidation of galantamine from "Leucojum aestivum". Isolation of the alkaloid constituents in "L. aestivum"…
Nature's Migraine Treatment: Isolation and Structure Elucidation of Parthenolide from "Tanacetum parthenium"
ERIC Educational Resources Information Center
Walsh, Emma L.; Ashe, Siobhan; Walsh, John J.
The purpose of this experiment is to provide students with the essential skills and knowledge required to perform the extraction, isolation, and structural elucidation of parthenolide from "Tanacetum parthenium" or feverfew. Students are introduced to a background of the traditional medicinal uses of parthenolide, while more modern applications of…
Isolation, Structure Elucidation, Biosynthesis, and Synthesis of Antalid, a Secondary Metabolite from Polyangium species.
Tautz, Thomas; Hoffmann, Judith; Hoffmann, Thomas; Steinmetz, Heinrich; Washausen, Peter; Kunze, Brigitte; Huch, Volker; Kitsche, Andreas; Reichenbach, Hans; Höfle, Gerhard; Müller, Rolf; Kalesse, Markus
The isolation, structure elucidation, and synthesis of antalid (1), a novel secondary metabolite from Polyangium sp., is described herein. The structure elucidation of 1 was performed with the aid of mass spectrometry, high field NMR experiments, and crystal structure analysis. The absolute configuration of antalid was confirmed through the Mosher ester method and ultimately by total synthesis. In addition, the biosynthetic origin of this hybrid PKS-NRPS natural product was unraveled by the in silico analysis of its biosynthetic gene cluster. PMID:27220069
Isolation, structure elucidation and DFT study on two novel oligosaccharides from yak milk
NASA Astrophysics Data System (ADS)
Singh, Meenakshi; Kumar, Alok; Srivastava, Gaurav; Deepak, Desh; Singh, M. P. V. V.
Two novel oligosaccharides were isolated from yak milk. The milk was processed by the method of Kobata and Ginsberg involving deproteination, centrifugation and lyophilization followed by gel filtrate chromatography acetylation and silica gel column chromatography of derivatized oligosaccharides while their homogeneity was confirmed by HPLC. The structures of these isolated oligosaccharides were elucidated by chemical transformation, chemical degradation, 1H, 13C NMR, 2D NMR (COSY, TOCSY and HSQC) and mass spectrometry. The geometry of compound A (Bosiose) and B (Bovisose) have been optimized at B3LYP method and 6-311 + G(d,p) basis set. The difference between the energies of A and B is 1.269 a.u. or 796.309 kcal/mol.
Meroparamycin production by newly isolated Streptomyces sp. strain MAR01: taxonomy, fermentation, purification and structural elucidation.
El-Naggar, Moustafa Y; El-Assar, Samy A; Abdul-Gawad, Sahar M
Twelve actinomycete strains were isolated from Egyptian soil. The isolated actinomycete strains were then screened with regard to their potential to generate antibiotics. The most potent of the producer strains was selected and identified. The cultural and physiological characteristics of the strain identified the strain as a member of the genus Streptomyces. The nucleotide sequence of the 16S rRNA gene (1.5 kb) of the most potent strain evidenced a 99% similarity with Streptomyces spp. and S. aureofaciens 16S rRNA genes, and the isolated strain was ultimately identified as Streptomyces sp. MAR01. The extraction of the fermentation broth of this strain resulted in the isolation of one major compound, which was active in vitro against gram-positive, gram-negative representatives and Candida albicans. The chemical structure of this bioactive compound was elucidated based on the spectroscopic data obtained from the application of MS, IR, UV, 1H NMR, 13C NMR, and elemental analysis techniques. Via comparison to the reference data in the relevant literature and in the database search, this antibiotic, which had a molecular formula of C19H29NO2 and a molecular weight of 303.44, was determined to differ from those produced by this genus as well as the available known antibiotics. Therefore, this antibiotic was designated Meroparamycin. PMID:16953179
Isolation, Characterization, Crystal Structure Elucidation, and Anticancer Study of Dimethyl Cardamonin, Isolated from Syzygium campanulatum Korth
Aisha, Abdalrahim F. A.; Al-Suede, Fouad Saleih Resq; Hamil, Mohammad Shahrul Ridzuan; Laghari, Madeeha; Abdul Majid, Amin Malik Shah
Syzygium campanulatum Korth is an equatorial, evergreen, aboriginal shrub of Malaysia. Conventionally it has been used as a stomachic. However, in the currently conducted study dimethyl cardamonin or 2′,4′-dihydroxy-6′-methoxy-3′,5′-dimethylchalcone (DMC) was isolated from S. campanulatum Korth, leaf extract. The structural characterization of DMC was carried out by making use of various techniques including UV, IR, NMR spectral followed by LC-MS, and X-ray crystallographic techniques. For determining the purity of compound, highly effective techniques including TLC, HPLC, and melting point were used. The cytotoxicity of DMC and three different extracts of S. campanulatum was evaluated against human colon cancer cell line (HT-29) by three different assays. DMC and ethanolic extract revealed potent and dose-dependent cytotoxic activity on the cancer cell line with IC50 12.6 and 90.1 µg/mL, respectively. Quite astonishingly to our knowledge, this is the very first report on S. campanulatum as being a rich source (3.5%) of DMC, X-ray crystallography, and anticancer activity on human colon cancer cells. PMID:25530783
Isolation and structural elucidation of two impurities from a diacerein bulk drug.
Ashok, Chaudhari; Golak, Maikap; Adwait, Deo; Krishna, Vivek; Himani, Agrawal; Umesh, Peshawe; Amol, Gawande; Srinivas, Sompalli; Sharad, Mane; Deepali, Jadhav; Atul, Chaudhari
Two impurities were found in the crude sample of diacerein. The level of these impurities 1.14% and 1.24% were detected by isocratic reverse-phase high performance liquid chromatography (HPLC). The molecular weights of the impurities were determined by liquid chromatography-mass spectroscopy (LC-MS) analysis. These impurities were isolated from crude sample of diacerein by reverse-phase preparative liquid chromatography. These impurities were characterized as 5-acetoxy-4-hydroxy-9,10-dioxo-9,10-dihydroanthracene-2-carboxylic acid (Impurity-1) and 4-acetoxy-5-hydroxy-9,10-dioxo-9,10-dihydroanthracene-2-carboxylic acid (Impurity-2) respectively. Structural elucidation of both the impurities were carried out by (1)H NMR, (13)C NMR, DEPT, 1D NOESY, MS and IR spectroscopy. PMID:19131202
Isolation and structure elucidation of the major degradation products of cefaclor in the solid state.
Dorman, D E; Lorenz, L J; Occolowitz, J L; Spangle, L A; Collins, M W; Bashore, F N; Baertschi, S W
Cefaclor is a beta-lactam antibiotic that degrades slowly under normal storage conditions to several minor products. To obtain samples large enough to permit structure elucidation, cefaclor was allowed to degrade at 40 degrees C (75% relative humidity) and at 85 degrees C. The profile of degradation products formed under these conditions is qualitatively similar to the profile of degradation products observed in samples of cefaclor aged for 14 years at room temperature, although some products found in the sample degraded at 85 degrees C are not formed at the lower temperatures. Using preparative reversed-phase high-performance liquid chromatography (rp-HPLC) and a combination of spectroscopic methods, we have isolated and characterized 17 of these degradation products. Some of these products were also isolated from studies of aqueous degradations. The major products appear to have arisen from five distinct pathways: (1) isomerization of the double bond in the dihydrothiazine ring; (2) decarboxylation; (3) ring contraction of the cephem nucleus to thiazole structures; (4) oxidative attack at carbon 4 of the dihydrothiazine ring; and (5) intramolecular attack of the primary amine of the side chain on either the beta-lactam carbonyl to form 3-phenyl-2,5-diketopiperazines or the "masked aldehyde" at carbon 6 to form 2-hydroxy-3-phenylpyrazine derivatives. The pathway involving oxidation at carbon 4 is particularly important at ambient temperatures and is unique to the solid-state degradation. PMID:9145376
Isolation and structure elucidation of thiazomycin- a potent thiazolyl peptide antibiotic from Amycolatopsis fastidiosa.
Jayasuriya, Hiranthi; Herath, Kithsiri; Ondeyka, John G; Zhang, Chaowei; Zink, Deborah L; Brower, Mark; Gailliot, Francis P; Greene, Joyce; Birdsall, Gwyneth; Venugopal, Jayashree; Ushio, Misti; Burgess, Bruce; Russotti, Greg; Walker, Andre; Hesse, Michelle; Seeley, Anna; Junker, Beth; Connors, Neal; Salazar, Oscar; Genilloud, Olga; Liu, Kun; Masurekar, Prakash; Barrett, John F; Singh, Sheo B
Thiazolyl peptides are a class of rigid macrocyclic compounds richly populated with thiazole rings. They are highly potent antibiotics but none have been advanced to clinic due to poor aqueous solubility. Recent progress in this field prompted a reinvestigation leading to the isolation of a new thiazolyl peptide, thiazomycin, a congener of nocathiacins. Thiazomycin possesses an oxazolidine ring as part of the amino-sugar moiety in contrast to the dimethyl amino group present in nocathiacin I. The presence of the oxazolidine ring provides additional opportunities for chemical modifications that are not possible with other nocathiacins. Thiazomycin is extremely potent against Gram-positive bacteria both in vitro and in vivo. The titer of thiazomycin in the fermentation broth was very low compared to the nocathiacins I and III. The lower titer together with its sandwiched order of elution presented significant challenges in large scale purification of thiazomycin. This problem was resolved by the development of an innovative preferential protonation based one- and/or two-step chromatographic method, which was used for pilot plant scale purifications of thiazomycin. The isolation and structure elucidation of thiazomycin is herein described. PMID:17917238
Isolation, structure elucidation and antibacterial activity of a new tetramic acid, ascosetin.
Ondeyka, John G; Smith, Scott K; Zink, Deborah L; Vicente, Francisca; Basilio, Angela; Bills, Gerald F; Polishook, Jon D; Garlisi, Charles; Mcguinness, Debra; Smith, Elizabeth; Qiu, Hongchen; Gill, Charles J; Donald, Robert G K; Phillips, John W; Goetz, Michael A; Singh, Sheo B
The ever-increasing bacterial resistance to clinical antibiotics is making many drugs ineffective and creating significant treatment gaps. This can be only circumvented by the discovery of antibiotics with new mechanisms of action. We report here the identification of a new tetramic acid, ascosetin, from an Ascomycete using the Staphylococcus aureus fitness test screening method. The structure was elucidated by spectroscopic methods including 2D NMR and HRMS. Relative stereochemistry was determined by ROESY and absolute configuration was deduced by comparative CD spectroscopy. Ascosetin inhibited bacterial growth with 2-16 μg ml(-1) MIC values against Gram-positive strains including methicillin-resistant S. aureus. It also inhibited the growth of Haemophilus influenzae with a MIC value of 8 μg ml(-1). It inhibited DNA, RNA, protein and lipid synthesis with similar IC50 values, suggesting a lack of specificity; however, it produced neither bacterial membrane nor red blood cell lysis. It showed selectivity for bacterial growth inhibition compared with fungal but not mammalian cells. The isolation, structure and biological activity of ascosetin have been detailed here. PMID:24690911
Separation by thin-layer chromatography and structure elucidation of bilirubin conjugates isolated from dog bile.
Heirwegh, K P; Fevery, J; Michiels, R; van Hees, G P; Compernolle, F
1. A system for separation of bile pigments by t.l.c. and for their structure elucidation is presented. Separated bile pigments are characterized by t.l.c. of derived dipyrrolic azopigments. 2. At the tetrapyrrolic stage hydrolysis in strongly alkaline medium followed by t.l.c. demonstrates the presence of bilirubin-IIIalpha, -IXalpha and -XIIIalpha and allows assessment of their relative amounts. 3. Most structural information is derived from analysis of dipyrrolic azopigments. Such derivatives, obtained by treatment of separated bile pigments with diazotized ethyl anthranilate, were separated and purified by t.l.c. Micro methods showed (a) the nature of the dipyrrolic aglycone, (b) the nature of the bonds connecting aglycone to a conjugating group, (c) the ratio of vinyl/isovinyl isomers present in the aglycone and, (d) the nature of the conjugating groups (by suitable derivative formation and t.l.c. with reference to known compounds). 4. In bile of normal dogs at least 20 tetrapyrrolic, diazo-positive bile pigments could be recognized. Except for two pigments the tetrapyrrolic nucleus corresponded predominantly to bilirubin-IXalpha. All conjugated pigments had their conjugating groups connected in ester linkage to the tetrapyrrolic aglycone, Apart from bilirubin-IXalpha, monoconjugates and homogeneous and mixed diconjugates of bilirubin were demonstrated; conjugating groups of major importance were xylose, glucose and glucuronic acid. 5. Bilirubin isomer determination on native bile and isolated bile pigments, and dipyrrole-exchange assays with [14C8]bilirubin indicated (a) that the conjugates pre-exist in bile, and (b) that no significant dipyrrole exchange occurs during isolation of the pigments. PMID:1156357
Nature's Cholesterol-Lowering Drug: Isolation and Structure Elucidation of Lovastatin from Red Yeast Rice-Containing Dietary Supplements
ERIC Educational Resources Information Center
Nazri, Maisarah Mohd; Samat, Farah D.; Kavanagh, Pierce V.; Walsh, John J.
Red yeast rice, produced by fermenting the fungus, "Monascus purpureus", on rice ("Oryza sativa" L. gramineae), is commonly used as a dietary supplement. It contains lovastatin, a member of the statin family of compounds, and is licensed for use as a cholesterol-lowering agent. This experiment involves the isolation and structure elucidation of…
Isolation and structural elucidation of a novel rotenoid from the seeds of Clitoria fairchildiana.
Mathias, Leda; Da Silva, Bernadete Pereira; Mors, Walter Baptist; Parente, José Paz
The seeds of Clitoria fairchildiana provided a new rotenoid, 6-hydroxy-2,3,9-trimethoxy-[1]benzopyrano[3,4-b][1]benzopyran-12(6H)-one. The structural elucidation was performed using detailed analyses of H- and 13C-NMR spectra including 2DNMR spectroscopic techniques (1H-13CHETCOR) and by comparison with spectrometric data from the literature. The anti-inflammatory activity was investigated using a capillary permeability assay. PMID:15938137
Isolation and structure elucidation of phenolic antioxidants from Tamarind (Tamarindus indica L.) seeds and pericarp.
Sudjaroen, Y; Haubner, R; Würtele, G; Hull, W E; Erben, G; Spiegelhalder, B; Changbumrung, S; Bartsch, H; Owen, R W
Although it is already known that Tamarind (Tamarindus indica L.) seeds contain phenolic substances, the individual components of the seeds have not been fully identified and quantitated, and in the case of Tamarind pericarp not reported. Therefore, major polyphenolic compounds were extracted using organic solvents and the metabolites were isolated by semi-preparative high performance liquid chromatography. Their structures were elucidated by liquid chromatography-electrospray-ionisation-mass spectrometry (LC-ESI-MS), nano-electrospray-ionisation mass spectrometry (ESI-MS), and where possible by gas chromatography-mass spectrometry (GC-MS) and 1H and 13C NMR. Quantitative analysis of polyphenolic compounds in Tamarind seeds and pericarp was conducted by analytical high performance liquid chromatography (HPLC), calculated against standard curves of authentic compounds. The yields of total phenolic compounds after Soxhlet extraction with methanol were 6.54 and 2.82 g/kg (dry weight) in the seeds and pericarp respectively. The profile (%) of polyphenolics in Tamarind pericarp was dominated by proanthcyanidins (73.4) in various forms (+)-catechin (2.0), procyanidin B2 (8.2), (-)-epicatechin (9.4), procyanidin trimer (11.3), procyanidin tetramer (22.2), procyanidin pentamer (11.6), procyanidin hexamer (12.8) along with taxifolin (7.4), apigenin (2.0), eriodictyol (6.9), luteolin (5.0) and naringenin (1.4) of total phenols, respectively. The content of Tamarind seeds comprised only procyanidins, represented (%) mainly by oligomeric procyanidin tetramer (30.2), procyanidin hexamer (23.8), procyanidin trimer (18.1), procyanidin pentamer (17.6) with lower amounts of procyanidin B2 (5.5) and (-)-epicatechin (4.8). Extraction of Tamarind pericarp and seeds using acetone:methanol:acetic acid gave only procyanidin oligomers, but in much higher yield and variety. The antioxidant capacities of the Soxhlet methanolic extracts were determined, and indicates that Tamarind may be an
Isolation and structure elucidation of radical scavengers from Thymus vulgaris leaves.
Dapkevicius, Airidas; van Beek, Teris A; Lelyveld, Gerrit P; van Veldhuizen, Albertus; de Groot, Aede; Linssen, Jozef P H; Venskutonis, Rimantas
2,2-Diphenyl-1-picrylhydrazyl radical (DPPH*) scavenging activity-guided fractionation of a leaf extract of Thymus vulgaris led to the isolation of the radical scavengers rosmarinic acid 1, eriodictyol, taxifolin, luteolin 7-glucuronide, p-cymene 2,3-diol, p-cymene 2,3-diol 6-6'-dimer, carvacrol, thymol, and a new compound, 2. The fractionation was considerably facilitated by using an on-line HPLC detector for radical scavenging activity. In this detector activity is monitored as the disappearance of the color of a postcolumn added stable radical after reacting with radical scavengers in a reaction coil. Compound 2, which consists of rosmarinic and caffeic acid moieties linked via a C-3'-C-8' ' ether bridge, was mainly elucidated by various NMR techniques and CD. Phenylpropanoid trimer 2 was a weaker and stronger radical scavenger than rosmarinic acid 1 in off-line TEAC and DPPH* assays, respectively. PMID:12088434
Isolation and extraction of lucidin primeveroside from Rubia tinctorum L. and crystal structure elucidation.
Henderson, Robert L; Rayner, Christopher M; Blackburn, Richard S
Madder (Rubia tinctorum L.) has been used as a dye for over 2000 years with alizarin and purpurin the major natural dyes analysed from extractions undertaken. The use of ethanol as the solvent in the extraction process produced an extract that yielded four anthraquinone compounds lucidin primeveroside, ruberythric acid, alizarin and lucidin-ω-ethyl ether. Gravitational separation of the extract was used to record the first crystal structure of lucidin primeveroside, which is also the first ever known crystal structure of a glycoside containing anthraquinone moiety. The crystal structure along with (1)H and (13)C NMR helped elucidate and confirm the structure of this overlooked natural dye which has been shown to be a major compound in R. tinctorum L. PMID:23891215
Isolation and structure elucidation of vicenistatin M, and importance of the vicenisamine aminosugar for exerting cytotoxicity of vicenistatin.
Matsushima, Y; Nakayama, T; Fujita, M; Bhandari, R; Eguchi, T; Shindo, K; Kakinuma, K
A new analogue of vicenistatin was isolated from the producing strain Streptomyces sp. HC-34. A characteristic of the elucidated structure involved the existence of a neutral sugar mycarose instead of an aminosugar vicenisamine of vicenistatin. The absolute stereochemistry of the new analogue (named as vicenistatin M) was determined by the synthesis of D-mycarose and of vicenistatin M itself. Biological testing of vicenistatin M suggested the importance of vicenisamine for exerting the cytotoxicity of vicenistatin. PMID:11372778
Accessible heavier s-block dihydropyridines: structural elucidation and reactivity of isolable molecular hydride sources.
Orr, Samantha A; Kennedy, Alan R; Liggat, John J; McLellan, Ross; Mulvey, Robert E; Robertson, Stuart D
The straightforward metathesis of 1-lithio-2-tbutyl-1,2-dihydropyridine using metal tert-butoxide (Na/K) has resulted in the first preparation and isolation of a series of heavier alkali metal dihydropyridines. By employing donors, TMEDA, PMDETA and THF, five new metallodihydropyridine compounds were isolated and fully characterised. Three distinct structural motifs have been observed; a dimer, a dimer of dimers and a novel polymeric dihydropyridylpotassium compound, and the influence of cation π-interactions therein has been discussed. Thermal volatility analysis has shown that these complexes have the potential to be used as simple isolable sodium or potassium hydride surrogates, which is confirmed in test reactions with benzophenone. PMID:26666219
Isolation and structure elucidation of azoricasterol, a new sterol of the deepwater sponge Macandrewia azorica
NASA Astrophysics Data System (ADS)
Gross, Harald; Reitner, Joachim; König, Gabriele M.
Chemical investigation of the deepwater sponge Macandrewia azorica, collected from the flanks of the Gettysburg and Ormonde Sea Mount, North Atlantic, from a depth of 600 m, has led to the isolation of a new sterol with an unusual side chain (1), along with S-methylergothioneine (2). The structures of compounds 1 and 2 were established by employing spectroscopic techniques (NMR, MS, UV, IR and polarimetry). This is the first report of metabolites of a sponge belonging to the genus Macandrewia.
Structure Elucidation and in Vitro Toxicity of New Azaspiracids Isolated from the Marine Dinoflagellate Azadinium poporum
Krock, Bernd; Tillmann, Urban; Potvin, Éric; Jeong, Hae Jin; Drebing, Wolfgang; Kilcoyne, Jane; Al-Jorani, Ahmed; Twiner, Michael J.; Göthel, Qun; Köck, Matthias
Two strains of Azadinium poporum, one from the Korean West coast and the other from the North Sea, were mass cultured for isolation of new azaspiracids. Approximately 0.9 mg of pure AZA-36 (1) and 1.3 mg of pure AZA-37 (2) were isolated from the Korean (870 L) and North Sea (120 L) strains, respectively. The structures were determined to be 3-hydroxy-8-methyl-39-demethyl-azaspiracid-1 (1) and 3-hydroxy-7,8-dihydro-39-demethyl-azaspiracid-1 (2) by 1H- and 13C-NMR. Using the Jurkat T lymphocyte cell toxicity assay, (1) and (2) were found to be 6- and 3-fold less toxic than AZA-1, respectively. PMID:26528990
Structure Elucidation and in Vitro Toxicity of New Azaspiracids Isolated from the Marine Dinoflagellate Azadinium poporum.
Krock, Bernd; Tillmann, Urban; Potvin, Éric; Jeong, Hae Jin; Drebing, Wolfgang; Kilcoyne, Jane; Al-Jorani, Ahmed; Twiner, Michael J; Göthel, Qun; Köck, Matthias
Two strains of Azadinium poporum, one from the Korean West coast and the other from the North Sea, were mass cultured for isolation of new azaspiracids. Approximately 0.9 mg of pure AZA-36 (1) and 1.3 mg of pure AZA-37 (2) were isolated from the Korean (870 L) and North Sea (120 L) strains, respectively. The structures were determined to be 3-hydroxy-8-methyl-39-demethyl-azaspiracid-1 (1) and 3-hydroxy-7,8-dihydro-39-demethyl-azaspiracid-1 (2) by ¹H- and (13)C-NMR. Using the Jurkat T lymphocyte cell toxicity assay, (1) and (2) were found to be 6- and 3-fold less toxic than AZA-1, respectively. PMID:26528990
Computer-Assisted Structure Elucidation of Black Chokeberry (Aronia melanocarpa) Fruit Juice Isolates with a New Fused Pentacyclic Flavonoid Skeleton
Naman, C. Benjamin; Li, Jie; Moser, Arvin; Hendrycks, Jeffery M.; Benatrehina, P. Annécie; Chai, Heebyung; Yuan, Chunhua; Keller, William J.; Kinghorn, A. Douglas
Melanodiol 4″-O-protocatechuate (1) and melanodiol (2) represent novel flavonoid derivatives isolated from a botanical dietary supplement ingredient, dried black chokeberry (Aronia melanocarpa) fruit juice. These non-crystalline compounds possess an unprecedented fused pentacyclic core with two contiguous hemiketals. Due to having significant hydrogen deficiency indices, their structures were determined using computer-assisted structure elucidation software. The in vitro hydroxyl radical-scavenging and quinone reductase-inducing activity of each compound are reported, and a plausible biogenetic scheme is proposed PMID:26030740
Computer-Assisted Structure Elucidation of Black Chokeberry (Aronia melanocarpa) Fruit Juice Isolates with a New Fused Pentacyclic Flavonoid Skeleton.
Naman, C Benjamin; Li, Jie; Moser, Arvin; Hendrycks, Jeffery M; Benatrehina, P Annécie; Chai, Heebyung; Yuan, Chunhua; Keller, William J; Kinghorn, A Douglas
Melanodiol 4″-O-protocatechuate (1) and melanodiol (2) represent novel flavonoid derivatives isolated from a botanical dietary supplement ingredient, dried black chokeberry (Aronia melanocarpa) fruit juice. These noncrystalline compounds possess an unprecedented fused pentacyclic core with two contiguous hemiketals. Due to having significant hydrogen deficiency indices, their structures were determined using computer-assisted structure elucidation software. The in vitro hydroxyl radical-scavenging and quinone reductase-inducing activity of each compound are reported, and a plausible biogenetic scheme is proposed. PMID:26030740
Moromycins A and B: Isolation and Structure Elucidation of C-Glycosylangucycline Type Antibiotics from Streptomyces sp.KY002
Abdelfattah, Mohamed S.; Kharel, Madan Kumar; Hitron, John Andrew; Baig, Irfan; Rohr, Jürgen
Two new anticancer antibiotics of the angucycline class, moromycins A and B (1, 2), along with the known microbial metabolites saquayamycin B (3) and fridamycin D (4) were isolated from the ethyl acetate extract of a culture broth of the terrestrial Streptomyces sp. KY002. The structures consist of a tetrangomycin core, and various C- and O-glycosidically linked deoxysugars. The chemical structures of the new secondary metabolites were elucidated by 1D and 2D NMR and by mass spectrometry. Moromycin B (2) showed significant cytotoxicity against H-460 human lung cancer and MCF-7 human breast cancer cells. PMID:18666798
Sulfated phenolic compounds from Limonium caspium: Isolation, structural elucidation, and biological evaluation
Gadetskaya, Anastassiya V.; Tarawneh, Amer H.; Zhusupova, Galiya E.; Gemejiyeva, Nadezhda G.; Cantrell, Charles L.; Cutler, Stephen J.; Ross, Samir A.
Three new compounds, (2S,3S)-5-methyldihydromyricetin (1), (2S,3S)-5-methyldihydromyricetin-3′-O-sulfate (2) and β-D-glucopyranoside, 3-methyl, but-3-en-1-yl 4-O-α-L-rhamnopyranosyl (3) have been isolated from the Limonium caspium, together with dihydromyricetin (4), dihydromyricetin-3′-O-sulfate (5), myricetin-3′-O-sulfate (6), 5-methylmyricetin (7), myricetin (8), myricetin-3-O-β-glucoside (9), as well as phloridzin (10), and tyramine (11). Compounds 5 and 6 were isolated for the first time as acids. This is the first report of all these compounds from this plant. Their structures were established by extensive NMR studies (1H NMR, 13C NMR, DEPT, 1H–1H COSY, HSQC, HMBC) as well as HRESIMS. All isolated compounds were evaluated for their antibacterial, antifungal, antimalarial and antileishmanial activities. Compounds 7, 8 and 9 exhibited good antifungal activity against Candida glabrata with IC50 values of 6.79, 15.37 and 8.53 μg/mL, respectively. Compound 8 displayed significant antimalarial activity against resistant and sensitive strains of Plasmodium falciparum with IC50 values of 1.82 and 1.51 μg/mL, respectively. Compounds 1, 4, 6, 8 and 9 showed excellent activity against Trypanosoma brucei with IC50 values of 6.93, 9.65, 8.52, 7.67 and 6.31 μg/mL, respectively. To date, this is the first report on the phytochemical and biological activity of secondary metabolites from L. caspium. PMID:26025854
Isolation, structure elucidation, and biological evaluation of 16,23-epoxycucurbitacin constituents from Eleaocarpus chinensis.
Pan, Li; Yong, Yeonjoong; Deng, Ye; Lantvit, Daniel D; Ninh, Tran Ngoc; Chai, Heebyung; Carcache de Blanco, Esperanza J; Soejarto, Djaja D; Swanson, Steven M; Kinghorn, A Douglas
Eight new 16,23-epoxycucurbitacin derivatives, designated as elaeocarpucins A-H (1-8), and five known cucurbitacins (9-13) were isolated from the chloroform-soluble partitions of separate methanol extracts of the fruits and stem bark of Elaeocarpus chinensis collected in Vietnam. Isolation work was facilitated using a LC/MS dereplication procedure, and bioassay-guided fractionation was monitored using HT-29 human cancer cells. The structures of compounds 1-8 were determined on the basis of spectroscopic data interpretation, with the absolute configurations of isomers 1 and 2 established by the Mosher ester method. Compounds 1-13 were evaluated in vitro against the HT-29 cell line and using a mitochondrial transmembrane potential assay. Elaeocarpucin C (3), produced by partial synthesis from 16α,23α-epoxy-3β,20β-dihydroxy-10αH,23βH-cucurbit-5,24-dien-11-one (13), was found to be inactive when evaluated in an in vivo hollow fiber assay using three different cancer cell types (dose range 0.5-10 mg/kg/day, i.p.). PMID:22239601
Isolation, Structure Elucidation, and Biological Evaluation of 16,23-Epoxycucurbitacin Constituents from Eleaocarpus chinensis#
Pan, Li; Yong, Yeonjoong; Deng, Ye; Lantvit, Daniel D.; Ninh, Tran Ngoc; Chai, Heebyung; de Blanco, Esperanza J. Carcache; Soejarto, Djaja D.; Swanson, Steven M.; Kinghorn, A. Douglas
Eight new 16,23-epoxycucurbitacin derivatives, designated as elaeocarpucins A–H (1–8), and five known cucurbitacins (9–13) were isolated from the chloroform-soluble partitions of separate methanol extracts of the fruits and stem bark of Elaeocarpus chinensis collected in Vietnam. Isolation work was facilitated using a LC/MS dereplication procedure, and bioassay-guided fractionation was monitored using HT-29 human cancer cells. The structures of compounds 1–8 were determined on the basis of spectroscopic data interpretation, with the absolute configurations of isomers 1 and 2 established by the Mosher ester method. Compounds 1–13 were evaluated in vitro against the HT-29 cell line and using a mitochondrial transmembrane potential assay. Elaeocarpucin C (3), produced by partial synthesis from 16α,23α-epoxy-3β,20β-dihydroxy-10αH,23βH-cucurbit-5,24-dien-11-one (13), was found to be inactive when evaluated in an in vivo hollow fiber assay using three different cancer cell types (dose range 0.5–10 mg/kg/day, ip). PMID:22239601
Isolation, Structure Elucidation and Total Synthesis of Lajollamide A from the Marine Fungus Asteromyces cruciatus
Gulder, Tobias A. M.; Hong, Hanna; Correa, Jhonny; Egereva, Ekaterina; Wiese, Jutta; Imhoff, Johannes F.; Gross, Harald
The marine-derived filamentous fungus Asteromyces cruciatus 763, obtained off the coast of La Jolla, San Diego, USA, yielded the new pentapeptide lajollamide A (1), along with the known compounds regiolone (2), hyalodendrin (3), gliovictin (4), 1N-norgliovicitin (5), and bis-N-norgliovictin (6). The planar structure of lajollamide A (1) was determined by Nuclear Magnetic Resonance (NMR) spectroscopy in combination with mass spectrometry. The absolute configuration of lajollamide A (1) was unambiguously solved by total synthesis which provided three additional diastereomers of 1 and also revealed that an unexpected acid-mediated partial racemization (2:1) of the L-leucine and L-N-Me-leucine residues occurred during the chemical degradation process. The biological activities of the isolated metabolites, in particular their antimicrobial properties, were investigated in a series of assay systems. PMID:23342379
Antineoplastic Agents. 570. Isolation and Structure Elucidation of Bacillistatins 1 and 2 from a Marine Bacillus silvestris†, ‡
Pettit, George R.; Knight, John C.; Herald, Delbert L.; Pettit, Robin K.; Hogan, Fiona; Mukku, Venugopal J. R. V.; Hamblin, John S.; Dodson, Michael J.; Chapuis, Jean-Charles
Two new cyclodepsipeptides designated bacillistatins 1 (1) and 2 (2) have been isolated from cultures of a sample of Bacillus silvestris that was obtained from a Pacific Ocean (southern Chile) crab. Each 12-unit cyclodepsipeptide strongly inhibited growth of a human cancer cell line panel, with GI50s of 10−4–10−5 μg/mL, and each compound was active against antibiotic-resistant Streptococcus pneumoniae. The structures were elucidated by a combination of X-ray diffraction and mass and 2D NMR spectroscopic analyses, together with chemical degradation. PMID:19226154
Fatty acid synthase inhibitors from plants: isolation, structure elucidation, and SAR studies.
Li, Xing-Cong; Joshi, Alpana S; ElSohly, Hala N; Khan, Shabana I; Jacob, Melissa R; Zhang, Zhizheng; Khan, Ikhlas A; Ferreira, Daneel; Walker, Larry A; Broedel, Sheldon E; Raulli, Robert E; Cihlar, Ronald L
Fatty acid synthase (FAS) has been identified as a potential antifungal target. FAS prepared from Saccharomyces cerevisiae was employed for bioactivity-guided fractionation of Chlorophora tinctoria,Paspalum conjugatum, Symphonia globulifera, Buchenavia parviflora, and Miconia pilgeriana. Thirteen compounds (1-13), including three new natural products (1, 4, 12), were isolated and their structures identified by spectroscopic interpretation. They represented five chemotypes, namely, isoflavones, flavones, biflavonoids, hydrolyzable tannin-related derivatives, and triterpenoids. 3'-Formylgenistein (1) and ellagic acid 4-O-alpha-l-rhamnopyranoside (9) were the most potent compounds against FAS, with IC(50) values of 2.3 and 7.5 microg/mL, respectively. Furthermore, 43 (14-56) analogues of the five chemotypes from our natural product repository and commercial sources were tested for their FAS inhibitory activity. Structure-activity relationships for some chemotypes were investigated. All these compounds were further evaluated for antifungal activity against Candida albicans and Cryptococcus neoformans. Although there were several antifungal compounds in the set, correlation between the FAS inhibitory activity and antifungal activity could not be defined. PMID:12502337
Phytochemicals of black bean seed coats: isolation, structure elucidation, and their antiproliferative and antioxidative activities.
Dong, Mei; He, Xiangjiu; Liu, Rui Hai
Bioactivity-guided fractionation of black bean (Phaseolus vulgaris) seed coats was used to determine the chemical identity of bioactive constituents, which showed potent antiproliferative and antioxidative activities. Twenty-four compounds including 12 triterpenoids, 7 flavonoids, and 5 other phytochemicals were isolated using gradient solvent fractionation, silica gel and ODS columns, and semipreparative and preparative HPLC. Their chemical structures were identified using MS, NMR, and X-ray diffraction analysis. Antiproliferative activities of isolated compounds against Caco-2 human colon cancer cells, HepG2 human liver cancer cells, and MCF-7 human breast cancer cells were evaluated. Among the compounds isolated, compounds 1, 2, 6, 7, 8, 13, 14, 15, 16, 19, and 20 showed potent inhibitory activities against the proliferation of HepG2 cells, with EC50 values of 238.8 +/- 19.2, 120.6 +/- 7.3, 94.4 +/- 3.4, 98.9 +/- 3.3, 32.1 +/- 6.3, 306.4 +/- 131.3, 156.9 +/- 11.8, 410.3 +/- 17.4, 435.9 +/- 47.7, 202.3 +/- 42.9, and 779.3 +/- 37.4 microM, respectively. Compounds 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 14, 15, 19, and 20 showed potent antiproliferative activities against Caco-2 cell growth, with EC50 values of 179.9 +/- 16.9, 128.8 +/- 11.6, 197.8 +/- 4.2, 105.9 +/- 4.7, 13.9 +/- 2.8, 35.1 +/- 2.9, 31.2 +/- 0.5, 71.1 +/- 11.9, 40.8 +/- 4.1, 55.7 +/- 8.1, 299.8 +/- 17.3, 533.3 +/- 126.0, 291.2 +/- 1.0, and 717.2 +/- 104.8 microM, respectively. Compounds 5, 7, 8, 9, 11, 19, 20 showed potent antiproliferative activities against MCF-7 cell growth in a dose-dependent manner, with EC50 values of 129.4 +/- 9.0, 79.5 +/- 1.0, 140.1 +/- 31.8, 119.0 +/- 7.2, 84.6 +/- 1.7, 186.6 +/- 21.1, and 1308 +/- 69.9 microM, respectively. Six flavonoids (compounds 14-19) showed potent antioxidant activity. These results showed the phytochemical extracts of black bean seed coats have potent antioxidant and antiproliferative activities. PMID:17602653
Acylated anthocyanins from sprouts of Raphanus sativus cv. Sango: isolation, structure elucidation and antioxidant activity.
Matera, Riccardo; Gabbanini, Simone; Berretti, Serena; Amorati, Riccardo; De Nicola, Gina Rosalinda; Iori, Renato; Valgimigli, Luca
Little is known on structure-activity relationships of antioxidant anthocyanins. Raphanus sativus cv Sango sprouts are among the richest sources (270 mg/100 g fresh weight). We isolated from sprouts' juice 9 acylated anthocyanins, including 4 new compounds. All comprise a cyanidin core bearing 3-4 glucose units, multiply acylated with malonic and phenolic acids (ferulic and sinapic). All compounds were equally effective in inhibiting the autoxidation of linoleic acid in aqueous micelles, with rate constant for trapping peroxyl radicals kinh=(3.8 ± 0.7) × 10(4)M(-1)s(-1) at 37 °C. In acetonitrile solution kinh varied with acylation: (0.9-2.1) × 10(5)M(-1)s(-1) at 30 °C. Each molecule trapped a number n of peroxyl radicals ranging from 4 to 7. Anthocyanins bearing sinapic acid were more effective than those bearing the ferulic moiety. Under identical settings, deacylated cyanin, ferulic and sinapic acids had kinh of 0.4 × 10(5), 0.3 × 10(5) and 1.6 × 10(5)M(-1)s(-1) respectively, with n ranging 2-3. Results show the major role of acylation on antioxidant performance. PMID:25053073
Nature's Sedative: Isolation and Structural Elucidation of Valtrate from Centranthus Ruber
ERIC Educational Resources Information Center
Doyle, Andrea M.; Reilly, Joe; Murphy, Niamh; Kavanagh, Pierce V.; O'Brien, John E.; Walsh, Martin S.; Walsh, John J.
A member of a related genus of the valerianaceae, Centranthus ruber, is used, that yields a higher percentage valtrate than other related species such as "Valeriana officinalis," there by making easier isolation in pure form.
Sulfated phenolic compounds from Limonium caspium: Isolation, structural elucidation, and biological evaluation
Technology Transfer Automated Retrieval System (TEKTRAN)
Three new compounds, 5-methyldihydromyricetin (1), 5-methyldihydromyricetin-3'-O-sulfate (2) and ß-D-glucopyranoside, 3-methyl, but-3-en-1-yl 4-O-a-L-rhamnopyranosyl (3) have been isolated from the Limonium caspium, together with dihydromyricetin (4), dihydromyricetin-3'-O-sulfate (5), myricetin-3'-...
Isolation and Structure Elucidation of the Terpene "[beta]"-Thujone from Cedar Leaf Oil
ERIC Educational Resources Information Center
French, Larry G.
Western red cedar leaf affords an essential oil characterized by high thujone content. Students in an advanced organic chemistry lab course isolate a single thujone diastereoisomer from commercially available cedar leaf oil. Treatment of crude oil, containing roughly 70% thujone, predominately as [alpha]-thujone (6.5:1), with ethanolic sodium…
Isolation and structure elucidation of a novel product of the acidic degradation of cefaclor.
Baertschi, S W; Dorman, D E; Occolowitz, J L; Spangle, L A; Collins, M W; Wildfeuer, M E; Lorenz, L J
The acidic aqueous degradation of cefaclor, an orally administered cephalosporin antibiotic, has been investigated. The most prominent peak in the high-performance liquid chromatography profile of a degraded solution of cefaclor was isolated by preparative high-performance liquid chromatography. Mechanistically, the formation of this degradent from cefaclor involves a condensation of two cefaclor degradation products in which both products have undergone contraction from a six-membered cephem ring to a five-membered thiazole ring, presumably via a common episulfonium ion intermediate. PMID:8331538
Constituents of Azadirachta indica: isolation and structure elucidation of a new antibacterial tetranortriterpenoid, mahmoodin, and a new protolimonoid, naheedin.
Siddiqui, S; Faizi, S; Siddiqui, B S; Ghiasuddin
Mahmoodin [1], a new limonoid, has been isolated from Azadirachta indica (neem) oil, along with seven known tetranortriterpenoids, azadirone, epoxyazadiradione, nimbin, gedunin, azadiradione, deacetylnimbin, and 17-hydroxyazadiradione. A new protolimonoid, naheedin [3], has been obtained from the neem fruits along with azadirachtol. Their structures have been elucidated through chemical and spectral analyses including 2D nmr studies. The absolute configuration of 1 was established by comparison of its cd spectrum with those of the known tetranortriterpenoids. Mahmoodin showed significant antibacterial activity against various Gram-positive and Gram-negative organisms. Four hydrocarbons, icosane, docosane, 2-methyltricosane, and docosene, have also been identified by gc-ms of the EtOH extract of the fruit coats. Only docosane has earlier been reported from neem, while the remaining three are unreported from this plant. PMID:1593280
Isolation, Structure Elucidation, and (Bio)Synthesis of Haprolid, a Cell-Type-Specific Myxobacterial Cytotoxin.
Steinmetz, Heinrich; Li, Jun; Fu, Chengzhang; Zaburannyi, Nestor; Kunze, Birgitte; Harmrolfs, Kirsten; Schmitt, Viktoria; Herrmann, Jennifer; Reichenbach, Hans; Höfle, Gerhard; Kalesse, Markus; Müller, Rolf
Myxobacteria are well-established sources for novel natural products exhibiting intriguing bioactivities. We here report on haprolid (1) isolated from Byssovorax cruenta Har1. The compound exhibits an unprecedented macrolactone comprising four modified amino acids and a polyketide fragment. As configurational assignment proved difficult, a bioinformatic analysis of the biosynthetic gene cluster was chosen to predict the configuration of each stereocenter. In-depth analysis of the corresponding biosynthetic proteins established a hybrid polyketide synthase/nonribosomal peptide synthetase origin of haprolid and allowed for stereochemical assignments. A subsequent total synthesis yielded haprolid and corroborated all predictions made. Intriguingly, haprolid showed cytotoxicity against several cell lines in the nanomolar range whereas other cells were almost unaffected by treatment with the compound. PMID:27404448
Isolation and structural elucidation of cytotoxic compounds from the root bark of Diospyros quercina (Baill.) endemic to Madagascar
Ruphin, Fatiany Pierre; Baholy, Robijaona; Emmanuel, Randrianarivo; Amelie, Raharisololalao; Martin, Marie-Therese; Koto–te-Nyiwa, Ngbolua
Objective To isolate and characterize the cytotoxic compounds from Diospyros quercina (Baill.) G.E. Schatz & Lowry (Ebenaceae). Methods An ethno-botanical survey was conducted in the south of Madagascar from July to August 2010. Bio-guided fractionation assay was carried out on the root bark of Diospyros quercina, using cytotoxicity bioassay on murine P388 leukemia cell lines as model. The structures of the cytotoxic compounds were elucidated by 1D and 2D NMR spectroscopy and mass spectrometry. Results Biological experiments resulted in the isolation of three bioactive pure compounds (named TR-21, TR-22, and TR-23) which exhibited very good in vitro cytotoxic activities with the IC50 values of (0.017 5±0.0060) µg/mL, (0.089±0.005) µg/mL and (1.027±0.070) µg/mL respectively. Thus, they support the claims of traditional healers and suggest the possible correlation between the chemical composition of this plant and its wide use in Malagasy folk medicine to treat cancer. Conclusions The ability of isolated compounds in this study to inhibit cell growth may represent a rational explanation for the use of Diospyros quercina root bark in treating cancer by Malagasy traditional healers. Further studies are, therefore, necessary to evaluate the in vivo anti-neoplastic activity of these cytotoxic compounds as effective anticancer drugs. PMID:25182433
Antimutagenic Compounds of White Shrimp (Litopenaeus vannamei): Isolation and Structural Elucidation.
López-Saiz, Carmen-María; Hernández, Javier; Cinco-Moroyoqui, Francisco-Javier; Velázquez, Carlos; Ocaño-Higuera, Víctor-Manuel; Plascencia-Jatomea, Maribel; Robles-Sánchez, Maribel; Machi-Lara, Lorena; Burgos-Hernández, Armando
According to the World Health Organization, cancer is the main cause of mortality worldwide; thus, the search of chemopreventive compounds to prevent the disease has become a priority. White shrimp (Litopenaeus vannamei) has been reported as a source of compounds with chemopreventive activities. In this study, shrimp lipids were extracted and then fractionated in order to isolate those compounds responsible for the antimutagenic activity. The antimutagenic activity was assessed by the inhibition of the mutagenic effect of aflatoxin B1 on TA98 and TA100 Salmonella tester strains using the Ames test. Methanolic fraction was responsible for the highest antimutagenic activity (95.6 and 95.9% for TA98 and TA100, resp.) and was further separated into fifteen different subfractions (M1-M15). Fraction M8 exerted the highest inhibition of AFB1 mutation (96.5 and 101.6% for TA98 and TA100, resp.) and, after further fractionation, four subfractions M8a, M8b, M8c, and M8d were obtained. Data from (1)H and (13)C NMR, and mass spectrometry analysis of fraction M8a (the one with the highest antimutagenic activity), suggest that the compound responsible for its antimutagenicity is an apocarotenoid. PMID:27006678
Antimutagenic Compounds of White Shrimp (Litopenaeus vannamei): Isolation and Structural Elucidation
López-Saiz, Carmen-María; Hernández, Javier; Cinco-Moroyoqui, Francisco-Javier; Velázquez, Carlos; Ocaño-Higuera, Víctor-Manuel; Plascencia-Jatomea, Maribel; Robles-Sánchez, Maribel; Machi-Lara, Lorena; Burgos-Hernández, Armando
According to the World Health Organization, cancer is the main cause of mortality worldwide; thus, the search of chemopreventive compounds to prevent the disease has become a priority. White shrimp (Litopenaeus vannamei) has been reported as a source of compounds with chemopreventive activities. In this study, shrimp lipids were extracted and then fractionated in order to isolate those compounds responsible for the antimutagenic activity. The antimutagenic activity was assessed by the inhibition of the mutagenic effect of aflatoxin B1 on TA98 and TA100 Salmonella tester strains using the Ames test. Methanolic fraction was responsible for the highest antimutagenic activity (95.6 and 95.9% for TA98 and TA100, resp.) and was further separated into fifteen different subfractions (M1–M15). Fraction M8 exerted the highest inhibition of AFB1 mutation (96.5 and 101.6% for TA98 and TA100, resp.) and, after further fractionation, four subfractions M8a, M8b, M8c, and M8d were obtained. Data from 1H and 13C NMR, and mass spectrometry analysis of fraction M8a (the one with the highest antimutagenic activity), suggest that the compound responsible for its antimutagenicity is an apocarotenoid. PMID:27006678
Isolation and Structural Elucidation of Antiproliferative Compounds of Lipidic Fractions from White Shrimp Muscle (Litopenaeus vannamei)
López-Saiz, Carmen-María; Velázquez, Carlos; Hernández, Javier; Cinco-Moroyoqui, Francisco-Javier; Plascencia-Jatomea, Maribel; Robles-Sánchez, Maribel; Machi-Lara, Lorena; Burgos-Hernández, Armando
Shrimp is one of the most popular seafood items worldwide, and has been reported as a source of chemopreventive compounds. In this study, shrimp lipids were separated by solvent partition and further fractionated by semi-preparative RP-HPLC and finally by open column chromatography in order to obtain isolated antiproliferative compounds. Antiproliferative activity was assessed by inhibition of M12.C3.F6 murine cell growth using the MTT (3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2-H-tetrazolium bromide) assay. The methanolic fraction showed the highest antiproliferative activity; this fraction was separated into 15 different sub-fractions (M1–M15). Fractions M8, M9, M10, M12, and M13 were antiproliferative at 100 µg/mL and they were further tested at lower concentrations. Fractions M12 and M13 exerted the highest growth inhibition with an IC50 of 19.5 ± 8.6 and 34.9 ± 7.3 µg/mL, respectively. Fraction M12 was further fractionated in three sub-fractions M12a, M12b, and M12c. Fraction M12a was identified as di-ethyl-hexyl-phthalate, fraction M12b as a triglyceride substituted by at least two fatty acids (predominantly oleic acid accompanied with eicosapentaenoic acid) and fraction M12c as another triglyceride substituted with eicosapentaenoic acid and saturated fatty acids. Bioactive triglyceride contained in M12c exerted the highest antiproliferative activity with an IC50 of 11.33 ± 5.6 µg/mL. Biological activity in shrimp had been previously attributed to astaxanthin; this study demonstrated that polyunsaturated fatty acids are the main compounds responsible for antiproliferative activity. PMID:25526568
Isolation and extraction of ruberythric acid from Rubia tinctorum L. and crystal structure elucidation.
Ford, Lauren; Rayner, Christopher M; Blackburn, Richard S
Madder (Rubia tinctorum L.) has been exploited as a dye throughout history. The roots of the plant are very rich in the highly coloured glycosidic compounds ruberythric acid and lucidin primeveroside, alongside the corresponding aglycons which can be readily formed by deglycosylation, particularly during extraction. Supported by (1)H and (13)C NMR data, the conclusive X-ray crystal structure of the natural dye ruberythric acid is presented for the first time. The solid state structure revealed extensive intermolecular hydrogen bonding interactions between the sugar moieties in the unit cell, but only intramolecular hydrogen bonding through the hydroxyquinone groups. There is also some additional π-π stacking from the anthraquinone moiety. PMID:26091962
Isolation and structural elucidation of a new tadalafil analogue in health supplements: bisprenortadalafil.
Lee, Ji Hyun; Park, Han Na; Ganganna, Bogonda; Jeong, Ji Hye; Park, Sung-Kwan; Lee, Jongkook; Baek, Sun Young
A new tadalafil analogue was found, along with nortadalafil, using HPLC-DAD during the inspection of a health product sold without official approval. The analogue was separated using a semi-preparative HPLC system and its structure was determined by a combination of mass spectrometry and NMR spectroscopy. The compound was identified as a tadalafil analogue in which the N-methyl group of tadalafil was replaced with a tadalafil precursor moiety. Nuclear Overhauser effect spectroscopy experiments suggested a cis-relationship between the substituents on a piperidine ring in the tadalafil moiety. PMID:27167568
Isolation, Structural Elucidation, and Synthesis of Lepteridine From Ma̅nuka (Leptospermum scoparium) Honey.
Daniels, Benjamin J; Prijic, Gordana; Meidinger, Sarah; Loomes, Kerry M; Stephens, Jonathan M; Schlothauer, Ralf C; Furkert, Daniel P; Brimble, Margaret A
Ma̅nuka honey, made from the nectar of Leptospermum scoparium, has garnered scientific and economical interest due to its nonperoxide antibacterial activity. Biomarkers for genuine ma̅nuka honey are increasingly in demand due to the presence of counterfeit ma̅nuka honey. This work reports the identification of a compound previously unreported in ma̅nuka honey by HPLC, and determination of the structure of the as 3,6,7-trimethyllumazine using NMR, MS, IR, and UV/vis spectroscopy. This assignment was confirmed by total synthesis. The natural product, renamed lepteridine, was only observed in ma̅nuka honeys and could potentially serve as a biomarker for genuine ma̅nuka honey. PMID:27210444
Isolation and structure elucidation of pectic polysaccharide from rose hip fruits (Rosa canina L.).
Ognyanov, Manol; Remoroza, Connie; Schols, Henk A; Georgiev, Yordan; Kratchanova, Maria; Kratchanov, Christo
A pectic polysaccharide from rose hip (RH) fruits has been obtained by extraction with 1% aqueous citric acid. It was found that the polysaccharide fraction mainly consisted of galacturonic acid (45.5%) next to galactose (5.5%) and arabinose (4.7%). RH pectin is having a relatively high degree of methylesterification (62%) and acetylation (10%) and consists of different molecular weight populations in the range of 10-100kDa. Enzymatic fingerprinting was performed using a combination of pectin lyase (PL) and endo-polygalacturonase. Detailed information about the structure and level of galacturonic acid oligomers released was obtained using LC-HILIC-MS/ELSD and HPAEC. Predominantly, unsaturated and methyl-esterified oligomers (DP 3-5) were released indicating that high proportions of methylesterified 'PL degradable' areas were present within the pectin. The data revealed that homogalacturonan is the main building block of the extracted pectin and consists of long methylesterified/acetylated GalA sequences interspersed with small blocks of non-methyl-esterified GalA units. PMID:27474627
Isolation and structure elucidation of avocado seed (Persea americana) lipid derivatives that inhibit Clostridium sporogenes endospore germination.
Rodríguez-Sánchez, Dariana Graciela; Pacheco, Adriana; García-Cruz, María Isabel; Gutiérrez-Uribe, Janet Alejandra; Benavides-Lozano, Jorge Alejandro; Hernández-Brenes, Carmen
Avocado fruit extracts are known to exhibit antimicrobial properties. However, the effects on bacterial endospores and the identity of antimicrobial compounds have not been fully elucidated. In this study, avocado seed extracts were tested against Clostridium sporogenes vegetative cells and active endospores. Bioassay-guided purification of a crude extract based on inhibitory properties linked antimicrobial action to six lipid derivatives from the family of acetogenin compounds. Two new structures and four compounds known to exist in nature were identified as responsible for the activity. Structurally, most potent molecules shared features of an acetyl moiety and a trans-enone group. All extracts produced inhibition zones on vegetative cells and active endospores. Minimum inhibitory concentrations (MIC) of isolated molecules ranged from 7.8 to 15.6 μg/mL, and bactericidal effects were observed for an enriched fraction at 19.5 μg/mL. Identified molecules showed potential as natural alternatives to additives and antibiotics used by the food and pharmaceutical industries to inhibit Gram-positive spore-forming bacteria. PMID:23829335
Isolation and structure elucidation of rebaudioside D2 from bioconversion reaction of rebaudioside A to rebaudioside D.
Prakash, Indra; Bunders, Cynthia; Devkota, Krishna P; Charan, Romila D; Ramirez, Catherine; Parikh, Maunik; Markosyan, Avetik
We report the isolation and complete structure of an isomer of rebaudioside D, known as rebaudioside D2. This novel steviol glycoside was isolated from a bioconversion reaction of rebaudioside A to rebaudioside D. Rebaudioside D2 possesses a relatively rare 1 --> 6 sugar linkage, which was discovered by extensive analysis of NMR (1H, 13C, COSY, HSQC-DEPT, HMBC, 1D TOCSY and NOESY) and mass spectral data. PMID:25233591
Isolation, structure elucidation and enzyme inhibition studies of a new hydroxy ester and other compounds from Berberis jaeschkeana Schneid stem.
Alamzeb, Muhammad; Khan, M Rafiullah; Mamoon-Ur-Rashid; Ali, Saqib; Khan, Ashfaq Ahmad
Bioassay-guided isolation and fractionation of Berberis jaeschkeana Schneid var. jaeschkeana stem resulted in the isolation and characterisation of a new long chain hydroxy ester named as berberinol (1) along with six known compounds (2-7). All the structures were established from 1D and 2D spectroscopic data. Crude extract, sub-fractions and all the isolated compounds were evaluated for their anti-fungal and urease enzyme inhibition properties. All of the sub-fractions and compounds showed good anti-fungal and urease enzyme inhibition properties. Minimum inhibitory concentrations (MICs) were calculated for all active samples in case of urease enzyme inhibition. MICs values were found to be in the range of 39.03-49.78 μg/mL for urease enzyme inhibition. PMID:25604951
Crystal Structure Elucidation and Anticancer Studies of (-)-Pseudosemiglabrin: A Flavanone Isolated from the Aerial Parts of Tephrosia apollinea
Ahmed Hassan, Loiy Elsir; Khadeer Ahamed, Mohamed B.; Abdul Majid, Aman Shah; Iqbal, Muhammad Adnan; Al Suede, Fouad Saleih R.; Haque, Rosenani A.; Ismail, Zhari; Ein, Oon Chern; Majid, Amin Malik Shah Abdul
Tephrosia apollinea is a perennial shrublet widely distributed in Africa and is known to have medicinal properties. The current study describes the bio-assay (cytotoxicity) guided isolation of (-)-pseudosemiglabrin from the aerial parts of T. apollinea. The structural and stereochemical features have been described using spectral and x-ray crystallographic techniques. The cytotoxicity of isolated compound was evaluated against nine cancer cell lines. In addition, human fibroblast was used as a model cell line for normal cells. The results showed that (-)-pseudosemiglabrin exhibited dose-dependent antiproliferative effect on most of the tested cancer cell lines. Selectively, the compound showed significant inhibitory effect on the proliferation of leukemia, prostate and breast cancer cell lines. Further studies revealed that, the compound exhibited proapoptotic phenomenon of cytotoxicity. Interestingly, the compound did not display toxicity against the normal human fibroblast. It can be concluded that (-)-pseudosemiglabrin is worthy for further investigation as a potential chemotherapeutic agent. PMID:24608571
Isolation and structure elucidation of secondary metabolites in Central and South American Calea species and their biochemical systematic implications
Ober, A.G.
Fourteen species of the genus Calea (Family Compositae, Tribe Heliantheae) from Central and northern South America, including the type species for the genus, were investigated chemically to determine their secondary metabolites. The taxa studied were C. leptocephala Blake, C. megacephala Rob, and Greenm., and C. trichotoma B. Smith from Mexico, C. prunifolia Kunth (syn. C. pittieri) from Costa Rica, C. prunifolia Kunth from Panama, C. jamaicensis L. from Jamaica, and the Venezuelan species C. berteriana DC., C. divaricata Benthem, C. oliverii Rob. and Greenm., C. prunifolia Kunth, C. septuplinervia Hieron., C. solidaginea Kunth, and C. subcordata Kunth. The chemical investigation of these Calea species, undertaken as part of biochemical systematic study, has resulted in the isolation of 83 compounds, of which 38 are new natural products. The isolated compounds were represented by a dioxin derivative, 3 benzofuranes, 5 chromenes, 12 flavones, and 62 sesquiterpene lactones. The structures of the new compounds were established by chemical and spectroscopic methods. These methods included MS, IR, UV, and CD, /sup 1/H NMR, /sup 13/C NMR, and single crystal x-ray diffraction analysis.
Isolation, structure elucidation and in vivo hepatoprotective potential of trans-tetracos-15-enoic acid from Indigofera tinctoria Linn.
Singh, B; Chandan, B K; Sharma, N; Bhardwaj, V; Satti, N K; Gupta, V N; Gupta, B D; Suri, K A; Suri, O P
The bioassay guided fractionation of the dried aerial part of Indigofera tinctoria Linn. led to the identification of an active fraction labelled as indigotin. On further chemical analysis, a compound isolated from indigotin was identified and characterized as trans-tetracos-15-enoic acid (TCA). The chemical structure of this compound was established on the basis of physical properties and spectral data, including NMR. It afforded significant hepatoprotection against carbon tetrachloride and paracetamol induced hepatotoxicity in experimental models. Silymarin, a well known plant based hepatoprotective agent, and N-acetylcysteine, which has proven efficacy as a replenisher of sulfhydryls, were used for relative efficacy. TCA was found to reverse the altered hepatic parameters in experimental liver damage. In the safety evaluation study the oral LD50 was found to be more than 2000 mg/kg, with no signs of abnormalities or any mortality for the 15 day period of observation after administration of a single dose of drug in mice. The studies revealed significant and concentration dependent hepatoprotective potential of TCA as it reversed the majority of the altered hepatic parameters in experimental liver damage in rats and mice and may be useful in the management of liver disorders. PMID:16841368
Isolation, structure elucidation, and biomimetic total synthesis of versicolamide B and the isolation of antipodal (-)-stephacidin A and (+)-notoamide B from Aspergillus versicolor
Technology Transfer Automated Retrieval System (TEKTRAN)
A new prenylated indole alkaloid, versicolamide B, was isolated from cultures of Aspergillus versicolor NRRL 35600. The structure was assigned by 2D NMR data, and confirmed by a biomimetic total synthesis. Versicolamide B is the first member of the paraherquamide-stephacidin family of alkaloids fo...
Nature's Chiral Catalyst and Anti-Malarial Agent: Isolation and Structure Elucidation of Cinchonine and Quinine from "Cinchona calisaya"
ERIC Educational Resources Information Center
Carroll, Anne-Marie; Kavanagh, David J.; McGovern, Fiona P.; Reilly, Joe W.; Walsh, John J.
Nature is a well-recognized source of compounds of interest, but access is often an issue. One pertinent example is the cinchona alkaloids from the bark of "Cinchona calisaya." In this experiment, students at the third-year undergraduate level undertake the selective isolation and characterization of two of the four main alkaloids present in the…
(#Issue1)Medium optimization of Streptomyces sp. 17944 for tirandamycin B production and isolation and structural elucidation of tirandamycins H, I, and J†
Rateb, Mostafa E.; Yu, Zhiguo; Yan, Yijun; Yang, Dong; Huang, Tingting; Vodanovic-Jankovic, Sanja; Kron, Michael A.; Shen, Ben
We have recently isolated tirandamycin (TAM) B from Streptomyces sp. 17944 as a Brugia malayi AsnRS (BmAsnRS) inhibitor that efficiently kills the adult B. malayi parasites and does not exhibit general cytotoxicity to human hepatic cells. We now report (i) the comparison of metabolite profiles of S. sp. 17944 in six different media, (ii) identification of a medium enabling the production of TAM B as essentially the sole metabolite, and with improved titer, and (iii) isolation and structural elucidation of three new TAM congeners. These findings shed new insights into the structure-activity relationship of TAM B as a BmAsnRS inhibitor, highlighting the δ-hydroxymethyl-α,β-epoxyketone moiety as the critical pharmacophore, and should greatly facilitate the production and isolation of sufficient quantities of TAM B for further mechanistic and preclinical studies to advance the candidacy of TAM B as an antifilarial drug lead. The current study also serves as an excellent reminder that traditional medium and fermentation optimization should continue to be very effective in improving metabolite flux and titer. PMID:23715040
Using Genomics for Natural Product Structure Elucidation.
Tietz, Jonathan I; Mitchell, Douglas A
Natural products (NPs) are the most historically bountiful source of chemical matter for drug development-especially for anti-infectives. With insights gleaned from genome mining, interest in natural product discovery has been reinvigorated. An essential stage in NP discovery is structural elucidation, which sheds light not only on the chemical composition of a molecule but also its novelty, properties, and derivatization potential. The history of structure elucidation is replete with techniquebased revolutions: combustion analysis, crystallography, UV, IR, MS, and NMR have each provided game-changing advances; the latest such advance is genomics. All natural products have a genetic basis, and the ability to obtain and interpret genomic information for structure elucidation is increasingly available at low cost to non-specialists. In this review, we describe the value of genomics as a structural elucidation technique, especially from the perspective of the natural product chemist approaching an unknown metabolite. Herein we first introduce the databases and programs of interest to the natural products chemist, with an emphasis on those currently most suited for general usability. We describe strategies for linking observed natural product-linked phenotypes to their corresponding gene clusters. We then discuss techniques for extracting structural information from genes, illustrated with numerous case examples. We also provide an analysis of the biases and limitations of the field with recommendations for future development. Our overview is not only aimed at biologically-oriented researchers already at ease with bioinformatic techniques, but also, in particular, at natural product, organic, and/or medicinal chemists not previously familiar with genomic techniques. PMID:26456468
A novel isoquinoline alkaloid, DD-carboxypeptidase inhibitor, with antibacterial activity isolated from Streptomyces sp. 8812. Part II: Physicochemical properties and structure elucidation.
Solecka, Jolanta; Sitkowski, Jerzy; Bocian, Wojciech; Bednarek, Elzbieta; Kawecki, Robert; Kozerski, Lech
A novel antimicrobial agent labeled JS-1, being a member of isoquinoline alkaloids, of molecular formula C10H9NO4 was isolated from the culture broth of Streptomyces sp. 8812. In this study, we present the structure based on physicochemical and spectroscopic NMR investigations and on quantum chemical structure modeling. The structure of a molecule suggests the biosynthetic path starting from 3'-hydroxy tyrosine. The synthesis was undertaken and it resulted in NMR data that fully agree with the presented analysis. PMID:19713991
Structure Elucidation of Nigricanoside A Through Enantioselective Total Synthesis
Chen, Jie; Koswatta, Panduka; DeBergh, J. Robb; Fu, Peng; Pan, Ende; MacMillan, John B.; Ready, Joseph M.
Nigricanoside A was isolated from green alga, and its dimethyl ester was found to display potent cytotoxicity. Its scarcity prevented a full structure elucidation, leaving total synthesis as the only means to determine its relative and absolute stereochemistry and to explore its biological activity. Here we assign the stereochemistry of the natural product through enantioselective total synthesis and provide initial studies of its cytotoxicity. PMID:26877863
A new series of natural antifungals that inhibit P450 lanosterol C-14 demethylase. I. Taxonomy, fermentation, isolation and structural elucidation.
Matsukuma, S; Ohtsuka, T; Kotaki, H; Shirai, H; Sano, T; Watanabe, K; Nakayama, N; Itezono, Y; Fujiu, M; Shimma, N
A new series of antifungal antibiotics, Ro 09-1470 and its 6 congeners were isolated from the fermentation broth of Penicillium sp. NR6564. Their structures were determined as tetrahydropyran derivatives with an alkenyl side chain on the basis of their spectroscopic and physico-chemical properties. Among these compounds, Ro 09-1470 and Ro 09-1545 possessing a glycyl N-substituted glycyl ester residue had high antifungal activity. Ro 09-1469, one of the congeners, was found in the fermentation broth of several strains of Aspergillus sclerotiorum Huber. PMID:1556006
Possible degradation/biotransformation of lutein in vitro and in vivo: isolation and structural elucidation of lutein metabolites by HPLC and LC-MS (atmospheric pressure chemical ionization).
Lakshminarayana, Rangaswamy; Aruna, Gorusupudi; Sangeetha, Ravi Kumar; Bhaskar, Narayan; Divakar, Sounder; Baskaran, Vallikannan
Metabolites of lutein are highly concentrated in the human macula and are known to provide protection against age-related macular degeneration. The aim of this investigation was to characterize the in vitro oxidation products of lutein obtained through photo-oxidation and to compare them with biologically transformed dietary lutein in intestine, plasma, liver, and eyes of rats. In vivo studies involved feeding rats a diet devoid of lutein for 2 weeks to induce deficiency. Rats were divided into two equal groups (n=6/group) and received either micellar lutein by gavage for 10 days or diet supplemented with fenugreek leaves as a lutein source for 4 weeks. Lutein metabolites/oxidation products obtained from in vivo and in vitro studies were characterized by HPLC and LC-MS (APCI) techniques to elucidate their structure. The characteristic fragmented ions resulting from photo-oxidation of lutein were identified as 523 (M(+)+H(+)-3CH(3)), 476 (M(+)+H(+)-6CH(3)), and 551 (M(+)+H(+)-H(2)O). In the eyes, the fragmented molecules resulting from lutein were 13-Z lutein, 13'-Z lutein, 13-Z zeaxanthin, all-E zeaxanthin, 9-Z lutein, 9'-Z lutein, and 3'-oxolutein. Epoxycarotenoids were identified in liver and plasma, whereas anhydrolutein was identified in intestine. This study emphasizes the essentiality of dietary lutein to maintain its status in the retina. PMID:18640265
Isolation, Characterization, Crystal Structure Elucidation of Two Flavanones and Simultaneous RP-HPLC Determination of Five Major Compounds from Syzygium campanulatum Korth.
Memon, Abdul Hakeem; Ismail, Zhari; Al-Suede, Fouad Saleih Resq; Aisha, Abdalrahim F A; Hamil, Mohammad Shahrul Ridzuan; Saeed, Mohammed Ali Ahmed; Laghari, Madeeha; Majid, Amin Malik Shah Abdul
Two flavanones named (2S)-7-Hydroxy-5-methoxy-6,8-dimethyl flavanone (1), (S)-5,7-dihydroxy-6,8-dimethyl-flavanone (2), along with known chalcone, namely, (E)-2',4'- dihydroxy-6'-methoxy-3',5'-dimethylchalcone (3) and two triterpenoids, namely, betulinic and ursolic acids (4 and 5), were isolated from the leaves of Syzygium campanulatum Korth (Myrtaceae). The structures of compounds (1 and 2) were determined on the basis of UV-visible, FTIR, NMR spectroscopies and LC-EIMS analytical techniques. Furthermore, new, simple, precise, selective, accurate, highly sensitive, efficient and reproducible RP-HPLC method was developed and validated for the quantitative analysis of the compounds (1-5) from S. campanulatum plants of five different age. RP-HPLC method was validated in terms of specificity, linearity (r2 ≤ 0.999), precision (2.0% RSD), and recoveries (94.4%-105%). The LOD and LOQ of these compounds ranged from 0.13-0.38 and 0.10-2.23 μg·mL-1, OPEN ACCESS respectively. Anti-proliferative activity of isolated flavanones (1 and 2) and standardized extract of S. campanulatum was evaluated on human colon cancer (HCT 116) cell line. Compounds (1 and 2) and extract revealed potent and dose-dependent activity with IC50 67.6, 132.9 and 93.4 μg·mL-1, respectively. To the best of our knowledge, this is the first study on isolation, characterization, X-ray crystallographic analysis of compounds (1 and 2) and simultaneous RP-HPLC determination of five major compounds (1-5) from different age of S. campanulatum plants. PMID:26248073
Structure Elucidation, Relative LC-MS Response and In Vitro Toxicity of Azaspiracids 7-10 Isolated from Mussels (Mytilus edulis).
Kilcoyne, Jane; Twiner, Michael J; McCarron, Pearse; Crain, Sheila; Giddings, Sabrina D; Foley, Barry; Rise, Frode; Hess, Philipp; Wilkins, Alistair L; Miles, Christopher O
Azaspiracids (AZAs) are marine biotoxins produced by dinoflagellates that can accumulate in shellfish, which if consumed can lead to poisoning events. AZA7-10, 7-10, were isolated from shellfish and their structures, previously proposed on the basis of only LC-MS/MS data, were confirmed by NMR spectroscopy. Purified AZA4-6, 4-6, and 7-10 were accurately quantitated by qNMR and used to assay cytotoxicity with Jurkat T lymphocyte cells for the first time. LC-MS(MS) molar response studies performed using isocratic and gradient elution in both selected ion monitoring and selected reaction monitoring modes showed that responses for the analogues ranged from 0.3 to 1.2 relative to AZA1, 1. All AZA analogues tested were cytotoxic to Jurkat T lymphocyte cells in a time- and concentration-dependent manner; however, there were distinct differences in their EC50 values, with the potencies for each analogue being: AZA6 > AZA8 > AZA1 > AZA4 ≈ AZA9 > AZA5 ≈ AZA10. This data contributes to the understanding of the structure-activity relationships of AZAs. PMID:25909151
New Isolated-Pentagon-Rule and Skeletally Transformed Isomers of C100 Fullerene Identified by Structure Elucidation of their Chloro Derivatives.
Wang, Song; Yang, Shangfeng; Kemnitz, Erhard; Troyanov, Sergey I
High-temperature chlorination of C100 fullerene followed by X-ray structure determination of the chloro derivatives enabled the identification of three isomers of C100 from the fullerene soot, specifically numbers 18, 425, and 417, which obey the isolated pentagon rule (IPR). Among them, isomers C1-C100 (425) and C2-C100 (18) afforded C1-C100 (425)Cl22 and C2-C100 (18)Cl28/30 compounds, respectively, which retain their IPR cage connectivities. In contrast, isomer C2v -C100 (417) gives Cs -C100 (417)Cl28 which undergoes a skeletal transformation by the loss of a C2 fragment, resulting in the formation of a nonclassical (NC) C1-C98 (NC)Cl26 with a heptagon in the carbon cage. Most probably, two nonclassical C1-C100 (NC)Cl18/22 chloro derivatives originate from the IPR isomer C1-C100 (382), although both C1-C100 (344) and even nonclassical C1-C100 (NC) can be also considered as the starting isomers. PMID:26848074
Structure elucidation of a process-related impurity of dapoxetine.
Darcsi, András; Tóth, Gergő; Kökösi, József; Béni, Szabolcs
Unknown by-product associated with the synthesis of dapoxetine was isolated. The structure elucidation of this new compound using accurate mass data and NMR spectroscopy is presented herein. The unambiguous resonance assignment concluded to the formation of a tricyclic compound 4-phenyl-2H,3H,4H-naphtho[1,2-b]pyran, a new impurity of dapoxetine which has never been reported previously. A proposed mechanism for the formation of the new carbon-carbon bond is discussed. For the separation of dapoxetine and the process-related impurities, a gradient HPLC method was developed. PMID:24793500
Ultrahigh-performance liquid chromatography-ion trap mass spectrometry characterization of the steroidal saponins of Dioscorea panthaica Prain et Burkill and its application for accelerating the isolation and structural elucidation of steroidal saponins.
Wang, Weihao; Zhao, Ye; Jing, Wenguang; Zhang, Jun; Xiao, Hui; Zha, Qin; Liu, An
Dioscorea panthaica is a traditional Chinese medicinal herb used in the treatment of various physiological conditions, including cardiovascular disease, gastropathy and hypertension. Steroidal saponins (SS) are the main active ingredients of this herb and have effects on myocardial ischemia and cancer. The phytochemical evaluation of SS is both time-consuming and laborious, and the isolation and structural determination steps can be especially demanding. For this reason, the development of new methods to accelerate the processes involved in the identification, isolation and structural elucidation of SS is highly desirable. In this study, a new ultrahigh performance liquid chromatography-ion trap mass spectrometry (UHPLC-IT/MS(n)) method has been developed for the identification of the SS in D. panthaica Prain et Burkill. Notably, the current method can distinguish between spirostanol and furostanol-type compounds based on the fragmentation patterns observed by electrospray ionization-ion trap mass spectrometry (ESI-IT/MS(n)) analysis. UHPLC-IT/MS(n) was used to conduct a detailed investigation of the number, structural class and order of the sugar moieties in the sugar chains of the SS present in D. panthaica. The established fragmentation features were used to analyze the compounds found in the 65% ethanol fraction of the water extracts of D. panthaica. Twenty-three SS were identified, including 11 potential new compounds and six groups of isomers. Two of these newly identified SS were selected as representative examples, and their chemical structures were confirmed by (1)H and (13)C NMR analyses. This newly developed UHPLC-IT/MS(n) method therefore allowed for the efficient identification, isolation and structural determination of the SS in D. panthaica. PMID:25575790
Isolation and Structural Elucidation of Brevibacillin, an Antimicrobial Lipopeptide from Brevibacillus laterosporus That Combats Drug-Resistant Gram-Positive Bacteria.
Yang, Xu; Huang, En; Yuan, Chunhua; Zhang, Liwen; Yousef, Ahmed E
A new environmental bacterial strain exhibited strong antimicrobial characteristics against methicillin-resistantStaphylococcus aureus, vancomycin-resistant strains ofEnterococcus faecalisandLactobacillus plantarum, and other Gram-positive bacteria. The producer strain, designated OSY-I1, was determined to beBrevibacillus laterosporusvia morphological, biochemical, and genetic analyses. The antimicrobial agent was extracted from cells of OSY-I1with isopropanol, purified by high-performance liquid chromatography, and structurally analyzed using mass spectrometry (MS) and nuclear magnetic resonance (NMR). The MS and NMR results, taken together, uncovered a linear lipopeptide consisting of 13 amino acids and an N-terminal C6fatty acid (FA) chain, 2-hydroxy-3-methylpentanoic acid. The lipopeptide (FA-Dhb-Leu-Orn-Ile-Ile-Val-Lys-Val-Val-Lys-Tyr-Leu-valinol, where Dhb is α,β-didehydrobutyric acid and valinol is 2-amino-3-methyl-1-butanol) has a molecular mass of 1,583.0794 Da and contains three modified amino acid residues: α,β-didehydrobutyric acid, ornithine, and valinol. The compound, designated brevibacillin, was determined to be a member of a cationic lipopeptide antibiotic family. In addition to its potency against drug-resistant bacteria, brevibacillin also exhibited low MICs (1 to 8 μg/ml) against selected foodborne pathogenic and spoilage bacteria, such asListeria monocytogenes,Bacillus cereus, andAlicyclobacillus acidoterrestris Purified brevibacillin showed no sign of degradation when it was held at 80°C for 60 min, and it retained at least 50% of its antimicrobial activity when it was held for 22 h under acidic or alkaline conditions. On the basis of these findings, brevibacillin is a potent antimicrobial lipopeptide which is potentially useful to combat drug-resistant bacterial pathogens and foodborne pathogenic and spoilage bacteria. PMID:26921428
Transcription initiation complex structures elucidate DNA opening.
Plaschka, C; Hantsche, M; Dienemann, C; Burzinski, C; Plitzko, J; Cramer, P
Transcription of eukaryotic protein-coding genes begins with assembly of the RNA polymerase (Pol) II initiation complex and promoter DNA opening. Here we report cryo-electron microscopy (cryo-EM) structures of yeast initiation complexes containing closed and open DNA at resolutions of 8.8 Å and 3.6 Å, respectively. DNA is positioned and retained over the Pol II cleft by a network of interactions between the TATA-box-binding protein TBP and transcription factors TFIIA, TFIIB, TFIIE, and TFIIF. DNA opening occurs around the tip of the Pol II clamp and the TFIIE 'extended winged helix' domain, and can occur in the absence of TFIIH. Loading of the DNA template strand into the active centre may be facilitated by movements of obstructing protein elements triggered by allosteric binding of the TFIIE 'E-ribbon' domain. The results suggest a unified model for transcription initiation with a key event, the trapping of open promoter DNA by extended protein-protein and protein-DNA contacts. PMID:27193681
NMR spectroscopy: structure elucidation of cycloelatanene A: a natural product case study.
Urban, Sylvia; Dias, Daniel Anthony
The structure elucidation of new secondary metabolites derived from marine and terrestrial sources is frequently a challenging task. The hurdles include the ability to isolate stable secondary metabolites of sufficient purity that are often present in <0.5 % of the dry weight of the sample. This usually involves a minimum of several chromatographic purification steps. The second issue is the stability of the compound isolated. It must always be assumed when dealing with the isolation of natural products that the compound may rapidly degrade during and/or after the isolation, due to sensitivity to light, air oxidation, and/or temperature. In this way, precautions need to be taken, as much as possible to avoid any such chemical inter-conversions and/or degradations. Immediately after purification, the next step is to rapidly acquire all analytical spectroscopic data in order to complete the characterization of the isolated secondary metabolite(s), prior to any possible decomposition. The final hurdle in this multiple step process, especially in the acquisition of the NMR spectroscopic and other analytical data (mass spectra, infrared and ultra-violet spectra, optical rotation, etc.), is to assemble the structural moieties/units in an effort to complete the structure elucidation. Often ambiguity with the elucidation of the final structure remains when structural fragments identified are difficult to piece together on the basis of the HMBC NMR correlations or when the relative configuration cannot be unequivocally identified on the basis of NOE NMR enhancements observed. Herein, we describe the methodology used to carry out the structure elucidation of a new C16 chamigrene, cycloelatanene A (5) which was isolated from the southern Australian marine alga Laurencia elata (Rhodomelaceae). The general approach and principles used in the structure determination of this compound can be applied to the structure elucidation of other small molecular weight compounds derived
Applications of a HOUDINI-based structure elucidation system.
Schulz, K-P; Korytko, A; Munk, M E
SESAMI, a comprehensive program for the elucidation of the structure of complex compounds of carbon, incorporates a structure reduction-based structure genearator (COCOA). Observed limitations with this program in the solution of higher molecular weight unknowns prompted the development of a structure generator (HOUDINI) which embodies a new concept, convergent structure generation. A comparison of the performance of COCOA-based and HOUDINI-based SESAMI using a set of complex, naturally occurring compounds as a test set of unknowns revealed faster execution times and more efficient processing of ambiguous structural information for the latter. PMID:14502477
Microscale Methodology for Structure Elucidation of Natural Products
Molinski, Tadeusz F.
1. Summary of Recent Advances Advances in microscale spectroscopic techniques, particularly microcryoprobe NMR, allow discovery and structure elucidation of new molecules down to only a few nanomole. Newer methods for utilizing circular dichroism (CD) have pushed the limits of detection to picomole levels. NMR and CD methods are complementary to the task of elucidation of complete stereostructures of complex natural products. Together, integrated microprobe NMR spectroscopy, microscale degradation and synthesis, are synergistic tools for discovery of bioactive natural products and have opened new realm for discovery among extreme sources including compounds from uncultured microbes, rare invertebrates and environmental samples. PMID:20880694
Elucidating the stop bands of structurally colored systems through recursion
NASA Astrophysics Data System (ADS)
Amir, Ariel; Vukusic, Peter
Interference is the source of some of the spectacular colors of animals and plants in nature. In some of these systems, the physical structure consists of an ordered array of layers with alternating high and low refractive indices. This periodicity leads to an optical band structure that is analogous to the electronic band structure encountered in semiconductor physics: specific bands of wavelengths (the stop bands) are perfectly reflected. Here, we present a minimal model for optical band structure in a periodic multilayer structure and solve it using recursion relations. The stop bands emerge in the limit of an infinite number of layers by finding the fixed point of the recursion. We compare to experimental data for various beetles, whose optical structure resembles the proposed model. Thus, using only the phenomenon of interference and the idea of recursion, we are able to elucidate the concept of band structure in the context of the experimentally observed high reflectance and iridescent appearance of structurally colored beetles.
Toward structural elucidation of the gamma-secretase complex
Li, H.; Wolfe, M. S.; Selkoe, D. J.
{gamma}-Secretase is an intramembrane protease complex that mediates the Notch signaling pathway and the production of amyloid {beta}-proteins. As such, this enzyme has emerged as an important target for development of novel therapeutics for Alzheimer disease and cancer. Great progress has been made in the identification and characterization of the membrane complex and its biological functions. One major challenge now is to illuminate the structure of this fascinating and important protease at atomic resolution. Here, we review recent progress on biochemical and biophysical probing of the structure of the four-component complex and discuss obstacles and potential pathways toward elucidating its detailed structure.
Toward structural elucidation of the γ-secretase complex
Li, Huilin; Wolfe, Michael S.; Selkoe, Dennis J.
γ-Secretase is an intramembrane protease complex that mediates the Notch signaling pathway and the production of amyloid β-proteins. As such, this enzyme has emerged as an important target for development of novel therapeutics for Alzheimer disease and cancer. Great progress has been made in the identification and characterization of the membrane complex and its biological functions. One major challenge now is to illuminate the structure of this fascinating and important protease at atomic resolution. Here, we review recent progress on biochemical and biophysical probing of the structure of the four-component complex and discuss barriers and potential pathways toward elucidating its detailed structure. PMID:19278647
Structure elucidation and complete NMR spectral assignments of four new diterpenoids from Smallantus sonchifolius.
Dou, De-Qiang; Tian, Fang; Qiu, Ying-Kun; Kang, Ting-Guo; Dong, Feng
Four new diterpenoids, named smaditerpenic acid A-D, together with five known compounds, were isolated from the H(2)O extract of the leaves of Smallantus sonchifolius (yacon) cultivated in Liaoning, China and their structures were elucidated on the basis of one- and two-dimensional NMR (including (1)H, (13)C-NMR, (1)H-(1)H COSY, HSQC, TOCSY, HMBC, and ROESY), electrospray ionization mass spectrometry (ESI-MS), and chemical methods. PMID:18470882
Crystal structure and spectroscopic elucidation of 3-phenylpyridinium hydrogensquarate.
Koleva, Bojidarka B; Kolev, Tsonko; Tsanev, Tsanko; Kotov, Stefan; Mayer-Figge, Heike; Spiteller, Michael; Sheldrick, William S
The novel 3-phenylpyridinium hydrogensquarate (1) has been synthesized and its structure and properties are elucidated spectroscopically, thermally and structurally, using single crystal X-ray diffraction, linear-polarized solid-state IR-spectroscopy, UV-spectroscopy, TGA, DSC, DTA and ESI MS. Quantum chemical calculations were used to obtain the electronic structure, vibrational data and electronic spectrum. 3-Phenylpyridinium hydrogensquarate, crystallizes in the space group P-1 and the ions in the unit cell are joined into layers by intermolecular NH...O=C((Sq)) bonds with bond lengths of 2.625 and 2.626 A, respectively. Hydrogentartarates form dimers by strong O=COH...OCO interactions (2.499 A). PMID:19931483
Tyrammonium 4-nitrophthalate dihydrate: structural and spectroscopic elucidation.
Kolev, Tsonko; Koleva, Bojidarka B; Seidel, Rüdiger W; Mayer-Figge, Heike; Spiteller, Michael; Sheldrick, William S
Tyrammonium 4-nitrophthalate has been synthesized and its structural and spectroscopic properties elucidated by single-crystal X-ray diffraction, solid-state polarized IR-spectroscopy of oriented colloids in a nematic host, HPLC with tandem mass spectrometry (HPLC ESI-MSMS), and TGV and DSC methods. The compound crystallizes in the monoclinic P2(1)/c space group and its structure consists of a 3D network of molecules joined by intermolecular interactions with the participation of cations, anions and two solvent molecules. The tyrammonium cation adopts a T trans configuration with corresponding angles of phi (1) = 76.0(4) degrees, phi (2 )= 54.8(1) degrees and phi (3) = 63.4(1) degrees, respectively. In the 4-nitrophthalate anion, the COO(-) and COOH groups are turned off the plane of the benzene ring at angles of tau (1) = 88.1(5) degrees and tau (2)= 22.1(7) degrees, respectively. PMID:18188664
Towards elucidation of dynamic structural changes of plant thylakoid architecture
Anderson, Jan M.; Horton, Peter; Kim, Eun-Ha; Chow, Wah Soon
Long-term acclimation of shade versus sun plants modulates the composition, function and structural organization of the architecture of the thylakoid membrane network. Significantly, these changes in the macroscopic structural organization of shade and sun plant chloroplasts during long-term acclimation are also mimicked following rapid transitions in irradiance: reversible ultrastructural changes in the entire thylakoid membrane network increase the number of grana per chloroplast, but decrease the number of stacked thylakoids per granum in seconds to minutes in leaves. It is proposed that these dynamic changes depend on reversible macro-reorganization of some light-harvesting complex IIb and photosystem II supracomplexes within the plant thylakoid network owing to differential phosphorylation cycles and other biochemical changes known to ensure flexibility in photosynthetic function in vivo. Some lingering grana enigmas remain: elucidation of the mechanisms involved in the dynamic architecture of the thylakoid membrane network under fluctuating irradiance and its implications for function merit extensive further studies. PMID:23148278
Advances in structure elucidation of small molecules using mass spectrometry
Fiehn, Oliver
The structural elucidation of small molecules using mass spectrometry plays an important role in modern life sciences and bioanalytical approaches. This review covers different soft and hard ionization techniques and figures of merit for modern mass spectrometers, such as mass resolving power, mass accuracy, isotopic abundance accuracy, accurate mass multiple-stage MS(n) capability, as well as hybrid mass spectrometric and orthogonal chromatographic approaches. The latter part discusses mass spectral data handling strategies, which includes background and noise subtraction, adduct formation and detection, charge state determination, accurate mass measurements, elemental composition determinations, and complex data-dependent setups with ion maps and ion trees. The importance of mass spectral library search algorithms for tandem mass spectra and multiple-stage MS(n) mass spectra as well as mass spectral tree libraries that combine multiple-stage mass spectra are outlined. The successive chapter discusses mass spectral fragmentation pathways, biotransformation reactions and drug metabolism studies, the mass spectral simulation and generation of in silico mass spectra, expert systems for mass spectral interpretation, and the use of computational chemistry to explain gas-phase phenomena. A single chapter discusses data handling for hyphenated approaches including mass spectral deconvolution for clean mass spectra, cheminformatics approaches and structure retention relationships, and retention index predictions for gas and liquid chromatography. The last section reviews the current state of electronic data sharing of mass spectra and discusses the importance of software development for the advancement of structure elucidation of small molecules. Electronic supplementary material The online version of this article (doi:10.1007/s12566-010-0015-9) contains supplementary material, which is available to authorized users. PMID:21289855
X-ray structure of dopamine transporter elucidates antidepressant mechanism.
Penmatsa, Aravind; Wang, Kevin H; Gouaux, Eric
Antidepressants targeting Na(+)/Cl(-)-coupled neurotransmitter uptake define a key therapeutic strategy to treat clinical depression and neuropathic pain. However, identifying the molecular interactions that underlie the pharmacological activity of these transport inhibitors, and thus the mechanism by which the inhibitors lead to increased synaptic neurotransmitter levels, has proven elusive. Here we present the crystal structure of the Drosophila melanogaster dopamine transporter at 3.0 Å resolution bound to the tricyclic antidepressant nortriptyline. The transporter is locked in an outward-open conformation with nortriptyline wedged between transmembrane helices 1, 3, 6 and 8, blocking the transporter from binding substrate and from isomerizing to an inward-facing conformation. Although the overall structure of the dopamine transporter is similar to that of its prokaryotic relative LeuT, there are multiple distinctions, including a kink in transmembrane helix 12 halfway across the membrane bilayer, a latch-like carboxy-terminal helix that caps the cytoplasmic gate, and a cholesterol molecule wedged within a groove formed by transmembrane helices 1a, 5 and 7. Taken together, the dopamine transporter structure reveals the molecular basis for antidepressant action on sodium-coupled neurotransmitter symporters and elucidates critical elements of eukaryotic transporter structure and modulation by lipids, thus expanding our understanding of the mechanism and regulation of neurotransmitter uptake at chemical synapses. PMID:24037379
Elucidation of the structures of all members of the Avsunviroidae family.
Giguère, Tamara; Adkar-Purushothama, Charith Raj; Bolduc, François; Perreault, Jean-Pierre
Viroids are small single-stranded RNA pathogens which cause significant damage to plants. As their nucleic acids do not encode for any proteins, they are dependant solely on their structure for their propagation. The elucidation of the secondary structures of viroids has been limited because of the exhaustive and time consuming nature of classic approaches. Here, the method of high-throughput selective 2'-hydroxyl acylation analysed by primer extension (hSHAPE) has been adapted to probe the viroid structure. The data obtained using this method were then used as input for computer-assisted structure prediction using RNA structure software in order to determine the secondary structures of the RNA strands of both (+) and (–) polarities of all Avsunviroidae members, one of the two families of viroids. The resolution of the structures of all of the members of the family provides a global view of the complexity of these RNAs. The structural differences between the two polarities, and any plausible tertiary interactions, were also analysed. Interestingly, the structures of the (+) and (–) strands were found to be different for each viroid species. The structures of the recently isolated grapevine hammerhead viroid-like RNA strands were also solved. This species shares several structural features with the Avsunviroidae family, although its infectious potential remains to be determined.To our knowledge, this article represents the first report of the structural elucidation of a complete family of viroids. PMID:25346967
Spectroscopic elucidation of chemical structure of plasma-polymerized pyridine
Hozumi, K.; Kitamura, K.; Hashimoto, H.; Hamaoka, T.; Fujisawa, H.; Ishizawa, T.
Chemical structure of the plasma-polymerized pyridine film produced on a glass reactor wall by means of the plasma technique in which the pyridine vapor was electronically excited by high-frequency power under a reduced pressure was elucidated. The polymer was highly hydrophilic and was soluble to some of the polar organic solvents so that nitrogen-containing polar functional groups were predicted to participate in the chemical structure of the polymer molecules. /sup 1/H-NMR, /sup 13/CNMR, and IR spectroscopies, high-resolution mass spectral data, and number-average molecular weight determination with some aid of microelemental analysis revealed the presence of various functional groups such as imine, nitrile, amine, pyridine ring, its N-oxide, and even amide. The oxygen atoms involved in the last two groups were supposedly introduced by contact with ambient air after the plasma process. The hydrophilic nature of the polymer which was essential for preparing reverse osmosis membrane was therefore due to the overall hydration effect of these polar functional groups.
Identification and structural elucidation of ozonation transformation products of estrone
Background Quantitative methods for the analysis of contaminants of emerging concern (CECs) are abundant in the scientific literature. However, there are few reports on systematic methods of identification and structural identification of transformation products. For this reason, a new method based on high-resolution mass spectrometry and differential analysis was developed in order to facilitate and accelerate the process of identification and structural elucidation of transformation products CECs. This method was applied to the study of ozonation transformation products (OTPs) of the natural hormone estrone (E1). Results A control compare trend experiment consisting in the comparison of a control sample to several samples having been exposed to decreasing concentrations of O3(aq) indicated that 593 peaks could be associated with OTPs. After applying various filters to remove background noise, sample contaminants and signal spikes, this data set was reduced to 16 candidate peaks. By inspection of the shape of these peaks, only two compounds OTP-276 (m/z 275.12930) and OTP-318 (m/z 317.14008) were considered as good candidates for further study. Multi-stage tandem mass spectrometry (MSn) experiments of SPE extracts of the ozonated samples of E1 and of a deuterium-labeled analogue (E1-d4) showed that OTP-276 and OTP-318 had carboxylic acid and hydroxyl functional groups, as previously reported for OTPs of other hormones. Structures for these two compounds were proposed based on their MSn spectra. Conclusion These results indicate that the method proposed is a systematic and rapid approach to study transformation products of CECs. PMID:23618537
Pyripyropenes, novel ACAT inhibitors produced by Aspergillus fumigatus. IV. Structure elucidation of pyripyropenes M to R.
Tomoda, H; Tabata, N; Yang, D J; Namatame, I; Tanaka, H; Omura, S; Kaneko, T
Six new pyripyropenes, M to R, were isolated from the ethyl acetate extracts of the jar fermentation broth of Aspergillus fumigatus FO-1289-2501. Structural elucidation indicated that all the pyripyropenes have the same pyridino-alpha-pyrone sesquiterpene core as pyripyropenes A to L. Among them pyripyropene M showed the most potent inhibition against acyl-CoA : cholesterol acyltransferase activity with an IC50 value of 3.80 microM in rat liver microsomes, but pyripyropenes N to R showed moderate inhibitory activity (IC50 11.0 approximately 78.0 microM). PMID:8626247
Pyripyropenes, Novel ACAT inhibitors produced by Aspergillus fumigatus. III. Structure elucidation of pyripyropenes E to L.
Tomoda, H; Tabata, N; Yang, D J; Takayanagi, H; Nishida, H; Omura, S; Kaneko, T
Eight new pyripyropenes, E to L, were isolated from the culture broth of Aspergillus fumigatus FO-1289-2501 selected as a higher producer by NTG mutation. Structural elucidation indicated that all the pyripyropenes have the same pyridino-alpha-pyrone sesquiterpene core as pyripyropenes A to D. Among them, pyripyropene L showed the most potent inhibition against acyl-CoA: cholesterol acyltransferase (ACAT) activity with an IC50 value of 0.27 microM in rat liver microsomes. PMID:7622436
Structure elucidation of organic compounds from natural sources using 1D and 2D NMR techniques
NASA Astrophysics Data System (ADS)
Topcu, Gulacti; Ulubelen, Ayhan
In our continuing studies on Lamiaceae family plants including Salvia, Teucrium, Ajuga, Sideritis, Nepeta and Lavandula growing in Anatolia, many terpenoids, consisting of over 50 distinct triterpenoids and steroids, and over 200 diterpenoids, several sesterterpenoids and sesquiterpenoids along with many flavonoids and other phenolic compounds have been isolated. For Salvia species abietanes, for Teucrium and Ajuga species neo-clerodanes for Sideritis species ent-kaurane diterpenes are characteristic while nepetalactones are specific for Nepeta species. In this review article, only some interesting and different type of skeleton having constituents, namely rearranged, nor- or rare diterpenes, isolated from these species will be presented. For structure elucidation of these natural diterpenoids intensive one- and two-dimensional NMR techniques ( 1H, 13C, APT, DEPT, NOE/NOESY, 1H- 1H COSY, HETCOR, COLOC, HMQC/HSQC, HMBC, SINEPT) were used besides mass and some other spectroscopic methods.
Structural elucidation of two new megastigmane glycosides from the leaves of Aquilaria sinensis.
Sun, Jian; Xia, Fang; Wang, Shu; Wang, Ke-Yuan; Chen, Jin-Ming; Tu, Peng-Fei
The present study was designed to determine the chemical constituents and identify new components of the leaves of Aquilaria sinensis (Lour.) Gilg. The compounds were isolated and purified by repeated silica gel, Sephadex LH-20, and ODS column chromatography and their structures were elucidated by NMR and HR-ESI-MS spectrometry. Eight megastigmane glycosides and two cucurbitacins were isolated and identified as (9S) megastigma-4,7-diene-2,3,9-triol 9-O-β-D-glucopyranoside (1), (9S) megastigma-4(13),7-diene-3,6,9-triol 9-O-β-D-glucopyranoside (2), macarangloside D (3), corchoionoside C (4), staphylionoside H (5), (+) 3-oxo-α-ionol-β-D-glucopyranoside (6), (-) 3-oxo-α-ionol-β-D-glucopyranoside (7), citroside B (8), 2-O-β-D-glucopyranosyl cucurbitacin I (9), bryoamaride (10). Compounds 1 and 2 were newly identified megstigmane glucosides and reported from this genus for the first time. PMID:25908626
Structural elucidation of humulone autoxidation products and analysis of their occurrence in stored hops.
Taniguchi, Yoshimasa; Taniguchi, Harumi; Matsukura, Yasuko; Kawachi, Yasuji; Shindo, Kazutoshi
The transformation of α-acids [in hops (Humulus lupulus L.)] to iso-α-acids (in beer) during the brewing process is well known, but the occurrence and structure of the oxidized α-acids during hop storage are not well documented. Because an understanding of these oxidized compounds is essential to optimize the effects of oxidized hops on the quality of beer, we investigated the autoxidation products of humulone (a representative congener of α-acids) using a simplified autoxidation model. Among the oxidation products, tricyclooxyisohumulones A (1) and B (2), tricycloperoxyisohumulone A (3), deisopropyltricycloisohumulone (4), and the hemiacetal 5 of tricycloperoxyhumulone A (5') were isolated, and their structures were elucidated for the first time. The occurrence of compounds 1-4 in stored hops was verified using LC/MS/MS analysis. We also monitored the levels of compounds 1-4 during hop storage using LC/MS/MS analysis. PMID:24875004
Structure elucidation of metabolites of swertiamarin produced by Aspergillus niger
NASA Astrophysics Data System (ADS)
Jun, Chang; Xue-Ming, Zhao; Chang-Xiao, Liu; Tie-Jun, Zhang
The in vitro metabolism of swertiamarin was carried out in preparative scale using the fungus Aspergillus niger and the metabolites were isolated by semi-preparative HPLC combined with liquid-liquid extraction. Two metabolites, erythrocentaurin and one new compound were obtained and identified by 1H, 13C and 2D NMR and high resolution MS. The anti-inflammatory activity of the novel metabolite was tested and compared with that of swertiamarin in a mice model.
Structure Elucidation and Immunomodulatory Activity of A Beta Glucan from the Fruiting Bodies of Ganoderma sinense
Yue, Rui-Qi; Dong, Cai-Xia; Chan, Chung-Lap; Ko, Chun-Hay; Cheung, Wing-Shing; Luo, Ke-Wang; Dai, Hui; Wong, Chun-Kwok; Leung, Ping-Chung; Han, Quan-Bin
A polysaccharide named GSP-2 with a molecular size of 32 kDa was isolated from the fruiting bodies of Ganoderma sinense. Its structure was well elucidated, by a combined utilization of chemical and spectroscopic techniques, to be a β-glucan with a backbone of (1→4)– and (1→6)–Glcp, bearing terminal- and (1→3)–Glcp side-chains at O-3 position of (1→6)–Glcp. Immunological assay exhibited that GSP-2 significantly induced the proliferation of BALB/c mice splenocytes with target on only B cells, and enhanced the production of several cytokines in human peripheral blood mononuclear cells and derived dendritic cells. Besides, the fluorescent labeled GSP-2 was phagocytosed by the RAW 264.7 cells and induced the nitric oxide secretion from the cells. PMID:25014571
Elucidation of kinematical and dynamical structure of the Galactic bulge
NASA Astrophysics Data System (ADS)
Yano, T.; Gouda, N.; Ueda, H.; Koyama, H.; Kan-ya, Y.; Taruya, A.
Future space mission of astrometric satellite, GAIA and JASMINE (Japan Astrometry Satellite Mission for Infrared Exploration), will produce astrometric parameter, such as positions, parallaxes, and proper motions of stars in the Galactic bulge. Then kinematical information will be obtained in the future. Accordingly it is expected that our understanding of the dynamical structure will be greatly improved. Therefore it is important to make a method to construct a kinematical and dynamical structure of the Galactic bulge immediately.
Structure elucidation and DNA binding specificity of natural compounds from Cassia siamea leaves: A biophysical approach.
Parveen, Mehtab; Ahmad, Faheem; Malla, Ali Mohammed; Khan, Mohd Sohrab; Rehman, Sayeed Ur; Tabish, Mohammad; Silva, Manuela Ramos; Silva, P S Pereira
A novel isoflavone, 5,6,7-trimethoxy-3-(3',4',5'-trimethoxyphenyl)-4H-chromen-4-one (1) along with a known pyranocoumarin, Seselin (2) have been isolated from the ethanolic extract of the leaves of Cassia siamea (Family: Fabaceae). Compound 1 has been reported for the first time from any natural source and has not been synthesized so far. Their structures were elucidated on the basis of chemical and physical evidences viz. elemental analysis, UV, FT-IR, (1)H-NMR, (13)C-NMR and mass spectral analysis. Structure of compound (1) was further authenticated by single-crystal X-ray analysis and density functional theory (DFT) calculations. A multi-technique approach employing UV-Visible spectroscopy, fluorescence, KI quenching studies, competitive displacement assay, circular dichroism and viscosity studies have been utilized to probe the extent of interaction and possible binding modes of isolated compounds (1-2) with calf thymus DNA (CT-DNA). Both the compounds were found to interact with DNA via non-intercalative binding mode with moderate proficiencies. Groove binding was the major interaction mode in the case of compound 2 while compound 1 probably interacts with DNA through electrostatic interactions. These studies provide deeper insight in understanding of DNA-drug (natural products) interaction which could be helpful to improve their bioavailability for therapeutic purposes. PMID:27085054
Optimization techniques in molecular structure and function elucidation.
Sahinidis, Nikolaos V
This paper discusses recent optimization approaches to the protein side-chain prediction problem, protein structural alignment, and molecular structure determination from X-ray diffraction measurements. The machinery employed to solve these problems has included algorithms from linear programming, dynamic programming, combinatorial optimization, and mixed-integer nonlinear programming. Many of these problems are purely continuous in nature. Yet, to this date, they have been approached mostly via combinatorial optimization algorithms that are applied to discrete approximations. The main purpose of the paper is to offer an introduction and motivate further systems approaches to these problems. PMID:20160866
Compositional analysis and structural elucidation of glycosaminoglycans in chicken eggs.
Liu, Zhangguo; Zhang, Fuming; Li, Lingyun; Li, Guoyun; He, Wenqing; Linhardt, Robert J
Glycosaminoglycans (GAGs) have numerous applications in the fields of pharmaceuticals, cosmetics, nutraceuticals, and foods. GAGs are also critically important in the developmental biology of all multicellular animals. GAGs were isolated from chicken egg components including yolk, thick egg white, thin egg white, membrane, calcified shell matrix supernatant, and shell matrix deposit. Disaccharide compositional analysis was performed using ultra high-performance liquid chromatography-mass spectrometry. The results of these analyses showed that all four families of GAGs were detected in all egg components. Keratan sulfate was found in egg whites (thick and thin) and shell matrix (calcified shell matrix supernatant and deposit) with high level. Chondroitin sulfates were much more plentiful in both shell matrix components and membrane. Hyaluronan was plentiful in both shell matrix components and membrane, but was only present in a trace of quantities in the yolk. Heparan sulfate was plentiful in the shell matrix deposit but was present in a trace of quantities in the egg content components (yolk, thick and thin egg whites). Most of the chondroitin and heparan sulfate disaccharides were present in the GAGs found in chicken eggs with the exception of chondroitin and heparan sulfate 2,6-disulfated disaccharides. Both CS and HS in the shell matrix deposit contained the most diverse chondroitin and heparan sulfate disaccharide compositions. Eggs might provide a potential new source of GAGs. PMID:25218438
Compositional analysis and structural elucidation of glycosaminoglycans in chicken eggs
Liu, Zhangguo; Zhang, Fuming; Li, Lingyun; Li, Guoyun; He, Wenqing; Linhardt, Robert J.
Glycosaminoglycans (GAGs) have numerous applications in the fields of pharmaceuticals, cosmetics, nutraceuticals, and foods. GAGs are also critically important in the developmental biology of all multicellular animals. GAGs were isolated from chicken egg components including yolk, thick egg white, thin egg white, membrane, calcified shell matrix supernatant, and shell matrix deposit. Disaccharide compositional analysis was performed using ultra high-performance liquid chromatography-mass spectrometry. The results of these analyses showed that all four families of GAGs were detected in all egg components. Keratan sulfate was found in egg whites (thick and thin) and shell matrix (calcified shell matrix supernatant and deposit) with high level. Chondroitin sulfates were much more plentiful in both shell matrix components and membrane. Hyaluronan was plentiful in both shell matrix components and membrane, but were only present in a trace of quantities in the yolk. Heparan sulfate was plentiful in the shell matrix deposit but was present in a trace of quantities in the egg content components (yolk, thick and thin egg whites). Most of the chondroitin and heparan sulfate disaccharides were present in the GAGs found in chicken eggs with the exception of chondroitin and heparan sulfate 2,6-disulfated disaccharides. Both CS and HS in the shell matrix deposit contained the most diverse chondroitin and heparan sulfate disaccharide compositions. Eggs might provide a potential new source of GAGs. PMID:25218438
Atomic structure of anthrax PA pore elucidates toxin translocation
Jiang, Jiansen; Pentelute, Bradley L.; Collier, R. John; Zhou, Z. Hong
Summary Anthrax toxin, comprising protective antigen (PA), lethal factor (LF) and edema factor (EF), is the major virulence factor of Bacillus anthracis, an agent that causes high mortality in human and animals. PA forms oligomeric prepores that undergo conversion to membrane-spanning pores by endosomal acidification, and these pores translocate the enzymes LF and EF into the cytosol of target cells1. PA is not only a vaccine component and therapeutic target for anthrax infections but also an excellent model system for understanding the mechanism of protein translocation. Based on biochemical and electrophysiological results, researchers have proposed that a Φ-clamp composed of Phe427 residues of PA catalyzes protein translocation via a charge-state dependent Brownian ratchet2–9. Although atomic structures of PA prepores are available10–14, how PA senses low pH, converts to active pore and translocates LF and EF are not well defined without an atomic model of the PA pore. Here, by cryo electron microscopy (cryoEM) with direct electron counting, we have determined the PA pore structure at 2.9-Å resolution. The structure reveals the long-sought-after catalytic Φ-clamp and the membrane-spanning translocation channel, and supports the Brownian ratchet model for protein translocation. Comparisons of four structures reveal conformational changes in prepore to pore conversion that support a multi-step mechanism by which low-pH is sensed and the membrane-spanning channel is formed. PMID:25778700
Atomic structure of anthrax protective antigen pore elucidates toxin translocation.
Jiang, Jiansen; Pentelute, Bradley L; Collier, R John; Zhou, Z Hong
Anthrax toxin, comprising protective antigen, lethal factor, and oedema factor, is the major virulence factor of Bacillus anthracis, an agent that causes high mortality in humans and animals. Protective antigen forms oligomeric prepores that undergo conversion to membrane-spanning pores by endosomal acidification, and these pores translocate the enzymes lethal factor and oedema factor into the cytosol of target cells. Protective antigen is not only a vaccine component and therapeutic target for anthrax infections but also an excellent model system for understanding the mechanism of protein translocation. On the basis of biochemical and electrophysiological results, researchers have proposed that a phi (Φ)-clamp composed of phenylalanine (Phe)427 residues of protective antigen catalyses protein translocation via a charge-state-dependent Brownian ratchet. Although atomic structures of protective antigen prepores are available, how protective antigen senses low pH, converts to active pore, and translocates lethal factor and oedema factor are not well defined without an atomic model of its pore. Here, by cryo-electron microscopy with direct electron counting, we determine the protective antigen pore structure at 2.9-Å resolution. The structure reveals the long-sought-after catalytic Φ-clamp and the membrane-spanning translocation channel, and supports the Brownian ratchet model for protein translocation. Comparisons of four structures reveal conformational changes in prepore to pore conversion that support a multi-step mechanism by which low pH is sensed and the membrane-spanning channel is formed. PMID:25778700
Fatty Acid Biosynthesis Revisited: Structure Elucidation and Metabolic Engineering
Beld, Joris; Lee, D. John
Fatty acids are primary metabolites synthesized by complex, elegant, and essential biosynthetic machinery. Fatty acid synthases resemble an iterative assembly line, with an acyl carrier protein conveying the growing fatty acid to necessary enzymatic domains for modification. Each catalytic domain is a unique enzyme spanning a wide range of folds and structures. Although they harbor the same enzymatic activities, two different types of fatty acid synthase architectures are observed in nature. During recent years, strained petroleum supplies have driven interest in engineering organisms to either produce more fatty acids or specific high value products. Such efforts require a fundamental understanding of the enzymatic activities and regulation of fatty acid synthases. Despite more than one hundred years of research, we continue to learn new lessons about fatty acid synthases' many intricate structural and regulatory elements. In this review, we summarize each enzymatic domain and discuss efforts to engineer fatty acid synthases, providing some clues to important challenges and opportunities in the field. PMID:25360565
Fatty acid biosynthesis revisited: structure elucidation and metabolic engineering.
Beld, Joris; Lee, D John; Burkart, Michael D
Fatty acids are primary metabolites synthesized by complex, elegant, and essential biosynthetic machinery. Fatty acid synthases resemble an iterative assembly line, with an acyl carrier protein conveying the growing fatty acid to necessary enzymatic domains for modification. Each catalytic domain is a unique enzyme spanning a wide range of folds and structures. Although they harbor the same enzymatic activities, two different types of fatty acid synthase architectures are observed in nature. During recent years, strained petroleum supplies have driven interest in engineering organisms to either produce more fatty acids or specific high value products. Such efforts require a fundamental understanding of the enzymatic activities and regulation of fatty acid synthases. Despite more than one hundred years of research, we continue to learn new lessons about fatty acid synthases' many intricate structural and regulatory elements. In this review, we summarize each enzymatic domain and discuss efforts to engineer fatty acid synthases, providing some clues to important challenges and opportunities in the field. PMID:25360565
Elucidating microscopic structure and dynamics in optically tweezed environments
NASA Astrophysics Data System (ADS)
Roy, Debjit; Mondal, Dipankar; Goswami, Debabrata
To probe the structure and dynamics of molecules under optical trapping conditions, we exploit the effect of femtosecond Fluorescence Resonance Energy Transfer (FRET) between dye molecules coated on the surface of polystyrene microspheres of various sizes suspended in water. The use of femtosecond laser pulses enables sensitive detection through two-photon fluorescence (TPF). Unlike conventional backscatter signal, the TPF signal shows a slow counterintuitive decay for the trapped microspheres when they are not fully within the laser illuminated volume. This decay is a characteristic sign of the occurrence of the FRET process. For microspheres with sizes less than the trapping focal volume, trapping of multiple particles can occur leading to the formation of optically bound clusters. Using different laser polarizations, we also extract information about the structure and dynamics of such optically bound clusters as a consequence of FRET.
N-methylcodeinium iodide—Crystal structure and spectroscopic elucidation
NASA Astrophysics Data System (ADS)
Seidel, R. W.; Bakalska, B. R.; Kolev, T.; Vassilev, D.; Mayer-Figge, H.; Spiteller, M.; Sheldrick, W. S.; Koleva, B. B.
The correlation between the structure and the spectroscopic properties of N-methylcodeinium iodide ( 1) has been studied, using the methods of single crystal X-ray diffraction, IR-LD spectroscopy of oriented samples as a suspension in nematic liquid crystals, UV-vis spectroscopy and 1H and 13C NMR spectroscopy. HPLC tandem mass spectrometry (HPLC ESI MS/MS) and thermal methods were also employed. Quantum chemical calculations have been performed with a view to obtaining the electronic structure and vibrational properties of the title compound. Compound ( 1) crystallizes in the space group P2 12 12 1 and its cations and anions are joined by moderate intermolecular OH…I - interaction of length 3.442 Å. The codeine molecule exhibits the classical T-shape for opiates. A dihedral angle value of 86.4(5)° between the A/B/C and D/E planes is obtained. Rings A and B are effectively coplanar with an interplanar angle of 3.6(3)°.
Janus-Cube Octasilsesquioxane: Facile Synthesis and Structure Elucidation.
Oguri, Naoki; Egawa, Yasunobu; Takeda, Nobuhiro; Unno, Masafumi
A perfect "Janus-cube" octasilsesquioxane, a nanometer-scale Janus particle with two different types of substituents, was synthesized through the cross-coupling of a "half-cube" cyclic sodium siloxanolate with another half-cube cyclic fluorosiloxane. The structure was confirmed by X-ray crystallography to be a Janus cube. The overall synthesis is simple and does not require drastic separation methods compared with previous methods. The synthesis of the Janus cube demonstrates a novel siloxane bond-forming reaction involving the coupling a silanol salt and fluorosilane. The reaction is mild, does not result in acid generation, and could be applied to the construction of other novel siloxane compounds. PMID:27225052
Structural elucidation of two photolytic degradation products of tetrabenazine.
Bourezg, Zouaoui; Cartiser, Nathalie; Ettouati, Laurent; Guillon, Jean; Lacoudre, Aline; Pinaud, Noël; Le Borgne, Marc; Fessi, Hatem
During solution formulation study of tetrabenazine (TBZ), a dopamine depleting agent, used in chorea associated with Huntington's disease and symptomatic treatment of hyperkinetic movement disorder it was observed a strong discoloration upon storage. We investigated this physico-chemical behavior by implementing forced degradation studies. It was observed yellowing only under Suntest(®) light exposure of TBZ solution. LC-MS (liquid chromatography coupled to mass spectrometer detection) analysis of light exposed TBZ samples allowed us to propose 1,11b-dedihydrotetrabenazine (DTBZ) and 1,3,4,11b-detetrahydrotetrabenazine (TTBZ) as the main TBZ impurities. Synthesis and complete structural determination of DTBZ and TTBZ·HCl by NMR and X-ray crystallography were carried out. They were identical in LC-MS with polar impurities found in light exposed TBZ samples. However, even if these TBZ degradation products are correlated with discoloration of TBZ solution there is no evidence they are directly responsible of it. PMID:24457996
Elucidating the chemical structure of native 1-deoxysphingosine.
Steiner, Regula; Saied, Essa M; Othman, Alaa; Arenz, Christoph; Maccarone, Alan T; Poad, Berwyck L J; Blanksby, Stephen J; von Eckardstein, Arnold; Hornemann, Thorsten
The 1-deoxysphingolipids (1-deoxySLs) are formed by an alternate substrate usage of the enzyme, serine-palmitoyltransferase, and are devoid of the C1-OH-group present in canonical sphingolipids. Pathologically elevated 1-deoxySL levels are associated with the rare inherited neuropathy, HSAN1, and diabetes type 2 and might contribute to β cell failure and the diabetic sensory neuropathy. In analogy to canonical sphingolipids, it was assumed that 1-deoxySLs also bear a (4E) double bond, which is normally introduced by sphingolipid delta(4)-desaturase 1. This, however, was never confirmed. We therefore supplemented HEK293 cells with isotope-labeled D3-1-deoxysphinganine and compared the downstream formed D3-1-deoxysphingosine (1-deoxySO) to a commercial synthetic SPH m18:1(4E)(3OH) standard. Both compounds showed the same m/z, but differed in their RPLC retention time and atmospheric pressure chemical ionization in-source fragmentation, suggesting that the two compounds are structural isomers. Using dimethyl disulfide derivatization followed by MS(2) as well as differential-mobility spectrometry combined with ozone-induced dissociation MS, we identified the carbon-carbon double bond in native 1-deoxySO to be located at the (Δ14) position. Comparing the chromatographic behavior of native 1-deoxySO to chemically synthesized SPH m18:1(14Z) and (14E) stereoisomers assigned the native compound to be SPH m18:1(14Z). This indicates that 1-deoxySLs are metabolized differently than canonical sphingolipids. PMID:27165858
Structure elucidation of two novel yak milk oligosaccharides and their DFT studies
NASA Astrophysics Data System (ADS)
Singh, Ashish Kumar; Ranjan, Ashok Kr.; Srivastava, Gaurav; Deepak, Desh
Milk is a primary dynamic biological fluid responsible for development of neonates. Besides the other regular constituents it have oligosaccharides in it which are responsible for antitumor, anticancer, antigenic and immunostimulant activities. In our endeavor to find biologically active novel oligosaccharides, yak milk was taken, which is a rich source of oligosaccharide and its milk is used as antihypertensive, antioxidative and heart strengthening agent in folk medicine. For this purpose yak milk was processed by method of Kobata and Ginsburg followed by gel filtration HPLC and CC which resulted in the isolation of two novel milk oligosaccharides namely (I) Grunniose and (II) Vakose. The structure of purified milk oligosaccharides were elucidated with the help of chemical degradation, chemical transformation, spectroscopic techniques like NMR (1H, 13C and 2D-NMR), structure reporter group theory and mass spectrometry. The optimized geometry of compound Grunniose and Vakose, at B3LYP method and 6-311 + G basis set on Gaussian 09 program, show that the compound Grunniose is lower in energy as compared to compound Vakose.
Methylbenzene-Containing Polyketides from a Streptomyces that Spontaneously Acquired Rifampicin Resistance: Structural Elucidation and Biosynthesis.
Thong, Wei Li; Shin-Ya, Kazuo; Nishiyama, Makoto; Kuzuyama, Tomohisa
Conventional screening for novel bioactive compounds in actinomycetes often results in the rediscovery of known compounds. In contrast, recent genome sequencing revealed that most of the predicted gene clusters for secondary metabolisms are not expressed under standard cultivation conditions. To explore the potential metabolites produced by these gene clusters, we implemented a cryptic gene activation strategy by screening mutants that acquire resistance to rifampicin. The induction of rifampicin resistance in 11 actinomycete strains generated 164 rifampicin-resistant mutants (rif mutants). The comparison of the metabolic profiles between the rif mutants and their wild-type strains indicated that one mutant (TW-R50-13) overproduced an unidentified metabolite (1). During the isolation and structural elucidation of metabolite 1, an additional metabolite was found; both are unprecedented compounds featuring a C5N unit and a methylbenzene moiety. Of these partial structures, the biosynthesis of the latter has not been reported. A feeding experiment using (13)C-labeled precursors demonstrated that the methylbenzene moiety is most likely synthesized by the action of polyketide synthase. The gene deletion experiments revealed that the genes for the methylbenzene moiety are located at a different locus than the genes for the C5N unit. PMID:26905826
Annotation and structural elucidation of bovine milk oligosaccharides and determination of novel fucosylated structures
Aldredge, Danielle L; Geronimo, Maria R; Hua, Serenus; Nwosu, Charles C; Lebrilla, Carlito B; Barile, Daniela
Bovine milk oligosaccharides (BMOs) are recognized by the dairy and food industries, as well as by infant formula manufacturers, as novel, high-potential bioactive food ingredients. Recent studies revealed that bovine milk contains complex oligosaccharides structurally related to those previously thought to be present in only human milk. These BMOs are microbiotic modulators involved in important biological activities, including preventing pathogen binding to the intestinal epithelium and serving as nutrients for a selected class of beneficial bacteria. Only a small number of BMO structures are fully elucidated. To better understand the potential of BMOs as a class of biotherapeutics, their detailed structure analysis is needed. This study initiated the development of a structure library of BMOs and a comprehensive evaluation of structure-related specificity. The bovine milk glycome was profiled by high-performance mass spectrometry and advanced separation techniques to obtain a comprehensive catalog of BMOs, including several novel, lower abundant neutral and fucosylated oligosaccharides that are often overlooked during analysis. Structures were identified using isomer-specific tandem mass spectroscopy and targeted exoglycosidase digestions to produce a BMO library detailing retention time, accurate mass and structure to allow their rapid identification in future studies. PMID:23436288
Structural Elucidation and Structure-Anti-inflammatory Activity Relationships of Cembranoids from Cultured Soft Corals Sinularia sandensis and Sinularia flexibilis.
Tsai, Tsung-Chang; Chen, Hsueh-Yu; Sheu, Jyh-Horng; Chiang, Michael Y; Wen, Zhi-Hong; Dai, Chang-Feng; Su, Jui-Hsin
New cembranoids 4-carbomethoxyl-10-epigyrosanoldie E (1), 7-acetylsinumaximol B (2), diepoxycembrene B (6), dihydromanaarenolide I (8), and isosinulaflexiolide K (9), along with 11 known related metabolites, were isolated from cultured soft corals Sinularia sandensis and Sinularia flexibilis. The structures were elucidated by means of infrared, mass spectrometry, and nuclear magnetic resonance techniques, and the absolute configurations of 1, 4, 9, and 15 were further confirmed by single-crystal X-ray diffraction analysis. The absolute configurations of these coral metabolites and comparison with known analogues showed that one hypothesis (that cembrane diterpenes possessing an absolute configuration of an isopropyl group at C1 obtained from Alcyonacean soft corals belong to the α series, whereas analogues isolated from Gorgonacean corals belong to the β series) is not applicable for a small number of cembranoids. An in vitro anti-inflammatory study using LPS-stimulated macrophage-like cell line RAW 264.7 revealed that compounds 9-14 significantly suppressed the accumulation of pro-inflammatory proteins, iNOS and COX-2. Structure-activity relationship analysis indicated that cembrane-type compounds with one seven-membered lactone moiety at C-1 are potential anti-inflammatory agents. This is the first culture system in the world that has successfully been used to farm S. sandensis. PMID:26260702
An Exercise on Structure Elucidation Based on a Tricky Aldol Reaction
ERIC Educational Resources Information Center
Sierra, Manuel Gonzalez; Pellegrinet, Silvina C.; Colombo, Maria I.; Ruveda, Edmundo A.
An exercise on structure elucidation for advanced undergraduate students is described. To determine the structure of an unknown product, students are required to use spectra together with an organic chemistry mechanism. This exercise exemplifies the procedure commonly used in research, thus helping students develop problem-solving skills. In…
The structural elucidation and antimicrobial activities of two isoflavane glycosides from Astragalus membranaceus (Fisch) Bge. var. mongholicus (Bge) Hsiao
NASA Astrophysics Data System (ADS)
Wang, Qing-Hu; Han, Na-ren-chao-ke-tu; Dai, Na-yin-tai; Wang, Xiu-lan; Ao, Wu-Li-Ji
Two isoflavane glycoside had been isolated from the EtOAc-soluble fraction of the roots of Astragalus membranaceus (Fisch) Bge. var. mongholicus (Bge) Hsiao. This is the first report on the structure elucidation of 2‧,5‧-dicarbonyl-3‧,4‧-dimethoxyisoflavanequinone-7-O-β-D-glucoside (1) based on spectroscopic methods including UV (Ultraviolet Spectrophotometry), IR (Infrared Absorption Spectroscopy), ESI-MS (Electrospray Ionization Mass Spectrometry), 1D NMR (Nuclear Magnetic Resonance Spectroscopy) and 2D NMR techniques. At the same time, antimicrobial activity of the two compounds was evaluated against various bacteria and fungi.
Consensus structure elucidation combining GC/EI-MS, structure generation, and calculated properties.
Schymanski, Emma L; Gallampois, Christine M J; Krauss, Martin; Meringer, Markus; Neumann, Steffen; Schulze, Tobias; Wolf, Sebastian; Brack, Werner
This article explores consensus structure elucidation on the basis of GC/EI-MS, structure generation, and calculated properties for unknown compounds. Candidate structures were generated using the molecular formula and substructure information obtained from GC/EI-MS spectra. Calculated properties were then used to score candidates according to a consensus approach, rather than filtering or exclusion. Two mass spectral match calculations (MOLGEN-MS and MetFrag), retention behavior (Lee retention index/boiling point correlation, NIST Kovat's retention index), octanol-water partitioning behavior (log K(ow)), and finally steric energy calculations were used to select candidates. A simple consensus scoring function was developed and tested on two unknown spectra detected in a mutagenic subfraction of a water sample from the Elbe River using GC/EI-MS. The top candidates proposed using the consensus scoring technique were purchased and confirmed analytically using GC/EI-MS and LC/MS/MS. Although the compounds identified were not responsible for the sample mutagenicity, the structure-generation-based identification for GC/EI-MS using calculated properties and consensus scoring was demonstrated to be applicable to real-world unknowns and suggests that the development of a similar strategy for multidimensional high-resolution MS could improve the outcomes of environmental and metabolomics studies. PMID:22414024
Chemical synthesis and structure elucidation of bovine {kappa}-casein (1-44)
Bansal, Paramjit S.; Grieve, Paul A.; Marschke, Ronald J.; Daly, Norelle L.; McGhie, Emily; Craik, David J.; Alewood, Paul F. . E-mail: firstname.lastname@example.com
The caseins ({alpha}{sub s1}, {alpha}{sub s2}, {beta}, and {kappa}) are phosphoproteins present in bovine milk that have been studied for over a century and whose structures remain obscure. Here we describe the chemical synthesis and structure elucidation of the N-terminal segment (1-44) of bovine {kappa}-casein, the protein which maintains the micellar structure of the caseins. {kappa}-Casein (1-44) was synthesised by highly optimised Boc solid-phase peptide chemistry and characterised by mass spectrometry. Structure elucidation was carried out by circular dichroism and nuclear magnetic resonance spectroscopy. CD analysis demonstrated that the segment was ill defined in aqueous medium but in 30% trifluoroethanol it exhibited considerable helical structure. Further, NMR analysis showed the presence of a helical segment containing 26 residues which extends from Pro{sup 8} to Arg{sup 34}. This is First report which demonstrates extensive secondary structure within the casein class of proteins.
Structure elucidation of fungal beauveriolide III, a novel inhibitor of lipid droplet formation in mouse macrophages.
Namatame, I; Tomoda, H; Tabata, N; Si, S; Omura, S
The structure of fungal beauveriolide III, an inhibitor of lipid droplet formation in mouse macrophages, was elucidated to be cyclo-[(3S,4S)-3-hydroxy-4-methyloctanoyl-L-phenylalanyl-L-alanyl- D-allo-isoleucyl] by spectral analyses and chemical degradation. PMID:10092190
Anti-inflammatory effects and structure elucidation of two new compounds from Astragalus membranaceus (Fisch) Bge. var. mongholicus (Bge) Hsiao
NASA Astrophysics Data System (ADS)
Wang, Qing-Hu; Han, Na-Ren-Chao-Ke-Tu; Dai, Na-Yin-Tai; Wang, Xiu-Lan; Ao, Wu-Li-Ji
Phytochemical study of the ethanol extract of Astragalus membranaceus (Fisch) Bge. var. mongholicus (Bge) Hsiao resulted to the isolation of two new compounds, 1-hydroxy-5-methylolbenzol-2-O-β-D-glucoside (1) and (3R, 4R)-4,7-hydroxy-2‧,3‧-dimethoxyisoflavane-4‧-O-β-D-glucoside (2). The structure of the isolated compounds were elucidated on the basis of the spectroscopic methods including UV, IR, ESI-MS, 1D NMR and 2D NMR techniques, and by comparison with those reported in the literature. The new compounds were investigated for its effect against inflammation induced by egg-albumin and carrageenan in rats.
Thermodynamic Properties of Asphaltenes: A Predictive Approach Based On Computer Assisted Structure Elucidation and Atomistic Simulations
Diallo, Mamadou S.; Cagin, Tahir; Faulon, Jean Loup; Goddard, William A.
The authors describe a new methodology for predicting the thermodynamic properties of petroleum geomacromolecules (asphaltenes and resins). This methodology combines computer assisted structure elucidation (CASE) with atomistic simulations (molecular mechanics and molecular dynamics and statistical mechanics). They use quantitative and qualitative structural data as input to a CASE program (SIGNATURE) to generate a sample of ten asphaltene model structures for a Saudi crude oil (Arab Berri). MM calculations and MD simulations are used to estimate selected volumetric and thermal properties of the model structures.
Elucidating the cellular uptake mechanism of aptamer-functionalized graphene-isolated-Au-nanocrystals with dual-modal imaging.
Wang, Shanshan; Liu, Zhangkun; Zou, Yuxiu; Lai, Xiaofang; Ding, Ding; Chen, Long; Zhang, Liqin; Wu, Yuan; Chen, Zhuo; Tan, Weihong
Elucidating the endocytosis and metabolism of nanoparticles in cells could improve the diagnostic sensitivity and therapeutic efficiency. In this work, we explore the cellular uptake mechanism of a biocompatible nanocrystal nanostructure, graphene-isolated-Au-nanocrystals (GIANs), by monitoring the intrinsic Raman and two-photon luminescence signals of GIANs in live cells. Aptamers functionalized on the GIAN nanostructure through simple, but strong, π-π interactions entered the cells through a clathrin-dependent pathway, while unmodified GIANs mainly entered the cells through a caveolae-mediated endocytosis pathway. Thus, it can be concluded that the mechanism of cellular uptake in these graphene-isolated-Au-nanocrystal nanostructures is determined by the presence or absence of aptamer modification. PMID:27111129
Toward efficient nanoporous catalysts: controlling site-isolation and concentration of grafted catalytic sites on nanoporous materials with solvents and colorimetric elucidation of their site-isolation.
Sharma, Krishna K; Anan, Abhishek; Buckley, Robert P; Ouellette, Wayne; Asefa, Tewodros
We report that the polarity and dielectric constants of solvents used for grafting organosilanes on mesoporous materials strongly affect the concentration of grafted organic groups, the degree of their site-isolation, and the catalytic properties of the resulting materials. Polar and nonpolar organosilanes as well as polar-protic, dipolar-aprotic, and nonpolar solvents were investigated. Polar-protic solvents, which have high dielectric constants, resulted in smaller concentrations ( approximately 1-2 mmol/g) of polar organic groups such as 3-aminopropyl groups, higher surface area materials, site-isolated organic groups, and more efficient catalytic properties toward the Henry reaction of p-hydroxybenzaldehyde with nitromethane. On the other hand, dipolar-aprotic and nonpolar solvents resulted in larger concentrations ( approximately 2-3 mmol/g) of grafted polar functional groups, lower-to-higher surface area materials, more densely populated catalytic groups, and poor-to-efficient catalytic properties toward the Henry reaction. Both the polar-protic and dipolar-aprotic solvents resulted in significantly lower concentration of grafted groups for nonpolar organosilanes such as (3-mercaptopropyl)trimethoxysilane compared to corresponding grafting of the polar amino-organosilanes. The relationship between the solvent properties and the percentage and degree of site-isolation of the grafted functional groups was attributed to differences in solvation of the organosilanes and silanols in various solvents and possible hydrogen-bonding between the organsilanes and the solvents. The degree of site-isolation of the amine groups, which affect the material's catalytic properties, was elucidated by a new colorimetric method involving probing of the absorption maxima (lambdamax) on the d-d electronic spectrum of Cu2+ complexes with the amine-functionalized materials and the colors of the samples. The absorption lambdamax and the colors of the materials were found to be
Elucidation of fluoranthene degradative characteristics in a newly isolated Achromobacter xylosoxidans DN002.
Ma, Yan-Ling; Lu, Wei; Wan, Li-Li; Luo, Na
Strain DN002 isolated from petroleum-contaminated soil was identified as Achromobacter xylosoxidans based on morphological and biochemical properties and 16S rRNA phylogeny, and investigated for its potential to utilize numerous polycyclic aromatic hydrocarbons (PAHs) such as fluoranthene and pyrene as sole carbon and energy resource. Biodegradation studies showed that 500 mg(·)l(-1)fluranthene was degraded to 35.6 ± 0.3 mg(·)l(-1) by DN002 after 14 days incubation. During fluoranthene biodegradation, catechol 2,3 dioxygenase (C23O) activity was augmented 1.5 times more than catechol 1,2 dioxygenase (C12O), which indicated that C23O played a major role in fluoranthene degradation by DN002. Protein profiles were examined by sodium dodecyl sulfate polyacrylamide gel electrophoresis and two-dimensional electrophoresis then analyzed by mass spectrometry induced by fluoranthene; a molecular mass range of 18 ∼ 66 kDa proteins were found upregulated compared with the uninduced control sample, including multiple isoenzymes of β-oxidation and dehydrogenases as well as dioxygenases. Besides, some new proteins, i.e., dihydrolipoamide succinyltransferase and aldehyde dehydrogenase family proteins and isocitrate lyase were also synthesized. PMID:25381650
Structural elucidation of fritillahupehin from bulbs of Fritillaria hupehensis Hsiao et K.C. Hsia.
Zhang, Yong-Hui; Ruan, Han-Li; Pi, Hui-Fang; Wu, Ji-Zhou; Sun, Han-Dong; Fujita, Tetsuro
A novel diterpenoid ester, fritillahupehin (1) and three known fatty acids, palmitic acid (2), lignoceric acid (3) and azelaric acid (4), have been isolated from the bulbs of Fritillaria hupehensis Hsiao et K.C. Hsia. The structure of fritillahupehin has been established to be ent-kauran-16beta-yl lignocerate by means of spectroscopic and chemical evidence. Compounds 2-4 were isolated from Fritillaria sp. for the first time. PMID:14989377
Structural elucidation of sulfaquinoxaline metabolism products and their occurrence in biological samples using high-resolution Orbitrap mass spectrometry.
Hoff, Rodrigo Barcellos; Meneghini, Leonardo; Pizzolato, Tânia Mara; Peralba, Maria do Carmo Ruaro; Díaz-Cruz, M Silvia; Barceló, Damià
Four previously unreported metabolism products of sulfaquinoxaline (SQX), a widely used veterinary medicine, were isolated and analyzed using liquid chromatography coupled to high-resolution Orbitrap mass spectrometry. Metabolites were structurally elucidated, and a fragmentation pathway was proposed. The combination of high-resolution MS(2) spectra, linear ion trap MS(2), in-source collision-induced dissociation (CID) fragmentation, and photolysis were used to analyze SQX and its metabolites. All metabolism products identified showed a similar fragmentation pattern to that of the original drug. Differential product ions were produced at m/z 162 and 253 which contain the radical moiety with more 16 Da units than sulfaquinoxaline. This occurs by a hydroxyl attachment to the quinoxaline moiety. With the exception of two low-intensity compounds, all the mass errors were below 5.0 ppm. The distribution of these metabolites in some animal species are also presented and discussed. PMID:24796379
Structural Elucidation of a Small Molecule Inhibitor of Protein Disulfide Isomerase
Compound libraries provide a starting point for multiple biological investigations, but the structural integrity of compounds is rarely assessed experimentally until a late stage in the research process. Here, we describe the discovery of a neuroprotective small molecule that was originally incorrectly annotated with a chemical structure. We elucidated the correct structure of the active compound using analytical chemistry, revealing it to be the natural product securinine. We show that securinine is protective in a cell model of Huntington disease and identify the binding site of securinine to its target, protein disulfide isomerase using NMR chemical shift perturbation studies. We show that securinine displays favorable pharmaceutical properties, making it a promising compound for in vivo studies in neurodegenerative disease models. In addition to finding this unexpected activity of securinine, this study provides a systematic roadmap to those who encounter compounds with incorrect structural annotation in the course of screening campaigns. PMID:26500720
New tricyclic and tetracyclic pyranocoumarins with an unprecedented C-4 substituent. Structure elucidation of tamanolide, tamanolide D and tamanolide P from Calophyllum inophyllum of French Polynesia.
Leu, T; Raharivelomanana, P; Soulet, S; Bianchini, J P; Herbette, G; Faure, R
Three new pyranocoumarin derivatives, tamanolide (1), tamanolide D (2) and tamanolide P (3), were isolated from the almond seeds of Calophyllum inophyllum L. (Clusiaceae) grown in French Polynesia. These compounds, having an unprecedented C-4 isobutyl substituent, have been characterized as a new class of pyranocoumarins called tamanolides. Their structures were elucidated on the basis of 1D and 2D NMR techniques (COSY, NOESY, HSQC and HMBC) in association with MS (HR-ESI-MS) data analysis. PMID:19603395
Structure elucidation of auxofuran, a metabolite involved in stimulating growth of fly agaric, produced by the mycorrhiza helper bacterium Streptomyces AcH 505.
Keller, Simone; Schneider, Kathrin; Süssmuth, Roderich D
Mycorrhiza helper bacterium Streptomyces strain AcH 505 stimulates ectomycorrhiza formation between spruce and fly agaric by supporting fungal growth whereas growth of pathogenic fungi is suppressed. A fungal growth promoting substance was isolated and the chemical structure elucidated by mass spectrometry and NMR spectroscopy. The absolute configuration of the novel fungal growth promoting compound auxofuran (1) was deduced from NMR data with the help of Mosher esters. PMID:17323648
Natural anthraquinone derivatives from a marine mangrove plant-derived endophytic fungus Eurotium rubrum: structural elucidation and DPPH radical scavenging activity.
Li, Dong-Li; Li, Xiao-Ming; Wang, Bin-Gui
There is considerable interest in the isolation of potent radical scavenging compounds from natural resources to treat diseases involving oxidative stress. In this report, four new fungal metabolites including one new bisdihydroanthracenone derivative (1, eurorubrin), two new seco-anthraquinone derivatives [3, 2-O-methyl-9-dehydroxyeurotinone and 4, 2-Omethyl- 4-O-(alpha-D-ribofuranosyl)-9-dehydroxyeurotinone], and one new anthraquinone glycoside [6, 3-O-(alpha-D-ribofuranosyl)- questin], were isolated and identified from Eurotium rubrum, an endophytic fungal strain that was isolated from the inner tissue of the stem of the marine mangrove plant Hibiscus tiliaceus. In addition, three known compounds including asperflavin (2), 2-O-methyleurotinone (5), and questin (7) were also isolated and identified. Their structures were elucidated on the basis of spectroscopic analysis. All of the isolated compounds were evaluated for 1,1-diphenyl-2-picrylhydrazyl(DPPH) radical scavenging activity. PMID:19652514
Towards the crystal structure elucidation of eukaryotic UDP-galactopyranose mutase
van Straaten, Karin E.; Routier, Francoise H.; Sanders, David A. R.
UDP-galactopyranose mutase (UGM) catalyzes the interconversion of UDP-galactopyranose and UDP-galactofuranose. Eukaryotic UGMs from Aspergillus fumigatus and Leishmania major have been purified to homogeneity by means of Ni2+-affinity chromatography and crystallized. Eukaryotic UGM structure elucidation was not straightforward owing to high pseudo-symmetry, twinning and very low anomalous signal. Phasing to 2.8 Å resolution using SAD was successful for L. major UGM. However, the maps could only be improved by iterative density modification and manual model building. High pseudo-symmetry and twinning prevented correct space-group assignment and the completion of structure refinement. The structure of A. fumigatus UGM to 2.52 Å resolution was determined by molecular replacement using the incomplete 2.8 Å resolution L. major UGM model. PMID:22505419
Bridging the gap between modules in isolation and as part of networks: A systems framework for elucidating interaction and regulation of signalling modules.
Menon, Govind; Krishnan, J
While signalling and biochemical modules have been the focus of numerous studies, they are typically studied in isolation, with no examination of the effects of the ambient network. In this paper we formulate and develop a systems framework, rooted in dynamical systems, to understand such effects, by studying the interaction of signalling modules. The modules we consider are (i) basic covalent modification, (ii) monostable switches, (iii) bistable switches, (iv) adaptive modules, and (v) oscillatory modules. We systematically examine the interaction of these modules by analyzing (a) sequential interaction without shared components, (b) sequential interaction with shared components, and (c) oblique interactions. Our studies reveal that the behaviour of a module in isolation may be substantially different from that in a network, and explicitly demonstrate how the behaviour of a given module, the characteristics of the ambient network, and the possibility of shared components can result in new effects. Our global approach illuminates different aspects of the structure and functioning of modules, revealing the importance of dynamical characteristics as well as biochemical features; this provides a methodological platform for investigating the complexity of natural modules shaped by evolution, elucidating the effects of ambient networks on a module in multiple cellular contexts, and highlighting the capabilities and constraints for engineering robust synthetic modules. Overall, such a systems framework provides a platform for bridging the gap between non-linear information processing modules, in isolation and as parts of networks, and a basis for understanding new aspects of natural and engineered cellular networks. PMID:27448907
Bridging the gap between modules in isolation and as part of networks: A systems framework for elucidating interaction and regulation of signalling modules
NASA Astrophysics Data System (ADS)
Menon, Govind; Krishnan, J.
While signalling and biochemical modules have been the focus of numerous studies, they are typically studied in isolation, with no examination of the effects of the ambient network. In this paper we formulate and develop a systems framework, rooted in dynamical systems, to understand such effects, by studying the interaction of signalling modules. The modules we consider are (i) basic covalent modification, (ii) monostable switches, (iii) bistable switches, (iv) adaptive modules, and (v) oscillatory modules. We systematically examine the interaction of these modules by analyzing (a) sequential interaction without shared components, (b) sequential interaction with shared components, and (c) oblique interactions. Our studies reveal that the behaviour of a module in isolation may be substantially different from that in a network, and explicitly demonstrate how the behaviour of a given module, the characteristics of the ambient network, and the possibility of shared components can result in new effects. Our global approach illuminates different aspects of the structure and functioning of modules, revealing the importance of dynamical characteristics as well as biochemical features; this provides a methodological platform for investigating the complexity of natural modules shaped by evolution, elucidating the effects of ambient networks on a module in multiple cellular contexts, and highlighting the capabilities and constraints for engineering robust synthetic modules. Overall, such a systems framework provides a platform for bridging the gap between non-linear information processing modules, in isolation and as parts of networks, and a basis for understanding new aspects of natural and engineered cellular networks.
Advances in ion trap mass spectrometry: Photodissociation as a tool for structural elucidation
Stephenson, J.L. Jr.; Booth, M.M.; Eyler, J.R.; Yost, R.A.
Photo-induced dissociation (PID) is the next most frequently used method (after collisional activation) for activation of Polyatomic ions in tandem mass spectrometry. The range of internal energies present after the photon absorption process are much narrower than those obtained with collisional energy transfer. Therefore, the usefulness of PID for the study of ion structures is greatly enhanced. The long storage times and instrumental configuration of the ion trap mass spectrometer are ideally suited for photodissociation experiments. This presentation will focus on both the fundamental and analytical applications of CO{sub 2} lasers in conjunction with ion trap mass spectrometry. The first portion of this talk will examine the fundamental issues of wavelength dependence, chemical kinetics, photoabsorption cross section, and collisional effects on photodissociation efficiency. The second half of this presentation will look at novel instrumentation for electrospray/ion trap mass spectrometry, with the concurrent development of photodissociation as a tool for structural elucidation of organic compounds and antibiotics.
Structure elucidation of anti-methicillin resistant Staphylococcus aureus (MRSA) flavonoids from balsam poplar buds.
Simard, François; Gauthier, Charles; Legault, Jean; Lavoie, Serge; Mshvildadze, Vakhtang; Pichette, André
There is nowadays an urgent need for developing novel generations of antibiotic agents due to the increased resistance of pathogenic bacteria. As a rich reservoir of structurally diverse compounds, plant species hold promise in this regard. Within this framework, we isolated a unique series of antibacterial flavonoids, named balsacones N-U, featuring multiple cinnamyl chains on the flavan skeleton. The structures of these compounds, isolated as racemates, were determined using extensive 1D and 2D NMR analysis in tandem with HRMS. Balsacones N-U along with previously isolated balsacones A-M were evaluated for their antibacterial activity against clinical isolates of methicillin resistant Staphylococcus aureus (MRSA). Several of the tested balsacones were potent anti-MRSA agents showing MIC values in the low micromolar range. Structure-activity relationships study highlighted some important parameters involved in the antibacterial activity of balsacones such as the presence of cinnamyl and cinnamoyl chains at the C-3 and C-8 positions of the flavan skeleton, respectively. These results suggest that balsacones could represent a potential novel class of naturally occurring anti-MRSA agents. PMID:27436809
Spectroscopic and structural elucidation of amino acid derivatives and small peptides: experimental and theoretical tools.
Kolev, Tsonko; Spiteller, Michael; Koleva, Bojidarka
This mini review deals with the modern aspects of the spectroscopy and structural elucidation of amino acid derivatives and small biologically active compounds. Free peptide bond rotation in these systems yields various conformers, which possess differing biological activities. Another phenomenon is the intermolecular or intramolecular stacking observed in aromatic small peptides. Specifically, the main aim is to illustrate the successful application of the "complex tool", consisting of a combination of the theoretical approximation methods with experimental linear polarized infrared (IR-LD) and/or Raman spectroscopy of oriented colloid suspensions in a nematic host. The possibilities and limitations of the approach for detailed vibrational assignment and structural elucidation of small peptides are discussed. Having in mind that physical and chemical properties of these systems can be precisely calculated by means of ab initio and DFT methods at Hartee-Fock, MP2 and B3LYP level of theory, varying basis sets, the results obtained allow a precise assignment of many vibrational bands to the corresponding normal modes, electronic structures and conformational state. The validity of the conclusions about the structure or vibrational properties of these systems have been supported, compared and/or additionally proved by the results from independent physical methods. In this respect (1)H and (13)C-NMR, single crystal X-ray diffraction, HPLC tandem mass spectrometry as well as thermal methods are all employed. A well ordered crystal must first be grown in order to determine the molecular structure by the absolute method of single crystal X-ray diffraction. Although the 3D structures of peptides have been determined over the past decades, peptide crystallization is still a major obstacle to X-ray diffraction work, the presence of chiral centre/s makes for this difficulty. For this reason the "complex tool" presented can be regarded as an alternative method for obtaining of
Comprehensive Secondary Structure Elucidation of Four Genera of the Family Pospiviroidae
Giguère, Tamara; Raj Adkar-Purushothama, Charith; Perreault, Jean-Pierre
Viroids are small, circular, single stranded RNA molecules that infect plants. Since they are non-coding, their structures play a critical role in their life cycles. To date, little effort has been spend on elucidating viroid structures in solution due to both the experimental difficulties and the time-consuming nature of the methodologies implicated. Recently, the technique of high-throughput selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) was adapted for the probing of the members of family Avsunviroidae, all of whom replicate in the chloroplast and demonstrate ribozyme activity. In the present work, twelve viroid species belonging to four different genera of the family Pospiviroidae, whose members are characterized by the presence of a central conserved region (CCR) and who replicate in nucleus of the host, were probed. Given that the structures of five distinct viroid species from the family Pospiviroidae have been previously reported, an overview of the different structural characteristics for all genera and the beginning of a manual classification of the different viroids based on their structural features are presented here. PMID:24897295
Comprehensive secondary structure elucidation of four genera of the family Pospiviroidae.
Giguère, Tamara; Adkar-Purushothama, Charith Raj; Perreault, Jean-Pierre
Viroids are small, circular, single stranded RNA molecules that infect plants. Since they are non-coding, their structures play a critical role in their life cycles. To date, little effort has been spend on elucidating viroid structures in solution due to both the experimental difficulties and the time-consuming nature of the methodologies implicated. Recently, the technique of high-throughput selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) was adapted for the probing of the members of family Avsunviroidae, all of whom replicate in the chloroplast and demonstrate ribozyme activity. In the present work, twelve viroid species belonging to four different genera of the family Pospiviroidae, whose members are characterized by the presence of a central conserved region (CCR) and who replicate in nucleus of the host, were probed. Given that the structures of five distinct viroid species from the family Pospiviroidae have been previously reported, an overview of the different structural characteristics for all genera and the beginning of a manual classification of the different viroids based on their structural features are presented here. PMID:24897295
Janthinocins A, B and C, novel peptide lactone antibiotics produced by Janthinobacterium lividum. II. Structure elucidation.
Johnson, J H; Tymiak, A A; Bolgar, M S
The structures of janthinocins A, B and C, three novel macrocyclic peptide lactone antibiotics isolated from fermentations of Janthinobacterium lividum, were determined. The janthinocins are of particular interest because they contain three amino acid residues that have not previously been reported in natural products: Each contains erythro-beta-hydroxy-D-leucine while janthinocins A and B also contain beta-hydroxytryptophan and beta-ketotryptophan, respectively. PMID:2211360
Elucidating Molecular Motion through Structural and Dynamic Filters of Energy-Minimized Conformer Ensembles
Complex RNA structures are constructed from helical segments connected by flexible loops that move spontaneously and in response to binding of small molecule ligands and proteins. Understanding the conformational variability of RNA requires the characterization of the coupled time evolution of interconnected flexible domains. To elucidate the collective molecular motions and explore the conformational landscape of the HIV-1 TAR RNA, we describe a new methodology that utilizes energy-minimized structures generated by the program "Fragment Assembly of RNA with Full-Atom Refinement (FARFAR)". We apply structural filters in the form of experimental residual dipolar couplings (RDCs) to select a subset of discrete energy-minimized conformers and carry out principal component analyses (PCA) to corroborate the choice of the filtered subset. We use this subset of structures to calculate solution T1 and T1ρ relaxation times for 13C spins in multiple residues in different domains of the molecule using two simulation protocols that we previously published. We match the experimental T1 times to within 2% and the T1ρ times to within less than 10% for helical residues. These results introduce a protocol to construct viable dynamic trajectories for RNA molecules that accord well with experimental NMR data and support the notion that the motions of the helical portions of this small RNA can be described by a relatively small number of discrete conformations exchanging over time scales longer than 1 μs. PMID:24479561
Identification tree based on fragmentation rules for structure elucidation of organophosphorus esters by electrospray mass spectrometry.
Schwarzenberg, Adrián; Ichou, Farid; Cole, Richard B; Machuron-Mandard, Xavier; Junot, Christophe; Lesage, Denis; Tabet, Jean-Claude
Organophosphorus compounds have played important roles as pesticides, chemical warfare agents and extractors of radioactive material. Structural elucidation of phosphonates poses a particular challenge because their initial forms can be hydrolyzed, thus, degradation products may predominate in samples acquired in the field. The analysis of non-volatile organophosphorus compounds and their degradation products is possible using electrospray tandem mass spectrometry ESI-MS/MS. Here, we present a generic strategy that allows the unambiguous identification of substituents for two families of organophosphorus compounds: the phosphonates and phosphates. General fragmentation rules were deduced based on the study of decomposition pathways of 55 organophosphorus esters, including examples found in the literature. Multistage MS (MS(n)) experiments at high resolution in a hybrid mass spectrometer provide accurate mass measurements, whereas collision-induced dissociation experiments in a triple quadrupole give access to small fragment ions. The creation of a specific nomenclature for each possible structure of organophosphorus compound, depending on the alkyl side chain linked to the oxygen, was achieved by applying these fragmentation rules. This led to the creation of an 'identification tree' based upon the unique consecutive decomposition pathways uncovered for each individual compound. Hence, seven structural motifs were created that orient an unequivocal identification using the 'identification tree'. Despite the similar structures of the ensemble of phosphate and phosphonate esters, distinct identifications based upon characteristic neutral losses and diagnostic fragment ions were possible in all cases. PMID:23674282
Elucidation of Peptide-Directed Palladium Surface Structure for Biologically Tunable Nanocatalysts
Bedford, Nicholas M.; Ramezani-Dakhel, Hadi; Slocik, Joseph M.; Briggs, Beverly D.; Ren, Yang; Frenkel, Anatoly I.; Petkov, Valeri; Heinz, Hendrik; Naik, Rajesh R.; Knecht, Mark R.
Peptide-enabled synthesis of inorganic nanostructures represents an avenue to access catalytic materials with tunable and optimized properties. This is achieved via peptide complexity and programmability that is missing in traditional ligands for catalytic nanomaterials. Unfortunately, there is limited information available to correlate peptide sequence to particle structure and catalytic activity to date. As such, the application of peptide-enabled nanocatalysts remains limited to trial and error approaches. In this paper, a hybrid experimental and computational approach is introduced to systematically elucidate biomolecule-dependent structure/function relationships for peptide-capped Pd nanocatalysts. Synchrotron X-ray techniques were used to uncover substantial particle surface structural disorder, which was dependent upon the amino acid sequence of the peptide capping ligand. Nanocatalyst configurations were then determined directly from experimental data using reverse Monte Carlo methods and further refined using molecular dynamics simulation, obtaining thermodynamically stable peptide-Pd nanoparticle configurations. Sequence-dependent catalytic property differences for C-C coupling and olefin hydrogenation were then eluddated by identification of the catalytic active sites at the atomic level and quantitative prediction of relative reaction rates. This hybrid methodology provides a clear route to determine peptide-dependent structure/function relationships, enabling the generation of guidelines for catalyst design through rational tailoring of peptide sequences
Cell division factors from crown gall tumors: a strategy for structural elucidation
Manning, K.S.
Mitogenic compounds present in extracts of Vinca rosea crown gall tumor tissue were investigated. An isolation procedure, consisting of solvent partitions and reverse phase chromatography, has yielded a group of isomeric compounds which show activity in the tobacco pith bioassay. Initial characterizations revealed an unsaturated base, a sugar residue, a ..beta..-linked glucose, an allylic alcohol, and two methyl groups. A two part strategy of mass spectrometry (MS) in combination with proton nuclear magnetic resonance (/sup 1/H NMR) was envisioned. The aglycone structure would be determined by MS and the regiochemical relationships among the structural units would be defined by /sup 1/H NMR data. The utility of this approach was demonstrated by the structure assignment of a specific inhibitor of ..beta..-D-glucuronidase, 2(S)-carboxy-3(R),4(R),5(S)-trihydroxypiperidine. The relative stereochemistry of the hydroxyls was revealed by /sup 1/H NMR and the absolute configuration was deduced by a comparison of Cotton effects with a model compound. The use of /sup 1/H NMR to establish regiochemical relationships was investigated. Terpenes containing quaternary carbons and methyl groups were excellent models for the regiochemical problems presented by the mitogenic factors. This /sup 1/H NMR spectroscopy has been applied to the cell division factor structure problem. These data, with information from two dimensional nOe experiments, have defined some of the regio-relationships among the structural units present in the isolated factors.
Developing New Isotope-Coded Mass Spectrometry-Cleavable Cross-Linkers for Elucidating Protein Structures
Structural characterization of protein complexes is essential for the understanding of their function and regulation. However, it remains challenging due to limitations in existing tools. With recent technological improvements, cross-linking mass spectrometry (XL-MS) has become a powerful strategy to define protein–protein interactions and elucidate structural topologies of protein complexes. To further advance XL-MS studies, we present here the development of new isotope-coded MS-cleavable homobifunctional cross-linkers: d0- and d10-labeled dimethyl disuccinimidyl sulfoxide (DMDSSO). Detailed characterization of DMDSSO cross-linked peptides further demonstrates that sulfoxide-containing MS-cleavable cross-linkers offer robust and predictable MS2 fragmentation of cross-linked peptides, permitting subsequent MS3 analysis for simplified, unambiguous identification. Concurrent usage of these reagents provides a characteristic doublet pattern of DMDSSO cross-linked peptides, thus aiding in the confidence of cross-link identification by MSn analysis. More importantly, the unique isotopic profile permits quantitative analysis of cross-linked peptides and therefore expands the capability of XL-MS strategies to analyze both static and dynamic protein interactions. Together, our work has established a new XL-MS workflow for future studies toward the understanding of structural dynamics of protein complexes. PMID:24471733
Developing new isotope-coded mass spectrometry-cleavable cross-linkers for elucidating protein structures.
Yu, Clinton; Kandur, Wynne; Kao, Athit; Rychnovsky, Scott; Huang, Lan
Structural characterization of protein complexes is essential for the understanding of their function and regulation. However, it remains challenging due to limitations in existing tools. With recent technological improvements, cross-linking mass spectrometry (XL-MS) has become a powerful strategy to define protein-protein interactions and elucidate structural topologies of protein complexes. To further advance XL-MS studies, we present here the development of new isotope-coded MS-cleavable homobifunctional cross-linkers: d0- and d10-labeled dimethyl disuccinimidyl sulfoxide (DMDSSO). Detailed characterization of DMDSSO cross-linked peptides further demonstrates that sulfoxide-containing MS-cleavable cross-linkers offer robust and predictable MS2 fragmentation of cross-linked peptides, permitting subsequent MS3 analysis for simplified, unambiguous identification. Concurrent usage of these reagents provides a characteristic doublet pattern of DMDSSO cross-linked peptides, thus aiding in the confidence of cross-link identification by MS(n) analysis. More importantly, the unique isotopic profile permits quantitative analysis of cross-linked peptides and therefore expands the capability of XL-MS strategies to analyze both static and dynamic protein interactions. Together, our work has established a new XL-MS workflow for future studies toward the understanding of structural dynamics of protein complexes. PMID:24471733
Cryo-EM and the elucidation of new macromolecular structures: Random Conical Tilt revisited
Sorzano, C. O. S.; Alcorlo, M.; de la Rosa-Trevín, J. M.; Melero, R.; Foche, I.; Zaldívar-Peraza, A.; del Cano, L.; Vargas, J.; Abrishami, V.; Otón, J.; Marabini, R.; Carazo, J. M.
Cryo-Electron Microscopy (cryo-EM) of macromolecular complexes is a fundamental structural biology technique which is expanding at a very fast pace. Key to its success in elucidating the three-dimensional structure of a macromolecular complex, especially of small and non-symmetric ones, is the ability to start from a low resolution map, which is subsequently refined with the actual images collected at the microscope. There are several methods to produce this first structure. Among them, Random Conical Tilt (RCT) plays a prominent role due to its unbiased nature (it can create an initial model based on experimental measurements). In this article, we revise the fundamental mathematical expressions supporting RCT, providing new expressions handling all key geometrical parameters without the need of intermediate operations, leading to improved automation and overall reliability, essential for the success of cryo-EM when analyzing new complexes. We show that the here proposed RCT workflow based on the new formulation performs very well in practical cases, requiring very few image pairs (as low as 13 image pairs in one of our examples) to obtain relevant 3D maps. PMID:26390853
Towards theory driven structure elucidation of complex natural products: mandelalides and coibamide A.
Snyder, Kevin M; Sikorska, Justyna; Ye, Tao; Fang, Lijing; Su, Wu; Carter, Rich G; McPhail, Kerry L; Cheong, Paul H-Y
The effectiveness of computational tools in determining relative configurations of complex molecules is investigated, using natural products mandelalides A-D and coibamide A, towards a generalized recipe for the scientific community at large. Ultimately, continuing efforts in this vein will accelerate and strengthen relative structure elucidation of complex molecules, such as natural products. Molecular mechanics conformational search, quantum mechanical NMR chemical shift predictions, and DP4 analyses led to confirmation of the revised structures of mandelalides A-D and coibamide A. All chiral centers in the northern hemisphere of mandelalides A-D are inverted with respect to the originally proposed structures, in agreement with recent total syntheses of mandelalide A by Ye, Fürstner & Carter. In the case of coibamide A, it was found that Fang & Su's revision, in which both the macrocycle [MeAla(11)] and the side chain [HIV(2)] residues are inverted from l to d, was consistent with the authentic natural product and computations. PMID:27152741
Bioactive Metabolites from Chaetomium aureum: Structure Elucidation and Inhibition of the Hsp90 Machine Chaperoning Activity
Kabbaj, Fatima Zahra; Lu, Su; Faouzi, My El Abbés; Meddah, Bouchra; Proksch, Peter; Cherrah, Yahya; Altenbach, Hans-Josef; Aly, Amal H.; Chadli, Ahmed; Debbab, Abdessamad
Chemical investigation of the EtOAc extract of the fungus Chaetomium aureum, an endophyte of the Moroccan medicinal plant Thymelaea lythroides, afforded one new resorcinol derivative named chaetorcinol, together with five known metabolites. The structures of the isolated compounds were determined on the basis of one- and two-dimensional NMR spectroscopy and high-resolution mass spectrometry as well as by comparison with the literature. All compounds were tested for their activity towards the Hsp90 chaperoning machine in vitro using the progesterone receptor (PR) and rabbit reticulocyte lysate (RRL). Among the isolated compounds, only sclerotiorin efficiently inhibited the Hsp90 machine chaperoning activity. However, sclerotiorin showed no cytotoxic effect on breast cancer Hs578T, MDA-MB-231 and prostate cancer LNCaP cell lines. Interestingly, deacetylation of sclerotiorin increased its cytotoxicity toward the tested cell lines over a period of 48h. PMID:25482429
A Mathematical Model to Elucidate Brain Tumor Abrogation by Immunotherapy with T11 Target Structure
Chaudhuri, Swapna
T11 Target structure (T11TS), a membrane glycoprotein isolated from sheep erythrocytes, reverses the immune suppressed state of brain tumor induced animals by boosting the functional status of the immune cells. This study aims at aiding in the design of more efficacious brain tumor therapies with T11 target structure. We propose a mathematical model for brain tumor (glioma) and the immune system interactions, which aims in designing efficacious brain tumor therapy. The model encompasses considerations of the interactive dynamics of glioma cells, macrophages, cytotoxic T-lymphocytes (CD8+ T-cells), TGF-β, IFN-γ and the T11TS. The system undergoes sensitivity analysis, that determines which state variables are sensitive to the given parameters and the parameters are estimated from the published data. Computer simulations were used for model verification and validation, which highlight the importance of T11 target structure in brain tumor therapy. PMID:25955428
Structure-Specific Ribonucleases for MS-Based Elucidation of Higher-Order RNA Structure
NASA Astrophysics Data System (ADS)
Scalabrin, Matteo; Siu, Yik; Asare-Okai, Papa Nii; Fabris, Daniele
Supported by high-throughput sequencing technologies, structure-specific nucleases are experiencing a renaissance as biochemical probes for genome-wide mapping of nucleic acid structure. This report explores the benefits and pitfalls of the application of Mung bean (Mb) and V1 nuclease, which attack specifically single- and double-stranded regions of nucleic acids, as possible structural probes to be employed in combination with MS detection. Both enzymes were found capable of operating in ammonium-based solutions that are preferred for high-resolution analysis by direct infusion electrospray ionization (ESI). Sequence analysis by tandem mass spectrometry (MS/MS) was performed to confirm mapping assignments and to resolve possible ambiguities arising from the concomitant formation of isobaric products with identical base composition and different sequences. The observed products grouped together into ladder-type series that facilitated their assignment to unique regions of the substrate, but revealed also a certain level of uncertainty in identifying the boundaries between paired and unpaired regions. Various experimental factors that are known to stabilize nucleic acid structure, such as higher ionic strength, presence of Mg(II), etc., increased the accuracy of cleavage information, but did not completely eliminate deviations from expected results. These observations suggest extreme caution in interpreting the results afforded by these types of reagents. Regardless of the analytical platform of choice, the results highlighted the need to repeat probing experiments under the most diverse possible conditions to recognize potential artifacts and to increase the level of confidence in the observed structural information.
Elucidation of structure-to-property relationships of piezoresistive polymer-carbon nanotube nanocomposites
NASA Astrophysics Data System (ADS)
Fang, Weiqing; Leung, Siu N.
Polymeric nanocomposites (PNC) filled with carbon nanotubes (CNTs) possess superior multifunctionality, including electrical, thermal, and mechanical properties, making them an emerging family of advanced and multifunctional materials. In recent years, flexible polymer/CNT nanocomposites are increasingly being considered as promising alternatives to conventional smart materials. Their piezoresistive behaviours have led to many potential applications in strain sensing. Despite extensive experimental and theoretical research, the underlying mechanisms for polymer/CNT nanocomposites' piezoresistive behaviours have yet been elucidated. This paper reports comprehensive investigations on the mechanisms and the structure-to-property relationships of these piezoresistive nanocomposites. Quantitative analyses revealed that piezoresistivity of polymer/CNT nanocomposites is predominantly governed by the three mechanisms related to the strain-induced morphological evolution of the CNT network embedded in the polymer matrix. Furthermore, both CNT content and CNT alignment are key structural parameters that affect the contribution of different mechanisms on PNCs' piezoresistivity and the sensitivity of flexible PNCs as strain sensors. For PNC filled with high content of randomly dispersed CNTs, the piezoresistivity was predominantly caused by the breakage of a complex conductive network into two or more simpler conductive paths. For PNC filled with low content of highly aligned CNTs, the piezoresistivity was mainly contributed by the complete disruption of originally interconnected CNTs in electrically conductive pathways.
Constructing kinetic models to elucidate structural dynamics of a complete RNA polymerase II elongation cycle
NASA Astrophysics Data System (ADS)
Yu, Jin; Da, Lin-Tai; Huang, Xuhui
The RNA polymerase II elongation is central in eukaryotic transcription. Although multiple intermediates of the elongation complex have been identified, the dynamical mechanisms remain elusive or controversial. Here we build a structure-based kinetic model of a full elongation cycle of polymerase II, taking into account transition rates and conformational changes characterized from both single molecule experimental studies and computational simulations at atomistic scale. Our model suggests a force-dependent slow transition detected in the single molecule experiments corresponds to an essential conformational change of a trigger loop (TL) opening prior to the polymerase translocation. The analyses on mutant study of E1103G and on potential sequence effects of the translocation substantiate this proposal. Our model also investigates another slow transition detected in the transcription elongation cycle which is independent of mechanical force. If this force-independent slow transition happens as the TL gradually closes upon NTP binding, the analyses indicate that the binding affinity of NTP to the polymerase has to be sufficiently high. Otherwise, one infers that the slow transition happens pre-catalytically but after the TL closing. Accordingly, accurate determination of intrinsic properties of NTP binding is demanded for an improved characterization of the polymerase elongation. Overall, the study provides a working model of the polymerase II elongation under a generic Brownian ratchet mechanism, with most essential structural transition and functional kinetics elucidated.
Structural Elucidation of Novel Saponins in the Sea Cucumber Holothuria lessoni
Bahrami, Yadollah; Zhang, Wei; Chataway, Tim; Franco, Chris
Sea cucumbers are prolific producers of a wide range of bioactive compounds. This study aimed to purify and characterize one class of compound, the saponins, from the viscera of the Australian sea cucumber Holothuria lessoni. The saponins were obtained by ethanolic extraction of the viscera and enriched by a liquid-liquid partition process and adsorption column chromatography. A high performance centrifugal partition chromatography (HPCPC) was applied to the saponin-enriched mixture to obtain saponins with high purity. The resultant purified saponins were profiled using MALDI-MS/MS and ESI-MS/MS which revealed the structure of isomeric saponins to contain multiple aglycones and/or sugar residues. We have elucidated the structure of five novel saponins, Holothurins D/E and Holothurinosides X/Y/Z, along with seven reported triterpene glycosides, including sulfated and non-sulfated saponins containing a range of aglycones and sugar moieties, from the viscera of H. lessoni. The abundance of novel compounds from this species holds promise for biotechnological applications. PMID:25110919
Synergic application of spectroscopic and theoretical methods to the chlorogenic acid structure elucidation.
Marković, Svetlana; Tošović, Jelena; Dimitrić Marković, Jasmina M
Although chlorogenic acid (5-O-caffeoylquinic acid, 5CQA) is a dietary polyphenol known for its pharmacological and nutritional properties, its structural features have not been completely elucidated. This is the first study whose aim is to contribute to clarification of the 5CQA structure by comparing the experimental and simulated IR, Raman, (1)H NMR, (13)C NMR, and UV spectra. For this purpose, a comprehensive conformational analysis of 5CQA was performed to reveal its most stable conformations in the gas-state and solution (DMSO and methanol). The lowest-energy conformers were used to predict the spectra at two levels of theory: B3LYP-D3/and M06-2X/6-311+G(d,p) in combination with the CPCM solvation model. Both methods provide very good agreement between all experimental and simulated spectra, thus indicating correct arrangement of the atoms in the 5CQA molecule. The quinic moiety is characterized with directed hydrogen bonds, where the carboxylic hydrogen is not oriented towards the carbonyl oxygen of the carboxylic group, but towards the oxygen of the proximate hydroxyl group. In the gas-state the lowest-energy conformers are characterized with the O4H4⋯O9' hydrogen bond, whereas in the solvated state the structures with the O4H4⋯O10' hydrogen bond prevail. Knowing the fine structural details, i.e. the proper conformation of 5CQA, provides a solid base for all further investigations related to this compound. PMID:27082653
Synergic application of spectroscopic and theoretical methods to the chlorogenic acid structure elucidation
NASA Astrophysics Data System (ADS)
Marković, Svetlana; Tošović, Jelena; Dimitrić Marković, Jasmina M.
Although chlorogenic acid (5-O-caffeoylquinic acid, 5CQA) is a dietary polyphenol known for its pharmacological and nutritional properties, its structural features have not been completely elucidated. This is the first study whose aim is to contribute to clarification of the 5CQA structure by comparing the experimental and simulated IR, Raman, 1H NMR, 13C NMR, and UV spectra. For this purpose, a comprehensive conformational analysis of 5CQA was performed to reveal its most stable conformations in the gas-state and solution (DMSO and methanol). The lowest-energy conformers were used to predict the spectra at two levels of theory: B3LYP-D3/and M06-2X/6-311+G(d,p) in combination with the CPCM solvation model. Both methods provide very good agreement between all experimental and simulated spectra, thus indicating correct arrangement of the atoms in the 5CQA molecule. The quinic moiety is characterized with directed hydrogen bonds, where the carboxylic hydrogen is not oriented towards the carbonyl oxygen of the carboxylic group, but towards the oxygen of the proximate hydroxyl group. In the gas-state the lowest-energy conformers are characterized with the O4sbnd H4 ⋯ O9‧ hydrogen bond, whereas in the solvated state the structures with the O4sbnd H4 ⋯ O10‧ hydrogen bond prevail. Knowing the fine structural details, i.e. the proper conformation of 5CQA, provides a solid base for all further investigations related to this compound.
Structural elucidation of olive pomace fed sea bass (Dicentrarchus labrax) polar lipids with cardioprotective activities.
Nasopoulou, Constantina; Smith, Terry; Detopoulou, Maria; Tsikrika, Constantina; Papaharisis, Leonidas; Barkas, Dimitris; Zabetakis, Ioannis
The purpose of this study was to structurally characterise the polar lipids of sea bass (Dicentrarchus labrax), fed with an experimental diet containing olive pomace (OP), that exhibit cardioprotective activities. OP has been added to conventional fish oil (FO) feed at 4% and this was the OP diet, having been supplemented as finishing diet to fish. Sea bass was aquacultured using either FO or OP diet. At the end of the dietary experiment, lipids in both samples of fish muscle were quantified and HPLC fractionated. The in vitro cardioprotective properties of the polar lipid fractions, using washed rabbit's platelets, have been assessed and the two most biologically active fractions were further analysed by mass spectrometry. The gas-chromatrograpy-mass spectrometric data shows that these two fractions contain low levels of myristic (14:0), oleic (18:1 cis ω-9) and linoleic acids (18:2 ω-6), but high levels of palmitic (16:0) and stearic acids (18:0) as well as eicosadienoic acid (20:2 ω-6). The first fraction (MS1) also contained significant levels of arachidonic acid (20:4 ω-6) and the omega-3 fatty acids: eicosapentaenoic acid (22:5) and docosahexaenoic acid (22:6). Electrospray-mass spectrometry elucidated that the lipid composition of the two fractions contained various diacyl-glycerophospholipids species, where the majority of them have either 18:0 or 18:1 fatty acids in the sn-1 position and either 22:6 or 20:2 fatty acids in the sn-2 position for MS1 and MS2, respectively. Our research focuses on the structure/function relationship of fish muscle polar lipids and cardiovascular diseases and structural data are given for polar lipid HPLC fractions with strong cardioprotective properties. PMID:24128590
Structure elucidation, proliferation effect on macrophage and its mechanism of a new heteropolysaccharide from Lactarius deliciosus Gray.
Hou, Yiling; Liu, Lu; Ding, Xiang; Zhao, Daqun; Hou, Wanru
A new heteropolysaccharide was isolated from the fruiting bodies of Lactarius deliciosus Gray which had a molecular weight of 16kDa and was mainly composed of the galactose and glucose. Structural elucidation results indicated that Lactarius deliciosus Gray polysaccharide (LDG-B) had a backbone of (1,6)-linked d-galactose and (1, 2, 6)-linked d-galactose which branches were mainly composed of 4-linked d-glucose and 6-linked d-galactose residue. Cell cycle test results showed that LDG-B could promote the proliferation of B cells and macrophage cells by affecting G0/G1 phase, S phases and G2/M phases. The analysis of transcriptomes sequence of macrophages showed a total of 1839 genes were identified as DEGs, and approximately 708 genes were up-regulated, whereas 1131 genes were down-regulated in LDG-B group. KEGG pathway enrichment analysis showed that the MAPK, JAK-STAT and NF-κB signaling pathways are significantly enriched for DEGs in LDG-B group. Analysis of transcriptome resources enabled us to examine gene expression profiles, verify differential gene expression, and select candidate signaling pathways as the mechanisms of the immunomodulatory activity of LDG-B. PMID:27516315
Hydrogen Rearrangement Rules: Computational MS/MS Fragmentation and Structure Elucidation Using MS-FINDER Software.
Tsugawa, Hiroshi; Kind, Tobias; Nakabayashi, Ryo; Yukihira, Daichi; Tanaka, Wataru; Cajka, Tomas; Saito, Kazuki; Fiehn, Oliver; Arita, Masanori
Compound identification from accurate mass MS/MS spectra is a bottleneck for untargeted metabolomics. In this study, we propose nine rules of hydrogen rearrangement (HR) during bond cleavages in low-energy collision-induced dissociation (CID). These rules are based on the classic even-electron rule and cover heteroatoms and multistage fragmentation. We evaluated our HR rules by the statistics of MassBank MS/MS spectra in addition to enthalpy calculations, yielding three levels of computational MS/MS annotation: "resolved" (regular HR behavior following HR rules), "semiresolved" (irregular HR behavior), and "formula-assigned" (lacking structure assignment). With this nomenclature, 78.4% of a total of 18506 MS/MS fragment ions in the MassBank database and 84.8% of a total of 36370 MS/MS fragment ions in the GNPS database were (semi-) resolved by predicted bond cleavages. We also introduce the MS-FINDER software for structure elucidation. Molecular formulas of precursor ions are determined from accurate mass, isotope ratio, and product ion information. All isomer structures of the predicted formula are retrieved from metabolome databases, and MS/MS fragmentations are predicted in silico. The structures are ranked by a combined weighting score considering bond dissociation energies, mass accuracies, fragment linkages, and, most importantly, nine HR rules. The program was validated by its ability to correctly calculate molecular formulas with 98.0% accuracy for 5063 MassBank MS/MS records and to yield the correct structural isomer with 82.1% accuracy within the top-3 candidates. In a test with 936 manually identified spectra from an untargeted HILIC-QTOF MS data set of human plasma, formulas were correctly predicted in 90.4% of the cases, and the correct isomer structure was retrieved at 80.4% probability within the top-3 candidates, including for compounds that were absent in mass spectral libraries. The MS-FINDER software is freely available at http
Deglycosylation of glycoproteins with trifluoromethanesulphonic acid: elucidation of molecular structure and function.
Edge, Albert S B
The alteration of proteins by post-translational modifications, including phosphorylation, sulphation, processing by proteolysis, lipid attachment and glycosylation, gives rise to a broad range of molecules that can have an identical underlying protein core. An understanding of glycosylation of proteins is important in clarifying the nature of the numerous variants observed and in determining the biological roles of these modifications. Deglycosylation with TFMS (trifluoromethanesulphonic acid) [Edge, Faltynek, Hof, Reichert, and Weber, (1981) Anal. Biochem. 118, 131-137] has been used extensively to remove carbohydrate from glycoproteins, while leaving the protein backbone intact. Glycosylated proteins from animals, plants, fungi and bacteria have been deglycosylated with TFMS, and the most extensively studied types of carbohydrate chains in mammals, the N-linked, O-linked and glycosaminoglycan chains, are all removed by this procedure. The method is based on the finding that linkages between sugars are sensitive to cleavage by TFMS, whereas the peptide bond is stable and is not broken, even with prolonged deglycosylation. The relative susceptibility of individual sugars in glycosidic linkage varies with the substituents at C-2 and the occurrence of amido and acetyl groups, but even the most stable sugars are removed under conditions that are sufficiently mild to prevent scission of peptide bonds. The post-translational modifications of proteins have been shown to be required for diverse biological functions, and selective procedures to remove these modifications play an important role in the elucidation of protein structure and function. PMID:12974674
Structural elucidation of a pectin from flowers of Lonicera japonica and its antipancreatic cancer activity.
Lin, Liyan; Wang, Peipei; Du, Zhenyun; Wang, Wucheng; Cong, Qifei; Zheng, Changping; Jin, Can; Ding, Kan; Shao, Chenghao
To investigate polysaccharide structure from Lonicera japonica, and study its effects on behavior of pancreatic cells, a homogenous polysaccharide, LJ-02-1, was extracted and purified from flowers of L. japonica by DEAE-cellulose and Sephacryl S-200HR column. The molecular weight was estimated to be 54kDa. Monosaccharide composition was determined to be rhamnose, galacturonic acid, galactose and arabinose in the molar ratio of 10.77:7.88:15.45:65.89 by analyzing the PMP derivatives of the monosaccharides from 2M trifluoracetic acid hydrolysis via HPLC. Based on methylation analysis, partial acid hydrolysis, and NMR spectra, the polysaccharide was elucidated to be a rhamnogalacturonan backbone and substituted partly at C-4 of rhamnose. The branches were determined to be T- and 1,4,6-linked β-d-Galp, T- and 1,5-linked α-l-Araf. The polysaccharide might inhibit BxPC-3 and PANC-1 pancreatic cancer cells growth at the concentration of 1mg/mL with inhibitory ratio of 66.7% and 52.1%, respectively. PMID:27000440
Structural elucidation of the interaction between neurodegenerative disease-related tau protein with model lipid membranes
NASA Astrophysics Data System (ADS)
Jones, Emmalee M.
A protein's sequence of amino acids determines how it folds. That folded structure is linked to protein function, and misfolding to dysfunction. Protein misfolding and aggregation into beta-sheet rich fibrillar aggregates is connected with over 20 neurodegenerative diseases, including Alzheimer's disease (AD). AD is characterized in part by misfolding, aggregation and deposition of the microtubule associated tau protein into neurofibrillary tangles (NFTs). However, two questions remain: What is tau's fibrillization mechanism, and what is tau's cytotoxicity mechanism? Tau is prone to heterogeneous interactions, including with lipid membranes. Lipids have been found in NFTs, anionic lipid vesicles induced aggregation of the microtubule binding domain of tau, and other protein aggregates induced ion permeability in cells. This evidence prompted our investigation of tau's interaction with model lipid membranes to elucidate the structural perturbations those interactions induced in tau protein and in the membrane. We show that although tau is highly charged and soluble, it is highly surface active and preferentially interacts with anionic membranes. To resolve molecular-scale structural details of tau and model membranes, we utilized X-ray and neutron scattering techniques. X-ray reflectivity indicated tau aggregated at air/water and anionic lipid membrane interfaces and penetrated into membranes. More significantly, membrane interfaces induced tau protein to partially adopt a more compact conformation with density similar to folded protein and ordered structure characteristic of beta-sheet formation. This suggests possible membrane-based mechanisms of tau aggregation. Membrane morphological changes were seen using fluorescence microscopy, and X-ray scattering techniques showed tau completely disrupts anionic membranes, suggesting an aggregate-based cytotoxicity mechanism. Further investigation of protein constructs and a "hyperphosphorylation" disease mimic helped
Structural elucidation and quantification of phenolic conjugates present in human urine after tea intake.
van der Hooft, Justin J J; de Vos, Ric C H; Mihaleva, Velitchka; Bino, Raoul J; Ridder, Lars; de Roo, Niels; Jacobs, Doris M; van Duynhoven, John P M; Vervoort, Jacques
In dietary polyphenol exposure studies, annotation and identification of urinary metabolites present at low (micromolar) concentrations are major obstacles. To determine the biological activity of specific components, it is necessary to have the correct structures and the quantification of the polyphenol-derived conjugates present in the human body. We present a procedure for identification and quantification of metabolites and conjugates excreted in human urine after single bolus intake of black or green tea. A combination of a solid-phase extraction (SPE) preparation step and two high pressure liquid chromatography (HPLC)-based analytical platforms was used, namely, accurate mass fragmentation (HPLC-FTMS(n)) and mass-guided SPE-trapping of selected compounds for nuclear magnetic resonance spectroscopy (NMR) measurements (HPLC-TOFMS-SPE-NMR). HPLC-FTMS(n) analysis led to the annotation of 138 urinary metabolites, including 48 valerolactone and valeric acid conjugates. By combining the results from MS(n) fragmentation with the one-dimensional (1D)-(1)H NMR spectra of HPLC-TOFMS-SPE-trapped compounds, we elucidated the structures of 36 phenolic conjugates, including the glucuronides of 3',4'-di- and 3',4',5'-trihydroxyphenyl-γ-valerolactone, three urolithin glucuronides, and indole-3-acetic acid glucuronide. We also obtained 26 h-quantitative excretion profiles for specific valerolactone conjugates. The combination of the HPLC-FTMS(n) and HPLC-TOFMS-SPE-NMR platforms results in the efficient identification and quantification of less abundant phenolic conjugates down to nanomoles of trapped amounts of metabolite corresponding to micromolar metabolite concentrations in urine. PMID:22827565
Adxanthromycins A and B, new inhibitors of ICAM-1/LFA-1 mediated cell adhesion molecule from Streptomyces sp. NA-148. II. Physico-chemical properties and structure elucidation.
Takahashi, S; Nakano, T; Koiwa, T; Noshita, T; Funayama, S; Koshino, H; Nakagawa, A
Adxanthromycins A and B are new inhibitors of ICAM-1/LFA-1 mediated cell adhesion molecule isolated from the fermentation broth of Streptomyces sp. NA-148. The molecular formula of adxanthromycins A and B were determined as C42H40O17 and C48H50O22, respectively by FAB-MS and NMR spectral analyses, and the structures of both compounds were elucidated to be a dimeric anthrone peroxide skeleton containing alpha-D-galactose by various NMR spectral analyses and chemical degradation. PMID:10805577
Secondary structure of double-stranded DNA under stretching: Elucidation of the stretched form
NASA Astrophysics Data System (ADS)
Maaloum, M.; Beker, A.-F.; Muller, P.
Almost two decades ago, measurements of force versus extension on isolated double-stranded DNA molecules revealed a force plateau. This unusual stretching phenomenon in DNA suggests that the long molecules may be extended from the usual B form into a new conformation. Different models have been proposed to describe the nature of DNA in its stretched form, S-DNA. Using atomic force microscopy combined with a molecular combing method, we identified the structure of λ-phage DNA for different stretching values. We provide strong evidence for the existence of a first-order transition between B form and S form. Beyond a certain extension of the natural length, DNA molecules adopt a new double-helix conformation characterized by a diameter of 1.2 nm and a helical pitch of 18 nm.
Secondary structure of double-stranded DNA under stretching: Elucidation of the stretched form
Maaloum, M.; Muller, P.; Beker, A-F.
Almost two decades ago, measurements of force versus extension on isolated double-stranded DNA molecules revealed a force plateau. This unusual stretching phenomenon in DNA suggests that the long molecules may be extended from the usual B form into a new conformation. Different models have been proposed to describe the nature of DNA in its stretched form, S-DNA. Using atomic force microscopy combined with a molecular combing method, we identified the structure of {lambda}-phage DNA for different stretching values. We provide strong evidence for the existence of a first-order transition between B form and S form. Beyond a certain extension of the natural length, DNA molecules adopt a new double-helix conformation characterized by a diameter of 1.2 nm and a helical pitch of18 nm.
pH-Controlled Oxidation of an Aromatic Ketone: Structural Elucidation of the Products of Two Green Chemical Reactions
ERIC Educational Resources Information Center
Ballard, C. Eric
A laboratory experiment emphasizing the structural elucidation of organic compounds has been developed as a discovery exercise. The "unknown" compounds are the products of the pH-controlled oxidation of 4'-methoxyacetophenone with bleach. The chemoselectivity of this reaction is highly dependent on the pH of the reaction media: under basic…
Isolation and chemical structure of aklanonic acid, an early intermediate in the biosynthesis of anthracyclines.
Eckardt, K; Tresselt, D; Schumann, G; Ihn, W; Wagner, C
The fermentation, isolation and structure elucidation of aklanonic acid are described. The compound was isolated from fermentations of Streptomyces strain ZIMET 43,717. Aklanonic acid is a yellow-orange crystalline substance, melting at 203-204 degrees C (dec), having the molecular formula C21H16O8, and possessing UV maxima at 258, 282 (sh) and 438 nm (CHCl3). In dimethyl sulfoxide or pyridine aklanonic acid is unstable and a new compound (aklanone) is formed as a conversion product. The elucidation of the structures has shown that aklanonic acid and aklanone are derivatives of 1,8-dihydroxyanthraquinone. PMID:3862658
Structure elucidation, anticancer and antioxidant activities of a novel polysaccharide from Gomphus clavatus Gray.
Ding, Xiang; Hou, Yiling; Zhu, Yuanxiu; Wang, Panpan; Fu, Lei; Zhu, Hongqing; Zhang, Nan; Qin, Hang; Qu, Wei; Wang, Fang; Hou, Wanru
A novel heteropolysaccharide from the fruiting bodies of Gomphus clavatus Gray was isolated through Sephadex G-200 and DEAE-cellulose columns. The Gomphus clavatus Gray polysaccharide (GCG-1) was mainly composed of β-D-glucosepyranose (β-D-Glu) and α-D-galactopyranose (α-D-Gal) in a ratio of 3:2 and had a molecular weight of ~50,000 Da. The structure of GCG-1 was investigated by a combination of total hydrolysis, gas chromatography-mass spectrometry, methylation analysis, nuclear magnetic resonance spectroscopy and infrared spectra. The results indicated that GCG-1 had a backbone of (1 → 4)-β-D-glucosepyranose residues with branches at O-6 and the branches consisted of two with (1 → 3)-α-D-galactopyranose residue. Antioxidation test in vitro showed that it possessed strong free radical scavenging activity, which may be comparable to vitamin C and butylated hydroxytoluene. GCG-1 also induced the apoptosis of HepG-2 cells and affected the mRNA expression of various housekeeping genes in the HepG-2 cells. The results indicated that Gomphus clavatus Gray may be an ideal sources for antioxidant and anticancer agents. PMID:25901792
Structural elucidation and biological studies of a novel exopolysaccaride from Klebsiella pneumoniae PB12.
Mandal, Amit K; Sen, Ipsita K; Maity, Prasenjit; Chattopadhyay, Sourav; Chakraborty, Ranadhir; Roy, Somenath; Islam, Syed S
An exopolysaccharide (KNPS) of an average molecular weight ∼1.8×10(5) Da was isolated from the culture medium of Klebsiella pneumoniae PB12. Structural characterization of KNPS was carried out using sugar and methylation analysis, Smith degradation and 1D/2D NMR experiments. Sugar analysis showed that the KNPS composed of arabinose, galactose, 3-O-methyl-galctose and glucose in a molar ratio of nearly 4:3:1:1. The proposed repeating unit of the KNPS has a backbone chain consisting of two (1→6)-galactopyranosyl residues, two (1→5)-arabinofuranosyl residues, one (1→6)-glucopyranosyl residue and one (1→3)-arabinopyranosyl residue, out of which one (1→6)-galactopyranosyl residue was branched at O-2 position with a (1→2)-linked-galactopyranosyl residue terminated with non reducing arabinofuranosyl residue and one (1→5)-arabinofuranosyl residue branched at O-3 position with non reducing end 3-O-Me-galactopyranosyl residue. KNPS was found non-toxic toward human lymphocyte up to the dosage of 100 μg/ml. KNPS enhanced malondialdehyde (MDA), reactive oxygen species (ROS), and have the potential to alter the ratio of oxidized glutathione (GSSG) and reduced glutathione (GSH) levels in the cellular system. PMID:25999015
Structure elucidation of hexabromocyclododecanes--a class of compounds with a complex stereochemistry.
Heeb, Norbert V; Schweizer, W Bernd; Kohler, Martin; Gerecke, Andreas C
Hexabromocyclododecanes (HBCDs) are high production volume chemicals (16700 t worldwide in 2001) used as flame-retardants for plastics and textiles. HBCDs exhibit typical properties of persistent organic pollutants (POPs). They are highly lipophilic and accumulate in biota. Increasing environmental concentrations of HBCDs, mostly reported as sum values, have been observed. As such, HBCDs have to be considered as potential emerging POPs, but their occurrence and environmental fate have not yet been addressed at the level of individual HBCD stereoisomers. Considering the six stereogenic centers of HBCDs, 16 stereoisomers, six diastereomeric pairs of enantiomers as well as four meso forms, can be deduced. Herein, we report spectroscopic and chromatographic data for eight out of 16 possible HBCD stereoisomers, which were isolated from a technical product. Six stereoisomers were identified as three pairs of enantiomers ((+/-) alpha-, beta-, and gamma-HBCDs), differing in optical rotation and chromatographic retention on a chiral phase. The crystal structures of these pairs of enantiomers were determined. Another two of these eight HBCD stereoisomers, not yet described in the literature, showed no optical rotation and are tentatively assigned as meso forms (delta- and epsilon-HBCD). The given spectroscopic and chromatographic information allows the unambiguous identification of eight HBCD stereoisomers and the occurrence, fate, and toxicology of these individual stereoisomers can now be studied. PMID:16157171
Seismic Behaviour of Vertical Mass Isolated Structures
Nekooei, M.; Ziyaeifar, M.
In this paper, the seismic behaviour of vertical mass isolated structures against the earthquake is studied. These structures are assumed to be consisted of two subsystems. Mass subsystem possesses low lateral stiffness but carries the major part of mass of the system. Stiffness subsystem, however, controls the deformation of the mass subsystem and attributes with much higher stiffness. The isolator layer is, therefore, located in between the mass and the stiffness subsystems and assumed to be a viscous damper layer. The analytical model used for this investigation is a dual mass-spring model which is an extended form of the three element Maxwell model. In this study, the ability of mass isolation techniques in reducing earthquake effects on buildings with two approaches, parametric and numerical approaches, is shown. In the parametric approach, by definition an isolation factor for structure and determination the dynamic characteristics of system, the relative optimum value of the isolator damping coefficient is obtained. The results provide an insight on role of relative stiffness and mass ratio of the two subsystems. Finally, in the numerical approach, the spectral responses of these structures due to the earthquake are investigated. The results show a noticeable decrease in earthquake input force to vertical mass isolated structures in comparison with non-isolated structures.
Microfabricated structures with electrical isolation and interconnections
NASA Technical Reports Server (NTRS)
Clark, William A. (Inventor); Juneau, Thor N. (Inventor); Roessig, Allen W. (Inventor); Lemkin, Mark A. (Inventor)
The invention is directed to a microfabricated device. The device includes a substrate that is etched to define mechanical structures at least some of which are anchored laterally to the remainder of the substrate. Electrical isolation at points where mechanical structures are attached to the substrate is provided by filled isolation trenches. Filled trenches may also be used to electrically isolate structure elements from each other at points where mechanical attachment of structure elements is desired. The performance of microelectromechanical devices is improved by 1) having a high-aspect-ratio between vertical and lateral dimensions of the mechanical elements, 2) integrating electronics on the same substrate as the mechanical elements, 3) good electrical isolation among mechanical elements and circuits except where electrical interconnection is desired.
Chemical structure elucidation from ¹³C NMR chemical shifts: efficient data processing using bipartite matching and maximal clique algorithms.
Koichi, Shungo; Arisaka, Masaki; Koshino, Hiroyuki; Aoki, Atsushi; Iwata, Satoru; Uno, Takeaki; Satoh, Hiroko
Computer-assisted chemical structure elucidation has been intensively studied since the first use of computers in chemistry in the 1960s. Most of the existing elucidators use a structure-spectrum database to obtain clues about the correct structure. Such a structure-spectrum database is expected to grow on a daily basis. Hence, the necessity to develop an efficient structure elucidation system that can adapt to the growth of a database has been also growing. Therefore, we have developed a new elucidator using practically efficient graph algorithms, including the convex bipartite matching, weighted bipartite matching, and Bron-Kerbosch maximal clique algorithms. The utilization of the two matching algorithms especially is a novel point of our elucidator. Because of these sophisticated algorithms, the elucidator exactly produces a correct structure if all of the fragments are included in the database. Even if not all of the fragments are in the database, the elucidator proposes relevant substructures that can help chemists to identify the actual chemical structures. The elucidator, called the CAST/CNMR Structure Elucidator, plays a complementary role to the CAST/CNMR Chemical Shift Predictor, and together these two functions can be used to analyze the structures of organic compounds. PMID:24655374
Elucidation and Structural Analysis of Conserved Pools for Genome-Scale Metabolic Reconstructions
Nikolaev, Evgeni V.; Burgard, Anthony P.; Maranas, Costas D.
In this article, we introduce metabolite concentration coupling analysis (MCCA) to study conservation relationships for metabolite concentrations in genome-scale metabolic networks. The analysis allows the global identification of subsets of metabolites whose concentrations are always coupled within common conserved pools. Also, the minimal conserved pool identification (MCPI) procedure is developed for elucidating conserved pools for targeted metabolites without computing the entire basis conservation relationships. The approaches are demonstrated on genome-scale metabolic reconstructions of Helicobacter pylori, Escherichia coli, and Saccharomyces cerevisiae. Despite significant differences in the size and complexity of the examined organism's models, we find that the concentrations of nearly all metabolites are coupled within a relatively small number of subsets. These correspond to the overall exchange of carbon molecules into and out of the networks, interconversion of energy and redox cofactors, and the transfer of nitrogen, sulfur, phosphate, coenzyme A, and acyl carrier protein moieties among metabolites. The presence of large conserved pools can be viewed as global biophysical barriers protecting cellular systems from stresses, maintaining coordinated interconversions between key metabolites, and providing an additional mode of global metabolic regulation. The developed approaches thus provide novel and versatile tools for elucidating coupling relationships between metabolite concentrations with implications in biotechnological and medical applications. PMID:15489308
Metabolic and genomic analysis elucidates strain-level variation in Microbacterium spp. isolated from chromate contaminated sediment
Henson, Michael W.; Santo Domingo, Jorge W.; Kourtev, Peter S.; Jensen, Roderick V.; Dunn, James A.
Hexavalent chromium [Cr(VI)] is a soluble carcinogen that has caused widespread contamination of soil and water in many industrial nations. Bacteria have the potential to aid remediation as certain strains can catalyze the reduction of Cr(VI) to insoluble and less toxic Cr(III). Here, we examine Cr(VI) reducing Microbacterium spp. (Cr-K1W, Cr-K20, Cr-K29, and Cr-K32) isolated from contaminated sediment (Seymore, Indiana) and show varying chromate responses despite the isolates' phylogenetic similarity (i.e., identical 16S rRNA gene sequences). Detailed analysis identified differences based on genomic metabolic potential, growth and general metabolic capabilities, and capacity to resist and reduce Cr(VI). Taken together, the discrepancies between the isolates demonstrate the complexity inter-strain variation can have on microbial physiology and related biogeochemical processes. PMID:26587353
Structure of Csm2 elucidates the relationship between small subunits of CRISPR-Cas effector complexes.
Venclovas, Česlovas
Type I and type III CRISPR-Cas effector complexes share similar architecture and have homologous key subunits. However, the relationship between the so-called small subunits of these complexes remains a contentious issue. Here, it is shown that the recently solved structure of Thermotoga maritima Csm2 represents a dimer with the extensive structure swapping between monomers. Unswapping the structure generates a compact globular monomer which shares similar structure and surface properties with Cmr5, the small subunit of a related Cmr complex. Detailed analysis of available structures of small subunits reveals that they all have a common fold suggesting their common origin. PMID:27091242
Elucidation of the biochemical pathway of 2-phenylethanol from shikimic acid using isolated protoplasts of rose flowers.
Yang, Ziyin; Sakai, Miwa; Sayama, Hironori; Shimeno, Taku; Yamaguchi, Koji; Watanabe, Naoharu
The isolated protoplasts of rose flowers were used to investigate the metabolic pathway in rose flower leading from shikimic acid or L-phenylalanine (L-Phe) to 2-phenylethanol (2PE), a dominant volatile compound in hybrid roses such as Rosa damascena Mill., R. 'Hoh-Jun', and R. 'Yves Piaget'. Deuterium-labeled L-Phe ([2H8]L-Phe) was supplied to the protoplasts isolated from R. 'Yves Piaget' petals. The volatile end products ([2Hn]-2PE, n=6-8) and their related intermediates ([2Hn]phenylacetaldehyde, n=6-8) were detected in the protoplasts by gas chromatography-mass spectrometry (GC-MS). In addition, we chemically synthesized [2,3,4,5,6-13C5]shikimic acid, a new stable isotopomer, to investigate the formation of 2PE from shikimic acid by GC-MS and nuclear magnetic resonance. We proposed the hypothetical biochemical pathway of 2PE from shikimic acid via chorismic acid, L-Phe, and phenylacetaldehyde. This protoplast system facilitates findings of metabolic intermediates and simplifies the complex branching biosynthetic pathways of floral scents to distinct individual events. PMID:19097671
Fragmentation follows structure: top-down mass spectrometry elucidates the topology of engineered cystine-knot miniproteins.
Reinwarth, Michael; Avrutina, Olga; Fabritz, Sebastian; Kolmar, Harald
Over the last decades the field of pharmaceutically relevant peptides has enormously expanded. Among them, several peptide families exist that contain three or more disulfide bonds. In this context, elucidation of the disulfide patterns is extremely important as these motifs are often prerequisites for folding, stability, and activity. An example of this structure-determining pattern is a cystine knot which comprises three constrained disulfide bonds and represents a core element in a vast number of mechanically interlocked peptidic structures possessing different biological activities. Herein, we present our studies on disulfide pattern determination and structure elucidation of cystine-knot miniproteins derived from Momordica cochinchinensis peptide MCoTI-II, which act as potent inhibitors of human matriptase-1. A top-down mass spectrometric analysis of the oxidised and bioactive peptides is described. Following the detailed sequencing of the peptide backbone, interpretation of the MS(3) spectra allowed for the verification of the knotted topology of the examined miniproteins. Moreover, we found that the fragmentation pattern depends on the knottin's folding state, hence, tertiary structure, which to our knowledge has not been described for a top-down MS approach before. PMID:25303319
Fragmentation Follows Structure: Top-Down Mass Spectrometry Elucidates the Topology of Engineered Cystine-Knot Miniproteins
Reinwarth, Michael; Avrutina, Olga; Fabritz, Sebastian; Kolmar, Harald
Over the last decades the field of pharmaceutically relevant peptides has enormously expanded. Among them, several peptide families exist that contain three or more disulfide bonds. In this context, elucidation of the disulfide patterns is extremely important as these motifs are often prerequisites for folding, stability, and activity. An example of this structure-determining pattern is a cystine knot which comprises three constrained disulfide bonds and represents a core element in a vast number of mechanically interlocked peptidic structures possessing different biological activities. Herein, we present our studies on disulfide pattern determination and structure elucidation of cystine-knot miniproteins derived from Momordica cochinchinensis peptide MCoTI-II, which act as potent inhibitors of human matriptase-1. A top-down mass spectrometric analysis of the oxidised and bioactive peptides is described. Following the detailed sequencing of the peptide backbone, interpretation of the MS3 spectra allowed for the verification of the knotted topology of the examined miniproteins. Moreover, we found that the fragmentation pattern depends on the knottin's folding state, hence, tertiary structure, which to our knowledge has not been described for a top-down MS approach before. PMID:25303319
Structure elucidation of membrane-associated peptides and proteins in oriented bilayers by solid-state NMR spectroscopy.
Naito, Akira
Solid-state NMR using magnetically oriented bilayer systems provides useful information on the structure and orientation of peptides and proteins bound to lipid bilayers. The ordering of the lipid bilayer along the magnetic field can be achieved in two ways. First, lipid can be macroscopically oriented by pressing lipid-water dispersion between flat glass plates, which is called a mechanically aligned system. Second, lipid molecules themselves can be aligned spontaneously in the magnetic field because of their diamagnetic anisotropy by forming bicelles or magnetically oriented vesicle systems. Structure and orientation of the membrane-associated peptides and proteins can be achieved by analyzing structural constraints obtained from anisotropic chemical shift interactions such as chemical shift oscillation or nuclear dipolar interactions such as dipolar wave and a combination of them such as PISA wheel. Detailed structure elucidation of various kinds of membrane peptides and proteins in such oriented bilayers is presented. PMID:19647984
Elucidation of Drug Metabolite Structural Isomers Using Molecular Modeling Coupled with Ion Mobility Mass Spectrometry.
Reading, Eamonn; Munoz-Muriedas, Jordi; Roberts, Andrew D; Dear, Gordon J; Robinson, Carol V; Beaumont, Claire
Ion mobility-mass spectrometry (IM-MS) in combination with molecular modeling offers the potential for small molecule structural isomer identification by measurement of their gas phase collision cross sections (CCSs). Successful application of this approach to drug metabolite identification would facilitate resource reduction, including animal usage, and may benefit other areas of pharmaceutical structural characterization including impurity profiling and degradation chemistry. However, the conformational behavior of drug molecules and their metabolites in the gas phase is poorly understood. Here the gas phase conformational space of drug and drug-like molecules has been investigated as well as the influence of protonation and adduct formation on the conformations of drug metabolite structural isomers. The use of CCSs, measured from IM-MS and molecular modeling information, for the structural identification of drug metabolites has also been critically assessed. Detection of structural isomers of drug metabolites using IM-MS is demonstrated and, in addition, a molecular modeling approach has been developed offering rapid conformational searching and energy assessment of candidate structures which agree with experimental CCSs. Here it is illustrated that isomers must possess markedly dissimilar CCS values for structural differentiation, the existence and extent of CCS differences being ionization state and molecule dependent. The results present that IM-MS and molecular modeling can inform on the identity of drug metabolites and highlight the limitations of this approach in differentiating structural isomers. PMID:26752623
Elucidation of the Covalent and Tertiary Structures of Biologically Active Ts3 Toxin.
Dang, Bobo; Kubota, Tomoya; Mandal, Kalyaneswar; Correa, Ana M; Bezanilla, Francisco; Kent, Stephen B H
Ts3 is an alpha scorpion toxin from the venom of the Brazilian scorpion Tityus serrulatus. Ts3 binds to the domain IV voltage sensor of voltage-gated sodium channels (Nav ) and slows down their fast inactivation. The covalent structure of the Ts3 toxin is uncertain, and the structure of the folded protein molecule is unknown. Herein, we report the total chemical synthesis of four candidate Ts3 toxin protein molecules and the results of structure-activity studies that enabled us to establish the covalent structure of biologically active Ts3 toxin. We also report the synthesis of the mirror image form of the Ts3 protein molecule, and the use of racemic protein crystallography to determine the folded (tertiary) structure of biologically active Ts3 toxin by X-ray diffraction. PMID:27244051
Structure elucidation of the Pribnow box consensus promoter sequence by racemic DNA crystallography.
Mandal, Pradeep K; Collie, Gavin W; Srivastava, Suresh C; Kauffmann, Brice; Huc, Ivan
It has previously been shown that the use of racemic mixtures of naturally chiral macromolecules such as protein and DNA can significantly aid the crystallogenesis process, thereby addressing one of the major bottlenecks to structure determination by X-ray crystallographic methods-that of crystal growth. Although previous studies have provided convincing evidence of the applicability of the racemic crystallization technique to DNA through the study of well-characterized DNA structures, we sought to apply this method to a historically challenging DNA sequence. For this purpose we chose a non-self-complementary DNA duplex containing the biologically-relevant Pribnow box consensus sequence 'TATAAT'. Four racemic crystal structures of this previously un-crystallizable DNA target are reported (with resolutions in the range of 1.65-2.3 Å), with further crystallographic studies and structural analysis providing insight into the racemic crystallization process as well as structural details of this highly pertinent DNA sequence. PMID:27137886
Structure elucidation of alkaline earth impregnated MCM-41 type mesoporous materials obtained by direct synthesis: An experimental and theoretical study
NASA Astrophysics Data System (ADS)
Paz, Gizeuda L.; Silva, Francisco das Chagas M.; Araújo, Maciel M.; Lima, Francisco das Chagas A.; Luz, Geraldo E.
In this work, MCM-41 were synthesized hydrothermally and functionalized with calcium and strontium salts by direct method, using the Si/M = 50 molar ratio, in order to elucidate the way as the alkaline earth is incorporated on MCM-41 molecular sieve. The materials were characterized by X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), Raman spectroscopy, nitrogen adsorption-desorption and theoretical calculations by DFT method. Experimental results and computer simulations showed that the alkaline earths were incorporated on MCM-41 through a complex structure, which negatively influences on basic sites formation.
Using FT-IR Spectroscopy to Elucidate the Structures of Ablative Polymers
NASA Technical Reports Server (NTRS)
Fan, Wendy
The composition and structure of an ablative polymer has a multifaceted influence on its thermal, mechanical and ablative properties. Understanding the molecular level information is critical to the optimization of material performance because it helps to establish correlations with the macroscopic properties of the material, the so-called structure-property relationship. Moreover, accurate information of molecular structures is also essential to predict the thermal decomposition pathways as well as to identify decomposition species that are fundamentally important to modeling work. In this presentation, I will describe the use of infrared transmission spectroscopy (FT-IR) as a convenient tool to aid the discovery and development of thermal protection system materials.
Structure elucidation of antiproliferative bisbenzylisoquinoline alkaloids from Anisocycla grandidieri from the Madagascar dry foresta
Liu, Yixi; Harinantenaina, Liva; Brodie, Peggy J.; Slebodnick, Carla; Callmander, Martin W.; Rakotondrajaona, R.; Rakotobe, Etienne; Rasamison, Vincent E.; TenDyke, Karen; Shen, Yongchun; Kingston, David G. I.
Antiproliferative bioassay-guided fractionation of the ethanol extract of the stems of Anisocycla grandidieri led to the isolation of the known alkaloids stebisimine (1), (+)-1,2-dehydrotelobine (2), (+)-2'-norcocsuline (3), and puetogaline B (4). Herein we report the full NMR assignments of all compounds and the X-ray crystallography of single crystals of compounds 1 and 3. Compounds 2 and 3 showed moderate antiproliferative activity against the A2780 human ovarian cancer cell line with IC50 values of 4.1 ± 0.3 and 2.7 ± 0.3 μM, respectively, and they also displayed selective activity towards the H460 (large cell lung cancer), MCF-7 (breast ductal carcinoma), and UACC-257 (melanoma) cell lines. PMID:23754698
Elucidating the Structure of Sugars: MW Spectroscopy Combined with Ultrafast UV Laser Vaporization
NASA Astrophysics Data System (ADS)
Cocinero, Emilio J.; Ecija, Patricia; Basterretxea, Francisco J.; Fernandez, Jose A.; Castano, Fernando; Lesarri, Alberto; Grabow, Jens-Uwe; Cimas, Alvaro
Carbohydrates are one of the most versatile biochemicalbuilding blocks, widely acting in energetic, structural or recognition processes. Even the small monosaccharides display unique structural and conformational freedom and may coexist in many open-chain or cyclic forms. We recently initiated the investigation of a series of monosaccharides using a combination of ultrafast laser vaporization and microwave spectroscopy in supersonic jet expansions. We present several structural studies on carbohydrates of aldoses and ketoses of five and six carbon sugars vaporized by UV ultrafast laser vaporization and stabilized in a jet expansion. The experimental evidence confirms that sugars exhibits a α-/β-pyranose conformation (6-membered ring), sharply contrasting with the furanose form (5-membered ring) found in the nature (as component of RNA, sucrose). In addition, thanks to the use of enriched samples, we have experimentally determined the substitution and effective structures. Finally, the structure of several monosaccharides was compared and common structural patterns of their conformational landscape will be showed. E. J. Cocinero, A. Lesarri, P. écija, F. J. Basterretxea, J. U. Grabow, J. A. Fernández and F. Castaño Angew. Chem. Int. Ed. 51, 3119-3124, 2012. E. J. Cocinero, A. Lesarri, P. écija, Á. Cimas, B. G. Davis, F. J. Basterretxea, J. A. Fernández and F. Castaño J. Am. Chem. Soc. 135, 2845-2852, 2013.
Polymer-Induced Heteronucleation for Protein Single Crystal Growth: Structural Elucidation of Bovine Liver Catalase and Concanavalin A Forms
Foroughi, Leila M.; Kang, You-Na; Matzger, Adam J.
Obtaining single crystals for X-ray diffraction remains a major bottleneck in structural biology; when existing crystal growth methods fail to yield suitable crystals, often the target rather than the crystallization approach is reconsidered. Here we demonstrate that polymer-induced heteronucleation, a powerful technique that has been used for small molecule crystallization form discovery, can be applied to protein crystallization by optimizing the heteronucleant composition and crystallization formats for crystallizing a wide range of protein targets. Applying these advances to two benchmark proteins resulted in dramatically increased crystal size, enabling structure determination, for a half century old form of bovine liver catalase (BLC) that had previously only been characterized by electron microscopy, and the discovery of two new forms of concanavalin A (conA) from the Jack bean and accompanying structural elucidation of one of these forms.
Structural elucidation of rapid solution-mediated phase transitions in pharmaceutical solids using in situ synchrotron SAXS/WAXS.
Boetker, Johan; Rades, Thomas; Rantanen, Jukka; Hawley, Adrian; Boyd, Ben J
In situ elucidation of kinetics of solution-mediated phase transformations using direct structural determination has been achieved using synchrotron SAXS/WAXS radiation. Using theophylline as a model drug with known phase transformation from anhydrate to monohydrate form in aqueous conditions within a few minutes, the kinetics of the structural transition were resolved at the second scale, and the results achieved agreed well with those determined using indirect approaches such as Raman spectroscopy. The recrystallization of the monohydrate in situ (due to its lower solubility) from dissolved anhydrate solution (higher solubility) is demonstrated directly, highlighting a major issue for such compounds in application. The technique has the additional benefit of having the potential to identify intermediate structures which are not readily achievable with in situ spectroscopic techniques, as well as being amenable to high throughput approaches. PMID:22871088
Elucidation of the EP defect in Diamond-Blackfan anemia by characterization and prospective isolation of human EPs.
Iskander, Deena; Psaila, Bethan; Gerrard, Gareth; Chaidos, Aristeidis; En Foong, Hui; Harrington, Yvonne; Karnik, Leena C; Roberts, Irene; de la Fuente, Josu; Karadimitris, Anastasios
Diamond-Blackfan anemia (DBA) is a disorder characterized by a selective defect in erythropoiesis. Delineation of the precise defect is hampered by a lack of markers that define cells giving rise to erythroid burst- and erythroid colony-forming unit (BFU-E and CFU-E) colonies, the clonogenic assays that quantify early and late erythroid progenitor (EEP and LEP) potential, respectively. By combining flow cytometry, cell-sorting, and single-cell clonogenic assays, we identified Lin(-)CD34(+)CD38(+)CD45RA(-)CD123(-)CD71(+)CD41a(-)CD105(-)CD36(-) bone marrow cells as EEP giving rise to BFU-E, and Lin(-)CD34(+/-)CD38(+)CD45RA(-)CD123(-)CD71(+)CD41a(-)CD105(+)CD36(+) cells as LEP giving rise to CFU-E, in a hierarchical fashion. We then applied these definitions to DBA and identified that, compared with controls, frequency, and clonogenicity of DBA, EEP and LEP are significantly decreased in transfusion-dependent but restored in corticosteroid-responsive patients. Thus, both quantitative and qualitative defects in erythroid progenitor (EP) contribute to defective erythropoiesis in DBA. Prospective isolation of defined EPs will facilitate more incisive study of normal and aberrant erythropoiesis. PMID:25755292
Structure elucidation of the Pribnow box consensus promoter sequence by racemic DNA crystallography
Mandal, Pradeep K.; Collie, Gavin W.; Srivastava, Suresh C.; Kauffmann, Brice; Huc, Ivan
It has previously been shown that the use of racemic mixtures of naturally chiral macromolecules such as protein and DNA can significantly aid the crystallogenesis process, thereby addressing one of the major bottlenecks to structure determination by X-ray crystallographic methods—that of crystal growth. Although previous studies have provided convincing evidence of the applicability of the racemic crystallization technique to DNA through the study of well-characterized DNA structures, we sought to apply this method to a historically challenging DNA sequence. For this purpose we chose a non-self-complementary DNA duplex containing the biologically-relevant Pribnow box consensus sequence 'TATAAT'. Four racemic crystal structures of this previously un-crystallizable DNA target are reported (with resolutions in the range of 1.65–2.3 Å), with further crystallographic studies and structural analysis providing insight into the racemic crystallization process as well as structural details of this highly pertinent DNA sequence. PMID:27137886
Determination and structural elucidation of triacylglycerols in krill oil by chromatographic techniques.
Araujo, Pedro; Zhu, Han; Breivik, Joar Fjørtoft; Hjelle, Jan Idar; Zeng, Yingxu
The content of triacylglycerols (TAG) in krill oil is generally omitted from the labels of commercial supplements and unacknowledged in studies aimed at proving its health benefits. The present study demonstrates that TAG compounds, in addition to phospholipids and lysophospholipids, are an important lipid class in pure krill oil. The fatty acid composition of TAG molecules from krill oil and their distribution on the backbone of TAG structures were determined by gas chromatography and liquid chromatography tandem mass spectrometric, respectively. The content of omega 3 polyunsaturated fatty acids (n-3 PUFA) was similar to those reported in the literature for fish oil. It was estimated that 21 % of n-3 PUFA were at the sn-2 position of TAG structures. To our knowledge, this is the first determination and structural characterization of TAG in pure krill oil supplements. PMID:24190513
Expression, crystallization and structure elucidation of γ-terpinene synthase from Thymus vulgaris.
Rudolph, Kristin; Parthier, Christoph; Egerer-Sieber, Claudia; Geiger, Daniel; Muller, Yves A; Kreis, Wolfgang; Müller-Uri, Frieder
The biosynthesis of γ-terpinene, a precursor of the phenolic isomers thymol and carvacrol found in the essential oil from Thymus sp., is attributed to the activitiy of γ-terpinene synthase (TPS). Purified γ-terpinene synthase from T. vulgaris (TvTPS), the Thymus species that is the most widely spread and of the greatest economical importance, is able to catalyze the enzymatic conversion of geranyl diphosphate (GPP) to γ-terpinene. The crystal structure of recombinantly expressed and purified TvTPS is reported at 1.65 Å resolution, confirming the dimeric structure of the enzyme. The putative active site of TvTPS is deduced from its pronounced structural similarity to enzymes from other species of the Lamiaceae family involved in terpenoid biosynthesis: to (+)-bornyl diphosphate synthase and 1,8-cineole synthase from Salvia sp. and to (4S)-limonene synthase from Mentha spicata. PMID:26750479
Spectroscopic and structural elucidation of alanyl-containing dipeptides and their hydrogensquarates
NASA Astrophysics Data System (ADS)
Koleva, Bojidarka B.; Kolev, Tsonko M.; Spiteller, Michael
The hydrogensquarates of alanyl-containing dipeptides glycylalanine ( H-Gly-Ala-OH) and alanylalanine ( H-Ala-Ala-OH) are characterized structurally by means of quantum chemical ab initio calculations, solid-state linear-dichroic infrared (IR-LD) spectroscopy, 1H and 13C NMR data, ESI-MS, HPLC-MS/MS, TGV and DSC methods. The structures consist in positive charged peptide moiety and negative hydrogensquarate anion (HSq -), stabilizing by strong intermolecular hydrogen bonds. The theoretical and IR-LD spectroscopic data are compared with corresponding ones of zwitterion dipeptides with a view to understanding the structural and conformational changes as well as the IR-spectroscopic ones as a result of hydrogensquarates formation. The strong overlapped and complicated IR-spectroscopic bands typical for hydrogensquarates in solid-state are assigned supporting with the presented vibrational analysis of the dipeptides and of the hydrogensqauarate anion.
Dioximate- and Bis(salicylaldiminate)-Bridged Titanium and Zirconium Alkoxides: Structure Elucidation by Mass Spectrometry
Maurer, Christian; Pittenauer, Ernst; Puchberger, Michael; Allmaier, Günter; Schubert, Ulrich
The treatment of titanium alkoxides with 1,5-pentanedioxime or 2,5-hexanedioxime resulted in the formation of complexes [{TiL(OR)2}2] in which the dioximate ligands (L) bridge a dimeric Ti2(μ2-OR)2 unit. The structures of the complexes were determined by single-crystal structure analysis, ESI mass spectrometry, and 1D and 2D solution NMR spectroscopy. In contrast, the treatment of titanium alkoxides with dioximes bearing cyclic linkers, such as cyclohexyl or aryl groups, resulted in insoluble polymeric compounds. The treatment of various bis(salicylaldiminates) with titanium and zirconium alkoxides resulted in compounds with the same composition [{TiL(OR)2}2], in which, however, two monomeric Ti(OR)2 units are bridged by the ligands L. The two structural possibilities can be distinguished by low-energy collision-induced dissociation owing to their different fragmentation patterns. PMID:23795338
Mechanism driven structural elucidation of forced degradation products from hydrocortisone in solution.
Zhang, Fa; Zhou, Jay; Shi, Yiqun; Tavlarakis, Panagiotis; Karaisz, Kenneth
Hydrocortisone degradation products 1, 2, 3, and 4 along with hemiacetal derivatives 5, 6, 7, and 8 were observed through stressed hydrocortisone in solution. Their structures were identified based on HPLC-UV, HPLC-MS, and HPLC-HRMS (high resolution/high accuracy mass spectrometry) analyses as well as reaction mechanistic investigation and synthesis for structural confirmation. 1 and 2 are a pair of E/Z isomers and they were generated through acid catalyzed tautomerization/dehydration of hydrocortisone. Incorporation of water to 1 and 2 resulted in the formation of 3. We also discovered new degradation product 4 which was converted from 3 by oxidation. The degradation products were synthesized by stressing hydrocortisone under the optimized conditions and their structures were characterized by NMR ((1)H/(13)C, COSY, HMBC, HSQC, NOESY) and HRMS analyses. The degradation pathway of hydrocortisone is postulated. PMID:27328360
Structural elucidation, optical, magnetic and nonlinear optical properties of oxystyryl dyes.
Koleva, Bojidarka B; Stoyanov, Stanimir; Kolev, Tsonko; Petkov, Ivan; Spiteller, Michael
Structure, magnetic and optical properties of tetraphenylborate salts of 2,5-[1-methyl-4-[2-(4-hydroxyphenyl)ethenyl]piridinium]-propane and butane are performed in gas and condense phase by means of solution and solid-state conventional and linear-polarized IR-spectroscopy of oriented colloids in nematic liquid crystal suspension, UV-vis and fluorescence methods, HPLC tandem ESI mess spectrometry (MS/MS), (1)H, (13)C and (1)H-(1)H COSY NMR, TGV and DSC methods. Quantum chemical DFT calculations are used for performing of the structures, optical and nonlinear optical properties of the studied compounds. PMID:18722806
Elucidation of the Fe(III) Gallate Structure in Historical Iron Gall Ink.
Ponce, Aldo; Brostoff, Lynn B; Gibbons, Sarah K; Zavalij, Peter; Viragh, Carol; Hooper, Joseph; Alnemrat, Sufian; Gaskell, Karen J; Eichhorn, Bryan
Synthetic, structural, spectroscopic and aging studies conclusively show that the main colorant of historical iron gall ink (IGI) is an amorphous form of Fe(III) gallate·xH2O (x = ∼1.5-3.2). Comparisons between experimental samples and historical documents, including an 18th century hand-written manuscript by George Washington, by IR and Raman spectroscopy, XRD, X-ray photoelectron spectroscopy, and Mössbauer spectroscopy confirm the relationship between the model and authentic samples. These studies settle controversy in the cultural heritage field, where an alternative structure for Fe(III) gallate has been commonly cited. PMID:27058399
Structural elucidation, optical, magnetic and nonlinear optical properties of oxystyryl dyes
NASA Astrophysics Data System (ADS)
Koleva, Bojidarka B.; Stoyanov, Stanimir; Kolev, Tsonko; Petkov, Ivan; Spiteller, Michael
Structure, magnetic and optical properties of tetraphenylborate salts of 2,5-[1-methyl-4-[2-(4-hydroxyphenyl)ethenyl]piridinium]-propane and butane are performed in gas and condense phase by means of solution and solid-state conventional and linear-polarized IR-spectroscopy of oriented colloids in nematic liquid crystal suspension, UV-vis and fluorescence methods, HPLC tandem ESI mess spectrometry (MS/MS), 1H, 13C and 1H- 1H COSY NMR, TGV and DSC methods. Quantum chemical DFT calculations are used for performing of the structures, optical and nonlinear optical properties of the studied compounds.
Isolation and structural elucidation of acidic terpenoid phytoalexins in maize and their interactions with Aspergillus flavus
Technology Transfer Automated Retrieval System (TEKTRAN)
Plants use a variety of physical and chemical defenses in response to herbivory and pathogen attack. Infection of maize by the fungal pathogen Aspergillus flavus results in the accumulation of aflatoxins, which are among the most detrimental biogenic substances known to man. The majority of maize de...
Structural elucidation and functional characterization of the Hyaloperonospora arabidopsidis effector protein ATR13.
Leonelli, Lauriebeth; Pelton, Jeffery; Schoeffler, Allyn; Dahlbeck, Douglas; Berger, James; Wemmer, David E; Staskawicz, Brian
The oomycete Hyaloperonospora arabidopsidis (Hpa) is the causal agent of downy mildew on the model plant Arabidopsis thaliana and has been adapted as a model system to investigate pathogen virulence strategies and plant disease resistance mechanisms. Recognition of Hpa infection occurs when plant resistance proteins (R-genes) detect the presence or activity of pathogen-derived protein effectors delivered to the plant host. This study examines the Hpa effector ATR13 Emco5 and its recognition by RPP13-Nd, the cognate R-gene that triggers programmed cell death (HR) in the presence of recognized ATR13 variants. Herein, we use NMR to solve the backbone structure of ATR13 Emco5, revealing both a helical domain and a disordered internal loop. Additionally, we use site-directed and random mutagenesis to identify several amino acid residues involved in the recognition response conferred by RPP13-Nd. Using our structure as a scaffold, we map these residues to one of two surface-exposed patches of residues under diversifying selection. Exploring possible roles of the disordered region within the ATR13 structure, we perform domain swapping experiments and identify a peptide sequence involved in nucleolar localization. We conclude that ATR13 is a highly dynamic protein with no clear structural homologues that contains two surface-exposed patches of polymorphism, only one of which is involved in RPP13-Nd recognition specificity. PMID:22194684
Using Jigsaw-Style Spectroscopy Problem-Solving to Elucidate Molecular Structure through Online Cooperative Learning
ERIC Educational Resources Information Center
Winschel, Grace A.; Everett, Renata K.; Coppola, Brian P.; Shultz, Ginger V.
Cooperative learning was employed as an instructional approach to facilitate student development of spectroscopy problem solving skills. An interactive online environment was used as a framework to structure weekly discussions around spectroscopy problems outside of class. Weekly discussions consisted of modified jigsaw-style problem solving…
Structural elucidation of sorghum lignins from an integrated biorefinery process based on hydrothermal and alkaline treatments.
Sun, Shao-Long; Wen, Jia-Long; Ma, Ming-Guo; Sun, Run-Cang
An integrated process based on hydrothermal pretreatment (HTP) (i.e., 110-230 °C, 0.5-2.0 h) and alkaline post-treatment (2% NaOH at 90 °C for 2.0 h) has been performed for the production of xylooligosaccharide, lignin, and digestible substrate from sweet sorghum stems. The yield, purity, dissociation mechanisms, structural features, and structural transformations of alkali lignins obtained from the integrated process were investigated. It was found that the HTP process facilitated the subsequent alkaline delignification, releasing lignin with the highest yield (79.3%) and purity from the HTP residue obtained at 190 °C for 0.5 h. All of the results indicated that the cleavage of the β-O-4 linkages and degradation of β-β and β-5 linkages occurred under the harsh HTP conditions. Depolymerization and condensation reactions simultaneously occurred at higher temperatures (≥ 170 °C). Moreover, the thermostability of lignin was positively related to its molecular weight, but was also affected by the inherent structures, such as β-O-4 linkages and condensed units. These findings will enhance the understanding of structural transformations of the lignins during the integrated process and maximize the potential utilizations of the lignins in a current biorefinery process. PMID:25090032
Elucidating the influence of polymorph-dependent interfacial solvent structuring at chitin surfaces.
Brown, Aaron H; Walsh, Tiffany R
Interfacial solvent structuring is thought to be influential in mediating the adsorption of biomolecules at aqueous materials interfaces. However, despite the enormous potential for exploitation of aqueous chitin interfaces in industrial, medical and drug-delivery applications, little is known at the molecular-level about such interfacial solvent structuring for chitin. Here we use molecular simulation to predict the structure of the [100] and [010] interfaces of α-chitin and β-chitin dihydrate in contact with liquid water and saline solution. We find the α-chitin [100] interface supports lateral high-density regions in the first water layer at the interface, which are also present, but not as pronounced, for β-chitin. The lateral structuring of interfacial ions at the saline/chitin interface is also more pronounced for α-chitin compared with β-chitin. Our findings provide a foundation for the systematic design of biomolecules with selective binding affinity for different chitin polymorphs. PMID:27474640
Structural Aspects of Several Oxide Glasses as Elucidated by Multinuclear NMR.
NASA Astrophysics Data System (ADS)
Zhong, Jianhui
NMR is sensitive to many interactions that the nucleus experiences with its environment. Included among these interactions are two that were heavily exploited in this thesis. They are the electric quadrupole interaction and the chemical shift interaction. These interactions yield structural information on short-range order and atom coordinations, which are very valuable and important to the understanding of properties and microstructures of glasses. Both the static or MASS NMR at high field and low field CW NMR were utilized to obtain information concerning the coordinations and local environments of several oxide glasses. For some systems, other spectroscopic methods (thermal analysis, X-ray and IR spectroscopies) were also used to assist NMR studies. In Chapter I relevant NMR theory and detection techniques used for this work are introduced. In Chapters 2-4, some structural aspects of alkali borate, borosilicate or alkali boroaluminate glasses are studied. In particular, boron coordinations in these glasses are carefully reinvestigated. The relationship between the change in boron coordinations and the changes in macroscopic characteristics of the glasses (such as electric conductivity and the mixed alkali effects) are studied. In mixed alkali glasses, the postulated alkali -pairing model provides a reasonable explanation for the structural changes. Chapter 5 is dedicated to the ^{71}Ga and ^{69 }Ga NMR studies of alkali gallate glasses. The glassforming range is explored and the gallium atom coordinations are studied. A structural model for the glass systems is suggested based on the distribution of galliums of different coordinations and structural parameters (quadrupole coupling constants, asymmetry parameters, and isotropic chemical shifts, etc.). A study of ^{31} P spectra in lead-iron-phosphate nuclear waste glasses is presented in Chapter 6. By subjecting the samples to various magnetic field strengths and different temperatures, information on the local
Structural elucidation and molecular characterization of Marinobacter sp. α-amylase.
Kumar, Sumit; Khan, Rizwan Hasan; Khare, S K
Halophiles have been perceived as potential source of novel enzymes in recent years. The interest emanates from their ability to catalyze efficiently under high salt and organic solvents. Marinobacter sp. EMB8 α-amylase was found to be active and stable in salt and organic solvents. A study was carried out using circular dichroism (CD), fluorescence spectroscopy, and bioinformatics analysis of similar protein sequence to ascertain molecular basis of salt and solvent adaptability of α-amylase. Structural changes recorded in the presence of varying amounts of NaCl exhibited an increase in negative ellipticity as a function of salt, confirming that salt stabilizes the protein and increases the secondary structure, making it catalytically functional. The data of intrinsic and extrinsic fluorescence (using 1-anilinonaphthalene 8-sulfonate [ANS] as probe) further confirmed the role of salt. The α-amylase was active in the presence of nonpolar solvents, namely, hexane and decane, but inactivated by ethanol. The decrease in the activity was correlated with the loss of tertiary structure in the presence of ethanol. Guanidine hydrochloride and pH denaturation indicated the molten globule state at pH 4.0. Partial N-terminal amino acid sequence of the purified α-amylase revealed the relatedness to Pseudoalteromonas sp. α-amylase. "FVHLFEW" was found as the N-terminal signature sequence. Bioinformatics analysis was done using M. algicola α-amylase protein having the same N-terminal signature sequence. The three-dimensional structure of Marinobacter α-amylase was deduced using the I-TASSER server, which reflected the enrichment of acidic amino acids on the surface, imparting the stability in the presence of salt. Our study clearly indicate that salt is necessary for maintaining the secondary and tertiary structure of halophilic protein, which is a necessary prerequisite for catalysis. PMID:26192048
High-Resolution Crystal Structures Elucidate the Molecular Basis of Cholera Blood Group Dependence
Heggelund, Julie Elisabeth; Burschowsky, Daniel; Bjørnestad, Victoria Ariel; Hodnik, Vesna; Anderluh, Gregor; Krengel, Ute
Cholera is the prime example of blood-group-dependent diseases, with individuals of blood group O experiencing the most severe symptoms. The cholera toxin is the main suspect to cause this relationship. We report the high-resolution crystal structures (1.1–1.6 Å) of the native cholera toxin B-pentamer for both classical and El Tor biotypes, in complexes with relevant blood group determinants and a fragment of its primary receptor, the GM1 ganglioside. The blood group A determinant binds in the opposite orientation compared to previously published structures of the cholera toxin, whereas the blood group H determinant, characteristic of blood group O, binds in both orientations. H-determinants bind with higher affinity than A-determinants, as shown by surface plasmon resonance. Together, these findings suggest why blood group O is a risk factor for severe cholera. PMID:27082955
Structure elucidation and gene cluster characterization of the O-antigen of Escherichia coli O80.
Senchenkova, Sof'ya N; Guo, Xi; Filatov, Andrei V; Perepelov, Andrei V; Liu, Bin; Shashkov, Alexander S; Knirel, Yuriy A
Mild alkaline degradation of the lipopolysaccharide of Escherichia coli O80 afforded a polysaccharide, which was studied by sugar analysis, selective cleavage of glycosidic linkages, and (1)H and (13)C NMR spectroscopy. Solvolysis of the polysaccharide with CF3CO2H cleaved the linkages of α-Fuc and β-linked GlcNAc and GalNAc residues to give two disaccharides. The following structure of the hexasaccharide repeating unit of the O-polysaccharide was established: The polysaccharide repeat also contains a minor O-acetyl group but its position was not determined. The O-antigen gene cluster of E. coli O80 between the conserved galF and gnd genes was analyzed and found to be consistent with the O-polysaccharide structure established. PMID:27454490
Structure elucidation of a bioactive polysaccharide from fruiting bodies of Hericium erinaceus in different maturation stages.
Li, Qiao-Zhen; Wu, Di; Zhou, Shuai; Liu, Yan-Fang; Li, Zheng-Peng; Feng, Jie; Yang, Yan
HPB-3, a heteropolysaccharide, with a mean molecular weight of 1.5×10(4)Da, was obtained from the maturating-stage IV, V and VI fruiting body of Hericium erinaceus, exhibited higher macrophages stimulation activities, was able to upregulate the functional events mediated by activated macrophages, such as production of nitric oxide (NO). Monosaccharide composition analysis showed that HPB-3 comprised l-fucose, d-galactose and d-glucose in the ratio of 5.2:23.9:1. Its chemical structure was characterized by sugar and methylation analysis, along with (1)H and (13)C NMR spectroscopy, including (1)H-(1)H COSY, TOCSY, NOESY, HMQC and HMBC experiments. The results indicated that HPB-3 contained a-(1/6)-linked galactopyranosyl backbone, partially with a side chain composed of α-l-fucopyranose at the O-2 position. The predicted primary structure of the polysaccharide was established as below. PMID:27083809
Cryo-EM structure of lysenin pore elucidates membrane insertion by an aerolysin family protein.
Bokori-Brown, Monika; Martin, Thomas G; Naylor, Claire E; Basak, Ajit K; Titball, Richard W; Savva, Christos G
Lysenin from the coelomic fluid of the earthworm Eisenia fetida belongs to the aerolysin family of small β-pore-forming toxins (β-PFTs), some members of which are pathogenic to humans and animals. Despite efforts, a high-resolution structure of a channel for this family of proteins has been elusive and therefore the mechanism of activation and membrane insertion remains unclear. Here we determine the pore structure of lysenin by single particle cryo-EM, to 3.1 Å resolution. The nonameric assembly reveals a long β-barrel channel spanning the length of the complex that, unexpectedly, includes the two pre-insertion strands flanking the hypothetical membrane-insertion loop. Examination of other members of the aerolysin family reveals high structural preservation in this region, indicating that the membrane-insertion pathway in this family is conserved. For some toxins, proteolytic activation and pro-peptide removal will facilitate unfolding of the pre-insertion strands, allowing them to form the β-barrel of the channel. PMID:27048994
Cryo-EM structure of lysenin pore elucidates membrane insertion by an aerolysin family protein
NASA Astrophysics Data System (ADS)
Bokori-Brown, Monika; Martin, Thomas G.; Naylor, Claire E.; Basak, Ajit K.; Titball, Richard W.; Savva, Christos G.
Lysenin from the coelomic fluid of the earthworm Eisenia fetida belongs to the aerolysin family of small β-pore-forming toxins (β-PFTs), some members of which are pathogenic to humans and animals. Despite efforts, a high-resolution structure of a channel for this family of proteins has been elusive and therefore the mechanism of activation and membrane insertion remains unclear. Here we determine the pore structure of lysenin by single particle cryo-EM, to 3.1 Å resolution. The nonameric assembly reveals a long β-barrel channel spanning the length of the complex that, unexpectedly, includes the two pre-insertion strands flanking the hypothetical membrane-insertion loop. Examination of other members of the aerolysin family reveals high structural preservation in this region, indicating that the membrane-insertion pathway in this family is conserved. For some toxins, proteolytic activation and pro-peptide removal will facilitate unfolding of the pre-insertion strands, allowing them to form the β-barrel of the channel.
Cryo-EM structure of lysenin pore elucidates membrane insertion by an aerolysin family protein
Bokori-Brown, Monika; Martin, Thomas G.; Naylor, Claire E.; Basak, Ajit K.; Titball, Richard W.; Savva, Christos G.
Lysenin from the coelomic fluid of the earthworm Eisenia fetida belongs to the aerolysin family of small β-pore-forming toxins (β-PFTs), some members of which are pathogenic to humans and animals. Despite efforts, a high-resolution structure of a channel for this family of proteins has been elusive and therefore the mechanism of activation and membrane insertion remains unclear. Here we determine the pore structure of lysenin by single particle cryo-EM, to 3.1 Å resolution. The nonameric assembly reveals a long β-barrel channel spanning the length of the complex that, unexpectedly, includes the two pre-insertion strands flanking the hypothetical membrane-insertion loop. Examination of other members of the aerolysin family reveals high structural preservation in this region, indicating that the membrane-insertion pathway in this family is conserved. For some toxins, proteolytic activation and pro-peptide removal will facilitate unfolding of the pre-insertion strands, allowing them to form the β-barrel of the channel. PMID:27048994
Membrane transporters studied by EPR spectroscopy: structure determination and elucidation of functional dynamics.
Mullen, Anna; Hall, Jenny; Diegel, Janika; Hassan, Isa; Fey, Adam; MacMillan, Fraser
During their mechanistic cycles membrane transporters often undergo extensive conformational changes, sampling a range of orientations, in order to complete their function. Such membrane transporters present somewhat of a challenge to conventional structural studies; indeed, crystallization of membrane-associated proteins sometimes require conditions that vary vastly from their native environments. Moreover, this technique currently only allows for visualization of single selected conformations during any one experiment. EPR spectroscopy is a magnetic resonance technique that offers a unique opportunity to study structural, environmental and dynamic properties of such proteins in their native membrane environments, as well as readily sampling their substrate-binding-induced dynamic conformational changes especially through complementary computational analyses. Here we present a review of recent studies that utilize a variety of EPR techniques in order to investigate both the structure and dynamics of a range of membrane transporters and associated proteins, focusing on both primary (ABC-type transporters) and secondary active transporters which were key interest areas of the late Professor Stephen Baldwin to whom this review is dedicated. PMID:27284059
Chemical profiling of the major components in natural waxes to elucidate their role in liquid oil structuring.
Doan, Chi Diem; To, Chak Ming; De Vrieze, Mike; Lynen, Frederic; Danthine, Sabine; Brown, Allison; Dewettinck, Koen; Patel, Ashok R
Elucidating the composition of waxes is of utmost importance to explain their behavior in liquid oil structuring. The chemical components (hydrocarbons - HCs, free fatty acids - FFAs, free fatty alcohols - FALs and wax esters - WEs) of natural waxes were analyzed using HPLC-ELSD and GC-MS followed by evaluation of their oil structuring properties. The gel strength, including the average storage modulus and oscillation yield stress, displayed a negative correlation with FALs and a positive correlation with HCs, FFAs and WEs. The components dictating the gel strength are HCs, FFAs and WEs in a descending order of importance. The consistency of the oleogels increased with the increasing amount of FFAs and HCs and the decreasing amount of WEs and FALs. The presence of more WEs results in a strong but brittle gel with a high initial flow yield stress. We believe these results might be useful in selecting the right waxes to combine in certain fat-based food products. PMID:27507530
Elucidating the pH-Dependent Structural Transition of T7 Bacteriophage Endolysin.
Sharma, Meenakshi; Kumar, Dinesh; Poluri, Krishna Mohan
Bacteriophages are the most abundant and diverse biological entities on earth. Bacteriophage endolysins are unique peptidoglycan hydrolases and have huge potential as effective enzybiotics in various infectious models. T7 bacteriophage endolysin (T7L), also known as N-acetylmuramoyl-l-alanine amidase or T7 lysozyme, is a 17 kDa protein that lyses a range of Gram-negative bacteria by hydrolyzing the amide bond between N-acetylmuramoyl residues and the l-alanine of the peptidoglycan layer. Although the activity profiles of several of the T7 family members have been known for many years, the molecular basis for their pH-dependent differential activity is not clear. In this study, we explored the pH-induced structural, stability, and activity characteristics of T7L by applying a variety of biophysical techniques and protein nuclear magnetic resonance (NMR) spectroscopy. Our studies established a reversible structural transition of T7L below pH 6 and the formation of a partially denatured conformation at pH 3. This low-pH conformation is thermally stable and exposed its hydrophobic pockets. Further, NMR relaxation measurements and structural analysis unraveled that T7L is highly dynamic in its native state and a network of His residues are responsible for the observed pH-dependent conformational dynamics and transitions. As bacteriophage chimeric and engineered endolysins are being developed as novel therapeutics against multiple drug resistance pathogens, we believe that our results are of great help in designing these entities as broadband antimicrobial and/or antibacterial agents. PMID:27513288
Elucidation of the effect of ionic liquid pretreatment on rice husk via structural analyses
Background In the present study, three ionic liquids, namely 1-butyl-3-methylimidazolium chloride ([BMIM]Cl), 1-ethyl-3-methylimidazolium acetate ([EMIM]OAc), and 1-ethyl-3-methylimidazolium diethyl phosphate ([EMIM]DEP), were used to partially dissolve rice husk, after which the cellulose were regenerated by the addition of water. The aim of the investigation is to examine the implications of the ionic liquid pretreatments on rice husk composition and structure. Results From the attenuated total reflectance Fourier transform-infrared (ATR FT-IR) spectroscopy, X-ray diffraction (XRD) and scanning electron microscopy (SEM) results, the regenerated cellulose were more amorphous, less crystalline, and possessed higher structural disruption compared with untreated rice husk. The major component of regenerated cellulose from [BMIM]Cl and [EMIM]DEP pretreatments was cellulose-rich material, while cellulose regenerated from [EMIM]OAc was a matrix of cellulose and lignin. Cellulose regenerated from ionic pretreatments could be saccharified via enzymatic hydrolysis, and resulted in relatively high reducing sugars yields, whereas enzymatic hydrolysis of untreated rice husk did not yield reducing sugars. Rice husk residues generated from the ionic liquid pretreatments had similar chemical composition and amorphousity to that of untreated rice husk, but with varying extent of surface disruption and swelling. Conclusions The structural architecture of the regenerated cellulose and rice husk residues showed that they could be used for subsequent fermentation or derivation of cellulosic compounds. Therefore, ionic liquid pretreatment is an alternative in the pretreatment of lignocellulosic biomass in addition to the conventional chemical pretreatments. PMID:22958710
Top-Down Strategies for the Structural Elucidation of Intact Gram-negative Bacterial Endotoxins
O'Brien, John P.; Needham, Brittany D.; Brown, Dusty B.; Trent, M. Stephen
Re-modelling of lipopolysaccharides, which are the primary constituent of the outer cell membrane of Gram-negative bacteria, modulates pathogenesis and resistance to microbials. Reported herein is the characterization of intact Gram-negative bacterial lipooligosaccharides (LOS) via a new strategy utilizing online liquid chromatography (LC) coupled with ultraviolet photodissociation (UVPD) mass spectrometry. Compared to collision-based MS/MS methods, UVPD and UVPD/HCD promoted a greater array of cleavages within both the glycan and lipid moieties, including C-C, C-N, C-O cleavages in the acyl chains as well as glycosidic and cross-ring cleavages, thus providing the most far-reaching structural characterization of LOS. This LC-MS/MS strategy affords a robust analytical method to structurally characterize complex mixtures of bacterial endotoxins that maintains the integrity of the core oligosaccharide and lipid A domains of LOS, providing direct feedback about the cell envelope architectures and LOS modification strategies involved in resistance host innate immune defense. PMID:25386333
Synthesis and Structural Elucidation of Triazolylmolybdenum(VI) Oxide Hybrids and Their Behavior as Oxidation Catalysts.
Lysenko, Andrey B; Senchyk, Ganna A; Domasevitch, Konstantin V; Hauser, Jürg; Fuhrmann, Daniel; Kobalz, Merten; Krautscheid, Harald; Neves, Patrícia; Valente, Anabela A; Gonçalves, Isabel S
A large family of bifunctional 1,2,4-triazole molecular tectons (tr) has been explored for engineering molybdenum(VI) oxide hybrid solids. Specifically, tr ligands bearing auxiliary basic or acidic groups were of the type amine, pyrazole, 1H-tetrazole, and 1,2,4-triazole. The organically templated molybdenum(VI) oxide solids with the general compositions [MoO3(tr)], [Mo2O6(tr)], and [Mo2O6(tr)(H2O)2] were prepared under mild hydrothermal conditions or by refluxing in water. Their crystal structures consist of zigzag chains, ribbons, or helixes of alternating cis-{MoO4N2} or {MoO5N} polyhedra stapled by short [N-N]-tr bridges that for bitriazole ligands convert the motifs into 2D or 3D frameworks. The high thermal (235-350 °C) and chemical stability observed for the materials makes them promising for catalytic applications. The molybdenum(VI) oxide hybrids were successfully explored as versatile oxidation catalysts with tert-butyl hydroperoxide (TBHP) or aqueous H2O2 as an oxygen source, at 70 °C. Catalytic performances were influenced by the different acidic-basic properties and steric hindrances of coordinating organic ligands as well as the structural dimensionality of the hybrid. PMID:26280712
Structural elucidation of a novel mechanism for the bacteriophage-based inhibition of the RNA degradosome.
Van den Bossche, An; Hardwick, Steven W; Ceyssens, Pieter-Jan; Hendrix, Hanne; Voet, Marleen; Dendooven, Tom; Bandyra, Katarzyna J; De Maeyer, Marc; Aertsen, Abram; Noben, Jean-Paul; Luisi, Ben F; Lavigne, Rob
In all domains of life, the catalysed degradation of RNA facilitates rapid adaptation to changing environmental conditions, while destruction of foreign RNA is an important mechanism to prevent host infection. We have identified a virus-encoded protein termed gp37/Dip, which directly binds and inhibits the RNA degradation machinery of its bacterial host. Encoded by giant phage фKZ, this protein associates with two RNA binding sites of the RNase E component of the Pseudomonas aeruginosa RNA degradosome, occluding them from substrates and resulting in effective inhibition of RNA degradation and processing. The 2.2 Å crystal structure reveals that this novel homo-dimeric protein has no identifiable structural homologues. Our biochemical data indicate that acidic patches on the convex outer surface bind RNase E. Through the activity of Dip, фKZ has evolved a unique mechanism to down regulate a key metabolic process of its host to allow accumulation of viral RNA in infected cells. PMID:27447594
Structure elucidation of a major fucopyranose-rich heteropolysaccharide (STP-II) from Sargassum thunbergii.
Luo, Dianhui; Yuan, Xiumei; Zeng, Yawei; Nie, Kaiying; Li, Zhiming; Wang, Zhaojing
A crude polysaccharide was extracted from the edible algae S. thunbergii. DEAE-Sepharose CL-6B column chromatography was used to separate and purify a major polysaccharide STP-II (63.75%) from the crude polysaccharide. STP-II was found to be a homogeneous polysaccharide with a single peak by high-performance size-exclusion chromatography with a Sugar KS-804 column, have a molecular weight of 550 kD, and consist mainly of fucose, xylose, galactose, glucose and glucuronic acid. The structural assignment of STP-II was carried out using Fourier transform infrared spectroscopy analysis, periodate oxidation-smith degradation, partial hydrolysis with acid, methylation analysis and nuclear magnetic resonance studies, and the repeating unit of STP-II was thus determined. The result indicated that (1→3)-linked-fucose, (1→3)-linked-xylose and (1→3)-linked-galactose formed the major components of the main-chain structure, and the branch ratios were 17.5%. The branching and terminal residues were (1→2)-linked-glucuronic acid, (1→4)-linked-glucose, (1→)-linked-xylose and (1→)-linked-4-O-acetyl-glucose, respectively. PMID:27083337
Structural elucidation of a novel mechanism for the bacteriophage-based inhibition of the RNA degradosome
Van den Bossche, An; Hardwick, Steven W; Ceyssens, Pieter-Jan; Hendrix, Hanne; Voet, Marleen; Dendooven, Tom; Bandyra, Katarzyna J; De Maeyer, Marc; Aertsen, Abram; Noben, Jean-Paul
In all domains of life, the catalysed degradation of RNA facilitates rapid adaptation to changing environmental conditions, while destruction of foreign RNA is an important mechanism to prevent host infection. We have identified a virus-encoded protein termed gp37/Dip, which directly binds and inhibits the RNA degradation machinery of its bacterial host. Encoded by giant phage фKZ, this protein associates with two RNA binding sites of the RNase E component of the Pseudomonas aeruginosa RNA degradosome, occluding them from substrates and resulting in effective inhibition of RNA degradation and processing. The 2.2 Å crystal structure reveals that this novel homo-dimeric protein has no identifiable structural homologues. Our biochemical data indicate that acidic patches on the convex outer surface bind RNase E. Through the activity of Dip, фKZ has evolved a unique mechanism to down regulate a key metabolic process of its host to allow accumulation of viral RNA in infected cells. DOI: http://dx.doi.org/10.7554/eLife.16413.001 PMID:27447594
X-ray Crystal Structures Elucidate the Nucleotidyl Transfer Reaction of Transcript Initiation Using Two Nucleotides
M Gleghorn; E Davydova; R Basu; L Rothman-Denes; K Murakami
We have determined the X-ray crystal structures of the pre- and postcatalytic forms of the initiation complex of bacteriophage N4 RNA polymerase that provide the complete set of atomic images depicting the process of transcript initiation by a single-subunit RNA polymerase. As observed during T7 RNA polymerase transcript elongation, substrate loading for the initiation process also drives a conformational change of the O helix, but only the correct base pairing between the +2 substrate and DNA base is able to complete the O-helix conformational transition. Substrate binding also facilitates catalytic metal binding that leads to alignment of the reactive groups of substrates for the nucleotidyl transfer reaction. Although all nucleic acid polymerases use two divalent metals for catalysis, they differ in the requirements and the timing of binding of each metal. In the case of bacteriophage RNA polymerase, we propose that catalytic metal binding is the last step before the nucleotidyl transfer reaction.
In vivo deuteration of a native bacterial biopolymer for structural elucidation using SANS
NASA Astrophysics Data System (ADS)
Holden, P. J.; Russell, R. A.; Stone, D. J. M.; Garvey, C. J.; Foster, L. J. R.
In order to facilitate future structural studies, biodeuteration of bacterial polyhydroxyalkanoates (PHAs) was investigated. We report here the in vivo deuteration of poly 3-hydroxyoctanoate (PHO) produced by its native host, the bacterium Pseudomonas oleovorans. Bacterial biomass was produced in bioreactor studies by growth on hydrogenated substrates and PHO was subsequently produced intracellularly (10-20% w/w) during batch fed growth on deuterated octanoic acid under oxygen limitation. GC-MS analyses of the PHO demonstrated that 13 of the 15 hydrogen atoms had been replaced with deuterium (except in position 3), the remaining two hydrogen presumably being derived from water. A SANS contrast variation study was conducted on whole cells and the results indicate the potential to discriminate inclusion bodies formed from deuterated precursor from an otherwise hydrogenated background.
Structural Elucidation and Antioxidant Activities of Proanthocyanidins from Chinese Bayberry (Myrica rubra Sieb. et Zucc.) Leaves
Fu, Yu; Qiao, Liping; Cao, Yuming; Zhou, Xiaozhou; Liu, Yu; Ye, Xingqian
Proanthocyanidins in Chinese bayberry leaves (PCBLs) were qualitatively analyzed. NMR data suggest that PCBLs are mostly composed of (epi)gallocatechin gallate units. Matrix-assisted laser desorption time-of-flight MS data indicate 95 possible prodelphinidin structures, ranging from dimers to tridecamers. Preparative normal-phase HPLC and further analysis by reverse-phase HPLC together with electrospray ionization MS enabled detection of 20 compounds, including seven newly identified compounds in Chinese bayberry leaves. The antioxidant capacity of PCBLs was evaluated by (1,1-diphenyl-2-picryl-hydrazyl), ferric-reducing antioxidant power, and oxygen radical absorption capacity assays. The EC50 of DPPH radical scavenging activities (as 50% decrease in the initial DPPH concentration) were 7.60 µg. The FRAP and ORAC values were 8859.33±978.39 and 12991.61±1553.34 µmol Trolox equivalents per gram, respectively. The results indicate the high antioxidant potency of PCBLs. PMID:24805126
Crystal Structure of Human Thymine DNA Glycosylase Bound to DNA Elucidates Sequence-Specific Mismatch Recognition
Maiti, A.; Morgan, M.T.; Pozharski, E.; Drohat, A.C.
Cytosine methylation at CpG dinucleotides produces m{sup 5}CpG, an epigenetic modification that is important for transcriptional regulation and genomic stability in vertebrate cells. However, m{sup 5}C deamination yields mutagenic G{center_dot}T mispairs, which are implicated in genetic disease, cancer, and aging. Human thymine DNA glycosylase (hTDG) removes T from G{center_dot}T mispairs, producing an abasic (or AP) site, and follow-on base excision repair proteins restore the G{center_dot}C pair. hTDG is inactive against normal A{center_dot}T pairs, and is most effective for G{center_dot}T mispairs and other damage located in a CpG context. The molecular basis of these important catalytic properties has remained unknown. Here, we report a crystal structure of hTDG (catalytic domain, hTDG{sup cat}) in complex with abasic DNA, at 2.8 {angstrom} resolution. Surprisingly, the enzyme crystallized in a 2:1 complex with DNA, one subunit bound at the abasic site, as anticipated, and the other at an undamaged (nonspecific) site. Isothermal titration calorimetry and electrophoretic mobility-shift experiments indicate that hTDG and hTDG{sup cat} can bind abasic DNA with 1:1 or 2:1 stoichiometry. Kinetics experiments show that the 1:1 complex is sufficient for full catalytic (base excision) activity, suggesting that the 2:1 complex, if adopted in vivo, might be important for some other activity of hTDG, perhaps binding interactions with other proteins. Our structure reveals interactions that promote the stringent specificity for guanine versus adenine as the pairing partner of the target base and interactions that likely confer CpG sequence specificity. We find striking differences between hTDG and its prokaryotic ortholog (MUG), despite the relatively high (32%) sequence identity.
Structural elucidation and genomic scrutiny of the C60-C100 mycolic acids of Segniliparus rotundus.
Lanéelle, Marie-Antoinette; Eynard, Nathalie; Spina, Lucie; Lemassu, Anne; Laval, Françoise; Huc, Emilie; Etienne, Gilles; Marrakchi, Hedia; Daffé, Mamadou
Mycolic acids, very long-chain α-alkyl, β-hydroxylated fatty acids, occur in the members of the order Corynebacteriales where their chain lengths (C(26)-C(88)) and structural features (oxygen functions, cis or trans double bonds, cyclopropane rings and methyl branches) are genus- and species-specific. The molecular composition and structures of the mycolic acids of two species belonging to the genus Segniliparus were determined by a combination of modern analytical chemical techniques, which include MS and NMR. They consist of mono-ethylenic C(62-)C(64) (α'), di-ethylenic C(77)-C(79) (α) and extremely long-chain mycolic acids (α(+)) ranging from 92 to 98 carbon atoms and containing three unsaturations, cis and/or trans double bonds and/or cyclopropanes. The double bonds in each class of mycolic acids were positioned by oxidative cleavage and exhibit locations similar to those of α- and α'-mycolic acids of mycobacteria. For the ultralong chain α-mycolic acids, the three double bonds were located at equally spaced carbon intervals (C(13)-C(16)), with the methyl branches adjacent to the proximal and distal trans double bonds. Examination of the Segniliparus rotundus genome compared with those of other members of the Corynebacteriales indicated two obvious differences in genes encoding the elongation fatty acid (FAS-II) enzymes involved in the biosynthesis of mycolic acids: the organization of 3-ketoacyl-ACP synthases (KasA and KasB) and (3R)-hydroxyacyl-ACP dehydratases (HadAB/BC), on one hand, and the presence of two copies of the hadB gene encoding the catalytic domain of the latter enzyme type, on the other. This observation is discussed in light of the most recent data accumulated on the biosynthesis of this hallmark of Corynebacteriales. PMID:23154972
Investigating the Web Structure by Isolated Stars
NASA Astrophysics Data System (ADS)
Uno, Yushi; Ota, Yoshinobu; Uemichi, Akio
The link structure of the Web is generally represented by the webgraph, and it is often used for web structure mining that mainly aims to find hidden communities on the Web. In this paper, we identify a common frequent substructure and give it a formal graph definition, which we call an isolated star (i-star), and propose an efficient enumeration algorithm of i-stars. We then investigate the structure of the Web by enumerating i-stars from real web data. As a result, we observed that most i-stars correspond to index structures in single domains, while some of them are verified to be candidates of communities, which implies the validity of i-stars as useful substructure for web structure mining and link spam detecting. We also observed that the distributions of i-star sizes show power-law, which is another new evidence of the scale-freeness of the webgraph.
Structural elucidation and physicochemical properties of mononuclear Uranyl(VI) complexes incorporating dianionic units.
Azam, Mohammad; Velmurugan, Gunasekaran; Wabaidur, Saikh Mohammad; Trzesowska-Kruszynska, Agata; Kruszynski, Rafal; Al-Resayes, Saud I; Al-Othman, Zeid A; Venuvanalingam, Ponnambalam
Two derivatives of organouranyl mononuclear complexes [UO2(L)THF] (1) and [UO2(L)Alc] (2), where L = (2,2'-(1E,1'E)-(2,2-dimethylpropane-1,3-dyl)bis(azanylylidene, THF = Tetrahydrofuran, Alc = Alcohol), have been prepared. These complexes have been determined by elemental analyses, single crystal X-ray crystallography and various spectroscopic studies. Moreover, the structure of these complexes have also been studied by DFT and time dependent DFT measurements showing that both the complexes have distorted pentagonal bipyramidal environment around uranyl ion. TD-DFT results indicate that the complex 1 displays an intense band at 458.7 nm which is mainly associated to the uranyl centered LMCT, where complex 2 shows a band at 461.8 nm that have significant LMCT character. The bonding has been further analyzed by EDA and NBO. The photocatalytic activity of complexes 1 and 2 for the degradation of rhodamine-B (RhB) and methylene blue (MB) under the irradiation of 500W Xe lamp has been explored, and found more efficient in presence of complex 1 than complex 2 for both dyes. In addition, dye adsorption and photoluminescence properties have also been discussed for both complexes. PMID:27595801
Structural elucidation and physicochemical properties of mononuclear Uranyl(VI) complexes incorporating dianionic units
Azam, Mohammad; Velmurugan, Gunasekaran; Wabaidur, Saikh Mohammad; Trzesowska-Kruszynska, Agata; Kruszynski, Rafal; Al-Resayes, Saud I.; Al-Othman, Zeid A.; Venuvanalingam, Ponnambalam
Two derivatives of organouranyl mononuclear complexes [UO2(L)THF] (1) and [UO2(L)Alc] (2), where L = (2,2′-(1E,1′E)-(2,2-dimethylpropane-1,3-dyl)bis(azanylylidene, THF = Tetrahydrofuran, Alc = Alcohol), have been prepared. These complexes have been determined by elemental analyses, single crystal X-ray crystallography and various spectroscopic studies. Moreover, the structure of these complexes have also been studied by DFT and time dependent DFT measurements showing that both the complexes have distorted pentagonal bipyramidal environment around uranyl ion. TD-DFT results indicate that the complex 1 displays an intense band at 458.7 nm which is mainly associated to the uranyl centered LMCT, where complex 2 shows a band at 461.8 nm that have significant LMCT character. The bonding has been further analyzed by EDA and NBO. The photocatalytic activity of complexes 1 and 2 for the degradation of rhodamine-B (RhB) and methylene blue (MB) under the irradiation of 500W Xe lamp has been explored, and found more efficient in presence of complex 1 than complex 2 for both dyes. In addition, dye adsorption and photoluminescence properties have also been discussed for both complexes. PMID:27595801
Experimental and theoretical studies on synthesis and structure elucidation of some polychlorinated biphenyl derivatives
NASA Astrophysics Data System (ADS)
Boyarskiy, Vadim P.; Boyarskaya, Irina А.; Savicheva, Elisaveta A.; Gdaniec, Maria; Fonari, Marina S.; Simonov, Yurii A.
The regioselective methoxycarbonylation of polychlorinated biphenyls (PCBs), 2,3,4'-trichlorobiphenyl (РСВ22), and 2,5,4'-trichlorobiphenyl (PCB31), carried out in the presence of modified Co 2(CO) 8 cobalt carbonyl catalyst proceeds with substitution of chlorine atom in the position 3 for РСВ22 and yields methyl 2-chloro-3-(4-chlorophenyl)benzoate 1, while for PCB31 results in methyl 4-chloro-2-(4-chlorophenyl)benzoate 2. The substitution of methoxycarbonyl group for chlorine in ortho-position of trichlorobiphenyls seems not to affect the twist angle of the biphenyl unit. However, the twist angle of the methoxycarbonyl group relative to the phenyl ring was found to be significantly larger in the meta-derivative 1 than the ortho-derivative 2. To rationalize conformational differences between the two esters 1 and 2 in their crystal structures the optimized geometries and potential energy curves (relative energy versus torsion angle) were calculated at the B3LYP/6-31+G(d,p) level of theory.
Facile synthesis, structural elucidation and spectral analysis of pyrrole 4-imidazole derivatives
NASA Astrophysics Data System (ADS)
Singh, R. N.; Rawat, Poonam; Baboo, Vikas
In this work pyrrole 4-imidazole derivatives (3A-3D): benzimidazoles and pyrrole 4-imidazoline have been synthesized by condensation, cyclization and oxidation of ethyl 4-formyl-3,5-dimethyl-1H-pyrrole carboxylate and phenylene diamine derivatives/ethylene diamine. The structure of these biheterocyclic compounds have been derived by elemental and spectroscopic - IR, UV, MS, 1H and 13C NMR analysis as well as theoretical study. The static first hyperpolarizability, β0 values for pyrrole 4-imidazole derivatives, (3A-3D) have been calculated as 10.901 × 10-31, 19.607 × 10-31, 40.323 × 10-31, 5.686 × 10-31 esu, respectively. The gradual increase in β0 value of synthesized pyrrole-benzimidazole derivatives from 3A to 3C is due to addition of acceptors -Cl atom in 3B to -NO2 group in 3C on benzimidazole side. The experimental absorption spectra found to be in UV region and the high β0 values show that the synthesized pyrrole-imidazoles are suitable as non-linear optical (NLO) materials.
Characteristic conformation of Mosher's amide elucidated using the cambridge structural database.
Ichikawa, Akio; Ono, Hiroshi; Mikata, Yuji
Conformations of the crystalline 3,3,3-trifluoro-2-methoxy-2-phenylpropanamide derivatives (MTPA amides) deposited in the Cambridge Structural Database (CSD) were examined statistically as Racid-enantiomers. The majority of dihedral angles (48/58, ca. 83%) of the amide carbonyl groups and the trifluoromethyl groups ranged from -30° to 0° with an average angle θ1 of -13°. The other conformational properties were also clarified: (1) one of the fluorine atoms was antiperiplanar (ap) to the amide carbonyl group, forming a staggered conformation; (2) the MTPA amides prepared from primary amines showed a Z form in amide moieties; (3) in the case of the MTPA amide prepared from a primary amine possessing secondary alkyl groups (i.e., Mosher-type MTPA amide), the dihedral angles between the methine groups and the carbonyl groups were syn and indicative of a moderate conformational flexibility; (4) the phenyl plane was inclined from the O-Cchiral bond of the methoxy moiety with an average dihedral angle θ2 of +21°; (5) the methyl group of the methoxy moiety was ap to the ipso-carbon atom of the phenyl group. PMID:26193245
Structural elucidation of Argonne premium coals: Molecular weights, heteroatom distributions and linkages between clusters
Winans, R.E.,; Kim, Y.; Hunt, J.E.; McBeth, R.L.
The objective of this study is to create a statistically accurate picture of important structural features for a group of coals representing a broad rank range. Mass spectrometric techniques are used to study coals, coal extracts and chemically modified coals and extracts. Laser desorption mass spectrometry is used to determine molecular weight distributions. Desorption chemical ionization high resolution mass spectrometry provides detailed molecular information on compound classes of molecules is obtained using tandem mass spectrometry. These results are correlated with other direct studies on these samples such as solid NMR, XPS and X-ray absorption spectroscopy. From the complex sets of data, several general trends are emerging especially for heteroatom containing species. From a statistical point of view, heteroatoms must play important roles in the reactivity of all coals. Direct characterization of sulfur containing species in the Argonne coals has been reported from XANES analysis. Indirect methods used include: TG-FTIR and HRMS which rely on thermal desorption and pyrolysis to vaporize the samples. Both XANES and XPS data on nitrogen has been reported, but at this time, the XPS information is probably more reliable. Results from HRMS are discussed in this paper. Most other information on nitrogen is limited to analysis of liquefaction products. However, nitrogen can be important in influencing characteristics of coal liquids and as a source of NO{sub x}`s in coal combustion.
Design, structural and spectroscopic elucidation, and the in vitro biological activities of new diorganotin dithiocarbamates.
Ferreira, Isabella P; de Lima, Geraldo M; Paniago, Eucler B; Rocha, Willian R; Takahashi, Jacqueline A; Pinheiro, Carlos B; Ardisson, José D
The reaction of 2,2-dimethoxy-N-methylethyllamine or 2-methyl-1,3-dioxolane with CS(2) in alkaline media produced two novel dithiocarbamate salts. Subsequent reactions with organotin halides yielded six new complexes: [SnMe(2){S(2)CNR(R(1))(2)}(2)] (1), [Sn(n-Bu)(2){S(2)CNR(R(1))(2)}(2)] (2), [SnPh(2){S(2)CNR(R(1))(2)}(2)] (3), [SnMe(2){S(2)CNR(R(2))(2)}(2)] (4), [Sn(n-Bu)(2){S(2)CNR(R(2))(2)}(2)] (5), [SnPh(2){S(2)CNR(R(2))(2)}(2)] (6), where R = methyl, R(1) = CH(2)CH(OMe)(2), and R(2) = 2-methyl-1,3-dioxolane. All compounds were identified in terms of infrared, (1)H and (13)C NMR, and the complexes were also characterized using (119)Sn NMR, (119)Sn Mössbauer and X-ray crystallography. The biological activity of all derivatives has been screened in terms of IC(90) and IC(50) against Aspergillus flavus, Aspergillus niger, Aspergillus parasiticus, Penicillium citrinum, Curvularia senegalensis, Staphylococcus aureus, Listeria monocytogenes, Bacillus cereus, Streptococcus sanguinis, Escherichia coli, Citrobacter freundii, Salmonella typhimurium, and Pseudomonas aeruginosa and the results correlated well with a performed study of structure-activity relationship (SAR). Complexes (3), (5) and (6) displayed the best IC(90) and IC(50) in the presence of the fungi, greater than that of miconazole, used as control drug. PMID:23159807
Structure and dynamics of retinal in rhodopsin elucidated by deuterium solid state NMR
NASA Astrophysics Data System (ADS)
Salgado, Gilmar Fernandes De Jesus
Rhodopsin is a seven transmembrane helix GPCR found which mediates dim light vision, in which the binding pocket is occupied by the ligand 11- cis-retinal. A site-directed 2H-labeling approach utilizing solid-state 2H NMR spectroscopy was used to investigate the structure and dynamics of retinal within its binding pocket in the dark state of rhodopsin, and as well the MetaI and MetaII. 11-cis-[5-C 2H3]-, 11-cis-[9-C 2H3]-, and 11-cis-[13-C2H 3]-retinal were used to regenerate bleached rhodopsin. Recombinant membranes comprising purified rhodopsin and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) were prepared (1:50 molar ratio). Solid-state 2H NMR spectra were obtained for the aligned rhodopsin/POPC recombinant membranes at temperatures below the order-disorder phase transition temperature of POPC. The solid-state NMR studies of aligned samples, give the orientations of the 2H nuclear coupling tensor relative to the membrane frame, which involve both the conformation and orientation of the bound retinal chromophore. Theoretical simulations of the experimental 2H NMR spectra employed a new lineshape treatment for a semi-random distribution due to static uniaxial disorder. The analysis gives the orientation of the 2H-labeled C-C2H3 methyl bond axes relative to the membrane plane as well as the extent of three-dimensional alignment disorder (mosaic spread). These results clearly demonstrate the applicability of site-directed 2H NMR methods for investigating conformational changes and dynamics of ligands bound to rhodopsin and other GPCRs in relation to their characteristic mechanisms of action.
Structural elucidation of rat biliary metabolites of corynoxeine and their quantification using LC-MS(n).
Wang, Wei; Li, Xinmei; Chen, Yaping; Hattori, Masao
Corynoxeine (COR) is one of 4 bioactive oxindole alkaloids in Uncaria species. In this work two phase I metabolites, namely 11-hydroxycorynoxeine (M1) and 10-hydroxycorynoxeine (M2), and two phase II metabolites, namely 11-hydroxycorynoxeine 11-O-β-d-glucuronide (M3) and 10-hydroxycorynoxeine 10-O-β-d-glucuronide (M4), were detected in rat bile after oral dose of COR (0.105 mmol/kg), by optimized high-performance liquid chromatography-tandem mass spectrometry (LC-MS(n) ) with electrospray ionization in positive ion mode. Structures of M1-4 were determined by LC-MS(n) , nuclear magnetic resonance, circular dichroism and high-resolution MS spectra. COR and its metabolites in rat bile were quantified by LC-MS(n) . The LC-MS(n) quantification methods for COR and its metabolites yielded a linearity with coefficient of determination ≥0.995 from 5.0 × 10(-10) to 5.0 × 10(-7) m. The recoveries of stability tests varied from 96.80 to 103.10%. Accuracy ranged from 91.00 to 105.20%. Relative standard deviation for intra-day and inter-day assay was <5.0%. After the oral dose 0.14% of COR was detected in rat bile from 0 to 8 h, in which in total 97.8% COR biotransformed into M1-4. M1 and M2 yielded 48.1 and 49.7%, which successively glucuronidated to M3 and M4 at 47.2 and 43.8%, respectively. PMID:24523045
Asparagine-linked oligosaccharides on lutropin, follitropin, and thyrotropin: structural elucidation of the sulfated and sialylated oligosaccharides on bovine, ovine, and human pituitary glycoprotein hormones
Green, E.D.; Baenziger, J.U.
The authors have elucidated the structures of the anionic asparagine-linked oligosaccharides present on the glycoprotein hormones lutropin (luteinizing hormone), follitropin (follicle-stimulating hormone), and thyrotropin (thyroid-stimulating hormone). Purified hormones, isolated from bovine, ovine, and human pituitaries, were digested with N-glycanase, and the released oligosaccharides were reduced with NaB(/sup 3/H)/sub 4/. The /sup 3/H-labeled oligosaccharides from each hormone were then fractionated by anion-exchange high performance liquid chromatography (HPLC) into populations differing in the number of sulfate and/or sialic acid moieties. The sulfated, sialylated, and sulfated/sialylated structures, which together comprised 67-90% of the asparagine-linked oligosaccharides on the pituitary glycoprotein hormones, were highly heterogeneous and displayed hormone- as well as animal species-specific features. A previously uncharacterized dibranched oligosaccharide, bearing one residue each of sulfate and sialic acid, was found on all of the hormones except bovine lutropin. In this study, they describe the purification and detailed structural characterizations of the sulfated, sialylated, and sulfated/sialylated oligosaccharides found on lutropin, follitropin, and thyrotropin from several animal species.
Isolation, structure, and HIV-1-integrase inhibitory activity of structurally diverse fungal metabolites.
Singh, Sheo B; Jayasuriya, Hiranthi; Dewey, Raymond; Polishook, Jon D; Dombrowski, Anne W; Zink, Deborah L; Guan, Ziqiang; Collado, Javier; Platas, Gonzalo; Pelaez, Fernando; Felock, Peter J; Hazuda, Daria J
HIV-1 integrase is a critical enzyme for replication of HIV, and its inhibition is one of the most promising new drug strategies for anti-retroviral therapy, with potentially significant advantages over existing therapies. In this report, a series of HIV-1 inhibitors isolated from the organic extract of fermentations from terrestrial fungi is described. These fungal species, belonging to a variety of genera, were collected from throughout the world following the strict guidelines of Rio Convention on Biodiversity. The polyketide- and terpenoid-derived inhibitors are represented by two naphthoquinones, a biphenyl and two triphenyls, a benzophenone, four aromatics with or without catechol units, a linear aliphatic terpenoid, a diterpenoid, and a sesterterpenoid. These compounds inhibited the coupled and strand-transfer reaction of HIV-1 integrase with an IC(50) value of 0.5-120 micro M. The bioassay-directed isolation, structure elucidation, and HIV-1 inhibitory activity of these compounds are described. PMID:14714192
Collision-Induced Dissociation Ion Mobility Mass Spectrometry for the Elucidation of Unknown Structures in Strained Polycyclic Aromatic Hydrocarbon Macrocycles.
Zhang, Wen; Quernheim, Martin; Räder, Hans Joachim; Müllen, Klaus
Structure determination of unexpected products obtained during synthesis of large carbon nanotube sidewall segments with more than 200 carbon atoms represents a challenging task for traditional analytical methods. Herein, we investigate a homologous series of four products having the same number of carbon atoms but slightly different hydrogen numbers ranging from 168 to 162. We demonstrate that the combination of mass spectrometry, ion mobility separation, and collision-induced dissociation (CID) can be used to finally elucidate the complete structures with high certainty. The postulated 1,2-phenyl shift as origin for the side reaction could be proven by changes in the minimum fragment sizes. A combination of CID and ion mobility spectrometry was applied for the first time to prove the cyclic nature of all molecules by the significant size increase upon ring opening. Thereby, also, more compact molecules were discovered in the gas phase with thus far unknown structures. Finally, the potential presence of numerous isomers could be ruled out by drift time measurements and molecular modeling together with theoretical collision cross-section (CCS) calculations. Surprisingly, only one defined structure could be assigned to each macrocycle in the homologous series, most likely as a result of natural selection rules driven by ring strain and steric hindrance. With a decreasing hydrogen content, the macrocycles undergo a stepwise transition from a cylindrical to conical shape. Overall, ion mobility mass spectrometry together with molecular modeling shows great potential to analyze unknown structures, especially in cases where structure determination by X-ray single-crystal analysis is not applicable. PMID:26613508
Structural elucidation of the hormonal inhibition mechanism of the bile acid cholate on human carbonic anhydrase II
Boone, Christopher D.; Tu, Chingkuang; McKenna, Robert
The structure of human carbonic anhydrase II in complex with cholate has been determined to 1.54 Å resolution. Elucidation of the novel inhibition mechanism of cholate will aid in the development of a nonsulfur-containing, isoform-specific therapeutic agent. The carbonic anhydrases (CAs) are a family of mostly zinc metalloenzymes that catalyze the reversible hydration/dehydration of CO{sub 2} into bicarbonate and a proton. Human isoform CA II (HCA II) is abundant in the surface epithelial cells of the gastric mucosa, where it serves an important role in cytoprotection through bicarbonate secretion. Physiological inhibition of HCA II via the bile acids contributes to mucosal injury in ulcerogenic conditions. This study details the weak biophysical interactions associated with the binding of a primary bile acid, cholate, to HCA II. The X-ray crystallographic structure determined to 1.54 Å resolution revealed that cholate does not make any direct hydrogen-bond interactions with HCA II, but instead reconfigures the well ordered water network within the active site to promote indirect binding to the enzyme. Structural knowledge of the binding interactions of this nonsulfur-containing inhibitor with HCA II could provide the template design for high-affinity, isoform-specific therapeutic agents for a variety of diseases/pathological states, including cancer, glaucoma, epilepsy and osteoporosis.
Structural Elucidation of Enzymatically Synthesized Galacto-oligosaccharides Using Ion-Mobility Spectrometry-Tandem Mass Spectrometry.
Carević, Milica; Bezbradica, Dejan; Banjanac, Katarina; Milivojević, Ana; Fanuel, Mathieu; Rogniaux, Hélène; Ropartz, David; Veličković, Dušan
Galacto-oligosaccharides (GOS) represent a diverse group of well-characterized prebiotic ingredients derived from lactose in a reaction catalyzed with β-galactosidases. Enzymatic transgalactosylation results in a mixture of compounds of various degrees of polymerization and types of linkages. Because structure plays an important role in terms of prebiotic activity, it is of crucial importance to provide an insight into the mechanism of transgalactosylation reaction and occurrence of different types of β-linkages during GOS synthesis. Our study proved that a novel one-step method, based on ion-mobility spectrometry-tandem mass spectrometry (IMS-MS/MS), enables complete elucidation of GOS structure. It has been shown that β-galactosidase from Aspergillus oryzae has the highest affinity toward formation of β-(1→3) or β-(1→6) linkages. Additionally, it was observed that the occurrence of different linkages varies during the reaction course, indicating that tailoring favorable GOS structures with improved prebiotic activity can be achieved by adequate control of enzymatic synthesis. PMID:27109424
Active isolation of vibrations with adaptive structures
NASA Technical Reports Server (NTRS)
Guigou, C.; Fuller, C. R.; Wagstaff, P. R.
Vibration transmission in structures is controlled by means of a technique which employs distributed arrays of piezoelectric transducers bonded to the supporting structure. Distributed PVDF piezoelectric strips are employed as error sensors, and a two-channel feedforward adaptive LMS algorithm is used for minimizing error signals and thereby controlling the structure. A harmonic force input excites a thick plate, and a receiving plate is configured with three pairs of piezoelectric actuators. Modal analyses are performed to determine the resonant frequencies of the system, and a scanning laser vibrometer is used to study the shape of the response of the receiving plate during excitation with and without the control algorithm. Efficient active isolation of the vibrations is achieved with modal suppression, and good control is noted in the on-resonance cases in which increased numbers of PVDF sensors and piezoelectric actuators are employed.
Seven naphtho-γ-pyrones from the marine-derived fungus Alternaria alternata: structure elucidation and biological properties
Eight bioactive pyrone derivatives were identified from the culture of Alternaria alternata strain D2006, isolated from the marine soft coral Denderonephthya hemprichi, which was selected as its profound antimicrobial activities. The compounds were assigned as pyrophen (1), rubrofusarin B (2), fonsecin (3), and fonsecin B (5) beside to the four dimeric naphtho-γ-pyrones; aurasperone A (6), aurasperone B (7), aurasperone C (8), and aurasperone F (9). Structures of the isolated compounds were identified on the basis of 1D and 2D NMR spectroscopy and mass (EI, ESI, HRESI) data, and by comparison with the literature. Configuration of the four dimeric naphtho-γ-pyrones 6-9 was analyzed by CD spectra, exhibiting an identical stereochemistry. PMID:22377027
Frequency response characteristics and response spectra of base-isolated and un-isolated structures
Mok, G.C.; Namba, H.
The transmissibility of seismic loads through a linear base-isolation system is analyzed using an impedance method. The results show that the system acts like a {open_quotes}low-pass{close_quotes} filter. It attenuates high-frequency loads but passes through low-frequency ones. The filtering effect depends on the vibration frequencies and damping of the isolated structure and the isolation system. This paper demonstrates the benefits and design principles of base isolation by comparing the transmissibilities and response spectra of isolated and un-isolated structures. Parameters of typical isolated buildings and ground motions of the 1994 Northridge earthquake are used for the demonstration.
Relationships between functional genes in Lactobacillus delbrueckii ssp. bulgaricus isolates and phenotypic characteristics associated with fermentation time and flavor production in yogurt elucidated using multilocus sequence typing.
Liu, Wenjun; Yu, Jie; Sun, Zhihong; Song, Yuqin; Wang, Xueni; Wang, Hongmei; Wuren, Tuoya; Zha, Musu; Menghe, Bilige; Heping, Zhang
Lactobacillus delbrueckii ssp. bulgaricus (L. bulgaricus) is well known for its worldwide application in yogurt production. Flavor production and acid producing are considered as the most important characteristics for starter culture screening. To our knowledge this is the first study applying functional gene sequence multilocus sequence typing technology to predict the fermentation and flavor-producing characteristics of yogurt-producing bacteria. In the present study, phenotypic characteristics of 35 L. bulgaricus strains were quantified during the fermentation of milk to yogurt and during its subsequent storage; these included fermentation time, acidification rate, pH, titratable acidity, and flavor characteristics (acetaldehyde concentration). Furthermore, multilocus sequence typing analysis of 7 functional genes associated with fermentation time, acid production, and flavor formation was done to elucidate the phylogeny and genetic evolution of the same L. bulgaricus isolates. The results showed that strains significantly differed in fermentation time, acidification rate, and acetaldehyde production. Combining functional gene sequence analysis with phenotypic characteristics demonstrated that groups of strains established using genotype data were consistent with groups identified based on their phenotypic traits. This study has established an efficient and rapid molecular genotyping method to identify strains with good fermentation traits; this has the potential to replace time-consuming conventional methods based on direct measurement of phenotypic traits. PMID:26547656
Application of Structural Equation Models for Elucidating the Ecological Drivers of Anopheles sinensis in the Three Gorges Reservoir
Duo-quan, Wang; Lin-hua, Tang; Heng-hui, Liu; Zhen-cheng, Gu; Xiang, Zheng
Objective To identify the major ecological drivers for malaria vector density using the structural equation model (SEM) in the Three Gorges Reservoir. Method An 11-year longitudinal surveillance of malaria vector as well as its related ecological factors was carried out in the Three Gorges Reservoir. The Delphi method was used to identify associated ecological factors. The structural equation model was repeatedly corrected and improved by the corrected index, combined with the actual situation. The final model was defined by relative simplicity, best fitting as well as the practicality. Result The final model indicated that the direct effects of temperature, livestock, humidity, and breeding on the vector were 0.015, −0.228, 0.450, 0.516 respectively, their total effects on the vector were 0.359, −0.112, 0.850, and 0.043 through different pathways. Conclusion SEM was effective and convenient in elucidating the mechanism by which malaria vector dynamics operated in this study. It identified that the breeding had the highest direct effect on vector and played a key role for mediating effect of temperature and humidity. PMID:23935887
Elucidating molecular iridium water oxidation catalysts using metal-organic frameworks: a comprehensive structural, catalytic, spectroscopic, and kinetic study.
Wang, Cheng; Wang, Jin-Liang; Lin, Wenbin
As a new class of porous, crystalline, molecular materials, metal-organic frameworks (MOFs) have shown great promise as recyclable and reusable single-site solid catalysts. Periodic order and site isolation of the catalytic struts in MOFs facilitate the studies of their activities and reaction mechanisms. Herein we report the construction of two highly stable MOFs (1 and 2) using elongated dicarboxylate bridging ligands derived from Cp*Ir(L)Cl complexes (L = dibenzoate-substituted 2,2'-bipyridine, bpy-dc, or dibenzoate-substituted 2-phenylpyridine, ppy-dc) and Zr(6)O(4)(OH)(4)(carboxylate)(12) cuboctahedral secondary building units (SBUs) and the elucidation of water oxidation pathways of the Cp*Ir(L)Cl catalysts using these MOFs. We carried out detailed kinetic studies of Ce(4+)-driven water oxidation reactions (WORs) catalyzed by the MOFs using UV-vis spectroscopy, phosphorescent oxygen detection, and gas chromatographic analysis. These results confirmed not only water oxidation activity of the MOFs but also indicated oxidative degradation of the Cp* rings during the WOR. The (bpy-dc)Ir(H(2)O)(2)XCl (X is likely a formate or acetate group) complex resulted from the oxidative degradation process was identified as a competent catalyst responsible for the water oxidation activity of 1. Further characterization of the MOFs recovered from WORs using X-ray photoelectron, diffuse-reflectance UV-vis absorption, luminescence, and infrared spectroscopies supported the identity of (bpy-dc)Ir(H(2)O)(2)XCl as an active water oxidation catalyst. Kinetics of MOF-catalyzed WORs were monitored by Ce(4+) consumptions and fitted with a reaction-diffusion model, revealing an intricate relationship between reaction and diffusion rates. Our work underscores the opportunity in using MOFs as well-defined single-site solid catalytic systems to reveal mechanistic details that are difficult to obtain for their homogeneous counterparts. PMID:23136923
Elucidating structural characteristics of biomass using solution-state 2 D NMR with a mixture of deuterated dimethylsulfoxide and hexamethylphosphoramide
Pu, Yunqiao; Ragauskas, Arthur J.; Yoo, Chang Geun; Li, Mi
In recent developments of NMR methods for characterization of lignocellulosic biomass allow improved understanding of plant cell-wall structures with minimal deconstruction and modification of biomass. This study introduces a new NMR solvent system composed of dimethylsulfoxide (DMSO-d6) and hexamethylphosphoramide (HMPA-d18). HMPA as a co-solvent enhanced swelling and mobility of the biomass samples; thereby it allowed enhancing signals of NMR spectra. Moreover, the structural information of biomass was successfully analyzed by the proposed NMR solvent system (DMSO-d6/HMPA-d18; 4:1, v/v) with different biomass. The proposed bi-solvent system does not require derivatization or isolation of biomass, facilitating a facile sample preparation and involvingmore » with no signals overlapping with biomass peaks. Furthermore, it also allows analyzing biomass with a room-temperature NMR probe instead of cryo-probes, which are traditionally used for enhancing signal intensities.« less
Elucidating the higher-order structure of biopolymers by structural probing and mass spectrometry: MS3D
Fabris, Daniele; Yu, Eizadora T.
Chemical probing represents a very versatile alternative for studying the structure and dynamics of substrates that are intractable by established high-resolution techniques. The implementation of MS-based strategies for the characterization of probing products has not only extended the range of applicability to virtually all types of biopolymers, but has also paved the way for the introduction of new reagents that would not have been viable with traditional analytical platforms. As the availability of probing data is steadily increasing on the wings of the development of dedicated interpretation aids, powerful computational approaches have been explored to enable the effective utilization of such information to generate valid molecular models. This combination of factors has contributed to making the possibility of obtaining actual 3D structures by MS-based technologies (MS3D) a reality. Although approaches for achieving structure determination of unknown substrates or assessing the dynamics of known structures may share similar reagents and development trajectories, they clearly involve distinctive experimental strategies, analytical concerns, and interpretation paradigms. This Perspective offers a commentary on methods aimed at obtaining distance constraints for the modeling of full-fledged structures, while highlighting common elements, salient distinctions, and complementary capabilities exhibited by methods employed in dynamics studies. We discuss critical factors to be addressed for completing effective structural determinations and expose possible pitfalls of chemical methods. We survey programs developed for facilitating the interpretation of experimental data and discuss possible computational strategies for translating sparse spatial constraints into all-atom models. Examples are provided to illustrate how the concerted application of very diverse probing techniques can lead to the solution of actual biological substrates. PMID:20648672
Structural elucidation, in vitro antioxidant and photoprotective capacities of a purified polyphenolic-enriched fraction from a saltmarsh plant.
Surget, Gwladys; Stiger-Pouvreau, Valérie; Le Lann, Klervi; Kervarec, Nelly; Couteau, Céline; Coiffard, Laurence J M; Gaillard, Fanny; Cahier, Karine; Guérard, Fabienne; Poupart, Nathalie
In temperate saltmarshes, halophytic plants have to daily protect their internal tissues against sunlight and UV rays. Consequently, they develop adaptive responses such as the synthesis of secondary metabolites, including polyphenols. The present study focused on the biological activities of fractions enriched in polyphenols from Salicornia ramosissima. Three different extracts were obtained by purification processes to concentrate polyphenols: a crude hydroalcoholic extract, and two purified fractions: an ethyl acetate fraction (EAF) and an aqueous fraction. Phenolic and flavonoid contents, antioxidant (DPPH radical-scavenging activity, reducing activity, β-carotene linoleic acid system and the ORAC method) and sunscreen properties (Sun Protection Factor and UVA-Protection Factor) were assessed by in vitro tests. The purification process was effective in increasing phenolic and flavonoid contents as well as antioxidant and sunscreen capacities of the EAF. The EAF appeared to be a broad spectrum UV absorber. The chemical structure of 10 EAF polyphenols was elucidated using 2D NMR and mass spectrometry spectra. Furthermore, a correlation was observed between phenolic composition and biological activity. These findings are encouraging for the future use of S. ramosissima as a potential source of antioxidant and photoprotectant molecules for industrial applications. PMID:25600264
Structure elucidation and in vitro cytotoxicity of ochratoxin α amide, a new degradation product of ochratoxin A.
Bittner, Andrea; Cramer, Benedikt; Harrer, Henning; Humpf, Hans-Ulrich
The mycotoxin ochratoxin A is a secondary metabolite occurring in a wide range of commodities. During the exposure of ochratoxin A to white and blue light, a cleavage between the carbon atom C-14 and the nitrogen atom was described. As a reaction product, the new compound ochratoxin α amide has been proposed based on mass spectrometry (MS) experiments. In the following study, we observed that this compound is also formed at high temperatures such as used for example during coffee roasting and therefore represents a further thermal ochratoxin A degradation product. To confirm the structure of ochratoxin α amide, the compound was prepared in large scale and complete structure elucidation via nuclear magnetic resonance (NMR) and MS was performed. Additionally, first studies on the toxicity of ochratoxin α amide were performed using immortalized human kidney epithelial (IHKE) cells, a cell line known to be sensitive against ochratoxin A with an IC50 value of 0.5 μM. Using this system, ochratoxin α amide revealed no cytotoxicity up to concentrations of 50 μM. Thus, these results propose that the thermal degradation of ochratoxin A to ochratoxin α amide might be a detoxification process. Finally, we present a sample preparation and a HPLC-tandem mass spectrometry (HPLC-MS/MS) method for the analysis of ochratoxin α amide in extrudates and checked its formation during the extrusion of artificially contaminated wheat grits at 150 and 180 °C, whereas no ochratoxin α amide was detectable under these conditions. PMID:25566949
Antineoplastic Agents. 556. Isolation and Structure of Coprinastatin 1 from Coprinus cinereus1⊥
Pettit, George R.; Meng, Yanhui; Pettit, Robin K.; Herald, Delbert L.; Cichacz, Zbigniew A.; Doubek, Dennis L.; Richert, Linda
Cancer cell line bioassay-guided separation of an ethyl acetate extract prepared from a plant-associated fungus, Coprinus cinereus, led to the isolation of three new sesquiterpenes, coprinastatin 1 (1), coprinol (2), and the epimer (4a) of the known sesquiterpene triol 4b. The previously described sesquiterpene 3 and oxazolinone 5 were also isolated. The structure and relative configuration of coprinastatin 1 (1) was determined by HRMS and by 1D- and 2D-NMR spectroscopic analyses. The structure of terpene 2 was elucidated by single-crystal X-ray diffraction experiments. The remaining structures were similarly determined, structure 3 by spectroscopic analyses and both 4a and 5 by X-ray crystal structure determination. Coprinastatin 1 (1) was found to inhibit growth of the murine P388 lymphocytic leukemia cell line and the pathogenic bacterium Neisseria gonorrhoeae. PMID:19919060
Porphyrins from Messel oil shale (Eocene, Germany): Structure elucidation, geochemical and biological significance, and distribution as a function of depth
Ocampo, R.; Bauder, C.; Callot, H.J.; Albrecht, P. )
The extraction and isolation procedures of twenty nickel porphyrins (seven alkylporphyrins, thirteen carboxylic acids) from lacustrine Messel shale (Eocene, Germany), as well as the unequivocal structural assignments (obtained using 200 and 400 MHz nuclear magnetic resonance (NMR), nuclear Overhauser effect, mass spectrometry, and total or partial synthesis of six reference compounds) are described. Ten porphyrins could be specifically correlated with biological precursors: algal chlorophyll c (4), bacteriochlorophylls d (3), and heme (3), while the remaining ones may arise from several chlorophylls. The structures of these fossil pigments mostly confirm the classical Treibs scheme,' including the origin of some porphyrins from nonchlorophyll sources. They also show that, even in a very immature sediment, deep modifications occur, including, in particular, extensive degradation of chlorophyll E ring. The composition of the porphyrin fractions of Messel oil shale was also studied as a function of depth. A porphyrin acids/alkylporphyrins ratio varying from 0.35 to 24.8 demonstrated that the apparent homogeneity of the shale is not reflected on the molecular scale. This was confirmed when the abundance of the twenty individual porphyrins of known structure was measured along the core. Significant correlations between individual porphyrins were found: fossils of bacteriochlorophylls d, homolog pairs of porphyrins (3-H/3-ethyl), etc.
Anti- and pro-lipase activity of selected medicinal, herbal and aquatic plants, and structure elucidation of an anti-lipase compound.
Ado, Muhammad Abubakar; Abas, Faridah; Mohammed, Abdulkarim Sabo; Ghazali, Hasanah M
Plants that help in slowing down the digestion of triacylglycerols (TAGs) in the pancreas and small intestine of humans play an important role in the reduction of obesity. On the other hand, there may be plants or plant parts that stimulate intestinal lipolytic activity, thus contributing to greater TAG assimilation. The aim of this study was to evaluate the aqueous methanolic extracts of ninety eight (98) medicinal, herbal and aquatic plant materials from Malaysia for their effect on porcine pancreatic lipase (PPL) activity and to identify the structure of an anti-lipase compound from one of the sources. The degree of inhibition was also quantified as relative to orlistat activity against PPL (orlistat equivalents). Results revealed that while 19.4% of the extracts were found to have anti-lipase activity ≥80%, 12% were actually found to promote PPL activity. Twenty two percent (22.4%) exhibited moderate inhibition (41%-80%) and 2% were neutral toward PPL activity. The ripe fruit of Averrhoa carambola and the leaves of Archidendron jiringa (Jack) I.C Nielsen L. (jering), Cynometra cauliflora (nam-nam) and Aleurites moluccana (L.) Willd (candle nut/buah keras) had the highest (100%) anti-lipase activity and are equivalent to 0.11 µg orlistat/mL. Plants that stimulated lipase activity included Pimpinella anisum L. (aniseed/jintan manis), activating the enzyme by 186.5%. Kaempferol 3-O-rhamnoside was isolated from the ethyl acetate fraction of C. cauliflora leaves and found to be an active lipase inhibitor. The structure was elucidated using 1H-NMR, 13C-NMR and 2D-NMR analyses. PMID:24287996
Fast in vitro hydrolytic degradation of polyester urethane acrylate biomaterials: structure elucidation, separation and quantification of degradation products.
Ghaffar, A; Verschuren, P G; Geenevasen, J A J; Handels, T; Berard, J; Plum, B; Dias, A A; Schoenmakers, P J; van der Wal, Sj
Synthetic biomaterials have evoked extensive interest for applications in the field of health care. Prior to administration to the body a quantitative study is necessary to evaluate their composition. An in vitro method was developed for the quick hydrolytic degradation of poly-2-hydroxyethyl methacrylate (pHEMA), poly(lactide-co-glycolide50/50)1550-diol (PLGA(50:50)(1550)-diol), PLGA(50:50)(1550)-diol(HEMA)(2) and PLGA(50:50)(1550)-diol(etLDI-HEMA)(2) containing ethyl ester lysine diisocyanate (etLDI) linkers using a microwave instrument. Hydrolysis time and temperature were optimized while monitoring the degree of hydrolysis by (1)H NMR spectroscopy. Complete hydrolytic degradation was achieved at 120°C and 3 bar pressure after 24 h. Chemical structure elucidations of the degradation products were carried out using (1)H and (13)C NMR spectroscopy. The molecular weight (MW) of the polymethacrylic backbone was estimated via size-exclusion chromatography coupled to refractive index detection (SEC-dRI). A bimodal MW distribution was found experimentally, also in the pHEMA starting material. The number average molecular weights (M(n)) of the PLGA-links (PLGA(50:50)(1550)-diol) were calculated by high pressure liquid chromatography-time-of-flight mass spectrometry (HPLC-TOF-MS) and (1)H NMR. The amounts of the high and low MW degradation products were determined by SEC-dRI and, HPLC-TOF-MS, respectively. The main hydrolysis products poly (methacrylic acid) (PMAA), ethylene glycol (EG), diethylene glycol (DEG), lactic acid (LA), glycolic acid (GA) and lysine were recovered almost quantitatively. The current method leads to the complete hydrolytic degradation of these materials and will be helpful to study the degradation behavior of these novel cross-linked polymeric biomaterials. PMID:21167489
3-D structural modeling of humic acids through experimental characterization, computer assisted structure elucidation and atomistic simulations 1. Chelsea soil humic acid.
Gassman, Paul; Hatcher, Patrick G.; Faulon, Jean-Loup Michel; Simpson, Andre; Goddard, William A., III; Diallo, Mamadou S.; Johnson, James H. Jr.
This paper describes an integrated experimental and computational framework for developing 3-D structural models for humic acids (HAs). This approach combines experimental characterization, computer assisted structure elucidation (CASE), and atomistic simulations to generate all 3-D structural models or a representative sample of these models consistent with the analytical data and bulk thermodynamic/structural properties of HAs. To illustrate this methodology, structural data derived from elemental analysis, diffuse reflectance FT-IR spectroscopy, 1-D/2-D {sup 1}H and {sup 13}C solution NMR spectroscopy, and electrospray ionization quadrupole time-of-flight mass spectrometry (ESI QqTOF MS) are employed as input to the CASE program SIGNATURE to generate all 3-D structural models for Chelsea soil humic acid (HA). These models are subsequently used as starting 3-D structures to carry out constant temperature-constant pressure molecular dynamics simulations to estimate their bulk densities and Hildebrand solubility parameters. Surprisingly, only a few model isomers are found to exhibit molecular compositions and bulk thermodynamic properties consistent with the experimental data. The simulated {sup 13}C NMR spectrum of an equimolar mixture of these model isomers compares favorably with the measured spectrum of Chelsea soil HA.
Elucidation, functional clustering and structural characterization of βTrCP1 substrates through a molecular dynamics study.
Shafique, Shagufta; Younis, Saima; Niaz, Hafsa; Rashid, Sajid
The current interest in the identification and characterization of βTrCP1 substrates necessitates a promising approach with broad structural constraints of WD40 potential binding sites. Here, we employed an in silico integrative approach to identify putative novel substrates of βTrCP1. Through a screened degradation motif (DSGXXS) for the entire human proteome and comparative substrate binding analysis of βTrCP1, we identified 344 substrates, sharing high sequence similarity with the consensus motif. Subsequent filtering on the basis of functional annotation and clustering resulted in the isolation of hits having clear roles in various cancer types. These substrates were phosphorylated at the Ser residues (Ser14 and Ser18) of the conserved motif. A comprehensive and thorough analysis of βTrCP1-phosphopeptide association indicated residual contributions located at the upper face of the β-propeller. Evidently, upon binding to phosphopeptides, the central channel of βTrCP1 attains a more open conformation to assist substrate binding. To elaborate the oncogenic function of βTrCP1, the SKP1-βTrCP1-CDH6 ternary complex was docked against CUL1-RBX1 and the acquired model exactly resembled the previously characterized SKP1-βTrCP1-β-catenin model. Overall, a deeper understanding of substrate targeting mechanisms coupled with the structural knowledge of βTrCP1 and associated proteins will be useful for designing novel targets for cancer therapeutics. PMID:27156994
Elucidating the electronic structure of supported gold nanoparticles and its relevance to catalysis by means of hard X-ray photoelectron spectroscopy
NASA Astrophysics Data System (ADS)
Reinecke, Benjamin N.; Kuhl, Kendra P.; Ogasawara, Hirohito; Li, Lin; Voss, Johannes; Abild-Pedersen, Frank; Nilsson, Anders; Jaramillo, Thomas F.
We report on the electronic structure of Au (gold) nanoparticles supported onto TiO2 with a goal of elucidating the most important effects that contribute to their high catalytic activity. We synthesize and characterize with high resolution transmission electron microscopy (HRTEM) 3.4, 5.3, and 9.5 nm diameter TiO2-supported Au nanoparticles with nearly spherical shape and measure their valence band using Au 5d subshell sensitive hard X-ray photoelectron spectroscopy (HAXPES) conducted at Spring-8. Based on density functional theory (DFT) calculations of various Au surface structures, we interpret the observed changes in the Au 5d valence band structure as a function of size in terms of an increasing percentage of Au atoms at corners/edges for decreasing particle size. This work elucidates how Au coordination number impacts the electronic structure of Au nanoparticles, ultimately giving rise to their well-known catalytic activity.
Structure of the lipopolysaccharide isolated from the novel species Uruburuella suis.
Silipo, Alba; Sturiale, Luisa; De Castro, Cristina; Lanzetta, Rosa; Parrilli, Michelangelo; Garozzo, Domenico; Molinaro, Antonio
Uruburuella suis is a novel species isolated from lungs and heart of pigs with pneumonia and pericarditis. Phenotypic and phylogenetic evidences showed that it represented a hitherto unknown subline within the family Neisseriaceae. In the present work we defined the whole structure of the LPS isolated from Uruburuella suis. The structural determination, which was achieved by chemical, spectroscopic and spectrometric approaches, indicates a novel rough type lipopolysaccharide rich in negatively charged groups in the lipid A-inner core region. The elucidation of the structural features of the LPS from Uruburuella suis is a first step toward the comprehension of the characteristics of the cell envelope in such new and interesting microorganisms. PMID:22704198
Combining Raman and infrared spectroscopy as a powerful tool for the structural elucidation of cyclodextrin-based polymeric hydrogels.
Venuti, V; Rossi, B; D'Amico, F; Mele, A; Castiglione, F; Punta, C; Melone, L; Crupi, V; Majolino, D; Trotta, F; Gessini, A; Masciovecchio, C
A detailed experimental and theoretical vibrational analysis of hydrogels of β-cyclodextrin nanosponges (β-CDNS), obtained by polymerization of β-cyclodextrin (β-CD) with the cross-linking agent ethylenediaminetetraacetic acid (EDTA), is reported here. Thorough structural characterization is achieved by exploiting the complementary selection rules of FTIR-ATR and Raman spectroscopies and by supporting the spectral assignments by DFT calculations of the spectral profiles. The combined analysis of the FTIR-ATR spectra of the polymers hydrated with H2O and D2O allowed us to isolate the HOH bending of water molecules not involved in symmetrical, tetrahedral environments. The analysis of the HOH bending mode was carried out as a function of temperature, showing the existence of a supercooled state of the water molecules. The highest level of cooperativity of the hydrogen bond scheme was reached at a value of the β-CD/EDTA molar ratio n = 6. Finally, the connectivity pattern of "uncoupled" water molecules bound to the nanosponge backbone was found to be weakened by increasing T. The temperature above which the population of non-tetracoordinated water molecules becomes predominant turned out to be independent of the parameter n. PMID:25798878
Synthesis, structural elucidation, and application of a pyrazolylpyridine-molybdenum oxide composite as a heterogeneous catalyst for olefin epoxidation.
Figueiredo, Sónia; Gomes, Ana C; Neves, Patrícia; Amarante, Tatiana R; Paz, Filipe A Almeida; Soares, Rosário; Lopes, André D; Valente, Anabela A; Pillinger, Martyn; Gonçalves, Isabel S
The reaction of [MoO(2)Cl(2)(pypzEA)] (1) (pypzEA = ethyl[3-(pyridin-2-yl)-1H-pyrazol-1-yl]acetate) with water in a Teflon-lined stainless steel autoclave (100 °C) or in an open reflux system leads to the isolation of the molybdenum oxide/pyrazolylpyridine composite material [Mo(2)O(6)(HpypzA)] (2; HpypzA = [3-(pyridinium-2-yl)-1H-pyrazol-1-yl]acetate). The solid state structure of 2 was solved through single crystal and powder X-ray diffraction analyses in conjunction with information derived from FT-IR and (13)C CP MAS NMR spectroscopies and elemental analyses. In the asymmetric unit of 2, two crystallographically distinct Mo(6+) centers are bridged by a syn,syn-carboxylate group of HpypzA. The periodic repetition of these units along the a axis of the unit cell leads to the formation of a one-dimensional composite polymer, (∞)(1)[Mo(2)O(6)(HpypzA)]. The outstretched pyrazolylpyridine groups of adjacent polymers interdigitate to form a zipper-like motif, generating strong onset π-π contacts between adjacent rings of coordinated HpypzA molecules. The composite oxide 2 is a stable heterogeneous catalyst for liquid-phase olefin epoxidation. PMID:22830308
Human serum albumin-benzo[a]pyrene anti-diol epoxide adduct structure elucidation by fluorescence line narrowing spectroscopy.
Day, B W; Doxtader, M M; Rich, R H; Skipper, P L; Singh, K; Dasari, R R; Tannenbaum, S R
Cryogenic (4-10 K) laser-induced vibrationless ground state and vibronic excited state fluorescence emission spectra of the adducts resulting from reaction in vitro of human serum albumin and the carcinogen (+-)-r-7,t-8-dihydroxy-c-9,c-10-epoxy-7,8,9,10- tetrahydrobenzo[a]-pyrene were recorded in order to determine the structures formed. Comparison of these fluorescence line-narrowed (FLN) spectra to those obtained from BaP-7,8,9,10- tetrahydrotetrols, synthetic N-t-BOC-alaninate ester, and N tau- and N pi-histidine amine anti-BaPDE adducts revealed that a mixture of adduct types are formed with the protein. Extensive dialysis of the adducted protein simplified the FLN spectrum, causing it to become nearly identical to the FLN spectrum obtained from the stable peptide adduct. Comparison of the FLN spectra of the synthetic histidine adducts to those obtained from peptide adducts isolated from enzymic digestion of the adducted protein indicated that only one of the imidazole nitrogens is the nucleophile which forms a stable adduct with anti-BaPDE. The FLN studies confirm that N tau-histidine adducts are formed between human serum albumin and the C-10 position of anti-BaPDE. PMID:1581540
Determination of the Chemical Structures of Tandyukisins B–D, Isolated from a Marine Sponge-Derived Fungus
Yamada, Takeshi; Umebayashi, Yoshihide; Kawashima, Maiko; Sugiura, Yuma; Kikuchi, Takashi; Tanaka, Reiko
Tandyukisins B–D (1–3), novel decalin derivatives, have been isolated from a strain of Trichoderma harzianum OUPS-111D-4 originally derived from the marine sponge Halichondria okadai, and their structures have been elucidated on the basis of spectroscopic analyses using 1D and 2D NMR techniques. In addition, their chemical structures were established by chemical transformation. They exhibited weak cytotoxicity, but selective growth inhibition on panel screening using 39 human cancer cell lines. PMID:26006715
Determination of the chemical structures of tandyukisins B-D, isolated from a marine sponge-derived fungus.
Yamada, Takeshi; Umebayashi, Yoshihide; Kawashima, Maiko; Sugiura, Yuma; Kikuchi, Takashi; Tanaka, Reiko
Tandyukisins B-D (1-3), novel decalin derivatives, have been isolated from a strain of Trichoderma harzianum OUPS-111D-4 originally derived from the marine sponge Halichondria okadai, and their structures have been elucidated on the basis of spectroscopic analyses using 1D and 2D NMR techniques. In addition, their chemical structures were established by chemical transformation. They exhibited weak cytotoxicity, but selective growth inhibition on panel screening using 39 human cancer cell lines. PMID:26006715
3-D Structural Modeling of Humic Acids through Experimental Characterization, Computer Assisted Structure Elucidation and Atomistic Simulations. 1. Chelsea Soil Humic Acid
Diallo, Mamadou S.; Simpson, Andre; Gassman, Paul L.; Faulon, Jean Loup; Johnson, Jr., James H.; Goddard, III, William A.; Hatcher, Patrick G.
This paper describes an integrated experimental and computational framework for developing 3-D structural models for humic acids (HAs). This approach combines experimental characterization, computer assisted structure elucidation (CASE), and atomistic simulations to generate all 3-D structural models or a representative sample of these models consistent with the analytical data and bulk thermodynamic/structural properties of HAs. To illustrate this methodology, structural data derived from elemental analysis, diffuse reflectance FT-IR spectroscopy, 1-D/2-D | 1H and 13C solution NMR spectroscopy, and electrospray ionization quadrupole time-of-flight mass spectrometry (ESI QqTOF MS) are employed as input to the CASE program SIGNATURE to generate all 3-D structural models for Chelsea soil humic acid (HA). These models are subsequently used as starting 3-D structures to carry out constant temperature-constant pressure molecular dynamics simulations to estimate their bulk densities and Hildebrand solubility parameters. Surprisingly, only a few model isomers are found to exhibit molecular compositions and bulk thermodynamic properties consistent with the experimental data. The simulated 13C NMR spectrum of * Corresponding author phone: (626)395-2730; fax: (626)585-0918; e-mail: firstname.lastname@example.com and firstname.lastname@example.com. Present address: Materials and Process Simulation Center,BeckmanInstitute 139-74, California Institute of Technology, Pasadena, CA 91125. † California Institute of Technology. ‡ Howard University. § University of Toronto. Pacific Northwest National Laboratory. ^ Sandia National Laboratories. # The Ohio State University. ã xxxx American Chemical Society PAGE EST: 11 10.1021/es0259638 CCC: $25.00 Published on Web 00/00/0000 an equimolar mixture of these model isomers compares favorably with the measured spectrum of Chelsea soil HA.
Structural elucidation and protective role of a polysaccharide from Sargassum fusiforme on ameliorating learning and memory deficiencies in mice.
Hu, Pei; Li, Zhixiong; Chen, Mingcang; Sun, Zhaolin; Ling, Yun; Jiang, Jian; Huang, Chenggang
A fucoidan, Sargassum fusiforme polysaccharide 65 (SFPS65) A, was isolated from a brown alga (S. fusiforme). SFPS65A had an estimated molecular weight of 90kDa and showed αD(20) -74.3288 (c 0.05, H2O). SFPS65A is composed of fucose, galactose, xylose, glucose, glucuronic acid, and mannose in the ratio of 19.23:9.58:6.64:1:6.52:2.57. The structural features of SFPS65A were investigated using composition analysis, methylation analysis, infrared spectrum, nuclear magnetic resonance spectroscopy, and electrospray ionization quadruple time-of-flight tandem mass spectroscopy. Results showed that SFPS65A has a main chain composed of →3)-β-l-Fucp-(1→3,4)-β-l-Fucp-(1→3,4)-β-l-Fucp-(1→ and connected with →3,4)-α-d-GlcAp-(1→, →4)-β-d-Xylp-(1→, →4)-α-d-Galp-(1→, →3,6)-α-d-Manp-(1→ alternately. The branches at O-3 of the fucosyl residue and O-3 of the hexosyl residues may include sulfate, →4)-β-l-Fucp-(1→, β-d-Xylp-(1→, and β-d-Xylp-(1→. SFPS65A exhibited an activity on Alzheimer's disease in vivo in the pharmacological experiments by increasing the cognitive abilities of scopolamine-, ethanol-, and sodium nitrite-treated mice against memory deficits. PMID:26794958
Chemical Structure of Lipid A Isolated from Flavobacterium meningosepticum Lipopolysaccharide
Kato, Hitomi; Haishima, Yuji; Iida, Takatoshi; Tanaka, Akira; Tanamoto, Ken-ichi
The chemical structure of the lipid A of the lipopolysaccharide component isolated from Flavobacterium meningosepticum IFO 12535 was elucidated. Methylation and nuclear magnetic resonance analyses showed that two kinds of hydrophilic backbone exist in the free lipid A: a β (1→6)-linked 2-amino-2-deoxy-d-glucose, which is usually present in enterobacterial lipid A's, and a 2-amino-6-O-(2,3-diamino-2,3-dideoxy-β-d-glucopyranosyl)-2-deoxy-d-glucose, in a molar ratio of 1.00:0.35. Both backbones were α-glycosidically phosphorylated in position 1, and the hydroxyl groups at positions 4, 4′, and 6′ were unsubstituted. Liquid secondary ion-mass spectrometry revealed a pseudomolecular ion at m/z 1673 [M-H]− as a major monophosphoryl lipid A component carrying five acyl groups. Fatty acid analysis showed that the lipid A contained 1 mol each of amide-linked (R)-3-OH iC17:0, ester-linked (R)-3-OH iC15:0, amide-linked (R)-3-O-(iC15:0)-iC17:0, and both amide- and ester-linked (R)-3-OH C16:0. Fatty acid distribution analyses using several mass spectrometry determinations demonstrated that the former two constituents were distributed on positions 2 and 3 of the reducing terminal unit of the backbones and that the latter two were attached to the 2′ and 3′ positions in the nonreducing terminal residue. PMID:9683486
Isolation and Structure of Kurahyne B and Total Synthesis of the Kurahynes.
Okamoto, Shinichiro; Iwasaki, Arihiro; Ohno, Osamu; Suenaga, Kiyotake
Kurahyne B (2), a new analogue of kurahyne (1), was isolated from the marine cyanobacterium Okeania sp. Its gross structure was elucidated based on spectroscopic analyses, and the absolute configuration was established by total synthesis. Kurahyne B (2) inhibited the growth of both HeLa and HL60 cells, with IC50 values of 8.1 and 9.0 μM, respectively. The growth-inhibitory activity of kurahyne B was the same as kurahyne (1). In parallel, the first total synthesis of kurahyne (1) was also achieved. PMID:26539973
Structure elucidation of degradation products of the antibiotic amoxicillin with ion trap MS(n) and accurate mass determination by ESI TOF.
Nägele, Edgar; Moritz, Ralf
Today, it is necessary to identify relevant compounds appearing in discovery and development of new drug substances in the pharmaceutical industry. For that purpose, the measurement of accurate molecular mass and empirical formula calculation is very important for structure elucidation in addition to other available analytical methods. In this work, the identification and confirmation of degradation products in a finished dosage form of the antibiotic drug amoxicillin obtained under stress conditions will be demonstrated. Structure elucidation is performed utilizing liquid chromatography (LC) ion trap MS/MS and MS3 together with accurate mass measurement of the molecular ions and of the collision induced dissociation (CID) fragments by liquid chromatography electro spray ionization time-of-flight mass spectrometry (LC/ESI-TOF). PMID:16099170
LC MS analysis in the e-beam and gamma radiolysis of metoprolol tartrate in aqueous solution: Structure elucidation and formation mechanism of radiolytic products
NASA Astrophysics Data System (ADS)
Slegers, Catherine; Maquille, Aubert; Deridder, Véronique; Sonveaux, Etienne; Habib Jiwan, Jean-Louis; Tilquin, Bernard
E-beam and gamma products from the radiolysis of aqueous solutions of (±)-metoprolol tartrate, saturated in nitrogen, are analyzed by HPLC with on-line mass and UV detectors. The structures of 10 radiolytic products common to e-beam and gamma irradiations are elucidated by comparing their fragmentation pattern to that of (±)-metoprolol. Two of the radiolytic products are also metabolites. Different routes for the formation of the radiolytic products are proposed.
Elucidation of the structure and reaction mechanism of sorghum hydroxycinnamoyltransferase and its structural relationship to other coenzyme a-dependent transferases and synthases.
Walker, Alexander M; Hayes, Robert P; Youn, Buhyun; Vermerris, Wilfred; Sattler, Scott E; Kang, ChulHee
Hydroxycinnamoyltransferase (HCT) from sorghum (Sorghum bicolor) participates in an early step of the phenylpropanoid pathway, exchanging coenzyme A (CoA) esterified to p-coumaric acid with shikimic or quinic acid as intermediates in the biosynthesis of the monolignols coniferyl alcohol and sinapyl alcohol. In order to elucidate the mode of action of this enzyme, we have determined the crystal structures of SbHCT in its apo-form and ternary complex with shikimate and p-coumaroyl-CoA, which was converted to its product during crystal soaking. The structure revealed the roles of threonine-36, serine-38, tyrosine-40, histidine-162, arginine-371, and threonine-384 in catalysis and specificity. Based on the exact chemistry of p-coumaroyl-CoA and shikimic acid in the active site and an analysis of kinetic and thermodynamic data of the wild type and mutants, we propose a role for histidine-162 and threonine-36 in the catalytic mechanism of HCT. Considering the calorimetric data, substrate binding of SbHCT should occur sequentially, with p-coumaroyl-CoA binding prior to the acyl acceptor molecule. While some HCTs can use both shikimate and quinate as an acyl acceptor, SbHCT displays low activity toward quinate. Comparison of the structure of sorghum HCT with the HCT involved in chlorogenic acid synthesis in coffee (Coffea canephora) revealed many shared features. Taken together, these observations explain how CoA-dependent transferases with similar structural features can participate in different biochemical pathways across species. PMID:23624856
Vibration isolation via a scissor-like structured platform
NASA Astrophysics Data System (ADS)
Sun, Xiuting; Jing, Xingjian; Xu, Jian; Cheng, Li
More and more attentions are attracted to the analysis and design of nonlinear vibration control/isolation systems for better isolation performance. In this study, an isolation platform with n-layer scissor-like truss structure is investigated to explore novel design of passive/semi-active/active vibration control/isolation systems and to exploit potential nonlinear benefits in vibration suppression. Due to the special scissor-like structure, the dynamic response of the platform has inherent nonlinearities both in equivalent damping and stiffness characteristics (although only linear components are applied), and demonstrates good loading capacity and excellent equilibrium stability. With the mathematical modeling and analysis of the equivalent stiffness and damping of the system, it is shown that: (a) the structural nonlinearity in the system is very helpful in vibration isolation, (b) both equivalent stiffness and damping characteristics are nonlinear and could be designed/adjusted to a desired nonlinearity by tuning structural parameters, and (c) superior vibration isolation performances (e.g., quasi-zero stiffness characteristics etc.) can be achieved with different structural parameters. This scissor-like truss structure can potentially be employed in different engineering practices for much better vibration isolation or control.
Viscous damping for base isolated structures
Lee, D.; Hussain, S.; Retamal, E.
Seismic Base Isolation can use elastomeric pads, sliding plates or inverted pendulums. Each method can include an energy dissipation means, but only as some kind of hysteretic damping. Hysteretic damping has limitations in terms of energy absorption and may tend to excite higher modes in some cases. It`s possible to avoid these problems with viscous dampers. Viscous damping adds energy dissipation through loads that are 900 out of phase with bending and shear loads so even with damping levels as high as 40% of critical adverse side effects tend to be minimal. This paper presents basic theory of viscous damping, and also describes a sample project. Viscous dampers being built for the new San Bernardino Medical Center reduce both deflections and loads by 50% compared with high damping elastomer base isolation bearings by themselves.
Spectroscopic and structural elucidation of merocyanine dye 2,5-[1-metyl-4-[2-(4-hydroxyphenyl)ethenyl)]piridinium]-hexane tetraphenylborate aggregation processes.
Koleva, Bojidarka B; Stoyanov, Stanimir; Kolev, Tsonko; Petkov, Ivan; Spiteller, Michael
Structural and spectroscopic elucidation of merocyanine dye, 2,5-[1-metyl-4-[2-(4-hydroxyphenyl)ethenyl)]piridinium]-hexane tetraphenylborate, is performed in gas and condense phase by means of solution and solid-state conventional and linear-polarized IR-spectroscopy of oriented colloids in nematic liquid crystal suspension, UV-vis and fluorescence methods, HPLC MS/MS tandem and ESI mass spectrometry, (1)H, (13)C and (1)H-(1)H COSY NMR, TGV and DSC methods. Quantum chemical DFT calculations are performed for structural optimization and spectroscopic properties prediction. PMID:18400554
Spectroscopic and structural elucidation of merocyanine dye 2,5-[1-metyl-4-[2-(4-hydroxyphenyl)ethenyl)]piridinium]-hexane tetraphenylborate. Aggregation processes
NASA Astrophysics Data System (ADS)
Koleva, Bojidarka B.; Stoyanov, Stanimir; Kolev, Tsonko; Petkov, Ivan; Spiteller, Michael
Structural and spectroscopic elucidation of merocyanine dye, 2,5-[1-metyl-4-[2-(4-hydroxyphenyl)ethenyl)]piridinium]-hexane tetraphenylborate, is performed in gas and condense phase by means of solution and solid-state conventional and linear-polarized IR-spectroscopy of oriented colloids in nematic liquid crystal suspension, UV-vis and fluorescence methods, HPLC MS/MS tandem and ESI mass spectrometry, 1H, 13C and 1H- 1H COSY NMR, TGV and DSC methods. Quantum chemical DFT calculations are performed for structural optimization and spectroscopic properties prediction.
Elucidation of Antimicrobial Susceptibility Profiles and Genotyping of Salmonella enterica Isolates from Clinical Cases of Salmonellosis in New Mexico in 2008
Smith, Kenneth P.; George, Jeffy; Cadle, Kathleen M.; Kumar, Sanath; Aragon, Steven J.; Hernandez, Ricardo L.; Jones, Suzanna E.; Floyd, Jody L.; Varela, Manuel F.
In this study, we investigated the antimicrobial susceptibility profiles and the distribution of some well known genetic determinants of virulence in clinical isolates of Salmonella enterica from New Mexico. The minimum inhibitory concentrations (MICs) for various antimicrobials were determined by using the E-test strip method according to CLSI guidelines. Virulence genotyping was performed by polymerase chain reaction (PCR) using primers specific for known virulence genes of Salmonella enterica. Of 15 isolates belonging to 11 different serovars analyzed, one isolate of Salmonella Typhimurium was resistant to multiple drugs namely ampicillin, amoxicillin / clavulanic acid, chloramphenicol and tetracycline, that also harbored class 1 intergron, blaTEM encoding genes for β-lactamase, chloramphenicol acetyl transferase (cat1), plus floR, tet(C) and tet(G). This strain was phage typed as DT104. PCR analysis revealed the presence of invA, hilA, stn, agfA and spvR virulence genes in all the isolates tested. The plasmid-borne pefA gene was absent in 11 isolates, while 5 isolates lacked sopE. One isolate belonging to serogroup E4 (Salmonella Sombre) was devoid of multiple virulence genes pefA, iroB, shdA and sopE. These results demonstrate that clinical Salmonella serotypes from New Mexico used here are predominantly sensitive to multiple antimicrobial agents, but vary in their virulence genotypes. Information on antimicrobial sensitivity and virulence genotypes will help in understanding the evolution and spread of epidemic strains of Salmonella enterica in the region of study. PMID:20514366
Sympatric species distribution, genetic diversity and population structure of Haemonchus isolates from domestic ruminants in Pakistan.
Hussain, Tanveer; Periasamy, Kathiravan; Nadeem, Asif; Babar, Masroor Ellahi; Pichler, Rudolf; Diallo, Adama
Haemonchus species are major gastro-intestinal parasites affecting ruminants across the world. The present study aimed to assess the sympatric species distribution, genetic diversity, population structure and frequency of β-tubulin isotype 1 alleles associated with benzimidazole resistance. Internal transcribed spacer 2 (ITS2) sequences revealed three sympatric species of Haemonchus, H. contortus, H. placei and H. longistipes with 12 distinct genotypes circulating among ruminant hosts in Pakistan. High genetic variability was observed in Pakistani Haemonchus isolates at nicotine amide dehydrogenase subunit 4 (ND4) and cytochrome oxidase subunit 1 (COI) gene loci. Intra-population diversity parameters were higher in H. contortus isolates than H. placei. Phylogenetic analysis of ND4 and COI sequences did not reveal clustering of haplotypes originating from a particular host indicating high rate of gene flow among Haemonchus parasites infecting sheep, goat and cattle in Pakistan. ND4 and COI haplotypes from Pakistan were compared to sequences of Haemonchus isolates from 11 countries to elucidate the population structure. Multidimensional scaling (MDS) plot of pairwise FST derived from 531 ND4 haplotypes revealed clustering together of H. contortus from Pakistan, China, Malaysia and Italy while the isolates from Yemen and United States were found to be genetically distinct. With respect to H. placei, isolates from Pakistan were found to be genetically differentiated from isolates of other countries. The tests for selective neutrality revealed negative D statistics and did not reveal significant deviations in Pakistani Haemonchus populations while significant deviation (P < 0.05) was observed in Brazilian and Chinese H. contortus populations. Median Joining (MJ) network of ND4 haplotypes revealed Yemenese H. contortus being closer to H. placei cluster. β-tubulin isotype 1 genotyping revealed 7.86% frequency of Y allele associated with benzimidazole resistance at F200Y
Stability-indicating HPLC method development and structural elucidation of novel degradation products in posaconazole injection by LC-TOF/MS, LC-MS/MS and NMR.
Yang, Yidi; Zhu, Xi; Zhang, Fei; Li, Wei; Wu, Ying; Ding, Li
Stress testing was carried out under acidic, alkaline, oxidative, thermal and photolytic conditions to evaluate the intrinsic stability of posaconazole injection. A total of four degradation products were detected and the drug was found to be susceptible to oxidative and thermal degradations. Three unknown degradants formed under oxidative stress condition were isolated by preparative HPLC and unambiguously elucidated by LC-TOF/MS, LC-MS/MS, (1)H NMR, (13)C NMR and 2D NMR techniques. Based on the spectrometric and spectroscopic information, these novel degradation products were unequivocally assigned as the N-oxides of posaconazole. Probable mechanisms for the formation of the degradants were proposed. A new and selective HPLC method was developed and validated to separate, detect and quantify all the degradants in posaconazole injection. PMID:27023129
Isolation, crystallization and crystal structure determination of bovine kidney Na(+),K(+)-ATPase.
Gregersen, Jonas Lindholt; Mattle, Daniel; Fedosova, Natalya U; Nissen, Poul; Reinhard, Linda
Na(+),K(+)-ATPase is responsible for the transport of Na(+) and K(+) across the plasma membrane in animal cells, thereby sustaining vital electrochemical gradients that energize channels and secondary transporters. The crystal structure of Na(+),K(+)-ATPase has previously been elucidated using the enzyme from native sources such as porcine kidney and shark rectal gland. Here, the isolation, crystallization and first structure determination of bovine kidney Na(+),K(+)-ATPase in a high-affinity E2-BeF3(-)-ouabain complex with bound magnesium are described. Crystals belonging to the orthorhombic space group C2221 with one molecule in the asymmetric unit exhibited anisotropic diffraction to a resolution of 3.7 Å with full completeness to a resolution of 4.2 Å. The structure was determined by molecular replacement, revealing unbiased electron-density features for bound BeF3(-), ouabain and Mg(2+) ions. PMID:27050261
Short Communication: Elucidation of bacterial community structure on thin-spined porcupine (Chaetomys subspinosus) spines by denaturing.
Bezerra, R A; Giné, G A F; Marques, E L S; Abreu-Tarazi, M F; Rezende, R P; Gaiotto, F A
Thin-spined porcupines (Chaetomys subspinosus) are threatened with extinction and are categorized as vulnerable. This is because of alteration to and loss of their habitat and possible hunting activities in their distribution area. Their spines constitute one of their defense mechanisms, which can be fomites for pathogens to humans. However, little is known about such pathogens. The present study aimed to detect bacteria on spines of C. subspinosus, from the Una Biological Reserve, South of Bahia, northeastern Brazil, by analyzing metagenomic DNA, isolating bacterial culture, using the denaturing gradient gel electrophoresis (DGGE) technique, and sequencing. Six anatomical points were selected for withdrawing spine samples from an individual C. subspinosus. At all sample points, bacteria were detected by bacteriological culture and/or DGGE and sequencing of excised bands. When all samples were combined, standard PCR-DGGE analysis of bacteria present in the spines identified 15 distinct bands, thereby revealing a distinct bacterial community. The main pathogens identified through sequencing were Bacillus cereus, B. thuringiensis, B. anthracis, and B. pumilus. The present study demonstrated the isolation and identification of non-pathogenic and pathogenic bacteria on the spines of C. subspinosus. PMID:26436511
Isolation and Structures of Axistatins 1-3 from the Republic of Palau Marine Sponge Agelas axifera Hentschel1
Pettit, George R.; Tang, Yuping; Zhang, Qingwen; Bourne, Gregory T.; Arm, Christoph A.; Leet, John E.; Knight, John C.; Pettit, Robin K.; Chapuis, Jean-Charles; Doubek, Dennis L.; Ward, Franklin J.; Weber, Christine; Hooper, John N. A.
An investigation begun in 1979 directed at the Republic of Palau marine sponge Agelas axifera Hentschel for cancer cell growth inhibitory constituents subsequently led to the isolation of three new pyrimidine diterpenes designated axistatins 1 (1), 2 (2), and 3 (3), together with the previously reported formamides 4, 5 and agelasine F (6). The structures were elucidated by analysis of 2D-NMR spectra and by HRMS. All of the isolated compounds were found to be moderate inhibitors of cancer cell growth. Axistatins 1–3 (1–3), formamide 4, and agelasine F (6) also exhibited antimicrobial activity. PMID:23410078
Isolation and structures of axistatins 1-3 from the Republic of Palau marine sponge Agelas axifera Hentschel .
Pettit, George R; Tang, Yuping; Zhang, Qingwen; Bourne, Gregory T; Arm, Christoph A; Leet, John E; Knight, John C; Pettit, Robin K; Chapuis, Jean-Charles; Doubek, Dennis L; Ward, Franklin J; Weber, Christine; Hooper, John N A
An investigation begun in 1979 directed at the Republic of Palau marine sponge Agelas axifera Hentschel for cancer cell growth inhibitory constituents subsequently led to the isolation of three new pyrimidine diterpenes designated axistatins 1 (1), 2 (2), and 3 (3), together with the previously reported formamides 4, 5, and agelasine F (6). The structures were elucidated by analysis of 2D-NMR spectra and by HRMS. All of the isolated compounds were found to be moderate inhibitors of cancer cell growth. Axistatins 1-3 (1-3), formamide 4, and agelasine F (6) also exhibited antimicrobial activity. PMID:23410078
Combined (Super 31)P and (Super 1)H NMR Experiments in the Structural Elucidation of Polynuclear Thiolate Complexes
ERIC Educational Resources Information Center
Cerrada, Elena; Laguna, Mariano
A facile synthesis of two gold(I) complexes with 1,2-benzenedithiolate ligand and two different bidentate phosphines are described. A detailed sequence of NMR experiments is suggested to determine the structure of the compounds.
An approximate procedure for solving base-isolated structures
Mohraz, B. . Mechanical Engineering Dept.); Jian, Y.C. )
Dynamic analysis of several shear-type structures with base isolation indicates that the response of these structures follows their fundamental mode shape. Based on this observation, this paper uses an approximate procedure for computing the response of base-isolated structures. The procedure consists of modeling the structure and its base by a two-degree of freedom system, one representing the base and the other the structure. The response from the two-degree of freedom model and mode shapes of the structure are used to compute the response of the structure to earthquake excitation. The approximate procedure is simple, requires substantially less computational time than other methods, and gives results that are in excellent agreement with those from direct integration. Nonlinear properties and nonproportional damping are easily included in the model. Savings of approximately 54--77 percent in computational time result by using the approximate model.
Molecular Mechanism for Conformational Dynamics of Ras·GTP Elucidated from In-Situ Structural Transition in Crystal.
Matsumoto, Shigeyuki; Miyano, Nao; Baba, Seiki; Liao, Jingling; Kawamura, Takashi; Tsuda, Chiemi; Takeda, Azusa; Yamamoto, Masaki; Kumasaka, Takashi; Kataoka, Tohru; Shima, Fumi
Ras•GTP adopts two interconverting conformational states, state 1 and state 2, corresponding to inactive and active forms, respectively. However, analysis of the mechanism for state transition was hampered by the lack of the structural information on wild-type Ras state 1 despite its fundamental nature conserved in the Ras superfamily. Here we solve two new crystal structures of wild-type H-Ras, corresponding to state 1 and state 2. The state 2 structure seems to represent an intermediate of state transition and, intriguingly, the state 1 crystal is successfully derived from this state 2 crystal by regulating the surrounding humidity. Structural comparison enables us to infer the molecular mechanism for state transition, during which a wide range of hydrogen-bonding networks across Switch I, Switch II and the α3-helix interdependently undergo gross rearrangements, where fluctuation of Tyr32, translocation of Gln61, loss of the functional water molecules and positional shift of GTP play major roles. The NMR-based hydrogen/deuterium exchange experiments also support this transition mechanism. Moreover, the unveiled structural features together with the results of the biochemical study provide a new insight into the physiological role of state 1 as a stable pool of Ras•GTP in the GDP/GTP cycle of Ras. PMID:27180801
Molecular Mechanism for Conformational Dynamics of Ras·GTP Elucidated from In-Situ Structural Transition in Crystal
Matsumoto, Shigeyuki; Miyano, Nao; Baba, Seiki; Liao, Jingling; Kawamura, Takashi; Tsuda, Chiemi; Takeda, Azusa; Yamamoto, Masaki; Kumasaka, Takashi; Kataoka, Tohru; Shima, Fumi
Ras•GTP adopts two interconverting conformational states, state 1 and state 2, corresponding to inactive and active forms, respectively. However, analysis of the mechanism for state transition was hampered by the lack of the structural information on wild-type Ras state 1 despite its fundamental nature conserved in the Ras superfamily. Here we solve two new crystal structures of wild-type H-Ras, corresponding to state 1 and state 2. The state 2 structure seems to represent an intermediate of state transition and, intriguingly, the state 1 crystal is successfully derived from this state 2 crystal by regulating the surrounding humidity. Structural comparison enables us to infer the molecular mechanism for state transition, during which a wide range of hydrogen-bonding networks across Switch I, Switch II and the α3-helix interdependently undergo gross rearrangements, where fluctuation of Tyr32, translocation of Gln61, loss of the functional water molecules and positional shift of GTP play major roles. The NMR-based hydrogen/deuterium exchange experiments also support this transition mechanism. Moreover, the unveiled structural features together with the results of the biochemical study provide a new insight into the physiological role of state 1 as a stable pool of Ras•GTP in the GDP/GTP cycle of Ras. PMID:27180801
Mitochondrial Structure and Function Are Disrupted by Standard Isolation Methods
Picard, Martin; Taivassalo, Tanja; Ritchie, Darmyn; Wright, Kathryn J.; Thomas, Melissa M.; Romestaing, Caroline; Hepple, Russell T.
Mitochondria regulate critical components of cellular function via ATP production, reactive oxygen species production, Ca2+ handling and apoptotic signaling. Two classical methods exist to study mitochondrial function of skeletal muscles: isolated mitochondria and permeabilized myofibers. Whereas mitochondrial isolation removes a portion of the mitochondria from their cellular environment, myofiber permeabilization preserves mitochondrial morphology and functional interactions with other intracellular components. Despite this, isolated mitochondria remain the most commonly used method to infer in vivo mitochondrial function. In this study, we directly compared measures of several key aspects of mitochondrial function in both isolated mitochondria and permeabilized myofibers of rat gastrocnemius muscle. Here we show that mitochondrial isolation i) induced fragmented organelle morphology; ii) dramatically sensitized the permeability transition pore sensitivity to a Ca2+ challenge; iii) differentially altered mitochondrial respiration depending upon the respiratory conditions; and iv) dramatically increased H2O2 production. These alterations are qualitatively similar to the changes in mitochondrial structure and function observed in vivo after cellular stress-induced mitochondrial fragmentation, but are generally of much greater magnitude. Furthermore, mitochondrial isolation markedly altered electron transport chain protein stoichiometry. Collectively, our results demonstrate that isolated mitochondria possess functional characteristics that differ fundamentally from those of intact mitochondria in permeabilized myofibers. Our work and that of others underscores the importance of studying mitochondrial function in tissue preparations where mitochondrial structure is preserved and all mitochondria are represented. PMID:21512578
Elucidating Common Structural Features of Human Pathogenic Variations Using Large-Scale Atomic-Resolution Protein Networks
Das, Jishnu; Lee, Hao Ran; Sagar, Adithya; Fragoza, Robert; Liang, Jin; Wei, Xiaomu; Wang, Xiujuan; Mort, Matthew; Stenson, Peter D.; Cooper, David N.; Yu, Haiyuan
With the rapid growth of structural genomics, numerous protein crystal structures have become available. However, the parallel increase in knowledge of the functional principles underlying biological processes, and more specifically the underlying molecular mechanisms of disease, has been less dramatic. This notwithstanding, the study of complex cellular networks has made possible the inference of protein functions on a large scale. Here, we combine the scale of network systems biology with the resolution of traditional structural biology to generate a large-scale atomic-resolution interactome-network comprising 3,398 interactions between 2,890 proteins with a well-defined interaction interface and interface residues for each interaction. Within the framework of this atomic-resolution network, we have explored the structural principles underlying variations causing human-inherited disease. We find that in-frame pathogenic variations are enriched at both the interface and in the interacting domain, suggesting that variations not only at interface "hot-spots," but in the entire interacting domain can result in alterations of interactions. Further, the sites of pathogenic variations are closely related to the biophysical strength of the interactions they perturb. Finally, we show that biochemical alterations consequent to these variations are considerably more disruptive than evolutionary changes, with the most significant alterations at the protein interaction interface. PMID:24599843
Structural Elucidation of the Cyclization Mechanism of α-1,6-Glucan by Bacillus circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase*
Suzuki, Nobuhiro; Fujimoto, Zui; Kim, Young-Min; Momma, Mitsuru; Kishine, Naomi; Suzuki, Ryuichiro; Suzuki, Shiho; Kitamura, Shinichi; Kobayashi, Mikihiko; Kimura, Atsuo; Funane, Kazumi
Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase belongs to the glycoside hydrolase family 66 and catalyzes an intramolecular transglucosylation reaction that produces cycloisomaltooligosaccharides from dextran. The crystal structure of the core fragment from Ser-39 to Met-738 of B. circulans T-3040 cycloisomaltooligosaccharide glucanotransferase, devoid of its N-terminal signal peptide and C-terminal nonconserved regions, was determined. The structural model contained one catalytic (β/α)8-barrel domain and three β-domains. Domain N with an immunoglobulin-like β-sandwich fold was attached to the N terminus; domain C with a Greek key β-sandwich fold was located at the C terminus, and a carbohydrate-binding module family 35 (CBM35) β-jellyroll domain B was inserted between the 7th β-strand and the 7th α-helix of the catalytic domain A. The structures of the inactive catalytic nucleophile mutant enzyme complexed with isomaltohexaose, isomaltoheptaose, isomaltooctaose, and cycloisomaltooctaose revealed that the ligands bound in the catalytic cleft and the sugar-binding site of CBM35. Of these, isomaltooctaose bound in the catalytic site extended to the second sugar-binding site of CBM35, which acted as subsite −8, representing the enzyme·substrate complex when the enzyme produces cycloisomaltooctaose. The isomaltoheptaose and cycloisomaltooctaose bound in the catalytic cleft with a circular structure around Met-310, representing the enzyme·product complex. These structures collectively indicated that CBM35 functions in determining the size of the product, causing the predominant production of cycloisomaltooctaose by the enzyme. The canonical sugar-binding site of CBM35 bound the mid-part of isomaltooligosaccharides, indicating that the original function involved substrate binding required for efficient catalysis. PMID:24616103
Elucidation of molecular structures at buried polymer interfaces and biological interfaces using sum frequency generation vibrational spectroscopy
Zhang, Chi; Myers, John; Chen, Zhan
Sum frequency generation (SFG) vibrational spectroscopy has been developed into an important technique to study surfaces and interfaces. It can probe buried interfaces in situ and provide molecular level structural information such as the presence of various chemical moieties, quantitative molecular functional group orientation, and time dependent kinetics or dynamics at such interfaces. This paper focuses on these three most important advantages of SFG and reviews some of the recent progress in SFG studies on interfaces related to polymer materials and biomolecules. The results discussed here demonstrate that SFG can provide important molecular structural information of buried interfaces in situ and in real time, which is difficult to obtain by other surface sensitive analytical techniques. PMID:23710244
Elucidation of the surface structure-selectivity relationship in ethanol electro-oxidation over platinum by density functional theory.
Sheng, Tian; Lin, Wen-Feng; Sun, Shi-Gang
We have successfully built a general framework to comprehend the structure-selectivity relationship in ethanol electrooxidation on platinum by density functional theory calculations. Based on the reaction mechanisms on three basal planes and five stepped surfaces, it was found that only (110) and n(111) × (110) sites can enhance CO2 selectivity but other non-selective step sites are more beneficial to activity. PMID:27181461
Use of XAS for the elucidation of metal structure and function: applications to nickel biochemistry, molecular toxicology, and carcinogenesis.
Carrington, Paul E; Al-Mjeni, Faizah; Zoroddu, Maria A; Costa, Max; Maroney, Michael J
Nickel has been shown to be an essential trace element involved in the metabolism of several species of bacteria, archea, and plants. In these organisms, nickel is involved in enzymes that catalyze both non-redox (e.g., urease, glyoxalase I) and redox (e.g., hydrogenase, carbon monoxide dehydrogenase, superoxide dismutase) reactions, and proteins involved in the transport, storage, metallocenter assembly, and regulation of nickel concentration have evolved. Studies of structure/function relationships in nickel biochemistry reveal that cysteine ligands are used to stabilize the Ni(III/II) redox couple. Certain nickel compounds have also been shown to be potent human carcinogens. A likely target for carcinogenic nickel is nuclear histone proteins. Here we present X-ray absorption spectroscopic studies of a model Ni peptide designed to help characterize the structure of the nickel complexes formed with histones and place them in the context of nickel structure/function relationships, to gain insights into the molecular mechanism of nickel carcinogenesis. PMID:12426116
Adsorption and Reaction of Acetaldehyde on Shape-Controlled CeO2 Nanocrystals: Elucidation of Structure-function Relationships
Mann, Amanda K; Wu, Zili; Calaza, Florencia; Overbury, Steven {Steve} H
CeO2 cubes with {100} facets, octahedra with {111} facets, and wires with highly defective structures were utilized to probe the structure-dependent reactivity of acetaldehyde. Using temperature-programmed desorption (TPD), temperature-programmed surface reactions (TPSR), and in situ infrared spectroscopy it was found that acetaldehyde desorbs unreacted or undergoes reduction, coupling, or C-C bond scission reactions depending on the surface structure of CeO2. Room temperature FTIR indicates that acetaldehyde binds primarily as 1-acetaldehyde on the octahedra, in a variety of conformations on the cubes, including coupling products and acetate and enolate species, and primarily as coupling products on the wires. The percent consumption of acetaldehyde follows the order of wires > cubes > octahedra. All the nanoshapes produce the coupling product crotonaldehyde; however, the selectivity to produce ethanol follows the order wires cubes >> octahedra. The selectivity and other differences can be attributed to the variation in the basicity of the surfaces, defects densities, coordination numbers of surface atoms, and the reducibility of the nanoshapes.
Nano-Structural Elucidation in Carbon Black Loaded NR Vulcanizate by 3D-TEM and In Situ WAXD Measurements
Ikeda,Y.; Kato, A.; Shimanuki, J.; Kohjiya, S.; Tosaka, M.; Poompradub, S.; Toki, S.; Hsiao, B.
Three dimensional (3D) visualization of nanometer structure of carbon black dispersion in rubbery matrix has successfully been studied and reported in this paper. Use of 3D-TEM, which is computerized tomography combined with transmission electron microscopy (TEM), enabled us to reconstruct 3D images of carbon black aggregates in natural rubber (NR) matrix. The TEM measurements were conducted by a bright-field method on thin samples without any electron staining. The sample was subject to uni-axial tilting (+65 degree to -65 degree with 2 degree increment) in the sample chamber, and 66 TEM images were taken on each sample. These TEM images were used for computerized tomography to reconstruct the 3D image. This technique is designated as 3D-TEM. The nano-structural features observed by 3D-TEM were in conformity with the electron-conductivity results, and the percolation behavior was recognized. These results were further supplemented by in situ wide-angle X-ray diffraction (WAXD), i.e., simultaneous WAXD and tensile measurements on the sample to observe the strain-induced crystallization in NR vulcanizate. Upon tensile elongation, the crystallization was clearly observed in WAXD in the presence of carbon black, and it contributed to the tensile properties. In order to understand the performances of filled NR vulcanizates, it surely is necessary to know the structural states of the mixed nano-filler and the crystallites produced upon elongation.
AptaTRACE Elucidates RNA Sequence-Structure Motifs from Selection Trends in HT-SELEX Experiments.
Dao, Phuong; Hoinka, Jan; Takahashi, Mayumi; Zhou, Jiehua; Ho, Michelle; Wang, Yijie; Costa, Fabrizio; Rossi, John J; Backofen, Rolf; Burnett, John; Przytycka, Teresa M
Aptamers, short RNA or DNA molecules that bind distinct targets with high affinity and specificity, can be identified using high-throughput systematic evolution of ligands by exponential enrichment (HT-SELEX), but scalable analytic tools for understanding sequence-function relationships from diverse HT-SELEX data are not available. Here we present AptaTRACE, a computational approach that leverages the experimental design of the HT-SELEX protocol, RNA secondary structure, and the potential presence of many secondary motifs to identify sequence-structure motifs that show a signature of selection. We apply AptaTRACE to identify nine motifs in C-C chemokine receptor type 7 targeted by aptamers in an in vitro cell-SELEX experiment. We experimentally validate two aptamers whose binding required both sequence and structural features. AptaTRACE can identify low-abundance motifs, and we show through simulations that, because of this, it could lower HT-SELEX cost and time by reducing the number of selection cycles required. PMID:27467247
Structure Elucidation of Poly-Faldaprevir: Polymer Backbone Solved Using Solid-State and Solution Nuclear Magnetic Resonance Spectroscopy.
Gonnella, Nina C; Busacca, Carl A; Zhang, Li; Saha, Anjan; Wu, Jiang-Ping; Li, Guisheng; Davis, Mark; Offerdahl, Thomas; Jones, Paul-James; Herfurth, Lars; Reddig, Tim; Wagner, Klaus; Niemann, Michael; Werthmann, Ulrike; Grupe, Julia; Roos, Helmut; Reckzügel, Gaby; Ding, Andreas
A large-scale synthesis of the hepatitis C virus drug Faldaprevir revealed precipitation of an unknown insoluble solid from methanol solutions of the drug substance. The unknown impurity was determined to be a polymer of Faldaprevir based on analytical methods that included size exclusion chromatography in combination with electrospray ionization mass spectrometry, solution nuclear magnetic resonance (NMR), matrix-assisted laser desorption ionization-time of flight, ultracentrifugation, elemental analysis, and sodium quantitation by atom absorption spectroscopy. Structure elucidation of the polymeric backbone was achieved using solid-state NMR cross-polarization/magic angle spinning (CP/MAS), cross polarization-polarization inversion, and heteronuclear correlation (HETCOR) experiments. The polymerization was found to occur at the vinyl cyclopropane via a likely free radical initiation mechanism. Full proton and carbon chemical shift assignments of the polymer were obtained using solution NMR spectroscopy. The polymer structure was corroborated with chemical synthesis of the polymer and solution NMR analysis. PMID:27238486
RNase R mutants elucidate the catalysis of structured RNA: RNA-binding domains select the RNAs targeted for degradation.
Matos, Rute Gonçalves; Barbas, Ana; Arraiano, Cecília Maria
The RNase II superfamily is a ubiquitous family of exoribonucleases that are essential for RNA metabolism. RNase II and RNase R degrade RNA in the 3'-->5' direction in a processive and sequence-independent manner. However, although RNase R is capable of degrading highly structured RNAs, the RNase II activity is impaired by the presence of secondary structures. RNase II and RNase R share structural properties and have a similar modular domain organization. The eukaryotic RNase II homologue, Rrp44/Dis3, is the catalytic subunit of the exosome, one of the most important protein complexes involved in the maintenance of the correct levels of cellular RNAs. In the present study, we constructed truncated RNase II and RNase R proteins and point mutants and characterized them regarding their exoribonucleolytic activity and RNA-binding ability. We report that Asp280 is crucial for RNase R activity without affecting RNA binding. When Tyr324 was changed to alanine, the final product changed from 2 to 5 nt in length, showing that this residue is responsible for setting the end-product. We have shown that the RNB domain of RNase II has catalytic activity. The most striking result is that the RNase R RNB domain itself degrades double-stranded substrates even in the absence of a 3'-overhang. Moreover, we have demonstrated for the first time that the substrate recognition of RNase R depends on the RNA-binding domains that target the degradation of RNAs that are 'tagged' by a 3'-tail. These results can have important implications for the study of poly(A)-dependent RNA degradation mechanisms. PMID:19630750
Structural, Spectroscopic, And Theoretical Elucidation of a Redox-Active Pincer-Type Ancillary Applied in Catalysis
Adhikari, D.; Mossin, S.; Basuli, F.; Huffman, J.C.; Szilagyi, R.K.; Meyer, K.; Mindiola, D.J.
Pincer-type ligands are believed to be very robust scaffolds that can support multifarious functionalities as well as highly reactive metal motifs applied in organometallic chemistry, especially in the realm of catalysis. In this paper, we describe the redox and, therefore, noninnocent behavior of a PNP (PNP{sup -} = N[2-P(CHMe{sub 2}){sub 2}-4-methylphenyl]{sub 2}) pincer ancillary bound to nickel. A combination of structural, spectroscopic, and theoretical techniques suggests that this type of framework can house an electron hole when coordinated to Ni(II).
Elucidating the native sources of an invasive tree species, Acacia pycnantha, reveals unexpected native range diversity and structure
Ndlovu, Joice; Richardson, David M.; Wilson, John R. U.; O'Leary, Martin; Le Roux, Johannes J.
Background and Aims Understanding the introduction history of invasive plant species is important for their management and identifying effective host-specific biological control agents. However, uncertain taxonomy, intra- and interspecific hybridization, and cryptic speciation may obscure introduction histories, making it difficult to identify native regions to explore for host-specific agents. The overall aim of this study was to identify the native source populations of Acacia pycnantha, a tree native to south-eastern Australia and invasive in South Africa, Western Australia and Portugal. Using a phylogeographical approach also allowed an exploration of the historical processes that have shaped the genetic structure of A. pycnantha in its native range. Methods Nuclear (nDNA) and plastid DNA sequence data were used in network and tree-building analyses to reconstruct phylogeographical relationships between native and invasive A. pycnantha populations. In addition, mismatch distributions, relative rates and Bayesian analyses were used to infer recent demographic processes and timing of events in Australia that led to population structure and diversification. Key Results The plastid network indicated that Australian populations of A. pycnantha are geographically structured into two informally recognized lineages, the wetland and dryland forms, whereas the nuclear phylogeny showed little geographical structure between these two forms. Moreover, the dryland form of A. pycnantha showed close genetic similarity to the wetland form based on nDNA sequence data. Hybrid zones may explain these findings, supported here by incongruent phylogenetic placement of some of these taxa between nuclear and plastid genealogies. Conclusions It is hypothesized that habitat fragmentation due to cycles of aridity inter-dispersed with periods of abundant rainfall during the Pleistocene (approx. 100 kya) probably gave rise to native dryland and wetland forms of A. pycnantha. Although the
Seismic Response Analysis and Design of Structure with Base Isolation
Rosko, Peter
The paper reports the study on seismic response and energy distribution of a multi-story civil structure. The nonlinear analysis used the 2003 Bam earthquake acceleration record as the excitation input to the structural model. The displacement response was analyzed in time domain and in frequency domain. The displacement and its derivatives result energy components. The energy distribution in each story provides useful information for the structural upgrade with help of added devices. The objective is the structural displacement response minimization. The application of the structural seismic response research is presented in base-isolation example.
Cobalt-Catalyzed [2π + 2π] Cycloadditions of Alkenes: Scope, Mechanism, and Elucidation of Electronic Structure of Catalytic Intermediates.
Schmidt, Valerie A; Hoyt, Jordan M; Margulieux, Grant W; Chirik, Paul J
Aryl-substituted bis(imino)pyridine cobalt dinitrogen compounds, ((R)PDI)CoN2, are effective precatalysts for the intramolecular [2π + 2π] cycloaddition of α,ω-dienes to yield the corresponding bicyclo[3.2.0]heptane derivatives. The reactions proceed under mild thermal conditions with unactivated alkenes, tolerating both amine and ether functional groups. The overall second order rate law for the reaction, first order with respect to both the cobalt precatalyst and the substrate, in combination with electron paramagnetic resonance (EPR) spectroscopic studies established the catalyst resting state as dependent on the identity of the precatalyst and diene substrate. Planar S = ½ κ(3)-bis(imino)pyridine cobalt alkene and tetrahedral κ(2)-bis(imino)pyridine cobalt diene complexes were observed by EPR spectroscopy and in the latter case structurally characterized. The hemilabile chelate facilitates conversion of a principally ligand-based singly occupied molecular orbital (SOMO) in the cobalt dinitrogen and alkene compounds to a metal-based SOMO in the diene intermediates, promoting C-C bond-forming oxidative cyclization. Structure-activity relationships on bis(imino)pyridine substitution were also established with 2,4,6-tricyclopentyl-substituted aryl groups, resulting in optimized catalytic [2π + 2π] cycloaddition. The cyclopentyl groups provide a sufficiently open metal coordination sphere that encourages substrate coordination while remaining large enough to promote a challenging, turnover-limiting C(sp(3))-C(sp(3)) reductive elimination. PMID:26030841
Structural elucidation of the hormonal inhibition mechanism of the bile acid cholate on human carbonic anhydrase II
Boone, Christopher D.; Tu, Chingkuang; McKenna, Robert
The carbonic anhydrases (CAs) are a family of mostly zinc metalloenzymes that catalyze the reversible hydration/dehydration of CO2 into bicarbonate and a proton. Human isoform CA II (HCA II) is abundant in the surface epithelial cells of the gastric mucosa, where it serves an important role in cytoprotection through bicarbonate secretion. Physiological inhibition of HCA II via the bile acids contributes to mucosal injury in ulcerogenic conditions. This study details the weak biophysical interactions associated with the binding of a primary bile acid, cholate, to HCA II. The X-ray crystallographic structure determined to 1.54 Å resolution revealed that cholate does not make any direct hydrogen-bond interactions with HCA II, but instead reconfigures the well ordered water network within the active site to promote indirect binding to the enzyme. Structural knowledge of the binding interactions of this nonsulfur-containing inhibitor with HCA II could provide the template design for high-affinity, isoform-specific therapeutic agents for a variety of diseases/pathological states, including cancer, glaucoma, epilepsy and osteoporosis. PMID:24914985
Templated Atom-Precise Galvanic Synthesis and Structure Elucidation of a [Ag24Au(SR)18](-) Nanocluster.
Bootharaju, Megalamane S; Joshi, Chakra P; Parida, Manas R; Mohammed, Omar F; Bakr, Osman M
Synthesis of atom-precise alloy nanoclusters with uniform composition is challenging when the alloying atoms are similar in size (for example, Ag and Au). A galvanic exchange strategy has been devised to produce a compositionally uniform [Ag24Au(SR)18](-) cluster (SR: thiolate) using a pure [Ag25(SR)18](-) cluster as a template. Conversely, the direct synthesis of Ag24Au cluster leads to a mixture of [Ag(25-x)Au(x)(SR)18](-), x=1-8. Mass spectrometry and crystallography of [Ag24Au(SR)18](-) reveal the presence of the Au heteroatom at the Ag25 center, forming Ag24Au. The successful exchange of the central Ag of Ag25 with Au causes perturbations in the Ag25 crystal structure, which are reflected in the absorption, luminescence, and ambient stability of the particle. These properties are compared with those of Ag25 and Ag24Pd clusters with same ligand and structural framework, providing new insights into the modulation of cluster properties with dopants at the single-atom level. PMID:26611172
Structure elucidation of a non-branched and entangled heteropolysaccharide from Tremella sanguinea Peng and its antioxidant activity.
Wang, Zhaojing; Zeng, Yawei; Luo, Dianhui
A crude polysaccharide was extracted from the edible fungi Tremella sanguinea Peng, and a polysaccharide TSP-II (31.56%) was separated and purified from the crude polysaccharide. TSP-II was a homogeneous polysaccharide by the high-performance size-exclusion chromatography (HPSEC), had a molecular weight of 356kD and consisted mainly of mannose, xylose, galactose and glucose at a molar ratio 5.9:2.4:1:1.1. The structural assignment of TSP-II was carried out using fourier transform infrared spectroscopy (FTIR) analysis, periodate oxidation-smith degradation, partial hydrolysis with acid, methylation analysis and nuclear magnetic resonance (NMR) studies, and the repeating unit of TSP-II was thus determined. The result indicated that →3)-α-d-Manp-(1→, →2)-α-d-Xylp-(1→, →6)-α-d-Glcp-(1→ and →3)-α-d-Galp-(1→ formed the major components of the main-chain structure, and TSP-II was a non-branched polysaccharide. Transmission electron microscopy (TEM) analysis revealed a primary non-branched and entangled state in its microstructure. TSP-II had higher scavenging activities on hydroxyl radical (EC50=0.088mg/ml) and superoxide radical (EC50=0.127mg/ml) than Vitamin C (Vc). PMID:27516247
In situ analysis and structural elucidation of sainfoin (Onobrychis viciifolia) tannins for high-throughput germplasm screening.
Gea, An; Stringano, Elisabetta; Brown, Ron H; Mueller-Harvey, Irene
A rapid thiolytic degradation and cleanup procedure was developed for analyzing tannins directly in chlorophyll-containing sainfoin ( Onobrychis viciifolia ) plants. The technique proved suitable for complex tannin mixtures containing catechin, epicatechin, gallocatechin, and epigallocatechin flavan-3-ol units. The reaction time was standardized at 60 min to minimize the loss of structural information as a result of epimerization and degradation of terminal flavan-3-ol units. The results were evaluated by separate analysis of extractable and unextractable tannins, which accounted for 63.6-113.7% of the in situ plant tannins. It is of note that 70% aqueous acetone extracted tannins with a lower mean degree of polymerization (mDP) than was found for tannins analyzed in situ. Extractable tannins had between 4 and 29 lower mDP values. The method was validated by comparing results from individual and mixed sample sets. The tannin composition of different sainfoin accessions covered a range of mDP values from 16 to 83, procyanidin/prodelphinidin (PC/PD) ratios from 19.2/80.8 to 45.6/54.4, and cis/trans ratios from 74.1/25.9 to 88.0/12.0. This is the first high-throughput screening method that is suitable for analyzing condensed tannin contents and structural composition directly in green plant tissue. PMID:21175139
Cryo-EM structures elucidate neutralizing mechanisms of anti-chikungunya human monoclonal antibodies with therapeutic activity
Long, Feng; Fong, Rachel H.; Austin, Stephen K.; Chen, Zhenguo; Klose, Thomas; Fokine, Andrei; Liu, Yue; Porta, Jason; Sapparapu, Gopal; Akahata, Wataru; Doranz, Benjamin J.; Crowe, James E.; Diamond, Michael S.; Rossmann, Michael G.
Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that causes severe acute and chronic disease in humans. Although highly inhibitory murine and human monoclonal antibodies (mAbs) have been generated, the structural basis of their neutralizing activity remains poorly characterized. Here, we determined the cryo-EM structures of chikungunya virus-like particles complexed with antibody fragments (Fab) of two highly protective human mAbs, 4J21 and 5M16, that block virus fusion with host membranes. Both mAbs bind primarily to sites within the A and B domains, as well as to the B domain's β-ribbon connector of the viral glycoprotein E2. The footprints of these antibodies on the viral surface were consistent with results from loss-of-binding studies using an alanine scanning mutagenesis-based epitope mapping approach. The Fab fragments stabilized the position of the B domain relative to the virus, particularly for the complex with 5M16. This finding is consistent with a mechanism of neutralization in which anti-CHIKV mAbs that bridge the A and B domains impede movement of the B domain away from the underlying fusion loop on the E1 glycoprotein and therefore block the requisite pH-dependent fusion of viral and host membranes. PMID:26504196
Characterization of the catalytic disulfide bond in E. coli 4-thiouridine synthetase to elucidate its functional quaternary structure.
Veerareddygari, Govardhan Reddy; Klusman, Thomas C; Mueller, Eugene G
4-Thiouridine at position 8 in prokaryotic tRNA serves as a photosensor for near-UV light, and the posttranscriptional conversion of uridine to 4-thiouridine is catalyzed by the 4-thiouridine synthetases (s(4) US, also named ThiI), which fall into two classes that differ in the presence of a C-terminal rhodanese homology domain. A cysteine residue in this domain first bears a persulfide group and then forms a disulfide bond with a cysteine residue that is conserved in both classes of s(4) US. Recent crystal structures suggest that s(4) US dimerizes in the presence of RNA substrate with domains from each subunit contributing to the binding and reaction of one RNA molecule, which raises the question of whether the catalytic disulfide bond in the longer class of s(4) US is formed within or between subunits. The E. coli enzyme is the best-characterized member of the longer class of s(4) US, and it was examined after quantitative installation of the disulfide bond during a single catalytic turnover. Gel electrophoresis and proteolysis/MALDI-MS results strongly imply that the disulfide bond forms within a single subunit, which provides a vital constraint for the structural modeling of the class of s(4) US with an appended rhodanese homology domain and the design and interpretation of experiments to probe the dynamics of the domains during catalysis. PMID:27293139
Metal Interactions at the Biochar-Water Interface: Energetics and Structure-Sorption Relationships Elucidated by Flow Adsorption Microcalorimetry
Harvey, Omar R.; Herbert, Bruce; Rhue, Roy D.; Kuo, Li-Jung
Interest in biochars and their role in the biogeochemical cycling of metals have increased in recent years. However, a systematic understanding of the mechanisms involved in biochar-metal interactions and conditions under which a given mechanism is predominant is still needed. We used flow adsorption micro-calorimetry to study structure-sorption relationships between twelve plant-derived biochars and two metals of different ionization potential (Ip). Biochar structure influenced the amount of K+ (Ip = 419 kJ mol-1) or Cd(II) (Ip = 868 kJ mol-17 ) sorption but had no effect on the mechanism of sorption. Irrespective of the biochar, K+ sorption was exothermic, surface-controlled and occurred via an ion-exchange mechanism on negatively- charged sites with molar heats of adsorption (_Hads) of -4 kJ mol-1 on wood versus -8 kJ mol-1 on grass biochars. In contrast, Cd(II) sorption was endothermic and favored surface complexation on uncharged biochar surfaces with _Hads of around +17 kJ mol-1. Cadmium sorption transitioned from surface- to diffusion-controlled on biochars formed at ≥ 350 oC and _Hads for Cd(II) sorption was the same on grass and wood biochars. We concluded that, in general, metals with lower Ip favor electrostatic interactions with biochars, while metals of higher Ip favor more covalent-like interactions.
Cryo-EM structures elucidate neutralizing mechanisms of anti-chikungunya human monoclonal antibodies with therapeutic activity.
Long, Feng; Fong, Rachel H; Austin, Stephen K; Chen, Zhenguo; Klose, Thomas; Fokine, Andrei; Liu, Yue; Porta, Jason; Sapparapu, Gopal; Akahata, Wataru; Doranz, Benjamin J; Crowe, James E; Diamond, Michael S; Rossmann, Michael G
Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that causes severe acute and chronic disease in humans. Although highly inhibitory murine and human monoclonal antibodies (mAbs) have been generated, the structural basis of their neutralizing activity remains poorly characterized. Here, we determined the cryo-EM structures of chikungunya virus-like particles complexed with antibody fragments (Fab) of two highly protective human mAbs, 4J21 and 5M16, that block virus fusion with host membranes. Both mAbs bind primarily to sites within the A and B domains, as well as to the B domain's β-ribbon connector of the viral glycoprotein E2. The footprints of these antibodies on the viral surface were consistent with results from loss-of-binding studies using an alanine scanning mutagenesis-based epitope mapping approach. The Fab fragments stabilized the position of the B domain relative to the virus, particularly for the complex with 5M16. This finding is consistent with a mechanism of neutralization in which anti-CHIKV mAbs that bridge the A and B domains impede movement of the B domain away from the underlying fusion loop on the E1 glycoprotein and therefore block the requisite pH-dependent fusion of viral and host membranes. PMID:26504196
Mass-spectrometric structure elucidation of dog bile azopigments as the acyl glycosides of glucopyranose and xylopyranose
Compernolle, F.; Van Hees, G. P.; Fevery, J.; Heirwegh, K. P. M.
1. The structures of the α2- and α3-azopigments, prepared by diazotization of dog bile with ethyl anthranilate, were shown by mass spectrometry and g.l.c. to correspond to azobilirubin β-d-xylopyranoside and azobilirubin β-d-glucopyranoside respectively. 2. Both azopigments consist of a mixture of two methyl vinyl isomers having structures (IIIa) and (IIIb) for the α2-azopigment and structures (IVa) and (IVb) for the α3-azopigment. Separation of methyl vinyl isomers was obtained by t.l.c. or column chromatography performed on the acetylated azopigments. Hydrolysis of the less polar acetates derived from components (IIIa) and (IVa) gave rise to the azopigment (Ia), whereas hydrolysis of the more polar acetates derived from components (IIIb) and (IVb) gave rise to the azopigment acid (Ib). The positions of methyl and vinyl substituents in compounds (Ia) and (Ib) were assigned on the basis of their n.m.r. spectra. 3. Molecular ions in the mass spectra of the trimethylsilyl and acetyl derivatives of the azopigments indicated the presence of a pentose and a hexose conjugating sugar. 4. The ester functions linking the sugars to the propionic acid side chain of azobilirubin were demonstrated by ammonolysis and identification of the amide of azobilirubin as the aglycone derivative. 5. The sugar moieties were shown to occur as xylopyranose (α2) and glucopyranose (α3), bound at C-1, by application of a sequence of reactions performed on a micro-scale. The sugar hydroxyl groups were acetylated and the 1-acyl aglycone removed selectively by treatment with hydrogen bromide in acetic acid. Hydrolysis of the 1-bromo sugar acetates followed by acetylation afforded the α- and β-xylopyranose tetra-acetates and α- and β-glucopyranose penta-acetates, identified by a combination of g.l.c. and mass spectrometry. 6. The validity of this degradation scheme was confirmed (a) by g.l.c.–mass spectrometry identification of the α- and β-1-propionyl derivatives of glucopyranose
Synthesis, spectral analysis, structural elucidation and quantum chemical studies of (E)-methyl-4-[(2-phenylhydrazono)methyl]benzoate
NASA Astrophysics Data System (ADS)
Şahin, Zarife Sibel; Şenöz, Hülya; Tezcan, Habibe; Büyükgüngör, Orhan
The title compound, (E)-methyl-4-[(2-phenylhydrazono)methyl]benzoate, (I), (C15H14N2O2), has been synthesized by condensation reaction of methyl-4-formylbenzoate and phenylhydrazine. The compound has been characterized by elemental analysis, IR, 1H NMR, 13C NMR, UV-Vis spectroscopies and single crystal X-ray diffraction techniques. Optimized molecular structure, harmonic vibrational frequencies, 1H and 13C NMR chemical shifts have been investigated by B3LYP/6-31G(d,p) method using density functional theory (DFT). Global chemical reactivity descriptors, natural population analysis (NPA), thermodynamic and non-linear optical (NLO) properties have also been studied. The energetic behavior of the compound has been examined in solvent media using the integral equation formalism polarizable continuum model (IEF-PCM).
Designer Reagents for Mass Spectrometry-Based Proteomics: Clickable Cross-Linkers for Elucidation of Protein Structures and Interactions
Sohn, Chang Ho; Agnew, Heather D.; Lee, J. Eugene; Sweredoski, Michael J.; Graham, Robert L.J.; Smith, Geoffrey T.; Hess, Sonja; Czerwieniec, Gregg; Loo, Joseph A.; Heath, James R.; Deshaies, Raymond J.; Beauchamp, J. L.
We present novel homobifunctional amine-reactive clickable cross-linkers (CXLs) for investigation of three-dimensional protein structures and protein-protein interactions (PPIs). CXLs afford consolidated advantages not previously available in a simple cross-linker, including (1) their small size and cationic nature at physiological pH, resulting in good water solubility and cell permeability, (2) an alkyne group for bio-orthogonal conjugation to affinity tags via the click reaction for enrichment of cross-linked peptides, (3) a nucleophilic displacement reaction involving the 1,2,3-triazole ring formed in the click reaction, yielding a lock-mass reporter ion for only clicked peptides, and (4) higher charge states of cross-linked peptides in the gas-phase for augmented electron transfer dissociation (ETD) yields. Ubiquitin, a lysine-abundant protein, is used as a model system to demonstrate structural studies using CXLs. To validate the sensitivity of our approach, biotin-azide labeling and subsequent enrichment of cross-linked peptides are performed for cross-linked ubiquitin digests mixed with yeast cell lysates. Cross-linked peptides are detected and identified by collision induced dissociation (CID) and ETD with linear quadrupole ion trap (LTQ)-Fourier transform ion cyclotron resonance (FTICR) and LTQ-Orbitrap mass spectrometers. The application of CXLs to more complex systems (e.g., in vivo cross-linking) is illustrated by Western blot detection of Cul1 complexes including known binders, Cand1 and Skp2, in HEK 293 cells, confirming good water solubility and cell-permeability. PMID:22339618
The elucidation of the structure of Thermotoga maritima peptidoglycan reveals two novel types of cross-link.
Boniface, Audrey; Parquet, Claudine; Arthur, Michel; Mengin-Lecreulx, Dominique; Blanot, Didier
Thermotoga maritima is a Gram-negative, hyperthermophilic bacterium whose peptidoglycan contains comparable amounts of L- and D-lysine. We have determined the fine structure of this cell-wall polymer. The muropeptides resulting from the digestion of peptidoglycan by mutanolysin were separated by high-performance liquid chromatography and identified by amino acid analysis after acid hydrolysis, dinitrophenylation, enzymatic determination of the configuration of the chiral amino acids, and mass spectrometry. The high-performance liquid chromatography profile contained four main peaks, two monomers, and two dimers, plus a few minor peaks corresponding to anhydro forms. The first monomer was the d-lysine-containing disaccharide-tripeptide in which the D-Glu-D-Lys bond had the unusual gamma-->epsilon arrangement (GlcNAc-MurNAc-L-Ala-gamma-D-Glu-epsilon-D-Lys). The second monomer was the conventional disaccharide-tetrapeptide (GlcNAc-MurNAc-L-Ala-gamma-D-Glu-L-Lys-D-Ala). The first dimer contained a disaccharide-L-Ala as the acyl donor cross-linked to the alpha-amine of D-Lys in a tripeptide acceptor stem with the sequence of the first monomer. In the second dimer, donor and acceptor stems with the sequences of the second and first monomers, respectively, were connected by a D-Ala4-alpha-D-Lys3 cross-link. The cross-linking index was 10 with an average chain length of 30 disaccharide units. The structure of the peptidoglycan of T. maritima revealed for the first time the key role of D-Lys in peptidoglycan synthesis, both as a surrogate of L-Lys or meso-diaminopimelic acid at the third position of peptide stems and in the formation of novel cross-links of the L-Ala1(alpha-->alpha)D-Lys3 and D-Ala4(alpha-->alpha)D-Lys3 types. PMID:19542229
Novel transglutaminase-like peptidase and C2 domains elucidate the structure, biogenesis and evolution of the ciliary compartment
Zhang, Dapeng
domains aid in the proper reconstruction of the Y-shaped linkers, which are key structures in the transitional zone of cilia, by allowing precise prediction of the multiple membrane-contacting and protein-protein interaction sites in these structures. These findings help decipher key events in the evolutionary separation of the ciliary and nuclear compartments in course of the emergence of the eukaryotic cell. PMID:22983010
Elucidation of Structural Elements for Selectivity across Monoamine Transporters: Novel 2-[(Diphenylmethyl)sulfinyl]acetamide (Modafinil) Analogues
2-[(Diphenylmethyl)sulfinyl]acetamide (modafinil, (±)-1) is a unique dopamine uptake inhibitor that binds the dopamine transporter (DAT) differently than cocaine and may have potential for the treatment of psychostimulant abuse. To further investigate structural requirements for this divergent binding mode, novel thio- and sulfinylacetamide and ethanamine analogues of (±)-1 were synthesized wherein (1) the diphenyl rings were substituted with methyl, trifluoromethyl, and halogen substituents and (2) substituents were added to the terminal amide/amine nitrogen. Halogen substitution of the diphenyl rings of (±)-1 gave several amide analogues with improved binding affinity for DAT and robust selectivity over the serotonin transporter (SERT), whereas affinity improved at SERT over DAT for the p-halo-substituted amine analogues. Molecular docking studies, using a subset of analogues with DAT and SERT homology models, and functional data obtained with DAT (A480T) and SERT (T497A) mutants defined a role for TM10 in the substrate/inhibitor S1 binding sites of DAT and SERT. PMID:24494745
Structure elucidation of a pungent compound in black cardamom: Amomum tsao-ko Crevost et Lemarié (Zingiberaceae).
Starkenmann, Christian; Mayenzet, Fabienne; Brauchli, Robert; Wunsche, Laurent; Vial, Christian
Natural plant extracts containing taste modifier compounds will gain more commercial interest in the future. Black cardamom, Amomum tsao-ko Crevost et Lemarié, used as a spice in Asia, produces a nice refreshing effect in the mouth. Therefore, an ethyl acetate extract was prepared, and constituents were separated by liquid chromatography. Guided by the tasting of each fraction (LC tasting), a new pungent compound was discovered, (+/-)-trans-2,3,3a,7a-tetrahydro-1H-indene-4-carbaldehyde. To confirm this new structure, a synthesis was performed starting from cyclopentene-1-carbaldehyde. The Wittig conditions were determined to control the stereochemistry of the ring fusion to prepare (+/-)-trans-(2,3,3a,7a-tetrahydro-1 H-inden-4-yl) methanol and (+/-)-cis-(2,3,3a,7a-tetrahydro-1H-inden-4-yl) methanol. After oxidation, (+/-)-trans-2,3,3a,7a-tetrahydro-1H-indene-4-carbaldehyde and (+/-)-cis-2,3,3a,7a-tetrahydro-1H-indene-4-carbaldehyde were tasted in water and only the trans-2,3,3a,7a-tetrahydro-1H-indene-4-carbaldehyde, present in black cardamom, produced a trigeminal effect in the mouth. PMID:18020415
Structural elucidation of direct analysis in real time ionized nerve agent simulants with infrared multiple photon dissociation spectroscopy.
Rummel, Julia L; Steill, Jeffrey D; Oomens, Jos; Contreras, Cesar S; Pearson, Wright L; Szczepanski, Jan; Powell, David H; Eyler, John R
Infrared multiple photon dissociation (IRMPD) was used to generate vibrational spectra of ions produced with a direct analysis in real time (DART) ionization source coupled to a 4.7 T Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. The location of protonation on the nerve agent simulants diisopropyl methylphosphonate (DIMP) and dimethyl methylphosphonate (DMMP) was studied while solutions of the compounds were introduced for extended periods of time with a syringe pump. Theoretical vibrational spectra were generated with density functional theory calculations. Visual comparison of experimental mid-IR IRMPD spectra and theoretical spectra could not establish definitively if a single structure or a mixture of conformations was present for the protonated parent of each compound. However, theoretical calculations, near-ir IRMPD spectra, and frequency-to-frequency and statistical comparisons indicated that the protonation site for both DIMP and DMMP was predominantly, if not exclusively, the phosphonyl oxygen instead of one of the oxygen atoms with only single bonds. PMID:21491962
Identification and structure elucidation of a novel antifungal compound produced by Pseudomonas aeruginosa PGPR2 against Macrophomina phaseolina.
Illakkiam, Devaraj; Ponraj, Paramasivan; Shankar, Manoharan; Muthusubramanian, Shanmugam; Rajendhran, Jeyaprakash; Gunasekaran, Paramasamy
Pseudomonas aeruginosa PGPR2 was found to protect mungbean plants from charcoal rot disease caused by Macrophomina phaseolina. Secondary metabolites from the culture supernatant of P. aeruginosa PGPR2 were extracted with ethyl acetate and the antifungal compound was purified by preparative HPLC using reverse phase chromatography. The purified compound showed antifungal activity against M. phaseolina and other phytopathogenic fungi (Fusarium sp., Rhizoctonia sp. Alternaria sp., and Aspergillus sp.). The structure of the purified compound was determined using (1)H, (13)C, 2D NMR spectra and liquid chromatography-mass spectrometry (LC-MS). Spectral data suggest that the antifungal compound is 3,4-dihydroxy-N-methyl-4-(4-oxochroman-2-yl)butanamide, with the chemical formula C14H17NO5 and a molecular mass of 279. Though chemically synthesized chromanone derivatives have been shown to have antifungal activity, we report for the first time, the microbial production of a chromanone derivative with antifungal activity. This ability of P. aeruginosa PGPR2 makes it a suitable strain for biocontrol. PMID:24037513
Structure and spectromagnetic properties of the superoxide radical adduct of DMPO in water: elucidation by theoretical investigations.
Houriez, Céline; Ferré, Nicolas; Siri, Didier; Tordo, Paul; Masella, Michel
In the field of spin trapping chemistry, the design of more efficient radical traps can be assisted by the development of theoretical methods able to give a quantitative evaluation of the electron paramagnetic resonance (EPR) spectrum features of the spin-adduct radical, even before initiating the experimental work. The superoxide radical adduct of the 5,5-dimethyl-1-pyrroline-N-oxide nitrone (DMPO-OOH) has been reported in a huge number of papers devoted to the study of the oxidative stress. Here, we present for the first time the theoretical study of DMPO-OOH in an explicit water solution, based on the combined QM/MM//MD protocol we recently proposed, featuring a full coupling between the solute and all the explicit water molecules. Our results show that the DMPO-OOH EPR spectrum, whose interpretation is still debated, can be explained in the light of two sites in chemical exchange, in agreement with the most recent experimental data. Moreover, we demonstrate that each site consists of an equilibrium between the two main 5-membered ring conformations of DMPO-OOH. We provide also an analysis of the solvent contribution to the hyperfine coupling constants (hcc's) as well as an exhaustive study of the possible relationship between the hcc's and the main structural characteristics of DMPO-OOH. Our QM/MM//MD protocol appears thus to be an accurate theoretical tool allowing the investigation of the magnetic properties of large nitroxide spin adducts in complex environments. PMID:20722404
Antimicrobial efficacy of phenanthrenequinone based Schiff base complexes incorporating methionine amino acid: Structural elucidation and in vitro bio assay
NASA Astrophysics Data System (ADS)
Arun, Thesingu Rajan; Raman, Natarajan
This work focuses the synthesis and characterization of few novel mixed ligand Schiff base metal complexes and their biological activities. For deriving the structural aspects, spectral techniques such as FT-IR, UV-Vis., 1H NMR, Raman, EPR and the physicochemical characterizations including elemental analysis, molar conductance and magnetic susceptibility method have been involved. All the complexes adopt square planar geometry. DNA binding ability of these complexes has been explored using diverse techniques viz. UV-Vis. absorption, fluorescence spectroscopy, viscometry and cyclic voltammetry. These studies prove that CT-DNA binding of the complexes follows the intercalation mode. Comparative DNA oxidative cleavage ability of the complexes has been done under ultraviolet photo radiation on pUC19 DNA. In addition, the biocidal action of the complexes has been investigated against few pathogenic bacteria and fungi by disc diffusion method. Importantly, the amylase inhibition activity of Cu(II) complex has been explored. The amylase inhibition property has been found to be increased upon increasing the complex concentration.
Isolation, Structural Modification, and HIV Inhibition of Pentacyclic Lupane-Type Triterpenoids from Cassine xylocarpa and Maytenus cuzcoina.
Callies, Oliver; Bedoya, Luis M; Beltrán, Manuela; Muñoz, Alejandro; Calderón, Patricia Obregón; Osorio, Alex A; Jiménez, Ignacio A; Alcamí, José; Bazzocchi, Isabel L
As a part of our investigation into new anti-HIV agents, we report herein the isolation, structure elucidation, and biological activity of six new (1-6) and 20 known (7-26) pentacyclic lupane-type triterpenoids from the stem of Cassine xylocarpa and root bark of Maytenus cuzcoina. Their stereostructures were elucidated on the basis of spectroscopic and spectrometric methods, including 1D and 2D NMR techniques. To gain a more complete understanding of the structural requirements for anti-HIV activity, derivatives 27-48 were prepared by chemical modification of the main secondary metabolites. Sixteen compounds from this series displayed inhibitory effects of human immunodeficiency virus type 1 replication with IC50 values in the micromolar range, highlighting compounds 12, 38, and 42 (IC50 4.08, 4.18, and 1.70 μM, respectively) as the most promising anti-HIV agents. PMID:25927586
Structure elucidation and anti-tumor activities of water-soluble oligosaccharides from Lactarius deliciosus (L. ex Fr.) Gray
Ding, Xiang; Hou, Yiling; Hou, Wanru; Zhu, Yuanxiu; Fu, Lei; Zhu, Hongqing
Background: Oligosaccharides are composed of a variable number of monosaccharide units and very important in the biologically diverse of biological systems. Materials and Methods: Crude water-soluble oligosaccharide was extracted from the fruiting bodies with water and then successively purified by DEAE–cellulose 52 and Sephadex G-100 column chromatography, yielding one major oligosaccharides fractions: LES-A. Structural features of Lactarius deliciosus (L. ex Fr.) Gray oligosaccharide (LDGO-A) were investigated by a combination of monosaccharide component analysis by thin layer chromatography, infrared spectra, nuclear magnetic resonance spectroscopy, scanning electron microscopy, and high-performance gel permeation chromatography analysis. Result: The results indicated that LDGO-A was composed of D-glucose and D-xylose, and the average molecular sizes was approximately 945 Da. The anti-tumor activity of LDGO-A was evaluated in vivo. The inhibitory rate in mice treated with 40 mg/kg LDGO-A can reach 40.02%, being the highest in the three doses, which may be comparable to mannatide. Histology of immune organs shows that the tissues arranged more regular and firmer, but the tumor tissue arranged looser in LDGO-A group than those in the control group. Meanwhile, there is no obvious damage to other organs, such as heart. The anti-tumor activity of the LDGO-A was usually believed to be a consequence of the stimulation of the cell-mediated immune response because it can significantly promote the lymphocyte and macrophage cells in the dose range of 100–400 μg/mL in vitro. LDGO-A also effected the expression of some housekeeping genes mRNA in S180 tumor. Conclusion: Accordingly, the LDGO-A might serve as an effective healthcare food and source of natural anti-tumor compounds. PMID:26600715
On the use of X-ray absorption spectroscopy to elucidate the structure of lutetium adenosine mono- and triphosphate complexes.
Mostapha, S; Berthon, C; Fontaine-Vive, F; Gaysinski, M; Guérin, L; Guillaumont, D; Massi, L; Monfardini, I; Solari, P L; Thomas, O P; Charbonnel, M C; Den Auwer, C
chemical calculations has been implemented in order to assess the lutetium coordination arrangement for the two nucleotides. In all the complexes described in the article, the lutetium cation is coordinated by the phosphate groups of the nucleotide plus additional putative water molecules with various tridimensional arrangements. With AMP 1:2 and ATP 1:1 solid-state compounds, polynuclear complexes are assumed to be obtained. In contrast, with ATP 1:2 soluble compound, the Lu coordination sphere is saturated by two ATP ligands, and this favors the formation of a mononuclear complex. In order to further interpret the EXAFS data obtained at the Lu LIII edge, model structures have been calculated for the 1:1 and 1:2 ATP complexes. They are discussed and compared to the EXAFS best fit metrical parameters. PMID:23727732
Two dimensional laser induced fluorescence spectroscopy: A powerful technique for elucidating rovibronic structure in electronic transitions of polyatomic molecules
NASA Astrophysics Data System (ADS)
Gascooke, Jason R.; Alexander, Ula N.; Lawrance, Warren D.
We demonstrate the power of high resolution, two dimensional laser induced fluorescence (2D-LIF) spectroscopy for observing rovibronic transitions of polyatomic molecules. The technique involves scanning a tunable laser over absorption features in the electronic spectrum while monitoring a segment, in our case 100 cm-1 wide, of the dispersed fluorescence spectrum. 2D-LIF images separate features that overlap in the usual laser induced fluorescence spectrum. The technique is illustrated by application to the S1-S0 transition in fluorobenzene. Images of room temperature samples show that overlap of rotational contours by sequence band structure is minimized with 2D-LIF allowing a much larger range of rotational transitions to be observed and high precision rotational constants to be extracted. A significant advantage of 2D-LIF imaging is that the rotational contours separate into their constituent branches and these can be targeted to determine the three rotational constants individually. The rotational constants determined are an order of magnitude more precise than those extracted from the analysis of the rotational contour and we find the previously determined values to be in error by as much as 5% [G. H. Kirby, Mol. Phys. 19, 289 (1970), 10.1080/00268977000101291]. Comparison with earlier ab initio calculations of the S0 and S1 geometries [I. Pugliesi, N. M. Tonge, and M. C. R. Cockett, J. Chem. Phys. 129, 104303 (2008), 10.1063/1.2970092] reveals that the CCSD/6-311G** and RI-CC2/def2-TZVPP levels of theory predict the rotational constants, and hence geometries, with comparable accuracy. Two ground state Fermi resonances were identified by the distinctive patterns that such resonances produce in the images. 2D-LIF imaging is demonstrated to be a sensitive method capable of detecting weak spectral features, particularly those that are otherwise hidden beneath stronger bands. The sensitivity is demonstrated by observation of the three isotopomers of fluorobenzene
Structural elucidation of monoterpene oxidation products by ion trap fragmentation using on-line atmospheric pressure chemical ionisation mass spectrometry in the negative ion mode.
Warscheid, B; Hoffmann, T
Based on ion trap mass spectrometry, an on-line method is described which provides valuable information on the molecular composition of structurally complex organic aerosols. The investigated aerosols were generated from the gas-phase ozonolysis of various C(10)H(16)-terpenes (alpha-pinene, beta-pinene, 3-carene, sabinene, limonene), and directly introduced into the ion source of the mass spectrometer. Negative ion chemical ionisation at atmospheric pressure (APCI(-)) enabled the detection of multifunctional carboxylic acid products by combining inherent sensitivity and molecular weight information. Sequential low-energy collision-induced product ion fragmentation experiments (MS(n)) were performed in order to elucidate characteristic decomposition pathways of the compounds. Dicarboxylic acids, oxocarboxylic acids and hydroxyketocarboxylic acid products could be clearly distinguished by multistage on-line MS. Furthermore, sabinonic acid and two C(9)-ether compounds were tentatively identified for the first time by applying on-line APCI(-)-MS(n). PMID:11746892
Fragmentation reactions using electrospray ionization mass spectrometry: an important tool for the structural elucidation and characterization of synthetic and natural products.
Demarque, Daniel P; Crotti, Antonio E M; Vessecchi, Ricardo; Lopes, João L C; Lopes, Norberto P
Over the last decade, the number of studies reporting the use of electrospray ionization mass spectrometry (ESI-MS) in combination with collision cells (or other activation methods) to promote fragmentation of synthetic and natural products for structural elucidation purposes has considerably increased. However, the lack of a systematic compilation of the gas-phase fragmentation reactions subjected to ESI-MS/MS conditions still represents a challenge and has led to many misunderstood results in the literature. This review article exploits the most common fragmentation reactions for ions generated by ESI in positive and negative modes using collision cells in an effort to stimulate the use of this technique by non-specialists, undergraduate students and researchers in related areas. PMID:26673733
Dhilirolides E-N, meroterpenoids produced in culture by the fungus Penicillium purpurogenum collected in Sri Lanka: structure elucidation, stable isotope feeding studies, and insecticidal activity.
Centko, Ryan M; Williams, David E; Patrick, Brian O; Akhtar, Yasmin; Garcia Chavez, Miguel Angel; Wang, Yan Alexander; Isman, Murray B; de Silva, E Dilip; Andersen, Raymond J
Extracts of laboratory cultures of the fungus Penicilium purpurogenum obtained from rotting fruit of the tree Averrhoa bilimbi growing in Sri Lanka have yielded 10 new meroterpenoids, dhilirolides E-N (5-14). The structures of the new dhilirolides have been elucidated by analysis of spectroscopic data and a single-crystal X-ray diffraction analysis of dhilirolide L (12). Dhilirolides A-N (1-14) represent the four unprecedented and rearranged dhilirane, isodhilirane, 14,15-dinordhilirane, and 23,24-dinorisodhilirane meroterpenoid carbon skeletons. Stable isotope feeding studies have confirmed the meroterpenoid biogenetic origin of the dhilirolides and provided support for a proposed genesis of the new carbon skeletons. Dhilirolide L (12) showed significant feeding inhibition and sublethal developmental disruption in the cabbage looper Trichoplusia ni, an important agricultural pest, at low concentrations. PMID:24684453
Shigella flexneri O-antigens revisited: final elucidation of the O-acetylation profiles and a survey of the O-antigen structure diversity.
Perepelov, Andrei V; Shekht, Maria E; Liu, Bin; Shevelev, Sergei D; Ledov, Vladimir A; Senchenkova, Sof'ya N; L'vov, Vyacheslav L; Shashkov, Alexander S; Feng, Lu; Aparin, Petr G; Wang, Lei; Knirel, Yuriy A
Shigella flexneri is an important human pathogen causing shigellosis. Strains of S. flexneri are serologically heterogeneous and, based on O-antigens, are currently classified into 14 types. Structures of the O-antigens (O-polysaccharides) of S. flexneri have been under study since 1960s but some gaps still remained. In this work, using one- and two-dimensional (1) H- and (13) C-NMR spectroscopy, the O-polysaccharides of several S. flexneri types were reinvestigated, and their structures were either confirmed (types 2b, 3b, 3c, 5b, X) or amended in respect to the O-acetylation pattern (types 3a, Y, 6, 6a). As a result, the O-acetylation sites were defined in all O-polysaccharides that had not been studied in detail earlier, and the long story of S. flexneri type strain O-antigen structure elucidation is thus completed. New and published data on the S. flexneri O-antigen structures are summarized and discussed in view of serological and genetic relationships of the O-antigens within the Shigella group and between S. flexneri and Escherichia coli. PMID:22724405
The α1B/D-adrenoceptor knockout mouse permits isolation of the vascular α1A-adrenoceptor and elucidates its relationship to the other subtypes
Methven, L; McBride, M; Wallace, GA; McGrath, JC
Background and purpose: Mesenteric and carotid arteries from the α1B/D-adrenoceptor knockout (α1B/D-KO) were employed to isolate α1A-adrenoceptor pharmacology and location and to reveal these features in the wild-type (WT) mouse. Experimental approach: Functional pharmacology by wire myography and receptor localization by confocal microscopy, using the fluorescent α1-adrenoceptor ligand BODIPY FL-Prazosin (QAPB), on mesenteric (an 'α1A-adrenoceptor' tissue) and carotid (an 'α1D-adrenoceptor' tissue) arteries. Key results: α1B/D-KO mesenteric arteries showed straightforward α1A-adrenoceptor agonist/antagonist pharmacology. WT had complex pharmacology with α1A- and α1D-adrenoceptor components. α1B/D-KO had a larger α1A-adrenoceptor response suggesting compensatory up-regulation: no increase in fluorescent ligand binding suggests up-regulation of signalling. α1B/D-KO carotid arteries had low efficacy α1A-adrenoceptor responses. WT had complex pharmacology consistent with co-activation of all three subtypes. Fluorescent binding had straightforward α1A-adrenoceptor characteristics in both arteries of α1B/D-KO. Fluorescent binding varied between cells in relative intracellular and surface distribution. Total fluorescence was reduced in the α1B/D-KO due to fewer smooth muscle cells showing fluorescent binding. WT binding was greater and sensitive to α1A- and α1D-adrenoceptor antagonists. Conclusions and implications: The straightforward pharmacology and fluorescent binding in the α1B/D-KO was used to interpret the properties of the α1A-adrenoceptor in the WT. Reduced total fluorescence in α1B/D-KO arteries, despite a clear difference in the functionally dominant subtype, indicates that measurement of receptor protein is unlikely to correlate with function. Fewer cells bound QAPB in the α1B/D-KO suggesting different cellular phenotypes of α1A-adrenoceptor exist. The α1B/D-KO provides robust assays for the α1A-adrenoceptor and takes us
Rhodomyrtials A and B, Two Meroterpenoids with a Triketone-Sesquiterpene-Triketone Skeleton from Rhodomyrtus tomentosa: Structural Elucidation and Biomimetic Synthesis.
Zhang, Ya-Long; Chen, Chen; Wang, Xiao-Bing; Wu, Lin; Yang, Ming-Hua; Luo, Jun; Zhang, Can; Sun, Hong-Bin; Luo, Jian-Guang; Kong, Ling-Yi
Rhodomyrtials A and B (1 and 2), two unprecedented triketone-sesquiterpene-triketone adducts, along with five biogenetically related intermediates, rhodomentone A (3) and tomentodiones A-D (4-7), were isolated from the leaves of Rhodomyrtus tomentosa. Their structures and absolute configurations were determined by a combination of NMR spectroscopy, chemical conversion, and X-ray diffraction analysis. Compounds 1 and 2 were biomimetically synthesized via 5 and 4, respectively, rather than 3, revealing their key ordering of biosynthetic events and confirming their structural assignments. Compound 7 exhibited potent metastatic inhibitory activity against DLD-1 cells by suppressing the activation of matrix metalloproteinase (MMP)-2 and MMP-9. PMID:27482941
Solution structure of the reduced form of human peroxiredoxin-6 elucidated using zero-length chemical cross-linking and homology modelling.
Rivera-Santiago, Roland F; Harper, Sandra L; Zhou, Suiping; Sriswasdi, Sira; Feinstein, Sheldon I; Fisher, Aron B; Speicher, David W
Peroxiredoxin-6 (PRDX6) is an unusual member of the peroxiredoxin family of antioxidant enzymes that has only one evolutionarily conserved cysteine. It reduces oxidized lipids and reactive oxygen species (ROS) by oxidation of the active-site cysteine (Cys(47)) to a sulfenic acid, but the mechanism for conversion back to a thiol is not completely understood. Moreover, it has phospholipase A2 (PLA2) activity in addition to its peroxidase activity. Interestingly, some biochemical data are inconsistent with a known high-resolution crystal structure of the catalytic intermediate of the protein, and biophysical data indicate that the protein undergoes conformational changes that affect enzyme activity. In order to further elucidate the solution structure of this important enzyme, we used chemical cross-linking coupled with high-resolution MS (CX-MS), with an emphasis on zero-length cross-links. Distance constraints from high confidence cross-links were used in homology modelling experiments to determine a solution structure of the reduced form of the protein. This structure was further evaluated using chemical cross-links produced by several homo-bifunctional amine-reactive cross-linking reagents, which helped to confirm the solution structure. The results show that several regions of the reduced version of human PRDX6 are in a substantially different conformation from that shown for the crystal structure of the peroxidase catalytic intermediate. The differences between these two structures are likely to reflect catalysis-related conformational changes. These studies also demonstrate that CX-MS using zero-length cross-linking is a powerful strategy for probing protein conformational changes that is complementary to alternative methods such as crystallographic, NMR and biophysical studies. PMID:25748205
The 3D model of the lipase/acyltransferase from Candida parapsilosis, a tool for the elucidation of structural determinants in CAL-A lipase superfamily.
Subileau, Maeva; Jan, Anne-Hélène; Nozac'h, Hervé; Pérez-Gordo, Marina; Perrier, Véronique; Dubreucq, Eric
Because lipids are hydrophobic, the development of efficient bioconversions in aqueous media free of organic solvents is particularly challenging for green oleochemistry. Within this aim, enzymes exhibiting various abilities to catalyze acyltransfer reaction in water/lipid systems have been identified. Among these, CpLIP2 from Candida parapsilosis has been characterized as a lipase/acyltransferase, able to catalyze acyltransfer reactions preferentially to hydrolysis in the presence of particularly low acyl acceptor concentration and high thermodynamic activity of water (aw>0.9). Lipase/acyltransferases are thus of great interest, being able to produce new esters at concentrations above the thermodynamic equilibrium of hydrolysis/esterification with limited to no release of free fatty acids. Here, we present a 3D model of CpLIP2 based on homologies with crystallographic structures of Pseudozyma antarctica lipase A. Indeed, the two enzymes have 31% of identity in their primary sequence, yielding a same general structure, but different catalytic properties. The quality of the calculated CpLIP2 model was confirmed by several methods. Limited proteolysis confirmed the location of some loops at the surface of the protein 3D model. Directed mutagenesis also supported the structural model constructed on CAL-A template: the functional properties of various mutants were consistent with their structure-based putative involvement in the oxyanion hole, substrate specificity, acyltransfer or hydrolysis catalysis and structural stability. The CpLIP2 3D model, in comparison with CAL-A 3D structure, brings insights for the elucidation and improvement of the structural determinants involved in the exceptional acyltransferase properties of this promising biocatalyst and of homologous enzymes of the same family. PMID:26123263
Structural confirmation of oligosaccharides newly isolated from sugar beet molasses
Background Sugar beet molasses is a viscous by-product of the processing of sugar beets into sugar. The molasses is known to contain sucrose and raffinose, a typical trisaccharide, with a well-established structure. Although sugar beet molasses contains various other oligosaccharides as well, the structures of those oligosaccharides have not been examined in detail. The purpose of this study was isolation and structural confirmation of these other oligosaccharides found in sugar beet molasses. Results Four oligosaccharides were newly isolated from sugar beet molasses using high-performance liquid chromatography (HPLC) and carbon-Celite column chromatography. Structural confirmation of the saccharides was provided by methylation analysis, matrix-assisted laser desorption/ionaization time of flight mass spectrometry (MALDI-TOF-MS), and nuclear magnetic resonance (NMR) measurements. Conclusion The following oligosaccharides were identified in sugar beet molasses: β-D-galactopyranosyl-(1- > 6)-β-D-fructofuranosyl-(2 <-> 1)-α-D-glucopyranoside (named β-planteose), α-D-galactopyranosyl-(1- > 1)-β-D-fructofuranosyl-(2 <-> 1)-α-D-glucopyranoside (named1-planteose), α-D-glucopyranosyl-(1- > 6)-α-D-glucopyranosyl-(1 <-> 2)-β-D-fructofuranoside (theanderose), and β-D-glucopyranosyl-(1- > 3)-α-D-glucopyranosyl-(1 <-> 2)-β-D-fructofuranoside (laminaribiofructose). 1-planteose and laminaribiofructose were isolated from natural sources for the first time. PMID:22925105
Elucidating the structure of carbon nanoparticles by ultra-performance liquid chromatography coupled with electrospray ionisation quadrupole time-of-flight tandem mass spectrometry.
Hu, Qin; Meng, Xiangpeng; Choi, Martin M F; Gong, Xiaojuan; Chan, Wan
A fast and accurate ultra-performance liquid chromatography coupled with electrospray ionisation quadrupole time-of-flight tandem mass spectrometry (UPLC-ESI-Q-TOF-MS/MS) method was developed for the separation and structural elucidation of fluorescent carbon nanoparticles (CNP). The CNP was synthesised from microwave-assisted pyrolysis of citric acid (CA) and 1,2-ethylenediamine (EDA). By using UPLC separation, the CNP product was well separated into ten fractions within 4.0 min. Based on high-accuracy MS and MS/MS analyses, the CNP species were revealed to display six kinds of chemical formulas, including (C10H20N4O5)n, (C8H12N2O5)n, (C16H22N4O9)n, (C6H8O7)n, (C14H18N2O11)n, and (C14H16N2O10)n. In particular, our study revealed for the first time that the CNP species exist as supramolecular clusters with their individual monomers units linked together through non-covalent bonding forces. These findings clearly indicated the usefulness of UPLC-ESI-Q-TOF-MS/MS in identifying the chemical composition of CNP product. It is anticipated that our proposed methodology can be applied to study the structure-property relationships of CNP, facilitating in the production of CNP with desirable spectral features. PMID:26893091
Synthesis, spectroscopic and structural elucidation of 1-butyl-4-[2-(3,5-dimethoxy-4-hydroxyphenyl)ethenyl)]pyridinium chloride tetrahydrate.
Koleva, B B; Kolev, T; Lamshöft, M; Mayer-Figge, H; Sheldrick, W S; Spiteller, M
The novel chloride salt of 1-butyl-4-[2-(4-hydroxyphenyl)ethenyl)]pyridine (1), has been synthesized as the tetrahydrate and its structure and properties elucidated in detail spectroscopically, thermally and structurally, using single crystal X-ray diffraction, linear-polarized solid-state IR-spectroscopy, UV-spectroscopy and mass spectrometry. Quantum chemical calculations were performed with a view to supporting and explaining the experimental structural and spectroscopic data. The compound (1) crystallizes in triclinic P1 space group and its unit cell contains two independent 1-butyl-4-[2-(3,5-dimethoxy4-hydroxyphenyl)ethenyl)]pyridinium] cations, differing with respect to the butyl chain torsion angle for which values of 80.0(9) degrees and 173.6(3) degrees are observed. The cations and anions are joined into infinite layers, formed by two different dimers and including solvent molecules. Hydrogen bonds OH...OH(2) (2.814 A), HOH...O(CH(3)) (2.960 A), OH...Cl (2.967 A), HOH...Cl(-) (3.034, 3.188, 3.161 and 3.062 A) and HOH...OH(2) (2.772 A) are observed. For first time in the literature, we are reporting the crystal structure of the dye with the syring-fragment in the molecule. The spectroscopic properties of the novel compound are compared and with those of the corresponding quinoide form (2). Both the forms (1) and (2) are characterized by 21 and 140 nm solvatochromic effects depending of the type of the solvent. The UV-spectroscopic data in solution confirm the formation of classical H-aggregates in polar protic solvent mixture. PMID:19833548
Synthesis, spectroscopic and structural elucidation of 1-butyl-4-[2-(3,5-dimethoxy-4-hydroxyphenyl)ethenyl)]pyridinium chloride tetrahydrate
NASA Astrophysics Data System (ADS)
Koleva, B. B.; Kolev, T.; Lamshöft, M.; Mayer-Figge, H.; Sheldrick, W. S.; Spiteller, M.
The novel chloride salt of 1-butyl-4-[2-(4-hydroxyphenyl)ethenyl)]pyridine ( 1), has been synthesized as the tetrahydrate and its structure and properties elucidated in detail spectroscopically, thermally and structurally, using single crystal X-ray diffraction, linear-polarized solid-state IR-spectroscopy, UV-spectroscopy and mass spectrometry. Quantum chemical calculations were performed with a view to supporting and explaining the experimental structural and spectroscopic data. The compound ( 1) crystallizes in triclinic P1¯ space group and its unit cell contains two independent 1-butyl-4-[2-(3,5-dimethoxy4-hydroxyphenyl)ethenyl)]pyridinium] cations, differing with respect to the butyl chain torsion angle for which values of 80.0(9)° and 173.6(3)° are observed. The cations and anions are joined into infinite layers, formed by two different dimers and including solvent molecules. Hydrogen bonds OH⋯OH 2 (2.814 Å), HOH⋯O(CH 3) (2.960 Å), OH⋯Cl (2.967 Å), HOH⋯Cl - (3.034, 3.188, 3.161 and 3.062 Å) and HOH⋯OH 2 (2.772 Å) are observed. For first time in the literature, we are reporting the crystal structure of the dye with the syring-fragment in the molecule. The spectroscopic properties of the novel compound are compared and with those of the corresponding quinoide form ( 2). Both the forms ( 1) and ( 2) are characterized by 21 and 140 nm solvatochromic effects depending of the type of the solvent. The UV-spectroscopic data in solution confirm the formation of classical H-aggregates in polar protic solvent mixture.
Structural analysis of proanthocyanidins isolated from fruit stone of Chinese hawthorn with potent antityrosinase and antioxidant activity.
Chai, Wei-Ming; Chen, Chih-Min; Gao, Yu-Sen; Feng, Hui-Ling; Ding, Yu-Mei; Shi, Yan; Zhou, Han-Tao; Chen, Qing-Xi
Proanthocyanidins were isolated from fruit stone of Chinese hawthorn (Crataegus pinnatifida Bge. var. major N.E.Br.). Their structures were analyzed and elucidated by methods of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and high performance liquid chromatography electrospray ionization mass spectrometry (HPLC-ESI-MS). The results demonstrated that these compounds are complicated mixtures of homo- and heteropolymers consisting of procyanidin/procyanidin gallate and prodelphinidin. They possessed structural heterogeneity in monomer units, polymer length, and interflavan linkage (A-type and B-type). Their antityrosinase and antioxidant activity were then investigated. The results revealed that they can inhibit tyrosinase activities, including the monophenolase activity and the diphenolase activity. In addition, proanthocyanidins possessed potent antioxidant activity. Our studies revealed that proanthocyanidins isolated from fruit stone of Chinese hawthorn may be applied in food, agriculture, pharmaceutical, and cosmetic industries. PMID:24313351
Structural Revisions of a Class of Natural Products: Scaffolds of Aglycon Analogues of Fusicoccins and Cotylenins Isolated from Fungi.
Tang, Ying; Xue, Yongbo; Du, Guang; Wang, Jianping; Liu, Junjun; Sun, Bin; Li, Xiao-Nian; Yao, Guangmin; Luo, Zengwei; Zhang, Yonghui
The reisolation and structural revision of brassicicene D is described, and inspired us to reassign the core skeletons of brassicicenes C-H, J and K, ranging from dicyclopenta[a,d]cyclooctane to tricyclo[188.8.131.52(3,7)]tetradecane using quantum-chemical predictions and experimental validation strategies. Three novel, highly modified fusicoccanes, brassicicenes L-N, were also isolated from the fungus Alternaria brassicicola, and their structures were unequivocally established by spectroscopic data, ECD calculations, and crystallography. The reassigned structures represent the first class of bridgehead double-bond-containing natural products with a bicyclo[6.2.1]undecane carbon skeleton. Furthermore, their stabilities were first predicted with olefin strain energy calculations. Collectively, these findings extend our view of the application of computational predictions and biosynthetic logic-based structure elucidation to address problems related to the structure and stability of natural products. PMID:26916098
Vibration isolation by exploring bio-inspired structural nonlinearity.
Wu, Zhijing; Jing, Xingjian; Bian, Jing; Li, Fengming; Allen, Robert
Inspired by the limb structures of animals/insects in motion vibration control, a bio-inspired limb-like structure (LLS) is systematically studied for understanding and exploring its advantageous nonlinear function in passive vibration isolation. The bio-inspired system consists of asymmetric articulations (of different rod lengths) with inside vertical and horizontal springs (as animal muscle) of different linear stiffness. Mathematical modeling and analysis of the proposed LLS reveal that, (a) the system has very beneficial nonlinear stiffness which can provide flexible quasi-zero, zero and/or negative stiffness, and these nonlinear stiffness properties are adjustable or designable with structure parameters; (b) the asymmetric rod-length ratio and spring-stiffness ratio present very beneficial factors for tuning system equivalent stiffness; (c) the system loading capacity is also adjustable with the structure parameters which presents another flexible benefit in application. Experiments and comparisons with existing quasi-zero-stiffness isolators validate the advantageous features above, and some discussions are also given about how to select structural parameters for practical applications. The results would provide an innovative bio-inspired solution to passive vibration control in various engineering practice. PMID:26448392
Elucidating Structural Characteristics of Biomass using Solution-State 2 D NMR with a Mixture of Deuterated Dimethylsulfoxide and Hexamethylphosphoramide.
Yoo, Chang Geun; Pu, Yunqiao; Li, Mi; Ragauskas, Arthur J
Recent developments of NMR methods for characterization of lignocellulosic biomass allow improved understanding of plant cell-wall structures with minimal deconstruction and modification of biomass. This study introduces a new NMR solvent system composed of dimethylsulfoxide (DMSO-d6 ) and hexamethylphosphoramide (HMPA-d18 ). HMPA as a co-solvent enhanced swelling and mobility of the biomass samples; thereby it allowed enhancing signals of NMR spectra. The structural information of biomass was successfully analyzed by the proposed NMR solvent system (DMSO-d6 /HMPA-d18 ; 4:1, v/v) with different biomass. The proposed bi-solvent system does not require derivatization or isolation of biomass, facilitating a facile sample preparation and involving with no signals overlapping with biomass peaks. It also allows analyzing biomass with a room-temperature NMR probe instead of cryo-probes, which are traditionally used for enhancing signal intensities. PMID:27116696
Structure Elucidation of Mixed-Linker Zeolitic Imidazolate Frameworks by Solid-State (1)H CRAMPS NMR Spectroscopy and Computational Modeling.
Jayachandrababu, Krishna C; Verploegh, Ross J; Leisen, Johannes; Nieuwendaal, Ryan C; Sholl, David S; Nair, Sankar
Mixed-linker zeolitic imidazolate frameworks (ZIFs) are nanoporous materials that exhibit continuous and controllable tunability of properties like effective pore size, hydrophobicity, and organophilicity. The structure of mixed-linker ZIFs has been studied on macroscopic scales using gravimetric and spectroscopic techniques. However, it has so far not been possible to obtain information on unit-cell-level linker distribution, an understanding of which is key to predicting and controlling their adsorption and diffusion properties. We demonstrate the use of (1)H combined rotation and multiple pulse spectroscopy (CRAMPS) NMR spin exchange measurements in combination with computational modeling to elucidate potential structures of mixed-linker ZIFs, particularly the ZIF 8-90 series. All of the compositions studied have structures that have linkers mixed at a unit-cell-level as opposed to separated or highly clustered phases within the same crystal. Direct experimental observations of linker mixing were accomplished by measuring the proton spin exchange behavior between functional groups on the linkers. The data were then fitted to a kinetic spin exchange model using proton positions from candidate mixed-linker ZIF structures that were generated computationally using the short-range order (SRO) parameter as a measure of the ordering, clustering, or randomization of the linkers. The present method offers the advantages of sensitivity without requiring isotope enrichment, a straightforward NMR pulse sequence, and an analysis framework that allows one to relate spin diffusion behavior to proposed atomic positions. We find that structures close to equimolar composition of the two linkers show a greater tendency for linker clustering than what would be predicted based on random models. Using computational modeling we have also shown how the window-type distribution in experimentally synthesized mixed-linker ZIF-8-90 materials varies as a function of their composition. The
Harnessing the Unique Structural Properties of Isolated α-Helices*
Swanson, Carter J.; Sivaramakrishnan, Sivaraj
The α-helix is a ubiquitous secondary structural element that is almost exclusively observed in proteins when stabilized by tertiary or quaternary interactions. However, beginning with the unexpected observations of α-helix formation in the isolated C-peptide in ribonuclease A, there is growing evidence that a significant percentage (0.2%) of all proteins contain isolated stable single α-helical domains (SAH). These SAH domains provide unique structural features essential for normal protein function. A subset of SAH domains contain a characteristic ER/K motif, composed of a repeating sequence of ∼4 consecutive glutamic acids followed by ∼4 consecutive basic arginine or lysine (R/K) residues. The ER/K α-helix, also termed the ER/K linker, has been extensively characterized in the context of the myosin family of molecular motors and is emerging as a versatile structural element for protein and cellular engineering applications. Here, we review the structure and function of SAH domains, as well as the tools to identify them in natural proteins. We conclude with a discussion of recent studies that have successfully used the modular ER/K linker for engineering chimeric myosin proteins with altered mechanical properties, as well as synthetic polypeptides that can be used to monitor and systematically modulate protein interactions within cells. PMID:25059657
Structural Elucidation and Toxicity Assessment of Degraded Products of Aflatoxin B1 and B2 by Aqueous Extracts of Trachyspermum ammi
Iram, Wajiha; Anjum, Tehmina; Iqbal, Mazhar; Ghaffar, Abdul; Abbas, Mateen
In this study aqueous extract of seeds and leaves of Trachyspermum ammi were evaluated for their ability to detoxify aflatoxin B1 and B2 (AFB1; 100 μg L−1 and AFB2; 50 μg L−1) by in vitro and in vivo assays. Results indicated that T. ammi seeds extract was found to be significant (P < 0.05) in degrading AFB1 and AFB2 i.e., 92.8 and 91.9% respectively. However, T. ammi leaves extract proved to be less efficient in degrading these aflatoxins, under optimized conditions i.e., pH 8, temperature 30°C and incubation period of 72 h. The structural elucidation of degraded toxin products by LCMS/MS analysis showed that eight degraded products of AFB1 and AFB2 were formed. MS/MS spectra showed that most of the products were formed by the removal of double bond in the terminal furan ring and modification of lactone group indicating less toxicity as compared to parent compounds. Brine shrimps bioassay further confirmed the low toxicity of degraded products, showing that T. ammi seeds extract can be used as an effective tool for the detoxification of aflatoxins. PMID:27064492
Structural elucidation and magnetic behavior evaluation of rare earth (La, Nd, Gd, Tb, Dy) doped BaCoNi-X hexagonal nano-sized ferrites
NASA Astrophysics Data System (ADS)
Majeed, Abdul; Khan, Muhammad Azhar; Raheem, Faseeh ur; Hussain, Altaf; Iqbal, F.; Murtaza, Ghulam; Akhtar, Majid Niaz; Shakir, Imran; Warsi, Muhammad Farooq
Rare-earth (RE=La3+, Nd3+, Gd3+, Tb3+, Dy3+) doped Ba2NiCoRExFe28-xO46 (x=0.25) hexagonal ferrites were synthesized for the first time via micro-emulsion route, which is a fast chemistry route for obtaining nano-sized ferrite powders. These nanomaterials were investigated by X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), as well as vibrating sample magnetometer (VSM). The XRD analysis exhibited that all the samples crystallized into single X-type hexagonal phase. The crystalline size calculated by Scherrer's formula was found in the range 7-19 nm. The variations in lattice parameters elucidated the incorporation of rare-earth cations in these nanomaterials. FTIR absorption spectra of these X-type ferrites were investigated in the wave number range 500-2400 cm-1. Each spectrum exhibited absorption bands in the low wave number range, thereby confirming the X-type hexagonal structure. The enhancement in the coercivity was observed with the doping of rare-earth cations. The saturation magnetization was lowered owing to the redistribution of rare-earth cations on the octahedral site (3bVI). The higher values of coercivity (664-926 Oe) of these nanomaterials suggest their use in longitudinal recording media.
Structural Elucidation and Toxicity Assessment of Degraded Products of Aflatoxin B1 and B2 by Aqueous Extracts of Trachyspermum ammi.
Iram, Wajiha; Anjum, Tehmina; Iqbal, Mazhar; Ghaffar, Abdul; Abbas, Mateen
In this study aqueous extract of seeds and leaves of Trachyspermum ammi were evaluated for their ability to detoxify aflatoxin B1 and B2 (AFB1; 100 μg L(-1) and AFB2; 50 μg L(-1)) by in vitro and in vivo assays. Results indicated that T. ammi seeds extract was found to be significant (P < 0.05) in degrading AFB1 and AFB2 i.e., 92.8 and 91.9% respectively. However, T. ammi leaves extract proved to be less efficient in degrading these aflatoxins, under optimized conditions i.e., pH 8, temperature 30°C and incubation period of 72 h. The structural elucidation of degraded toxin products by LCMS/MS analysis showed that eight degraded products of AFB1 and AFB2 were formed. MS/MS spectra showed that most of the products were formed by the removal of double bond in the terminal furan ring and modification of lactone group indicating less toxicity as compared to parent compounds. Brine shrimps bioassay further confirmed the low toxicity of degraded products, showing that T. ammi seeds extract can be used as an effective tool for the detoxification of aflatoxins. PMID:27064492
Identification of the chemical constituents of Chinese medicine Yi-Xin-Shu capsule by molecular feature orientated precursor ion selection and tandem mass spectrometry structure elucidation.
Wang, Hong-ping; Chen, Chang; Liu, Yan; Yang, Hong-Jun; Wu, Hong-Wei; Xiao, Hong-Bin
The incomplete identification of the chemical components of traditional Chinese medicinal formula has been one of the bottlenecks in the modernization of traditional Chinese medicine. Tandem mass spectrometry has been widely used for the identification of chemical substances. Current automatic tandem mass spectrometry acquisition, where precursor ions were selected according to their signal intensity, encounters a drawback in chemical substances identification when samples contain many overlapping signals. Compounds in minor or trace amounts could not be identified because most tandem mass spectrometry information was lost. Herein, a molecular feature orientated precursor ion selection and tandem mass spectrometry structure elucidation method for complex Chinese medicine chemical constituent analysis was developed. The precursor ions were selected according to their two-dimensional characteristics of retention times and mass-to-charge ratio ranges from herbal compounds, so that all precursor ions from herbal compounds were included and more minor chemical constituents in Chinese medicine were identified. Compared to the conventional automatic tandem mass spectrometry setups, the approach is novel and can overcome the drawback for chemical substances identification. As an example, 276 compounds from the Chinese Medicine of Yi-Xin-Shu capsule were identified. PMID:26311399
Structure elucidation of an artifact discharging from rubber-based vial closures by means of gas chromatography/tandem mass spectrometry.
Kapp, Thomas; Vetter, Walter
The use of vial closures equipped with butyl rubber septa may lead to sample contamination by rubber additives discharging from the septum material. In this study, the structure elucidation of an artifact causing intense signals in gas chromatography/electron capture negative ion mass spectrometry (GC/ECNI-MS) and gas chromatographic analyses with electron capture detection is described. Tentative identification of the leached compound was achieved by employing tandem mass spectrometric techniques both in electron capture negative ion and in electron ionization modes. The artifact could thus be characterized as 2-benzothiazolyl-N,N-dimethyl dithiocarbamate, which is a known vulcanization accelerator for rubber. It is conceivable that the identified compound or related substances are also used in other applications. Therefore, two food-related matrixes were investigated for a possible migration of this compound into foods. During these analyses, the tentatively identified rubber additive was detected in an aqueous extract of a rubber seal ring for canning jars. GC/ECNI-MS provided better sensitivity and selectivity than GC/EI-MS for the determination of the rubber additive and other mercaptobenzothiazole-derived substances. PMID:17134153
Elucidating the band structure and free charge carrier dynamics of pure and impurities doped CH3NH3PbI(3-x)Cl(x) perovskite thin films.
Zhang, Zhen-Yu; Chen, Xin; Wang, Hai-Yu; Xu, Ming; Gao, Bing-Rong; Chen, Qi-Dai; Sun, Hong-Bo
CH3NH3PbI3-xClx perovskite material has been commonly used as the free charge generator and reservoir in highly efficient perovskite-based solid-state solar photovoltaic devices. However, many of the underlying fundamental photophysical mechanisms in this material such as the perovskite transition band structure as well as the dependent relationship between the carrier properties and lattice properties still lack sufficient understanding. Here, we elucidated the fundamental band structure of the pure CH3NH3PbI3-xClx pervoskite lattice, and then reported about the dependent relationship between the free charge carrier characteristic and the different CH3NH3PbI3-xClx pervoskite lattice thin films utilizing femtosecond time-resolved pump-probe technologies. The data demonstrated that the pure perovskite crystal band structure should only have one conduction and one valence band rather than dual valences, and the pure perovskite lattice could trigger more free charge carriers with a slower recombination rate under an identical pump intensity compared with the impurities doped perovskite crystal. We also investigated the perovskite film performance when exposed to moisture and water, the corresponding results gave us a dip in the optimization of the performance of perovskite based devices, and so as a priority this material should be isolated from moisture (water). This work may propose a deeper perspective on the comprehension for this material and it is useful for future optimization of applications in photovoltaic and light emission devices. PMID:26497219
Bioassay-Guided Isolation and Structural Modification of the Anti-TB Resorcinols from Ardisia gigantifolia.
Guan, Yi-Fu; Song, Xun; Qiu, Ming-Hua; Luo, Shi-Hong; Wang, Bao-Jie; Van Hung, Nguyen; Cuong, Nguyen M; Soejarto, Djaja Doel; Fong, Harry H S; Franzblau, Scott G; Li, Sheng-Hong; He, Zhen-Dan; Zhang, Hong-Jie
Tuberculosis (TB) is a highly contagious disease mainly caused by Mycobacterium tuberculosis H37 RV . Antitubercular (anti-TB) bioassay-guided isolation of the CHCl3 extract of the leaves and stems of the medicinal plant Ardisia gigantifolia led to the isolation of two anti-TB 5-alkylresorcinols, 5-(8Z-heptadecenyl) resorcinol (1) and 5-(8Z-pentadecenyl) resorcinol (2). We further synthesized 15 derivatives based on these two natural products. These compounds (natural and synthetic) were evaluated for their anti-TB activity against Mycobacterium tuberculosis H37 RV . Resorcinols 1 and 2 exhibited anti-TB activity with MIC values at 34.4 and 79.2 μm in MABA assay, respectively, and 91.7 and 168.3 μm in LORA assay, respectively. Among these derivatives, compound 8 was found to show improved anti-TB activity than its synthetic precursor (2) with MIC values at 42.0 μm in MABA assay and 100.2 μm in LORA assay. The active compounds should be regarded as new hits for further study as a novel class of anti-TB agents. The distinct structure-activity correlations of the parent compound were elucidated based on these derivatives. PMID:26992112
Dke1--structure, dynamics, and function: a theoretical and experimental study elucidating the role of the binding site shape and the hydrogen-bonding network in catalysis.
Brkić, Hrvoje; Buongiorno, Daniela; Ramek, Michael; Straganz, Grit; Tomić, Sanja
This study elucidates the role of the protein structure in the catalysis of β-diketone cleavage at the three-histidine metal center of diketone cleaving enzyme (Dke1) by computational methods in correlation with kinetic and mutational analyses. Molecular dynamics simulations, using quantum mechanically deduced parameters for the nonheme Fe(II) cofactor, were performed and showed a distinct organization of the hydrophilic triad in the free and substrate-ligated wild-type enzyme. It is shown that in the free species, the Fe(II) center is coordinated to three histidines and one glutamate, whereas the substrate-ligated, catalytically competent enzyme-substrate complex has an Fe(II) center with three-histidine coordination, with a small fraction of three-histidine, one-glutamate coordination. The substrate binding modes and channels for the traffic of water and ligands (2,4-pentandionyl anion, methylglyoxal, and acetate) were identified. To characterize the impact of the hydrophobic protein environment around the metal center on catalysis, a set of hydrophobic residues close to the active site were targeted. The variations resulted in an up to tenfold decrease of the O(2) reduction rates for the mutants. Molecular dynamics studies revealed an impact of the hydrophobic residues on the substrate stabilization in the active site as well as on the orientations of Glu98 and Arg80, which have previously been shown to be crucial for catalysis. Consequently, the Glu98-His104 interaction in the variants is weaker than in the wild-type complex. The role of protein structure in stabilizing the primary O(2) reduction step in Dke1 is discussed on the basis of our results. PMID:22526564
Systematic Structural Elucidation for the Protonated Form of Rare Earth Bis(porphyrinato) Double-Decker Complexes: Direct Structural Evidence of the Location of the Attached Proton.
Yamashita, Ken-Ichi; Sakata, Naoya; Ogawa, Takuji
Direct structural evidence of the presence and location of the attached proton in the protonated form of rare earth bis(porphyrinato) double-decker complexes is obtained from an X-ray diffraction study of single crystals for a series of protonated forms of bis(tetraphenylporphyrinato) complexes [M(III)(tpp)(tppH)] (M = Tb, Y, Sm, Nd, and La). When CHCl3 is used as a solvent for crystallization of the complexes, their nondisordered molecular structures are obtained and the attached proton is identified on one of the eight nitrogen atoms. Use of other solvents affords another type of crystal, in which the position of the proton is disordered and thus the molecular structure is averaged. La complex also affords the disordered average structure even when CHCl3 is used for crystallization. A variable-temperature diffraction study for the Tb complex reveals that the dynamics of the proton in the nondisordered crystal is restricted. PMID:27541189
Elucidation of a masked repeating structure of the O-specific polysaccharide of the halotolerant soil bacteria Azospirillum halopraeferens Au4.
Sigida, Elena N; Fedonenko, Yuliya P; Shashkov, Alexander S; Arbatsky, Nikolay P; Zdorovenko, Evelina L; Konnova, Svetlana A; Ignatov, Vladimir V; Knirel, Yuriy A
An O-specific polysaccharide was obtained by mild acid hydrolysis of the lipopolysaccharide isolated by the phenol-water extraction from the halotolerant soil bacteria Azospirillum halopraeferens type strain Au4. The polysaccharide was studied by sugar and methylation analyses, selective cleavages by Smith degradation and solvolysis with trifluoroacetic acid, one- and two-dimensional (1)H and (13)C NMR spectroscopy. The following masked repeating structure of the O-specific polysaccharide was established: →3)-α-L-Rhap2Me-(1→3)-[β-D-Glcp-(1→4)]-α-D-Fucp-(1→2)-β-D-Xylp-(1→, where non-stoichiometric substituents, an O-methyl group (~45%) and a side-chain glucose residue (~65%), are shown in italics. PMID:27340454
Elucidation of a masked repeating structure of the O-specific polysaccharide of the halotolerant soil bacteria Azospirillum halopraeferens Au4
Fedonenko, Yuliya P; Shashkov, Alexander S; Arbatsky, Nikolay P; Zdorovenko, Evelina L; Konnova, Svetlana A; Ignatov, Vladimir V; Knirel, Yuriy A
Summary An O-specific polysaccharide was obtained by mild acid hydrolysis of the lipopolysaccharide isolated by the phenol–water extraction from the halotolerant soil bacteria Azospirillum halopraeferens type strain Au4. The polysaccharide was studied by sugar and methylation analyses, selective cleavages by Smith degradation and solvolysis with trifluoroacetic acid, one- and two-dimensional 1H and 13C NMR spectroscopy. The following masked repeating structure of the O-specific polysaccharide was established: →3)-α-L-Rhap2Me-(1→3)-[β-D-Glcp-(1→4)]-α-D-Fucp-(1→2)-β-D-Xylp-(1→, where non-stoichiometric substituents, an O-methyl group (~45%) and a side-chain glucose residue (~65%), are shown in italics. PMID:27340454
First attempts at an elucidation of the interface structure resulting from the interaction between methacrylonitrile and a platinum anode: an experimental and theoretical (ab initio) study
NASA Astrophysics Data System (ADS)
Bureau, Christophe; Deniau, Guy; Valin, Françoise; Guittet, Marie-Joseph; Lécayon, Gérard; Delhalle, Joseph
The aim of the present paper is to contribute to the elucidation of the molecular structures obtained on a platinum surface as this surface is submitted to an anodic potential (with respect to a silver reference electrode) when dipped into pure 2-methyl 2-propenenitrile (methacrylonitrile). Modified surfaces are examined using X- and UV-photoelectron spectroscopies (UPS and XPS). The results evidence the formation of an ultra-thin (20-40 Å) grafted oligomer film, which is not classical polymethacrylonitrile (PMAN), as obtained through a radical or anionic mechanism: spectral characteristics argue in the sense of a cationic polymerization of methacrylonitrile through its nitrile groups, as evidenced by a lowering of the gap as well as by the UPS and XPS (N 1s region) spectra. Molecular models of the reactants and reaction intermediates are proposed for the cationic polymerization of methacrylonitrile, and show that this polymerization is about as feasible as that of acetonitrile, at least on kinetic control grounds. Two different mechanisms are nonetheless possible, leading either to a quasi conjugated poly-imine type -(N C) n-, or to a poly-cumulene type -(N C C) n- network. Theoretical consierations on reactants properties lead us to select the poly-imine way as the most plausible. Along with literature data concerning chemisorbed nitriles on platinum surfaces, a molecular model of the final state of the poly-imine reaction is then designed, comprising a three atom cluster to render the grafting site, and a dimer to render the grafted structure. A full geometry optimization is performed on the organic moiety at the Hartree-Fock (ab initio) level of theory, and a rough evaluation of the spectral footprint of the interface bond in the N 1s region is performed on the basis of Koopmans theorem with calibration on the bulk polymer peak. A preliminary 2.7 eV downward shift is predicted for N 1s interface nitrogens with respect to the polymer peak, which can
Structural Elucidation of Diglycosyl Diacylglycerol and Monoglycosyl Diacylglycerol from Streptococcus pneumoniae by Multiple-Stage Linear Ion-Trap Mass Spectrometry with Electrospray Ionization
Tatituri, Raju Venkata Veera; Brenner, Michael B.; Turk, John; Hsu, Fong-Fu
The cell wall of the pathogenic bacterium Streptococcus pneumoniae (S. pneumoniae) contains glucopyranosyl diacylglycerol (GlcDAG) and galactoglucopyranosyldiacylglycerol (GalGlcDAG). The specific GlcDAG consisting of vaccenic acid substituent at sn-2 was recently identified as another glycolipid antigen family recognized by invariant natural killer T cells (iNKT cells). Here, we describe a linear ion-trap (LIT) multiple-stage (MSn) mass spectrometric approach towards structural analysis of GalGlcDAG and GlcDAG. Structural information derived from MSn (n = 2,3) on the [M + Li]+ adduct ions desorbed by electrospray ionization (ESI) affords identification of the fatty acid substituents, assignment of the fatty acyl groups on the glycerol backbone, as well as the location of double bond along the fatty acyl chain. The identification of the fatty acyl groups and determination of their regio-specificity were confirmed by MSn (n = 2,3) on the [M + NH4]+ ions. We establish the structures of GalGlcDAG and GlcDAG isolated from S. pneumoniae, in which the major species consists of a 16:1- or 18:1-fatty acid substituent mainly at sn-2, and the double bond of the fatty acid is located at ω-7 (n-7). More than one isomers were found for each mass in the family. This mass spectrometric approach provides a simple method to achieve structure identification of this important lipid family that would be very difficult to define using the traditional method. PMID:22282097
Structural properties of rutile TiO2 nanoparticles accumulated in a model of gastrointestinal epithelium elucidated by micro-beam x-ray absorption fine structure spectroscopy
NASA Astrophysics Data System (ADS)
Veronesi, G.; Brun, E.; Fayard, B.; Cotte, M.; Carrière, M.
Micro-beam x-ray absorption fine structure spectroscopy was used to investigate rutile TiO2 nanoparticles internalized into gastrointestinal cells during their crossing of a gut model barrier. Nanoparticles diluted in culture medium tend to accumulate in cells after 48 h exposure; however, no spectral differences arise between particles in cellular and in acellular environments, as corroborated by quantitative analysis. This finding establishes that no modification of the lattice properties of the nanoparticles occurs upon interaction with the barrier. These measurements demonstrate the possibility of interrogating nanoparticles in situ within cells, suggesting a way to investigate their fate when incorporated in biological hosts.
Microbial Communities in Sediments of Lagos Lagoon, Nigeria: Elucidation of Community Structure and Potential Impacts of Contamination by Municipal and Industrial Wastes.
Obi, Chioma C; Adebusoye, Sunday A; Ugoji, Esther O; Ilori, Mathew O; Amund, Olukayode O; Hickey, William J
Estuarine sediments are significant repositories of anthropogenic contaminants, and thus knowledge of the impacts of pollution upon microbial communities in these environments is important to understand potential effects on estuaries as a whole. The Lagos lagoon (Nigeria) is one of Africa's largest estuarine ecosystems, and is impacted by hydrocarbon pollutants and other industrial and municipal wastes. The goal of this study was to elucidate microbial community structure in Lagos lagoon sediments to identify groups that may be adversely affected by pollution, and those that may serve as degraders of environmental contaminants, especially polycyclic aromatic hydrocarbons (PAHs). Sediment samples were collected from sites that ranged in types and levels of anthropogenic impacts. The sediments were characterized for a range of physicochemical properties, and microbial community structure was determined by Illumina sequencing of the 16S rRNA genes. Microbial diversity (species richness and evenness) in the Apapa and Eledu sediments was reduced compared to that of the Ofin site, and communities of both of the former two were dominated by a single operational taxonomic unit (OTU) assigned to the family Helicobacteraceae (Epsilonproteobacteria). In the Ofin community, Epsilonproteobacteria were minor constituents, while the major groups were Cyanobacteria, Bacteroidetes, and Firmicutes, which were all minor in the Apapa and Eledu sediments. Sediment oxygen demand (SOD), a broad indicator of contamination, was identified by multivariate analyses as strongly correlated with variation in alpha diversity. Environmental variables that explained beta diversity patterns included SOD, as well as levels of naphthalene, acenaphthylene, cobalt, cadmium, total organic matter, or nitrate. Of 582 OTU identified, abundance of 167 was significantly correlated (false discovery rate q≤ 0.05) to environmental variables. The largest group of OTU correlated with PAH levels were PAH
Microbial Communities in Sediments of Lagos Lagoon, Nigeria: Elucidation of Community Structure and Potential Impacts of Contamination by Municipal and Industrial Wastes
Obi, Chioma C.; Adebusoye, Sunday A.; Ugoji, Esther O.; Ilori, Mathew O.; Amund, Olukayode O.; Hickey, William J.
Estuarine sediments are significant repositories of anthropogenic contaminants, and thus knowledge of the impacts of pollution upon microbial communities in these environments is important to understand potential effects on estuaries as a whole. The Lagos lagoon (Nigeria) is one of Africa's largest estuarine ecosystems, and is impacted by hydrocarbon pollutants and other industrial and municipal wastes. The goal of this study was to elucidate microbial community structure in Lagos lagoon sediments to identify groups that may be adversely affected by pollution, and those that may serve as degraders of environmental contaminants, especially polycyclic aromatic hydrocarbons (PAHs). Sediment samples were collected from sites that ranged in types and levels of anthropogenic impacts. The sediments were characterized for a range of physicochemical properties, and microbial community structure was determined by Illumina sequencing of the 16S rRNA genes. Microbial diversity (species richness and evenness) in the Apapa and Eledu sediments was reduced compared to that of the Ofin site, and communities of both of the former two were dominated by a single operational taxonomic unit (OTU) assigned to the family Helicobacteraceae (Epsilonproteobacteria). In the Ofin community, Epsilonproteobacteria were minor constituents, while the major groups were Cyanobacteria, Bacteroidetes, and Firmicutes, which were all minor in the Apapa and Eledu sediments. Sediment oxygen demand (SOD), a broad indicator of contamination, was identified by multivariate analyses as strongly correlated with variation in alpha diversity. Environmental variables that explained beta diversity patterns included SOD, as well as levels of naphthalene, acenaphthylene, cobalt, cadmium, total organic matter, or nitrate. Of 582 OTU identified, abundance of 167 was significantly correlated (false discovery rate q≤ 0.05) to environmental variables. The largest group of OTU correlated with PAH levels were PAH
Synthesis, structural elucidation, and catalytic properties in olefin epoxidation of the polymeric hybrid material [Mo3O9(2-[3(5)-pyrazolyl]pyridine)]n.
Amarante, Tatiana R; Neves, Patrícia; Gomes, Ana C; Nolasco, Mariela M; Ribeiro-Claro, Paulo; Coelho, Ana C; Valente, Anabela A; Paz, Filipe A Almeida; Smeets, Stef; McCusker, Lynne B; Pillinger, Martyn; Gonçalves, Isabel S
The reaction of [MoO2Cl2(pzpy)] (1) (pzpy = 2-[3(5)-pyrazolyl]pyridine) with water in an open reflux system (16 h), in a microwave synthesis system (120 °C, 2 h), or in a Teflon-lined stainless steel digestion bomb (100 °C, 19 h) gave the molybdenum oxide/pyrazolylpyridine polymeric hybrid material [Mo3O9(pzpy)]n (2) as a microcrystalline powder in yields of 72–79%. Compound 2 can also be obtained by the hydrothermal reaction of MoO3, pzpy, and H2O at 160 °C for 3 d. Secondary products isolated from the reaction solutions included the salt (pzpyH)2(MoCl4) (3) (pzpyH = 2-[3(5)-pyrazolyl]pyridinium), containing a very rare example of the tetrahedral MoCl4(2–) anion, and the tetranuclear compound [Mo4O12(pzpy)4] (4). Reaction of 2 with excess tert-butylhydroperoxide (TBHP) led to the isolation of the oxodiperoxo complex [MoO(O2)2(pzpy)] (5). Single-crystal X-ray structures of 3 and 5 are described. Fourier transform (FT)-IR and FT Raman spectra for 1, 4, and 5 were assigned based on density functional theory calculations. The structure of 2 was determined from synchrotron powder X-ray diffraction data in combination with other physicochemical information. In 2, a hybrid organic–inorganic one-dimensional (1D) polymer, ∞(1)[Mo3O9(pzpy)], is formed by the connection of two very distinct components: a double ladder-type inorganic core reminiscent of the crystal structure of MoO3 and 1D chains of corner-sharing distorted {MoO4N2} octahedra. Compound 2 exhibits moderate activity and high selectivity when used as a (pre)catalyst for the epoxidation of cis-cyclooctene with TBHP. Under the reaction conditions used, 2 is poorly soluble and is gradually converted into 5, which is at least partly responsible for the catalytic reaction. PMID:24520803
Structure elucidation and gene cluster annotation of the O-antigen of Escherichia coli O39; application of anhydrous trifluoroacetic acid for selective cleavage of glycosidic linkages.
Perepelov, Andrei V; Filatov, Andrei V; Wang, Quan; L'vov, Vyacheslav L; Qian, Ye; Shashkov, Alexander S; Wang, Lei; Knirel, Yuriy A
O-Polysaccharide (O-antigen) accompanied by a minor mannan was isolated from the lipopolysaccharide of Escherichia coli O39 and studied by component analyses, methylation, Smith degradation, mass spectrometry, and 1D and 2D NMR spectroscopy. In addition, a new approach, solvolysis with anhydrous trifluoroacetic acid, was applied to cleave selectively the rhamnosidic linkage. The following structure of the O-polysaccharide was established: α--D-Galpl-->3-->3)-β-D-Quip4N(R3Hb)-(1-->2)-α-D-Manp-(l-->4)-α-L-Rhap-(1-->3)-α-D-GlcpNAc-(1--> where D-Qui4N(R3Hb) indicates 4,6-dideoxy-4-[(R)-3-hydroxybutanoylamino]-d-glucose. The O-antigen gene cluster of E. coli O39 has been sequenced. The gene functions were tentatively assigned by a comparison with sequences in the available databases and found to be in agreement with the O-polysaccharide structure. PMID:24607538
[Isolation and structural identification of flavonoids from Aurantii Fructus].
Ding, Yi-qiang; Xiong, Ying; Zhou, Bin; Deng, Min-zhi; Deng, Ke-zhong
Aurantii Fructus is the dried and immature fruit of Citrus aurantium and its cultivars. To investigate the chemical constituents of Aurantii Fructus, the separation and purification of constituents were performed by column chromatography on silica gel LH-20, HW-40, ODS, PHPLC and PTLC. Fourteen flavonoids, including four flavone glycosides and ten polymethoxyflavones (PMFs) were isolated from the EtOAc fraction and Petroleum ether fraction of Aurantii Fructus and their structures were identified by physicochemical properties and spectral data (NMR and MS) as (2R) -and (2S)-6"-O-acetylprunin (1,2), naringenin-7-O-β-D-glucopyranside (3), 5,7,4'-trihydroxy-8,3'-dimethoxyflavone-3-O-6"-(3-hydroxyl-3-methylglutaroyl)-β-D-glucopyranoside(4), 4'-hydroxy-5,6, 7-trimethoxyflavone (5), natsudaidain (6), nobiletin (7), sinensetin (8), 5,6,7,4'-tetramethoxyflavone (9), 5,7,8,4'-tetramethoxyflavone (10), 3,5,6,7,8,3',4'-heptamethoxyflavone (11), tangeretin (12), 5-demethyl nobiletin (13), and 5-hydroxy-6,7,3', 4'-tetramethoxyflavone (14). Compound 3-5 s were isolated from this plant for the first time and compound 1 was a new one. PMID:26591524
Response of seismic-isolated structures under long-period motions
Ma, D.C.
In the past decade, considerable progress has been made on reducing the seismic response of structures through seismic isolation. Application of seismic-isolation techniques to nuclear power facilities is currently being investigated. This paper presents an analysis of the effect of long period motions on a seismic-isolated nuclear structure. Preliminary analysis indicates that long-period earthquake motions increase structural accelerations and relative displacements between the upper and lower mats. Relative displacement between the mats can be represented by spectral displacement at the frequency of the structure, and can be effectively reduced by increasing viscous damping in the isolator. The isolated structure behaves as a system with one degree of freedom. Future analysis of seismic effects on seismic-isolated structures should include the linear and nonlinear effects of soil-structure interactions. 3 refs., 12 figs., 3 tabs.
Preparative isolation and structural characterization of sucrose ester isomers from oriental tobacco.
Jia, Chunxiao; Wang, Yingying; Zhu, Yonghua; Xu, Chunping; Mao, Duobin
To date, the structures of the sucrose tetraester (STE) isomers, a main kind of sucrose esters (SEs) in Solanum, have not been conclusively assigned. In this study, three groups of STE isomers with the molecular weight 650, 664 and 678 (designated as STE I, STE II and STE III, respectively) have been isolated and purified from the oriental tobacco-Komotini Basma using a semi-preparative RP-HPLC method. The full characterization of the isomers in the three groups of STE were investigated for the first time by MS (HRMS, MS(2)) and NMR ((1)H, (13)C, HSQC) spectroscopy combined with alkaline hydrolysis and STE derivation experiments. The STE III (a single compound) was confirmed as a known sucrose tetraester. Furthermore, the STE II was found to contain three isomers and the structures were first unambiguously established as 6-O-acetyl (2,3 or 2,4 or 3,4)-di-O-3-methylvaleryl-(4 or 3 or 2)-O-2-methylbutyryl-α-d-glucopyranosyl-β-d-fructofuranoside. Finally, the STE I was discovered to contain seven isomers and the structures were elucidated as 6-O-acetyl (2 or 3 or 4)-O-3-methylvaleryl-(3,4 or 2,4 or 2,3)-di-O-2-methylbutyryl-α-d-glucopyranosyl-β-d-fructofuranoside, 6-O-acetyl (2 or 3 or 4)-O-3-methylvaleryl-(3,4 or 2,4 or 2,3)-di-O-isovaleryl-α-d-glucopyranosyl-β-d-fructofuranoside and 6-O-acetyl (2,3 or 2,4 or 3,4)-di-O-3-methylvaleryl-(4 or 3 or 2)-O-isobutyryl-α-d-glucopyranosyl-β-d-fructofuranoside (one of the 3 isomers). PMID:23542308
Analysis and reduction of leakage current of 2 kV monolithic isolator with wide trench spiral isolation structure
NASA Astrophysics Data System (ADS)
Takeuchi, Yusuke; Kuroda, Rihito; Sugawa, Shigetoshi
In this work, the origin of the leakage current of a highly area-efficient silicon-on-insulator (SOI) monolithic isolator using a spiral trench isolation structure is clarified by experimental and simulation analyses and its reduction method is proposed. It was found that parasitic MOSFET inversion and accumulation channels formed at the SOI and buried oxide (BOX) interface are the origins of leakage current. To reduce the leakage current, adequate SOI spiral length and width and BOX layer thickness are proposed for various voltage usages and show the possibility of 4 kV voltage tolerance and 500 MΩ isolation resistivity.
Structure of turbulent wedges created by isolated surface roughness
NASA Astrophysics Data System (ADS)
Kuester, Matthew S.; White, Edward B.
Isolated surface roughness in a laminar boundary layer can create a wedge of turbulence that spreads laterally into the surrounding laminar flow. Some recent studies have identified high- and low-speed streaks along the exterior of turbulent wedges. In this experiment, developing turbulent wedges are measured to observe the creation of these streaks. Naphthalene shear stress surface visualization and hotwire measurements are utilized to investigate the details of turbulent wedges created by cylinders in a laminar flat-plate boundary layer. Both the surface visualization and the hotwire measurements show high- and low-speed streaks in the wake of the cylinder that devolve into a turbulent wedge. The turbulent wedge spreading is associated with the emergence of these high- and low-speed streaks along the outside of the wedge. As the wedge evolves in the streamwise direction, these streaks persist inside of the core of the wedge, while new, lower amplitude streaks form along the outside of the wedge. Adding asymmetry to the cylinder moved the virtual origin closer to the roughness and increased the vortex shedding frequency, while adding small-scale roughness features did not strongly affect turbulent wedge development. Intermittency calculations additionally show the origin of the turbulent core inside of the wedge. The structure and spacing of the high-speed streaks along the extremities of the turbulent wedge give insight into the spreading angle of the turbulent wedge.
Population structure and genetic diversity within California Citrus tristeza virus (CTV) isolates.
Kong, P; Rubio, L; Polek, M; Falk, B W
The Closterovirus, Citrus tristeza virus (CTV) is an aphid-borne RNA virus that is the causal agent of important worldwide economic losses in citrus. Biological and molecular variation has been observed for many CTV isolates. In this work we detected and analyzed sequence variants (haplotypes) within individual CTV isolates. We studied the population structure of five California CTV isolates by single strand conformation polymorphism (SSCP) analysis of four CTV genomic regions. Also, we estimated the genetic diversity within and between isolates by analysis of haplotype nucleotide sequences. Most CTV isolates were composed of a population of genetically related variants (haplotypes), one being predominant. However in one case, we found a high nucleotide divergence between haplotypes of the same isolate. Comparison of these haplotypes with those from other isolates suggests that some CTV isolates could have arisen as result of a mixed infection of two divergent isolates. PMID:11129629
Structural confirmation of novel oligosaccharides isolated from sugar beet molasses.
Abe, Tatsuya; Kikuchi, Hiroto; Aritsuka, Tsutomu; Takata, Yusuke; Fukushi, Eri; Fukushi, Yukiharu; Kawabata, Jun; Ueno, Keiji; Onodera, Shuichi; Shiomi, Norio
Eleven oligosaccharides were isolated from sugar beet molasses using carbon-Celite column chromatography and HPLC. The constituent sugars and linkage positions were determined using methylation analysis, MALDI-TOF-MS, and NMR measurements. The configurations of isolated oligosaccharides were confirmed based on detailed NMR analysis. Based on our results, three of the 11 oligosaccharides were novel. PMID:26920296
A novel polysaccharide isolated from mulberry fruits (Murus alba L.) and its selenide derivative: structural characterization and biological activities.
Chen, Chun; Zhang, Bin; Fu, Xiong; Liu, Rui Hai
A novel polysaccharide (MFP3P) was isolated from Murus alba L. through the hot water extraction method followed by chromatographic purification. The chemical structure of MFP3P was elucidated by acid hydrolysis, Smith degradation and methylation analysis, along with FT-IR, GC-MS, (1)H and (13)C NMR spectroscopy. Its morphological properties were further characterized by SEM and AFM. The selenide of the polysaccharide (MFP3P-Se) was obtained by the Na2SeO3/BaCl2 method. The antioxidant properties showed that MFP3P-Se exhibited higher peroxy radical-scavenging capacity than MFP3P in vitro. Moreover, MFP3P-Se had more significant hypoglycemic effects than MFP3P through promoting pancreatic cell proliferation and increasing glucose metabolism and insulin secretion. PMID:27241036
Structural and biological characterization of one antibacterial acylpolyamine isolated from the hemocytes of the spider Acanthocurria gomesiana
Pereira, Lourivaldo S.; Silva, Pedro I.; Miranda, M. Teresa M.; Almeida, Igor C.; Naoki, Hideo; Konno, Katsuhiro; Daffre, Sirlei . E-mail: email@example.com
We have isolated a 417 Da antibacterial molecule, named mygalin, from the hemocytes of the spider Acanthoscurria gomesiana. The structure of mygalin was elucidated by tandem mass spectrometry (MS/MS) and by two spectroscopic techniques, nuclear magnetic resonance (NMR) and ultraviolet (UV) spectroscopy. Mygalin was identified as bis-acylpolyamine N1,N8-bis(2,5-dihydroxybenzoyl)spermidine, in which the primary amino groups of the spermidine are acylated with the carboxyl group of the 2,5-dihydroxybenzoic acid. Mygalin was active against Escherichia coli at 85 {mu}M, being this activity inhibited completely by catalase. Therefore, the antibacterial activity of mygalin was attributed to its production of hydrogen peroxide (H{sub 2}O{sub 2}). The putative mechanisms of formation of H{sub 2}O{sub 2} from mygalin are discussed. To our knowledge this is the first report of one bis-acylpolyamine with antibacterial activity purified from animal source.
Scopariusicides, Novel Unsymmetrical Cyclobutanes: Structural Elucidation and Concise Synthesis by a Combination of Intermolecular [2 + 2] Cycloaddition and C-H Functionalization.
Zhou, Min; Li, Xing-Ren; Tang, Jian-Wei; Liu, Yang; Li, Xiao-Nian; Wu, Bin; Qin, Hong-Bo; Du, Xue; Li, Li-Mei; Wang, Wei-Guang; Pu, Jian-Xin; Sun, Han-Dong
Scopariusicides A (1) and B (2), two novel immunosuppressive unsymmetrical cyclobutane derivatives, were isolated from the aerial parts of Isodon scoparius. Moreover, based on the results of phytochemical investigation, a concise stereocontrolled synthesis of scopariusicide A and its analogues with enhanced biological activities was efficiently achieved using the main diterpenoid (3) isolated from this plant as a readily available starting material. A crossed intermolecular [2 + 2] photocycloaddition and a Pd-catalyzed sp(3) C-H bond β-arylation were used synergistically to access the highly congested unsymmetrical cyclobutane core with four contiguous stereocenters. PMID:26617269
Quantitative structure toxicity relationships for phenols in isolated rat hepatocytes.
Moridani, Majid Y; Siraki, Arno; O'Brien, Peter J
Quantitative structure toxicity relationship (QSTR) equations were obtained to predict and describe the cytotoxicity of 31 phenols using logLD(50) as a concentration to induce 50% cytotoxicity of isolated rat hepatocytes in 2 h and logP as octanol/water partitioning: logLD(50) (microM)=-0.588(+/-0.059)logP+4.652(+/-0.153) (n=27, r(2)=0.801, s=0.261, P<1 x 10(-9)). Hydroquinone, catechol, 4-nitrophenol, and 2,4-dinitrophenol were outliers for this equation. When the ionization constant pK(a) was considered as a contributing factor a two-parameter QSTR equation was derived: logLD(50) (microM)=-0.595(+/-0.051)logP+0.197(+/-0.029)pK(a)+2.665(+/-0.281) (n=28, r(2)=0.859, s=0.218, P<1 x 10(-6)). Using sigma+, the Brown variation of the Hammet electronic constant, as a contributing parameter, the cytotoxicity of phenols towards hepatocytes were defined by logLD(50) (microM)=-0.594(+/-0.052)logP-0.552(+/-0.085)sigma+ +4.540(+/-0.132) (n=28, r(2)=0.853, s=0.223, P<1 x 10(-6)). Replacing sigma+ with the homolytic bond dissociation energy (BDE) for (X-PhOH+PhO.-->X-PhO.+PhOH) led to logLD(50) (microM)=-0.601(+/-0.066)logP-0.040(+/-0.018)BDE+4.611(+/-0.166) (n=23, r(2)=0.827, s=0.223, P<0.05). Hydroquinone, catechol and 2-nitrophenol were outliers for the above equations. Using redox potential and logP led to a new correlation: logLD(50) (microM)=-0.529(+/-0.135)logP+2.077(+/-0.892)E(p/2)+2.806(+/-0.592) (n=15, r(2)=0.561, s=0.383, P<0.05) with 4-nitrophenol as an outlier. Our findings indicate that phenols with higher lipophilicity, BDE, or sigma+ values or with lower pK(a) and redox potential were more toxic towards hepatocytes. We also showed that a collapse of hepatocyte mitochondrial membrane potential preceded the cytotoxicity of most phenols. Our study indicates that one or a combination of mechanisms; i.e. mitochondrial uncoupling, phenoxy radicals, or phenol metabolism to quinone methides and quinones, contribute to phenol cytotoxicity towards hepatocytes depending on
Biosynthesis and structural characterization of silver nanoparticles from bacterial isolates
Zaki, Sahar; El Kady, M.F.; Abd-El-Haleem, Desouky
Graphical abstract: In this study five bacterial isolates belong to different genera were found to be able to biosynthesize silver nanoparticles. Biosynthesis and spectral characterization are reported here. Highlights: {yields} About 300 bacterial isolates were screened for their ability to produce nanosilvers {yields} Five of them were potential candidates for synthesis of silver nanoparticles {yields} Production of silver nanoparticles was examined using UV-Vis, XRD, SEM and EDS. {yields} The presence of nanoparticles with all five bacterial isolates was confirmed. -- Abstract: This study aimed to develop a green process for biosynthesis of silver nanomaterials by some Egyptian bacterial isolates. This target was achieved by screening an in-house culture collection consists of 300 bacterial isolates for silver nanoparticle formation. Through screening process, it was observed that strains belonging to Escherichia coli (S30, S78), Bacillus megaterium (S52), Acinetobacter sp. (S7) and Stenotrophomonas maltophilia (S54) were potential candidates for synthesis of silver nanoparticles. The extracellular production of silver nanoparticles by positive isolates was investigated by UV-Vis spectroscopy, X-ray diffraction (XRD), transmission electron microscope (TEM), scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDS). The results demonstrated that UV-visible spectrum of the aqueous medium containing silver ion showed a peak at 420 nm corresponding to the plasmon absorbance of silver nanoparticles. Scanning electron microscopy micrograph showed formation of silver nanoparticles in the range of 15-50 nm. XRD-spectrum of the silver nanoparticles exhibited 2{theta} values corresponding to the silver nanocrystal that produce in hexagonal and cubic crystal configurations with different plane of orientation. In addition, the signals of the silver atoms were observed by EDS-spectrum analysis that confirms the presence of silver nanoparticles (Ag
Semi-active control of isolated and damaged structures using online damage detection
NASA Astrophysics Data System (ADS)
Amini, Fereidoun; Mohajeri, Seyed Ahmad; Javanbakht, Majd
The idea of using semi-active or active control devices within a base isolation system has been developed recently, since applying this system to building structures has some shortcomings such as the creation of large displacements at the base level and the system's lack of adaptability to different seismic excitations. In this study, an integrated structural health monitoring and semi-active control scheme is proposed to enhance the seismic behavior of damaged isolated structures. The nonlinear behavior of an isolated structure is limited to the isolator level and the superstructure is assumed to remain linear. Then, using an online damage detection algorithm based on identified system Markov parameters and a semi-active fuzzy controller, the damage in the base isolator is mitigated and the seismic response of the structure is reduced. In addition, a magnetorheological damper is utilized as a well-studied semi-active actuator in the control system. The effectiveness of the proposed control system is evaluated through the numerical study of a six-degrees-of-freedom model of base-isolated buildings excited by various near-fault and far-field earthquake records. The results of the simulation show that the integrated algorithm is substantially effective in improving the dynamic behavior of isolated structures and reducing the damage in the isolator.
Interplay between the structural and magnetic probes in the elucidation of the structure of a novel 2D layered [V4O4(OH)2(O2CC6H4CO2)4]·DMF.
Djerdj, Igor; Škapin, Srečo D; Ceh, Miran; Jagličić, Zvonko; Pajić, Damir; Kozlevčar, Bojan; Orel, Bojan; Orel, Zorica Crnjak
The title compound has been synthesized under solvothermal conditions by reacting vanadium(V) oxytriisopropoxide with terephthalic acid in N,N-dimethylformamide. A combination of synchrotron powder diffraction, infrared spectroscopy, scanning and transmission electron microscopy, and thermal and chemical analysis elucidated the chemical, structural and microstructural features of a new 2D layered inorganic-organic framework. Due to the low-crystallinity of the final material, its crystal structure has been solved from synchrotron X-ray powder diffraction data using a direct space global optimization technique and subsequent constraint Rietveld refinement. [V(4)O(4)(OH)(2)(O(2)CC(6)H(4)CO(2))(4)]·DMF crystallizes in the monoclinic system (space group P2/m (No. 10)); cell parameters: a = 20.923(4) Å, b = 5.963(4) Å, c = 20.425(1) Å, β = 123.70(6)°, V = 2120.1(9) Å(3), Z = 2. The overall structure can be described as an array of parallel 2D layers running along [-101] direction, consisting of two types of vanadium oxidation states and coordination polyhedra: face-shared trigonal prisms (V(4+)) and distorted corner-shared square pyramids (V(5+)). Both configurations form independent parallel chains oriented along the 2-fold symmetry crystallographic b-axis mutually interlinked with terephthalate ligands in a monodentate mode perpendicular to it. The morphology of the compound exhibits long nanofibers, with the growth direction along the layered [-101] axis. The magnetic susceptibility measurements show that the magnetic properties of [V(4)O(4)(OH)(2)(O(2)CC(6)H(4)CO(2))(4)]·DMF can be described by a linear antiferromagnetic chain model, with the isotropic exchange interaction of J = -75 K between the nearest V(4+) neighbours of S = 1/2. PMID:22042096
Development of adaptive seismic isolators for ultimate seismic protection of civil structures
NASA Astrophysics Data System (ADS)
Li, Jianchun; Li, Yancheng; Li, Weihua; Samali, Bijan
Base isolation is the most popular seismic protection technique for civil engineering structures. However, research has revealed that the traditional base isolation system due to its passive nature is vulnerable to two kinds of earthquakes, i.e. the near-fault and far-fault earthquakes. A great deal of effort has been dedicated to improve the performance of the traditional base isolation system for these two types of earthquakes. This paper presents a recent research breakthrough on the development of a novel adaptive seismic isolation system as the quest for ultimate protection for civil structures, utilizing the field-dependent property of the magnetorheological elastomer (MRE). A novel adaptive seismic isolator was developed as the key element to form smart seismic isolation system. The novel isolator contains unique laminated structure of steel and MR elastomer layers, which enable its large-scale civil engineering applications, and a solenoid to provide sufficient and uniform magnetic field for energizing the field-dependent property of MR elastomers. With the controllable shear modulus/damping of the MR elastomer, the developed adaptive seismic isolator possesses a controllable lateral stiffness while maintaining adequate vertical loading capacity. In this paper, a comprehensive review on the development of the adaptive seismic isolator is present including designs, analysis and testing of two prototypical adaptive seismic isolators utilizing two different MRE materials. Experimental results show that the first prototypical MRE seismic isolator can provide stiffness increase up to 37.49%, while the second prototypical MRE seismic isolator provides amazing increase of lateral stiffness up to1630%. Such range of increase of the controllable stiffness of the seismic isolator makes it highly practical for developing new adaptive base isolation system utilizing either semi-active or smart passive controls.
X-ray absorption spectroscopy elucidates the impact of structural disorder on electron mobility in amorphous zinc-tin-oxide thin films
Siah, Sin Cheng E-mail: email@example.com; Lee, Yun Seog; Buonassisi, Tonio E-mail: email@example.com; Lee, Sang Woon; Gordon, Roy G.; Heo, Jaeyeong; Shibata, Tomohiro; Segre, Carlo U.
We investigate the correlation between the atomic structures of amorphous zinc-tin-oxide (a-ZTO) thin films grown by atomic layer deposition (ALD) and their electronic transport properties. We perform synchrotron-based X-ray absorption spectroscopy at the K-edges of Zn and Sn with varying [Zn]/[Sn] compositions in a-ZTO thin films. In extended X-ray absorption fine structure (EXAFS) measurements, signal attenuation from higher-order shells confirms the amorphous structure of a-ZTO thin films. Both quantitative EXAFS modeling and X-ray absorption near edge spectroscopy (XANES) reveal that structural disorder around Zn atoms increases with increasing [Sn]. Field- and Hall-effect mobilities are observed to decrease with increasing structural disorder around Zn atoms, suggesting that the degradation in electron mobility may be correlated with structural changes.
Elucidation of the Teixobactin Pharmacophore.
Yang, Hyunjun; Chen, Kevin H; Nowick, James S
This paper elucidates the teixobactin pharmacophore by comparing the arginine analogue of teixobactin Arg10-teixobactin to seven homologues with varying structure and stereochemistry. The roles of the guanidinium group at position 10, the stereochemistry of the macrolactone ring, and the "tail" comprising residues 1-5 are investigated. The guanidinium group is not necessary for activity; Lys10-teixobactin is more active than Arg10-teixobactin against Gram-positive bacteria in minimum inhibitory concentration (MIC) assays. The relative stereochemistry of the macrolactone ring is important. Diastereomer l-Thr8,Arg10-teixobactin is inactive, and diastereomer d-allo-Ile11,Arg10-teixobactin is less active. The macrolactone ring is critical; seco-Arg10-teixobactin is inactive. The absolute stereochemistry is not important; the enantiomer ent-Arg10-teixobactin is comparable in activity. The hydrophobic N-terminal tail is important. Truncation of residues 1-5 results in loss of activity, and replacement of residues 1-5 with a dodecanoyl group partially restores activity. These findings pave the way for developing simpler homologues of teixobactin with enhanced pharmacological properties. PMID:27232661
Persistent cystic fibrosis isolate Pseudomonas aeruginosa strain RP73 exhibits an under-acylated LPS structure responsible of its low inflammatory activity.
Di Lorenzo, Flaviana; Silipo, Alba; Bianconi, Irene; Lore', Nicola Ivan; Scamporrino, Andrea; Sturiale, Luisa; Garozzo, Domenico; Lanzetta, Rosa; Parrilli, Michelangelo; Bragonzi, Alessandra; Molinaro, Antonio
Pseudomonas aeruginosa, the major pathogen involved in lethal infections in cystic fibrosis (CF) population, is able to cause permanent chronic infections that can persist over the years. This ability to chronic colonize CF airways is related to a series of adaptive bacterial changes involving the immunostimulant lipopolysaccharide (LPS) molecule. The structure of LPSs isolated from several P. aeruginosa strains showed conserved features that can undergo chemical changes during the establishment of the chronic infection. In the present paper, we report the elucidation of the structure and the biological activity of the R-LPS (lipooligosaccharide, LOS) isolated from the persistent CF isolate P. aeruginosa strain RP73, in order to give further insights in the adaptation mechanism of the pathogen in the CF environment. The complete structural analysis of P. aeruginosa RP73 LOS was achieved by chemical analyses, NMR spectroscopy and MALDI MS spectrometry, while the assessment of the biological activity was attained testing the in vivo pro-inflammatory capacity of the isolated LOS molecule. While a typical CF LPS is able to trigger a high immune response and production of pro-inflammatory molecules, this P. aeruginosa RP73 LOS showed to possess a low pro-inflammatory capacity. This was possible due to a singular chemical structure possessing an under-acylated lipid A very similar to the LPS of P. aeruginosa found in chronic lung diseases such as bronchiectstasis. PMID:24856407
Engine isolation for structural-borne interior noise reduction in a general aviation aircraft
NASA Technical Reports Server (NTRS)
Unruh, J. F.; Scheidt, D. C.
Engine vibration isolation for structural-borne interior noise reduction is investigated. A laboratory based test procedure to simulate engine induced structure-borne noise transmission, the testing of a range of candidate isolators for relative performance data, and the development of an analytical model of the transmission phenomena for isolator design evaluation are addressed. The isolator relative performance test data show that the elastomeric isolators do not appear to operate as single degree of freedom systems with respect to noise isolation. Noise isolation beyond 150 Hz levels off and begins to decrease somewhat above 600 Hz. Coupled analytical and empirical models were used to study the structure-borne noise transmission phenomena. Correlation of predicted results with measured data show that (1) the modeling procedures are reasonably accurate for isolator design evaluation, (2) the frequency dependent properties of the isolators must be included in the model if reasonably accurate noise prediction beyond 150 Hz is desired. The experimental and analytical studies were carried out in the frequency range from 10 Hz to 1000 Hz.
Pyripyropenes, novel inhibitors of acyl-CoA:cholesterol acyltransferase produced by Aspergillus fumigatus. II. Structure elucidation of pyripyropenes A, B, C and D.
Kim, Y K; Tomoda, H; Nishida, H; Sunazuka, T; Obata, R; Omura, S
The structures of pyripyropenes A, B, C and D, novel acyl-CoA:cholesterol acyltransferase (ACAT) inhibitors, were determined mainly by spectroscopic studies including various NMR measurements. Pyripyropenes have a common structure which consists of pyridine, alpha-pyrone and sesquiterpene moieties. One of the three O-acetyl residues in the sesquiterpene moiety of pyripyropene A is replaced with an O-propionyl residue in pyripyropenes B, C and D. PMID:8150710
Population Structure of Blueberry Mosaic Associated Virus: Evidence of Genetic Exchange in Geographically Distinct Isolates
Technology Transfer Automated Retrieval System (TEKTRAN)
The population structure of blueberry mosaic associated virus (BlMaV), a putative member of the family Ophioviridae, was examined using 59 isolates collected from North America and Slovenia. The studied isolates displayed low genetic diversity in the movement and nucleoprotein regions and low ratios...
Crystal structures and mutagenesis of PPP-family ser/thr protein phosphatases elucidate the selectivity of cantharidin and novel norcantharidin-based inhibitors of PP5C.
Chattopadhyay, Debasish; Swingle, Mark R; Salter, Edward A; Wood, Eric; D'Arcy, Brandon; Zivanov, Catherine; Abney, Kevin; Musiyenko, Alla; Rusin, Scott F; Kettenbach, Arminja; Yet, Larry; Schroeder, Chad E; Golden, Jennifer E; Dunham, Wade H; Gingras, Anne-Claude; Banerjee, Surajit; Forbes, David; Wierzbicki, Andrzej; Honkanen, Richard E
Cantharidin is a natural toxin and an active constituent in a traditional Chinese medicine used to treat tumors. Cantharidin acts as a semi-selective inhibitor of PPP-family ser/thr protein phosphatases. Despite sharing a common catalytic mechanism and marked structural similarity with PP1C, PP2AC and PP5C, human PP4C was found to be insensitive to the inhibitory activity of cantharidin. To explore the molecular basis for this selectivity, we synthesized and tested novel C5/C6-derivatives designed from quantum-based modeling of the interactions revealed in the co-crystal structures of PP5C in complex with cantharidin. Structure-activity relationship studies and analysis of high-resolution (1.25Å) PP5C-inhibitor co-crystal structures reveal close contacts between the inhibitor bridgehead oxygen and both a catalytic metal ion and a non-catalytic phenylalanine residue, the latter of which is substituted by tryptophan in PP4C. Quantum chemistry calculations predicted that steric clashes with the bulkier tryptophan side chain in PP4C would force all cantharidin-based inhibitors into an unfavorable binding mode, disrupting the strong coordination of active site metal ions observed in the PP5C co-crystal structures, thereby rendering PP4C insensitive to the inhibitors. This prediction was confirmed by inhibition studies employing native human PP4C. Mutation of PP5C (F446W) and PP1C (F257W), to mimic the PP4C active site, resulted in markedly suppressed sensitivity to cantharidin. These observations provide insight into the structural basis for the natural selectivity of cantharidin and provide an avenue for PP4C deselection. The novel crystal structures also provide insight into interactions that provide increased selectivity of the C5/C6 modifications for PP5C versus other PPP-family phosphatases. PMID:27002182
Isolation and structures of schleicherastatins 1-7 and schleicheols 1 and 2 from the teak forest medicinal tree Schleichera oleosa.
Pettit, G R; Numata, A; Cragg, G M; Herald, D L; Takada, T; Iwamoto, C; Riesen, R; Schmidt, J M; Doubek, D L; Goswami, A
Bioassay (P-388 lymphocytic leukemia cell line)-guided separation of an extract prepared from the bark and stem of the Sri Lankan tree Schleichera oleosa led to the isolation of seven cancer cell growth inhibitory hydroxylated sterols designated schleicherastatins 1-7 (1-7) and two related sterols, schleicheols 1 and 2 (8, 9). The structure of schleicherastatin 1 (1) was completely elucidated by X-ray crystal structure determination. Based upon that defined structure, the remaining new sterol structures were deduced by highfield (300 and 500 MHz) NMR and MS interpretations. In this new series of sterols, hydroxylation at C-22 appears to be important for promoting cancer cell growth inhibition. PMID:10650082
Isolation, structural characterization and immunological activity of an exopolysaccharide produced by Bacillus licheniformis 8-37-0-1.
Liu, Chunhui; Lu, Juan; Lu, Lili; Liu, Yuhong; Wang, Fengshan; Xiao, Min
A strain of Bacillus licheniformis 8-37-0-1 with high exopolysaccharide (EPS) production ability was isolated and identified based on morphological and physiological characteristics and phylogenetic analysis of 16S rDNA sequences. A new type of EPS was isolated from the strain fermentation broth by enzymolysis, isopropanol precipitation, anion-exchange, and gel-filtration chromatography. The new EPS was determined as homogeneous, with a molecular weight of 2.826 x 10(4), as determined by High-Performance Size-Exclusion Chromatography Multi-Angle Laser Light Scattering analysis. Its structural characteristics were investigated and elucidated by methylation analysis, partial acid hydrolysis, gas-liquid chromatography mass spectrometry, Fourier transform infrared, and nuclear magnetic resonance spectroscopy. Based on obtained data, the EPS was found to be a levan containing a (2-->6)-linked backbone with a single beta-d-fructose at the C-1 position every seven residue, on average, along the main chain. Preliminary in vitro tests revealed that EPS could significantly stimulate the proliferation of spleen lymphocyte. PMID:20199860
Structure Elucidation of Coxsackievirus A16 in Complex with GPP3 Informs a Systematic Review of Highly Potent Capsid Binders to Enteroviruses
Tijsma, Aloys; Neyts, Johan; Spyrou, John A. B.; Ren, Jingshan; Grimes, Jonathan M.; Puerstinger, Gerhard; Leyssen, Pieter; Fry, Elizabeth E.; Rao, Zihe; Stuart, David I.
The replication of enterovirus 71 (EV71) and coxsackievirus A16 (CVA16), which are the major cause of hand, foot and mouth disease (HFMD) in children, can be inhibited by the capsid binder GPP3. Here, we present the crystal structure of CVA16 in complex with GPP3, which clarifies the role of the key residues involved in interactions with the inhibitor. Based on this model, in silico docking was performed to investigate the interactions with the two next-generation capsid binders NLD and ALD, which we show to be potent inhibitors of a panel of enteroviruses with potentially interesting pharmacological properties. A meta-analysis was performed using the available structural information to obtain a deeper insight into those structural features required for capsid binders to interact effectively and also those that confer broad-spectrum anti-enterovirus activity. PMID:26485389
The fumarate sensor DcuS: progress in rapid protein fold elucidation by combining protein structure prediction methods with NMR spectroscopy.
Meiler, Jens; Baker, David
We illustrate how moderate resolution protein structures can be rapidly obtained by interlinking computational prediction methodologies with un- or partially assigned NMR data. To facilitate the application of our recently described method of ranking and subsequent refining alternative structural models using unassigned NMR data [Proc. Natl. Acad. Sci. USA 100 (2003) 15404] for such "structural genomics"-type experiments it is combined with protein models from several prediction techniques, enhanced to utilize partial assignments, and applied on a protein with an unknown structure and fold. From the original NMR spectra obtained for the 140 residue fumarate sensor DcuS, 1100 1H, 13C, and 15N chemical shift signals, 3000 1H-1H NOESY cross peak intensities, and 209 backbone residual dipolar couplings were extracted and used to rank models produced by de novo structure prediction and comparative modeling methods. The ranking proceeds in two steps: first, an optimal assignment of the NMR peaks to atoms is found for each model independently, and second, the models are ranked based on the consistency between the NMR data and the model assuming these optimal assignments. The low-resolution model selected using this ranking procedure had the correct overall fold and a global backbone RMSD of 6.0 angstrom, and was subsequently refined to 3.7 angstrom RMSD. With the incorporation of a small number of NOE and residual dipolar coupling constraints available very early in the traditional spectral assignment process, a model with an RMSD of 2.8 angstrom could rapidly be built. The ability to generate moderate resolution models within days of NMR data collection should facilitate large scale NMR structure determination efforts. PMID:15780923
Seismic Performance of a Base Isolated Structure by Shake Table Tests
Yenidogan, Cem; Uckan, Eren
A 1/4 scaled model structure has been tested on a shake table to investigate the effectiveness of a passive-hybrid isolation system for a three-storey mass concentric steel structure. The isolation system consists of two high damping rubber bearings (HDRB) and four flat sliding bearings (PTFE), which are located below the central and corner columns, respectively. To maintain dynamic similitude, each earthquake record was compressed in time by a factor of two. Measurements were taken at structural points and at the bearings. Two different type of HDRB's were tested. A numerical model for the structure was developed and calibrated by the data from the experimental studies. The effectiveness of the hybrid isolation system is verified by comparing the results obtained from both isolated and fixed base models.
Structural design of active seismic isolation floor with a charging function
NASA Astrophysics Data System (ADS)
Nakakoji, Hayato; Miura, Nanako
This study shows an optimum structure of a seismic isolation floor against horizontal ground motions. Although a seismic isolation floor is effective with vibration reduction, the response of the floor becomes larger when excited by long-period ground motions. It is shown that caster equipment move and suffer damage in a seismic isolation structure by an experiment. Moreover, the permissible displacement of the floor is limited. Therefore, the focus is on an active seismic isolation. About active control, the system cannot operate without power supply. To solve these problems an energy regeneration is considered in our previous study. These studies only analyze simple model and did not choose the suitable structure for active control and energy regeneration. This research propose a new structure which has regenerated energy exceeds the energy required for the active control by numerical simulation.
Elucidating a Key Anti-HIV-1 and Cancer-Associated Axis: The Structure of CCL5 (Rantes) in Complex with CCR5
NASA Astrophysics Data System (ADS)
Tamamis, Phanourios; Floudas, Christodoulos A.
CCL5 (RANTES) is an inflammatory chemokine which binds to chemokine receptor CCR5 and induces signaling. The CCL5:CCR5 associated chemotactic signaling is of critical biological importance and is a potential HIV-1 therapeutic axis. Several studies provided growing evidence for the expression of CCL5 and CCR5 in non-hematological malignancies. Therefore, the delineation of the CCL5:CCR5 complex structure can pave the way for novel CCR5-targeted drugs. We employed a computational protocol which is primarily based on free energy calculations and molecular dynamics simulations, and report, what is to our knowledge, the first computationally derived CCL5:CCR5 complex structure which is in excellent agreement with experimental findings and clarifies the functional role of CCL5 and CCR5 residues which are associated with binding and signaling. A wealth of polar and non-polar interactions contributes to the tight CCL5:CCR5 binding. The structure of an HIV-1 gp120 V3 loop in complex with CCR5 has recently been derived through a similar computational protocol. A comparison between the CCL5 : CCR5 and the HIV-1 gp120 V3 loop : CCR5 complex structures depicts that both the chemokine and the virus primarily interact with the same CCR5 residues. The present work provides insights into the blocking mechanism of HIV-1 by CCL5.
Temperature-Dependence of Lipid A Acyl Structure in Psychrobacter cryohalolentis and Arctic Isolates of Colwellia hornerae and Colwellia piezophila.
Sweet, Charles R; Watson, Rebecca E; Landis, Corinne A; Smith, Joseph P
Lipid A is a fundamental Gram-negative outer membrane component and the essential element of lipopolysaccharide (endotoxin), a potent immunostimulatory molecule. This work describes the metabolic adaptation of the lipid A acyl structure by Psychrobacter cryohalolentis at various temperatures in its facultative psychrophilic growth range, as characterized by MALDI-TOF MS and FAME GC-MS. It also presents the first elucidation of lipid A structure from the Colwellia genus, describing lipid A from strains of Colwellia hornerae and Colwellia piezophila, which were isolated as primary cultures from Arctic fast sea ice and identified by 16S rDNA sequencing. The Colwellia strains are obligate psychrophiles, with a growth range restricted to 15 °C or less. As such, these organisms have less need for fluidity adaptation in the acyl moiety of the outer membrane, and they do not display alterations in lipid A based on growth temperature. Both Psychrobacter and Colwellia make use of extensive single-methylene variation in the size of their lipid A molecules. Such single-carbon variations in acyl size were thought to be restricted to psychrotolerant (facultative) species, but its presence in these Colwellia species shows that odd-chain acyl units and a single-carbon variation in lipid A structure are present in obligate psychrophiles, as well. PMID:26264000
Temperature-Dependence of Lipid A Acyl Structure in Psychrobacter cryohalolentis and Arctic Isolates of Colwellia hornerae and Colwellia piezophila
Sweet, Charles R.; Watson, Rebecca E.; Landis, Corinne A.; Smith, Joseph P.
Lipid A is a fundamental Gram-negative outer membrane component and the essential element of lipopolysaccharide (endotoxin), a potent immunostimulatory molecule. This work describes the metabolic adaptation of the lipid A acyl structure by Psychrobacter cryohalolentis at various temperatures in its facultative psychrophilic growth range, as characterized by MALDI-TOF MS and FAME GC-MS. It also presents the first elucidation of lipid A structure from the Colwellia genus, describing lipid A from strains of Colwellia hornerae and Colwellia piezophila, which were isolated as primary cultures from Arctic fast sea ice and identified by 16S rDNA sequencing. The Colwellia strains are obligate psychrophiles, with a growth range restricted to 15 °C or less. As such, these organisms have less need for fluidity adaptation in the acyl moiety of the outer membrane, and they do not display alterations in lipid A based on growth temperature. Both Psychrobacter and Colwellia make use of extensive single-methylene variation in the size of their lipid A molecules. Such single-carbon variations in acyl size were thought to be restricted to psychrotolerant (facultative) species, but its presence in these Colwellia species shows that odd-chain acyl units and a single-carbon variation in lipid A structure are present in obligate psychrophiles, as well. PMID:26264000
Demographic structure and microevolution of an Italian alpine isolated population.
Sella, G; Marin, A; Santovito, A; Girotti, M; Cervella, P; Delpero, M
The isonymic method has been generally accepted in population genetic studies and surnames have been successfully used to investigate human populations as if they were genetic markers associated to the Y chromosome. In this study we analysed the microevolution dynamics of Postua, a mountain village of North Western Italy, by means of demographic methods. The uniqueness of this community is due to its past geographical and cultural isolation and to the high frequency of marriage between relatives. During the study period considered (1640-1989) the population underwent several fluctuations in size and other demographic parameters such as the endogamy, isonimy and consanguinity rates. Until the first half of the XIX century Postua appears to be a village characterised by a closed and isolated community, with high endogamy (80-90%) and isonimy (up to 34.4%). Only at the beginning of the XX century, when the population started to be subjected to significant immigration fluxes, data show a progressive reduction of the isolation. The population showed two demographic peaks, the first around the second half of the XVIII century (1639 inhabitants) and the second at the end of the XIX century (1464 inhabitants). The S/Nratio was low (0.2-0.3) and relatively constant until the beginning of the last century, and only in the last three decades of the XX century, when the population was subjected to immigration, Postua showed a significant increase in the S/Nratio values (to about 0.9). The surname frequency was constant until the 1850 when almost all surnames were the same as those already present in the XVII century. From the first half of the XIX century, the founder surnames decreased, whereas new surnames started to increase and became persistent in the population. PMID:20873211
Sensor failure detection and isolation in flexible structures using system realization redundancy
NASA Astrophysics Data System (ADS)
Zimmerman, David C.; Lyde, Terri L.
Sensor failure detection and isolation for flexible structures is approached from a system realization perspective. Instead of using hardware or analytical model redundancy, system realization is utilized to provide an experimental based model redundancy. The failure detection and isolation algorithm utilizes the eigensystem realization algorithm to determine a minimum-order state-space realization of the structure in the presence of noisy measurements. The failure detection and isolation algorithm utilizes statistical comparisons of successive realizations to detect and isolate the failed sensor component. Because of the nature in which the failure detection and isolation algorithm is formulated, it is also possible to classify the failure mode of the sensor. Results are presented using both numerically simulated and actual experimental data.
Elucidating Structure-Bioactivity Relationships of Methyl-Branched Alkanes in the Contact Sex Pheromone of the Parasitic Wasp Lariophagus distinguendus
Kühbandner, Stephan; Bello, Jan E.; Mori, Kenji; Millar, Jocelyn G.; Ruther, Joachim
The exoskeletons of insects are covered by complex mixtures of cuticular hydrocarbons (CHCs) which are involved in social and sexual communication. However, little is known about the relationship between the structures of CHCs and their behavioral activity. The key component of the contact sex pheromone of the parasitoid Lariophagus distinguendus is 3-methylheptacosane (3-MeC27), which is present in CHC profiles of both females and newly emerged males. The CHCs of females and young males elicit wing-fanning behavior in older males. However, as young males age, 3-MeC27 disappears from their CHC profiles and they no longer elicit wing-fanning responses from other males. We applied enantiopure 3-MeC27 and structurally related CHCs (with respect to chain length or methyl-branch position) to the cuticle of aged male dummies and recorded the wing-fanning behavior of responding males. Only the two enantiomers of 3-MeC27 restored the dummies' attractiveness. The addition of structurally related CHCs or various n-alkanes to bioactive dummies of young males and females significantly decreased wing-fanning by test males. Hence, L. distinguendus males respond specifically but not enantioselectively to 3-MeC27, and perceive the CHC profiles as a whole. Both removal (as is the case with 3-MeC27 in aging males) and addition of individual compounds may disrupt the behavioral response. PMID:26462534
Evaluation of structural issues related to isolation of the 100-KE/100-KW discharge chute
Winkel, B.V.; Hyde, L.L.
The issue of excessive post-seismic leakage in the discharge chute of the K East and K West fuel storage basins was resolved by designing isolation barriers to maintain basin water levels if the discharge chute should drain. This report addresses the structural issues associated with isolation of the discharge chute. The report demonstrates the structural adequacy of the components associated with chute isolation for normal and seismic loading. Associated issues, such as hardware drop accidents and seismic slosh heights are also addressed.
Hydrolyzable tannins of tamaricaceous plants. V. Structures of monomeric-trimeric tannins and cytotoxicity of macrocyclic-type tannins isolated from Tamarix nilotica (1).
Orabi, Mohamed A A; Taniguchi, Shoko; Sakagami, Hiroshi; Yoshimura, Morio; Yoshida, Takashi; Hatano, Tsutomu
Three new ellagitannin monomers, nilotinins M5-M7 (1-3), a dimer, nilotinin D10 (4), and a trimer, nilotinin T1 (5), together with three known dimers, hirtellin D (7) and tamarixinins B (8) and C (9), and a trimer, hirtellin T2 (6), were isolated from Tamarix nilotica dried leaves. The structures of the tannins were elucidated by intensive spectroscopic methods and chemical conversions into known tannins. The new trimer (5) is a unique macrocyclic type whose monomeric units are linked together by an isodehydrodigalloyl and two dehydrodigalloyl moieties. Additionally, dimeric and trimeric macrocyclic-type tannins isolated from T. nilotica in this study were assessed for possible cytotoxic activity against four human tumor cell lines. Tumor-selective cytotoxicities of the tested compounds were higher than those of synthetic and natural potent cytotoxic compounds, including polyphenols, and comparable with those of 5-fluorouracil and melphalan. PMID:23675651
Starfish saponins. 55. Isolation, structure elucidation, and biological activity of the steroid oligoglycosides from an Antarctic starfish of the family Asteriidae.
De Marino, S; Iorizzi, M; Palagiano, E; Zollo, F; Roussakis, C
This paper reports an analysis of the chemical constituents from an Antarctic starfish of the family Asteriidae. Different steroid glycoside types are represented among its constituents, including the five hexaglycoside steroidal sulfates ("asterosaponins") asteriidosides A-E (1-5), differing in their oligosaccharide chain, and the two nonsulfated diglycosides asteriidoside F (6) and G (7), in which 6 is the 26-methyl analogue of 7. Also present are the two sulfated diglycosides asteriidoside H (8) and I (9) and one sulfated monoglycoside asteriidoside L (10). Eight of the compounds were tested against human nonsmall-cell lung carcinoma cells (NSCLC-L16) and found to be moderately cytotoxic. PMID:9834144
Structural and Functional Elucidation of the Mechanism Promoting Error-prone Synthesis by Human DNA Polymerase [kappa] Opposite the 7,8-Dihydro-8-oxo-2'-deoxyguanosine Adduct
Irimia, Adriana; Eoff, Robert L.; Guengerich, F.Peter; Egli, Martin
Human polymerase kappa (hPol {kappa}) is one of four eukaryotic Y-class DNA polymerases and may be an important element in the cellular response to polycyclic aromatic hydrocarbons such as benzo[a]pyrene, which can lead to reactive oxygenated metabolite-mediated oxidative stress. Here, we present a detailed analysis of the activity and specificity of hPol {kappa} bypass opposite the major oxidative adduct 7,8-dihydro-8-oxo-2{prime}-deoxyguanosine (8-oxoG). Unlike its archaeal homolog Dpo4, hPol {kappa} bypasses this lesion in an error-prone fashion by inserting mainly dATP. Analysis of transient-state kinetics shows diminished 'bursts' for dATP:8-oxoG and dCTP:8-oxoG incorporation, indicative of non-productive complex formation, but dATP:8-oxoG insertion events that do occur are 2-fold more efficient than dCTP:G insertion events. Crystal structures of ternary hPol {kappa} complexes with adducted template-primer DNA reveal non-productive (dGTP and dATP) alignments of incoming nucleotide and 8-oxoG. Structural limitations placed upon the hPol {kappa} by interactions between the N-clasp and finger domains combined with stabilization of the syn-oriented template 8-oxoG through the side chain of Met-135 both appear to contribute to error-prone bypass. Mutating Leu-508 in the little finger domain of hPol {kappa} to lysine modulates the insertion opposite 8-oxoG toward more accurate bypass, similar to previous findings with Dpo4. Our structural and activity data provide insight into important mechanistic aspects of error-prone bypass of 8-oxoG by hPol {kappa} compared with accurate and efficient bypass of the lesion by Dpo4 and polymerase {eta}.
The structural elucidation of the Salmonella enterica subsp. enterica, reveals that it contains both O-factors 4 and 5 on the LPS antigen.
De Castro, Cristina; Lanzetta, Rosa; Leone, Serena; Parrilli, Michelangelo; Molinaro, Antonio
Spectroscopic investigation of the O-antigen from Salmonella enterica subsp. enterica revealed fine details on the acetylation pattern, the biological repeating unit and the polymerization degree. Acetylation at O-2 of the abequose residue, defined both O-factors 4 and 5 in the O-antigen chain of the lipopolysaccharide. NMR observation of the terminal non-reducing end of the polymer confirmed previous data regarding the biological repeating unit and showed an average polymerization degree of 5. The information about these structural elements might contribute to the understanding of key features of the biology of this pathogen, as phase variation and/or adaptation to the external environment. PMID:23419941
Measurement of long range H,C couplings in natural products in orienting media: a tool for structure elucidation of natural products
NASA Astrophysics Data System (ADS)
Verdier, Laurent; Sakhaii, Peyman; Zweckstetter, Markus; Griesinger, Christian
In this paper we show that water insoluble compounds dissolved in poly-γ-benzyl-glutamate are amenable to the measurement of a number of homo- and heteronuclear dipolar couplings. The sensitivity and experimental precision of dipolar couplings are sufficient to obtain a good match with the structure. In order to achieve the necessary precision for H,C dipolar couplings between protons and carbons that are not directly bound a new method for the measurement of heteronuclear long range couplings is introduced that allows a one-parameter fit to a HSQC-based experiment as reference experiment. The methodology is applied to menthol (1R, 3S, 4R).
Application of Molecular Techniques To Elucidate the Influence of Cellulosic Waste on the Bacterial Community Structure at a Simulated Low-Level-Radioactive-Waste Site▿ †
Field, Erin K.; D'Imperio, Seth; Miller, Amber R.; VanEngelen, Michael R.; Gerlach, Robin; Lee, Brady D.; Apel, William A.; Peyton, Brent M.
Low-level-radioactive-waste (low-level-waste) sites, including those at various U.S. Department of Energy sites, frequently contain cellulosic waste in the form of paper towels, cardboard boxes, or wood contaminated with heavy metals and radionuclides such as chromium and uranium. To understand how the soil microbial community is influenced by the presence of cellulosic waste products, multiple soil samples were obtained from a nonradioactive model low-level-waste test pit at the Idaho National Laboratory. Samples were analyzed using 16S rRNA gene clone libraries and 16S rRNA gene microarray (PhyloChip) analyses. Both methods revealed changes in the bacterial community structure with depth. In all samples, the PhyloChip detected significantly more operational taxonomic units, and therefore relative diversity, than the clone libraries. Diversity indices suggest that diversity is lowest in the fill and fill-waste interface (FW) layers and greater in the wood waste and waste-clay interface layers. Principal-coordinate analysis and lineage-specific analysis determined that the Bacteroidetes and Actinobacteria phyla account for most of the significant differences observed between the layers. The decreased diversity in the FW layer and increased members of families containing known cellulose-degrading microorganisms suggest that the FW layer is an enrichment environment for these organisms. These results suggest that the presence of the cellulosic material significantly influences the bacterial community structure in a stratified soil system. PMID:20305022
Structural elucidation, density functional calculations and contribution of intermolecular interactions in cholest-4-en-3-one crystals: Insights from X-ray and Hirshfeld surface analysis
NASA Astrophysics Data System (ADS)
Khanam, Hena; Mashrai, Ashraf; Siddiqui, Nazish; Ahmad, Musheer; Alam, Mohammad Jane; Ahmad, Shabbir; Shamsuzzaman
The foremost objective of the present work is systematic analysis of intermolecular interactions in crystal structure of cholest-4-en-3-one (2) molecule. It is accomplished by Hirshfeld surface analysis and fingerprint plot. Hirshfeld surface analysis has been used to visualize the fidelity of the crystal structure. This method permitted for the identification of individual types of intermolecular contacts and their impact on the complete packing. Molecules are linked by a combination of Cdbnd O---H, Csbnd H---H, and C---H contacts, which have clear signatures in the fingerprint plots. The theoretical study was attempted to predict the optimized geometry and computed spectra by the Density Functional Theory (DFT) using the B3LYP function with the 6-311++G(d,p) basis set. Atomic charges, MEP mapping, HOMO-LUMO, various thermodynamic and molecular properties have been reported. In addition thermal stability, optical, morphological, and microstructral properties of the title compound (2) have also been explored.
Application of molecular techniques to elucidate the influence of cellulosic waste on the bacterial community structure at a simulated low-level-radioactive-waste site.
Field, Erin K; D'Imperio, Seth; Miller, Amber R; VanEngelen, Michael R; Gerlach, Robin; Lee, Brady D; Apel, William A; Peyton, Brent M
Low-level-radioactive-waste (low-level-waste) sites, including those at various U.S. Department of Energy sites, frequently contain cellulosic waste in the form of paper towels, cardboard boxes, or wood contaminated with heavy metals and radionuclides such as chromium and uranium. To understand how the soil microbial community is influenced by the presence of cellulosic waste products, multiple soil samples were obtained from a nonradioactive model low-level-waste test pit at the Idaho National Laboratory. Samples were analyzed using 16S rRNA gene clone libraries and 16S rRNA gene microarray (PhyloChip) analyses. Both methods revealed changes in the bacterial community structure with depth. In all samples, the PhyloChip detected significantly more operational taxonomic units, and therefore relative diversity, than the clone libraries. Diversity indices suggest that diversity is lowest in the fill and fill-waste interface (FW) layers and greater in the wood waste and waste-clay interface layers. Principal-coordinate analysis and lineage-specific analysis determined that the Bacteroidetes and Actinobacteria phyla account for most of the significant differences observed between the layers. The decreased diversity in the FW layer and increased members of families containing known cellulose-degrading microorganisms suggest that the FW layer is an enrichment environment for these organisms. These results suggest that the presence of the cellulosic material significantly influences the bacterial community structure in a stratified soil system. PMID:20305022
Atomistic structure of a spinel Li4Ti5O12(111) surface elucidated by scanning tunneling microscopy and medium energy ion scattering spectrometry
NASA Astrophysics Data System (ADS)
Kitta, Mitsunori; Matsuda, Taishi; Maeda, Yasushi; Akita, Tomoki; Tanaka, Shingo; Kido, Yoshiaki; Kohyama, Masanori
Spinel lithium titanate (Li4Ti5O12, LTO) is one of the promising anode materials for high-performance lithium-ion batteries (LIBs). It is crucial to investigate atomistic structures of LTO surfaces to understand the phenomena at LTO/electrolyte interfaces such as CO2-gas generation which greatly affects the performance and safety of LIBs. By applying scanning tunneling microscopy (STM) and medium energy ion scattering spectrometry (MEIS) to a LTO(111) film prepared from a TiO2 wafer, we found that there exist two kinds of Li-terminated (111) terraces bounded by steps with different heights. In the major terraces, the top hexagonal Li layer is stacked above the oxygen layer, while the top Li layer is stacked above the Ti-Li layer in the minor terraces. The relative stability between the two surface structures seems to depend on the atmosphere due to different stoichiometry. For the major terraces, the LTO surface should have electronic holes due to oxygen-rich stoichiometry, which is a possible origin of CO2 generation via redox interaction with electrolyte molecules.
How to produce a chemical defense: structural elucidation and anatomical distribution of aplysioviolin and phycoerythrobilin in the sea hare Aplysia californica.
Kamio, Michiya; Nguyen, Linh; Yaldiz, Seymanur; Derby, Charles D
We previously used bioassay-guided fractionation to identify phycoerythrobilin (1) and its monomethyl ester, aplysioviolin (2), as components in the ink secretion of a marine gastropod, the sea hare Aplysia californica, that act as chemical deterrents against predatory blue crabs. This was the first report of 1 as a natural product. Compound 2 was previously reported as a natural product from three species of Aplysia (A. fasciata, A. dactylomela, and A. parvula), but the reported structure and composition of stereoisomers of 2 are different among these species. Sea hares are thought to produce 2 from phycoerythrin, a photosynthetic pigment in their red-algal diet composed of a phycobiliprotein covalently linked to the chromophore 1, by cleavage of the covalent bond and methylation of 1, but neither the sequence nor the anatomical location of the cleavage and methylation is known. In this study, we clarify the structure of 1 and 2 in ink secretion of A. californica, and describe the distribution of 1 and 2 in the tissues of sea hares. We conclude that cleavage of the covalent bond in phycoerythrin occurs first, forming 1 in the digestive gland, followed by methylation of 1 to yield 2 in the ink gland. PMID:20491075
Use of Protein Cross-Linking and Radiolytic Labeling To Elucidate the Structure of PsbO within Higher-Plant Photosystem II.
Mummadisetti, Manjula P; Frankel, Laurie K; Bellamy, Henry D; Sallans, Larry; Goettert, Jost S; Brylinski, Michal; Bricker, Terry M
We have used protein cross-linking with the zero-length cross-linker 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide, and radiolytic footprinting coupled with high-resolution tandem mass spectrometry, to examine the structure of higher-plant PsbO when it is bound to Photosystem II. Twenty intramolecular cross-linked residue pairs were identified. On the basis of this cross-linking data, spinach PsbO was modeled using the Thermosynechococcus vulcanus PsbO structure as a template, with the cross-linking distance constraints incorporated using the MODELLER program. Our model of higher-plant PsbO identifies several differences between the spinach and cyanobacterial proteins. The N-terminal region is particularly interesting, as this region has been suggested to be important for oxygen evolution and for the specific binding of PsbO to Photosystem II. Additionally, using radiolytic mapping, we have identified regions on spinach PsbO that are shielded from the bulk solvent. These domains may represent regions on PsbO that interact with other components, as yet unidentified, of the photosystem. PMID:27203407
Application of Molecular Techniques to Elucidate the Influence of Cellulosic Waste on the Bacterial Community Structure at a Simulated Low-Level-Radioactive-Waste Site
Erin K. Field; Seth D'Imperio; Amber R. Miller; Michael R. VanEngelen; Robin Gerlach; Brady D. Lee; William A. Apel; Brent M. Peyton
Low-level radioactive waste sites, including those at various U.S. Department of Energy (DOE) sites, frequently contain cellulosic waste in the form of paper towels, cardboard boxes, or wood contaminated with heavy metals and radionuclides such as chromium and uranium. To understand how the soil microbial community is influenced by the presence of cellulosic waste products, multiple soil samples were obtained from a non-radioactive model low-level waste test pit at the Idaho National Laboratory. Samples were analyzed using 16S rDNA clone libraries and 16S rRNA gene microarray (PhyloChip) analyses. Both the clone library and PhyloChip results revealed changes in the bacterial community structure with depth. In all samples, the PhyloChip detected significantly more unique Operational Taxonomic Units (OTUs), and therefore more relative diversity, than the clone libraries. Calculated diversity indices suggest that diversity is lowest in the Fill (F) and Fill Waste (FW) layers and greater in the Wood Waste (WW) and Waste Clay (WC) layers. Principal coordinates analysis and lineage specific analysis determined that Bacteroidetes and Actinobacteria phyla account for most of the significant differences observed between the layers. The decreased diversity in the FW layer and increased members of families containing known cellulose degrading microorganisms suggests the FW layer is an enrichment environment for cellulose degradation. Overall, these results suggest that the presence of the cellulosic material significantly influences the bacterial community structure in a stratified soil system.
The Structure of Dasatinib (BNS-354825) Bound to Activated ABL Kinase Domain Elucidates its Inhibitory Activity Against Imatinib-Resistant ABL Mutants
Tokarski,J.; Newitt, J.; Chang, C.; Cheng, J.; Wittekind, M.; Kiefer, S.; Kish, K.; Lee, F.; Borzilerri, R.; et al.
Chronic myeloid leukemia (CML) is caused by the constitutively activated tyrosine kinase breakpoint cluster (BCR)-ABL. Current frontline therapy for CML is imatinib, an inhibitor of BCR-ABL. Although imatinib has a high rate of clinical success in early phase CML, treatment resistance is problematic, particularly in later stages of the disease, and is frequently mediated by mutations in BCR-ABL. Dasatinib (BMS-354825) is a multitargeted tyrosine kinase inhibitor that targets oncogenic pathways and is a more potent inhibitor than imatinib against wild-type BCR-ABL. It has also shown preclinical activity against all but one of the imatinib-resistant BCR-ABL mutants tested to date. Analysis of the crystal structure of dasatinib-bound ABL kinase suggests that the increased binding affinity of dasatinib over imatinib is at least partially due to its ability to recognize multiple states of BCR-ABL. The structure also provides an explanation for the activity of dasatinib against imatinib-resistant BCR-ABL mutants.
Elucidating the structural basis of diphenyl ether derivatives as highly potent enoyl-ACP reductase inhibitors through molecular dynamics simulations and 3D-QSAR study.
Kamsri, Pharit; Punkvang, Auradee; Saparpakorn, Patchareenart; Hannongbua, Supa; Irle, Stephan; Pungpo, Pornpan
Diphenyl ether derivatives are good candidates for anti-tuberculosis agents that display a promising potency for inhibition of InhA, an essential enoyl-acyl carrier protein (ACP) reductase involved in fatty acid biosynthesis pathways in Mycobacterium tuberculosis. In this work, key structural features for the inhibition were identified by 3D-QSAR CoMSIA models, constructed based on available experimental binding properties of diphenyl ether inhibitors, and a set of four representative compounds was subjected to MD simulations of inhibitor-InhA complexes for the calculation of binding free energies. The results show that bulky groups are required for the R1 substituent on the phenyl A ring of the inhibitors to favor a hydrophobic pocket formed by residues Phe149, Met155, Pro156, Ala157, Tyr158, Pro193, Met199, Val203, Leu207, Ile215, and Leu218. Small substituents with a hydrophilic property are required at the R3 and R4 positions of the inhibitor phenyl B rings to form hydrogen bonds with the backbones of Gly96 and Met98, respectively. For the R2 substituent, small substituents with simultaneous hydrophilic or hydrophobic properties are required to favor the interaction with the pyrophosphate moiety of NAD(+) and the methyl side chain of Ala198, respectively. The reported data provide structural guidance for the design of new and potent diphenyl ether-based inhibitors with high inhibitory activities against M. tuberculosis InhA. PMID:24935113
Crystal structure of a bioactive sesquiterpene isolated from Artemisia reticulata.
Bauri, A K; Foro, Sabine; Do, Nhu Quynh Nguyen
The title compound, C15H24O2 {systematic name: 1-[6-hy-droxy-7-(propan-2-yl)-4-methyl-idene-2,3,3a,4,5,6,7,7a-octa-hydro-1H-inden-1-yl]ethanone} was iso-la-ted from A. reticulata by column chromatography over silica gel by gradient solvent elution. The mol-ecule comprises a bi-cyclo-[4.3.0]nonane ring bearing acet-oxy, hy-droxy and isopropyl substituents, and an exocyclic double bond on the cyclo-hexane ring. In the bicyclic skeleton, the cyclo-hexane ring adopts a chair conformation ring and the cyclo-pentane ring is in an envelope conformation. In the crystal, mol-ecules are linked by O-H⋯O hydrogen bonds, forming chains along [010]. These chains are cross-linked by C-H⋯O hydrogen bonds. PMID:27375864
Coumarin as attractive casein kinase 2 (CK2) inhibitor scaffold: an integrate approach to elucidate the putative binding motif and explain structure-activity relationships.
Chilin, Adriana; Battistutta, Roberto; Bortolato, Andrea; Cozza, Giorgio; Zanatta, Samuele; Poletto, Giorgia; Mazzorana, Marco; Zagotto, Giuseppe; Uriarte, Eugenio; Guiotto, Adriano; Pinna, Lorenzo A; Meggio, Flavio; Moro, Stefano
Casein kinase 2 (CK2) is an ubiquitous, essential, and highly pleiotropic protein kinase whose abnormally high constitutive activity is suspected to underlie its pathogenic potential in neoplasia and other diseases. Recently, using different virtual screening approaches, we have identified several novel CK2 inhibitors. In particular, we have discovered that coumarin moiety can be considered an attractive CK2 inhibitor scaffold. In the present work, we have synthetized and tested a small library of coumarins (more than 60), rationalizing the observed structure-activity relationship. Moreover, the most promising inhibitor, 3,8-dibromo-7-hydroxy-4-methylchromen-2-one (DBC), has been also crystallized in complex with CK2, and the experimental binding mode has been used to derive a linear interaction energy (LIE) model. PMID:18251491
3-Naphthoylindazoles and 2-naphthoylbenzoimidazoles as novel chemical groups of synthetic cannabinoids: chemical structure elucidation, analytical characteristics and identification of the first representatives in smoke mixtures.
Shevyrin, Vadim; Melkozerov, Vladimir; Nevero, Alexander; Eltsov, Oleg; Morzherin, Yuri; Shafran, Yuri
By means of gas chromatography with mass spectrometry detection (GC-MS), including high resolution mass spectrometry (GC-HRMS) together with ultra-high performance liquid chromatography in combination with high resolution tandem mass spectrometry (UHPLC-HRMS), nuclear magnetic resonance spectroscopy (NMR) and Fourier transform infrared spectroscopy (FT-IR), structure of novel synthetic cannabinoids, namely, 1-(5-fluoropentyl)-1H-indazol-3-yl(naphthalen-1-yl)methanone, naphthalen-1-yl(1-pentyl-1H-benzo[d]imidazol-2-yl)methanone and 1-(5-fluoropentyl)-1H-benzo[d]imidazol-2-yl(naphthalen-1-yl)methanone was established. Analytical data obtained in the paper enable reliable identification of these compounds during qualitative analysis of seizures, including smoke mixtures. PMID:25036783
Coupling multistripe laser triangulation with hyperspectral imaging VisNIR spectroscopy to elucidate the feedbacks between soil structure, hydrology, and organic matter
NASA Astrophysics Data System (ADS)
Hirmas, Daniel; Steffens, Markus; Sullivan, Pamela; Zhang, Chi; Giménez, Daniel
Recent advances in three-dimensional (3-D) laser scanning techniques and reflectance spectroscopy provide the high-resolution quantitative measures needed to unravel the feedbacks mechanism between soil structure, hydrology, and organic matter at the pedon scale. Multistripe laser triangulation (MLT) can be used to quantify the shape, size, orientation, abundance, and spatial distribution of soil peds and associated macropore networks, while imaging visible light near infrared spectroscopy (imVisIR) can be used to examine the spatial distribution, quality and quantity of total, labile, and non-labile organic matter (SOM), iron, and manganese oxides at high spatial resolutions. In this work, we sought to investigate the potential for coupling these two disparate sensors (MLT and imVisIR) to examine relationships between soil structure, soil hydrology, and SOM. Soils were sampled from four landscape positions (summit, backslope, footslope, and toeslope) along an oak-hickory forest catena at the University of Kansas Field Station (KUFS) Fitch Natural History Reserve in conjunction with the installation of a National Ecological Observatory Network (NEON) site. Soil pits were excavated at each position to 1 m, described in detail by US Department of Agriculture-Natural Resource Conservation (USDA-NRCS) soil scientists, and sampled by morphological horizon for standard chemical and physical soil analyses. In addition, samples were taken from each horizon for root density and size determination, cores sampled to estimate water content, pore-size distribution, and hydraulic conductivity via low field nuclear magnetic resonance (NMR), and clods taken for water retention determination. Two intact soil monoliths per pit, carefully carved from the excavation walls at two depths (0-40 and 30-70 cm), were sampled in custom steel trays that were 15 cm wide by 40 cm long with a lip around the edge approximately 2 cm deep. The monoliths were prepared and dried at 40° C for 12
Synthesis, Structural Elucidation, and Biological Evaluation of NSC12, an Orally Available Fibroblast Growth Factor (FGF) Ligand Trap for the Treatment of FGF-Dependent Lung Tumors.
Castelli, Riccardo; Giacomini, Arianna; Anselmi, Mattia; Bozza, Nicole; Vacondio, Federica; Rivara, Silvia; Matarazzo, Sara; Presta, Marco; Mor, Marco; Ronca, Roberto
NSC12 is an orally available pan-FGF trap able to inhibit FGF2/FGFR interaction and endowed with promising antitumor activity. It was identified by virtual screening from a NCI small molecule library, but no data were available about its synthesis, stereochemistry, and physicochemical properties. We report here a synthetic route that allowed us to characterize and unambiguously identify the structure of the active compound by a combination of NMR spectroscopy and in silico conformational analysis. The synthetic protocol allowed us to sustain experiments aimed at assessing its therapeutic potential for the treatment of FGF-dependent lung cancers. A crucial step in the synthesis generated a couple of diastereoisomers, with only one able to act as a FGF trap molecule and to inhibit FGF-dependent receptor activation, cell proliferation, and tumor growth when tested in vitro and in vivo on murine and human lung cancer cells. PMID:27138345
Elucidation of the Nature of Structural Heterogeneity During Alkali Leaching of Non-activated and Mechanically Activated Boehmite ( γ-AlOOH)
NASA Astrophysics Data System (ADS)
Kumar, Rakesh; Alex, Thomas C.
Crystal joints and faces in non-activated boehmite and, state of agglomeration of particles, degree of amorphization, microcrystallite dimension and, strain in mechanically activated boehmite are indicators of structural heterogeneity which influences reactivity of the solid phase. The focus of this paper is on understanding the manifestation of the heterogeneity during alkali leaching of a boehmite (specific surface area—263 m2/g), without and with mechanical activation using planetary milling up to 240 minutes. A two-prong strategy is used for this purpose which involved analysis of the kinetics of leaching by a model-free approach using `isoconversional method' and, in parallel, characterization of the reacting solid after different durations of leaching. Unlike model-fitting methods, the kinetic analysis revealed sample-dependent variation of apparent activation energy with fraction leached. Changes observed in the morphology of samples (by SEM), particle size distribution (by laser diffraction), and crystalline nature (by powder X-ray diffraction) are used to explain activation energy changes and propose mechanisms of leaching. The effect of mechanical activation on rate constant is assessed and it has been found that up to ~23-fold increase in rate is possible depending on the activation time, leaching temperature, and fraction leached. Further, based on binary correlations between activation energy at different fractions leached and initial characteristics of the samples, it is found that the leaching is predominantly influenced by structural changes during milling, namely, degree of amorphization, microcrystallite dimension, and strain, vis-à-vis specific surface area. Significantly, the paper highlights limitation of model-fitting methods used by most researchers to analyze the kinetics of leaching, especially for mechanically activated minerals.
The Collaboratory for MS3D: A New Cyberinfrastructure for the Structural Elucidation of Biological Macromolecules and their Assemblies Using Mass Spectrometry-based Approaches
Yu, Eizadora T.; Hawkins, Arie; Kuntz, Irwin D.; Rahn, Larry A.; Rothfuss, Andrew; Sale, Kenneth; Young, Malin M.; Yang, Christine L.; Pancerella, Carmen M.; Fabris, Daniele
Modern biomedical research is evolving with the rapid growth of diverse data types, biophysical characterization methods, computational tools and extensive collaboration among researchers spanning various communities and having complementary backgrounds and expertise. Collaborating researchers are increasingly dependent on shared data and tools made available by other investigators with common interests, thus forming communities that transcend the traditional boundaries of the single research lab or institution. Barriers, however, remain to the formation of these virtual communities, usually due to the steep learning curve associated with becoming familiar with new tools, or with the difficulties associated with transferring data between tools. Recognizing the need for shared reference data and analysis tools, we are developing an integrated knowledge environment that supports productive interactions among researchers. Here we report on our current collaborative environment, which focuses on bringing together structural biologists working in the area of mass spectrometric based methods for the analysis of tertiary and quaternary macromolecular structures (MS3D) called the Collaboratory for MS3D (C-MS3D). C-MS3D is a web-portal designed to provide collaborators with a shared work environment that integrates data storage and management with data analysis tools. Files are stored and archived along with pertinent meta data in such a way as to allow file handling to be tracked (data provenance) and data files to be searched using keywords and modification dates. While at this time the portal is designed around a specific application, the shared work environment is a general approach to building collaborative work groups. The goal of which is to not only provide a common data sharing and archiving system but also to assist in the building of new collaborations and to spur the development of new tools and technologies. PMID:18817429
Food web structure and seasonality of slope megafauna in the NW Mediterranean elucidated by stable isotopes: Relationship with available food sources
NASA Astrophysics Data System (ADS)
Papiol, V.; Cartes, J. E.; Fanelli, E.; Rumolo, P.
The food-web structure and seasonality of the dominant taxa of benthopelagic megafauna (fishes and decapods) on the middle slope of the Catalan Sea (Balearic Basin, NW Mediterranean) were investigated using the carbon and nitrogen stable isotope ratios of 29 species. Macrofauna (infauna, suprabenthos and zooplankton) were also analysed as potential prey. Samples were collected on a seasonal basis from 600 to 1000 m depth between February 2007 and February 2008. The fishes and decapods were classified into feeding groups based on the literature: benthic feeders (including suprabenthos) and zooplankton feeders, the latter further separated into migratory and non-migratory species. Decapods exhibited depleted δ15N and enriched δ13C compared to fishes. Annual mean δ13C of fishes ranged from - 19.15‰ (Arctozenus risso) to - 16.65‰ (Phycis blennoides) and of δ15N from 7.27‰ (Lampanyctus crocodilus) to 11.31‰ (Nezumia aequalis). Annual mean values of δ13C of decapods were from - 18.94‰ (Sergestes arcticus) to - 14.78‰ (Pontophilus norvegicus), and of δ15N from 6.36‰ (Sergia robusta) to 9.72‰ (Paromola cuvieri). Stable isotopes distinguished well amongst the 3 feeding guilds established a priori, pointing to high levels of resource partitioning in deep-sea communities. The trophic structure of the community was a function of the position of predators along the benthic-pelagic gradient, with benthic feeders isotopically enriched relative to pelagic feeders. This difference allowed the identification of two food webs based on pelagic versus benthic consumption. Prey and predator sizes were also important in structuring the community. The most generalised seasonal pattern was δ13C depletion from winter to spring and summer, especially amongst migratory macroplankton feeders. This suggests greater consumption of pelagic prey, likely related with increases in pelagic production or with ontogenic migrations of organisms from mid-water to the Benthic
Synthesis, structure elucidation, and redox properties of 99Tc complexes of lacunary Wells-Dawson polyoxometalates: insights into molecular 99Tc-metal oxide interactions.
McGregor, Donna; Burton-Pye, Benjamin P; Howell, Robertha C; Mbomekalle, Israel M; Lukens, Wayne W; Bian, Fang; Mausolf, Edward; Poineau, Frederic; Czerwinski, Kenneth R; Francesconi, Lynn C
The isotope (99)Tc (β(max), 293.7; half-life, 2.1 × 10(5) years) is an abundant product of uranium-235 fission in nuclear reactors and is present throughout the radioactive waste stored in underground tanks at the Hanford and Savannah River sites. Understanding and controlling the extensive redox chemistry of (99)Tc is important in identifying tunable strategies to separate (99)Tc from spent fuel and from waste tanks and, once separated, to identify and develop an appropriately stable waste form for (99)Tc. Polyoxometalates (POMs), nanometer-sized models for metal oxide solid-state materials, are used in this study to provide a molecular level understanding of the speciation and redox chemistry of incorporated (99)Tc. In this study, (99)Tc complexes of the (α(2)-P(2)W(17)O(61))(10-) and (α(1)-P(2)W(17)O(61))(10-) isomers were prepared. Ethylene glycol was used as a "transfer ligand" to minimize the formation of TcO(2)·xH(2)O. The solution structures, formulations, and purity of Tc(V)O(α(1)/α(2)-P(2)W(17)O(61))(7-) were determined by multinuclear NMR. X-ray absorption spectroscopy of the complexes is in agreement with the formulation and structures determined from (31)P and (183)W NMR. Preliminary electrochemistry results are consistent with the EXAFS results, showing a facile reduction of the Tc(V)O(α(1)-P(2)W(17)O(61))(7-) species compared to the Tc(V)O(α(2)-P(2)W(17)O(61))(7-) analog. The α(1) defect is unique in that a basic oxygen atom is positioned toward the α(1) site, and the Tc(V)O center appears to form a dative metal-metal bond with a framework W site. These attributes may lead to the assistance of protonation events that facilitate reduction. Electrochemistry comparison shows that the Re(V) analogs are about 200 mV more difficult to reduce in accordance with periodic trends. PMID:21268605
Synthesis, structure elucidation, biological screening, molecular modeling and DNA binding of some Cu(II) chelates incorporating imines derived from amino acids
NASA Astrophysics Data System (ADS)
Abdel-Rahman, Laila H.; Abu-Dief, Ahmed M.; Ismael, Mohammed; Mohamed, Mounir A. A.; Hashem, Nahla Ali
Three tridentate Schiff bases amino acids were prepared by direct condensation of 3-methoxysalicylaldehyde (MS) or 4-diethylaminosalicylaldehyde (DS) with α-amino acid ligands [L-phenylalanine (P), L-histidine (H) and DL-tryptophan (T)]. The prepared Schiff bases amino acids were investigated by melting points, elemental analysis, 1HNMR and 13CNMR, IR, UV-Vis spectra, conductivity and magnetic measurements analyses. Subsequently, copper was introduced and Cu(II) complexes formed. These complexes were analyzed by thermal and elemental analyses and further investigated by FT-IR and UV/Vis spectroscopies. The experimental results indicating that all Cu(II) complexes contain hydrated water molecules (except DSPCu complex) and don't contain coordinated water molecules. The kinetic and thermal parameters were extracted from the thermal data using Coast and Redfern method. The molar conductance values of the Schiff base amino acid ligands and their Cu(II) complexes were relatively low, showing that these compounds have non-electrolytic nature. Magnetic susceptibility measurements showed the diamagnetic nature of the Schiff base amino acid ligands and paramagnetic nature of their complexes. Additionally, a spectrophotometric method was determined to extract their stability constants. It was found that the complexes possess 1:2 (M:L) stoichiometry. The results suggested that 3-methoxysalicylaldehyde and 4-diethylaminosalicylaldehyde amino acid Schiff bases behave as monobasic tridentate ONO ligands and coordinate Cu(II) ions in octahedral geometry according to the general formula [Cu(HL)2]·nH2O. To further understanding the structural and electronic properties of these complexes, Density Functional Theory (DFT) calculations were employed and provided a satisfactory description. The optimized structures of MST Schiff base ligand and its complex were calculated using DFT. The antimicrobial activity of the Schiff base ligands and their complexes were screened against some
Synthesis, structure elucidation and redox properties of 99Tc complexes of lacunary Wells Dawson polyoxometalates: insights into molecular 99Tc - metal oxide interactions
McGregor, Donna; Burton-Pye, Benjamin P.; Howell, Robertha C.; Mbomekalle, Israel M.; Lukens Jr, Wayne W.; Bian, Fang; Mausolf, Edward; Poineau, Frederic; Czerwinski, Kenneth R; Francesconi, Lynn C.
The isotope 99Tc (beta max: 250 keV, half-life: 2 x 105 year) is an abundant product of uranium-235 fission in nuclear reactors and is present throughout the radioactive waste stored in underground tanks at Hanford and Savannah River. Understanding and controlling the extensive redox chemistry of 99Tc is important to identify tunable strategies to separate 99Tc from spent fuel and from waste tanks and once separated, to identify and develop an appropriately stable waste-form for 99Tc. Polyoxometalates (POMs), nanometer sized models for metal oxide solid-state materials, are used in this study to provide a molecular level understanding of the speciation and redox chemistry of incorporated 99Tc. In this study, 99Tc complexes of the (alpha 2-P2W17O61)10- and (alpha 1-P2W17O61)10- isomers were prepared. Ethylene glycol was used as a"transfer ligand" to minimize the formation of TcO2 cdot xH2O. The solution structures, formulations, and purity of TcVO(alpha 1/alpha 2-P2W17O61)7- were determined by multinuclear NMR. X-ray Absorption Spectroscopy of the complexes are in agreement with the formulation and structures determined from 31P and 183W NMR. Preliminary electrochemistry results are consistent with the EXAFS results, showing a facile reduction of the TcVO(alpha 1-P2W17O61)7- species compared to the TcVO(alpha 2-P2W17O61)7- analog. The alpha1- defect is unique in that a basic oxygen atom is positioned toward the alpha1- site and the TcVO center appears to form a dative metal-metal bond with a framework W site. These attributes may lead to the assistance of protonation events that facilitate reduction. Electrochemistry comparison shows that the ReV analogs are about 200 mV more difficult to reduce in accordance with periodic trends.
Structure Elucidation at the Nanomole-Scale. 1. Trisoxazole Macrolides and Thiazole-containing Cyclic Peptides from the Nudibranch Hexabranchus sanguineus
Dalisay, Doralyn S.; Rogers, Evan W.; Edison, Arthur S.; Molinski, Tadeusz F.
A single specimen of Hexabranchus sanguineus, a nudibranch from the Indo-Pacific that is known to sequester kabiramides B, C and other trisoxazole macrolides, yielded new kabiramide analogs – 9-desmethylkabiramide B and 33-methyltetrahydrohalichondramide – and two new unexpected thiazole-containing cyclic peptides in sub-micromole amounts. The structures of these cyclic peptides were determined by analyses of 1D and 2D NMR spectra recorded with a state-of-the-art 1-mm 1H NMR high-temperature superconducting micro-cryoprobe, together with mass spectra. In addition to two proline residues, each peptide contains a thiazole- or oxazole-modified amino acid residue, together with conventional amino acid residues. All of the amino acid residues were L- as determined by Marfey's analysis of the acid hydrolysates of the peptides. This is the first report of cyclic thiazole peptides from H. sanguineus. Since thiazole-oxazole modified peptides are typically associated with cyanobacteria and tunicates, the finding may imply a dietary component of the H. sanguineus that was previously overlooked. PMID:19254038
Design, structural and spectroscopic elucidation of new nitroaromatic carboxylic acids and semicarbazones for the in vitro screening of anti-leishmanial activity
NASA Astrophysics Data System (ADS)
Dias, L. C.; de Lima, G. M.; Pinheiro, C. B.; Rodrigues, B. L.; Donnici, C. L.; Fujiwara, R. T.; Bartholomeu, D. C.; Ferreira, R. A.; Ferreira, S. R.; Mendes, T. A. O.; da Silva, J. G.; Alves, M. R. A.
In this paper we report the synthesis and characterization of four new nitroaromatic compounds, 2-{6-nitrobenzo[1,3]dioxol-5-(methyleneamino)}benzoic acid (1), 2-{[5-(2-nitrophenyl)furan-2-yl]methylene-amino}benzoic acid (2), 2-{(6-nitrobenzo[1,3]dioxol-5-yl)methylene}hydrazinecarboxamide (3) and 2-{[5-(2-nitrophenyl)furan-2-yl]methylene}hydrazinecarboxamide (4). Compounds (1)-(4) have been authenticated by infrared and NMR spectroscopy, and the structure of (1), (2) and (4) have been determined by X-ray diffraction. In addition, the in vitro ability of compounds (1)-(4) to inhibit the growth of Leishmania infantum has been evaluated. Comparisons of the redox potential of the compounds and leishmanicidal activity indicate that the presence of the electroactive nitro group is important for the biological activity. The inhibition activity of compound (3) is comparable to that of the reference drug, SbCl3. Considering the important side effects and the low efficiency of SbCl3 in the case of resistance, compound (3) deserves further attention as a promising anti-leishmanicidal drug for veterinary use.
Bio-sensitive activities of coordination compounds containing 1,10-phenanthroline as co-ligand: Synthesis, structural elucidation and DNA binding properties of metal(II) complexes
NASA Astrophysics Data System (ADS)
Raman, Natarajan; Mahalakshmi, Rajkumar; Mitu, Liviu
Present work reports the DNA binding and cleavage characteristics of a series of mixed-ligand complexes having the composition [M(L)(phen)2]Cl2 (where M = Cu(II), Ni(II), Co(II) and Zn(II) and phen as co-ligand) in detail. Their structural features and other properties have been deduced from their elemental analyses, magnetic susceptibility and molar conductivity as well as from IR, UV-Vis, 1H NMR and EPR spectral studies. The UV-Vis, magnetic susceptibility and EPR spectral data of metal complexes suggest an octahedral geometry. The binding properties of these complexes with calf thymus DNA (CT-DNA) have been explored using electronic absorption spectroscopy, viscosity measurement, cyclic voltammetry and differential pulse voltammetry. The DNA-binding constants for Cu(II), Ni(II), Co(II), and Zn(II) complexes are 6.14 × 105 M-1, 1.8 × 105 M-1, 6.7 × 104 M-1 and 2.5 × 104 M-1 respectively. Detailed analysis reveals that these complexes interact with DNA through intercalation binding. Nuclease activity has also been investigated by gel electrophoresis. Moreover, the synthesized Schiff base and its mixed-ligand complexes have been screened for antibacterial and antifungal activities. The data reveal that the complexes exhibit higher activity than the parent ligand.
Population structure and acquisition of the vanB resistance determinant in German clinical isolates of Enterococcus faecium ST192
Bender, Jennifer K.; Kalmbach, Alexander; Fleige, Carola; Klare, Ingo; Fuchs, Stephan; Werner, Guido
In the context of the global action plan to reduce the dissemination of antibiotic resistances it is of utmost importance to understand the population structure of resistant endemic bacterial lineages and to elucidate how bacteria acquire certain resistance determinants. Vancomycin resistant enterococci represent one such example of a prominent nosocomial pathogen on which nation-wide population analyses on prevalent lineages are scarce and data on how the bacteria acquire resistance, especially of the vanB genotype, are still under debate. With respect to Germany, an increased prevalence of VRE was noted in recent years. Here, invasive infections caused by sequence type ST192 VRE are often associated with the vanB-type resistance determinant. Hence, we analyzed 49 vanB-positive and vanB-negative E. faecium isolates by means of whole genome sequencing. Our studies revealed a distinct population structure and that spread of the Tn1549-vanB-type resistance involves exchange of large chromosomal fragments between vanB-positive and vanB-negative enterococci rather than independent acquisition events. In vitro filter-mating experiments support the hypothesis and suggest the presence of certain target sequences as a limiting factor for dissemination of the vanB element. Thus, the present study provides a better understanding of how enterococci emerge into successful multidrug-resistant nosocomial pathogens. PMID:26902259
Population structure and acquisition of the vanB resistance determinant in German clinical isolates of Enterococcus faecium ST192.
Bender, Jennifer K; Kalmbach, Alexander; Fleige, Carola; Klare, Ingo; Fuchs, Stephan; Werner, Guido
In the context of the global action plan to reduce the dissemination of antibiotic resistances it is of utmost importance to understand the population structure of resistant endemic bacterial lineages and to elucidate how bacteria acquire certain resistance determinants. Vancomycin resistant enterococci represent one such example of a prominent nosocomial pathogen on which nation-wide population analyses on prevalent lineages are scarce and data on how the bacteria acquire resistance, especially of the vanB genotype, are still under debate. With respect to Germany, an increased prevalence of VRE was noted in recent years. Here, invasive infections caused by sequence type ST192 VRE are often associated with the vanB-type resistance determinant. Hence, we analyzed 49 vanB-positive and vanB-negative E. faecium isolates by means of whole genome sequencing. Our studies revealed a distinct population structure and that spread of the Tn1549-vanB-type resistance involves exchange of large chromosomal fragments between vanB-positive and vanB-negative enterococci rather than independent acquisition events. In vitro filter-mating experiments support the hypothesis and suggest the presence of certain target sequences as a limiting factor for dissemination of the vanB element. Thus, the present study provides a better understanding of how enterococci emerge into successful multidrug-resistant nosocomial pathogens. PMID:26902259
Isolation, structural determination, synthesis and quantitative determination of impurities in Intron-A, leached from a silicone tubing.
Chan, Tze-Ming; Pramanik, Birendra; Aslanian, Robert; Gullo, Vincent; Patel, Mahesh; Cronin, Bart; Boyce, Chris; McCormick, Kevin; Berlin, Mike; Zhu, Xiaohong; Buevich, Alexei; Heimark, Larry; Bartner, Peter; Chen, Guodong; Pu, Haiyan; Hegde, Vinod
Investigation of unexpected levels of impurities in Intron product has revealed the presence of low levels of impurities leached from the silicone tubing (Rehau RAU-SIK) on the Bosch filling line. In order to investigate the effect of these compounds (1a, 1b and 2) on humans, they were isolated identified and synthesized. They were extracted from the tubing by stirring in Intron placebo at room temperature for 72 h and were enriched on a reverse phase CHP-20P column, eluting with gradient aqueous ACN and were separated by HPLC. Structural elucidation of 1a, 1b and 2 by MS and NMR studies demonstrated them to be halogenated biphenyl carboxylic acids. The structures were confirmed by independent synthesis. Levels of extractable impurities in first filled vials of actual production are estimated to be in the range of 0.01-0.55 microg/vial for each leached impurity. Potential toxicity of these extractables does not represent a risk for patients under the conditions of clinical use. PMID:19150187
Crystallographic analysis of human hemoglobin elucidates the structural basis of the potent and dual antisickling activity of pyridyl derivatives of vanillin
Abdulmalik, Osheiza; Ghatge, Mohini S.; Musayev, Faik N.; Parikh, Apurvasena; Chen, Qiukan; Yang, Jisheng; Nnamani, Ijeoma; Danso-Danquah, Richmond; Eseonu, Dorothy N.; Asakura, Toshio; Abraham, Donald J.; Venitz, Jurgen; Safo, Martin K.
Pyridyl derivatives of vanillin increase the fraction of the more soluble oxygenated sickle hemoglobin and/or directly increase the solubility of deoxygenated sickle hemoglobin. Crystallographic analysis reveals the structural basis of the potent and dual antisickling activity of these derivatives. Vanillin has previously been studied clinically as an antisickling agent to treat sickle-cell disease. In vitro investigations with pyridyl derivatives of vanillin, including INN-312 and INN-298, showed as much as a 90-fold increase in antisickling activity compared with vanillin. The compounds preferentially bind to and modify sickle hemoglobin (Hb S) to increase the affinity of Hb for oxygen. INN-312 also led to a considerable increase in the solubility of deoxygenated Hb S under completely deoxygenated conditions. Crystallographic studies of normal human Hb with INN-312 and INN-298 showed that the compounds form Schiff-base adducts with the N-terminus of the α-subunits to constrain the liganded (or relaxed-state) Hb conformation relative to the unliganded (or tense-state) Hb conformation. Interestingly, while INN-298 binds and directs its meta-positioned pyridine-methoxy moiety (relative to the aldehyde moiety) further down the central water cavity of the protein, that of INN-312, which is ortho to the aldehyde, extends towards the surface of the protein. These studies suggest that these compounds may act to prevent sickling of SS cells by increasing the fraction of the soluble high-affinity Hb S and/or by stereospecific inhibition of deoxygenated Hb S polymerization.
Elucidating the Physical and Chemical Structural Changes of Proteins on Clay Mineral Surfaces using Large-scale Molecular Dynamics Simulations in Tandem with NMR Spectroscopy
NASA Astrophysics Data System (ADS)
Andersen, A.; Govind, N.; Washton, N.; Reardon, P.; Chacon, S. S.; Burton, S.; Lipton, A.; Kleber, M.; Qafoku, N. P.
Carbon cycling among the three major Earth's pools, i.e., atmosphere, terrestrial systems and oceans, has received increased attention because the concentration of CO2 in the atmosphere has increased significantly in recent years reaching concentrations greater than 400 ppm that have never been recorded before, warming the planet and changing the climate. Within the terrestrial system, soil organic matter (SOM) represents an important sub-pool of carbon. The associations of SOM with soil mineral interfaces and particles, creating micro-aggregates, are believed to regulate the bioavailability of the associated organic carbon by protecting it from transformations and mineralization to carbon dioxide. Nevertheless, the molecular scale interactions of different types of SOM with a variety of soil minerals and the controls on the extent and rate of SOM transformation and mineralization are not well documented in the current literature. Given the importance of SOM fate and persistence in soils and the current knowledge gaps, the application of atomistic scale simulations to study SOM/mineral associations in abiotic model systems offers rich territory for original and impactful science. Molecular modeling and simulation of SOM is a burgeoning and challenging avenue for aiding the characterization of these complex compounds and chemical systems and for studying their interactions in self-assembled aggregates composed of different organic matter compounds and with mineral surfaces of different types and common in soils, which are thought to contribute to their reactive properties including recalcitrance potential and resistance to mineralization. Here, we will discuss our large-scale molecular dynamics simulation efforts to explore the interaction of proteins with clay minerals (i.e., phyllosilicates such as kaolinite, smectite and micas), including the potential physical and chemical structural changes of proteins, protein adsorption by polar and permanently charged
Prediction Models of Retention Indices for Increased Confidence in Structural Elucidation during Complex Matrix Analysis: Application to Gas Chromatography Coupled with High-Resolution Mass Spectrometry.
Dossin, Eric; Martin, Elyette; Diana, Pierrick; Castellon, Antonio; Monge, Aurelien; Pospisil, Pavel; Bentley, Mark; Guy, Philippe A
Monitoring of volatile and semivolatile compounds was performed using gas chromatography (GC) coupled to high-resolution electron ionization mass spectrometry, using both headspace and liquid injection modes. A total of 560 reference compounds, including 8 odd n-alkanes, were analyzed and experimental linear retention indices (LRI) were determined. These reference compounds were randomly split into training (n = 401) and test (n = 151) sets. LRI for all 552 reference compounds were also calculated based upon computational Quantitative Structure-Property Relationship (QSPR) models, using two independent approaches RapidMiner (coupled to Dragon) and ACD/ChromGenius software. Correlation coefficients for experimental versus predicted LRI values calculated for both training and test set compounds were calculated at 0.966 and 0.949 for RapidMiner and at 0.977 and 0.976 for ACD/ChromGenius, respectively. In addition, the cross-validation correlation was calculated at 0.96 from RapidMiner and the residual standard error value obtained from ACD/ChromGenius was 53.635. These models were then used to predict LRI values for several thousand compounds reported present in tobacco and tobacco-related fractions, plus a range of specific flavor compounds. It was demonstrated that using the mean of the LRI values predicted by RapidMiner and ACD/ChromGenius, in combination with accurate mass data, could enhance the confidence level for compound identification from the analysis of complex matrixes, particularly when the two predicted LRI values for a compound were in close agreement. Application of this LRI modeling approach to matrixes with unknown composition has already enabled the confirmation of 23 postulated compounds, demonstrating its ability to facilitate compound identification in an analytical workflow. The goal is to reduce the list of putative candidates to a reasonable relevant number that can be obtained and measured for confirmation. PMID:27403731
High accuracy NMR chemical shift corrected for bulk magnetization as a tool for structural elucidation of dilutable microemulsions. Part 1 - Proof of concept.
Hoffman, Roy E; Darmon, Eliezer; Aserin, Abraham; Garti, Nissim
In microemulsions, changes in droplet size and shape and possible transformations occur under various conditions. They are difficult to characterize by most analytical tools because of their nano-sized structure and dynamic nature. Several methods are usually combined to obtain reliable information, guiding the scientist in understanding their physical behavior. We felt that there is a need for a technique that complements those in use today in order to provide more information on the microemulsion behavior, mainly as a function of dilution with water. The improvement of NMR chemical shift measurements independent of bulk magnetization effects makes it possible to study the very weak intermolecular chemical shift effects. In the present study, we used NMR high resolution magic angle spinning to measure the chemical shift very accurately, free of bulk magnetization effects. The chemical shift of microemulsion components is measured as a function of the water content in order to validate the method in an interesting and promising, U-type dilutable microemulsion, which had been previously studied by a variety of techniques. Phase transition points of the microemulsion (O/W, bicontinuous, W/O) and changes in droplet shape were successfully detected using high-accuracy chemical shift measurements. We analyzed the results and found them to be compatible with the previous studies, paving the way for high-accuracy chemical shifts to be used for the study of other microemulsion systems. We detected two transition points along the water dilution line of the concentrate (reverse micelles) corresponding to the transition from swollen W/O nano-droplets to bicontinuous to the O/W droplets along with the changes in the droplets' sizes and shapes. The method seems to be in excellent agreement with other previously studied techniques and shows the advantage of this easy and valid technique. PMID:25113928
Structure Elucidation of New Acetylated Saponins, Lessoniosides A, B, C, D, and E, and Non-Acetylated Saponins, Lessoniosides F and G, from the Viscera of the Sea Cucumber Holothuria lessoni
Bahrami, Yadollah; Franco, Christopher M. M.
Sea cucumbers produce numerous compounds with a wide range of chemical structural diversity. Among these, saponins are the most diverse and include sulfated, non-sulfated, acetylated and methylated congeners with different aglycone and sugar moieties. In this study, MALDI and ESI tandem mass spectrometry, in the positive ion mode, were used to elucidate the structure of new saponins extracted from the viscera of H. lessoni. Fragmentation of the aglycone provided structural information on the presence of the acetyl group. The presence of the O-acetyl group was confirmed by observing the mass transition of 60 u corresponding to the loss of a molecule of acetic acid. Ion fingerprints from the glycosidic cleavage provided information on the mass of the aglycone (core), and the sequence and type of monosaccharides that constitute the sugar moiety. The tandem mass spectra of the saponin precursor ions [M + Na]+ provided a wealth of detailed structural information on the glycosidic bond cleavages. As a result, and in conjunction with existing literature, we characterized the structure of five new acetylated saponins, Lessoniosides A–E, along with two non-acetylated saponins Lessoniosides F and G at m/z 1477.7, which are promising candidates for future drug development. The presented strategy allows a rapid, reliable and complete analysis of native saponins. PMID:25603350
Isolation, antimicrobial activities, and primary structures of hamster neutrophil defensins.
Mak, P; Wójcik, K; Thogersen, I B; Dubin, A
Hamster (Mesocricetus auratus) neutrophil granules contain at least four microbicidal peptides belonging to the defensin family. These compounds were purified from granule acid extracts by reverse-phase chromatography and termed HaNP-1 to -4 (hamster neutrophil peptide). HaNP-1 and HaNP-3 revealed the most bactericidal activity, with a 50% inhibitory concentration of 0.3 to 0.8 microg/ml for Staphylococcus aureus and Streptococcus pyogenes strains. The HaNP-4 was always isolated in concentrations exceeding about 10 times the concentrations of other hamster peptides, but its antibacterial activity as well as that of HaNP-2 was relatively lower, probably as a result of conserved Arg residue substitutions. Other microorganisms were also tested, and generally, hamster defensins exhibited less potency against gram-negative bacteria. The amino acid sequence of hamster defensins showed a high percentage of identity to the sequence of mouse enteric defensins, reaching about 60% identical residues in the case of HaNP-3 and cryptdin 3. PMID:8890190
Mounting Systems for Structural Members, Fastening Assemblies Thereof, and Vibration Isolation Systems Including the Same
NASA Technical Reports Server (NTRS)
Young, Ken (Inventor); Hindle, Timothy (Inventor); Barber, Tim Daniel (Inventor)
Mounting systems for structural members, fastening assemblies thereof, and vibration isolation systems including the same are provided. Mounting systems comprise a pair of mounting brackets, each clamped against a fastening assembly forming a mounting assembly. Fastening assemblies comprise a spherical rod end comprising a spherical member having a through opening and an integrally threaded shaft, first and second seating members on opposite sides of the spherical member and each having a through opening that is substantially coaxial with the spherical member through opening, and a partially threaded fastener that threadably engages each mounting bracket forming the mounting assembly. Structural members have axial end portions, each releasably coupled to a mounting bracket by the integrally threaded shaft. Axial end portions are threaded in opposite directions for permitting structural member rotation to adjust a length thereof to a substantially zero strain position. Structural members may be vibration isolator struts in vibration isolation systems.
Isolation, Characterization, and Aggregation of a Structured Bacterial Matrix Precursor*
Chai, Liraz; Romero, Diego; Kayatekin, Can; Akabayov, Barak; Vlamakis, Hera; Losick, Richard; Kolter, Roberto
Biofilms are surface-associated groups of microbial cells that are embedded in an extracellular matrix (ECM). The ECM is a network of biopolymers, mainly polysaccharides, proteins, and nucleic acids. ECM proteins serve a variety of structural roles and often form amyloid-like fibers. Despite the extensive study of the formation of amyloid fibers from their constituent subunits in humans, much less is known about the assembly of bacterial functional amyloid-like precursors into fibers. Using dynamic light scattering, atomic force microscopy, circular dichroism, and infrared spectroscopy, we show that our unique purification method of a Bacillus subtilis major matrix protein component results in stable oligomers that retain their native α-helical structure. The stability of these oligomers enabled us to control the external conditions that triggered their aggregation. In particular, we show that stretched fibers are formed on a hydrophobic surface, whereas plaque-like aggregates are formed in solution under acidic pH conditions. TasA is also shown to change conformation upon aggregation and gain some β-sheet structure. Our studies of the aggregation of a bacterial matrix protein from its subunits shed new light on assembly processes of the ECM within bacterial biofilms. PMID:23632024
Composition, Structure and Functional Properties of Protein Concentrates and Isolates Produced from Walnut (Juglans regia L.)
Mao, Xiaoying; Hua, Yufei
In this study, composition, structure and the functional properties of protein concentrate (WPC) and protein isolate (WPI) produced from defatted walnut flour (DFWF) were investigated. The results showed that the composition and structure of walnut protein concentrate (WPC) and walnut protein isolate (WPI) were significantly different. The molecular weight distribution of WPI was uniform and the protein composition of DFWF and WPC was complex with the protein aggregation. H0 of WPC was significantly higher (p < 0.05) than those of DFWF and WPI, whilst WPI had a higher H0 compared to DFWF. The secondary structure of WPI was similar to WPC. WPI showed big flaky plate like structures; whereas WPC appeared as a small flaky and more compact structure. The most functional properties of WPI were better than WPC. In comparing most functional properties of WPI and WPC with soybean protein concentrate and isolate, WPI and WPC showed higher fat absorption capacity (FAC). Emulsifying properties and foam properties of WPC and WPI in alkaline pH were comparable with that of soybean protein concentrate and isolate. Walnut protein concentrates and isolates can be considered as potential functional food ingredients. PMID:22408408
Population structure of blueberry mosaic associated virus: Evidence of reassortment in geographically distinct isolates.
Thekke-Veetil, Thanuja; Polashock, James J; Marn, Mojca V; Plesko, Irena M; Schilder, Annemiek C; Keller, Karen E; Martin, Robert R; Tzanetakis, Ioannis E
The population structure of blueberry mosaic associated virus (BlMaV), a putative member of the family Ophioviridae, was examined using 61 isolates collected from North America and Slovenia. The studied isolates displayed low diversity in the movement and nucleocapsid proteins and low ratios of non-synonymous to synonymous nucleotide substitutions, indicative of strong purifying selection. Phylogenetic analyses revealed grouping primarily based on geography with some isolates deviating from this rule. Phylogenetic incongruence in the two regions, coupled with detection of reassortment events, indicated the possible role of genetic exchange in the evolution of BlMaV. PMID:25733053
Population structure and virulence content of avian pathogenic Escherichia coli isolated from outbreaks in Sri Lanka.
Dissanayake, D R A; Octavia, Sophie; Lan, Ruiting
Avian pathogenic Escherichia coli (APEC) causes economically significant infections in poultry. The genetic diversity of APEC and phylogenetic relationships within and between APEC and other pathogenic E. coli are not yet well understood. We used multilocus sequence typing (MLST), PCR-based phylogrouping and virulence genotyping to analyse 75 avian E. coli strains, including 55 isolated from outbreaks of colisepticaemia and 20 from healthy chickens. Isolates were collected from 42 commercial layer and broiler chicken farms in Sri Lanka. MLST identified 61 sequence types (ST) with 44 being novel. The most frequent ST, ST48, was represented by only six isolates followed by ST117 with four isolates. Phylogenetic clusters based on MLST sequences were mostly comparable to phylogrouping by PCR and MLST further differentiated phylogroups B1 and D into two subgroups. Genotyping of 16 APEC associated virulence genes found that 27 of the clinical isolates and one isolate from a healthy chicken belonged to highly virulent genotype according to previously established classification schemes. We found that a combination of four genes, ompT, hlyF, iroN and papC, gave a comparable prediction to that of using five and nine genes by other studies. Four STs (ST10, ST48, ST117 and ST2016) contained APEC isolates from this study and human UPEC isolates reported by others, suggesting that these STs are potentially zoonotic. Our results enhanced the understanding of APEC population structure and virulence association. PMID:24388626
Arbutin: Isolation, X-ray structure and computional studies
NASA Astrophysics Data System (ADS)
Nycz, Jacek E.; Malecki, Grzegorz; Morag, Monika; Nowak, Gerard; Ponikiewski, Lukasz; Kusz, Joachim; Switlicka, Anna
Arbutin, an active component originated from Serratula quinquefolia for skin-whitening use and treating skin related allergic inflammation, was characterized by microanalysis, FTIR, UV-Vis, multinuclear NMR spectroscopy, and single crystal X-ray diffraction method. The geometries of the studied compound were optimized in singlet states using the density functional theory (DFT) method with B3LYP functional. Electronic spectra were calculated by TDDFT method. In general, the predicted bond lengths and angles are in a good agreement with the values based on the X-ray crystal structure data.
Isolation and structural characterization of chondroitin sulfate from bony fishes.
Maccari, Francesca; Galeotti, Fabio; Volpi, Nicola
Chondroitin sulfate (CS) was purified from the bones of common fishes, monkfish, cod, spiny dogfish, salmon and tuna, and characterized in an effort to find alternative sources and new peculiar structures of this complex biomacromolecule utilized in the pharmaceutical and nutraceutical industry. Quantitative analyses yielded a CS content ranging from 0.011% for cod up to 0.34% for monkfish. The disaccharide pattern showed the presence of nonsulfated disaccharide, monosulfated species ΔDi6s and ΔDi4s, and disulfated disaccharides in different percentages. The disulfated species ΔDi2,6dis was present in all CS extracts in a range of 1.3-10.5%. The presence of these disulfated disaccharides may be a useful marker for the marine origin of CS. The newly identified sources would certainly enable the production of CS with unique disaccharide composition and properties. PMID:26050899
Structural and Electronic Properties of Isolated Nanodiamonds: A Theoretical Perspective
Raty, J; Galli, G
Nanometer sized diamond has been found in meteorites, proto-planetary nebulae and interstellar dusts, as well as in residues of detonation and in diamond films. Remarkably, the size distribution of diamond nanoparticles appears to be peaked around 2-5 nm, and to be largely independent of preparation conditions. Using ab-initio calculations, we have shown that in this size range nanodiamond has a fullerene-like surface and, unlike silicon and germanium, exhibit very weak quantum confinement effects. We called these carbon nanoparticles bucky-diamonds: their atomic structure, predicted by simulations, is consistent with many experimental findings. In addition, we carried out calculations of the stability of nanodiamond which provided a unifying explanation of its size distribution in extra-terrestrial samples, and in ultra-crystalline diamond films. Here we present a summary of our theoretical results and we briefly outline work in progress on doping of nanodiamond with nitrogen.
Structure analysis and laxative effects of oligosaccharides isolated from bananas.
Wang, Juan; Huang, Hui Hua; Cheng, Yan Feng; Yang, Gong Ming
Banana oligosaccharides (BOS) were extracted with water, and then separated and purified using column chromatography. Gel penetration chromatography was used to determine the molecular weights. Thin layer chromatogram and capillary electrophoresis were employed to analyze the monosaccharide composition. The indican bond and structure of the BOS molecule were determined using Fourier transform infrared spectroscopy and nuclear magnetic resonance. Results showed that BOS were probably composed of eight β-D-pyran glucose units linked with 1→6 indican bonds. The laxative effects of BOS were investigated in mice using the method described in "Handbook of Technical Standards for Testing and Assessment of Health Food in China." The length of the small intestine over which a carbon suspension solution advanced in mice treated with low-, middle-, and high-dose BOS was significantly greater than that in the model group, suggesting that BOS are effective in accelerating the movement of the small intestine. PMID:23039112
Recent Research and Application on Seismic Isolation, Energy Dissipation and Control for Structures in China
Zhou Fulin; Tan Ping; Cui Jie; Xian Qiaoling; Wei Lushun; Huang Dongyang
This paper briefly introduces the recent research, testing analysis, design and application on seismic isolation, energy dissipation, tuned mass damper and active control for buildings and bridges in mainland China. Paper introduces some typical researches, testing and analysis, including the mechanical tests for bearings and control devices, and the shaking table tests for structural models with different control systems. Paper also introduces the Chinese design codes for structures with seismic isolation and energy dissipation. Paper describes the recent application status and typical examples, especially introduces the largest isolation buildings group in the world, and the using passive and semi active control for structures. Also the paper makes discussion some problems existed on passive and active control technique now and the tendency of development on seismic control in future.
Seismic response analyses of base isolated structures with high damping elastomeric bearings
Wang, C.Y.; Tang, Y.; Chang, Y.W.; Seidensticker, R.W. ); Marchertas, A.H. )
Seismic response analysis of base-isolated structures with high damping elastomeric bearings is described. Emphasis is placed on the adaptation of a nonlinear constitutive model for the isolation bearing together with the treatment of foundation embedment for the soil-structure-interaction analysis. The constitutive model requires six input parameters derived from bearing experimental data under sinusoidal loading. The characteristic behavior of bearing, such as the variation of shear modulus and material damping with the change of maximum shear deformation, can be captured closely by the formulation. In the treatment of soil embedment a spring method is utilized to evaluate the foundation input motion as well as soil stiffness and damping. The above features have been incorporated into a three-dimensional system response program, SISEC, developed at Argonne National Laboratory. Sample problems are presented to illustrate the relative response of isolated and unisolated structures. 11 refs., 12 figs.
Sensor failure detection and isolation in flexible structures using the eigensystem realization algorithm
NASA Astrophysics Data System (ADS)
Zimmerman, David C.; Lyde, Terri L.
Sensor failure detection and isolation (FDI) for flexible structures is approached from a system realization perspective. Instead of using hardware or analytical model redundancy, system realization is utilized to provide an experimental model based redundancy. The FDI algorithm utilizes the eigensystem realization algorithm to determine a minimum-order state space realization of the structure in the presence of noisy measurements. The FDI algorithm utilizes statistical comparisons of successive realizations to detect and isolate the failed sensor component. Due to the nature in which the FDI algorithm is formulated, it is also possible to classify the failure mode of the sensor. Results are presented using both numerically simulated and actual experimental data.
Isolation, structural characterization, and properties of mattacin (polymyxin M), a cyclic peptide antibiotic produced by Paenibacillus kobensis M.
Martin, Nathaniel I; Hu, Haijing; Moake, Matthew M; Churey, John J; Whittal, Randy; Worobo, Randy W; Vederas, John C
Mattacin is a nonribosomally synthesized, decapeptide antibiotic produced by Paenibacillus kobensis M. The producing strain was isolated from a soil/manure sample and identified using 16 S rRNA sequence homology along with chemical and morphological characterization. An efficient production and isolation procedure was developed to afford pure mattacin. Structure elucidation using a combination of chemical degradation, multidimensional NMR studies (COSY, HMBC, HMQC, ROESY), and mass spectrometric (MALDI MS/MS) analyses showed that mattacin is identical to polymyxin M, an uncommon antibiotic reported previously in certain Bacillus species by Russian investigators. Mattacin (polymyxin M) is cyclic and possesses an amide linkage between the C-terminal threonine and the side chain amino group of the diaminobutyric acid residue at position 4. It contains an (S)-6-methyloctanoic acid moiety attached as an amide at the N-terminal amino group, one D-leucine, six L-alpha,gamma-diaminobutyric acid, and three L-threonine residues. Transfer NOE experiments on the conformational preferences of mattacin when bound to lipid A and microcalorimetry studies on binding to lipopolysaccharide showed that its behavior was very similar to that observed in previous studies of polymyxin B (a commercial antibiotic), suggesting an identical mechanism of action. It was capable of inhibiting the growth of a wide variety of Gram-positive and Gram-negative bacteria, including several human and plant pathogens with activity comparable with purified polymyxin B. The biosynthesis of mattacin was also examined briefly using transpositional mutagenesis by which 10 production mutants were obtained, revealing a set of genes involved in production. PMID:12569104
Isolation, Purification, and Structural Identification of an Antifungal Compound from a Trichoderma Strain.
Li, Chong-Wei; Song, Rui-Qing; Yang, Li-Bin; Deng, Xun
Trichoderma strain T-33 has been demonstrated to have inhibitory effect on the fungus species Cytospora chrysosperma. Here, an active antifungal compound was obtained from Trichoderma strain T-33 extract via combined separation technologies, including organic solvent extraction, liquid chromatography, and thin-layer chromatography. The purified compound was further characterized by advanced analytical technologies to elucidate its chemical structure. Results indicated that the active antifungal compound in Trichoderma strain T-33 extract is 2,5- cyclohexadiene-1,4-dione-2,6-bis (1,1-dimethylethyl). PMID:25876599
Isolated magnetic field structures in Mercury's magnetosheath as possible analogues for terrestrial magnetosheath plasmoids and jets
NASA Astrophysics Data System (ADS)
Karlsson, Tomas; Liljeblad, Elisabet; Kullen, Anita; Raines, Jim M.; Slavin, James A.; Sundberg, Torbjörn
We have investigated MESSENGER magnetic field data from the Mercury magnetosheath and near solar wind, to identify isolated magnetic field structures (defined as clear, isolated changes in the field magnitude). Their properties are studied in order to determine if they may be considered as analogues to plasmoids and jets known to exist in Earth's magnetosheath. Both isolated decreases of the magnetic field absolute value ('negative magnetic field structures') and increases ('positive structures') are found in the magnetosheath, whereas only negative structures are found in the solar wind. The similar properties of the solar wind and magnetosheath negative magnetic field structures suggests that they are analogous to diamagnetic plasmoids found in Earth's magnetosheath and near solar wind. The latter have earlier been identified with solar wind magnetic holes. Positive magnetic field structures are only found in the magnetosheath, concentrated to a region relatively close to the magnetopause. Their proximity to the magnetopause, their scale sizes, and the association of a majority of the structures with bipolar magnetic field signatures identify them as flux transfer events (which generally are associated with a decrease of plasma density in the magnetosheath). The positive magnetic field structures are therefore not likely to be analogous to terrestrial paramagnetic plasmoids but possibly to a sub-population of magnetosheath jets. At Earth, a majority of magnetosheath jets are associated with the quasi-parallel bow shock. We discuss some consequences of the findings of the present investigation pertaining to the different nature of the quasi-parallel bow shock at Mercury and Earth.
Structure Elucidation of the Diagnostic Product Ion at m/z 97 Derived from Androst-4-en-3-One-Based Steroids by ESI-CID and IRMPD Spectroscopy
NASA Astrophysics Data System (ADS)
Thevis, Mario; Beuck, Simon; Höppner, Sebastian; Thomas, Andreas; Held, Joseph; Schäfer, Mathias; Oomens, Jos; Schänzer, Wilhelm
Structure elucidation of steroids by mass spectrometry has been of great importance to various analytical arenas and numerous studies were conducted to provide evidence for the composition and origin of (tandem) mass spectrometry-derived product ions used to characterize and identify steroidal substances. The common product ion at m/z 97 generated from androst-4-ene-3-one analogs has been subject of various studies, including stable isotope-labeling and (high resolution/high accuracy) tandem mass spectrometry, but its gas-phase structure has never been confirmed. Using high resolution/high accuracy mass spectrometry and low resolution tandem mass spectrometry, density functional theory (DFT) calculation, and infrared multiple photon dissociation (IRMPD) spectroscopy employing a free electron laser, the structure of m/z 97 derived from testosterone was assigned to protonated 3-methyl-2-cyclopenten-1-one. This ion was identified in a set of six cyclic C6H9O+ isomers as computed at the B3LYP/6-311++G(2d,2p) level of theory (protonated 3-methyl-2-cyclopenten-1-one, 2-methyl-2-cyclopenten-1-one and 2-cyclohexen-1-one). Product ions of m/z 97 obtained from MS2 and MS3 experiments of protonated 3-methyl-2-cyclopenten-1-one, 2-methyl-2-cyclopenten-1-one, 2-cyclohexen-1-one, and testosterone corroborated the suggested gas-phase ion structure, which was eventually substantiated by IRMPD spectroscopy yielding a spectrum that convincingly matched the predicted counterpart. Finally, the dissociation pathway of the protonated molecule of testosterone to m/z 97 was revisited and an alternative pathway was suggested that considers the exclusion of C-10 along with the inclusion of C-5, which was experimentally demonstrated with stable isotope labeling.
Charge‐Induced Unzipping of Isolated Proteins to a Defined Secondary Structure
González Flórez, Ana Isabel; Mucha, Eike; Ahn, Doo‐Sik; Gewinner, Sandy; Schöllkopf, Wieland; Pagel, Kevin
Abstract Here we present a combined experimental and theoretical study on the secondary structure of isolated proteins as a function of charge state. In infrared spectra of the proteins ubiquitin and cytochrome c, amide I (C=O stretch) and amide II (N–H bend) bands can be found at positions that are typical for condensed‐phase proteins. For high charge states a new band appears, substantially red‐shifted from the amide II band observed at lower charge states. The observations are interpreted in terms of Coulomb‐driven transitions in secondary structures from mostly helical to extended C5‐type hydrogen‐bonded structures. Support for this interpretation comes from simple energy considerations as well as from quantum chemical calculations on model peptides. This transition in secondary structure is most likely universal for isolated proteins that occur in mass spectrometric experiments. PMID:26847383
Charge-Induced Unzipping of Isolated Proteins to a Defined Secondary Structure.
González Flórez, Ana Isabel; Mucha, Eike; Ahn, Doo-Sik; Gewinner, Sandy; Schöllkopf, Wieland; Pagel, Kevin; von Helden, Gert
Here we present a combined experimental and theoretical study on the secondary structure of isolated proteins as a function of charge state. In infrared spectra of the proteins ubiquitin and cytochrome c, amide I (C=O stretch) and amide II (N-H bend) bands can be found at positions that are typical for condensed-phase proteins. For high charge states a new band appears, substantially red-shifted from the amide II band observed at lower charge states. The observations are interpreted in terms of Coulomb-driven transitions in secondary structures from mostly helical to extended C5 -type hydrogen-bonded structures. Support for this interpretation comes from simple energy considerations as well as from quantum chemical calculations on model peptides. This transition in secondary structure is most likely universal for isolated proteins that occur in mass spectrometric experiments. PMID:26847383
Effect of structural flexibility on the design of vibration-isolating mounts for aircraft engines
NASA Technical Reports Server (NTRS)
Phillips, W. H.
Previous analyses of the design of vibration-isolating mounts for a rear-mounted engine to decouple linear and rotational oscillations are extended to take into account flexibility of the engine-mount structure. Equations and curves are presented to allow the design of mount systems and to illustrate the results for a range of design conditions.
On inertia nonlinearity in irregular-plan isolated structures under seismic excitations
NASA Astrophysics Data System (ADS)
Amin Afshar, Majid; Aghaei Pour, Sepehr
The influence of nonlinear inertia as a function of acceleration, velocity, and displacement is investigated for an asymmetric isolated structure. Six degrees of freedom (6-DOFs) are defined to illustrate translational and rotational displacements of the superstructure and base isolation. Motion equations of such DOFs are derived using the Lagrangian formalism. Two coordinate systems of the reference are defined, one fixed on the building base (global coordinate) and the other at the torsional isolation level (local coordinate). The motion governing equations in the conventional approach is formulated on a linear form in the global coordinate system, whereas in the novel approach, the local coordinate system leads to a nonlinear form of dynamic equations. The difference between two linear and nonlinear models is appeared because of the existence of nonlinear inertia terms just in the nonlinear one. Afterwards, three particular types of isolated structures are employed with the peculiar ratio of torsional-lateral coupled frequency on symmetric frequency. Numerical analysis is applied to investigate the performance of two structural models by exerting harmonic excitations and earthquakes. The results are obtained while analyzing time history and frequency content and show that the coupling effects of nonlinear inertia lead to differences in the responses of linear and nonlinear models of such structures; also, some nonlinear phenomena such as energy transfer between modes, saturation, rigid displacement, and super-harmonic created due to geometrical (inertial) nonlinearities are studied.
Structure of complex cell wall polysaccharides isolated from Trichoderma and Hypocrea species.
Prieto, A; Leal, J A; Poveda, A; Jiménez-Barbero, J; Gómez-Miranda, B; Domenech, J; Ahrazem, O; Bernabé, M
The structure of fungal polysaccharides isolated from the cell wall of Trichoderma reesei, T. koningii, and Hypocrea psychrophila, have been investigated by means of chemical analyses and 1D and 2D NMR spectroscopy. The polysaccharides have an irregular structure, idealized as follows: [formula: see text] The proportions of the different side chains vary from a species to another, being n above some three times larger in H. psychrophila than in T. reesei or T. koningii. PMID:9468630
Structure Elucidation of the Metabolites of 2', 3', 5'-Tri-O-Acetyl-N6-(3-Hydroxyphenyl) Adenosine in Rat Urine by HPLC-DAD, ESI-MS and Off-Line Microprobe NMR
Miao, Zhaoxia; Qu, Kai; Liu, Xia; Zhang, Peicheng; Qin, Hailin; Zhu, Haibo; Wang, Yinghong
2', 3', 5'-tri-O-acetyl-N6-(3-hydroxyphenyl) adenosine (also known as WS070117) is a new adenosine analog that displays anti-hyperlipidemic activity both in vitro and in vivo experiments as shown in many preliminary studies. Due to its new structure, little is known about the metabolism of WS070117. Hence, the in vivo metabolites of WS070117 in rat urine following oral administration were investigated. Identification of the metabolites was conducted using the combination of high-performance liquid chromatography (HPLC) coupled with diode array detector (DAD), ion trap electrospray ionization-mass spectrometry (ESI-MS), and off-line microprobe nuclear magnetic resonance (NMR) measurements. Seven metabolites were obtained as pure compounds at the sub-milligram to milligram levels. Results of structure elucidation unambiguously revealed that the phase I metabolite, N6-(3-hydroxyphenyl) adenosine (M8), was a hydrolysate of WS070117 by hydrolysis on the three ester groups. N6-(3-hydr-oxyphenyl) adenine (M7), also one of the phase I metabolites, was the derivative of M8 by the loss of ribofuranose. In addition to two phase I metabolites, there were five phase II metabolites of WS070117 found in rat urine. 8-hydroxy-N6-(3-hydroxy-phenyl) adenosine (M6) was the product of M7 by hydrolysis at position 8. The other four were elucidated to be N6-(3-O-β-D-glucuronyphenyl) adenine (M2), N8-hydroxy-N6-(3-O-sulfophenyl) adenine (M3), N6-(3-O-β-D-glucuronyphenyl) adenosine (M4), and N6-(3-O- sulfophenyl) adenosine (M5). Phase II metabolic pathways were proven to consist of hydroxylation, glucuronidation and sulfation. This study provides new and valuable information on the metabolism of WS070117, and also demonstrates the HPLC/MS/off-line microprobe NMR approach as a robust means for rapid identification of metabolites. PMID:26029929
Inner structural vibration isolation method for a single control moment gyroscope
NASA Astrophysics Data System (ADS)
Zhang, Jingrui; Guo, Zixi; Zhang, Yao; Tang, Liang; Guan, Xin
Assembling and manufacturing errors of control moment gyros (CMG) often generate high frequency vibrations which are detrimental to spacecrafts with high precision pointing requirement. In this paper, some design methods of vibration isolation between CMG and spacecraft is dealt with. As a first step, the dynamic model of the CMG with and without supporting isolation structures is studied and analyzed. Subsequently, the frequency domain analysis of CMG with isolation system is performed and the effectiveness of the designed system is ascertained. Based on the above studies, an adaptive design suitable with appropriate design parameters are carried out. A numerical analysis is also performed to understand the effectiveness of the system and the comparison made. The simulation results clearly indicate that when the ideal isolation structure was implemented in the spacecraft, the vibrations generated by the rotor were found to be greatly reduced, while the capacity of the output torque was not lost, which means that the isolation system will not affect the performance of attitude control.
Band stop vibration suppression using a passive X-shape structured lever-type isolation system
NASA Astrophysics Data System (ADS)
Liu, Chunchuan; Jing, Xingjian; Chen, Zhaobo
In the paper, band-stop vibration suppression property using a novel X-shape structured lever-type isolation system is studied. The geometrical nonlinear property of an X-shape supporting structure is used to improve the band-stop characteristics in the low frequency range of the lever-type vibration isolator. With the dynamics modeling of this hybrid structural system, it is shown that the proposed hybrid vibration system has very beneficial nonlinear stiffness and damping properties which are helpful to achieve much wider stop bandwidth. Theoretical results demonstrate that the anti-resonant frequencies, width and magnitude of the stop band can all be flexibly designed with structural parameters, and the parameters of the X-shape supporting structure are very critical for designing the band-stop frequency to achieve excellent low-frequency isolation performance. The results in the study provide a new approach to the design of the passive vibration suppression system in the low frequency region.
Metalorganic chemical vapour deposition of junction isolated GaAlAs/GaAs LED structures
NASA Astrophysics Data System (ADS)
Bradley, R. R.; Ash, R. M.; Forbes, N. W.; Griffiths, R. J. M.; Jebb, D. P.
A low-cost high-radiance Ga(1-x)Al(x)As/GaAs LED has been developed using p-n junction isolation to achieve current confinement in an inverted Burrus LED structure. Using this structure devices with a high internal quantum efficiency of 87 percent which launch up to 1.5 mW into 200-micron, 0.3 nA fiber at 150 mA and have rise and fall times of less than 5 ns, have been fabricated. The LED structure involved a two-stage growth process in which initially an n-type isolation layer was grown on a p-type substrate, followed by infill growth, through contact holes, of the inverted LED structure. This paper will describe in detail the growth and preparation of the optimized junction isolated LED structure, including growth rate and composition control, layer uniformity and deliberate interface grading. Exploration of the use of magnesium doping and triethylaluminum for precise control of active layer doping and composition will be discussed, and finally details of device characteristics and performance are presented.
Finite element prediction of seismic response modification of monumental structures utilizing base isolation
NASA Astrophysics Data System (ADS)
Spanos, Konstantinos; Anifantis, Nikolaos; Kakavas, Panayiotis
The analysis of the mechanical behavior of ancient structures is an essential engineering task concerning the preservation of architectural heritage. As many monuments of classical antiquity are located in regions of earthquake activity, the safety assessment of these structures, as well as the selection of possible restoration interventions, requires numerical models capable of correctly representing their seismic response. The work presented herein was part of a research project in which a better understanding of the dynamics of classical column-architrave structures was sought by means of numerical techniques. In this paper, the seismic behavior of ancient monumental structures with multi-drum classical columns is investigated. In particular, the column-architrave classical structure under strong ground excitations was represented by a finite element method. This approach simulates the individual rock blocks as distinct rigid blocks interconnected with slidelines and incorporates seismic isolation dampers under the basement of the structure. Sliding and rocking motions of individual stone blocks and drums are modeled utilizing non-linear frictional contact conditions. The seismic isolation is modeled through the application of pad bearings under the basement of the structure. These pads are interpreted by appropriate rubber and steel layers. Time domain analyses were performed, considering the geometric and material non-linear behavior at the joints and the characteristics of pad bearings. The deformation and failure modes of drum columns subject to seismic excitations of various types and intensities were analyzed. The adverse influence of drum imperfections on structural safety was also examined.
Analysis of population structure among Korean and Japanese Legionella pneumophila isolates using hsp60 sequences.
Park, Chan Geun; Kim, Byoung Jun; Kim, Hee-Youn; Yun, Yeo-Jun; Ko, Kwan Soo; Miyamoto, Hiroshi; Kim, Bum-Joon; Kook, Yoon-Hoh
The population structure of Korean (150 strains) and Japanese (92 strains) Legionella pneumophila isolates along with 18 reference strains were investigated using hsp60 sequence (1647 bp) analysis. Twelve clonal subgroups (hsP-I to hsP-X and hsF-I and hsF-II) were designated on the hsp60 tree, inferred from representative sequences using the neighbor-joining method. Some of the isolates showed unique subgroups depending on the source of isolates, including hsP-I, hsF-I, and hsF-II from cooling tower water, and subgroups hsP-VIII and hsP-X from circulating hot water bath. These subgroups may be useful for epidemiological studies to chase or specify sources of infection in Korea and Japan. PMID:22672106
The population structure of Escherichia coli isolated from subtropical and temperate soils
Byappanahalli, Muruleedhara N.; Yan, Tao; Hamilton, Matthew J.; Ishii, Satoshi; Fujioka, Roger S.; Whitman, Richard L.; Sadowsky, Michael J.
While genotypically-distinct naturalized Escherichia coli strains have been shown to occur in riparian soils of Lake Michigan and Lake Superior watersheds, comparative analyses of E. coli populations in diverse soils across a range of geographic and climatic conditions have not been investigated. The main objectives of this study were to: (a) examine the population structure and genetic relatedness of E. coli isolates collected from different soil types on a tropical island (Hawaii), and (b) determine if E. coli populations from Hawaii and temperate soils (Indiana, Minnesota) shared similar genotypes that may be reflective of biome-related soil conditions. DNA fingerprint and multivariate statistical analyses were used to examine the population structure and genotypic characteristics of the E. coli isolates. About 33% (98 of 293) of the E. coli from different soil types and locations on the island of Oahu, Hawaii, had unique DNA fingerprints, indicating that these bacteria were relatively diverse; the Shannon diversity index for the population was 4.03. Nearly 60% (171 of 293) of the E. coli isolates from Hawaii clustered into two major groups and the rest, with two or more isolates, fell into one of 22 smaller groups, or individual lineages. Multivariate analysis of variance of 89, 21, and 106 unique E. coli DNA fingerprints for Hawaii, Indiana, and Minnesota soils, respectively, showed that isolates formed tight cohesive groups, clustering mainly by location. However, there were several instances of clonal isolates being shared between geographically different locations. Thus, while nearly identical E. coli strains were shared between disparate climatologically- and geographically-distinct locations, a vast majority of the soil E. coli strains were genotypically diverse and were likely derived from separate lineages. This supports the hypothesis that these bacteria are not unique and multiple genotypes can readily adapt to become part of the soil autochthonous
Isolation of an Isocoumarin and an Isobenzofuran Derivatives from a Fungicolous Isolate of Acremonium crotocinigenum
Technology Transfer Automated Retrieval System (TEKTRAN)
6,8-dimethoxy-4,5-dimethyl-3-methyleneisochroman-1-one (1) and 5,7-dimethoxy-3,4-dimethyl-3-hydroxy-isobenzofuranone (2), have been isolated from an organic extract of the fungicolous fungus Acremonium crotocinigenum (NRRL 40192). The structures of these compounds were elucidated on the basis of NM...
Characterization of structures in biofilms formed by a Pseudomonas fluorescens isolated from soil
Background Microbial biofilms represent an incompletely understood, but fundamental mode of bacterial growth. These sessile communities typically consist of stratified, morphologically-distinct layers of extracellular material, where numerous metabolic processes occur simultaneously in close proximity. Limited reports on environmental isolates have revealed highly ordered, three-dimensional organization of the extracellular matrix, which may hold important implications for biofilm physiology in vivo. Results A Pseudomonas spp. isolated from a natural soil environment produced flocculent, nonmucoidal biofilms in vitro with unique structural features. These mature biofilms were made up of numerous viable bacteria, even after extended culture, and contained up to 50% of proteins and accumulated 3% (by dry weight) calcium, suggesting an important role for the divalent metal in biofilm formation. Ultrastructurally, the mature biofilms contained structural motifs consisting of dense, fibrillary clusters, nanofibers, and ordered, honeycomb-like chambers enveloped in thin sheets. Conclusion Mature biofilms contained living bacteria and were structurally, chemically, and physiologically heterogeneous. The principal architectural elements observed by electron microscopy may represent useful morphological clues for identifying bacterial biofilms in vivo. The complexity and reproducibility of the structural motifs observed in bacterial biofilms appear to be the result of organized assembly, suggesting that this environmental isolate may possess ecological advantages in its natural habitat. PMID:19460161
Population structure of Staphylococcus aureus isolated from bulk tank goat's milk.
Spanu, Vincenzo; Scarano, Christian; Virdis, Salvatore; Melito, Sara; Spanu, Carlo; De Santis, Enrico Pietro Luigi
The presence of Staphylococcus aureus in raw milk can represent a potential threat to human health, due to the introduction of pathogenic strains into dairy food supply chain. The present study was performed to investigate the genetic variation among S. aureus strains isolated from bulk tank goat's milk. The virulence profiles were also assessed to link the isolates with the potential source of milk contamination. A population study was performed on 60 strains using distance-based methods such as pulsed-field gel electrophoresis (PFGE), and the output was analyzed using Structure statistical software (University of Chicago; http://pritch.bsd.uchicago.edu/structure.html ). This Bayesian clustering model tool allows one to assign individuals into a population with no predefined structure. In order to assess partition of genetic variability among isolates, groups obtained by Structure were also investigated using analysis of molecular variance. S. aureus was recovered in 60 out of 78 samples (76.9%) collected from 26 farms. According to PFGE analysis, the strains were divided into 25 different pulsotypes and grouped into two main clusters. Restriction profiles, analyzed by Structure, allowed us to identify two distinct S. aureus genetic groups. Within each group, the strains showed a high coefficient of membership. A great part of genetic variability was attributable to within-groups variation. On the basis of the virulence profile, 45% of the isolates were linked to "animal" biovar, while 6.7% could be assigned to "human" biovar. Out of 60 strains, 27 were characterized by in vitro production of either enterotoxins A (5.0%), C (38.3%), or D (1.7%). The present study showed a high prevalence of bulk tank goat's milk contamination with S. aureus of animal origin. The presence in goat's milk of S. aureus strains able to produce enterotoxins and their potential introduction into dairy chain may represent a serious threat to human health. PMID:23458027
Active pneumatic vibration isolation system using negative stiffness structures for a vehicle seat
NASA Astrophysics Data System (ADS)
Danh, Le Thanh; Ahn, Kyoung Kwan
In this paper, an active pneumatic vibration isolation system using negative stiffness structures (NSS) for a vehicle seat in low excitation frequencies is proposed, which is named as an active system with NSS. Here, the negative stiffness structures (NSS) are used to minimize the vibratory attraction of a vehicle seat. Owing to the time-varying and nonlinear behavior of the proposed system, it is not easy to build an accurate dynamic for model-based controller design. Thus, an adaptive intelligent backstepping controller (AIBC) is designed to manage the system operation for high-isolation effectiveness. In addition, an auxiliary control effort is also introduced to eliminate the effect of the unpredictable perturbations. Moreover, a radial basis function neural network (RBFNN) model is utilized to estimate the optimal gain of the auxiliary control effort. Final control input and the adaptive law for updating coefficients of the approximate series can be obtained step by step using a suitable Lyapunov function. Afterward, the isolation performance of the proposed system is assessed experimentally. In addition, the effectiveness of the designed controller for the proposed system is also compared with that of the traditional backstepping controller (BC). The experimental results show that the isolation effectiveness of the proposed system is better than that of the active system without NSS. Furthermore, the undesirable chattering phenomenon in control effort is quite reduced by the estimation mechanism. Finally, some concluding remarks are given at the end of the paper.
Multilevel NLTE radiative transfer in isolated atmospheric structures: implementation of the MALI-technique.
NASA Astrophysics Data System (ADS)
Heinzel, P.
We have developed and extensively tested a new multilevel NLTE transfer code for isolated solar atmospheric structures (loops, prominences, spicules etc.). The code is based on the MALI approach of Rybicki & Hummer (1991, 1992) to multilevel accelerated lambda iterations. It is demonstrated that this method is fully capable of treating a difficult problem of NLTE hydrogen excitation and ionization equilibrium, provided that we linearize the preconditioned statistical equilibrium equations with respect to atomic level populations and the electron density. With this generalization of the original MALI approach, the numerical code is robust and stable. As compared to the standard linearization method of Auer & Mihalas (1969), the new MALI code designed for 1D slabs is more than one order of magnitude faster and its accuracy is quite satisfactory. We discuss several details of our implementation of the MALI technique to isolated, externally irradiated, 1D structures and finally draw some future prospects.
Structure-Activity Relationships of Retro-dihydrochalcones Isolated from Tacca sp
Peng, Jiangnan; Risinger, April L.; Da, Chenxiao; Fest, Gary A.; Kellogg, Glen E.; Mooberry, Susan L.
Several biologically active compounds have been identified from Tacca species, including glycosides, diarylheptanoids, saponins, withanolides, and the taccalonolide class of microtubule stabilizers. More recently, two cytotoxic retro-dihydrochalcones named evelynin A (7) and taccabulin A (6) were isolated and their biological activities characterized, including the finding that taccabulin has microtubule destabilizing effects. Here we describe the identification and characterization of five new retro-chalcones, named taccabulins B – E (1–4) and evelynin B (5) from Tacca sp. extracts. Their structures were determined using 1D and 2D NMR as well as mass spectroscopic data and modeled into the colchicine binding site of tubulin. The antiproliferative and microtubule effects of each compound were determined experimentally and found to be well correlated with modeling studies. The isolation and biological characterization of several retro-dihydrochalcones facilitated preliminary structure-activity relationships for this compound class concerning its antiproliferative and microtubule depolymerizing activities. PMID:24303844
The isolation and structure of 13,18-dehydroglaucarubinone, a new antineoplastic quassinoid from Simarouba amara.
Polonsky, J; Varon, Z; Jacquemin, H; Pettit, G R
An investigation of the Guyana plant Simarouba amara Aubl. (Simaroubaceae) for antineoplastic quassinoids led to isolation and structural determination of the new quassinoids 2'-acetylglaucarubine (1a) and 13,18-dehydroglaucarubinone (2). The previously known 2'-acetylglaucarubinone (3a) and glaucarubinone (3b) were also obtained. The new quassinoid 2 was found significantly to inhibit growth of the murine lymphocytic leukemia P388. PMID:720499
Isolation and Structure of Cancer Cell Growth Inhibitory Tetracyclic Triterpenoids from the Zimbabwean Monadenium lugardae.
Pettit, George R; Ye, Qinghua; Herald, Delbert L; Knight, John C; Hogan, Fiona; Melody, Noeleen; Mukku, Venugopal J R V; Doubek, Dennis L; Chapuis, Jean-Charles
The Zimbabwean medicinal plant Monadenium lugardae was evaluated as a potential source of new anticancer constituents. Four new tetracyclic triterpene (1-4) were isolated, accompanied by four previously known triterpenes (5-8). Against a panel of human tumor cell lines, lugardstatins 1 (1) and 2 (2) had good cancer cell growth inhibitory activity. All of the triterpene structures (1-8) were established by 1D and 2D NMR spectrometric and HR mass spectrometric analysis. PMID:27214528
Design and Nuclear Magnetic Resonance (NMR) Structure Determination of the Second Extracellular Immunoglobulin Tyrosine Kinase A (TrkAIg2) Domain Construct for Binding Site Elucidation in Drug Discovery
The tyrosine kinase A (TrkA) receptor is a validated therapeutic intervention point for a wide range of conditions. TrkA activation by nerve growth factor (NGF) binding the second extracellular immunoglobulin (TrkAIg2) domain triggers intracellular signaling cascades. In the periphery, this promotes the pain phenotype and, in the brain, cell survival or differentiation. Reproducible structural information and detailed validation of protein–ligand interactions aid drug discovery. However, the isolated TrkAIg2 domain crystallizes as a β-strand-swapped dimer in the absence of NGF, occluding the binding surface. Here we report the design and structural validation by nuclear magnetic resonance spectroscopy of the first stable, biologically active construct of the TrkAIg2 domain for binding site confirmation. Our structure closely mimics the wild-type fold of TrkAIg2 in complex with NGF (1WWW.pdb), and the 1H–15N correlation spectra confirm that both NGF and a competing small molecule interact at the known binding interface in solution. PMID:25454499
Isolation and structural characterization of the water-extractable polysaccharides from Cassia obtusifolia seeds.
Shang, Mingsheng; Zhang, Xiaoman; Dong, Qun; Yao, Jian; Liu, Qin; Ding, Kan
The seed of Cassia obtusifolia is a food or herbal medicine used for improving eyesight, treating constipation and other disorders, and polysaccharides have been implicated in these pharmacological activities. The endosperm of the seeds, Cassia gum, is a commercial thickening or gelling agent, composed mainly of galactomannans. However, the whole seeds of C. obtusifolia, rather than the endosperm, are used in folk medicine or food, which might contain more complex constituents of polysaccharides. In this study, the whole seeds of C. obtusifolia were extracted with boiling water, and from the water extract, three homogeneous fractions were isolated, designated CFAA-1, CFAA-3, and CFBB2, respectively, after treatment with Fehling solution followed by anion-exchange and gel permeation chromatography. Using chemical and spectroscopic methods, CFAA-1, and CFAA-3 were elucidated to be both branched galactomannans with different molecular weights, consisting of 1,4-linked β-d-mannopyranosyl backbone with single-unit α-d-galactopyranosyl branches attached to O-6 of mannose, while CFBB2 was shown to be a linear (1→4)-α-polygalacturonic acid. PMID:22840008
Structural degradation of Thar lignite using MW1 fungal isolate: optimization studies
Haider, Rizwan; Ghauri, Muhammad A.; Jones, Elizabeth J.; Orem, William H.; SanFilipo, John R.
Biological degradation of low-rank coals, particularly degradation mediated by fungi, can play an important role in helping us to utilize neglected lignite resources for both fuel and non-fuel applications. Fungal degradation of low-rank coals has already been investigated for the extraction of soil-conditioning agents and the substrates, which could be subjected to subsequent processing for the generation of alternative fuel options, like methane. However, to achieve an efficient degradation process, the fungal isolates must originate from an appropriate coal environment and the degradation process must be optimized. With this in mind, a representative sample from the Thar coalfield (the largest lignite resource of Pakistan) was treated with a fungal strain, MW1, which was previously isolated from a drilled core coal sample. The treatment caused the liberation of organic fractions from the structural matrix of coal. Fungal degradation was optimized, and it showed significant release of organics, with 0.1% glucose concentration and 1% coal loading ratio after an incubation time of 7 days. Analytical investigations revealed the release of complex organic moieties, pertaining to polyaromatic hydrocarbons, and it also helped in predicting structural units present within structure of coal. Such isolates, with enhanced degradation capabilities, can definitely help in exploiting the chemical-feedstock-status of coal.
Solution structure of the isolated histone H2A-H2B heterodimer
Moriwaki, Yoshihito; Yamane, Tsutomu; Ohtomo, Hideaki; Ikeguchi, Mitsunori; Kurita, Jun-ichi; Sato, Masahiko; Nagadoi, Aritaka; Shimojo, Hideaki; Nishimura, Yoshifumi
During chromatin-regulated processes, the histone H2A-H2B heterodimer functions dynamically in and out of the nucleosome. Although detailed crystal structures of nucleosomes have been established, that of the isolated full-length H2A-H2B heterodimer has remained elusive. Here, we have determined the solution structure of human H2A-H2B by NMR coupled with CS-Rosetta. H2A and H2B each contain a histone fold, comprising four α-helices and two β-strands (α1–β1–α2–β2–α3–αC), together with the long disordered N- and C-terminal H2A tails and the long N-terminal H2B tail. The N-terminal αN helix, C-terminal β3 strand, and 310 helix of H2A observed in the H2A-H2B nucleosome structure are disordered in isolated H2A-H2B. In addition, the H2A α1 and H2B αC helices are not well fixed in the heterodimer, and the H2A and H2B tails are not completely random coils. Comparison of hydrogen-deuterium exchange, fast hydrogen exchange, and {1H}-15N hetero-nuclear NOE data with the CS-Rosetta structure indicates that there is some conformation in the H2A 310 helical and H2B Lys11 regions, while the repression domain of H2B (residues 27–34) exhibits an extended string-like structure. This first structure of the isolated H2A-H2B heterodimer provides insight into its dynamic functions in chromatin. PMID:27181506
Solution structure of the isolated histone H2A-H2B heterodimer.
Moriwaki, Yoshihito; Yamane, Tsutomu; Ohtomo, Hideaki; Ikeguchi, Mitsunori; Kurita, Jun-Ichi; Sato, Masahiko; Nagadoi, Aritaka; Shimojo, Hideaki; Nishimura, Yoshifumi
During chromatin-regulated processes, the histone H2A-H2B heterodimer functions dynamically in and out of the nucleosome. Although detailed crystal structures of nucleosomes have been established, that of the isolated full-length H2A-H2B heterodimer has remained elusive. Here, we have determined the solution structure of human H2A-H2B by NMR coupled with CS-Rosetta. H2A and H2B each contain a histone fold, comprising four α-helices and two β-strands (α1-β1-α2-β2-α3-αC), together with the long disordered N- and C-terminal H2A tails and the long N-terminal H2B tail. The N-terminal αN helix, C-terminal β3 strand, and 310 helix of H2A observed in the H2A-H2B nucleosome structure are disordered in isolated H2A-H2B. In addition, the H2A α1 and H2B αC helices are not well fixed in the heterodimer, and the H2A and H2B tails are not completely random coils. Comparison of hydrogen-deuterium exchange, fast hydrogen exchange, and {(1)H}-(15)N hetero-nuclear NOE data with the CS-Rosetta structure indicates that there is some conformation in the H2A 310 helical and H2B Lys11 regions, while the repression domain of H2B (residues 27-34) exhibits an extended string-like structure. This first structure of the isolated H2A-H2B heterodimer provides insight into its dynamic functions in chromatin. PMID:27181506
Antihyperglycemic activities of cryptolepine analogues: an ethnobotanical lead structure isolated from Cryptolepis sanguinolenta.
Bierer, D E; Dubenko, L G; Zhang, P; Lu, Q; Imbach, P A; Garofalo, A W; Phuan, P W; Fort, D M; Litvak, J; Gerber, R E; Sloan, B; Luo, J; Cooper, R; Reaven, G M
Cryptolepine (1) is a rare example of a natural product whose synthesis was reported prior to its isolation from nature. In the previous paper we reported the discovery of cryptolepine's antihyperglycemic properties. As part of a medicinal chemistry program designed to optimize natural product lead structures originating from our ethnobotanical and ethnomedical field research, a series of substituted and heterosubstituted cryptolepine analogues was synthesized. Antihyperglycemic activity was measured in vitro and in an NIDDM mouse model to generate the first structure-bioactivity study about the cryptolepine nucleus. PMID:9667966
High-spatial-resolution Raman microscopy of stress in shallow-trench-isolated Si structures
NASA Astrophysics Data System (ADS)
Poborchii, Vladimir; Tada, Tetsuya; Kanayama, Toshihiko
Stress in single and periodic shallow-trench-isolated Si structures was examined by 364nm excitation confocal resonance Raman microscopy, laser penetration being restricted to the near-surface region. Using a 1.3 numerical aperture microobjective lens with a theoretical ˜140nm spatial resolution, the authors show that the configuration with both incident and scattered lights polarized parallel to each other and perpendicular to Si stripes is favorable for stress detection in the middle of the stripes, suppressing contributions from their edges. The stresses located in different areas of the structures were identified and analyzed.
Glycolonitrile oligomerization: structure of isolated oxazolines, potential heterocycles on the early earth
NASA Technical Reports Server (NTRS)
Arrhenius, G.; Baldridge, K. K.; Richards-Gross, S.; Siegel, J. S.; Bada, J. L. (Principal Investigator)
A study of glycolonitrile polymerization has led to the isolation and characterization of two 2,5-dihydro-4-aminooxazoles, 4 and 5. Previous reports have misassigned these structures as s-triazines or pyrimidines. X-ray diffraction analysis of crystals of 4 and an acetylated oxazole derivative of 5 (6) confirm the proposed structures. Ab initio computations are used to assess the relative thermodynamic stability of three trimer isomers (an s-triazine, an aminohydroxypyrimidine, and an aminooxazoline), and the results indicate that 4 is a novel kinetic product. Mechanistic considerations rationalize kinetic oxazole formation over the more customary triazine or pyrimidine trimers.
Roles of soil-structure interaction and damping in base-isolated structures built on numerous soil layers overlying a half-space
NASA Astrophysics Data System (ADS)
Tsai, C. S.; Hsueh, C. I.; Su, H. C.
This study examines the roles of soil-structure interaction (SSI), higher modes, and damping in a base-isolated structure built on multiple layers of soil overlying a half space. Closed-form solutions for the entire system, including a superstructure, seismic isolator, and numerous soil layers overlying a half-space, were obtained. The formulations obtained in this study simply in terms of well-known frequencies and mechanical impedance ratios can explicitly interpret the dynamic behavior of a base-isolated structure interacting with multiple soil layers overlying a half-space. The key factors influencing the performance of the isolation system are the damping ratio of the isolator and the ratio of the natural frequency of the fixed-base structure to that of the isolated structure by assuming that the superstructure moves as a rigid body. This study reveals that higher damping in the base isolator is unfavorable to higher mode responses that usually dominate the responses of the superstructure and that the damping mechanism plays an important role in transmitting energy in addition to absorbing energy. It is also concluded that it is possible to design a soft soil layer as an isolation system for isolating vibration energy.
Isolation and Characterization of Sclerienone C from Scleria striatinux.
Nyongbela, Kennedy D; Makolo, Felix L; Hoye, Thomas R; Efange, Simon M N
Herein, we report the isolation and characterization of sclerienone C, a novel sesquiterpene isolated from the methylene chloride/methanol (1:1) extract of Scleria striatinux that we have deduced to have structure 1. This medicinal spice of Cameroon has been shown to display antimicrobial and antiplasmodial activities. The isolation and purification involved a combination of methods including silica gel column chromatography, Sephadex LH-20, and semi-prep HPLC separations. Structure elucidation was carried-out by means of spectroscopic analysis and comparison with previously isolated sesquiterpene derivatives from the plant. PMID:26996004
Vibration control of platform structures with magnetorheological elastomer isolators based on an improved SAVS law
NASA Astrophysics Data System (ADS)
Xu, Zhao-Dong; Suo, Si; Lu, Yong
This paper presents a study on the vibration control of platform structures with magnetorheological elastomer (MRE) isolators. Firstly, a novel MRE isolator design is put forward based on the mechanical properties of MREs, and subsequently a single-degree-of-freedom (SDOF) dynamic model and a multiple-degree-of-freedom (MDOF) dynamic model for platform systems incorporating such isolators are developed. In order to overcome the shortcomings of the conventional on–off control law, an improved semi-active variable stiffness (SAVS) control law is proposed. The proposed SAVS scheme makes full use of the continuously variable stiffness of MREs, and it takes into account the influence of the sampling interval such that the field-dependent restoring force is made to do negative work during the whole sampling interval as far as possible. The results of numerical simulations demonstrate that the improved SAVS control law can achieve better vibration-control effectiveness than the on–off control law. The comparative results are discussed through examining the mechanisms of these two control laws in light of the power spectral density and the energy input. For an MDOF platform a simplified approach is proposed to combine the local response signals with an equivalent SDOF representation to generate the control parameters for individual isolators, and the effectiveness of such a scheme is also verified through numerical simulation.
The spectral elucidation versus the X-ray structure of the critical precursor complex in bimolecular electron transfers: application of experimental/theoretical solvent probes to ion-radical (redox) dyads.
Rosokha, Sergiy V; Newton, Marshall D; Jalilov, Almaz S; Kochi, Jay K
The mechanistic conundrum is commonly posed by the intrinsic structural disconnect between a bimolecular (reactive) intermediate that is fleetingly detected spectroscopically in solution versus that rigorously defined by isolation and X-ray crystallography. We resolve this ambiguity by the combined experimental and theoretical application of the solvent media probe to the transient (1:1) precursor complex in the simplest chemical reaction involving direct adiabatic electron transfer (ET) among various donor/acceptor pairs. Of particular help in our resolution of such an important ET problem is the characterization of the bimolecular precursor complex as Robin-Day class II (localized) or class III (delocalized) from either the solvent-dependent or the solvent-independent response of the diagnostic intervalence absorption bands for the quantitative evaluation of the electronic coupling elements. The magnitudes of these intracomplex bindings are confirmed by theoretical (ab initio and DFT) computations that derive from X-ray structures and Marcus-Hush theories. Most importantly, the experimental solvent-induced ET barriers evaluated from the intervalence absorption bands are also quantitatively verified by the calculated outer-shell reorganization energies to establish unambiguously the intimate interconnection between the loosely bound bimolecular intermediate identified concurrently in solution and in the solid state. PMID:18211069
Studies in the Chemical Constituents of Azadirachta indica Part II: Isolation and Structure of the New Triterpenoid Azadirachtol.
Siddiqui, S; Siddiqui, B S; Faizi, S
A new triterpenoid named azadirachtol ( 1) has been isolated from the fruits of AZADIRACHTA INDICA Juss. (neem) of which the structure is reported on the basis of chemical and spectral data. Azadirachtol appears to be the first apo-tirucallol (apo-euphol) derivative possessing an eight carbons side-chain with an oxygenated ring system isolated from neem. Moreover, it is the first instance of the isolation of an 11-hydroxy triterpenoid from any of the various parts of neem. PMID:17345262
Qualitative Fault Isolation of Hybrid Systems: A Structural Model Decomposition-Based Approach
NASA Technical Reports Server (NTRS)
Bregon, Anibal; Daigle, Matthew; Roychoudhury, Indranil
Quick and robust fault diagnosis is critical to ensuring safe operation of complex engineering systems. A large number of techniques are available to provide fault diagnosis in systems with continuous dynamics. However, many systems in aerospace and industrial environments are best represented as hybrid systems that consist of discrete behavioral modes, each with its own continuous dynamics. These hybrid dynamics make the on-line fault diagnosis task computationally more complex due to the large number of possible system modes and the existence of autonomous mode transitions. This paper presents a qualitative fault isolation framework for hybrid systems based on structural model decomposition. The fault isolation is performed by analyzing the qualitative information of the residual deviations. However, in hybrid systems this process becomes complex due to possible existence of observation delays, which can cause observed deviations to be inconsistent with the expected deviations for the current mode in the system. The great advantage of structural model decomposition is that (i) it allows to design residuals that respond to only a subset of the faults, and (ii) every time a mode change occurs, only a subset of the residuals will need to be reconfigured, thus reducing the complexity of the reasoning process for isolation purposes. To demonstrate and test the validity of our approach, we use an electric circuit simulation as the case study.
The phylogenetic structure of plant-pollinator networks increases with habitat size and isolation.
Aizen, Marcelo A; Gleiser, Gabriela; Sabatino, Malena; Gilarranz, Luis J; Bascompte, Jordi; Verdú, Miguel
Similarity among species in traits related to ecological interactions is frequently associated with common ancestry. Thus, closely related species usually interact with ecologically similar partners, which can be reinforced by diverse co-evolutionary processes. The effect of habitat fragmentation on the phylogenetic signal in interspecific interactions and correspondence between plant and animal phylogenies is, however, unknown. Here, we address to what extent phylogenetic signal and co-phylogenetic congruence of plant-animal interactions depend on habitat size and isolation by analysing the phylogenetic structure of 12 pollination webs from isolated Pampean hills. Phylogenetic signal in interspecific interactions differed among webs, being stronger for flower-visiting insects than plants. Phylogenetic signal and overall co-phylogenetic congruence increased independently with hill size and isolation. We propose that habitat fragmentation would erode the phylogenetic structure of interaction webs. A decrease in phylogenetic signal and co-phylogenetic correspondence in plant-pollinator interactions could be associated with less reliable mutualism and erratic co-evolutionary change. PMID:26493295
A VO-seeded Approach for the Growth of Star-shaped VO2 and V2O5 Nanocrystals: Facile Synthesis Structural Characterization and Elucidation of Electronic Structure
L Whittaker; J Velazquez; S Banerjee
Obtaining shape and size control of strongly correlated materials is imperative to obtain a fundamental understanding of the influence of finite size and surface restructuring on electronic instabilities in the proximity of the Fermi level. We present here a novel synthetic approach that takes advantage of the intrinsic octahedral symmetry of rock-salt-structured VO to facilitate the growth of six-armed nanocrystallites of related, technologically important binary vanadium oxides VO2 and V2O5. The prepared nanostructures exhibit clear six-fold symmetry and most notably show remarkable retention of electronic structure. The latter has been evidenced through extensive X-ray absorption spectroscopy measurements.
Genome sequencing of disease and carriage isolates of nontypeable Haemophilus influenzae identifies discrete population structure.
De Chiara, Matteo; Hood, Derek; Muzzi, Alessandro; Pickard, Derek J; Perkins, Tim; Pizza, Mariagrazia; Dougan, Gordon; Rappuoli, Rino; Moxon, E Richard; Soriani, Marco; Donati, Claudio
One of the main hurdles for the development of an effective and broadly protective vaccine against nonencapsulated isolates of Haemophilus influenzae (NTHi) lies in the genetic diversity of the species, which renders extremely difficult the identification of cross-protective candidate antigens. To assess whether a population structure of NTHi could be defined, we performed genome sequencing of a collection of diverse clinical isolates representative of both carriage and disease and of the diversity of the natural population. Analysis of the distribution of polymorphic sites in the core genome and of the composition of the accessory genome defined distinct evolutionary clades and supported a predominantly clonal evolution of NTHi, with the majority of genetic information transmitted vertically within lineages. A correlation between the population structure and the presence of selected surface-associated proteins and lipooligosaccharide structure, known to contribute to virulence, was found. This high-resolution, genome-based population structure of NTHi provides the foundation to obtain a better understanding, of NTHi adaptation to the host as well as its commensal and virulence behavior, that could facilitate intervention strategies against disease caused by this important human pathogen. PMID:24706866
Photochemistry of matrix-isolated and thin film acid chlorides: Quantum yields and product structures
Rowland, B.; Hess, W.P.; Winter, P.R.; Ellison, G.B.; Radziszewski, J.G.
Ultraviolet photoexcitation of matrix-isolated CH{sub 3}COCl, CH{sub 3}CH{sub 2}COCl, and CH{sub 3}CH{sub 2}CH{sub 2}CH{sub 2}COCl produces HCl{center_dot}CH{sub 2}{double_bond}C{double_bond}O, HCl{center_dot}CH{sub 3}CHC{double_bond}C{double_bond}O, and HCl{center_dot}CH{sub 3}CH{sub 2}CH{sub 2}CHC{double_bond}C{double_bond}O complexes. The authors report precursor and matrix dependent reaction quantum yields. Quantum yield values decrease with increasing alkyl chain length due to a reduced number of {alpha} H-atoms available for the elimination reaction and steric considerations. The authors found quantum yields in neat matrixes to be roughly half that in argon or xenon matrixes and assign structures for HCL and ketene complexes in argon and xenon matrixes by comparing IR spectra ab initio electronic structure calculations. In argon matrixes, the product complex HCl frequently is strongly shifted whereas the ketene remains unshifted with respect to matrix-isolated ketene. In xenon matrixes, HCl{center_dot}ketene complexes display absorption bands indicative of two distinct structures. Differences between HCl{center_dot}ketene structures in argon and xenon matrixes are attributed to size differences of the matrix lattice.
Zebrafish Cardiac Muscle Thick Filaments: Isolation Technique and Three-Dimensional Structure
González-Solá, Maryví; AL-Khayat, Hind A.; Behra, Martine; Kensler, Robert W.
To understand how mutations in thick filament proteins such as cardiac myosin binding protein-C or titin, cause familial hypertrophic cardiomyopathies, it is important to determine the structure of the cardiac thick filament. Techniques for the genetic manipulation of the zebrafish are well established and it has become a major model for the study of the cardiovascular system. Our goal is to develop zebrafish as an alternative system to the mammalian heart model for the study of the structure of the cardiac thick filaments and the proteins that form it. We have successfully isolated thick filaments from zebrafish cardiac muscle, using a procedure similar to those for mammalian heart, and analyzed their structure by negative-staining and electron microscopy. The isolated filaments appear well ordered with the characteristic 42.9 nm quasi-helical repeat of the myosin heads expected from x-ray diffraction. We have performed single particle image analysis on the collected electron microscopy images for the C-zone region of these filaments and obtained a three-dimensional reconstruction at 3.5 nm resolution. This reconstruction reveals structure similar to the mammalian thick filament, and demonstrates that zebrafish may provide a useful model for the study of the changes in the cardiac thick filament associated with disease processes. PMID:24739166
Use of polymerase chain reaction-amplified Helicobacter pylori urease structural genes for differentiation of isolates.
Foxall, P A; Hu, L T; Mobley, H L
Helicobacter pylori has been demonstrated as an etiologic agent of human gastritis and peptic ulcer formation. However, there is no straightforward basis to distinguish different isolates. We used the polymerase chain reaction (PCR) to amplify the urease structural subunit genes, ureA and ureB, which, when digested with appropriate restriction endonucleases, allow the differentiation of patterns on agarose gels. PCR amplification was possible with DNA rapidly extracted from H. pylori by alkaline lysis and phenol-chloroform. The 2.4-kb PCR products amplified from 22 clinical isolates and subjected to HaeII restriction endonuclease digestion produced 10 distinct patterns on agarose gels, with two patterns being shared between five and six strains. PCR amplification of the urease genes may enable the differentiation of closely related H. pylori strains by restriction digest analysis of PCR-amplified ureA and ureB genes. Images PMID:1313051
Structural characterization of the O-polysaccharide isolated from Franconibacter helveticus LMG23732(T).
Szulta, Sylwia; Czerwicka, Małgorzata; Forsythe, Stephen J; Ossowska, Karolina; Dziadziuszko, Halina; Kaczyński, Zbigniew
The bacterial strain Franconibacter helveticus LMG 23732(T) was previously misidentified as the neonatal pathogen Cronobacter zurichensis. O-polysaccharide (OPS) is a part of lipopolysaccharide (LPS), which is an important cell envelope compound of Gram-negative bacteria. OPS isolated from the bacterium Franconibacter helveticus LMG23732(T) was characterized by chemical analyses as well as 1D and 2D NMR experiments. Compositional analyses indicated the presence of glucose and unusual 6-deoxy sugar - 6-deoxy-talose (6-dTal). The studied strain produced OPS, which consists of 6-l-dTalp in main chain and terminal d-Glcp as a branch: This is the first structural determination of the OPS isolated from genus Franconibacter. PMID:27288973
Isolation and structure of whiskey polyphenols produced by oxidation of oak wood ellagitannins.
Fujieda, Miho; Tanaka, Takashi; Suwa, Yoshihide; Koshimizu, Seiichi; Kouno, Isao
Three new phenolic compounds named whiskey tannins A and B and carboxyl ellagic acid were isolated from commercial Japanese whiskey, along with gallic acid, ellagic acid, brevifolin carboxylic acid, three galloyl glucoses, a galloyl ester of phenolic glucoside, 2,3-(S)-hexahydroxydiphenoylglucose, and castacrenin B. Whiskey tannins A and B were oxidation products of a major oak wood ellagitannin, castalagin, in which the pyrogallol ring at the glucose C-1 position of castalagin was oxidized to a cyclopentenone moiety. These tannins originated from ellagitannins contained in the oak wood used for barrel production; however, the original oak wood ellagitannins were not detected in the whiskey. To examine whether the whiskey tannins were produced during the charring process of barrel production, pyrolysis products of castalagin were investigated. Dehydrocastalagin and a new phenolcarboxylic acid trislactone having an isocoumarin structure were isolated, along with castacrenin F and ellagic acid. However, whiskey tannins were not detected in the products. PMID:18672883
Structural analyses of novel glycerophosphorylated alpha-cyclosophorohexadecaoses isolated from X. campestris pv. campestris.
Jung, Yunjung; Park, Heylin; Cho, Eunae; Jung, Seunho
Novel periplasmic anionic cyclic glucans produced by Xanthomonas campestris pv. campestris were isolated by trichloroacetic acid treatment and various chromatographic techniques. No report has been made on the presence of substituted cyclic glucans of the Xanthomonas species. We show, for the first time, that X. campestris pv. campestris produces the anionic cyclic glucans with phosphoglycerol residues, the presence of which can be predicted by analyzing the sequence database with the aid of the NCBI RefSeq database. To analyze the structure of isolated anionic cyclic glucans analyses, we used NMR spectroscopy, matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOFMS) and electrospray-ionization mass spectrometry (ESIMS). The results suggest that the novel anionic forms of the cyclic glucans of X. campestris pv. campestris are glycerophosphorylated alpha-cyclosophorohexadecaose with one or two phosphoglycerol substituents at the C-6 positions of the glucose residues. PMID:15721339
Population genetic structure of Theileria parva field isolates from indigenous cattle populations of Uganda.
Muwanika, Vincent; Kabi, Fredrick; Masembe, Charles
Theileria parva causes East Coast Fever (ECF) a protozoan infection which manifests as a non-symptomatic syndrome among endemically stable indigenous cattle populations. Knowledge of the current genetic diversity and population structure of T. parva is critical for predicting pathogen evolutionary trends to inform development of effective control strategies. In this study the population genetic structure of 78 field isolates of T. parva from indigenous cattle (Ankole, n=41 and East African shorthorn Zebu (EASZ), n=37) sampled from the different agro ecological zones (AEZs) of Uganda was investigated. A total of eight mini- and micro-satellite markers encompassing the four chromosomes of T. parva were used to genotype the study field isolates. The genetic diversity of the surveyed T. parva populations was observed to range from 0.643±0.55 to 0.663±0.41 among the Central and Western AEZs respectively. The overall Wright's F index showed significant genetic variation between the surveyed T. parva populations based on the different AEZs and indigenous cattle breeds (FST=0.133, p<0.01) and (FST=0.101, p<0.01) respectively. Significant pairwise population genetic differentiations (p<0.05) were observed with FST values ranging from 0.048 to 0.173 between the eastern and northern, eastern and western populations respectively. The principal component analysis (PCA) showed a high level of genetic and geographic sub-structuring among populations. Linkage disequilibrium was observed when populations from all the study AEZs were treated as a single population and when analysed separately. On the overall, the significant genetic diversity and geographic sub-structuring exhibited among the study T. parva isolates has critical implications for ECF control. PMID:26613662
Investigation of olefinic structures in class I resinites by isolation and characterization of soluble polylabdanoids
Clifford, D.J.; Botto, R.E.; Anderson, K.B.
Resinites derived from labdatriene structures (Class I) are ubiquitous throughout the geosphere. A soluble polylabdanoid material has been isolated by sequential extraction with organic solvents. Solid- and liquid-state NMR spectroscopy, and Py-GC-MS, indicate that at least for immature resinites, the extractable polymer is representative of the insoluble, polylabdanoid material, which constitutes the bulk of most Class I resinites. With increasing maturity, the dominant chemical transformation that occurs in these materials is the {open_quotes}loss{close_quotes} of exomethylene structures and depletion of olefinic character from {approximately}two to {approximately}one olefin per monomer unit. To investigate the fate of olefinic structures and to determine the nature of the residual olefin distribution in these materials, two-dimensional NMR correlation spectroscopies (COSY and HMQC) and nuclear Overhauser experiments (NOESY) have been undertaken. Results from these analyses and their implications to the maturation of Class-I resinites will be discussed.
Disrupted topological organization of structural and functional brain connectomes in clinically isolated syndrome and multiple sclerosis.
Shu, Ni; Duan, Yunyun; Xia, Mingrui; Schoonheim, Menno M; Huang, Jing; Ren, Zhuoqiong; Sun, Zheng; Ye, Jing; Dong, Huiqing; Shi, Fu-Dong; Barkhof, Frederik; Li, Kuncheng; Liu, Yaou
The brain connectome of multiple sclerosis (MS) has been investigated by several previous studies; however, it is still unknown how the network changes in clinically isolated syndrome (CIS), the earliest stage of MS, and how network alterations on a functional level relate to the structural level in MS disease. Here, we investigated the topological alterations of both the structural and functional connectomes in 41 CIS and 32 MS patients, compared to 35 healthy controls, by combining diffusion tensor imaging and resting-state functional MRI with graph analysis approaches. We found that the structural connectome showed a deviation from the optimal pattern as early as the CIS stage, while the functional connectome only showed local changes in MS patients, not in CIS. When comparing two patient groups, the changes appear more severe in MS. Importantly, the disruptions of structural and functional connectomes in patients occurred in the same direction and locally correlated in sensorimotor component. Finally, the extent of structural network changes was correlated with several clinical variables in MS patients. Together, the results suggested early disruption of the structural brain connectome in CIS patients and provided a new perspective for investigating the relationship of the structural and functional alterations in MS. PMID:27403924
Disrupted topological organization of structural and functional brain connectomes in clinically isolated syndrome and multiple sclerosis
Shu, Ni; Duan, Yunyun; Xia, Mingrui; Schoonheim, Menno M.; Huang, Jing; Ren, Zhuoqiong; Sun, Zheng; Ye, Jing; Dong, Huiqing; Shi, Fu-Dong; Barkhof, Frederik; Li, Kuncheng; Liu, Yaou
The brain connectome of multiple sclerosis (MS) has been investigated by several previous studies; however, it is still unknown how the network changes in clinically isolated syndrome (CIS), the earliest stage of MS, and how network alterations on a functional level relate to the structural level in MS disease. Here, we investigated the topological alterations of both the structural and functional connectomes in 41 CIS and 32 MS patients, compared to 35 healthy controls, by combining diffusion tensor imaging and resting-state functional MRI with graph analysis approaches. We found that the structural connectome showed a deviation from the optimal pattern as early as the CIS stage, while the functional connectome only showed local changes in MS patients, not in CIS. When comparing two patient groups, the changes appear more severe in MS. Importantly, the disruptions of structural and functional connectomes in patients occurred in the same direction and locally correlated in sensorimotor component. Finally, the extent of structural network changes was correlated with several clinical variables in MS patients. Together, the results suggested early disruption of the structural brain connectome in CIS patients and provided a new perspective for investigating the relationship of the structural and functional alterations in MS. PMID:27403924
New theoretical methodology for elucidating the solution structure of peptides from NMR data. II. Free energy of dominant microstates of Leu-enkephalin and population-weighted average nuclear Overhauser effects intensities.
Meirovitch, E; Meirovitch, H
A small linear peptide in solution may populate several stable states (called here microstates) in thermodynamic equilibrium; elucidating its dynamic three dimensional structure by multi- dimensional nmr is complex since the experimentally measured nuclear Overhauser effect intensities (NOEs) represent averages over the individual contributions. We propose a new methodology based on statistical mechanical considerations for analyzing nmr data of such peptides. In a previous paper (called paper I, H. Meirovitch et al. (1995) Journal of Physical Chemistry, 99, 4847-4854] we have developed theoretical methods for determining the contribution to the partition function Z of the most stable microstates, i.e. those that pertain to a given energy range above the global energy minimum (GEM). This relatively small set of dominant microstates provides the main contribution to medium- and long-range NOE intensities. In this work the individual populations and NOEs of the dominant microstates are determined, and then weighted averages are calculated and compared with experiment. Our methodology is applied to the pentapeptide Leu-enkephalin H-Tyr-Gly-Gly-Phe-Leu-OH, described by the potential energy function ECEPP. Twenty one significantly different energy minimized structures are first identified within the range of 2 kcal/mol above the GEM by an extensive conformational search; this range has been found in paper I to contribute 0.6 of Z. These structures then become "seeds" for Monte Carlo (MC) simulations designed to keep the molecule relatively close to its seed. Indeed, the MC samples (called MC microstates) illustrate what we define as intermediate chain flexibility; some dihedral angles remain in the vicinity of their seed value, while others visit the full range of [-180 degrees, 180 degrees]. The free energies of the MC microstates (which lead to the populations) are calculated by the local states method, which (unlike other techniques) can handle any chain flexibility
Dissipativity analysis of the base isolated benchmark structure with magnetorheological fluid dampers
NASA Astrophysics Data System (ADS)
Erkus, Baris; Johnson, Erik A.
This paper investigates the dissipativity and performance characteristics of the semiactive control of the base isolated benchmark structure with magnetorheological (MR) fluid dampers. Previously, the authors introduced the concepts of dissipativity and dissipativity indices in the semiactive control of structures with smart dampers and studied the dissipativity characteristics of simple structures with idealized dampers. To investigate the effects of semiactive controller dissipativity characteristics on the overall performance of the base isolated benchmark building, a clipped optimal control strategy with a linear quadratic Gaussian (LQG) controller and a 20 ton MR fluid damper model is used. A cumulative index is proposed for quantifying the overall dissipativity of a control system with multiple control devices. Two control designs with different dissipativity and performance characteristics are considered as the primary controller in clipped optimal control. Numerical simulations reveal that the dissipativity indices can be classified into two groups that exhibit distinct patterns. It is shown that the dissipativity indices identify primary controllers that are more suitable for application with MR dampers and provide useful information in the semiactive design process that complements other performance indices. The computational efficiency of the proposed dissipativity indices is verified by comparing computation times.
Structural investigations on a linear isolated depsipeptide: the importance of dispersion interactions.
Stamm, A; Bernhard, D; Gerhards, M
In this paper we present the first investigations on an isolated linear depsipetide CyCO-Gly-Lac-NH-PhOMe (cyclohexylcarbonyl-glycine-lactate-2-anisidine abbreviated as MOC) in a molecular beam experiment. Depsipeptides are a special subclass of peptides which contain at least one ester bond replacing a peptide bond. This leads to a different folding behavior and a different biological activity compared to a "normal" peptide. In order to analyze the folding of an isolated depsipeptide on a molecular level a variety of combined IR/UV methods including IR/IR/UV experiments are applied to MOC. Three different isomers are identified in combination with DFT calculations using the hybrid functional B3LYP-D3 with a TZVP basis set. The most stable structure shows a tweezer-like arrangement between the aromatic chromophore and the aliphatic cyclohexyl ring. A characteristic feature of this structure is that it is stabilized by dispersion interactions resulting from CH/π interactions. If dispersion is not taken into account this structural arrangement is no longer a minimum on the potential energy surface indicating the importance of dispersion interactions. PMID:27211924
Isolation, Co-Crystallization and Structure-Based Characterization of Anabaenopeptins as Highly Potent Inhibitors of Activated Thrombin Activatable Fibrinolysis Inhibitor (TAFIa)
Schreuder, Herman; Liesum, Alexander; Lönze, Petra; Stump, Heike; Hoffmann, Holger; Schiell, Matthias; Kurz, Michael; Toti, Luigi; Bauer, Armin; Kallus, Christopher; Klemke-Jahn, Christine; Czech, Jörg; Kramer, Dan; Enke, Heike; Niedermeyer, Timo H. J.; Morrison, Vincent; Kumar, Vasant; Brönstrup, Mark
Mature thrombin activatable fibrinolysis inhibitor (TAFIa) is a carboxypeptidase that stabilizes fibrin clots by removing C-terminal arginines and lysines from partially degraded fibrin. Inhibition of TAFIa stimulates the degradation of fibrin clots and may help to prevent thrombosis. Applying a lead finding approach based on literature-mining, we discovered that anabaenopeptins, cyclic peptides produced by cyanobacteria, were potent inhibitors of TAFIa with IC50 values as low as 1.5 nM. We describe the isolation and structure elucidation of 20 anabaenopeptins, including 13 novel congeners, as well as their pronounced structure-activity relationships (SAR) with respect to inhibition of TAFIa. Crystal structures of the anabaenopeptins B, C and F bound to the surrogate protease carboxypeptidase B revealed the binding modes of these large (~850 Da) compounds in detail and explained the observed SAR, i.e. the strong dependence of the potency on a basic (Arg, Lys) exocyclic residue that addressed the S1' binding pocket, and a broad tolerance towards substitutions in the pentacyclic ring that acted as a plug of the active site. PMID:27604544
Isolation, Co-Crystallization and Structure-Based Characterization of Anabaenopeptins as Highly Potent Inhibitors of Activated Thrombin Activatable Fibrinolysis Inhibitor (TAFIa).
Schreuder, Herman; Liesum, Alexander; Lönze, Petra; Stump, Heike; Hoffmann, Holger; Schiell, Matthias; Kurz, Michael; Toti, Luigi; Bauer, Armin; Kallus, Christopher; Klemke-Jahn, Christine; Czech, Jörg; Kramer, Dan; Enke, Heike; Niedermeyer, Timo H J; Morrison, Vincent; Kumar, Vasant; Brönstrup, Mark
Mature thrombin activatable fibrinolysis inhibitor (TAFIa) is a carboxypeptidase that stabilizes fibrin clots by removing C-terminal arginines and lysines from partially degraded fibrin. Inhibition of TAFIa stimulates the degradation of fibrin clots and may help to prevent thrombosis. Applying a lead finding approach based on literature-mining, we discovered that anabaenopeptins, cyclic peptides produced by cyanobacteria, were potent inhibitors of TAFIa with IC50 values as low as 1.5 nM. We describe the isolation and structure elucidation of 20 anabaenopeptins, including 13 novel congeners, as well as their pronounced structure-activity relationships (SAR) with respect to inhibition of TAFIa. Crystal structures of the anabaenopeptins B, C and F bound to the surrogate protease carboxypeptidase B revealed the binding modes of these large (~850 Da) compounds in detail and explained the observed SAR, i.e. the strong dependence of the potency on a basic (Arg, Lys) exocyclic residue that addressed the S1' binding pocket, and a broad tolerance towards substitutions in the pentacyclic ring that acted as a plug of the active site. PMID:27604544
Concerning the structure of islandoquinone isolated from the lichen Cetraria islandica.
Borisova, Ksenia L; Pelageev, Dmitry N; Kochergina, Tatiana Yu; Pokhilo, Nataly D; Pushilin, Michael A; Denisenko, Vladimir A; Berdyshev, Dmitry V; Anufriev, Victor Ph
An investigation of the oxidative coupling products of some substituted hydroxynaphthazarins led to a revision of the proposed structure of islandoquinone, previously isolated from the lichen Cetraria islandica, and yielding (7aS*, 13aS*)-6,7a-diethyl-2,5,9,11,12,13a-hexahydroxy-7, 4-dioxabenzo[a]tetracene-1,4,8,13(7aH, 13aH)-tetraone through X-ray diffraction analysis of its 2,11-dimethyl ether. PMID:25115094
Isolation and structures of oligomeric wine pigments by bisulfite-mediated ion-exchange chromatography.
Asenstorfer, R E; Hayasaka, Y; Jones, G P
Methods have been developed that are based on cation exchange chromatography in the absence and presence of excess bisulfite for the isolation of wine pigments from Australian red wine and grape marc extract. The pigments were identified using HPLC and electrospray ionization mass spectrometry. The mass spectral data indicate that these pigments are C4-substituted anthocyanins with a tetracyclic structure. The pigments form a series of closely related oligomeric pigments which include those previously described in the literature, such as pigment A and vitisin A, as well as some newly identified pigments. PMID:11743792
Structural gene isolation and prepeptide sequence of gallidermin, a new lanthionine containing antibiotic.
Schnell, N; Entian, K D; Götz, F; Hörner, T; Kellner, R; Jung, G
Peptide antibiotics containing lanthionine and 3-methyllanthionine bridges, named lantibiotics are of increasing interest. A new lantibiotic, gallidermin, has been isolated from Staphyloccus gallinarum. Here we report the isolation of its structural gene which we name gdmA. In all lantibiotics so far studied genetically, three peptides can be formally distinguished: (i) the primary translation product, which we call the prepeptide; (ii) the propeptide lacking the leader sequence and (iii) the mature lantibiotic. Unlike the plasmid-coded epidermin, gdmA is located on the chromosome. The gdmA locus codes for a 52 amino acid residue prepeptide, consisting of an alpha-helical leader sequence of hydrophilic character, which is separated from the C-terminus (propeptide) by a characteristic proteolytic processing site (Pro-2 Arg-1 Ile1). Although pro-gallidermin differs from pro-epidermin (a recently isolated lantibiotic) only by a single amino acid residue exchange. Leu instead of Ile, the N-terminus of the prepeptide differs by an additional two exchanges. PMID:2765032
Leucaena leucocephala (Lam.) de Wit., "subabul" stem lignin: Isolation, structural characterization and thermal properties.
Yearla, Srinivasa Rao; Padmasree, Kollipara
Lignin is the second most abundant renewable biopolymer on earth after cellulose. It is being used in many industrial applications due to its abundance. In the present study, lignin was isolated from the stems of Leucaena leucocephala (Lam.) de Wit., a high biomass yielding plant using acidic dioxane under N2 atmosphere. Structural characterization of isolated dioxane lignin (DL) was performed by analytical techniques: UV, FT-IR, ¹H NMR and ¹³C NMR. Their monolignol content was determined by nitrobenzene oxidation followed by HPLC-MS/MS analysis. The data was compared with commercial alkali lignin (AL). The results showed that DL is of hardwood guaiacyl-syringyl (GS) type, whereas AL is softwood type with more guaiacyl units and trace amounts of p-hydroxyphenyl units (H). Thermogravimetric analysis (TGA) of DL showed two stage thermal degradation profile similar to AL. The DTGmax for DL and AL were found in the second major loss event of second stage of TGA at 424°C and 404°C, respectively. Differential scanning calorimetry (DSC) study exhibited the glass transition temperatures (Tg) at 132°C and 122°C for DL and AL, respectively. The results from thermal stability studies suggest that dioxane lignin isolated from the "miracle tree" (subabul) can be exploited in various thermoplastic industrial applications. PMID:27468468
On the molecular structure of the amylopectin fraction isolated from "high-amylose" ae maize starches.
Peymanpour, Ghazal; Marcone, Massimo; Ragaee, Sanaa; Tetlow, Ian; Lane, Christopher C; Seetharaman, Koushik; Bertoft, Eric
The amylopectin fractions from starch of a series of amylose-extender (ae) maize samples (HYLON(®) V, VII and VIII starches) were isolated and analysed for their molecular composition and structure. The fractions from all samples contained both a high and a low molecular weight fraction (HMF and LMF), of which LMF increased with the amylose content of the starch and appeared to have substantially more of long chains than HMF. A normal amylose-containing maize starch (NMS), which served as a reference sample, contained very little LMF, which suggested that LMF was the inherent result of the effect of the loss of starch branching enzyme IIb activity in the ae mutants. Clusters were isolated from the amylopectin fractions using Bacillus amyloliquefaciens α-amylase, which effectively hydrolyses long internal chain segments between clusters. During the hydrolysis process, clearly more of small dextrins were released from the ae starches in comparison to NMS. It appeared that some of these small dextrins did not precipitate in methanol together with the majority of the clusters. Nevertheless, isolated clusters from the HYLON starch samples were smaller than in NMS and the clusters possessed a lower density of branches with longer chains. The composition of small, branched building blocks was also clearly different: HYLON starch samples possessed much more of single-branched blocks and less multiple-branched blocks than NMS. PMID:27296443