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Thermodynamics of Enzyme-Catalyzed Reactions Database
National Institute of Standards and Technology Data Gateway
SRD 74 Thermodynamics of Enzyme-Catalyzed Reactions Database (Web, free access)ĀĀ The Thermodynamics of Enzyme-Catalyzed Reactions Database contains thermodynamic data on enzyme-catalyzed reactions that have been recently published in the Journal of Physical and Chemical Reference Data (JPCRD). For each reaction the following information is provided: the reference for the data, the reaction studied, the name of the enzyme used and its Enzyme Commission number, the method of measurement, the data and an evaluation thereof.
Microorganisms detected by enzyme-catalyzed reaction
NASA Technical Reports Server (NTRS)
Enzymes detect the presence of microorganisms in soils. The enzyme lysozymi is used to release the enzyme catalase from the microorganisms in a soil sample. The catalase catalyzes the decomposition of added hydrogen peroxide to produce oxygen which is detected manometrically. The partial pressure of the oxygen serves as an index of the samples bacteria content.
Vango, S. P.; Weetall, H. H.; Weliky, N.
Representing Rate Equations for Enzyme-Catalyzed Reactions
ERIC Educational Resources Information Center
Rate equations for enzyme-catalyzed reactions are derived and presented in a way that makes it easier for the nonspecialist to see how the rate of an enzyme-catalyzed reaction depends upon kinetic constants and concentrations. This is done with distribution equations that show how the rate of the reaction depends upon the relative quantities ofģ
Ault, Addison
Oxidative tailoring reactions catalyzed by nonheme iron-dependent enzymes: streptorubin B biosynthesis as an example.
Tailoring enzymes catalyze reactions that modify natural product backbone structures before, during, or after their biosynthesis to create a final product with specific biological activities. Such reactions can be catalyzed by a myriad of different enzyme families and are responsible for a wide variety of transformations including regio- and/or stereospecific acylation, alkylation, glycosylation, halogenation, and oxidation. Within a broad group of oxidative tailoring enzymes, there is a rapidly growing family of nonheme iron- and oxygen-dependent enzymes that catalyze a variety of remarkable hydroxylation, desaturation, halogenation, and oxidative cyclization reaction in the biosynthesis of several important metabolites, including carbapenems, penicillins, cephalosporins, clavams, prodiginines, fosfomycin, syringomycin, and coronatine. In this chapter, we report an expedient method for analyzing tailoring enzymes that catalyze oxidative cyclization reactions in prodiginine biosynthesis via expression of the corresponding genes in a heterologous host, feeding of putative biosynthetic intermediates to the resulting strains, and liquid chromatography-mass spectrometry analyses of the metabolites produced. PMID:23034230
Sydor, Paulina K; Challis, Gregory L
Mutagenicity screening of reaction products from the enzyme-catalyzed oxidation of phenolic pollutants
SciTech Connect
Phenol-oxidizing enzymes such as peroxidases, laccases, and mushroom polyphenol oxidase are capable of catalyzing the oxidation of a wide range of phenolic pollutants. Although the use of these enzymes in waste-treatment applications has been proposed by a number of investigators, little information exists on the toxicological characteristics of the oxidation products. The enzymes chloroperoxidase, horseradish peroxidase, lignin peroxidase, and mushroom polyphenol oxidase were used in this study to catalyze the oxidation of phenol, several mono-substituted phenols, and pentachlorophenol. Seventeen reaction mixtures representing selected combinations of enzyme and parent phenol were subjected to mutagenicity screening using the Ames Salmonella typhimurium plate incorporation assay; five selected mixtures were also incubated with the S9 microsomal preparation to detect the possible presence of promutagens. The majority of reaction mixtures tested were not directly mutagenic, and none of those tested with S9 gave a positive response. Such lack of mutagenicity of enzymatic oxidation products provides encouragement for establishing the feasibility of enzyme-catalyzed oxidation as a waste-treatment process. The only positive responses were obtained with reaction products from the lignin peroxidase-catalyzed oxidation of 2-nitrophenol and 4-nitrophenol. Clear positive responses were observed when strain TA100 was incubated with 2-nitrophenol reaction-product mixtures, and when strain TA98 was incubated with the 4-nitrophenol reaction mixture. Additionally, 2,4-dinitrophenol was identified as a reaction product from 4-nitrophenol, and preliminary evidence indicates that both 2,4- and 2,6-dinitrophenol are produced from the oxidation of 2-nitrophenol. Possible mechanism by which these nitration reactions occur are discussed.
Massey, I.J.; Aitken, M.D.; Ball, L.M.; Heck, P.E. (Univ. of North Carolina, Chapel Hill, NC (United States). Dept. of Environmental Sciences and Engineering)
Mechanistic studies of an unprecedented enzyme-catalyzed 1,2-phosphono migration reaction
PubMed Central
(S)-2-Hydroxypropylphosphonate ((S)-2-HPP) epoxidase (HppE) is a mononuclear non-heme iron-dependent enzyme1,2,3 responsible for the last step in the biosynthesis of the clinically useful antibiotic fosfomycin4. Enzymes of this class typically catalyze oxygenation reactions that proceed via the formation of substrate radical intermediates. In contrast, HppE catalyzes an unusual dehydrogenation reaction while converting the secondary alcohol of (S)-2-HPP to the epoxide ring of fosfomycin1,5. HppE is shown here to also catalyze a biologically unprecedented 1,2-phosphono migration with the alternative substrate (R)-1-HPP. This transformation likely involves an intermediary carbocation based on observations with additional substrate analogues, such as (1R)-1-hydroxy-2-aminopropylphosphonate, and model reactions for both radical- and carbocation-mediated migration. The ability of HppE to catalyze distinct reactions depending on the regio- and stereochemical properties of the substrate is given a structural basis using X-ray crystallography. These results provide compelling evidence for the formation of a substrate-derived cation intermediate in the catalytic cycle of a mononuclear non-heme iron-dependent enzyme. The underlying chemistry of this unusual phosphono migration may represent a new paradigm for the in vivo construction of phosphonate-containing natural products that can be exploited for the preparation of novel phosphonate derivatives.
Chang, Wei-chen; Dey, Mishtu; Liu, Pinghua; Mansoorabadi, Steven O.; Moon, Sung-Ju; Zhao, Zongbao K.; Drennan, Catherine L.; Liu, Hung-wen
Folylpolyglutamate synthetase: direct evidence for an acyl phosphate intermediate in the enzyme-catalyzed reaction
The nature of the intermediate in the reaction catalyzed by folylpoly-..gamma..-glutamate synthetase (FPGS) has been investigated. Incubation of ..cap alpha..,..gamma..-(/sup 18/O)methotrexate with ATP, glutamate, and FPGS resulted in the formation of (/sup 18/O)phosphate, thus providing strong evidence for the formation of a ..gamma..-glutamyl phosphate during catalysis. The inorganic phosphate formed in the enzyme-catalyzed reaction was separated from other products and substrates by chromatography on DEAE-cellulose, then converted to the trimethyl ester, and analyzed by mass spectroscopy. Stoichiometric formation of (/sup 18/O)phosphate was observed in the case of the E. coli enzyme, isolated from a transformant containing the cloned FPGS-dihydrofolate synthetase (folC) gene. In addition, /sup 31/P-NMR analysis of the phosphate isolated from the reaction using E. coli FPGS showed the expected /sup 18/O-isotopic perturbations due to both singly bonded and doubly bonded P-/sup 18/O species. Similar experiments were carried out with FPGS isolated from hog liver. In this case, the small amounts of pure enzyme available precluded use of the NMR technique. However, mass spectral analysis of the derivatized phosphate product revealed the presence of (/sup 18/O)-trimethyl phosphate, thus indicating that the reaction catalyzed by the mammalian enzyme also proceeds via an acyl phosphate intermediate.
Banerjee, R.; McGuire, J.J.; Shane, B.; Coward, J.K.
Estimation of kinetic parameters when modifiers are bound in enzyme-catalyzed reactions.
Modifiers of enzyme-catalyzed reactions can have various types of effects on the velocity, but the most important effect is that they provide multiple pathways to products. The rapid-equilibrium kinetic effects of modifiers are explored for the enzyme-catalyzed reaction A --> products. When a single molecule of modifier X is bound, the mechanism involves three independent equilibrium expressions and two rate constants. But when two molecules of X are bound are bound in two reactions, there are five independent equilibria and three paths to products. The advantages of using a computer to derive rapid-equilibrium rate equations are that more complicated rate equations can be derived and the kinetic parameters can be estimated using the minimum number of velocity measurements. The mechanism with three paths to products is of special interest because the effects of cooperativity can be studied. Thermodynamic cycles can be used to estimate additional kinetic parameters. PMID:20055362
Alberty, Robert A
Starting D-optimal designs for batch kinetics studies of enzyme-catalyzed reactions in the presence of enzyme deactivation.
This paper describes a strategy for the starting experimental design of experiments required by general research in the field of biochemical kinetics. The type of experiments that qualify for this analysis involve batch reactions catalyzed by soluble enzymes where the activity of the enzyme decays with time. Assuming that the catalytic action of the enzyme obeys a Michaelis-Menten rate expression and that the deactivation of the enzyme follows a first-order decay, the present analysis employs the dimensionless, integrated form of the overall rate expression to obtain a criterion (based on the maximization of the determinant of the derivative matrix) that relates the a priori estimates of the parameters with the times at which samples should be withdrawn from the reacting mixture. The analysis indicates that the initial concentration of substrate should be as large as possible, and that the samples should be taken at times corresponding to substrate concentrations of approximately 2/3, 1/4, and I/epsilon of the initial concentration (where epsilon should be as large as possible). PMID:1420847
Malcata, F X
Determination of kinetic parameters of enzyme-catalyzed reactions with a minimum number of velocity measurements.
Duggleby [Duggleby, R.G., 1979. Experimental designs for estimating kinetic parameters for enzyme-catalyzed reactions. J. Theor. Biol. 81, 672-684] discussed the "design of several replicate measurements of the velocity at as many experimental conditions as there are parameters to be estimated." He discussed the application of this method to A-->products, without and with competitive inhibition, and commented briefly on A+B-->products. The availability of computer applications that can solve large sets of simultaneous equations makes it possible to use this method to calculate kinetic parameters for more complicated enzyme mechanisms. This article is concerned with rapid-equilibrium rate equations, but this method can also be used with steady-state rate equations. Computer programs are provided for the calculation of the three kinetic parameters for ordered A+B-->products from three velocity measurements and for the calculation of the four kinetic parameters for random A+B-->products from four velocity measurements. Computer programs are also provided for competitive inhibition, uncompetitive inhibition, and mixed inhibition of ordered A+B-->products. PMID:18582902
Asymmetric Effect of Mechanical Stress on the Forward and Reverse Reaction Catalyzed by an Enzyme
The concept of modulating enzymatic activity by exerting a mechanical stress on the enzyme has been established in previous work. Mechanical perturbation is also a tool for probing conformational motion accompanying the enzymatic cycle. Here we report measurements of the forward and reverse kinetics of the enzyme Guanylate Kinase from yeast (Saccharomyces cerevisiae). The enzyme is held in a state of stress using the DNA spring method. The observation that mechanical stress has different effects on the forward and reverse reaction kinetics suggests that forward and reverse reactions follow different paths, on average, in the enzyme's conformational space. Comparing the kinetics of the stressed and unstressed enzyme we also show that the maximum speed of the enzyme is comparable to the predictions of the relaxation model of enzyme action, where we use the independently determined dissipation coefficient for the enzyme's conformational motion. The present experiments provide a mean to explore enzyme kinetics beyond the static energy landscape picture of transition state theory.
Joseph, Collin; Tseng, Chiao-Yu; Zocchi, Giovanni; Tlusty, Tsvi
Reformulation of the Michaelis-Menten Equation: How Enzyme-Catalyzed Reactions Depend on Gibbs Energy
The impact of raising Gibbs energy of the enzyme-substrate complex (G[subscript 3]) and the reformulation of the Michaelis-Menten equation are discussed. The maximum velocity of the reaction (v[subscript m]) and characteristic constant for the enzyme (K[subscript M]) will increase with increase in Gibbs energy, indicating that the rate of reactionģ
Bozlee, Brian J.
Catalyzed enzyme electrodes
An enzyme electrode is prepared with a composite coating on an electrical conductor. The composite coating is formed from a casting solution of a perfluorosulfonic acid polymer, an enzyme, and a carbon supported catalyst. The solution may be cast directly on the conductor surface or may be formed as a membrane and applied to the surface. The perfluorosulfonic acid ionomer formed from the casting solution provides an insoluble biocompatible protective matrix for the enzyme and acts to retain the enzyme for long term availability in the electrode structure. The carbon supported catalyst provides catalytic sites throughout the layer for the oxidation of hydrogen peroxide from the enzyme reactions. The carbon support then provides a conductive path for establishing an electrical signal to the electrical conductor. In one embodiment, the electrical conductor is a carbon cloth that permits oxygen or other gas to be introduced to the perfluorosulfonic polymer to promote the enzyme reaction independent of oxygen in the solution being tested.
Zawodzinski, T.A.; Wilson, M.S.; Rishpon, J.; Gottesfeld, S.
Enzyme Reactions
NSDL National Science Digital Library
This video shows an enzyme reaction lab. The teacher demonstrates how the enzyme, catalase, reacts with hydrogen peroxide (a substrate found in cells). The teacher first demonstrates a normal enzyme reaction. He or she then goes on to show how manipulating temperature and pH will affect the reaction of an enzyme.
School, Minerva D.
Quantitative Analysis of the Time Courses of Enzyme-Catalyzed Reactions
Microsoft Academic Search
The catalytic properties of enzymes are usually evaluated by measuring and analyzing reaction rates. However, analyzing the complete time course can be advantageous because it contains additional information about the properties of the enzyme. Moreover, for systems that are not at steady state, the analysis of time courses is the preferred method. One of the major barriers to the wide
Ronald G. Duggleby
Asymmetric effect of mechanical stress on the forward and reverse reaction catalyzed by an enzyme.
The concept of modulating enzymatic activity by exerting a mechanical stress on the enzyme has been established in previous work. Mechanical perturbation is also a tool for probing conformational motion accompanying the enzymatic cycle. Here we report measurements of the forward and reverse kinetics of the enzyme Guanylate Kinase from yeast (Saccharomyces cerevisiae). The enzyme is held in a state of stress using the DNA spring method. The observation that mechanical stress has different effects on the forward and reverse reaction kinetics suggests that forward and reverse reactions follow different paths, on average, in the enzyme's conformational space. Comparing the kinetics of the stressed and unstressed enzyme we also show that the maximum speed of the enzyme is comparable to the predictions of the relaxation model of enzyme action, where we use the independently determined dissipation coefficient [Formula: see text] for the enzyme's conformational motion. The present experiments provide a mean to explore enzyme kinetics beyond the static energy landscape picture of transition state theory. PMID:25000118
Multiple intensified performance of an enzyme-catalyzed reaction in organic medium.
A lipase-catalyzed glycerolysis reaction (a transesterification between polyunsaturated fatty acid ethyl ester [PUFA] and glycerol) was investigated. Its performance was multiply intensified by (1) using a lipase having high specific activity, high activity in organic solvent, and high tolerance in organic solvent; (2) immobilization on fine CaCO3 powder (cheap and safe material, easy physical adsorption method of immobilization, reusable); (3) reaction in vacuo resulting in 100% conversion and effective avoidance of oxidative deterioration of PUFA; (4) high volumetric productivity because of no use of solvent; and (5) no need of further separation and purification of the oil product. It is emphasized that performance of biocatalytic reactions in organic media should be enhanced manifold for industrial implementation. PMID:10075632
Yamane, T; Iwasaki, Y; Roxana, R; Shimidzu, N; Doisaki, N
Synthesis of 2-monoacylglycerols and structured triacylglycerols rich in polyunsaturated fatty acids by enzyme catalyzed reactions.
This paper studies the synthesis of structured triacylglycerols (STAGs) by a four-step process: (i) obtaining 2-monoacylglycerols (2-MAGs) by alcoholysis of cod liver oil with several alcohols, catalyzed by lipases Novozym 435, from Candida antartica and DF, from Rhizopus oryzae, (ii) purification of 2-MAGs, (iii) formation of STAGs by esterification of 2-MAGs with caprylic acid catalyzed by lipase DF, from R. oryzae, and (iv) purification of these STAGs. For the alcoholysis of cod liver oil, absolute ethanol, ethanol 96% (v/v) and 1-butanol were compared; the conditions with ethanol 96% were then optimized and 2-MAG yields of around 54-57% were attained using Novozym 435. In these 2-MAGs, DHA accounted for 24-31% of total fatty acids. In the operational conditions this lipase maintained a stable level of activity over at least 11 uses. These results were compared with those obtained with lipase DF, which deactivated after only three uses. The alcoholysis of cod liver oil and ethanol 96% catalyzed by Novozym 435 was scaled up by multiplying the reactant amounts 100-fold and maintaining the intensity of treatment constant (IOT=3g lipase h/g oil). In these conditions, the 2-MAG yield attained was about 67%; these 2-MAGs contained 36.6% DHA. The synthesized 2-MAGs were separated and purified from the alcoholysis reaction products by solvent extraction using solvents of low toxicity (ethanol and hexane); 2-MAG recovery yield and purity of the target product were approximately 96.4% and 83.9%, respectively. These 2-MAGs were transformed to STAGs using the optimal conditions obtained in a previous work. After synthesis and purification, 93% pure STAGs were obtained, containing 38% DHA at sn-2 position and 60% caprylic acid (CA) at sn-1,3 positions (of total fatty acids at these positions), i.e. the major TAG is the STAG with the structure CA-DHA-CA. PMID:22759534
RodrĒguez, Alicia; Esteban, Luis; MartĒn, Lorena; Jimķnez, MarĒa Josķ; Hita, Estrella; Castillo, Beatriz; Gonzßlez, Pedro A; Robles, Alfonso
Ester synthesis in lipase-catalyzed reactions
This review discusses the myriad of reaction systems employed in ester production catalyzed by lipases. Enzyme behavior in reaction systems is a consequence of certain structural patterns typical of lipases. Water has a profound effect on the lipase behavior either directly by affecting the hydration of the enzyme or indirectly by changing the nature of the reaction media and\\/or enzyme
Ahmad R. M Yahya; William A Anderson; Murray Moo-Young
Monitoring enzyme-catalyzed reactions in micromachined nanoliter wells using a conventional microscope-based microarray reader
NASA Astrophysics Data System (ADS)
Yeast-Saccharomyces cerevisiae - it widely used as a model system for other higher eukaryotes, including man. One of the basic fermentation processes in yeast is the glycolytic pathway, which is the conversion of glucose to ethanol and carbon dioxide. This pathway consists of 12 enzyme-catalyzed reactions. With the approach of microarray technology we want to explore the metabolic regulation of this pathway in yeast. This paper will focus on the design of a conventional microscope based microarray reader, which is used to monitor these enzymatic reactions in microarrays. These microarrays are fabricated in silicon and have sizes of 300 by 300 micrometers 2. The depth varies from 20 to 50 micrometers . Enzyme activity levels can be derived by monitoring the production or consumption rate of NAD(P)H, which is excited at 360nm and emits around 450nm. This fluorophore is involved in all 12 reactions of the pathway. The microarray reader is equipped with a back-illuminated CCD camera in order to obtain a high quantum efficiency for the lower wavelengths. The dynamic range of our microarray reader varies form 5(mu) Molar to 1mMolar NAD(P)H. With this microarray reader enzyme activity levels down to 0.01 unit per milliliter can be monitored. The acquisition time per well is 0.1s. The total scan cycle time for a 5 X 5 microarray is less than half a minute. The number of cycles for a proper estimation of the enzyme activity is inversely proportional to the enzyme activity: long measurement times are needed to determine low enzyme activity levels.
van den Doel, L. Richard; Moerman, R.; van Dedem, G. W. K.; Young, Ian T.; van Vliet, Lucas J.
The lactate dehydrogenase catalyzed pyruvate adduct reaction: simultaneous general acid-base catalysis involving an enzyme and an external catalyst.
The pH dependence of the reaction catalyzed by lactate dehydrogenase, where pyruvate adds covalently to NAD to yield a NAD-Pyr adduct, together with published data on the pH dependence of parameters in the normal redox reaction suggests similar binding modes for enolpyruvate and lactate in their complexes with E X NAD (where E is one-fourth of the tetramer), for ketopyruvate in its complexes with the protonated species, E X H X NAD and E X H X NADH, and for the NAD--Pyr adduct and NADH plus pyruvate in their complexes with E X H. These similarities, together with previous data, suggest a reaction scheme for the formation of the enzyme-adduct complex that includes the relevant proton-transfer steps. Seven different amine chloride buffers were used in a study of the reverse adduct reaction, i.e., the decomposition of E X H X NAD--Pyr. These act with varying efficiencies as external general acid catalysts; the enzyme apparently acts as a (internal) general base. The involvement of the amine chloride buffers as external general catalysts is supported by the concentration dependence of the buffer effect, by a Br÷nsted plot, and by solvent deuterium isotope effects. The involvement of the enzyme as an internal general catalyst is inferred from the pH dependence of the reaction and the identities of the nearby groups in the E X H X NAD--Pyr complex (from crystallographic studies). The dependence of the adduct reaction on chloride concentration indicates the presence of dead-end inhibitor complexes of E X H X Cl and E X H X NAD X Cl. Chloride also accelerates the decomposition of the adduct in the complex E X H X NAD--Pyr by binding to this complex. PMID:6477888
Burgner, J W; Ray, W J
Catalase-like oxygen production by horseradish peroxidase must predominantly be an enzyme-catalyzed reaction.
When hydrogen peroxide (H2O2) was provided as the only substrate for horseradish peroxidase C (HRP-C) the catalase-like emission of oxygen gas was observed. The reaction was favored at neutral compared to acidic pH. Addition of the superoxide radical scavengers tetranitromethane (TNM) or superoxide dismutase (SOD) increased activity. TNM's effect was concentration dependent but SOD's was not, indicating that only some of the superoxide generated was released into solution. Manganous ions (Mn2+) react with superoxide radicals to regenerate H2O2 but not oxygen; when added to the reaction medium oxygen production was reduced but not abolished. The effect was essentially concentration independent, suggesting that most oxygen was produced enzymatically and not by chemical disproportionation of superoxide. The catalase-like activities of some site-directed mutants of HRP-C suggest that active site residues histidine 42 and arginine 38 are influential in determining this activity. A clear correlation also existed between catalase activity and the enzymes' resistance to inactivation by H2O2. Computer simulation of a reaction scheme that included catalase-like activity agreed well with experimental data. PMID:11488605
Hiner, A N; Hernßndez-Ruiz, J; Williams, G A; Arnao, M B; GarcĒa-Cßnovas, F; Acosta, M
An "Aufbau" Approach to Understanding How the King-Altman Method of Deriving Rate Equations for Enzyme-Catalyzed Reactions Works
The King-Altman method of deriving rate equations for enzymatic reactions is applied to the derivation of the Michaelis-Menten equation, along with an explanation for how (or why) the King-Altman method works in this case. The slightly more complicated cases of competitive inhibition and a two-substrate enzyme-catalyzed reaction are then treatedģ
Sims, Paul A.
Mechanosensitive liposomes as artificial chaperones for shear-driven acceleration of enzyme-catalyzed reaction.
Mechanosensitive liposomes were prepared and applied to continuously accelerate the glucose oxidase (GO) reaction in shear flow. The liposome membrane was composed of a ternary lipid mixture containing 20 mol % negatively charged lipid and 30 mol % cholesterol. The liposomes encapsulating GO and catalase were passed through microtubes with inner diameter of 190 or 380 ?m at 25 ░C to induce the catalytic oxidation of 10 mM glucose with simultaneous decomposition of H2O2 produced. The liposomal GO showed significantly low reactivity in the static liquid system because of the permeation resistance of lipid membranes to glucose. On the other hand, the enzyme activity of liposomal GO observed at the average shear rate of 7.8 ū 10(3) s(-1) was significantly larger than its intrinsic activity free of mass transfer effect in the static liquid system. The structure of liposomes was highly shear-sensitive as elucidated on the basis of shear rate-dependent physical stability of liposomes and membrane permeability to 5(6)-carboxyfluorescein as well as to GO. Thus, the above shear-driven acceleration of GO reaction was indicated to be caused by the free GO molecules released from the structurally altered liposomes at high shear rates. Moreover, the shear-induced denaturation of free GO was completely depressed by the interaction with the sheared liposomes with the chaperone-like function. The shear-sensitive liposomal GO system can be a unique catalyst that continuously accelerates and also decelerates the oxidation reaction depending on the applied shear rate. PMID:24547684
Natsume, Tomotaka; Yoshimoto, Makoto
Determination of rapid-equilibrium kinetic parameters of ordered and random enzyme-catalyzed reaction A+B=P+Q.
This article deals with the rapid-equilibrium kinetics of the forward and reverse reactions together for the ordered and random enzyme-catalyzed A+B=P+Q and emphasizes the importance of reporting the values of the full set of equilibrium constants. Equilibrium constants that are not in the rate equation can be calculated for random mechanisms using thermodynamic cycles. This treatment is based on the use of a computer to derive rate equations for three mechanisms and to estimate the kinetic parameters with the minimum number of velocity measurements. The most general of these three programs is the one to use first when the mechanism for A+B=P+Q is studied for the first time. This article shows the effects of experimental errors in velocity measurements on the values of the kinetic parameters and on the apparent equilibrium constant calculated using the Haldane relation. PMID:19558174
Determination of Rapid-Equilibrium Kinetic Parameters of Ordered and Random Enzyme-Catalyzed Reaction A + B = P + Q
This article deals with the rapid-equilibrium kinetics of the forward and reverse reactions together for the ordered and random enzyme-catalyzed A + B = P + Q and emphasizes the importance of reporting the values of the full set of equilibrium constants. Equilibrium constants that are not in the rate equation can be calculated for random mechanisms using thermodynamic cycles. This treatment is based on the use of a computer to derive rate equations for three mechanisms and to estimate the kinetic parameters with the minimum number of velocity measurements. The most general of these three programs is the one to use first when the mechanism for A + B = P + Q is studied for the first time. This article shows the effects of experimental errors in velocity measurements on the values of the kinetic parameters and on the apparent equilibrium constant calculated using the Haldane relation.
Enzyme-free and ultrasensitive electrochemical detection of nucleic acids by target catalyzed hairpin assembly followed with hybridization chain reaction.
An isothermal, enzyme-free and ultrasensitive protocol for electrochemical detection of DNA is proposed based on the ingenious combination of target catalyzed hairpin assembly and hybridization chain reaction (HCR) strategies for two-step signal amplification. The DNA hairpin assembly on the electrode is triggered by target DNA, accompanied by the release of target DNA for the successive hybridization and assembly process. The newly emerging DNA fragment on the electrode after hairpin assembly is further used to propagate the HCR between methylene blue-labeled signal probe and auxiliary probe, inducing a remarkably amplified electrochemical signal. The current dual signal amplification strategy is relatively simple and inexpensive owing to avoid the use of any kind of enzyme or sophisticated equipment. It can achieve a sensitivity of 0.1 fM with a wide linear dynamic range from 1 ū 10(-15) to 1 ū 10(-10)M and discriminate mismatched DNA from perfect matched target DNA with a high selectivity. The high sensitivity and selectivity make this method a great potential for early diagnosis in gene-related diseases. PMID:23811481
Liu, Shufeng; Wang, Ying; Ming, Jingjing; Lin, Ying; Cheng, Chuanbin; Li, Feng
The Effect of Temperature on the Enzyme-Catalyzed Reaction: Insights from Thermodynamics
When teaching the effect of temperature on biochemical reactions, the problem is usually oversimplified by confining the thermal effect to the catalytic constant, which is identified with the rate constant of the elementary limiting step. Therefore, only positive values for activation energies and values greater than 1 for temperature coefficientsģ
Aledo, Juan Carlos; Jimenez-Riveres, Susana; Tena, Manuel
Quantitation of low molecular mass substrates and products of enzyme catalyzed reactions using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.
Relative peak-height ratios of products to substrates determined by MALDI-TOFMS allow the quantitative analysis of enzyme catalyzed reactions for screening purposes. Two examples were investigated: the first one was a lipase catalyzed reaction which produces 2-methoxy-N-[(1R)-1-phenylethyl]acetamide (MET) using rac-alpha-phenylethylamine (PEA) as substrate. The second one was the pyruvate decarboxylase catalyzed formation of (1R)-1-hydroxy-1-phenyl-2-propanone (PAC) with benzaldehyde (BzA) as substrate. Here the corresponding oximes were analyzed after derivatization using hydroxylamine. The standard curves (r2 = 0.985 for MET, r2 = 0.991 for PAC) were linear over two orders of magnitude for MET and PAC concentrations. After optimization of the sample preparation an average relative standard deviation of 12.5% was obtained in both cases. PMID:11085406
Kang, M J; Tholey, A; Heinzle, E
Enzyme-Catalyzed Processes in Organic Solvents
Three different lipases (porcine pancreatic, yeast, and mold) can vigorously act as catalysts in a number of nearly anhydrous organic solvents. Various transesterification reactions catalyzed by porcine pancreatic lipase in hexane obey Michaelis-Menten kinetics. The dependence of the catalytic activity of the enzyme in organic media on the pH of the aqueous solution from which it was recovered is bell-shaped,
Aleksey Zaks; Alexander M. Klibanov
Visualization of enzyme-catalyzed reactions using pH indicators: rapid screening of hydrolase libraries and estimation of the enantioselectivity
The use of pH indicators to monitor hydrolase-catalyzed reactions is described. The formation of acid following an enzyme-mediated hydrolysis causes a drop in the pH that can be visualized by a change in the color of the indicator-containing solution. The best indicators are those showing a color transition within the operational pH range of the hydrolases, like bromothymol blue and
Francisco Mor??s-Varas; Amit Shah; John Aikens; Neelesh P Nadkarni; J. David Rozzell; David C Demirjian
Kinetic Studies on Enzyme-Catalyzed Reactions: Oxidation of Glucose, Decomposition of Hydrogen Peroxide and Their Combination
The kinetics of the glucose oxidase-catalyzed reaction of glucose with O2, which produces gluconic acid and hydrogen peroxide, and the catalase-assisted breakdown of hydrogen peroxide to generate oxygen, have been measured via the rate of O2 depletion or production. The O2 concentrations in air-saturated phosphate-buffered salt solutions were monitored by measuring the decay of phosphorescence from a Pd phosphor in solution; the decay rate was obtained by fitting the tail of the phosphorescence intensity profile to an exponential. For glucose oxidation in the presence of glucose oxidase, the rate constant determined for the rate-limiting step was k = (3.0 ▒ 0.7) ū104 M?1s?1 at 37░C. For catalase-catalyzed H2O2 breakdown, the reaction order in [H2O2] was somewhat greater than unity at 37░C and well above unity at 25░C, suggesting different temperature dependences of the rate constants for various steps in the reaction. The two reactions were combined in a single experiment: addition of glucose oxidase to glucose-rich cell-free media caused a rapid drop in [O2], and subsequent addition of catalase caused [O2] to rise and then decrease to zero. The best fit of [O2] to a kinetic model is obtained with the rate constants for glucose oxidation and peroxide decomposition equal to 0.116 s?1 and 0.090 s?1 respectively. Cellular respiration in the presence of glucose was found to be three times as rapid as that in glucose-deprived cells. Added NaCN inhibited O2 consumption completely, confirming that oxidation occurred in the cellular mitochondrial respiratory chain.
Tao, Zhimin; Raffel, Ryan A.; Souid, Abdul-Kader; Goodisman, Jerry
Mechanism of enzyme-catalyzed phospho group transfer
To understand more fully the mechanism of enzyme-catalyzed phospho group transfer, the stereochemical course at phosphorus of four enzymes has been determined. First, using adenosine (..gamma..-(S)-/sup 16/O, /sup 17/O, /sup 18/O)triphosphate as the substrate, the reaction catalyzed by creatine kinase has been found to proceed with overall inversion of configuration at phosphorus. Second, using adenosine (..beta..-(S)-/sup 16/O, /sup 17/O, /sup 18/O)diphosphate as the substrate, the reaction catalyzed by adenylate kinase has been found also to proceed with overall inversion. Third, the reaction catalyzed by phosphoenolpyruvate carboxylase has been studied using ((S/sub p/)-/sup 16/O, /sup 17/O)thiophospoenolpyruvate as the substrate in H/sub 2/ /sup 18/O. Fourth, using adenosine 5'-O-((..gamma..S/sub p/)-..beta gamma..-/sup 17/O,..gamma..-/sup 17/O,/sup 18/O)(3-thiotriphosphate) as the substrate, the reaction catalyzed by pyruvate carboxylase has been shown to proceed with inversion at phosphorus. This results rules out the chemically and enzymatically precendented composite mechanism that had been proposed for this enzyme and supports a stepwise pathway again involving the intermediacy of carboxyphosphate. The first pair of results supports the growing body of evidence that enzyme-catalyzed phospho group transfer proceeds by an in-line associative mechanism. The second pair of results eliminate mechanistic suggestions of concerted electrocyclic processes in bicarbonate dependent carboxylation reactions.
Hansen, D.E.
Strictosidine Synthase: Mechanism of a Pictet-Spengler Catalyzing Enzyme
The Pictet¢Spengler reaction, which yields either a ?-carboline or a tetrahydroquinoline product from an aromatic amine and an aldehyde, is widely utilized in plant alkaloid biosynthesis. Here we deconvolute the role that the biosynthetic enzyme strictosidine synthase plays in catalyzing the stereoselective synthesis of a ?-carboline product. Notably, the rate-controlling step of the enzyme mechanism, as identified by the appearance of a primary kinetic isotope effect (KIE), is the rearomatization of a positively charged intermediate. The KIE of a nonenzymatic Pictet¢Spengler reaction indicates that rearomatization is also rate-controlling in solution, suggesting that the enzyme does not significantly change the mechanism of the reaction. Additionally, the pH dependence of the solution and enzymatic reactions provides evidence for a sequence of acid¢base catalysis steps that catalyze the Pictet¢Spengler reaction. An additional acid-catalyzed step, most likely protonation of a carbinolamine intermediate, is also significantly rate controlling. We propose that this step is efficiently catalyzed by the enzyme. Structural analysis of a bisubstrate inhibitor bound to the enzyme suggests that the active site is exquisitely tuned to correctly orient the iminium intermediate for productive cyclization to form the diastereoselective product. Furthermore, ab initio calculations suggest the structures of possible productive transition states involved in the mechanism. Importantly, these calculations suggest that a spiroindolenine intermediate, often invoked in the Pictet¢Spengler mechanism, does not occur. A detailed mechanism for enzymatic catalysis of the ?-carboline product is proposed from these data.
Maresh, Justin J.; Giddings, Lesley-Ann; Friedrich, Anne; Loris, Elke A.; Panjikar, Santosh; Trout, Bernhardt L.
4-alkyl-o-quinone/2-hydroxy-p-quinone methide isomerase from the larval hemolymph of Sarcophaga bullata. I. Purification and characterization of enzyme-catalyzed reaction.
An enzyme which catalyzes the conversion of certain 4-alkyl-o-benzoquinones to 2-hydroxy-p-quinone methides has been purified to apparent homogeneity from the hemolymph of Sarcophaga bullata by employing conventional protein purification techniques. The purified enzyme migrated with an approximate molecular weight of 98,000 on gel filtration chromatography. On sodium dodecyl sulfate-polyacrylamide gel electrophoresis, it migrated as a single band with a molecular weight of 46,000, indicating that it is made up of two identical subunits. It exhibited a pH optimum of 6.0 and readily converted chemically synthesized as well as enzymatically generated quinones derived from N-acetyldopamine, N-beta-alanyldopamine, and 3,4-dihydroxyphenethyl alcohol to highly unstable 2-hydroxy-p-quinone methides. The quinone methides thus formed were rapidly and nonenzymatically hydrated to form side chain hydroxylated o-diphenols as the stable product. In support of this proposition, when the enzyme reaction with N-acetyldopamine quinone was conducted in the presence of 10% methanol, racemic beta-methoxy-N-acetyldopamine was recovered as an additional product. The quinones of N-acetylnorepinephrine, N-beta-alanylnorepinephrine, and 3,4-dihydroxyphenylglycol were also attacked by the isomerase, resulting in the formation of N-acetylarterenone, N-beta-alanylarterenone and 2-hydroxy-3',4'-dihydroxyacetophenone, respectively as the stable products. The isomerase converted the dihydrocaffeiyl methyl amide quinone to its quinone methide analog which rapidly tautomerized to yield caffeiyl methyl amide. The importance of quinone isomerase in insect immunity and sclerotization of insect cuticle is discussed. PMID:2211605
Saul, S J; Sugumaran, M
Homologous (beta/alpha)8-barrel enzymes that catalyze unrelated reactions: orotidine 5'-monophosphate decarboxylase and 3-keto-L-gulonate 6-phosphate decarboxylase.
The 3-keto-L-gulonate 6-phosphate decarboxylase (KGPDC) encoded by the ulaD gene in the Escherichia coli genome [Yew, W. S., and Gerlt, J. A. (2002) J. Bacteriol. 184, 302-306] and orotidine 5'-monophosphate decarboxylase (OMPDC) are homologous (derived from a common ancestor) but catalyze different reactions. The metal-independent decarboxylation reaction catalyzed by OMPDC avoids the formation of a vinyl anion intermediate; the Mg2+-dependent decarboxylation reaction catalyzed by KGPDC involves the formation of an enediolate anion intermediate. Based on the available structures of OMPDC, a sequence alignment allows the predictions that (1) KGPDC is a dimer of (beta/alpha)8-barrels, with the active sites located at the dimer interface; (2) KGPDC and OMPDC share an aspartate residue at the end of the first beta-strand and an Asp-x-Lys-x-x-Asp motif at the end of the third beta-strand with OMPDC; but (3) KGPDC has a Glu instead of a Lys at the end of the second beta-strand. The structure of KGPDC has been determined in the presence of Mg2+ and the substrate analogue L-gulonate 6-phosphate and confirms these predictions. The carboxylate functional groups at the ends of the first, second, and third beta-strands in KGPDC are ligands of the Mg2+; in OMPDC, the homologues of these residues participate in a hydrogen-bonded network that facilitates the decarboxylation reaction. The 3-OH group of the substrate analogue is coordinated to the Mg2+, supporting the hypothesis that the mechanism of the decarboxylation catalyzed by KGPDC involves stabilization of an enediolate anion intermediate. These structural studies establish the existence of the OMPDC "suprafamily," in which members catalyze reactions that occur in different metabolic pathways and share no mechanistic relationship. The existence of this suprafamily demonstrates that divergent evolution can be opportunistic, conscripting active site features of a progenitor to catalyze unrelated functions. Accordingly, sequence or structure homology alone cannot be used to infer the functions of new proteins discovered in genome projects. PMID:11900527
Wise, Eric; Yew, Wen Shan; Babbitt, Patricia C; Gerlt, John A; Rayment, Ivan
Enzyme reaction annotation using cloud techniques.
An understanding of the activities of enzymes could help to elucidate the metabolic pathways of thousands of chemical reactions that are catalyzed by enzymes in living systems. Sophisticated applications such as drug design and metabolic reconstruction could be developed using accurate enzyme reaction annotation. Because accurate enzyme reaction annotation methods create potential for enhanced production capacity in these applications, they have received greater attention in the global market. We propose the enzyme reaction prediction (ERP) method as a novel tool to deduce enzyme reactions from domain architecture. We used several frequency relationships between architectures and reactions to enhance the annotation rates for single and multiple catalyzed reactions. The deluge of information which arose from high-throughput techniques in the postgenomic era has improved our understanding of biological data, although it presents obstacles in the data-processing stage. The high computational capacity provided by cloud computing has resulted in an exponential growth in the volume of incoming data. Cloud services also relieve the requirement for large-scale memory space required by this approach to analyze enzyme kinetic data. Our tool is designed as a single execution file; thus, it could be applied to any cloud platform in which multiple queries are supported. PMID:24222895
Huang, Chuan-Ching; Lin, Chun-Yuan; Chang, Cheng-Wen; Tang, Chuan Yi
Spectroscopic, steady-state kinetic, and mechanistic characterization of the radical SAM enzyme QueE, which catalyzes a complex cyclization reaction in the biosynthesis of 7-deazapurines
7-Carboxy-7-deazaguanine (CDG) synthase (QueE) catalyzes the complex heterocyclic radical-mediated conversion of 6-carboxy-5,6,7,8-tetrahydropterin (CPH4) to CDG in the third step of the biosynthetic pathway to all 7-deazapurines. Here we present a detailed characterization of QueE from Bacillus subtilis to delineate the mechanism of conversion of CPH4 to CDG. QueE is a member of the radical S-adenosyl-L-methionine (SAM) superfamily, all of which use a bound [4Fe-4S]+ cluster to catalyze the reductive cleavage of SAM cofactor to generate methionine and a 5?-deoxyadenosyl radical (5?-dAdoĢ), which initiates enzymatic transformations requiring H-atom abstraction. The UV-visible, EPR, and M÷ssbauer spectroscopic features of the homodimeric QueE point to the presence of a single [4Fe-4S] cluster per monomer. Steady-state kinetic experiments indicate a Km of 20 ▒ 7 ?M for CPH4 and kcat of 5.4 ▒ 1.2 min-1 for the overall transformation. The kinetically determined Kapp for SAM is 45 ▒ 1 ?M. QueE is also magnesium-dependent and exhibits a Kapp for the divalent metal ion of 0.21 ▒ 0.03 mM. The SAM cofactor supports multiple turnovers, indicating that it is regenerated at the end of each catalytic cycle. The mechanism of rearrangement of QueE was probed with CPH4 isotopologs containing deuterium at C-6 or the two prochiral positions at C-7. These studies implicate 5?-dAdoĢ as initiating the ring contraction reaction catalyzed by QueE by abstraction of the H-atom from C-6 of CPH4.
McCarty, Reid M.; Krebs, Carsten; Bandarian, Vahe
Fronts and pulses in an enzymatic reaction catalyzed by glucose oxidase
Waves and patterns in living systems are often driven by biochemical reactions with enzymes as catalysts and regulators. We present a reaction¢diffusion system catalyzed by the enzyme glucose oxidase that exhibits traveling wave patterns in a spatially extended medium. Fronts and pulses propagate as a result of the coupling between the enzyme-catalyzed autocatalytic production and diffusion of hydrogen ions. A mathematical model qualitatively explains the experimental observations.
Miguez, David G.; Vanag, Vladimir K.; Epstein, Irving R.
Palladium-catalyzed oxidative carbonylation reactions.
Palladium-catalyzed coupling reactions have become a powerful tool for advanced organic synthesis. This type of reaction is of significant value for the preparation of pharmaceuticals, agrochemicals, as well as advanced materials. Both, academic as well as industrial laboratories continuously investigate new applications of the different methodologies. Clearly, this area constitutes one of the major topics in homogeneous catalysis and organic synthesis. Among the different palladium-catalyzed coupling reactions, several carbonylations have been developed and widely used in organic syntheses and are even applied in the pharmaceutical industry on ton-scale. Furthermore, methodologies such as the carbonylative Suzuki and Sonogashira reactions allow for the preparation of interesting building blocks, which can be easily refined further on. Although carbonylative coupling reactions of aryl halides have been well established, palladium-catalyzed oxidative carbonylation reactions are also interesting. Compared with the reactions of aryl halides, oxidative carbonylation reactions offer an interesting pathway. The oxidative addition step could be potentially avoided in oxidative reactions, but only few reviews exist in this area. In this Minireview, we summarize the recent development in the oxidative carbonylation reactions. PMID:23307763
Wu, Xiao-Feng; Neumann, Helfried; Beller, Matthias
Unusual Cytochrome P450 Enzymes and Reactions*
Cytochrome P450 enzymes primarily catalyze mixed-function oxidation reactions, plus some reductions and rearrangements of oxygenated species, e.g. prostaglandins. Most of these reactions can be rationalized in a paradigm involving Compound I, a high-valent iron-oxygen complex (FeO3+), to explain seemingly unusual reactions, including ring couplings, ring expansion and contraction, and fusion of substrates. Most P450s interact with flavoenzymes or iron-sulfur proteins to receive electrons from NAD(P)H. In some cases, P450s are fused to protein partners. Other P450s catalyze non-redox isomerization reactions. A number of permutations on the P450 theme reveal the diversity of cytochrome P450 form and function.
Guengerich, F. Peter; Munro, Andrew W.
Gold(I)-catalyzed enantioselective cycloaddition reactions
Summary In recent years there have been extraordinary developments of gold(I)-catalyzed enantioselective processes. This includes progress in the area of cycloaddition reactions, which are of particular interest due to their potential for the rapid construction of optically active cyclic products. In this article we will summarize some of the most remarkable examples, emphasizing reaction mechanisms and key intermediates involved in the processes.
Surface catalyzed mercury transformation reactions
Mercury is a known pollutant that has detrimental effect on human health and environment. The anthropogenic emissions of mercury account for 10 to 30% of worldwide mercury emissions. There is a need to control/reduce anthropogenic mercury emissions. Many mercury control technologies are available but their effectiveness is dependent on the chemical form of mercury, because different chemical forms of mercury have different physical and chemical properties. Mercury leaves the boiler in its elemental form but goes through various transformations in the post-combustion zone. There is a need to understand how fly ash and flue gas composition affect speciation, partitioning, and reactions of mercury under the full range of post-combustion zone conditions. This knowledge can then be used to predict the chemical transformation of mercury (elemental, oxidized or particulate) in the post combustion zone and thus help with the control of mercury emissions from coal-burning power plants. To accomplish this goal present study was conducted using five coal fly ashes. These ashes were characterized and their catalytic activity was compared under selected reaction conditions in a fixed bed reactor. Based on the results from these fly ash experiments, three key components (carbon, iron oxide and calcium oxide) were chosen. These three components were then used to prepare model fly ashes. Silica/alumina was used as a base for these model fly ashes. One, two or three component model fly ashes were then prepared to investigate mercury transformation reactions. The third set of experiments was performed with five different oxidation catalysts to further understand the mercury oxidation process. Based on the results of these three studies the key components were predicted for different fly ash compositions under variety of flue gas conditions. A fixed bed reactor system was used to conduct this study. In all the experiments, the inlet concentration of Hg0(g) was maintained at 35 mug/m 3 using a diffusion tube as the source of Hg0(g). All experiments were conducted using 4% O2 in nitrogen mix as a reaction gas, and other reactants (HCl, H2O and SO2, NO 2, Br2) were added as required. The fixed bed reactor was operated over a temperature range of 200 to 400░C. In each experiment, the reactor effluent was analyzed using the modified Ontario-Hydro method. After each experiment, fly ash particles were also analyzed for mercury. The results show that the ability of fly ash to adsorb and/or oxidize mercury is primarily dependent on its carbon, iron and calcium content. There can be either one or more than one key component at a particular temperature and flue gas condition. Surface area played a secondary role in effecting the mercury transformations when compared to the concentration of the key component in the fly ash. Amount carbon and surface area played a key important role in the adsorption of mercury. Increased concentration of gases in the flue gas other than oxygen and nitrogen caused decreased the amount of mercury adsorbed on carbon surface. Mercury adsorption by iron oxide primarily depended on the crystalline structure of iron oxide. alpha-iron oxide had no effect on mercury adsorption or oxidation under most of the flue gas conditions, but gamma-iron oxide adsorbed mercury under most of the flue gas conditions. Bromine is a very good oxidizing agent for mercury. But in the presence of calcium oxide containing fly ashes, all the oxidized mercury would be reduced to elemental form. Among the catalysts, it was observed that presence of free lattice chlorine in the catalyst was very important for the oxidation of mercury. But instead of using the catalyst alone, using it along with carbon may better serve the purpose by providing the adsorption surface for mercury and also some extra surface area for the reaction to occur (especially for fly ashes with low surface area).
Varanasi, Patanjali
Enzyme-catalyzed synthesis of aliphatic-aromatic oligoamides.
Enzymatically catalyzed polycondensation of p-xylylenediamine and diethyl sebacate resulted in oligo(p-xylylene sebacamide) with high melting temperatures (223-230 ░C) and the enzymatic polycondensation of dimethyl terephthalate and 1,8-diaminooctane leads to oligo(octamethylene terephthalamide) with two melting temperatures at 186 and 218 ░C. No oligoamides, but products 1 and 2, were formed from the enzymatic reaction of dimethyl terephthalate and p-xylylenediamine. All reactions were catalyzed by CAL-B, icutinase, or CLEA cutinase. All reactions catalyzed by CAL-B show higher conversion than reactions catalyzed by icutinase or CLEA cutinase. The highest DPmax of 15 was achieved in a one-step and two-step synthesis of oligo(p-xylylene sebacamide) catalyzed by CLEA cutinase. PMID:23544613
Stavila, E; Alberda van Ekenstein, G O R; Loos, K
Hydrogen Location in Stages of an Enzyme-Catalyzed Reaction: Time-of-Flight Neutron Structure of D-Xylose Isomerase with Bound D-Xylulose
The time-of-flight neutron Laue technique has been used to determine the location of hydrogen atoms in the enzyme D-xylose isomerase (XI). The neutron structure of crystalline XI with bound product, D-xylulose, shows, unexpectedly, that O5 of D-xylulose is not protonated but is hydrogen-bonded to doubly protonated His54. Also, Lys289, which is neutral in native XI, is protonated (positively charged), while the catalytic water in native XI has become activated to a hydroxyl anion which is in the proximity of C1 and C2, the molecular site of isomerization of xylose. These findings impact our understanding of the reaction mechanism.
Coates, Leighton [ORNL
Potential of Mean Force Calculation for the Proton and Hydride Transfer Reactions Catalyzed by Medium-Chain Acyl-CoA Dehydrogenase:Ā Effect of Mutations on Enzyme Catalysis å
ABSTRACT: Potential of mean,force calculations have been,performed,on the wild-type medium-chain acyl-CoA dehydrogenase,(MCAD) and two of its mutant,forms. Initial simulation and analysis of the active site of the enzyme reveal that an arginine residue (Arg256), conserved in the substrate-binding domain of this group of enzymes, exists in two alternate conformations, only one of which makes the enzyme,active. This active conformation,was used
Sudeep Bhattacharyya; Shuhua Ma; Marian T. Stankovich; Donald G. Truhlar; Jiali Gao
Atomic Description of an Enzyme Reaction Dominated by Proton Tunneling
We present an atomic-level description of the reaction chemistry of an enzyme-catalyzed reaction dominated by proton tunneling. By solving structures of reaction intermediates at near-atomic resolution, we have identified the reaction pathway for tryptamine oxidation by aromatic amine dehydrogenase. Combining experiment and computer simulation, we show proton transfer occurs predominantly to oxygen O2 of Asp128beta in a reaction dominated by
Laura Masgrau; Anna Roujeinikova; Linus O. Johannissen; Parvinder Hothi; Jaswir Basran; Kara E. Ranaghan; Adrian J. Mulholland; Michael J. Sutcliffe; Nigel S. Scrutton; David Leys
Mechanistic considerations of guanidine-catalyzed reactions.
This feature article discusses the various mechanistic aspects of guanidine-catalyzed reactions. Guanidines are well known as strong organic bases; however, in the first section, three most common commercially available guanidines, TMG, TBD and MTBD, will be used to illustrate the use of guanidines as nucleophilic catalysts. In the second section, different modes of hydrogen bonding interactions of the conjugate acid of guanidine, the guanidinium, are discussed. Particularly interesting are the possibilities of mono-functional or bifunctional activation of a nucleophile and an electrophile by guanidinium. PMID:21541409
Fu, Xiao; Tan, Choon-Hong
Enantioselective Imidation of Sulfides via Enzyme-Catalyzed Intermolecular Nitrogen-Atom Transfer.
Engineering enzymes with novel reaction modes promises to expand the applications of biocatalysis in chemical synthesis and will enhance our understanding of how enzymes acquire new functions. The insertion of nitrogen-containing functional groups into unactivated C-H bonds is not catalyzed by known enzymes but was recently demonstrated using engineered variants of cytochrome P450BM3 (CYP102A1) from Bacillus megaterium. Here, we extend this novel P450-catalyzed reaction to include intermolecular insertion of nitrogen into thioethers to form sulfimides. An examination of the reactivity of different P450BM3 variants toward a range of substrates demonstrates that electronic properties of the substrates are important in this novel enzyme-catalyzed reaction. Moreover, amino acid substitutions have a large effect on the rate and stereoselectivity of sulfimidation, demonstrating that the protein plays a key role in determining reactivity and selectivity. These results provide a stepping stone for engineering more complex nitrogen-atom-transfer reactions in P450 enzymes and developing a more comprehensive biocatalytic repertoire. PMID:24901646
Farwell, Christopher C; McIntosh, John A; Hyster, Todd K; Wang, Z Jane; Arnold, Frances H
Biginelli Reaction Catalyzed by Copper Nanoparticles
We recently reported a novel synthesis of copper nanoparticles from copper sulphate utilizing the charge-compensatory effect of ionic liquid [bmim]BF4 and ethylene glycol. The nanoparticles were characterized and found to be stable for one year. Here we hypothesize that the stabilized nanoparticles should be able to catalyze one-pot multicomponent organic reactions. We show that the nanoparticles catalyzed Biginelli reaction at room temperature to give the product 3,4-dihydopyrimidinone (>90% yield in ?15 minutes) from aldehydes, ?-diketoester (ethylacetoacetate) and urea (or thiourea). ). Remarkably, such high yields and rapid kinetics was found to be independent of the electronic density on the reactant aryl-aldehyde. This was probably because even the surface-active particles reacted faster in the presence of ionic liquid as compared to conventional methods. The heterocyclic dihydropyrimidinones (DHPMs) and their derivatives are widely used in natural and synthetic organic chemistry due to their wide spectrum of biological and therapeutic properties (resulting from their antibacterial, antiviral, antitumor and anti-inflammatory activities. Our method has an easy work-up procedure and the nanoparticles could be recycled with minimal loss of efficiency.
Dewan, Manika; Kumar, Ajeet; Saxena, Amit; De, Arnab; Mozumdar, Subho
A model study of sequential enzyme reactions and electrostatic channeling.
We study models of two sequential enzyme-catalyzed reactions as a basic functional building block for coupled biochemical networks. We investigate the influence of enzyme distributions and long-range molecular interactions on reaction kinetics, which have been exploited in biological systems to maximize metabolic efficiency and signaling effects. Specifically, we examine how the maximal rate of product generation in a series of sequential reactions is dependent on the enzyme distribution and the electrostatic composition of its participant enzymes and substrates. We find that close proximity between enzymes does not guarantee optimal reaction rates, as the benefit of decreasing enzyme separation is countered by the volume excluded by adjacent enzymes. We further quantify the extent to which the electrostatic potential increases the efficiency of transferring substrate between enzymes, which supports the existence of electrostatic channeling in nature. Here, a major finding is that the role of attractive electrostatic interactions in confining intermediate substrates in the vicinity of the enzymes can contribute more to net reactive throughput than the directional properties of the electrostatic fields. These findings shed light on the interplay of long-range interactions and enzyme distributions in coupled enzyme-catalyzed reactions, and their influence on signaling in biological systems. PMID:24628210
Eun, Changsun; Kekenes-Huskey, Peter M; Metzger, Vincent T; McCammon, J Andrew
A novel enzyme-catalyzed synthesis of N-substituted pyrrole derivatives.
A novel method for the synthesis of substituted pyrroles catalyzed by ?-amylase from hog pancreas via Paal-Knorr reaction was developed. A series of pyrrole derivatives were synthesized under mild conditions and the products were obtained with good to excellent yields (60-99 %). The impact of factors, such as solvents, enzyme amount, and temperature, on the reaction were investigated. This study reports an efficient route for the synthesis of N-substituted pyrrole derivatives. PMID:23361455
Zheng, Hui; Shi, Qiaoyue; Du, Kui; Mei, Yijia; Zhang, Pengfei
Detoxification of sulfur mustard by enzyme-catalyzed oxidation using chloroperoxidase.
One of the most interesting methods for the detoxification of sulfur mustard is enzyme-catalyzed oxidation. This study examined the oxidative destruction of a sulfur mustard by the enzyme chloroperoxidase (EC 18.104.22.168). Chloroperoxidase (CPO) belongs to a group of enzymes that catalyze the oxidation of various organic compounds by peroxide in the presence of a halide ion. The enzymatic oxidation reaction is affected by several factors: pH, presence or absence of chloride ion, temperature, the concentrations of hydrogen peroxide and enzyme and aqueous solubility of the substrate. The optimum reaction conditions were determined by analyzing the effects of all factors, and the following conditions were selected: solvent, Britton-Robinson buffer (pH=3) with tert-butanol (70:30 v/v); CPO concentration, 16U/mL; hydrogen peroxide concentration, 40mmol/L; sodium chloride concentration, 20mmol/L. Under these reaction conditions, the rate constant for the reaction is 0.006s(-1). The Michaelis constant, a measure of the affinity of an enzyme for a particular substrate, is 1.87ū10(-3)M for this system. The Michaelis constant for enzymes with a high affinity for their substrate is in the range of 10(-5) to 10(-4)M, so this value indicates that CPO does not have a very high affinity for sulfur mustard. PMID:24034427
Popiel, S; Nawa?a, J
Mammalian Tyrosinase Catalyzes Three Reactions in the Biosynthesis of Melanin
The biosynthesis of melanin is initiated by the catalytic oxidation of tyrosine to dopa by tyrosinase in a reaction that requires dopa as a cofactor. Tyrosinase then catalyzes the dehydrogenation of dopa to dopaquinone. The subsequent reactions can proceed spontaneously in vitro. Tyrosinase, purified from murine melanomas and the skins of brown mice, has now been shown to catalyze a
Ann Korner; John Pawelek
Internal friction in enzyme reactions.
The empirical concept of internal friction was introduced 20 years ago. This review summarizes the results of experimental and theoretical studies that help to uncover the nature of internal friction. After the history of the concept, we describe the experimental challenges in measuring and interpreting internal friction based on the viscosity dependence of enzyme reactions. We also present speculations about the structural background of this viscosity dependence. Finally, some models about the relationship between the energy landscape and internal friction are outlined. Alternative concepts regarding the viscosity dependence of enzyme reactions are also discussed. PMID:23281036
Rauscher, Anna; Derķnyi, Imre; Grßf, Lßszl¾; Mßlnßsi-Csizmadia, Andrßs
Enzyme-catalyzed biocathode in a photoelectrochemical biofuel cell
A novel double-enzyme photoelectrochemical biofuel cell (PEBFC) has been developed by taking glucose dehydrogenase (GDH) and horseradish peroxidase (HRP) as the enzyme of the photoanode and biocathode to catalyze the oxidation of glucose and the reduction of oxygen. A H2-mesoporphyrin IX is used as a dye for a TiO2 film electrode to fabricate a photoanode. The horseradish peroxidase (HRP) is immobilized on a glassy carbon (GC) electrode to construct a biocathode which is used to catalyze the reduction of oxygen in the PEBFC for the first time. The biocathode exhibits excellent electrocatalytic activity in the presence of O2. The performances of the PEBFC are obtained by current-voltage and power-voltage curves. The short-circuit current density (Isc), the open-circuit voltage (Voc), maximum power density (Pmax), fill factor (FF) and energy conversion efficiency (?) are 439Ā?AĀcm-2, 678ĀmV, 79Ā?WĀcm-2, 0.39 and 0.016%, respectively, and the incident photon-to-collected electron conversion efficiency (IPCE) is 32% at 350Ānm. The Isc is higher than that of the PEBFC with Pt cathode, and the Voc is higher than that of the dye-sensitized solar cell or the enzyme-catalyzed biofuel cell operating individually, which demonstrates that the HRP is an efficient catalyst for the biocathode in the PEBFC.
Yang, Jing; Hu, Donghua; Zhang, Xiaohuan; Wang, Kunqi; Wang, Bin; Sun, Bo; Qiu, Zhidong
Kinetic Determination of Drug Particles Concentration via Enzyme-Catalyzed Decomposition of Hydrogen Peroxide
The inhibition effect of blood pressure control drug particles, metoprolol (C34H56N2O12), and atenolol (C14H22N2O3), on the enzyme catalyzed decomposition of hydrogen peroxide reaction has been investigated by ultraviolet spectrophotometry. The results obtained when hydrogen peroxide was spectrophotometrically monitored were compared with those previously obtained from electrochemical measurements. As expected, the two series of measurements were shown to be consistent with
F. Pogacean; I. Baldea; L. Olenic; S. Pruneanu; A. S. Biris
[Synthesis and acceptor properties of 11-[(9'-anthracenyl)methoxy]undecyl phosphate and P1-{11-[(9'-anthracenyl)methoxy]undecyl}-P2-(alpha-D-galactopyranosyl) diphosphate in the enzymic reactions catalyzed by galactosylphosphotransferase and mannosyltransferase from Salmonella newport].
Fluorescent 11-[(9'-anthracenyl)methoxy]undecyl phosphate and P1-{11-[(9'-anthracenyl)methoxy]undecyl}-P2-(alpha-D-galactopyranosyl) diphosphate were chemically synthesized for the first time. The ability of the first compound to serve as substrate-acceptor ofgalactosyl phosphate residue and the second compound of mannosyl residue in enzymic reactions catalyzed by galactosylphosphotransferase and mannosyltransferase from Salmonella newport membrane preparation was demonstrated. PMID:23844511
Vinnikova, A N; Utkina, N S; Danilov, L L; Torgov, V I; Druzhinina, T N; Veselovski?, V V
Probing the Mechanism of 1,4-Conjugate Elimination Reactions Catalyzed by Terpene Synthases
The reaction mechanisms of (E)-?-farnesene synthase (EBFS) and isoprene synthase (ISPS), enzymes that catalyze a formal regioespecific 1,4-conjugate elimination of hydrogen-diphosphate from (E, E)-farnesyl and dimethylallyl diphosphate (FDP and DMADP) to generate the semiochemicals (E)-?-farnesene and isoprene, respectively, were probed with substrate analogs and kinetic measurements. The results support stepwise reaction mechanisms through analogous enzyme-bound allylic cationic intermediates. For EBFS, we demonstrate that the elimination reaction can proceed via the enzyme-bound intermediate trans-nerolidyl diphosphate, while for ISPS the intermediacy of 2-methylbut-3-enyl 2-diphosphate can be inferred from the product outcome when deuterated DMADPs are used as substrates. Possible implications derived from the mechanistic details of the EBFS catalyzed reaction for the evolution of sesquiterpene synthases are discussed.
Faraldos, Juan A.; Gonzalez, Veronica; Li, Amang; Yu, Fanglei; Koksal, Mustafa; Christianson, David W.; Allemann, Rudolf K.
Carotenoid biosynthesis: Isolation and characterization of a bifunctional enzyme catalyzing the synthesis of phytoene
Phytoene is the first C40 intermediate in the biogenesis of carotenoids. It is formed by two enzyme activities, catalyzing (i) the coupling of two molecules of geranylgeranyl diphosphate to yield prephytoene diphosphate and (ii) the conversion of prephytoene diphosphate into phytoene. We show now, with Capsicum chromoplast stroma, that the overall activity resides in a single protein, which has been purified to homogeneity by affinity chromatography. The monomeric structure and the molecular size (Mr 47,500) were demonstrated by NaDodSO4/PAGE and glycerol gradient centrifugation. Further characterization was achieved by using specific antibodies which allowed immunofractionation and immunoprecipitation of the enzymatic activity from chromoplast stroma. The two reactions followed conventional Michaelis-Menten kinetics, with Km values of 0.30 ?M and 0.27 ?M, respectively, for geranylgeranyl diphosphate and prephytoene diphosphate. The activity of the enzyme depends strictly upon the presence of Mn2+. This selectivity may be one of the factors regulating the competition with potentially rival enzymes converting geranylgeranyl diphosphate into other plastid terpenoids. The two enzymatic reactions were inhibited by inorganic pyrophosphate and by the arginine-specific reagent hydroxyphenylglyoxal. In no instance were the two reactions kinetically uncoupled. These properties strongly suggest that the same enzyme catalyzes the two consecutive reactions, and we propose to name it phytoene synthase. Images
Dogbo, Odette; Laferriere, Andre; D'Harlingue, Alain; Camara, Bilal
Glutaminase catalyzes reaction of Glutamate to GABA.
Here, for the first time, we report an NMR spectroscopy study of l-Glutamine (Gln) conversion by Glutaminase (Glnase), which shows that the reaction involves two distinct steps. In the first step, Glnase rapidly hydrolyzes Gln to Glutamate (Glu) (?16.87 ?mol of Gln/min/mg of Glnase) and in the second step, Glu generated in the first step is decarboxylated into gamma-amino butyric acid (GABA) with a much slower rate (?0.185 ?mol/min/mg). When Glnase was added to the sample containing l-Glu alone, it was also converted to GABA, at a similar rate as in the second step mentioned above. The rate of Glu decarboxylation into GABA by Glnase is about an order of magnitude lower than that by commonly known enzyme, Glutamate decarboxylase. Potential impact of these findings, on the mechanistic aspects of Gln-Glu shuttle in neuroscience and glutaminolysis in tumors, is discussed. PMID:24755074
Nanga, Ravi Prakash Reddy; DeBrosse, Catherine; Singh, Anup; D'Aquilla, Kevin; Hariharan, Hari; Reddy, Ravinder
PathPred: an enzyme-catalyzed metabolic pathway prediction server.
The KEGG RPAIR database is a collection of biochemical structure transformation patterns, called RDM patterns, and chemical structure alignments of substrate-product pairs (reactant pairs) in all known enzyme-catalyzed reactions taken from the Enzyme Nomenclature and the KEGG PATHWAY database. Here, we present PathPred (http://www.genome.jp/tools/pathpred/), a web-based server to predict plausible pathways of muti-step reactions starting from a query compound, based on the local RDM pattern match and the global chemical structure alignment against the reactant pair library. In this server, we focus on predicting pathways for microbial biodegradation of environmental compounds and biosynthesis of plant secondary metabolites, which correspond to characteristic RDM patterns in 947 and 1397 reactant pairs, respectively. The server provides transformed compounds and reference transformation patterns in each predicted reaction, and displays all predicted multi-step reaction pathways in a tree-shaped graph. PMID:20435670
Moriya, Yuki; Shigemizu, Daichi; Hattori, Masahiro; Tokimatsu, Toshiaki; Kotera, Masaaki; Goto, Susumu; Kanehisa, Minoru
Improved enzyme stability in lipase-catalyzed synthesis of fatty acid ethyl ester from soybean oil.
In this work, we describe the optimization of the ethanolysis of soybean oil by the enzyme Lipozyme TL-IM in the lipase-catalyzed biodiesel synthesis and the improvement of the enzyme stability over repeated batches. The studied process variables were: reaction temperature, substrate molar ratio, enzyme content, and volume of added water. Fractional factorial design was used to analyze the variables so as to select those with higher influence on the reaction and then perform a central composite design to find the optimal reaction conditions. The optimal conditions found were: temperature, 26 degrees C; substrate molar ratio, 7.5:1 (ethanol/oil); enzyme content, 25% in relation to oil weight; and added water, 4% in relation to oil weight. Under these conditions, the yield conversion obtained was 69% in 12 h. The enzyme stability assessment in repeated batches was carried out by washing the immobilized enzyme with different solvents (n-hexane, water, ethanol, and propanol) after each batch. In the treatment with n-hexane, around 80% of the enzyme activity still remains after seven cycles of synthesis, suggesting its economical application on biodiesel production. PMID:18548204
Costa Rodrigues, Rafael; Volpato, Giandra; Wada, Keiko; Zßchia Ayub, Marco Ant¶nio
Enzyme-catalyzed oxidation facilitates the return of fluorescence for single-walled carbon nanotubes.
In this work, we studied enzyme-catalyzed oxidation of single-walled carbon nanotubes (SWCNTs) produced by the high-pressure carbon monoxide (HiPco) method. While oxidation via strong acids introduced defect sites on SWCNTs and suppressed their near-infrared (NIR) fluorescence, our results indicated that the fluorescence of SWCNTs was restored upon enzymatic oxidation, providing new evidence that the reaction catalyzed by horseradish peroxidase (HRP) in the presence of H2O2 is mainly a defect-consuming step. These results were further supported by both UV-vis-NIR and Raman spectroscopy. Therefore, when acid oxidation followed by HRP-catalyzed enzyme oxidation was employed, shortened (<300 nm in length) and NIR-fluorescent SWCNTs were produced. In contrast, upon treatment with myeloperoxidase, H2O2, and NaCl, the oxidized HiPco SWCNTs underwent complete oxidation (i.e., degradation). The shortened, NIR-fluorescent SWCNTs resulting from HRP-catalyzed oxidation of acid-cut HiPco SWCNTs may find applications in cellular NIR imaging and drug delivery systems. PMID:23672715
Chiu, Cheuk Fai; Barth, Brian A; Kotchey, Gregg P; Zhao, Yong; Gogick, Kristy A; Saidi, Wissam A; Petoud, Stķphane; Star, Alexander
Complex Biotransformations Catalyzed by Radical S-Adenosylmethionine Enzymes*
The radical S-adenosylmethionine (AdoMet) superfamily currently comprises thousands of proteins that participate in numerous biochemical processes across all kingdoms of life. These proteins share a common mechanism to generate a powerful 5?-deoxyadenosyl radical, which initiates a highly diverse array of biotransformations. Recent studies are beginning to reveal the role of radical AdoMet proteins in the catalysis of highly complex and chemically unusual transformations, e.g. the ThiC-catalyzed complex rearrangement reaction. The unique features and intriguing chemistries of these proteins thus demonstrate the remarkable versatility and sophistication of radical enzymology.
Zhang, Qi; Liu, Wen
Steroid hydroxylations: A paradigm for cytochrome P450 catalyzed mammalian monooxygenation reactions
The present article reviews the history of research on the hydroxylation of steroid hormones as catalyzed by enzymes present in mammalian tissues. The report describes how studies of steroid hormone synthesis have played a central role in the discovery of the monooxygenase functions of the cytochrome P450s. Studies of steroid hydroxylation reactions can be credited with showing that: (a) the adrenal mitochondrial enzyme catalyzing the 11{beta}-hydroxylation of deoxycorticosterone was the first mammalian enzyme shown by O{sup 18} studies to be an oxygenase; (b) the adrenal microsomal enzyme catalyzing the 21-hydroxylation of steroids was the first mammalian enzyme to show experimentally the proposed 1:1:1 stoichiometry (substrate:oxygen:reduced pyridine nucleotide) of a monooxygenase reaction; (c) application of the photochemical action spectrum technique for reversal of carbon monoxide inhibition of the 21-hydroxylation of 17{alpha}-OH progesterone was the first demonstration that cytochrome P450 was an oxygenase; (d) spectrophotometric studies of the binding of 17{alpha}-OH progesterone to bovine adrenal microsomal P450 revealed the first step in the cyclic reaction scheme of P450, as it catalyzes the 'activation' of oxygen in a monooxygenase reaction; (e) purified adrenodoxin was shown to function as an electron transport component of the adrenal mitochondrial monooxygenase system required for the activity of the 11{beta}-hydroxylase reaction. Adrenodoxin was the first iron-sulfur protein isolated and purified from mammalian tissues and the first soluble protein identified as a reductase of a P450; (f) fractionation of adrenal mitochondrial P450 and incubation with adrenodoxin and a cytosolic (flavoprotein) fraction were the first demonstration of the reconstitution of a mammalian P450 monooxygenase reaction.
Estabrook, Ronald W. [Virginia Lazenby O'Hara Professor of Biochemistry, Ida and Cecil Green Chair in the Biomedical Sciences, Department of Biochemistry, Room Y7.206B, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd., Dallas, TX 75390-9038 (United States)]. E-mail: firstname.lastname@example.com
Stereochemistry and mechanism of reactions catalyzed by tryptophanase Escherichia coli.
Several beta replacement and alpha,beta elimination reactions catalyzed by tryptophanase from Escherichia coli are shown to proceed stereospecifically with retention of configuration. These conversions include synthesis of tryptophan from (2S,3R)- and (2s,3s)-[3(-3H)]serine in the presence of indole, deamination of these serines in D2O to pyruvate and ammonia, and cleavage of (2S,3R)-and (2S,3S)-[3(-3H)]tryptophan in D2O to indole, pyruvate, and ammonia. A coupled reaction with lactate dehydrogenase was used to trap the stereospecifically labeled [3-H,2H,3H]pryuvates as lactate, which was oxidized to acetate for chirality analysis of the methyl group. During deamination of tryptophan there is significant intramolecular transfer of the alpha proton of the amino acid to C-3 of indole. To determine the exposed face of the cofactor.substrate complex on the enzyme surface and to analyze its conformational orientation, sodium boro[3H]hydride was used to reduce tryptophanase-bound alaninepyridoxal phosphate Schiff's base. Degradation of the resulting pyridoxylalanine to (2S)-[2(-3H)]alanine and (4'S)-[4'(-3H)]pyridoxamine demonstrates that reduction occurs from the exposed si face at C-4' of the complex and that the ketimine double bond is trans. PMID:353050
Vederas, J C; Schleicher, E; Tsai, M D; Floss, H G
Influencing Enzymes: A Lesson on Enzyme Reactions
This teaching resource was developed by a K-12 science teacher in the American Physiological Society├┬s 2007 Frontiers in Physiology Program. For more information on this program, please visit www.frontiersinphys.org. Students will investigate the catabolic properties of the enzyme amylase and its role in digestion of breaking down starch molecules. Prior to this activity, students should be able to identify the structural and functional properties of carbohydrates and proteins. Upon completion of this activity, students will be able to predict the effect of different environments on enzyme activity.
Camia Steinmann (Clear Creek High School)
Iron-catalyzed asymmetric haloamination reactions.
The first iron(III)/N,N'-dioxide-catalyzed asymmetric haloamination of 3-alkylidene- and 3-arylidene-indolin-2-ones was developed, affording the corresponding chiral oxindole derivatives bearing vicinal haloamine substituents with excellent results (up to 99% yield, 99% ee, >19?:?1 dr). This iron catalyst also exhibits perfect enantioselectivity for chalcone derivatives. The cooperative activation of the substrate and the reagent in concert guarantees the high stereoselectivity. PMID:23903004
Cai, Yunfei; Liu, Xiaohua; Zhou, Pengfei; Kuang, Yulong; Lin, Lili; Feng, Xiaoming
Enzyme catalyzed electricity-driven water softening system.
Hardness in water, which is caused by divalent cations such as calcium and magnesium ions, presents a major water quality problem. Because hard water must be softened before use in residential applications, there is great interest in the saltless water softening process because, unlike ion exchange softeners, it does not introduce additional ions into water. In this study, a saltless hardness removal driven by bioelectrochemical energy produced through enzymatic oxidation of glucose was proposed and investigated. Glucose dehydrogenase was coated on a carbon electrode to catalyze glucose oxidation in the presence of NAD? as a cofactor/mediator and methylene green as an electrocatalyst. The results showed that electricity generation stimulated hardness removal compared with non-electricity conditions. The enzymatic water softener worked upon a 6h batch operation per day for eight days, and achieved an average hardness removal of 46% at a high initial concentration of 800 mg/L as CaCO?. More hardness was removed at a lower initial concentration. For instance, at 200mg/L as CaCO? the enzymatic water softener removed 76.4▒4.6% of total hardness. The presence of magnesium ions decreased hardness removal because of its larger hydrated radius than calcium ions. The enzymatic water softener removed 70-80% of total hardness from three actual hard water samples. These results demonstrated a proof-of-concept that enzyme catalyzed electricity generation can be used to soften hard water. PMID:23040397
Arugula, Mary A; Brastad, Kristen S; Minteer, Shelley D; He, Zhen
Ligand Intermediates in Metal-Catalyzed Reactions
The longest-running goal of this project has been the synthesis, isolation, and physical chemical characterization of homogeneous transition metal complexes containing ligand types believed to be intermediates in the metal-catalyzed conversion of CO/H{sub 2}, CO{sub 2}, CH{sub 4}, and similar raw materials to organic fuels, feedstocks, etc. In the current project period, complexes that contain unusual new types of C{sub x}(carbide) and C{sub x}O{sub y} (carbon oxide) ligands have been emphasized. A new program in homogeneous fluorous phase catalysis has been launched as described in the final report.
Gladysz, John A.
Rearrangement reactions catalyzed by cytochrome P450s.
Cytochrome P450s promote a variety of rearrangement reactions both as a consequence of the nature of the radical and other intermediates generated during catalysis, and of the neighboring structures in the substrate that can interact either with the initial radical intermediates or with further downstream products of the reactions. This article will review several kinds of previously published cytochrome P450-catalyzed rearrangement reactions, including changes in stereochemistry, radical clock reactions, allylic rearrangements, "NIH" and related shifts, ring contractions and expansions, and cyclizations that result from neighboring group interactions. Although most of these reactions can be carried out by many members of the cytochrome P450 superfamily, some have only been observed with select P450s, including some reactions that are catalyzed by specific endoperoxidases and cytochrome P450s found in plants. PMID:20971058
Ortiz de Montellano, Paul R; Nelson, Sidney D
Rearrangement Reactions Catalyzed by Cytochrome P450s
Cytochrome P450s promote a variety of rearrangement reactions both as a consequence of the nature of the radical and other intermediates generated during catalysis, and of the neighboring structures in the substrate that can interact either with the initial radical intermediates or with further downstream products of the reactions. This article will review several kinds of previously published cytochrome P450-catalyzed rearrangement reactions, including changes in stereochemistry, radical clock reactions, allylic rearrangements, ōNIHö and related shifts, ring contractions and expansions, and cyclizations that result from neighboring group interactions. Although most of these reactions can be carried out by many members of the cytochrome P450 superfamily, some have only been observed with select P450s, including some reactions that are catalyzed by specific endoperoxidases and cytochrome P450s found in plants.
Ortiz de Montellano, Paul R.; Nelson, Sidney D.
A novel palladium-catalyzed intramolecular redox reaction.
[reaction: see text] A new type of palladium-catalyzed redox reaction is described, forming enones from 2-(2-bromobenzyl)-ketones with an overall loss of HBr. The scope and limitations of the reaction are demonstrated by a series of cyclic and acyclic substrates. The mechanism most probably involves the formation of an intramolecular arylpalladium enolate and is related to the oxidation of silyl enol ethers with palladium acetate. PMID:11388850
H÷genauer, K; Mulzer, J
Diamine Ligands in Copper-Catalyzed Reactions
The utility of copper-mediated cross-coupling reactions has been significantly increased by the development of mild reaction conditions and the ability to employ catalytic amounts of copper. The use of diamine-based ligands has been important in these advances and in this review we discuss these systems, including the choice of reaction conditions and applications in the synthesis of pharmaceuticals, natural products and designed materials.
Surry, David S.
Enzyme catalysis in organic solvents: influence of water content, solvent composition and temperature on Candida rugosa lipase catalyzed transesterification.
In the present study the influence of water content, solvent composition and reaction temperature on the transesterification of 1-phenylpropan-2-ol catalyzed by Candida rugosa lipase was examined. Reactions were carried out in different mixtures of hexane and tetrahydrofurane. The studies showed that an increasing water content of the organic solvent results in an increasing enzyme activity and a decreasing enantiomeric excess. Furthermore, a significant influence of the solvent hydrophilicity both on the enzyme activity and on the enantiomeric excess was found. An increase in solvent hydrophilicity leads to a decrease of enzyme activity and an increase of the enantiomeric excess. This indicates that the enzyme becomes more selective with decreasing flexibility. Similar effects were found by variation of the reaction temperature. Taken together, the decrease in conversion and the increase in selectivity with increasing solvent hydrophilicity are induced by the different water contents on the enzyme surface and not by the solvent itself. PMID:22465292
Herbst, Daniela; Peper, Stephanie; Niemeyer, Bernd
In vitro analysis of RNA degradation catalyzed by deadenylase enzymes.
In this chapter, we describe a method for purification and analysis of the enzymatic activity of deadenylase enzymes. Nearly all eukaryotic messenger RNAs are modified at the 3' end by the addition of an adenosine polymer: the poly-adenosine tail. The poly(A) tail plays a central role in protein expression and mRNA fate. The poly(A) tail promotes translation of the mRNA. Shortening of the poly(A) tail, referred to as deadenylation, reduces protein synthesis and initiates destruction of the mRNA. A specialized class of exoribonucleases, called deadenylase enzymes, carries out this process. Deadenylases are found throughout eukarya, but their functions remain largely unexplored. We present a detailed protocol to analyze deadenylase activity in vitro. First, recombinant deadenylase enzyme is over-expressed and purified from bacteria. Next, labeled RNA substrate is prepared. Deadenylation reactions are performed, and reaction products are analyzed by denaturing gel electrophoresis. Reaction rates are then determined quantitatively. Crucial controls and experimental parameters are described along with practical tips that promote success. PMID:24590800
Hrit, Joel; Raynard, Nathan; Van Etten, Jamie; Sankar, Kamya; Petterson, Adam; Goldstrohm, Aaron C
Adenosyl radical: reagent and catalyst in enzyme reactions.
Adenosine is undoubtedly an ancient biological molecule that is a component of many enzyme cofactors: ATP, FADH, NAD(P)H, and coenzyme A, to name but a few, and, of course, of RNA. Here we present an overview of the role of adenosine in its most reactive form: as an organic radical formed either by homolytic cleavage of adenosylcobalamin (coenzyme B(12), AdoCbl) or by single-electron reduction of S-adenosylmethionine (AdoMet) complexed to an iron-sulfur cluster. Although many of the enzymes we discuss are newly discovered, adenosine's role as a radical cofactor most likely arose very early in evolution, before the advent of photosynthesis and the production of molecular oxygen, which rapidly inactivates many radical enzymes. AdoCbl-dependent enzymes appear to be confined to a rather narrow repertoire of rearrangement reactions involving 1,2-hydrogen atom migrations; nevertheless, mechanistic insights gained from studying these enzymes have proved extremely valuable in understanding how enzymes generate and control highly reactive free radical intermediates. In contrast, there has been a recent explosion in the number of radical-AdoMet enzymes discovered that catalyze a remarkably wide range of chemically challenging reactions; here there is much still to learn about their mechanisms. Although all the radical-AdoMet enzymes so far characterized come from anaerobically growing microbes and are very oxygen sensitive, there is tantalizing evidence that some of these enzymes might be active in aerobic organisms including humans. PMID:20191656
Marsh, E Neil G; Patterson, Dustin P; Li, Lei
Palladium-Catalyzed Coupling Reactions of Aryl Chlorides
Collectively, palladium-catalyzed cou- pling reactions represent some of the most powerful and versatile tools avail- able to synthetic organic chemists. Their widespread popularity stems in part from the fact that they are gen- erally tolerant to a large number of functional groups, which allows them to be employed in a wide range of applications. However, for many years a major
Adam F. Littke; Gregory C. Fu
Cross-ligation and exchange reactions catalyzed by hairpin ribozymes.
The negative strand of the satellite RNA of tobacco ringspot virus (sTobRV(-)) contains a hairpin catalytic domain that shows self-cleavage and self-ligation activities in the presence of magnesium ions. We describe here that the minimal catalytic domain can catalyze a cross-ligation reaction between two kinds of substrates in trans. The cross-ligated product increased when the reaction temperature was decreased during the reaction from 37 degrees C to 4 degrees C. A two-stranded hairpin ribozyme, divided into two fragments between G45 and U46 in a hairpin loop, showed higher ligation activity than the nondivided ribozyme. The two stranded ribozyme also catalyzed an exchange reaction of the 3'-portion of the cleavage site. Images
Komatsu, Y; Koizumi, M; Sekiguchi, A; Ohtsuka, E
Silver and gold-catalyzed multicomponent reactions
Summary Silver and gold salts and complexes mainly act as soft and carbophilic Lewis acids even if their use as ?-activators has been rarely reported. Recently, transformations involving Au(I)/Au(III)-redox catalytic systems have been reported in the literature. In this review we highlight all these aspects of silver and gold-mediated processes and their application in multicomponent reactions.
Abbiati, Giorgio
Can Chlorine Anion Catalyze the Reaction fo HOCl with HCl?
The reaction of HOCl + HCl -> Cl2 + H20 in the presence of Cl has been studied using ab initio methods. This reaction has been shown to have a high activation barrier of 46.5 kcal/mol. The chlorine anion, Cl- is found to catalyze the reaction, viz. two mechanisms. The first involves Cl- interacting through the concerted four-center transition state of the neutral reaction. The other mechanism involves the formation of a HCl-HOCl-Cl- intermediate which dissociates into Cl2 + Cl- + H20. The steps are found to have no barriers. The overall exothermicity is 15.5 kcal/mol.
Richardson, S. L.; Francisco, J. S.; Mebel, A. M.; Morokuma, K.
Kinetic parameters for the elimination reaction catalyzed by triosephosphate isomerase and an estimation of the reaction's physiological significance.
Kinetic parameters for triosephosphate isomerase catalysis of the elimination reaction of an equilibrium mixture of dihydroxyacetone phosphate (DHAP) and D-glyceraldehyde-3-phosphate (DGAP) to form methylglyoxal and phosphate ion are reported for the enzyme from rabbit muscle. Pseudo-first-order rate constants for the disappearance of substrate (kelim) were determined for reactions at [Enzyme] much greater than [Substrate]. The second-order rate constant kEnz = 10.1 M-1 s-1 was determined from a plot of kelim against enzyme concentration. The kinetic parameters, determined from a steady-state kinetic analysis at [Substrate] much greater than [Enzyme], are kcat = 0.011 s-1, Km = 0.76 mM, and kcat/Km = 14 M-1 s-1. The estimated rate-constant ratio for partitioning of the enzyme-bound intermediate between protonation at carbon 2 and elimination, 1,000,000, is much larger than the ratio of 6.5 determined for the reaction of the enediolate phosphate in a loose complex with quinuclidinonium cation, a small buffer catalyst. There is a 10(5)-10(8)-fold decrease in the rate constant for the elimination reaction of the enediolate phosphate when this species binds to triosephosphate isomerase. The kinetic parameters for the elimination reaction catalyzed by the native triosephosphate isomerase and for the reaction catalyzed by a mutant form of the enzyme, which is missing a segment that forms hydrogen bonds with the phosphate group of substrate [Pompliano, D. L., Peyman, A., & Knowles, J. R. (1990) Biochemistry 29, 3186-3194] are similar.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:2021650
Richard, J P
Catalyzed reactions at illuminated semiconductor interfaces
It is pointed out that thermodynamically unfavorable chemical redox reactions can be effected by using optical energy as the driving force. To date, the best man-contrived systems for the direct conversion of optical energy to high energy redox products are semiconductor-based photoelectrochemical devices. The present investigation is concerned with the possibility that the minority carrier redox process at a semiconductor electrode may be too slow to compete with the recombination of photogenerated carriers. Attention is given to the photoelectrochemical generation of hydrogen, the photoelectrochemical reduction of carbon dioxide, the photo-oxidation of halides to halogens, and photo-oxidation of water. It is concluded that redox reactions of possible significance in solar fuel generation require rate acceleration to achieve high solar energy conversion efficiency.
Wrighton, M. S.
The role and source of 5'-deoxyadenosyl radical in a carbon skeleton rearrangement catalyzed by a plant enzyme.
The last step in the biosynthesis of tropane alkaloids is the carbon skeleton rearrangement of littorine to hyoscyamine. The reaction is catalyzed by a cell-free extract prepared from cultured hairy roots of Datura stramonium. Adenosylmethionine stimulated the rearrangement 10-20-fold and showed saturation kinetics with an apparent Km of 25 microM. It is proposed that S-adenosylmethionine is the source of a 5'-deoxyadenosyl radical which initiates the rearrangement in a similar manner as it does in analogous rearrangements catalyzed by coenzyme B12-dependent enzymes. Possible roles of S-adenosylmethionine as a radical source in higher plants are discussed. PMID:9824314
Ollagnier, S; Kervio, E; Rķtey, J
Differential Quantum Tunneling Contributions in Nitroalkane Oxidase Catalyzed and the Uncatalyzed Proton Transfer Reaction
The proton transfer reaction between the substrate nitroethane and Asp-402 catalyzed by nitroalkane oxidase and the uncatalyzed process in water have been investigated using a path-integral free-energy perturbation method. Although the dominating effect in rate acceleration by the enzyme is the lowering of the quasiclassical free energy barrier, nuclear quantum effects also contribute to catalysis in nitroalkane oxidase. In particular, the overall nuclear quantum effects have greater contributions to lowering the classical barrier in the enzyme, and there is a larger difference in quantum effects between proton and deuteron transfer for the enzymatic reaction than that in water. Both experiment and computation show that primary KIEs are enhanced in the enzyme, and the computed Swain-Schaad exponent for the enzymatic reaction is exacerbated relative to that in the absence of the enzyme. In addition, the computed tunneling transmission coefficient is approximately three times greater for the enzyme reaction than the uncatalyzed reaction, and the origin of the difference may be attributed to a narrowing effect in the effective potentials for tunneling in the enzyme than that in aqueous solution.
Major , D.; Heroux , A; Orville , A; Valley , M; Fitzpatrick , P; Gao , J
Density Functional Study of Mo-Carbonyl-Catalyzed Alkynol Cycloisomerization: Comparison with W-Catalyzed Reaction
Mo-catalyzed endo-cycloisomerizations of alkynes tethered to alcohols have been studied using density functional theory, and comparisons were made with the W-catalyzed reaction. The cycloisomerization is initiated with the formation of metal alkyne ? complex and is followed by the rate-determining step, which transforms the ? complex to a vinylidene carbene complex, considered to be critical for endo-mode cyclization. Several different alkynols have been selected to investigate five- and six-membered ring endo-cycloisomerizations in the presence of Mo(CO)5 catalyst. The energy barriers calculated for five- and six-membered ring cycloisomerizations are within a range of 25¢30 kcal/mol for most cases studied, showing no significant energy difference between the two metals. The stabilization effect of THF and Et3N solvents and the substitution reaction of THF by alkynol substrates in the reaction process with Mo and W complexes are studied as well. The principal difference between Mo- and W-catalyzed cycloisomerization processes appears to be the initial formation of a ? complex, which is more stabilizing for formation of the W-alkyne vs Mo-alkyne complexes.
Nowroozi-Isfahani, Taraneh; Musaev, Djamaladdin G.; McDonald, Frank E.; Morokuma, Keiji
Enzyme-Catalyzed Gel Proteolysis: An Anomalous Diffusion-Controlled Mechanism
Enzyme-catalyzed proteolysis of gelatin gels has been studied. We report a gel degradation rate varying as the square of the enzyme concentration. The diffusion motion of enzymes in the gel has been measured by two-photon fluorescence correlation spectroscopy and identified as being anomalously slow. These experimental results are discussed from a theoretical point of view and interpreted in terms of a diffusion-controlled mechanism for the gel degradation. These results make a step toward the understanding of enzyme-catalyzed gel degradation and give new insight on biological processes such as the action of metalloproteinases in the extracellular matrix involved in cellular invasion.
Fadda, G. C.; Lairez, D.; Arrio, B.; Carton, J.-P.; Larreta-Garde, V.
Regioselective enzyme-catalyzed synthesis of sophorolipid esters, amides, and multifunctional monomers.
Novel enzyme-mediated synthetic routes were developed to provide a new family of sophorolipid derivatives and glycolopid-based amphiphilic monomers. These compounds are of great interest for their potential use in immunoregulation, as well as for other biological properties. In the present work, an efficient lipase-catalyzed conversion of sophorolipid ethyl ester to (a) the 6'-monoacylated derivatives using Novozym 435, (b) 6' '-monoacylated derivatives using Lipase PS-C, (c) secondary amide derivatives using Novozym 435, and (d) 6',6' '-diacylated amide derivatives using Novozym 435 in an one-pot reaction and (e) the regioselective monoacylation of an amide derivative at the 6'- and 6' '-positions using Novozym 435 and Lipase PS-C, respectively, are described. The ethyl ester produced by esterification of the sophorolipid mixture with sodium ethoxide was subjected to acylation catalyzed by Novozym 435 in dry tetrahedrofuran (THF) with vinyl acetate and vinyl methacrylate to produce 6'-monoacylated derivatives. In contrast, Lipase PS-C catalyzed acylations of sophorolipid ethyl ester in dry THF with vinyl acetate and vinyl methacrylate to give the corresponding 6'-monoacylated derivatives. Novozym 435 mediated amidation of sophorolipid ethyl ester in dry THF with phenethylamine, tyramine, p-methoxyphenethylamine, 2-(p-tolyl)ethylamine, and p-fluorophenethylamine generated the corresponding secondary amides but not tertiary amides. The formation of diacyl derivatives of amides was achieved by their treatment with vinyl acetate and vinyl methacrylate in dry THF using Novozym 435 as catalyst. The conversion of sophorolipid ethyl ester to the same diacyl derivatives of amide (i.e., both amidation and acylation) in high yield was also demonstrated in dry THF by a one-pot reaction using Novozym 435. Furthermore, regioselective monoacylation of a sophorolipid amide at 6' and 6' ' in dry THF with vinyl acetate and vinyl methacrylate using Novozym 435 and Lipase PS-C was also demonstrated. PMID:12839437
Singh, Sanjay K; Felse, Arthur P; Nunez, Alberto; Foglia, Thomas A; Gross, Richard A
Density function studies on the PtCl2-catalyzed asymmetric cycloisomerization reaction of hydroxylated enynes
The PtCl2-catalyzed asymmetric cycloisomerization reaction of hydroxylated enynes was studied using density functional theory (DFT). All structures have been optimized completely at the B3LYP/6-311G(d,p) level. As shown, the cycloisomerization reaction is exothermic. The cycloisomerization reaction mainly undergoes the formation of catalyst-hydroxylated enzyme coordination, the asymmetric cyclopropyl platinum carbene, catalyst-cyclopropyl enol coordination, and catalyst-cyclopropyl ketone coordination. The chirality-limiting step for the asymmetric cycloisomerization reaction is the formation of the asymmetric cyclopropyl platinum carbene, and the rate-determining step for this reaction is the formation of the catalyst-cyclopropyl ketone coordination. The dominant products predicted theoretically are (R,S) -syn_5a, in agreement with the experiment.
Meng, Qingxi; Li, Ming; Zhang, Jinsheng; Shen, Wei
Predicting enzyme targets for cancer drugs by profiling human Metabolic reactions in NCI60 cell lines
BACKGROUND: Drugs can influence the whole metabolic system by targeting enzymes which catalyze metabolic reactions. The existence of interactions between drugs and metabolic reactions suggests a potential way to discover drug targets. RESULTS: In this paper, we present a computational method to predict new targets for approved anti-cancer drugs by exploring drug-reaction interactions. We construct a Drug-Reaction Network to provide
Limin Li; Xiaobo Zhou; Wai-Ki Ching; Ping Wang
Signal enhancement strategy for a micro-arrayed polydiacetylene (PDA) immunosensor using enzyme-catalyzed precipitation.
This paper describes a signal enhancement strategy to improve the sensitivity of an antibody-based immunosensor that uses polydiacetylene (PDA) liposomes to detect a target protein (human immunoglobulin E [hIgE]). To achieve ultrasensitive detection, multiple stimuli applied to PDA immunosensor chips offer a signal enhancement method that combines the primary immune reaction between antigen and antibody with the sandwich method of polyclonal antibody (pAb)-conjugated horseradish peroxidase (HRP). In the second step, fluorescence is enhanced by the mechanical pressure from the precipitate formed by enzyme catalysis. In order to detect hIgE, the surface of immobilized PDA liposomes was conjugated with monoclonal antibodies against hIgE, and fluorescence signals were detected after the antigen-antibody reaction. In this step, hIgE concentrations as low as 10ng/mL were detected. Fluorescence signals slightly increased when anti-hIgE pAb-HRP was used as an amplifying agent after primary immunoresponse. After secondary immunoresponse, HRP-catalyzed oxidation of 3,3'-diaminobenzidine produced an insoluble precipitate that strongly stimulated PDA liposomes by their weight and pressure, thereby dramatically increasing the fluorescence signal. Thus, PDA liposome immunosensor could detect hIgE concentrations as low as 0.01ng/mL, representing a 1000-fold increase in sensitivity over the signal generated by the primary immunoresponse. This study indicates that increasing the external mechanical force applied to PDA liposomes by enzyme-catalyzed precipitate formation enhanced the sensitivity of the PDA liposome immunosensor chip. This strategy can be applied to the detection of other biomolecules in experimental or clinical settings where ultrasensitive and highly specific biosensing is required. PMID:24907539
Lee, Jong Uk; Jeong, Ji Hoon; Lee, Doo Sung; Sim, Sang Jun
Optimization of the enzyme-catalyzed synthesis of amino acid-based surfactants from palm oil fractions.
The feasibility of using palm oil fractions as cheap and abundant sources of raw material for the synthesis of amino acid surfactants was investigated. Of a number of enzymes screened, the best results were obtained with the immobilized enzyme, Lipozyme. The effects of temperature, solvent, incubation period, fatty substrate/amino acid molar ratio, enzyme amount, and water removal on the reactions were analyzed and compared to those on reactions with free fatty acids and pure triglycerides as fatty substrates. All reactions were most efficient when carried out at high temperatures (70-80 degrees C) in hexane as a solvent. However, while reactions with free fatty acids proceeded better when a slight excess of the free fatty acids over the amino acids was used, reactions with triglycerides and palm oil fractions were best performed at equimolar ratios. Also, the addition of molecular sieves slightly enhanced reactions with free fatty acids but adversely affected reactions with triglycerides and palm oil fractions. Although reactions with palm oil fractions took longer (6 d) to reach equilibrium compared to reactions with free fatty acids (4 d) and pure triglycerides (4 d), better yields were obtained. Such lipase-catalyzed transacylation of palm oil fractions with amino acids is potentially useful in the production of mixed medium- to long-chain surfactants for specific applications. PMID:16233420
Soo, Ee Lin; Salleh, Abu Bakar; Basri, Mahiran; Zaliha Raja Abdul Rahman, Raja Noor; Kamaruddin, Kamarulzaman
Rapid sampling of multiple enzyme reactions.
A simple method of initiating and sampling six simultaneous reactions was devised. A commercially available vial rack was fitted with a Plexiglas overlaying sheet to stabilize the vials for the addition and sampling procedures. Glass vials were routinely used because of their thermal conductivity advantages. Samples were added and removed, and the reactions were mixed with a multichannel pipet using every other channel. The data showing six simultaneous progress curves for the rapid inactivation of herpes simplex virus ribonucleotide reductase were presented and analyzed. In addition, the time course of 12 reactions catalyzed by varicella zoster virus thymidine kinase were assayed at one min intervals generating 96 data points within 8.5 min. A second experiment generated data points every 30 s for six simultaneous replicate thymidine kinase reactions. The ease of use and high reproducibility of the method are demonstrated by these data. PMID:2559105
Spector, T; Harrington, J A
Gold-catalyzed cyclization reactions of allenol and alkynol derivatives.
Although gold is chemically inert as a bulk metal, the landmark discovery that gold nanoparticles can be effective catalysts has opened up new and exciting research opportunities in the field. In recent years, there has been growth in the number of reactions catalyzed by gold complexes [gold(I) and gold(III)], usually as homogeneous catalysts, because they are soft Lewis acids. In addition, alkynes and allenes have interesting reactivities and selectivities, notably their ability to produce complex structures in very few steps. In this Account, we describe our work in gold catalysis with a focus on the formation of C-C and C-O bonds using allenes and alkynes as starting materials. Of these, oxa- and carbo-cyclizations are perhaps the best known and most frequently studied. We have divided those contributions into sections arranged according to the nature of the starting material (allene versus alkyne). Gold-catalyzed carbocyclizations in allenyl C2-linked indoles, allenyl-?-lactams, and allenyl sugars follow different mechanistic pathways. The cyclization of indole-tethered allenols results in the efficient synthesis of carbazole derivatives, for example. However, the compound produced from gold-catalyzed 9-endo carbocyclization of (aryloxy)allenyl-tethered 2-azetidinones is in noticeable contrast to the 5-exo hydroalkylation product that results from allenyl sugars. We have illustrated the unusual preference for the 4-exo-dig cyclization in allene chemistry, as well as the rare ?-hydride elimination reaction, in gold catalysis from readily available ?-allenols. We have also observed in ?-allenols that a (methoxymethyl)oxy protecting group not only masks a hydroxyl functionality but also exerts directing effects as a controlling unit in a gold-catalyzed regioselectivity reversal. Our recent work has also led to a combined experimental and computational study on regioselective gold-catalyzed synthetic routes to 1,3-oxazinan-2-ones (kinetically controlled products) and 1,3-oxazin-2-one derivatives (thermodynamically favored) from easily accessible allenic carbamates. In addition, we discuss the direct gold-catalyzed cycloketalization of alkynyldioxolanes, as well as aminoketalization of alkynyloxazolidines. We performed labeling studies and density functional calculations to gain insight into the mechanisms of the bis-heterocyclization reactions. We also describe the controlled gold-catalyzed reactions of primary and secondary propargylic hydroperoxides with a variety of nucleophiles including alcohols and phenols, allowing the direct synthesis of ?-functionalized ketones. Through computations and (18)O-labeling experiments, we discovered various aspects of the controlled reactivity of propargylic hydroperoxides with external nucleophiles under gold catalysis. The mechanism resembles a Meyer-Schuster rearrangement, but notably, the presence and geometry characteristics of the OOH functional group allow a new pathway to happen, which cannot apply to propargylic alcohols. PMID:24428670
Alcaide, Benito; Almendros, Pedro
Engineering entropy-driven reactions and networks catalyzed by DNA.
Artificial biochemical circuits are likely to play as large a role in biological engineering as electrical circuits have played in the engineering of electromechanical devices. Toward that end, nucleic acids provide a designable substrate for the regulation of biochemical reactions. However, it has been difficult to incorporate signal amplification components. We introduce a design strategy that allows a specified input oligonucleotide to catalyze the release of a specified output oligonucleotide, which in turn can serve as a catalyst for other reactions. This reaction, which is driven forward by the configurational entropy of the released molecule, provides an amplifying circuit element that is simple, fast, modular, composable, and robust. We have constructed and characterized several circuits that amplify nucleic acid signals, including a feedforward cascade with quadratic kinetics and a positive feedback circuit with exponential growth kinetics. PMID:18006742
Zhang, David Yu; Turberfield, Andrew J; Yurke, Bernard; Winfree, Erik
A Paradigm for Enzyme-Catalyzed Proton Transfer at Carbon: Triosephosphate Isomerase
Triosephosphate isomerase (TIM) catalyzes the stereospecific 1,2-proton shift at dihydroxyacetone phosphate (DHAP) to give (R)-glyceraldehyde 3-phosphate through a pair of isomeric enzyme-bound cis-enediolate phosphate intermediates. The chemical transformations that occur at the active site of TIM were well understood by the early 1990s. The mechanism for enzyme-catalyzed isomerization is similar to that for the nonenzymatic reaction in water, but the origin of the catalytic rate acceleration is not understood. We review the results of experimental work which show that a substantial fraction of the large 12 kcal/mol intrinsic binding energy of the non-reacting phosphodianion fragment of TIM is utilized to activate the active site side chains for catalysis of proton transfer. Evidence is presented that this activation is due to a phosphodianion driven conformational change, the most dramatic feature of which is closure of loop 6 over the dianion. The kinetic data are interpreted within the framework of a model where activation is due to the stabilization by the phosphodianion of a rare, desolvated, loop closed form of TIM. The dianion binding energy is proposed to drive the otherwise thermodynamically unfavorable desolvation of the solvent-exposed active site. This reduces the effective local dielectric constant of the active site, in order to enhance stabilizing electrostatic interactions between polar groups and the anionic transition state; and, increases the basicity of the carboxylate side chain of Glu-165 that functions to deprotonate the bound carbon acid substrate. A rebuttal is presented to the recent proposal [Samanta, M., Murthy, M. R. N., Balaram, H., and Balaram, P. (2011) Chembiochem 12, 1886¢1895] that the cationic side chain of K12 functions as an active site electrophile to protonate the carbonyl oxygen of DHAP.
Richard, John P.
Mechanism of maltal hydration catalyzed by. beta. -amylase: Role of protein structure in controlling the steric outcome of reactions catalyzed by a glycosylase
Crystalline (monomeric) soybean and (tetrameric) sweet potato {beta}-amylase were shown to catalyze the cis hydration of maltal ({alpha}-D-glucopyranosyl-2-deoxy-D-arabino-hex-1-enitol) to form {beta}-2-deoxymaltose. As reported earlier with the sweet potato enzyme, maltal hydration in D{sub 2}O by soybean {beta}-amylase was found to exhibit an unusually large solvent deuterium kinetic isotope effect (V{sub H}/V{sub D}=6.5), a reaction rate linearly dependent on the mole fraction of deuterium, and 2-deoxy-(2(a)-{sup 2}H)maltose as product. These results indicate (for each {beta}-amylase) that protonation is the rate-limiting step in a reaction involving a nearly symmetric one-proton transition state and that maltal is specifically protonated from above the double bond. That maltal undergoes cis hydration provides evidence in support of a general-acid-catalyzed, carbonium ion mediated reaction. Of fundamental significance is that {beta}-amylase protonates maltal from a direction opposite that assumed for protonating strach, yet creates products of the same anomeric configuration from both. Such stereochemical dichotomy argues for the overriding role of protein structures is dictating the steric outcome of reactions catalyzed by a glycosylase, by limiting the approach and orientation of water or other acceptors to the reaction center.
Kitahata, Sumio (Osaka Municipal Technical Research Inst. (Japan)); Chiba, S. (Hokkaido Univ. (Japan)); Brewer, C.F.; Hehre, E.J. (Albert Einstein Coll. of Medicine, Bronx, NY (United States))
Probing the Regiospecificity of Enzyme-Catalyzed Steroid Glycosylation
The potential of a uniquely permissive engineered glycosyltransferase (OleD ASP) as a catalyst for steroid glycosylation is highlighted. The ability of OleD ASP to glucosylate a range of cardenolides and bufadienolides was assessed using a rapid LC-UV/MS-SPE-NMR analytical platform. While a bias toward OleD-catalyzed C3 mono-glucosylation was observed, subtle alterations of the steroidal architecture in some cases, invoked diglucosylation or, in one case (digoxigenin), C12 glucosylation. This latter case represents the first, and highly efficient, synthesis of digoxigenin 12-O-?-D-glucoside.
Zhou, Maoquan; Hou, Yanpeng; Hamza, Adel; Zhan, Chang-Guo; Bugni, Tim S.; Thorson, Jon S.
The Enzyme-Catalyzed Synthesis of Sucrose from Starch.
National Technical Information Service (NTIS)
The most abundant food sugar is sucrose and world demand for sucrose and other sweeteners has outstripped production. Commercial processes have been developed for enzymic production of glucose-fructose mixtures from cornstarch. This report very briefly de...
S. J. Kelly L. G. Butler R. G. Squires
Electrostatic effects on the rates of DNA-catalyzed reactions
Diol-epoxide metabolites of many genotoxic polycyclic aromatic hydrocarbons are hydrolyzed to tetraols in a detoxification reaction. The hydrolysis reaction has both spontaneous and acid-catalyzed components; moreover, the reaction rate increases in the presence of DNA. The best studied of these diol epoxide metabolites are the trans 7,8 diol-9,10 epoxides of benzo[a]pyrene: anti-BPDE, the proximate carcinogen, in which the oxirane ring is anti with respect to the 7-hydroxyl group, and its syn diastereomer, syn-BPDE. Jerina and coworkers have studied the kinetics of the hydrolysis of syn- and anti-BPDE as a function of pH and DNA concentration and have measured the equilibrium constant for the formation of a noncovalent complex with DNA. They constructed a two-state model in which the diol epoxide is either free or statically bound: the free fraction is hydrolyzed with the same kinetics as it exhibits in solution without DNA; the bound diol epoxide reacts at faster rates. In this model, the dependence of the observed hydrolysis rates on both DNA concentration and pH is explained by using the rate constants, k0 and kH, for reactions of the free diol epoxide, the rate constants, kcat0 and kcatH, for the bound molecule, and the binding constant, Keq. The present work uses an acidic-domain interpretation of the two-state model to explain the catalytic effect of DNA on the acid-catalyzed hydrolysis of syn- and anti-BPDE. Postulating that the rate enhancement is a result of acidic domains at the DNA surface, we assumed the relationship k catH = k H [H +] b, where [H +] b is the hydrogen ion concentration near the bound molecule. Using numerical solutions to the Poisson-Boltzmann equation, the pH dependence of acidic domains at the surface of the polyelectrolyte, DNA, was calculated. Energy-minimization calculations were used to estimate the conformations of diol epoxide-DNA intercalation complexes. Poisson-Boltzmann (PB) calculations on these structures yielded hydrogen-ion concentrations near the epoxide group consistent with the k catH/k H ratio over a range of added-salt concentrations. The results strongly suggest that DNA catalysis of diol-epoxide hydrolysis is a polyelectrolyte effect. The mechanisms and rate constants observed for the acid-catalyzed hydrolysis in the absence of DNA are consistent with the increase in the rate constant induced by DNA. It may be concluded that the catalysis is primarily an effect of the acidic domains in the surface grooves of the nucleic acid.
Pack, George R.; Wong, Linda
Enzyme Reactions in Nanoporous, Picoliter Volume Containers
Advancements in nanoscale fabrication allow creation of small volume reaction containers that can facilitate the screening and characterization of enzymes. A porous, ~19 pL volume vessel has been used in this work to carry out enzyme reactions under varying substrate concentrations. Assessment of small molecule and Green Fluorescent Protein diffusion from the vessels indicates that pore sizes on order of 10 nm can be obtained, allowing capture of proteins and diffusive exchange of small molecules. Glucose oxidase and horseradish peroxidase can be contained in these structures and diffusively fed with a solution containing glucose and the fluorogenic substrate Amplex RedÖ through the engineered nanoscale pore structure. Fluorescent microscopy was used to monitor the reaction, which was carried out under microfluidic control. Kinetic characteristics of the enzyme (Km and Vmax) were evaluated and compared with results from conventional scale reactions. These picoliter, nanoporous containers can facilitate quick determination of enzyme kinetics in microfluidic systems without the requirement of surface tethering and can be used for applications in drug discovery, clinical diagnostics and high-throughput screening.
Siuti, Piro; Retterer, Scott T.; Choi, Chang-Kyoung; Doktycz, Mitchel J.
Utilization of peroxide and its relevance in oxygen insertion reactions catalyzed by chloroperoxidase
Chloroperoxidase (CPO) catalyzed oxygen insertions are highly enantioselective and hence of immense biotechnological potential. A peroxide activation step is required to give rise to the compound I species that catalyzes this chiral reaction. A side reaction, a catalase type peroxide dismutation, is another feature of CPOÆs versatility. This work systematically investigates the utilization of different peroxides for the two reactions,
Kelath Murali Manoj; Lowell P. Hager
Acid-catalyzed reactions of hexanal on sulfuric acid particles: Identification of reaction products
While it is well established that organics compose a large fraction of the atmospheric aerosol mass, the mechanisms through which organics are incorporated into atmospheric aerosols are not well understood. Acid-catalyzed reactions of compounds with carbonyl groups have recently been suggested as important pathways for transfer of volatile organics into acidic aerosols. In the present study, we use the aerodyne
Rebecca M. Garland; Matthew J. Elrod; Kristi Kincaid; Melinda R. Beaver; Jose L. Jimenez; Margaret A. Tolbert
Synthesis of eugenol esters by lipase-catalyzed reaction in solvent-free system.
Enzymatic esterification of eugenol is a matter of great scientific and technological interest due to the well-known drawbacks of the chemical-catalyzed route as well as the potential use of produced compounds as natural antimicrobials. This work reports the maximization of eugenil acetate production by esterification of eugenol and acetic anhydride in a solvent-free system using Novozym 435 as catalyst. The antimicrobial activity of eugenol and eugenil acetate was also determined. The operating conditions that maximized eugenil acetate production were 50 ░C, eugenol to acetic anhydride of 1:3, 150 rpm, and 5.5 wt% of enzyme, with a conversion of 99 %. A kinetic study was performed to assess the influence of substrates molar ratio, enzyme concentration, and temperature on eugenil acetate yield. Results show that an excess of anhydride, low enzyme concentration (1 wt%), and 60 ░C afforded nearly complete conversion after 6 h of reaction. The highest antimicrobial activity of eugenil acetate was observed against Acinetobacter sp. (48.66 mm) at concentration of 20 ?L. Results indicate that the esterification of eugenol improved its antimicrobial properties. New experimental data on enzymatic esterification of eugenol and acetic anhydride are reported in this work, showing a promising perspective to overcome the inconvenient of the chemical-catalyzed route for obtaining antimicrobial natural compounds. PMID:22864649
Chiaradia, V; Paroul, N; Cansian, R L; J·nior, C V; Detofol, M R; Lerin, L A; Oliveira, J Vladimir; Oliveira, D
Acid-catalyzed Heterogeneous Reactions in SOA Formation
The importance of heterogeneous reactions in secondary organic aerosol (SOA) formation has recently excited a great deal of interest in the aerosol community. Jang and Kamens (2001) showed enhanced aerosol yield from aldehydes, which can be produced by atmospheric photochemical reactions, in the presence of acidic seed. They suggest that the carbonyl functional groups of the aldehydes further react in the aerosol phase via hydration, polymerization, and hemiacetal/acetal formation with alcohols at an accelerated rate in the presence of acid. Jang et al. (2003) demonstrated similar results using a flow reactor and Czoschke et al. (in press) qualitatively showed increased yields for isoprene and alpha-pinene ozonolysis in the presence of acidic seed. While these findings are intriguing and important, the conditions under which the experiments were carried out were atmospherically unrealistic. A series of SOA formation experiments have been carried out in the Caltech Indoor Chamber Facility, which is comprised of dual 28 m3 FEP Teflon chambers, with the flexibility to carry out both dark ozonolysis and photochemical OH oxidation reactions. Cycloheptene and alpha-pinene were oxidized in the presence of neutral seed under dry (<10% RH) and humid (50% RH) conditions and in the presence of acidic seed under humid (50% RH) conditions. The SOA yields for these experiments will be presented, and the extent of the influence of acid-catalyzed reactions on SOA yield will be discussed. Reference List 1. Cocker, D. R. III. and R. C. Flagan and J. H. Seinfeld, State-of-the-art chamber facility for studying atmospheric aerosol chemistry, Environmental Science and Technology, 35, 2594-2601, 2001. 2. Czoschke, N. M., M. Jang, and R. M. Kamens, Effect of acid seed on biogenic sceondary organic aerosol growth, Atmospheric Environment, In press. 3. Jang, M., S. Lee, and R. M. Kamens, Organic aerosol growth by acid-catalyzed heterogeneous reactions of octanal in a flow reactor, Atmospheric Environment, 37, 2125-2138, 2003. 4. Jang, M. S. and R. M Kamens, Atmospheric secondary aerosol formation by heterogeneous reactions of aldehydes in the presence of a sulfuric acid aerosol catalyst. Environmental Science and Technology, 35, 4758-4766,2001.
Ng, N.; Keywood, M.; Varutbangkul, V.; Gao, S.; Loewer, E.; Surratt, J.; Richard, F. C.; John, S. H.
Quantitative Comparison of Catalytic Mechanisms and Overall Reactions in Convergently Evolved Enzymes: Implications for Classification of Enzyme Function
Functionally analogous enzymes are those that catalyze similar reactions on similar substrates but do not share common ancestry, providing a window on the different structural strategies nature has used to evolve required catalysts. Identification and use of this information to improve reaction classification and computational annotation of enzymes newly discovered in the genome projects would benefit from systematic determination of reaction similarities. Here, we quantified similarity in bond changes for overall reactions and catalytic mechanisms for 95 pairs of functionally analogous enzymes (non-homologous enzymes with identical first three numbers of their EC codes) from the MACiE database. Similarity of overall reactions was computed by comparing the sets of bond changes in the transformations from substrates to products. For similarity of mechanisms, sets of bond changes occurring in each mechanistic step were compared; these similarities were then used to guide global and local alignments of mechanistic steps. Using this metric, only 44% of pairs of functionally analogous enzymes in the dataset had significantly similar overall reactions. For these enzymes, convergence to the same mechanism occurred in 33% of cases, with most pairs having at least one identical mechanistic step. Using our metric, overall reaction similarity serves as an upper bound for mechanistic similarity in functional analogs. For example, the four carbon-oxygen lyases acting on phosphates (EC 4.2.3) show neither significant overall reaction similarity nor significant mechanistic similarity. By contrast, the three carboxylic-ester hydrolases (EC 3.1.1) catalyze overall reactions with identical bond changes and have converged to almost identical mechanisms. The large proportion of enzyme pairs that do not show significant overall reaction similarity (56%) suggests that at least for the functionally analogous enzymes studied here, more stringent criteria could be used to refine definitions of EC sub-subclasses for improved discrimination in their classification of enzyme reactions. The results also indicate that mechanistic convergence of reaction steps is widespread, suggesting that quantitative measurement of mechanistic similarity can inform approaches for functional annotation.
Almonacid, Daniel E.; Yera, Emmanuel R.; Mitchell, John B. O.; Babbitt, Patricia C.
Diversity synthesis using the complimentary reactivity of rhodium(II)- and palladium(II)-catalyzed reactions.
Rhodium(II)-catalyzed reactions of aryldiazoacetates can be conducted in the presence of iodide, triflate, organoboron, and organostannane functionality, resulting in the formation of a variety of cyclopropanes or C-H insertion products with high stereoselectivity. The combination of the rhodium(II)-catalyzed reaction with a subsequent palladium(II)-catalyzed Suzuki coupling offers a novel strategy for diversity synthesis. PMID:16839138
Ni, Aiwu; France, Jessica E; Davies, Huw M L
A unifying kinetic framework for modeling oxidoreductase-catalyzed reactions
Motivation: Oxidoreductases are a fundamental class of enzymes responsible for the catalysis of oxidation¢reduction reactions, crucial in most bioenergetic metabolic pathways. From their common root in the ancient prebiotic environment, oxidoreductases have evolved into diverse and elaborate protein structures with specific kinetic properties and mechanisms adapted to their individual functional roles and environmental conditions. While accurate kinetic modeling of oxidoreductases is thus important, current models suffer from limitations to the steady-state domain, lack empirical validation or are too specialized to a single system or set of conditions. Results: To address these limitations, we introduce a novel unifying modeling framework for kinetic descriptions of oxidoreductases. The framework is based on a set of seven elementary reactions that (i) form the basis for 69 pairs of enzyme state transitions for encoding various specific microscopic intra-enzyme reaction networks (micro-models), and (ii) lead to various specific macroscopic steady-state kinetic equations (macro-models) via thermodynamic assumptions. Thus, a synergistic bridge between the micro and macro kinetics can be achieved, enabling us to extract unitary rate constants, simulate reaction variance and validate the micro-models using steady-state empirical data. To help facilitate the application of this framework, we make available RedoxMech: a MathematicaÖ software package that automates the generation and customization of micro-models. Availability: The MathematicaÖ source code for RedoxMech, the documentation and the experimental datasets are all available from: http://www.igb.uci.edu/tools/sb/metabolic-modeling. Contact: firstname.lastname@example.com Supplementary information: Supplementary data are available at Bioinformatics online.
Chang, Ivan; Baldi, Pierre
The isolation and characterization of a rhodacycle intermediate implicated in metal-catalyzed reactions of alkylidenecyclopropanes.
The isolation and characterization of a rhodacycle intermediate implicated in rhodium-catalyzed reactions of alkylidenecyclopropanes (ACPs) is described. The structure of the metallacycle was unambiguously determined by X-ray crystallography and is catalytically competent in the rhodium-catalyzed carbocyclization and ene-cycloisomerization reactions of ACPs. This work represents a rare example of the isolation of a metallacycle in a metal-catalyzed higher-order carbocyclization reaction and thereby provides important insight into the ligand requirements for the insertion of ?-components. Furthermore, it serves as a convenient synthon for the development of challenging higher-order carbocyclization reactions, as exemplified by the reaction with an activated allene. PMID:24616050
Inglesby, Phillip A; Bacsa, John; Negru, Daniela E; Evans, P Andrew
Pd/C catalyzed Suzuki-Miyaura cross coupling reaction: Is it heterogeneous or homogeneous?
The Suzuki-Miyaura cross-coupling reaction is a popular industrial method of creating covalent bonds between two carbons. This reaction can be catalyzed by a myriad of palladium catalyst including heterogeneous and homogeneous. The objective of this research is to study whether the Suzuki cross coupling reaction catalyzed by solid supported palladium catalysts is truly heterogeneous in nature (i.e. does the reaction occurs on the surface of the catalyst or does palladium leach from the solid support and catalyze the reaction in a homogenous manner).
Hoang, Tony Phuc
Trapping of an intermediate in the reaction catalyzed by flavin-dependent thymidylate synthase.
Thymidylate is a DNA nucleotide that is essential to all organisms and is synthesized by the enzyme thymidylate synthase (TSase). Several human pathogens rely on an alternative flavin-dependent thymidylate synthase (FDTS), which differs from the human TSase both in structure and molecular mechanism. It has recently been shown that FDTS catalysis does not rely on an enzymatic nucleophile and that the proposed reaction intermediates are not covalently bound to the enzyme during catalysis, an important distinction from the human TSase. Here we report the chemical trapping, isolation, and identification of a derivative of such an intermediate in the FDTS-catalyzed reaction. The chemically modified reaction intermediate is consistent with currently proposed FDTS mechanisms that do not involve an enzymatic nucleophile, and it has never been observed during any other TSase reaction. These findings establish the timing of the methylene transfer during FDTS catalysis. The presented methodology provides an important experimental tool for further studies of FDTS, which may assist efforts directed toward the rational design of inhibitors as leads for future antibiotics. PMID:22295882
Mishanina, Tatiana V; Koehn, Eric M; Conrad, John A; Palfey, Bruce A; Lesley, Scott A; Kohen, Amnon
Trapping of an intermediate in the reaction catalyzed by flavin-dependent thymidylate synthase (FDTS)
Thymidylate is a DNA nucleotide that is essential to all organisms and is synthesized by the enzyme thymidylate synthase (TSase). Several human pathogens rely on an alternative flavin-dependent thymidylate synthase (FDTS), which differs from the human TSase both in structure and molecular mechanism. Recently it has been shown that FDTS catalysis does not rely on an enzymatic nucleophile and the proposed reaction intermediates are not covalently bound to the enzyme during catalysis, an important distinction from the human TSase. Here we report the chemical trapping, isolation, and identification of a derivative of such an intermediate in the FDTS-catalyzed reaction. The chemically modified reaction intermediate is consistent with currently proposed FDTS mechanisms that do not involve an enzymatic nucleophile, and has never been observed during any other TSase reaction. These findings establish the timing of the methylene transfer during FDTS catalysis. The presented methodology provides an important experimental tool for further studies of FDTS, which may assist the efforts to rationally design inhibitors as leads for future antibiotics.
Mishanina, Tatiana V.; Koehn, Eric M.; Conrad, John A.; Palfey, Bruce A.; Lesley, Scott A.
Enzyme-catalyzed acylation of homoserine: mechanistic characterization of the Escherichia coli metA-encoded homoserine transsuccinylase.
The first unique step in bacterial and plant methionine biosynthesis involves the activation of the gamma-hydroxyl of homoserine. In Escherichia coli, this activation is accomplished via a succinylation reaction catalyzed by homoserine transsuccinylase. The activity of this enzyme is closely regulated in vivo and therefore represents a critical control point for cell growth and viability. We have cloned homoserine transsuccinylase from E. coli and present the first detailed enzymatic study of this enzyme. Steady-state kinetic experiments demonstrate that the enzyme utilizes a ping-pong kinetic mechanism in which the succinyl group of succinyl-CoA is initially transferred to an enzyme nucleophile before subsequent transfer to homoserine to form the final product, O-succinylhomoserine. The maximal velocity, V/K(succinyl)(-)(CoA), and V/K(homoserine) all exhibited a bell-shaped pH dependence with apparent pK's of 6.6 and approximately 7.9. The enzyme was inhibited by iodoacetamide in a pH-dependent manner, with an apparent pK of the group being inactivated of 6.4. This suggests the presence of an active site cysteine which forms a succinyl-cysteine intermediate during enzymatic turnover. Solvent kinetic isotope effect studies yielded inverse effects of 0.7 on V and 0.61 on V/K in the reverse reaction only. On the basis of these observations, we propose a detailed chemical mechanism for this important member of the acyltransferase family. PMID:10572016
Born, T L; Blanchard, J S
Nanoparticle-catalyzed reductive bleaching for fabricating turn-off and enzyme-free amplified colorimetric bioassays.
Nanoparticle-catalyzed reductive bleaching reactions of colored substrates are emerging as a class of novel indicator reactions for fabricating enzyme-free amplified colorimetric biosensing (turn-off mode), which are exactly opposite to the commonly used oxidative coloring processes of colorless substrates in traditional enzyme-catalyzed amplified colorimetric bioassays (turn-on mode). In this work, a simple theoretical analysis shows that the sensitivity of this colorimetric bioassay can be improved by increasing the amplification factor (kcat?t), or enhancing the binding affinity between analyte and receptor (Kd), or selecting the colored substrates with high extinction coefficients (?). Based on this novel strategy, we have developed a turn-off and cost-effective amplified colorimetric thrombin aptasensor. This aptasensor made full use of sandwich binding of two affinity aptamers for increased specificity, magnetic particles for easy separation and enrichment, and gold nanoparticle (AuNP)-catalyzed reductive bleaching reaction to generate the amplified colorimetric signal. With 4-nitrophenol (4-NP) as the non-dye colored substrate, colorimetric bioassay of thrombin was achieved by the endpoint method with a detection limit of 91pM. In particular, when using methylene blue (MB) as the substrate, for the first time, a more convenient and efficient kinetic-based colorimetric thrombin bioassay was achieved without the steps of acidification termination and magnetic removal of particles, with a low detection limit of 10pM, which was superior to the majority of the existing colorimetric thrombin aptasensors. The proposed colorimetric protocol is expected to hold great promise in field analysis and point-of-care applications. PMID:23962710
Li, Wei; Qiang, Weibing; Li, Jie; Li, Hui; Dong, Yifan; Zhao, Yaju; Xu, Danke
[Organophosphorus compounds: classification and enzyme reactions].
Organophosphorus compounds are derivatives of phosphoric, phosphonic or phosphinic acids whose oxygen atoms bound directly to the phosphorus atom can be substituted by sulphur or nitrogen atoms. These compounds represent a large group of organic compounds used primarily as pesticides. Some are used as drugs and the most toxic compounds as nerve agents. Acute toxicity of organophosphorus compounds is due to the inhibition of acetylcholinesterase, the critical enzyme in neurotransmission. Organophosphorus compounds whose sulphur atom creates a coordinative covalent bond with the phosphor atom are not acetylcholinesterase inhibitors. To become biologically active these compounds must transform into their oxo analogues, passing through spontaneous or biotransformation reactions. Biotransformation reactions of organophosphorus compounds involve a large number of enzymatic reactions that can make them more or less toxic, or even non-toxic for acetylcholinesterase. The classification of organophosphorus compounds in this paper considers the nature of groups bound directly to the central phosphorus atom. The paper describes the enzymes taking part in biotransformation of organophosphorus compounds and gives examples of their reactions. PMID:17265684
Bosak, Anita
Gold-catalyzed reactions of 2-alkynyl-phenylamines with alpha,beta-enones.
[reaction: see text] The gold-catalyzed reaction of 2-alkynyl-phenylamines with alpha,beta-enones represents a new general one-pot entry into C-3-alkyl-indoles by sequential reactions. Gold-catalyzed sequential cyclization/alkylation, N-alkylation/cyclization, or N-alkylation/cyclization/alkylation reactions leading to different indoles can be directed by changing the 2-alkynyl-phenylamine 1/alpha,beta-enone 3 ratio and the reaction temperature. Unusual gold-catalyzed rearrangement reaction of indoles are observed at 140 degrees C. New gold-catalyzed formation of propargyl-alkyl ether under mild conditions and the hydration reaction of N-acetyl-2-ethynyl-phenylamine are reported. PMID:15760214
Alfonsi, Maria; Arcadi, Antonio; Aschi, Massimiliano; Bianchi, Gabriele; Marinelli, Fabio
Activation Energies for an Enzyme-Catalyzed and Acid-Catalyzed Hydrolysis: An Introductory Interdisciplinary Experiment for Chemists and Biochemists.
Background information, procedures used, and typical results obtained are provided for an experiment in which students determine and compare the Arrhenius activation energies (Ea) for the hydrolysis of salicin. This reaction is subject to catalysis both by acid and by the enzyme emulsin (beta-d-glucoside glycohydrolase). (JN)
Adams, K. R.; Meyers, M. B.
Separation of the two reactions, oxidation and isomerization, catalyzed by Streptomyces cholesterol oxidase.
Site-directed mutagenesis was used to identify key amino acid residues of the cholesterol oxidase from Streptomyces sp., which catalyzes the oxidation of cholesterol and the isomerization of 5-cholesten-3-one. Eight mutant enzymes were constructed and the following amino acid substitutions were identified: N318A, N318H, E356A, E356D, H441A, H441N, N480A and N480Q. Mutants N318A and N318H retained both oxidation and isomerization activities. The mutant E356D retained oxidation but not isomerization activity. On the other hand, mutants N480A and N480Q showed no oxidation activity but retained their isomerization activities. The two catalytic reactions, oxidation and isomerization, in cholesterol oxidase were thus successfully separated. When the H441A or H441N mutation was introduced, both the oxidase and isomerase activities were completely lost. The H441, E356 and N480 residues thus appear to participate in the catalysis of cholesterol oxidase, whereas N318 does not. An analysis of the products of these mutant enzymes suggested that the previously proposed 6-hydroxylation reaction by cholesterol oxidase is actually autooxidation from 5-cholesten-3-one. Kinetic studies of the purified wild-type and mutant enzymes showed that the k(cat)/Km values for oxidation in E356D and for isomerization in N480A increased six- and threefold, respectively, over those in the wild-type. These mutational effects and the reaction mechanisms are discussed in terms of the three-dimensional structure of the enzyme constructed on the basis of homology modeling. PMID:9876929
Yamashita, M; Toyama, M; Ono, H; Fujii, I; Hirayama, N; Murooka, Y
Phospholipid:diacylglycerol acyltransferase: An enzyme that catalyzes the acyl-CoA-independent formation of triacylglycerol in yeast and plants
Triacylglycerol (TAG) is known to be synthesized in a reaction that uses acyl-CoA as acyl donor and diacylglycerol (DAG) as acceptor, and which is catalyzed by the enzyme acyl-CoA:diacylglycerol acyltransferase. We have found that some plants and yeast also have an acyl-CoA-independent mechanism for TAG synthesis, which uses phospholipids as acyl donors and DAG as acceptor. This reaction is catalyzed by an enzyme that we call phospholipid:diacylglycerol acyltransferase, or PDAT. PDAT was characterized in microsomal preparations from three different oil seeds: sunflower, castor bean, and Crepis palaestina. We found that the specificity of the enzyme for the acyl group in the phospholipid varies between these species. Thus, C. palaestina PDAT preferentially incorporates vernoloyl groups into TAG, whereas PDAT from castor bean incorporates both ricinoleoyl and vernoloyl groups. We further found that PDAT activity also is present in yeast microsomes. The substrate specificity of this PDAT depends on the head group of the acyl donor, the acyl group transferred, and the acyl chains of the acceptor DAG. The gene encoding the enzyme was identified. The encoded PDAT protein is related to lecithin:cholesterol acyltransferase, which catalyzes the acyl-CoA-independent synthesis of cholesterol esters. However, budding yeast PDAT and its relatives in fission yeast and Arabidopsis form a distinct branch within this protein superfamily, indicating that a separate PDAT enzyme arose at an early point in evolution.
Dahlqvist, Anders; Stahl, Ulf; Lenman, Marit; Banas, Antoni; Lee, Michael; Sandager, Line; Ronne, Hans; Stymne, Sten
Exploring chain length selectivity in HIC-catalyzed polycondensation reactions.
Polyester synthesis activity of immobilized Humicola insolens (HiC) was systematically studied with three-series of substrates varying in (i) omega-hydroxyalkanoic acid (omegaHA), (ii) alpha,omega-n-alkane diol, and (iii) alpha,omega-n-alkane diacid chain length. Covalent immobilization of HiC on Amberzyme oxirane (AO) resin (i.e., AO-HiC) was prepared. HiC-AO's activity for omegaHA substrates with 6, 10, 12, and 16 carbons was C16 > C12, where C10-omegaHA and C6-omegaHA were not polymerized. In contrast, N435's activity for omegaHA substrates was C16 = C12 > C10, where C6-omegaHA was not polymerized. HiC-AO activity for copolymerization of sebacic acid (C10-diacid) with alpha,omega-n-alkane diols with 3-, 4-, 5-, 6-, and 8-carbon chain lengths was C8 > C6, where C3, C4, and C5 diols were not polymerized. N435's relative activity for diol substrates was C8 = C6 = C5 > C4 > C3. HiC-AO activity for copolymerizations of 1,8-octanediol with alpha,omega-n-alkane diacids with 6-, 8-, 9-, 10-, and 13-carbon chain lengths was C13 = C10, where HiC showed little activity for C6, C8, and C9 diacid copolymerization. N435 displayed similar activity for all these diacid chain lengths. Thus, N435 has a broader substrate promiscuity than HiC-AO. This is most apparent for shorter chain length omegaHA, diol, and diacid monomers. These trends were similarly observed for a series of small molecule esterification reactions. Comparison of HiC-AO- and N435-catalyzed C16-HA homopolymerization at 8 h gave polymers with M(n) 40.4 and 25.5 kg/mol, respectively. Furthermore, HiC-AO- and N435-catalyzed copolymerization of 1,8-octanediol/C13-diacid polymerizations at 8 h gave polymers with M(n) of 11.0 and 9.6 kg/mol, respectively. PMID:20095578
Feder, David; Gross, Richard A
Adrenodoxin supports reactions catalyzed by microsomal steroidogenic cytochrome P450s
The interaction of adrenodoxin (Adx) and NADPH cytochrome P450 reductase (CPR) with human microsomal steroidogenic cytochrome P450s was studied. It is found that Adx, mitochondrial electron transfer protein, is able to support reactions catalyzed by human microsomal P450s: full length CYP17, truncated CYP17, and truncated CYP21. CPR, but not Adx, supports activity of truncated CYP19. Truncated and the full length CYP17s show distinct preference for electron donor proteins. Truncated CYP17 has higher activity with Adx compared to CPR. The alteration in preference to electron donor does not change product profile for truncated enzymes. The electrostatic contacts play a major role in the interaction of truncated CYP17 with either CPR or Adx. Similarly electrostatic contacts are predominant in the interaction of full length CYP17 with Adx. We speculate that Adx might serve as an alternative electron donor for CYP17 at the conditions of CPR deficiency in human.
Pechurskaya, Tatiana A. [Institute of Bioorganic Chemistry, Academy of Sciences of Belarus, Kuprevicha st., 5/2, Minsk 220141 (Belarus); Harnastai, Ivan N. [Institute of Bioorganic Chemistry, Academy of Sciences of Belarus, Kuprevicha st., 5/2, Minsk 220141 (Belarus); Grabovec, Irina P. [Institute of Bioorganic Chemistry, Academy of Sciences of Belarus, Kuprevicha st., 5/2, Minsk 220141 (Belarus); Gilep, Andrei A. [Institute of Bioorganic Chemistry, Academy of Sciences of Belarus, Kuprevicha st., 5/2, Minsk 220141 (Belarus); Usanov, Sergey A. [Institute of Bioorganic Chemistry, Academy of Sciences of Belarus, Kuprevicha st., 5/2, Minsk 220141 (Belarus)]. E-mail: email@example.com
Entropy is Key to the Formation of Pentacyclic Terpenoids by Enzyme-Catalyzed Polycyclization.
Polycyclizations constitute a cornerstone of chemistry and biology. Multicyclic scaffolds are generated by terpene cyclase enzymes in nature through a carbocationic polycyclization cascade of a prefolded polyisoprene backbone, for which electrostatic stabilization of transient carbocationic species is believed to drive catalysis. Computational studies and site-directed mutagenesis were used to assess the contribution of entropy to the polycyclization cascade catalyzed by the triterpene cyclase from A. acidocaldarius. Our results show that entropy contributes significantly to the rate enhancement through the release of water molecules through specific channels. A single rational point mutation that results in the disruption of one of these water channels decreased the entropic contribution to catalysis by 60?kcal?mol(-1) . This work demonstrates that entropy is the key to enzyme-catalyzed polycyclizations, which are highly relevant in biology since 90?% of all natural products contain a cyclic subunit. PMID:24711227
Syrķn, Per-Olof; Hammer, Stephan C; Claasen, Birgit; Hauer, Bernhard
The dynamic determinants of reaction specificity in the IMPDH/GMPR family of (?/?)8 barrel enzymes
The IMPDH/GMPR family of (?/?)8 enzymes presents an excellent opportunity to investigate how subtle changes in enzyme structure change reaction specificity. IMP dehydrogenase (IMPDH) and GMP reductase (GMPR) bind the same ligands with similar affinities and share a common set of catalytic residues. Both enzymes catalyze a hydride transfer reaction involving a nicotinamide cofactor hydride, and both reactions proceed via the same covalent intermediate. In the case of IMPDH, this intermediate reacts with water while in GMPR it reacts with ammonia. In both cases, the two chemical transformations are separated by a conformational change. In IMPDH, the conformational change involves a mobile protein flap while in GMPR the cofactor moves. Thus reaction specificity is controlled by differences in dynamics, which in turn are controlled by residues outside the active site. These findings have some intriguing implications for the evolution of the IMPDH/GMPR family.
Hedstrom, Lizbeth
Organic reactions catalyzed by methylrhenium trioxide: Reactions of ethyl diazoacetate and organic azides
Methylrhenium trioxide (CH{sub 3}ReO{sub 3} or MTO) catalyzes several classes of reactions of ethyl diazoacetate, EDA. It is the first high valent oxo complex for carbene transfer. Under mild conditions and in the absence of other substrates, EDA was converted to a 9:1 mixture of diethyl maleate and diethyl fumarate. In the presence of alcohols, {alpha}-alkoxy ethyl acetates were obtained in good yield. The yields dropped for the larger and more branched alcohols, the balance of material being diethyl maleate and fumarate. An electron-donating group in the para position of phenols favors the formation of {alpha}-phenoxy ethyl acetates. The use of EDA to form {alpha}-thio ethyl acetates and N-substituted glycine ethyl esters, on the other hand, is hardly affected by the size or structure of the parent thiol or amine, with all of these reactions proceeding in high yield. MTO-catalyzed cycloaddition reactions occur between EDA and aromatic imines, olefins, and carbonyl compounds. Three-membered ring products are formed: aziridines, cyclopropanes, and epoxides, respectively. The reactions favor the formation of trans products, and provide a convenient route for the preparation of aziridines. Intermediate carbenoid and nitrenoid species have been proposed. In the presence of an oxygen source such as an epoxide, ethyl diazoacetate and azibenzil are converted to an oxalic acid monoethyl ester and to benzil; at the same time the epoxide was converted to an olefin. 75 refs., 1 fig., 7 tabs.
Zhu, Z.; Espenson, J.H. [Ames Lab., IA (United States)] [Ames Lab., IA (United States); [Iowa State Univ., Ames, IA (United States)
DNA strand transfer reactions catalyzed by vaccinia topoisomerase: hydrolysis and glycerololysis of the covalent protein-DNA intermediate.
Vaccinia topoisomerase forms a covalent protein-DNA intermediate at sites containing the sequence 5'-CCCTT. The T nucleotide is linked via a 3'-phosphodiester bond to Tyr-274 of the enzyme. Here, we report that the enzyme catalyzes hydrolysis of the covalent intermediate, resulting in formation of a 3'-phosphate-terminated DNA cleavage product. The hydrolysis reaction is pH-dependent (optimum pH = 9.5) and is slower, by a factor of 10(-5), than the rate of topoisomerase-catalyzed strand transfer to a 5'-OH terminated DNA acceptor strand. Mutants of vaccinia topoisomerase containing serine or threonine in lieu of the active site Tyr-274 form no detectable covalent intermediate and catalyze no detectable DNA hydrolysis. This suggests that hydrolysis occurs subsequent to formation of the covalent protein-DNA adduct and not via direct attack by water on DNA. Vaccinia topoisomerase also catalyzes glycerololysis of the covalent intermediate. The rate of glycerololysis is proportional to glycerol concentration and is optimal at pH 9.5.
Petersen, B O; Shuman, S
A unique enzyme from Saccharothrix sp. catalyzing D-amino acid transfer.
A newly isolated actinomycete belonging to Saccharothrix sp. was found to produce a unique enzyme catalyzing D-amino acid transfer. The enzyme, which was tentatively named D-amino acid transferase, was purified 2600-fold to electrophoretic homogeneity and the molecular mass was 41 kDa. The enzyme was D-configuration specific and recognized aromatic D-amino acid esters to form oligo D-amino acid esters. D-Phenylalanine ester was favored as substrate over other D-amino acid esters. The optimum conditions for oligo D-phenylalanine ester formation by D-amino acid transferase were pH 7.0 and 40 degrees C. The enzyme was inhibited by DAN, EPNP and DFP. PMID:9003435
Watanabe, Y; Muro, T; Sugihara, A; Shimada, Y; Nagao, T; Takenishi, S; Tominaga, Y
Accumulation of the Quinonoid Intermediate in the Reaction Catalyzed by Aspartate Aminotransferase with Cysteine Sulfinic Acid
The pyridoxal phosphate form of aspartate aminotransferase from Escherichia coli catalyzes the irreversible conversion of L-cysteine sulfinate to the pyridoxamine phosphate form of the enzyme, bisulfite, and pyruvate. The addition of L-cysteine sulfinate to a solution containing a high concentration of enzyme (?10 ?M) yields a rapidly appearing red color (?max = 520 nm) which decays with a rate constant
N. C. Furumo; J. F. Kirsch
Recent developments in gold-catalyzed cycloaddition reactions
Summary In the last years there have been extraordinary advances in the development of gold-catalyzed cycloaddition processes. In this review we will summarize some of the most remarkable examples, and present the mechanistic rational underlying the transformations.
Mechanistic evaluation of substrate inhibition kinetics observed from aldehyde oxidase-catalyzed reactions.
While most enzyme-catalyzed reactions are adequately described by Michaelis-Menten kinetics, Aldehyde Oxidase (AOX) metabolism might exhibit atypical kinetics due to possible substrate inhibition. Ignoring this phenomenon may lead to erroneous estimates of kinetic parameters and over simplification of the enzyme mechanism. In this study, in vitro metabolism data for 3 AOX substrates exhibiting varying degrees of substrate inhibition were analyzed with the following kinetic models: A) Michaelis-Menten (na've) model; B) Substrate inhibition (empirical) model; and C) Twobinding site (mechanistic) model. The application of this mechanistic model is a novel interpretation for kinetic analysis of AOX metabolism whereby substrate can presumably bind to two enzymes' active site(s). Unlike the other models, this mechanistic model quantitatively captures the degree of substrate inhibition observed. Analysis by this model showed: A) All tested substrates have simultaneous access to the metabolic and inhibitory site of the enzyme with Ks (binding affinity for inhibitory site) greater (1.3- to 28-fold) than Km (binding affinity for metabolic site); B) Dissociation constants for binding of a second substrate in either the productive and nonproductive enzyme conformations decreased with factor ? ranging from 2.58 to 15.6 between compounds; and C) In addition, a drastic decrease (from 64%-98%) in the metabolism rates between compounds was exhibited by factor ? (ranging from 0.02-0.36). Overall, the mechanistic two-binding site model best fitted the experimental data. Moreover, the observed differences between kinetic parameters generated by these models highlight the importance of appropriate model selection to adequately fit the substrate inhibition kinetics of AOX metabolism. PMID:24151826
Wang, Stephen W J; Abdul-Hadi, Kojo; Cohen, Lawrence; Xia, Cindy Q
'Single addition' and 'transnucleotidation' reactions catalyzed by polynucleotide phosphorylase. Effect of enzymatic removal of inorganic phosphate during reaction.
The reaction of the tetranucleotide, pA-A(2)-A, with 2'(3')-0-(alpha-methoxyethyl)uridine 5'-diphosphate, Mg(2+) ions, and M. luteus polynucleotide phosphorylase followed by mild acid treatment to remove the blocking groups results in a 49% yield of the desired single addition product, pA-A(3)-U, together with smaller amounts of pA-A-U, pA-A-A, pA-A(2)-U, pA-A(2)-A, pA-A(3)-A, pA-A(4)-U, and pA-A(4)-A. The side products are thought to arise from the phosphorolysis of the acceptor molecule by the inorganic phosphate formed in the reaction mixture and from subsequent additions to the various oligonucleotide species by the resulting adenosine 5'-diphosphate. A system developed for the removal of inorganic phosphate as it is formed in the synthesis involves the addition to the reaction mixture of calf spleen nucleoside phosphorylase and nicotinamide riboside and, under these conditions, pA-A(3)-U can be prepared in 90% yield with essentially no side products. Under similar conditions, pA-A(3)-A, pA-A(3)-G, and pA-A(3)-C may be prepared from pA-A(2)-A and the appropriate blocked nucleoside diphosphate in yields of 85-94%. The incubation of pA-A(2)-A alone with polynucleotide phosphorylase exhibits the phenomenon of "transnucleotidation" in that the molecule is partially converted to oligonucleotides of smaller and larger chain lengths. In the presence of the phosphate removal system, however, the tetranucleotide is not attacked by the enzyme, and thus, "transnucleotidation" appears to be simply a combination of phosphorolytic and addition reactions catalyzed by trace amounts of inorganic phosphate contaminating the enzyme and/or the substrate. PMID:4281080
Sninsky, J J; Bennett, G N; Gilham, P T
Recent Developments in Pd-Catalyzed Alkene Aminoarylation Reactions for the Synthesis of Nitrogen Heterocycles
This short review describes new developments in Pd-catalyzed aminoarylation reactions between aryl halides and alkenes bearing pendant nitrogen nucleophiles. These transformations provide a novel and powerful method for accessing numerous 3-, 5-, 6-, and 7-membered nitrogen heterocycles.
Schultz, Danielle M.; Wolfe, John P.
Efficient and enantioselective nitroaldol reaction catalyzed by copper Schiff-base complexes
Mild and efficient enantioselective nitroaldol reactions of nitromethane with various aldehydes were catalyzed by chiral copper Schiff-base complexes, which can be readily prepared from amino acid, yielding the corresponding adducts with high yields and good enantiometric excess (ee).
Changsheng Gan; Guoyin Lai; Zuhui Zhang; Zhiyong Wang; Ming-Ming Zhou
N-heterocyclic carbene catalyzed nucleophilic substitution reaction for construction of benzopyrones and benzofuranones.
N-Heterocyclic carbene as an efficient organic catalyst was employed to catalyze an intramolecular nucleophilic substitution reaction. When R(2) was a phenyl group, the cyclization process underwent isomerization, leading to generation of benzofuranone. PMID:16986969
He, Jinmei; Zheng, Jiyue; Liu, Jian; She, Xuegong; Pan, Xinfu
Addition reaction of dialkyl disulfides to terminal alkynes catalyzed by a rhodium complex and trifluoromethanesulfonic acid.
[reaction: see text]. Addition of dialkyl disulfides to terminal alkynes is catalyzed by a rhodium-phosphine complex and trifluoromethanesulfonic acid giving (Z)-bis(alkylthio)olefins stereoselectively. PMID:11259056
Arisawa, M; Yamaguchi, M
EPA Science Inventory
The use of ionic liquids in various synthetic transformations is gaining significance due to the enhanced reaction rates, potential for recycling and compatibility with various organic compounds and organometallic catalysts. Palladium-catalyzed oxidation of styrene and other alk...
Mechanistic insight into transition metal-catalyzed reaction of enynal/enynone with alkenes: metal-dependent reaction pathway.
A systematic study of the transition metal-catalyzed reaction of enynal/enynone with alkenes has been reported. It was found that the reaction has two metal-dependent reaction pathways. One led to the formation of 1,2-DHN, while another led to cyclic-o-QDM. PMID:24911212
Zhu, Shifa; Huang, Hua; Zhang, Zhicai; Ma, Tongmei; Jiang, Huanfeng
First evidence for the use of organosilver compounds in Pd-catalyzed coupling reactions; a mechanistic rationale for the Pd/Ag-catalyzed enyne synthesis?
Silver acetylides have been prepared and used in Pd-catalyzed coupling reactions. Enynes have thus been obtained in good yields. This work demonstrates that organosilver compounds could enter the Pd catalytic cycle; it also supports the role of silver acetylides as intermediates in the new Pd/Ag-catalyzed coupling reaction. PMID:11405680
Dillinger, S; Bertus, P; Pale, P
Predicting enzyme targets for cancer drugs by profiling human Metabolic reactions in NCI-60 cell lines
Background Drugs can influence the whole metabolic system by targeting enzymes which catalyze metabolic reactions. The existence of interactions between drugs and metabolic reactions suggests a potential way to discover drug targets. Results In this paper, we present a computational method to predict new targets for approved anti-cancer drugs by exploring drug-reaction interactions. We construct a Drug-Reaction Network to provide a global view of drug-reaction interactions and drug-pathway interactions. The recent reconstruction of the human metabolic network and development of flux analysis approaches make it possible to predict each metabolic reaction's cell line-specific flux state based on the cell line-specific gene expressions. We first profile each reaction by its flux states in NCI-60 cancer cell lines, and then propose a kernel k-nearest neighbor model to predict related metabolic reactions and enzyme targets for approved cancer drugs. We also integrate the target structure data with reaction flux profiles to predict drug targets and the area under curves can reach 0.92. Conclusions The cross validations using the methods with and without metabolic network indicate that the former method is significantly better than the latter. Further experiments show the synergism of reaction flux profiles and target structure for drug target prediction. It also implies the significant contribution of metabolic network to predict drug targets. Finally, we apply our method to predict new reactions and possible enzyme targets for cancer drugs.
Nuclear physics of the muon-catalyzed d+d reactions.
A Coulomb-corrected, charge independent R-matrix calculation of the four-nucleon reactions accounts for the surprisingly large branching ratio, as well as for the absolute fusion rate measured for the muon- catalyzed d(plus)d reactions. Reaction constants...
G. M. Hale
Palladium-catalyzed three-component reaction of N-tosylhydrazone, norbornene and aryl halide.
A palladium-catalyzed three-component reaction of N-tosylhydrazone, norbornene and aryl halide has been demonstrated. In this reaction, an intermolecular Heck-type reaction occurs, which is followed by the alkyl palladium carbene migratory insertion process. This transformation provides an efficient and convenient methodology for the double functionalization of norbornene with good to excellent yields. PMID:24777124
Hu, Fangdong; Xia, Ying; Liu, Zhenxing; Ma, Chen; Zhang, Yan; Wang, Jianbo
Enzyme-catalyzed acylation of homoserine: mechanistic characterization of the Haemophilus influenzae met2-encoded homoserine transacetylase.
The first unique step in bacterial and plant methionine biosynthesis involves the acylation of the gamma-hydroxyl of homoserine. In Haemophilus influenzae, acylation is accomplished via an acetyl-CoA-dependent acetylation catalyzed by homoserine transacetylase. The activity of this enzyme regulates flux of homoserine into multiple biosynthetic pathways and, therefore, represents a critical control point for cell growth and viability. We have cloned homoserine transacetylase from H. influenzae and present the first detailed enzymatic study of this enzyme. Steady-state kinetic experiments demonstrate that the enzyme utilizes a ping-pong kinetic mechanism in which the acetyl group of acetyl-CoA is initially transferred to an enzyme nucleophile before subsequent transfer to homoserine to form the final product, O-acetylhomoserine. The maximal velocity and V/K(homoserine) were independent of pH over the range of values tested, while V/K(acetyl)(-)(CoA) was dependent upon the ionization state of a single group exhibiting a pK value of 8.6, which was required to be protonated. Solvent kinetic isotope effect studies yielded inverse effects of 0.75 on V and 0.74 on V/K(CoA) on the reverse reaction and effects of 1.2 on V and 1.7 on V/K(homoserine) on the forward reaction. Direct evidence for the formation of an acetyl-enzyme intermediate was obtained using rapid-quench labeling studies. On the basis of these observations, we propose a chemical mechanism for this important member of the acyltransferase family and contrast its mechanism with that of homoserine transsuccinylase. PMID:10913262
Born, T L; Franklin, M; Blanchard, J S
A free-standing condensation enzyme catalyzing ester bond formation in C-1027 biosynthesis
Nonribosomal peptide synthetases (NRPSs) catalyze the biosynthesis of many biologically active peptides and typically are modular, with each extension module minimally consisting of a condensation, an adenylation, and a peptidyl carrier protein domain responsible for incorporation of an amino acid into the growing peptide chain. C-1027 is a chromoprotein antitumor antibiotic whose enediyne chromophore consists of an enediyne core, a deoxy aminosugar, a benzoxazolinate, and a ?-amino acid moiety. Bioinformatics analysis suggested that the activation and incorporation of the ?-amino acid moiety into C-1027 follows an NRPS mechanism whereby biosynthetic intermediates are tethered to the peptidyl carrier protein SgcC2. Here, we report the biochemical characterization of SgcC5, an NRPS condensation enzyme that catalyzes ester bond formation between the SgcC2-tethered (S)-3-chloro-5-hydroxy-?-tyrosine and (R)-1-phenyl-1,2-ethanediol, a mimic of the enediyne core. SgcC5 uses (S)-3-chloro-5-hydroxy-?-tyrosyl-SgcC2 as the donor substrate and exhibits regiospecificity for the C-2 hydroxyl group of the enediyne core mimic as the acceptor substrate. Remarkably, SgcC5 is also capable of catalyzing amide bond formation, albeit with significantly reduced efficiency, between (S)-3-chloro-5-hydroxy-?-tyrosyl-(S)-SgcC2 and (R)-2-amino-1-phenyl-1-ethanol, an alternative enediyne core mimic bearing an amine at its C-2 position. Thus, SgcC5 is capable of catalyzing both ester and amide bond formation, providing an evolutionary link between amide- and ester-forming condensation enzymes.
Lin, Shuangjun; Van Lanen, Steven G.; Shen, Ben
Sequential Aldol Condensation - Transition Metal-Catalyzed Addition Reactions of Aldehydes, Methyl Ketones and Arylboronic Acids
Sequential aldol condensation of aldehydes with methyl ketones followed by transition metal-catalyzed addition reactions of arylboronic acids to form ?-substituted ketones is described. By using the 1,1?-spirobiindane-7,7?-diol (SPINOL)-based phosphite, an asymmetric version of this type of sequential reaction, with up to 92% ee, was also realized. Our study provided an efficient method to access ?-substituted ketones and might lead to the development of other sequential/tandem reactions with transition metal-catalyzed addition reactions as the key step.
Liao, Yuan-Xi; Xing, Chun-Hui; Israel, Matthew; Hu, Qiao-Sheng
Iron-catalyzed cycloaddition reaction of diynes and cyanamides at room temperature.
An iron-catalyzed [2 + 2 + 2] cycloaddition reaction of diynes and cyanamides at room temperature is reported. Highly substituted 2-aminopyridines were obtained in good to excellent yields with high regioselectivity. Insights toward the reaction process were investigated through in situ IR spectra and control experiments. In this iron-catalyzed cycloaddition reaction, the active iron species was generated only in the presence of both alkynes and nitriles. The lower reaction temperature, broad substrates scope, and inversed regioselectivity make it a complementary method to the previously developed iron catalytic system. PMID:23373593
Wang, Chunxiang; Wang, Dongping; Xu, Fen; Pan, Bin; Wan, Boshun
Improvements of enzyme activity and enantioselectivity in lipase-catalyzed alcoholysis of ( R, S)-azolides
With Candida antarctica lipase B (CALB)-catalyzed alcoholysis of (R,S)-naproxenyl 1,2,4-triazolide at the optimal conditions (i.e. anhydrous MTBE as the solvent, and methanol as the acyl acceptor at 45░C) as the model system, the enzyme enantioselectivity in terms of VR\\/VS=105.8 and specific activity for the fast-reacting (R)-azolide VR\\/(Et)=0.979mmol\\/(hg) were greatly improved in comparison with VR\\/VS=8.0 and VR\\/(Et)=0.113mmol\\/(hg) of using (R,S)-naproxenyl 2,2,2-trifluoroethyl
An-Chi Wu; Pei-Yun Wang; Yi-Sheng Lin; Min-Fang Kao; Jin-Ru Chen; Jyun-Fen Ciou; Shau-Wei Tsai
The reaction mechanism for dehydration process catalyzed by type I dehydroquinate dehydratase from Gram-negative Salmonella enterica
The fundamental reaction mechanism for the dehydration process catalyzed by type I dehydroquinate dehydratase from Gram-negative Salmonella enterica has been studied by density functional theory calculations. The results indicate that the dehydration process undergoes a two-step cis-elimination mechanism, which is different from the previously proposed one. The catalytic roles of both the highly conserved residue His143 and the Schiff base formed between the substrate and Lys170 have also been elucidated. The structural and mechanistic insight presented here may direct the design of type I dehydroquinate dehydratase enzyme inhibitors as non-toxic antimicrobials, anti-fungals, and herbicides.
Yao, Yuan; Li, Ze-Sheng
Identification and characterization of the two-enzyme system catalyzing oxidation of EDTA in the EDTA-degrading bacterial strain DSM 9103.
In a gram-negative isolate (DSM 9103) able to grow with EDTA as the sole source of carbon, nitrogen, and energy, the first two steps of the catabolic pathway for EDTA were elucidated. They consisted of the sequential oxidative removal of two acetyl groups, resulting in the formation of glyoxylate. An enzyme complex that catalyzes the removal of two acetyl groups was purified and characterized. In the reaction, ethylenediaminetriacetate (ED3A) was formed as an intermediate and N,N'-ethylenediaminediacetate was the end product. The enzyme complex consisted of two components: component A' (cA'), most likely a monooxygenase, which catalyzes the cleavage of EDTA and ED3A while consuming oxygen and reduced flavin mononucleotide (FMN)-H2, and component B' (cB'), an NADH2:FMN oxidoreductase that provides FMNH2 for cA'. cB' could be replaced by other NADH2:FMN oxidoreductases such as component B of the nitrilotriacetate monooxygenase or the NADH2:FMN oxidoreductase from Photobacterium fischeri. The EDTA-oxidizing enzyme complex accepted EDTA as a substrate only when it was complexed with Mg2+, Zn2+, Mn2+, Co2+, or Cu2+. Moreover, the enzyme complex catalyzed the removal of acetyl groups from several other aminopolycarboxylic acids that possess three or more acetyl groups.
Witschel, M; Nagel, S; Egli, T
Explaining the Atypical Reaction Profiles of Heme Enzymes with a Novel Mechanistic Hypothesis and Kinetic Treatment
Many heme enzymes show remarkable versatility and atypical kinetics. The fungal extracellular enzyme chloroperoxidase (CPO) characterizes a variety of one and two electron redox reactions in the presence of hydroperoxides. A structural counterpart, found in mammalian microsomal cytochrome P450 (CYP), uses molecular oxygen plus NADPH for the oxidative metabolism (predominantly hydroxylation) of substrate in conjunction with a redox partner enzyme, cytochrome P450 reductase. In this study, we employ the two above-mentioned heme-thiolate proteins to probe the reaction kinetics and mechanism of heme enzymes. Hitherto, a substrate inhibition model based upon non-productive binding of substrate (two-site model) was used to account for the inhibition of reaction at higher substrate concentrations for the CYP reaction systems. Herein, the observation of substrate inhibition is shown for both peroxide and final substrate in CPO catalyzed peroxidations. Further, analogy is drawn in the ōsteady state kineticsö of CPO and CYP reaction systems. New experimental observations and analyses indicate that a scheme of competing reactions (involving primary product with enzyme or other reaction components/intermediates) is relevant in such complex reaction mixtures. The presence of non-selective reactive intermediate(s) affords alternate reaction routes at various substrate/product concentrations, thereby leading to a lowered detectable concentration of ōthe product of interestö in the reaction milieu. Occam's razor favors the new hypothesis. With the new hypothesis as foundation, a new biphasic treatment to analyze the kinetics is put forth. We also introduce a key concept of ōsubstrate concentration at maximum observed rateö. The new treatment affords a more acceptable fit for observable experimental kinetic data of heme redox enzymes.
Manoj, Kelath Murali; Baburaj, Arun; Ephraim, Binoy; Pappachan, Febin; Maviliparambathu, Pravitha Parapurathu; Vijayan, Umesh K.; Narayanan, Sivaprasad Valiyaveettil; Periasamy, Kalaiselvi; George, Ebi Ashley; Mathew, Lazar T.
Prostacyclin synthase (PGIS) and thromboxane synthase (TXAS) are atypical cytochrome P450s. They do not require NADPH or dioxygen for isomerization of prostaglandin H2 (PGH2) to produce prostacyclin (PGI2) and thromboxane A2 (TXA2). PGI2 and TXA2 have opposing actions on platelet aggregation and blood vessel tone. In this report, we use a lipid hydroperoxide, 15-hydroperoxyeicosatetraenoic acid (15-HPETE), to explore the active site characteristics of PGIS and TXAS. The two enzymes transformed 15-HPETE not only into 13-hydroxy-14,15-epoxy-5,8,11-eicosatrienoic acid (13-OH-14,15-EET), like many microsomal P450s, but also to 15-ketoeicosatetraenoic acid (15-KETE) and 15-hydroxyeicosatetraenoic acid (15-HETE). 13-OH-14,15-EET and 15-KETE result from homolytic cleavage of the O¢O bond, whereas 15-HETE results from heterolytic cleavage, a common peroxidase pathway. About 80% of 15-HPETE was homolytically cleaved by PGIS and 60% was homolytically cleaved by TXAS. The Vmax of homolytic cleavage is 3.5-fold faster than heterolytic cleavage for PGIS-catalyzed reactions (1100 min?1 vs. 320 min?1) and 1.4-fold faster for TXAS (170 min?1 vs. 120 min?1). Similar KM values for homolytic and heterolytic cleavages were found for PGIS (?60 ?M 15-HPETE) and TXAS (?80 ?M 15-HPETE), making PGIS a more efficient catalyst for the 15-HPETE reaction.
Yeh, Hui-Chun; Tsai, Ah-Lim; Wang, Lee-Ho
Bulk Gold-Catalyzed Reactions of Isocyanides, Amines, and Amine N-Oxides
Bulk gold powder (5¢50 ?m particles) catalyzes the reactions of isocyanides with amines and amine N-oxides to produce ureas. The reaction of n-butyl isocyanide (nBu¢N?C) with di-n-propylamine and N-methylmorpholine N-oxide in acetonitrile, which was studied in the greatest detail, produced 3-butyl-1,1-dipropylurea (O?C(NHnBu)(NnPr2)) in 99% yield at 60 ░C within 2 h. Sterically and electronically different isocyanides, amines, and amine N-oxides react successfully under these conditions. Detailed studies support a two-step mechanism that involves a gold-catalyzed reaction of adsorbed isocyanide with the amine N-oxide to form an isocyanate (RN?C?O), which rapidly reacts with the amine to give the urea product. These investigations show that bulk gold, despite its reputation for poor catalytic activity, is capable of catalyzing these reactions.
Klobukowski, Erik; Angelici, Robert; Woo, Keith L.
Iron-catalyzed radical oxidative coupling reaction of aryl olefins with 1,3-dithiane.
An alternative method to an iron-catalyzed radical oxidative cross-coupling reaction followed by 2-chloro-1,3-dithiane and aryl olefins for the synthesis of ?-chloro substituent 1,3-dithiane products is presented. The described method has the advantage of mildness of the reaction conditions and tolerates a variety of functional groups. Preliminary mechanistic studies have confirmed the first example of a coupling of 1,3-dithiane with unactivated alkenes that proceeds via an iron-catalyzed oxidative radical intermediate along the reaction pathway. PMID:24749868
Du, Wenbin; Tian, Lixia; Lai, Junshan; Huo, Xing; Xie, Xingang; She, Xuegong; Tang, Shouchu
C1-symmetric aminosulfoximines in copper-catalyzed asymmetric vinylogous Mukaiyama aldol reactions.
Vinylogous Mukaiyama-type aldol reactions have been catalyzed by a combination of Cu(OTf)2 and readily available C1-symmetric aminosulfoximines. After a fine-tuning of the reaction conditions and an optimization of the modularly assembled ligand structure, high stereoselectivities and excellent yields have been achieved in catalyzed reactions involving various electrophile/nucleophile combinations. The relative and absolute configurations of two products were assigned by X-ray single crystal structure analysis and a comparison of calculated and experimental CD spectra. PMID:20229533
Frings, Marcus; Atodiresei, Iuliana; Wang, Yutian; Runsink, Jan; Raabe, Gerhard; Bolm, Carsten
Stereoselective synthesis of 2,5-disubstituted morpholines using a palladium-catalyzed hydroamination reaction.
A palladium-catalyzed hydroamination reaction is the key step in a stereoselective synthesis of 2,5-disubstituted and 2,3,5-trisubsituted morpholines from carbamate-protected aziridines. Aziridines are selectively attacked at the more substituted position by unsaturated alcohol nucleophiles using Lewis acid catalysts. Palladium-catalyzed hydroamination of the resulting aminoalkenes gives morpholines as a single diastereomer in excellent yield. PMID:23784260
McGhee, Alicia; Cochran, Brian M; Stenmark, Torrey A; Michael, Forrest E
C3-Symmetric chiral trisimidazoline-catalyzed Friedel-Crafts (FC)-type reaction.
Imidazoline-catalyzed enantioselective Friedel-Crafts (FC)-type reactions were established using C3-symmetric chiral trisimidazolines. The imidazoline catalysts promoted the FC-type reaction of aldimines with 2-naphthols to produce the corresponding adducts in high yields with up to 99% ee. PMID:24971875
Takizawa, Shinobu; Hirata, Shuichi; Murai, Kenichi; Fujioka, Hiromichi; Sasai, Hiroaki
Enantioselective Formal Aza-Diels-Alder Reactions of Enones with Cyclic Imines Catalyzed by Primary Aminothioureas
A highly enantio- and diastereoselective synthesis of indolo- and benzoquinolizidine compounds has been developed through the formal aza-Diels¢Alder reaction of enones with cyclic imines. This transformation is catalyzed by a new bifunctional primary aminothiourea that achieves simultaneous activation of both the enone and imine reaction components.
Lalonde, Mathieu P.; McGowan, Meredeth A.; Rajapaksa, Naomi S.; Jacobsen, Eric N.
Iron-catalyzed rearrangements and cycloaddition reactions of 2H-chromenes.
Iron(III) salts catalyze the tandem rearrangement/hetero-Diels-Alder reaction of 2H-chromenes to yield tetrahydrochromeno heterocycles. The process can occur as a homodimerization and cycloaddition process using electron-rich dienophiles. Deuterium labeling and mechanistic studies revealed a hydride shift and ortho-quinone methide cycloaddition reaction pathway. PMID:22098535
Luan, Yi; Sun, Huan; Schaus, Scott E
Fluorenone Synthesis by Palladacycle-Catalyzed Sequential Reactions of 2-Bromobenzaldehydes with Arylboronic Acids
A new, anionic four-electron donor-based (Type I) palladacycle-catalyzed sequential reaction of 2-bromobenzaldehydes with arylboronic acids based on the addition reaction, cyclization via C-H activation-oxidation sequence is described. Our study provided an efficient access to a variety of substituted fluorenones/indenofluorenediones from readily available arylboronic acids and 2-bromobenzaldehydes.
Liu, Tao-Ping; Liao, Yuan-Xi; Xing, Chun-Hui; Hu, Qiao-Sheng
Fluorenone synthesis by palladacycle-catalyzed sequential reactions of 2-bromobenzaldehydes with arylboronic acids.
A new, anionic four-electron donor-based (type I) palladacycle-catalyzed sequential reaction of 2-bromobenzaldehydes with arylboronic acids based on the addition reaction, cyclization via C-H activation-oxidation sequence is described. Our study provided an efficient access to a variety of substituted fluorenones/indenofluorenediones from readily available arylboronic acids and 2-bromobenzaldehydes. PMID:21480660
Direct asymmetric dearomatization of pyridines and pyrazines by iridium-catalyzed allylic amination reactions.
The first iridium-catalyzed intramolecular asymmetric allylic dearomatization reaction of pyridines and pyrazines has been realized. 2,3-Dihydroindolizine and 6,7-dihydropyrrolo[1,2-a]pyrazine derivatives were obtained with excellent yields and enantioselectivity. This methodology features dearomatization by direct N-allylic alkylation of pyridines or pyrazines under mild reaction conditions. PMID:24861469
Yang, Ze-Peng; Wu, Qing-Feng; You, Shu-Li
ENZYME: Enzyme Nomenclature Database
Recently updated, the ENZYME: Enzyme Nomenclature Database is based mainly on recommendations by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and "describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided." An online user manual describes how to access and use the database, which may be searched by EC number, enzyme class, official description or alternative name(s), chemical compound, or cofactor. Typical returns include Names, Reaction catalyzed, Comments, Human Genetic Diseases, and a host of hyperlinked cross-references. ENZYME is provided by the Swiss Institute of Bioinformatics.
Continuous In Vitro Evolution of a Ribozyme that Catalyzes Three Successive Nucleotidyl Addition Reactions
Variants of the class I ligase ribozyme, which catalyzes joining of the 3' end of a template bound oligonucleotide to its own 5' end, have been made to evolve in a continuous manner by a simple serial transfer procedure that can be carried out indefinitely. This process was expanded to allow the evolution of ribozymes that catalyze three successive nucleotidyl addition reactions, two template-directed mononucleotide additions followed by RNA ligation. During the development of this behavior, a population of ribozymes was maintained against an overall dilution of more than 10(exp 406). The resulting ribozymes were capable of catalyzing the three-step reaction pathway, with nucleotide addition occurring in either a 5' yieldig 3' or a 3' yielding 5' direction. This purely chemical system provides a functional model of a multi-step reaction pathway that is undergoing Darwinian evolution.
McGinness, Kathleen E.; Wright, Martin C.; Joyce, Gerald F.
Iron and xanthine oxidase catalyze formation of an oxidant species distinguishable from OH. : comparison with the Haber-Weiss reaction
O2- was produced by gamma irradiation of formate solutions, by the action of xanthine oxidase on hypoxanthine and O2, and by the action of ferredoxin reductase on NADPH and paraquat in the presence of O2. Its reaction with H2O2 and various iron chelates was studied. Oxidation of deoxyribose to thiobarbituric acid-reactive products that was appropriately inhibited by OH. scavengers, or formate oxidation to CO2, was used to detect OH(.). With each source of O2-, and by these criteria, Fe(EDTA) efficiently catalyzed this (Haber-Weiss) reaction, but little catalysis was detectable with iron bound to DTPA, citrate, ADP, ATP, or pyrophosphate, or without chelator in phosphate buffer. O2- produced from xanthine oxidase, but not from the other sources, underwent another iron-dependent reaction with H2O2, to produce an oxidant that did not behave as free OH(.). It was formed in phosphate or bicarbonate buffer, and caused deoxyribose oxidation that was readily inhibited by mannitol or Tris, but not by benzoate, formate, or dimethyl sulfoxide. It did not oxidize formate to CO2. Addition of EDTA changed the pattern of inhibition to that expected for a reaction of OH(.). The other chelators all inhibited deoxyribose oxidation, provided their concentrations were high enough. The results are compatible with iron bound to xanthine oxidase catalyzing production of a strong oxidant (which is not free OH.) from H2O2 and O2- produced by the enzyme.
Winterbourn, C.C.; Sutton, H.C.
Tandem Aldol Condensation - Platinacycle-Catalyzed Addition Reactions of Aldehydes, Methyl Ketones and Arylboronic Acids
Tandem aldol condensation of aldehydes with methyl ketones followed by anionic four-electron donor-based (Type I) platinacycle-catalyzed addition reactions of arylboronic acids to form ?-arylated ketones is described. Good to excellent yields of ?-arylated ketones were obtained for the tandem reactions of aromatic/aliphatic aldehydes, methyl ketones and arylboronic acids, and moderate yields were observed for the tandem reaction with ?, ?-unsaturated aldehydes as the aldehyde source.
Liao, Yuan-Xi; Hu, Qiao-Sheng
Magnesium halide-catalyzed anti-aldol reactions of chiral N-acylthiazolidinethiones.
[reaction: see text] Diastereoselective direct aldol reactions of chiral N-acylthiazolidinethiones occur in high yield with preference for the illustrated anti diastereomer. This reaction is catalyzed by 10% MgBr2.OEt2 in the presence of triethylamine and chlorotrimethylsilane. Yields range from 56 to 93% with diastereoselectivity up to 19:1 for a variety of N-acylthiazolidinethiones and unsaturated aldehydes. PMID:11922799
Evans, David A; Downey, C Wade; Shaw, Jared T; Tedrow, Jason S
Nuclear physics of the muon-catalyzed d+d reactions
A Coulomb-corrected, charge independent R-matrix calculation of the four-nucleon reactions accounts for the surprisingly large branching ratio, as well as for the absolute fusion rate measured for the muon- catalyzed d{plus}d reactions. Reaction constants are given for both S-wave and P-wave transitions that would result in the sort of temperature dependence for the branching ratio that has recently been observed. 6 refs., 1 fig., 1 tab.
Hale, G.M.
Role of a guanidinium cation-phosphodianion pair in stabilizing the vinyl carbanion intermediate of orotidine 5'-phosphate decarboxylase-catalyzed reactions.
The side chain cation of Arg235 provides a 5.6 and 2.6 kcal/mol stabilization of the transition states for orotidine 5'-monophosphate (OMP) decarboxylase (OMPDC) from Saccharomyces cerevisiae catalyzed reactions of OMP and 5-fluoroorotidine 5'-monophosphate (FOMP), respectively, a 7.2 kcal/mol stabilization of the vinyl carbanion-like transition state for enzyme-catalyzed exchange of the C-6 proton of 5-fluorouridine 5'-monophosphate (FUMP), but no stabilization of the transition states for enzyme-catalyzed decarboxylation of truncated substrates 1-(?-d-erythrofuranosyl)orotic acid and 1-(?-d-erythrofuranosyl) 5-fluorouracil. These observations show that the transition state stabilization results from formation of a protein cation-phosphodianion pair, and that there is no detectable stabilization from an interaction between the side chain and the pyrimidine ring of substrate. The 5.6 kcal/mol side chain interaction with the transition state for the decarboxylation reaction is 50% of the total 11.2 kcal/mol transition state stabilization by interactions with the phosphodianion of OMP, whereas the 7.2 kcal/mol side chain interaction with the transition state for the deuterium exchange reaction is a larger 78% of the total 9.2 kcal/mol transition state stabilization by interactions with the phosphodianion of FUMP. The effect of the R235A mutation on the enzyme-catalyzed deuterium exchange is expressed predominantly as a change in the turnover number kex, whereas the effect on the enzyme-catalyzed decarboxylation of OMP is expressed predominantly as a change in the Michaelis constant Km. These results are rationalized by a mechanism in which the binding of OMP, compared with that for FUMP, provides a larger driving force for conversion of OMPDC from an inactive open conformation to a productive, active, closed conformation. PMID:24053466
Goryanova, Bogdana; Goldman, Lawrence M; Amyes, Tina L; Gerlt, John A; Richard, John P
Concise, convergent syntheses of (▒)-trichostatin A utilizing a Pd-catalyzed ketone enolate ?-alkenylation reaction.
Two concise, convergent syntheses of (▒)-trichostatin A (1), a potent histone deacetylase inhibitor, have been accomplished. The key step in both is a Pd-catalyzed ?-alkenylation reaction between ketone 2 and either dienyl bromide 3 or alkenyl bromide 9 using a modification of cross-coupling conditions described by Negishi and Hartwig. A brief investigation has shown the potential utility of a Ni-catalyzed version of this reaction. The overall synthetic routes are short and amenable to scaleup, providing access to trichostatin A via trichostatic acid as a direct precursor. PMID:21688856
Cosner, Casey C; Helquist, Paul
Gold-Catalyzed Oxidative Coupling Reactions with Aryltrimethylsilanes
During continuing studies with a novel oxidative gold oxyarylation reaction, arylsilanes were found to be competent coupling partners, providing further evidence for an intramolecular electrophilic aromatic substitution mechanism. While providing complementary yields to the previously described boronic acid methods, the use of trimethylsilanes reduces the observation of homocoupling byproducts and allows for facile intramolecular coupling reactions.
Brenzovich, William E.; Brazeau, Jean-Francois; Toste, F. Dean
Highly Selective Fluorogenic Multianalyte Biosensors Constructed via Enzyme-Catalyzed Coupling and Aggregation-Induced Emission.
The development of a highly selective and fast responsive fluorogenic biosensor for diverse analytes ranging from bioactive small molecules to specific antigens is highly desirable but remains a considerable challenge. We herein propose a new approach by integrating substrate-selective enzymatic reactions with fluorogens exhibiting aggregation-induced emission feature. Tyrosine-functionalized tetraphenylethene, TPE-Tyr, molecularly dissolves in aqueous media with negligible fluorescence emission; upon addition of horseradish peroxidase (HRP) and H2O2, effective cross-linking occurs due to HRP-catalyzed oxidative coupling of tyrosine moieties in TPE-Tyr. This leads to fluorescence emission turn-on and fast detection of H2O2 with high sensitivity and selectivity. As a validation of the new strategy's generality, we further configure it into the biosensor design for glucose through cascade enzymatic reactions and for pathologically relevant antigens (e.g., human carcinoembryonic antigen) by combining with the ELISA kit. PMID:24983204
Wang, Xiaorui; Hu, Jinming; Zhang, Guoying; Liu, Shiyong
Phospholipids chiral at phosphorus. Steric course of the reactions catalyzed by phosphatidylserine synthase from Escherichia coli and yeast
The steric courses of the reactions catalyzed by phosphatidylserine (PS) synthase from Escherichia coli and yeast were elucidated by the following procedure. R/sub P/ and S/sub P/ isomers of 1,2-dipalmitoyl-sn-glycero-3-(/sup 17/O, /sup 18/O)phosphoethanolamine ((/sup 17/O, /sup 18/O)DPPE) were synthesized and converted to (R/sub P/)- and (S/sub P/)-1,2-dipalmitoyl-sn-glycero-3-(/sup 16/O, /sup 17/O, /sup 18/O)DPPA), respectively, by incubating with phospholipase D. Condensation of (/sup 16/O, /sup 17/O, /sup 18/O)DPPA with cytidine 5'-monophosphomorpholidate in pyridine gave the desired substrate for PS synthase, (/sup 17/O, /sup 18/O)cytidine 5'-diphospho-1,2-dipalmitoyl-sn-glycerol ((/sup 17/O,/sup 18/O)CDP-DPG), as a mixture of several isotopic and configurational isomers. Incubation of (/sup 17/O, /sup 18/O)CDP-DPG), as a mixture of several isotopic and configurational isomers. Incubation of (/sup 17/O, /sup 18/O) CDP-DPG with a mixture of L-serine, PS synthase and PS decarboxylase gave (/sup 17/O, /sup 18/O)DPPE. The configuration and isotopic enrichments of the starting (/sup 17/O, /sup 18/O)DPPE and the product were analyzed by /sup 31/P NMR following trimethylsilylation of the DPPE. The results indicate that the reaction of E. coli PS synthase proceeds with retention of configuration at phosphorus, which suggests a two-step mechanism involving a phosphatidyl-enzyme intermediate, while the yeast PS synthase catalyzes the reaction with inversion of configuration, which suggests a single-displacement mechanism. Such results lend strong support to the ping-pong mechanism proposed for the E. coli enzyme and the sequential Bi-Bi mechanism proposed for the yeast enzyme, both based on previous isotopic exchange experiments.
Raetz, C.R.H.; Carman, G.M.; Dowhan, W.; Jiang, R.T.; Waszkuc, W.; Loffredo, W.; Tsai, M.D.
Synthesis of polycyclic indole skeletons by a gold(I)-catalyzed cascade reaction.
The conversion of simple, easily available urea-substituted 3-phenylpropargyl alcohols catalyzed by a simple IPr-gold(I) catalyst in a gold(I)-catalyzed cascade reaction composing of a gold-catalyzed nucleophilic addition and a subsequent gold-catalyzed substitution reaction delivers 1H-imidazo[1,5-a]indol-3(2H)-ones. Other gold(I) catalysts or silver catalysts gave lower yields and often gave other side products. Gold(III) and copper(II) catalysts decomposed the starting material. Twelve examples, including donor and acceptor substituents on the distal nitrogen of the urea substructure, are provided. An X-ray crystal structure analysis confirmed the structural assignment. The mechanistic investigation including isolation and further conversion of intermediates and reactions with enantiopure starting materials indicated that after the nucleophilic-addition step, the substrate undergoes an S(N)1-type benzylic substitution reaction at the indolyl alcohol intermediate or an intramolecular hydroamination reaction of the 2-vinylindole intermediate. PMID:24375591
Wang, Tao; Shi, Shuai; Pflõsterer, Daniel; Rettenmeier, Eva; Rudolph, Matthias; Rominger, Frank; Hashmi, A Stephen K
Influence of surface morphology and chemistry on the enzyme catalyzed biodegradation of polycarbonate-urethanes.
Polycarbonate based polyurethanes were synthesized with varying hard segment content as well as hard segment chemistry based on three different diisocyanates,1,6-hexane diisocyanate (HDI), 4.4'-methylene bisphenyl diisocyanate (MDI) and 4,4-methylene biscyclohexyl diisocyanate (HMDI). The surface chemistry and morphology were characterized using X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM). The polymers were incubated with cholesterol esterase (CE) in a phosphate buffer solution at 37 degrees C over 10 weeks. XPS results showed that the surface chemistry changed as the size and chemistry of the hard segment varied within the materials. AFM images exhibited distinctive surface morphologies for all polymers, and this was particularly apparent with changes in the hard segment chemistry. The results showed that the surface of HDI polymers consisted of relatively stiff rod-like structures, which corresponded to the soft segment domains. Polymers with a higher HDI content exhibited a dense top layer containing a relatively higher hard segment component, covering the sub-surface matrix of rod like structures. The MDI based polyurethane had large aggregates on its top surface, which corresponded to the aggregation of harder components. The HMDI based polycarbonate-urethane presented a relatively homogeneous surface where no phase separation could be detected. The relative differences in hard and soft segment content in their surface structure was supported by XPS findings. The analysis of the biodegradation results, concluded that enzyme catalyzed biodegradation within these materials was initiated in amorphous soft segment regions located in the region of the interface between hard and soft segments. A higher hard segment content at the surface contributed significantly to an increase in biostability. The findings provided an enhanced understanding for the role of surface molecular structure in the enzyme catalyzed biodegradation of polyurethanes. PMID:12160304
Tang, Y W; Labow, R S; Revenko, I; Santerre, J P
The methylthiolation reaction mediated by the Radical-SAM enzymes.
Over the past 10 years, considerable progress has been made in our understanding of the mechanistic enzymology of the Radical-SAM enzymes. It is now clear that these enzymes appear to be involved in a remarkably wide range of chemically challenging reactions. This review article highlights mechanistic and structural aspects of the methylthiotransferases (MTTases) sub-class of the Radical-SAM enzymes. The mechanism of methylthio insertion, now observed to be performed by three different enzymes is an exciting unsolved problem. This article is part of a Special Issue entitled: Radical SAM enzymes and Radical Enzymology. PMID:22178611
Atta, Mohamed; Arragain, Simon; Fontecave, Marc; Mulliez, Etienne; Hunt, John F; Luff, Jon D; Forouhar, Farhad
AgOTf-catalyzed one-pot reactions of 2-alkynylbenzaldoximes with ?,?-unsaturated carbonyl compounds
Summary AgOTf-catalyzed one-pot reactions of 2-alkynylbenzaldoximes with various ?,?-unsaturated carbonyl compounds under mild conditions are described, which provides a facile and efficient pathway for the synthesis of 1-alkylated isoquinoline derivatives. The method tolerates a wide range of substrates and allows for the preparation of the products of interest in moderate to excellent yields.
Ding, Qiuping; Wang, Dan; Liu, Meiling; Zhou, Liyun
AgOTf-catalyzed one-pot reactions of 2-alkynylbenzaldoximes with ?,?-unsaturated carbonyl compounds.
AgOTf-catalyzed one-pot reactions of 2-alkynylbenzaldoximes with various ?,?-unsaturated carbonyl compounds under mild conditions are described, which provides a facile and efficient pathway for the synthesis of 1-alkylated isoquinoline derivatives. The method tolerates a wide range of substrates and allows for the preparation of the products of interest in moderate to excellent yields. PMID:24204406
Ding, Qiuping; Wang, Dan; Luo, Puying; Liu, Meiling; Pu, Shouzhi; Zhou, Liyun
A Novel Cyclic Carbamate from the Acid-Catalyzed Reaction of D-Glucose and Urea
The acid-catalyzed reaction of D-glucose with urea in a phenol-water solution has provided ?-D-glucopyranosylamine 1,2-(cyclic carbamate) (1). The use of H-C correlated NMR spectroscopy involving indirectly-bonded hydrogens and carbons proved to be indispensable in determining the structure.
Richard F. Helm; Joseph J. Karchesy
Influence of an internal trifluoromethyl group on the rhodium(II)-catalyzed reactions of vinyldiazocarbonyl compounds.
Incorporation of a trifluoromethyl group into the structure of 4-(alkoxycarbonyl)vinyldiazocarbonyl compounds greatly decreases the tendency of the carbenoid intermediates formed during Rh(II)-catalyzed reactions to undergo intermolecular processes. Instead, they are prone to experience intramolecular [1,5]- and [1,3]-electrocyclizations to produce reactive cyclopropenes and furans, and these are capable of further transformations. PMID:23614681
Nikolaev, Valerij A; Supurgibekov, Murat B; Davies, Huw M L; Sieler, Joachim; Zakharova, Valerija M
Pd-catalyzed coupling reaction of fluorinated propargyl amidines with aryl iodides.
Catalyzed by ligand free Pd(OAc)(2), 2,5-disubstituted imidazole was prepared in good yield by the reaction of fluorinated propargyl amidines with iodoarene. Mechanistic studies indicated that this transformation occurs through a nitropalladation-reductive elimination pathway. PMID:23117859
Li, Shan; Yuan, Yafen; Li, Yajun; Li, Zhengke; Zhang, Lisi; Wu, Yongming
Hydrosilylation reactions catalyzed by rhodium complexes with phosphine ligands functionalized with imidazolium salts
Hydrosilylation reactions of styrene with triethoxysilane catalyzed by rhodium complexes with phosphine ligands functionalized with imidazolium salts are reported. In comparison with WilkinsonÆs catalyst, Rh(PPh3)3Cl, all of the present rhodium complexes with phosphines functionalized with imidazolium salts exhibit higher catalytic activity and selectivity.
Jiayun Li; Jiajian Peng; Diliang Wang; Ying Bai; Jianxiong Jiang; Guoqiao Lai
Textured catalysts, methods of making textured catalysts, and methods of catalyzing reactions conducted in hydrothermal conditions
A textured catalyst having a hydrothermally-stable support, a metal oxide and a catalyst component is described. Methods of conducting aqueous phase reactions that are catalyzed by a textured catalyst are also described. The invention also provides methods of making textured catalysts and methods of making chemical products using a textured catalyst.
Werpy, Todd (West Richland, WA) [West Richland, WA; Frye, Jr., John G. (Richland, WA); Wang, Yong (Richland, WA) [Richland, WA; Zacher, Alan H. (Kennewick, WA) [Kennewick, WA
The effect of Mg/2+/ and Ca/2+/ on urea-catalyzed phosphorylation reactions
The effect of Mg(2+) and Ca(2+) on phosphorylation reactions catalyzed by urea is investigated, showing that Mg(2+) improves markedly the yield of products containing pyrophosphate bonds. Yields of up to 25% of uridine diphosphate can be obtained with struvite at temperatures as low as 65 C.
Handschuk, G. J.; Lohrmann, R.; Orgel, L. E.
Micellar catalysis using a photochromic surfactant: application to the Pd-catalyzed Tsuji-Trost reaction in water.
The first example of a Pd-catalyzed Tsuji-Trost reaction, applied in a photochromic micellar media under conventional heating and microwave irradiation, is reported. The surfactant activity and recycling ability were investigated and compared with those of a few commercially available surfactants. The synthetic photochromic surfactant proved to be efficient, recyclable, and versatile for Pd-catalyzed coupling reactions. PMID:24295431
Billamboz, Muriel; Mangin, Floriane; Drillaud, Nicolas; Chevrin-Villette, Carole; Banaszak-Lķonard, Estelle; Len, Christophe
Stereochemical outcome of copper-catalyzed C-H insertion reactions. An experimental and theoretical study.
The combination of chiral preparative HPLC separation, VCD measurements, and theoretical calculations allows the unambiguous determination of the absolute configuration of the conformationally flexible products of copper-catalyzed carbene insertion reactions. DFT calculations were used to predict the stereochemical outcome of the copper-bis(oxazoline)-catalyzed C-H insertion reaction between methyl diazophenylacetate and tetrahydrofuran and also to predict the absolute configuration of the major stereoisomers derived from the same reaction with different cyclic ethers. These predictions were verified experimentally through NMR and VCD spectroscopy and allowed rationalization of the stereochemical outcome of these reactions without further derivatization of the products, which can be prblematic under certain conditions as described herein. PMID:23701290
Jimķnez-Osķs, Gonzalo; Vispe, Eugenio; Roldßn, Marta; RodrĒguez-RodrĒguez, Sergio; L¾pez-Ram-de-Viu, Pilar; Salvatella, Luis; Mayoral, Josķ A; Fraile, Josķ M
Reaction mechanism for the acid-catalyzed hydrolysis of saccharose
1.A polarimetric study was made of the reaction for the hydrolysis of saccharose in inorganic acid solutions.2.The A-1 mechanism, on the assumption that saccharose is a base of the type of a Hammett indicator, does not describe the experimental data.
N. A. Khalturinskii; Yu. V. Moiseev; G. E. Zaikov
Catalyzed vinylogous Mukaiyama aldol reactions with controlled enantio- and diastereoselectivities.
In control: A new catalytic vinylogous Mukaiyama aldol reaction provides products with high diastereo- and enantioselectivities (up to 99 % de and ee; see scheme). The relative and absolute stereochemistry of a representative product was rigorously assigned by NMR and CD spectroscopies (measured and calculated), X-ray diffraction, and quantum-chemical calculations. PMID:19123229
Frings, Marcus; Atodiresei, Iuliana; Runsink, Jan; Raabe, Gerhard; Bolm, Carsten
Enzyme-Substrate Reactions in Very High Magnetic Fields. I
The availability of very high magnetic fields of up to 170,000 gauss made it worthwhile to pursue the search for a critical change in the rate of four enzyme substrate reactions. The four enzymes were ribonuclease, polyphenol oxidase, peroxidase, and aldolase. The experiments showed that, to within ▒3%, no detectable change was observable in the rate of reaction of any of the systems for periods of exposure to the magnetic field of up to 20 min.
Rabinovitch, B.; Maling, J. E.; Weissbluth, M.
Rhodium(I)/Diene-Catalyzed Addition Reactions of Arylborons with Ketones
Rh(I)/diene-catalyzed addition reactions of arylboroxines/arylboronic acids with unactivated ketones to form tertiary alcohols in good to excellent yields are described. By using C2-symmetric (3aR,6aR)-3,6-diaryl-1,3a,4,6a-tetrahydropentalenes as ligands, the asymmetric version of such an addition reaction, with up to 68% ee, was also realized.
Liao, Yuan-Xi; Xing, Chun-Hui; Hu, Qiao-Sheng
Bifunctional Metalloporphyrins-Catalyzed Coupling Reaction of Epoxides and CO 2 to Cyclic Carbonates
New catalysts of water soluble bifunctional metalloporphyrins M(TTMAPP)I4(X) (M = Co, Fe, Mn, and Cr; X = OAc, CF3COO, CCl3COO, OTs, Cl, Br, and I) were synthesized and used to catalyze the synthesis of cyclic carbonate through the coupling reaction of terminal epoxides and CO2. The effects of reaction temperature, various metals as the Lewis acidic center, counterions, and recycling
Dongsheng BAI; Xiaoxuan WANG; Yingying SONG; Bo LI; Lilong ZHANG; Peng YAN; Huanwang JING
The role of silica gel in lipase-catalyzed esterification reactions of high-polar substrates
The crucial role of silica gel in lipase-catalyzed esterification reactions using adsorbed high-polar substates was established.\\u000a It was found that in these kinds of reactions, the presence of silica gel-adsorbed substrates did not alter the kinetic mechanisms\\u000a of the synthesis of acylglycerides but improved significantly the conversion yields. An explanation for the critical role\\u000a of silica gel in these kinds
Edmundo Castillo; Valķrie Dossat; Alain Marty; J. Stķphane Condoret; Didier Combes
Iridium-catalyzed asymmetric ring-opening reactions of oxabicyclic alkenes with secondary amine nucleophiles
Summary Iridium-catalyzed asymmetric ring-opening reactions of oxabicyclic alkenes with various aliphatic and aromatic secondary amines are reported for the first time. The reaction gave the corresponding trans-1,2-dihydronaphthalenol derivatives in good yields with moderate enantioselectivities in the presence of 2.5 mol % [Ir(COD)Cl]2 and 5 mol % bisphosphine ligand (S)-p-Tol-BINAP. The trans-configuration of 3f was confirmed by X-ray crystallography.
Hu, Ping; Long, Yuhua; Wu, Yujuan; Zeng, Heping; Wang, Hui; Zuo, Xiongjun
Copper-catalyzed reaction of ketenimine and in situ generated immonium ion: access to ?,?-unsaturated amidines.
A Cu-catalyzed three-component reaction of alkyne, azides (sulfonyl or phosphoryl azides), and N,N-dialkyloxyformamide dialkyl acetal via electrophilic addition of immonium ion to copper ketenimine is reported. This new protocol for the preparation of ?,?-unsaturated amidine derivatives appears to offer high yield, mild conditions, and wide substrate scope. The reaction might involve the processes of copper ketenimine intermediate formation, electrophilic addition, and isomerization. PMID:24392993
Yao, Bangben; Shen, Chuang; Liang, Zunjun; Zhang, Yuhong
Synthesis of substituted tetrahydroindoloisoquinoline derivatives via intramolecular Pd-catalyzed alkene carboamination reactions.
Intramolecular Pd-catalyzed alkene carboamination reactions of substituted 2-allyl-N-(2-bromobenzyl)anilines are described. The substrates for these reactions are generated in two steps from readily available 2-allylanilines and 2-bromobenzaldehyde derivatives. The transformations afford substituted tetrahydroindoloisoquinolines, an uncommon class of fused bicyclic heterocycles, in good yield. The mechanism of these transformations is described, and a model that accounts for the observed product stereochemistry is proposed. PMID:24724560
Alicea, Jeremiah; Wolfe, John P
NAD deamidation "a new reaction" by an enzyme from Aspergillus terreus DSM 826.
NAD deamidation is a non-previously recognized reaction. This reaction has been found to be catalyzed by extracts of Aspergillus terreus DSM 826. Conversion of NAD to the biosynthetic intermediate, deamido NAD, by these extracts, at the optimum pH and temperature did not exceed about 55 of the amount of the substrate added. Completion of the reaction was achieved when the extracts were pre-heated at 50 degrees C for 15 min in absence of the substrate. In a very similar manner, the extracts catalyzed hydrolytic cleavage of the amide linkages of different biomolecules such as nicotinamide, nicotinamide riboside, nicotinamide mononucleotide, L-glutamine, L-asparagine and acetamide. Polyacrylamide was also deamidated under the same conditions. In addition, complete dephosphorylation of the dinucleotide molecule was also effected by the same extracts. Separation of the NAD deamidating enzyme from the NAD dephosphorylating enzyme was achieved on using either DEAE - Sephadex A-25 or Sephadex G-200 column chromatography. The obtained phosphohydrolase-free-deamidase showed optimum activity at pH 8 of 0.1 M phosphate buffer and 50 degrees C. It exhibited broad substrate specificity and hyperbolic substrate saturation kinetics. It was isosterically inhibited by the product of its activity and this inhibition was prevented by heating the extracts at 50 degrees C for 15 min. Its activity was not affected in presence of sodium fluoride, partially inhibited in presence of magnesium chloride and was retained in the freezer for some months. PMID:15793621
Elzainy, Tahany A; Ali, Thanaa H
Palladium-catalyzed cross-coupling reaction of organoindiums with aryl halides in aqueous media.
[reaction: see text] Diaryl-, divinyl-, and dialkylindium proved to be stable in aqueous media and to undergo a palladium-catalyzed cross-coupling reaction with aryl halides in aqueous THF. Treatment of 3-iodophenol with diphenylindium compound, generated from indium trichloride and two equimolar amounts of a phenyl Grignard reagent, in aqueous media under palladium catalysis provided the corresponding coupling product in excellent yield. Divinyl- and diethylindium can be used for the coupling reaction in the presence of water. A wide range of functional groups, including a hydroxy group and a formyl group, are compatible with this reaction. PMID:11418033
Takami, K; Yorimitsu, H; Shinokubo, H; Matsubara, S; Oshima, K
Catalyst system for catalyzing the water gas shift reaction
The improved catalyst system developed by the University of Rochester for the water-gas shift reaction is very active at relatively low temperatures and is efficient in its utilization of the components forming the catalyst system. The homogeneous catalyst system contains rhodium carbonyl iodide in a water\\/acetic acid solvent. The system can be formed from (Rh(CO)ŌCl)Ō, aqueous HI, and glacial acetic
R. Eisenberg; C. H. Cheng
Enantioselective TADMAP-Catalyzed Carboxyl Migration Reactions for the Synthesis of Stereogenic Quaternary Carbon
The chiral, nucleophilic catalyst TADMAP (1) has been prepared from 3-lithio-4-dimethylamino-pyridine (5) and triphenylacetaldehyde (3), followed by acylation and resolution. TADMAP catalyzes the carboxyl migration of oxazolyl, furanyl, and benzofuranyl enol carbonates with good to excellent levels of enantioselection. The oxazole reactions are especially efficient, and are used to prepare chiral lactams (23) and lactones (30) containing a quaternary asymmetric carbon. TADMAP-catalyzed carboxyl migrations in the indole series are relatively slow and proceed with inconsistent enantioselectivity. Modeling studies (B3LYP/6-31G*) have been used in qualitative correlations of catalyst conformation, reactivity, and enantioselectivity.
Shaw, Scott A.; Aleman, Pedro; Christy, Justin; Kampf, Jeff W.; Va, Porino
Combination of stereospecific dihydroxylation and enzyme catalyzed enantioselective resolution for synthesis of enantiopure vicinal diols
By employing a combination of stereospecific osmium catalyzed dihydroxylation of selected alkenes, and enantioselective lipase catalyzed kinetic resolution, nine alkenes were converted into nine enantiopure vicinal diols and nine enantiopure hydroxy butanoates.
Anders Riise Moen; Kjersti Ruud; Thorleif Anthonsen
Influence of Catalyst Structure and Reaction Conditions on anti- versus syn-Aminopalladation Pathways in Pd-Catalyzed Alkene Carboamination Reactions of N-Allylsulfamides.
The Pd-catalyzed coupling of N-allylsulfamides with aryl and alkenyl triflates to afford cyclic sulfamide products is described. In contrast to other known Pd-catalyzed alkene carboamination reactions, these transformations may be selectively induced to occur by way of either anti- or syn-aminopalladation mechanistic pathways by modifying the catalyst structure and reaction conditions. PMID:24938206
Fornwald, Ryan M; Fritz, Jonathan A; Wolfe, John P
?-Complexation in nickel-catalyzed cross-coupling reactions.
The kinetic isotope effect (KIE) is used to experimentally elucidate the first irreversible step in oxidative addition reactions of a zerovalent nickel catalyst to a set of haloarene substrates. Halogenated o-methylbenzene, dimethoxybenzene, and thiophene derivatives undergo intramolecular oxidative addition through irreversible ?-complexation. Density functional theory computations at the B3LYP-D3/TZ2P-LANL2TZ(f)-LANL08d level predict ?(2)-bound ?-complexes are generally stable relative to a solvated catalyst plus free substrate and that ring-walking of the Ni(0) catalyst and intramolecular oxidative addition are facile in these intermediates. PMID:24490934
Sontag, S Kyle; Bilbrey, Jenna A; Huddleston, N Eric; Sheppard, Gareth R; Allen, Wesley D; Locklin, Jason
Development of Safe and Scalable Continuous-Flow Methods for Palladium-Catalyzed Aerobic Oxidation Reactionså
Summary The synthetic scope and utility of Pd-catalyzed aerobic oxidation reactions has advanced significantly over the past decade, and these reactions have potential to address important green-chemistry challenges in the pharmaceutical industry. This potential has been unrealized, however, because safety concerns and process constraints hinder large-scale applications of this chemistry. These limitations are addressed by the development of a continuous-flow tube reactor, which has been demonstrated on several scales in the aerobic oxidation of alcohols. Use of a dilute oxygen gas source (8% O2 in N2) ensures that the oxygen/organic mixture never enters the explosive regime, and efficient gas-liquid mixing in the reactor minimizes decomposition of the homogeneous catalyst into inactive Pd metal. These results provide the basis for large-scale implementation of palladium-catalyzed (and other) aerobic oxidation reactions for pharmaceutical synthesis.
Ye, Xuan; Diao, Tianning
Exploring the scope of the 29G12 antibody catalyzed 1,3-dipolar cycloaddition reaction.
[Chemical reaction: See text] 29G12 is a murine monoclonal antibody programmed to catalyze the regio- and enantioselective 1,3-dipolar cycloaddition reaction between 4-acetamidobenzonitrile N-oxide 1a and N,N-dimethylacrylamide 2a (Toker, J. D.; Wentworth, P., Jr.; Hu, Y.; Houk, K. N.; Janda, K. D. J. Am. Chem. Soc. 2000, 122, 3244). Given the unique nature of 29G12 as a protein biocatalyst for this chemical reaction, we have investigated both the substrate specificity and mechanistic parameters of the 29G12-catalyzed process. These studies have shown that while 29G12 is specific for its dipole substrate 1a, the antibody is highly promiscuous with respect to the dipolarophiles it can process. 29G12 accepts a bulky hydrophobic dipolarophile cosubstrate, with rates of product formation up to 70-fold faster than with the original substrate 2a. In all cases, the respective isoxazoline products are produced with exquisite regio- and stereochemical control (78-98% ee). Comparison between the steady-state kinetic parameters from the 29G12-catalyzed reaction of 1a with the most efficient versus the original dipolarophile cosubstrate (2m and 2a, respectively), reveals that while the effective molarities (EM)s are almost identical (EM(2m)) 26 M; EM((2a)) 23 M), the affinity of 29G12 for the larger dipolarophile 2m is more than 1 order of magnitude higher than for 2a [Km(2m) 0.44 +/- 0.04 mM; Km(2a) 5.8 +/- 0.4 mM]. Furthermore, when 2m is the cosubstrate, the affinity of 29G12 for its dipole 1a is also greatly improved [Km(1a) 0.82 +/- 0.1 mM compared to Km(1a) 3.4 +/- 0.4 mM when 2a is the cosubstrate]. An analysis of the temperature dependence of the 29G12-catalyzed reaction between 1a and 2m reveals that catalysis is achieved via a decrease in enthalpy of activation (DeltaDeltaH 4.4 kcal mol(-1)) and involves a large increase in the entropy of activation (DeltaDeltaS 10.4 eu). The improved affinity of 29G12 for the nitrile oxide 1a in the presence of 2m, coupled with the increase in DeltaDeltaS during the 29G12-catalyzed reaction between 1a and 2m supports the notion of a structural reorganization of the active site to facilitate this antibody-catalyzed reaction. PMID:16277300
Toker, Jonathan D; Tremblay, Martin R; Yli-Kauhaluoma, Jari; Wentworth, Anita D; Zhou, Bin; Wentworth, Paul; Janda, Kim D
Macromolecular Crowding Effect upon in Vitro Enzyme Kinetics: Mixed Activation-Diffusion Control of the Oxidation of NADH by Pyruvate Catalyzed by Lactate Dehydrogenase.
Enzyme kinetics studies have been usually designed as dilute solution experiments, which differ substantially from in vivo conditions. However, cell cytosol is crowded with a high concentration of molecules having different shapes and sizes. The consequences of such crowding in enzymatic reactions remain unclear. The aim of the present study is to understand the effect of macromolecular crowding produced by dextran of different sizes and at diverse concentrations in the well-known reaction of oxidation of NADH by pyruvate catalyzed by l-lactate dehydrogenase (LDH). Our results indicate that the reaction rate is determined by both the occupied volume and the relative size of dextran obstacles with respect to the enzyme present in the reaction. Moreover, we analyzed the influence of macromolecular crowding on the Michaelis-Menten constants, vmax and Km. The obtained results show that only high concentrations and large sizes of dextran reduce both constants suggesting a mixed activation-diffusion control of this enzymatic reaction due to the dextran crowding action. From our knowledge, this is the first experimental study that depicts mixed activation-diffusion control in an enzymatic reaction due to the effect of crowding. PMID:24660904
Balcells, Cristina; Pastor, Isabel; Vilaseca, Eudald; Madurga, Sergio; Cascante, Marta; Mas, Francesc
Existence of efficient divalent metal ion-catalyzed and inefficient divalent metal ion-independent channels in reactions catalyzed by a hammerhead ribozyme
The hammerhead ribozyme is generally accepted as a well characterized metalloenzyme. However, the precise nature of the interactions of the RNA with metal ions remains to be fully defined. Examination of metal ion-catalyzed hammerhead reactions at limited concentrations of metal ions is useful for evaluation of the role of metal ions, as demonstrated in this study. At concentrations of Mn2+ ions from 0.3 to 3 mM, addition of the ribozyme to the reaction mixture under single-turnover conditions enhances the reaction with the product reaching a fixed maximum level. Further addition of the ribozyme inhibits the reaction, demonstrating that a certain number of divalent metal ions is required for proper folding and also for catalysis. At extremely high concentrations, monovalent ions, such as Na+ ions, can also serve as cofactors in hammerhead ribozyme-catalyzed reactions. However, the catalytic efficiency of monovalent ions is extremely low and, thus, high concentrations are required. Furthermore, addition of monovalent ions to divalent metal ion-catalyzed hammerhead reactions inhibits the divalent metal ion-catalyzed reactions, suggesting that the more desirable divalent metal ion¢ribozyme complexes are converted to less desirable monovalent metal ion¢ribozyme complexes via removal of divalent metal ions, which serve as a structural support in the ribozyme complex. Even though two channels appear to exist, namely an efficient divalent metal ion-catalyzed channel and an inefficient monovalent metal ion-catalyzed channel, it is clear that, under physiological conditions, hammerhead ribozymes are metalloenzymes that act via the significantly more efficient divalent metal ion-dependent channel. Moreover, the observed kinetic data are consistent with LilleyÆs and DeRoseÆs two-phase folding model that was based on ground state structure analyses.
Zhou, Jing-Min; Zhou, De-Min; Takagi, Yasuomi; Kasai, Yasuhiro; Inoue, Atsushi; Baba, Tadashi; Taira, Kazunari
Pre-Steady-State Kinetic Analysis of Enzyme-monitored Turnover during Cystathionine ?-Synthase-catalyzed H2S-Generationå
Cystathionine ?-synthase (CBS) catalyzes the first step in the transsulfuration pathway in mammals, i.e., the condensation of serine and homocysteine to produce cystathionine and water. Recently, we have reported a steady-state kinetic analysis of the three hydrogen sulfide (H2S)-generating reactions that are catalyzed by human and yeast CBS (Singh et al (2009) J Biol Chem 284: 22457-66). In the current study, we report a pre-steady-state kinetic analysis of intermediates in the H2S-generating reactions catalyzed by yeast CBS (yCBS). Because yCBS does not have a heme cofactor, in contrast to human CBS, it is easier to observe reaction intermediates with yCBS. The most efficient route for H2S generation by yCBS is the ?-replacement of the cysteine thiol by homocysteine. In this reaction, yCBS first reacts with cysteine to release H2S and forms an aminoacrylate intermediate (kobs=1.61 ▒ 0.04 mM?1 s?1 at low cysteine and 2.8 ▒ 0.1 mM?1 s?1 at high cysteine concentrations, at 20 ░C), which has an absorption maximum at 465 nm. Homocysteine binds to the EĢaminoacrylate intermediate with a bimolecular rate constant of 142 mM?1 s?1 and rapidly condenses to form the enzyme-bound external aldimine of cystathionine. The reactions could be partially rate limited by release of the products, cystathionine and H2S.
Singh, Sangita; Ballou, David P.; Banerjee, Ruma
Investigation of the stereodynamics of molecules and catalyzed reactions by CE.
The investigation of the molecular dynamics of stereoisomers and the study of the kinetics of reactions, in particular of catalyzed reactions, is of fundamental interest in chemistry, biochemistry, and medicine. Understanding how to control the transition state of a reaction allows for a directed design of new catalysts and benign processes. The integration of reactions and capillary or microchip-based electrophoretic separations is highly attractive to perform on-column derivatizations or enzymatic on-column digests of peptides and proteins for further characterization. The present review article focuses on the recent advances to study the stereodynamics of molecules and reaction kinetics of catalyzed processes by means of CE. Models and algorithms to evaluate interconversion profiles obtained by electrophoretic separation techniques are discussed with respect to the challenging demands of high separation efficiencies typical for electrophoretic techniques. Models used for evaluation are based on iterative computer simulation algorithms using the theoretical plate model or stochastic model of chromatography, empirical calculation methods, derived from equations used in chemical engineering, namely Damk÷hler analysis, and direct access with the approximation function and more recently with the unified equation, which can be applied to all kinds of first-order reactions taking place during a chromatographic or a electrophoretic separation. Furthermore, areas of applications are presented and discussed to give a guideline for using dynamic CE and on-column reaction electrophoresis to study kinetics of reactions and dynamic processes. PMID:20191543
Trapp, Oliver
Rhodium complex-catalyzed Pauson-Khand-type reaction with aldehydes as a CO source.
With aldehydes as a CO source under solvent-free conditions, rhodium complex efficiently catalyzed an intramolecular carbonylative alkene-alkyne coupling (Pauson-Khand-type reaction) and various bicyclic enones were obtained in high yield. Experiments under argon flow and a 13C-labeling experiment suggested that almost no free carbon monoxide was generated in this reaction. When noncationic rhodium complex with chiral phosphine was used as a chiral catalyst, the reaction proceeded enantioselectively to give various chiral cyclopentenones in up to 90% ee under solvent-free conditions. PMID:12375978
Shibata, Takanori; Toshida, Natsuko; Takagi, Kentaro
Palladium-catalyzed Hiyama-type cross-coupling reactions of arenesulfinates with organosilanes.
Palladium-catalyzed Hiyama-type cross-coupling reactions of various arenesulfinates with organosilanes were achieved in good to excellent yields under aerobic conditions at 70 ░C. Fluoride is essential, and tetrabutylammonium fluoride (TBAF) was shown to be the most efficient additive for these cross-coupling reactions. These cross-coupling reactions of the arenesulfinates provide high yields and show wide functional group tolerance, making them attractive alternative transformations to traditional cross-coupling approaches for carbon-carbon bond construction. PMID:23656304
Cheng, Kai; Hu, Sai; Zhao, Baoli; Zhang, Xian-Man; Qi, Chenze
Intramolecular Pd(II)-catalyzed oxidative biaryl synthesis under air: reaction development and scope.
New reaction conditions for intramolecular palladium(II)-catalyzed oxidative carbon-carbon bond formation under air are described. The use of pivalic acid as the reaction solvent, instead of acetic acid, results in greater reproducibility, higher yields, and broader scope. This includes the use of electron-rich diarylamines as illustrated in the synthesis of three naturally occurring carbazole products: Murrayafoline A, Mukonine, and Clausenine. A variety of side products have also been isolated, casting light on competing reaction pathways and revealing new reactivity with palladium(II) catalysis. PMID:18543991
Liķgault, BenoŅt; Lee, Doris; Huestis, Malcolm P; Stuart, David R; Fagnou, Keith
Enzyme-Catalyzed Synthesis of Unsaturated Aliphatic Polyesters Based on Green Monomers from Renewable Resources
Bio-based commercially available succinate, itaconate and 1,4-butanediol are enzymatically co-polymerized in solution via a two-stage method, using Candida antarctica Lipase B (CALB, in immobilized form as Novozyme« 435) as the biocatalyst. The chemical structures of the obtained products, poly(butylene succinate) (PBS) and poly(butylene succinate-co-itaconate) (PBSI), are confirmed by 1H- and 13C-NMR. The effects of the reaction conditions on the CALB-catalyzed synthesis of PBSI are fully investigated, and the optimal polymerization conditions are obtained. With the established method, PBSI with tunable compositions and satisfying reaction yields is produced. The 1H-NMR results confirm that carbon-carbon double bonds are well preserved in PBSI. The differential scanning calorimetry (DSC) and thermal gravimetric analysis (TGA) results indicate that the amount of itaconate in the co-polyesters has no obvious effects on the glass-transition temperature and the thermal stability of PBS and PBSI, but has significant effects on the melting temperature.
Jiang, Yi; Woortman, Albert J.J.; Alberda van Ekenstein, Gert O.R.; Loos, Katja
Enzyme catalyzed cross-linking of spruce galactoglucomannan improves its applicability in barrier films.
Hemicelluloses are one of the main constituents of plant cell walls and thereby one of the most abundant biopolymers on earth. They can be obtained as by-products from different wood based processes, most importantly from the mechanical pulping. Hemicelluloses have interesting properties in e.g. barrier film applications. However, their relatively low molecular weight after isolation and co-extraction with lignin has limited their use. In this work, we present a novel technique for increasing the molecular weight of different wood hemicelluloses from mechanical pulping process waters as well as from pre-hydrolysis extracts. This is achieved by enzyme-catalyzed cross-linking of aromatic moieties bound to the hemicelluloses. The cross-linking treatment resulted in significantly improved mechanical properties in barrier films made with spruce galactoglucomannan. To our knowledge, this is the first time that wood hemicelluloses have been cross-linked by utilizing the bound aromatic moieties and creates new possibilities for utilizing this raw material source. PMID:23648031
Oinonen, Petri; Areskogh, Dimitri; Henriksson, Gunnar
Zinc Enzymes.
Discusses the role of zinc in various enzymes concerned with hydration, hydrolysis, and redox reactions. The binding of zinc to protein residues, properties of noncatalytic zinc(II) and catalytic zinc, and the reactions catalyzed by zinc are among the topics considered. (JN)
Bertini, I.; And Others
Reaction kinetics of substrate transglycosylation catalyzed by TreX of Sulfolobus solfataricus and effects on glycogen breakdown.
We studied the activity of a debranching enzyme (TreX) from Sulfolobus solfataricus on glycogen-mimic substrates, branched maltotetraosyl-?-cyclodextrin (Glc?-?-CD), and natural glycogen to better understand substrate transglycosylation and the effect thereof on glycogen debranching in microorganisms. The validation test of Glc?-?-CD as a glycogen mimic substrate showed that it followed the breakdown process of the well-known yeast and rat liver extract. TreX catalyzed both hydrolysis of ?-1,6-glycosidic linkages and transglycosylation at relatively high (>0.5 mM) substrate concentrations. TreX transferred maltotetraosyl moieties from the donor substrate to acceptor molecules, resulting in the formation of two positional isomers of dimaltotetraosyl-?-1,6-?-cyclodextrin [(Glc?)?-?-CD]; these were 6(1),6(3)- and 6(1),6(4)-dimaltotetraosyl-?-1,6-?-CD. Use of a modified Michaelis-Menten equation to study substrate transglycosylation revealed that the kcat and Km values for transglycosylation were 1.78 ū 10(3) s(-1) and 3.30 mM, respectively, whereas the values for hydrolysis were 2.57 ū 10(3) s(-1) and 0.206 mM, respectively. Also, enzyme catalytic efficiency (the kcat/Km ratio) increased as the degree of polymerization of branch chains rose. In the model reaction system of Escherichia coli, glucose-1-phosphate production from glycogen by the glycogen phosphorylase was elevated ?1.45-fold in the presence of TreX compared to that produced in the absence of TreX. The results suggest that outward shifting of glycogen branch chains via transglycosylation increases the number of exposed chains susceptible to phosphorylase action. We developed a model of the glycogen breakdown process featuring both hydrolysis and transglycosylation catalyzed by the debranching enzyme. PMID:24610710
Nguyen, Dang Hai Dang; Park, Jong-Tae; Shim, Jae-Hoon; Tran, Phuong Lan; Oktavina, Ershita Fitria; Nguyen, Thi Lan Huong; Lee, Sung-Jae; Park, Cheon-Seok; Li, Dan; Park, Sung-Hoon; Stapleton, David; Lee, Jin-Sil; Park, Kwan-Hwa
Mechanism and Stereochemical Course at Phosphorus of the Reaction Catalyzed by a Bacterial Phosphotriesterase,
Abstract: The reaction mechanism for the phosphotriesterase from Pseudomonas diminuta has been examined. When paraoxon (diethyl 4-nitrophenyl phosphate) is hydrolyzed by this enzyme in oxygen-18-labeled water, the oxygen-18 label is found exclusively in t...
V. E. Lewis W. J. Donarski J. R. Wild F. M. Raushel
Optimization of the enzyme-catalyzed synthesis of amino acid-based surfactants from palm oil fractions
The feasibility of using palm oil fractions as cheap and abundant sources of raw material for the synthesis of amino acid surfactants was investigated. Of a number of enzymes screened, the best results were obtained with the immobilized enzyme, Lipozyme. The effects of temperature, solvent, incubation period, fatty substrate\\/amino acid molar ratio, enzyme amount, and water removal on the reactions
Ee Lin Soo; Abu Bakar Salleh; Mahiran Basri; Raja Noor Zaliha Raja Abdul Rahman; Kamarulzaman Kamaruddin
Efficient and Stereoselective Synthesis of Yellow Scale Pheromone via Alkyne Haloboration, Zr-Catalyzed Asymmetric Carboalumination of Alkenes (ZACA Reaction), and Pd-Catalyzed Tandem Negishi Coupling
A Pd-catalyzed reaction of allylzincs with the 1-octyne bromoboration product gives the desired allyl-alkenyl coupling products in good yields except with H2C=CHCH2ZnBr. This reaction is suitable for converting an alkyne bromoboration product 3 into 4 with no isomerization or ?-elimination. The Pd-catalyzed isoalkyl-alkenyl coupling of 4 with the isoalkylzinc reagent derived from 2 provides yellow scale pheromone (1) of ?98% isomeric purity in 34% in six steps from TBDPS-protected homoallyl alcohol.
Xu, Zhaoqing; Negishi*, Ei-ichi
Lipoxygenase from banana leaf: purification and characterization of an enzyme that catalyzes linoleic acid oxygenation at the 9-position.
The objective of the present study was to purify and characterize the lipoxygenase (LOX) from banana leaf (Giant Cavendishii, AAA), an unutilized bioresource. LOX was extracted, isolated, and purified 327-fold using 25-50% saturation of ammonium sulfate fractionation, hydroxyapatite column separation, and gel filtration on Superdex 200. The molecular mass of the purified LOX was 85 kDa, K(m) was 0.15 mM, and V(max) was 2.4 microM/min.mg using linoleic acid as substrate. Triton X-100 was required in the extraction medium; otherwise, no LOX activity was detected. LOX activity increased with the concentration of Triton X-100 with an optimum at 0.1%. The optimal pH of the purified LOX from banana leaf was 6.2, and optimal temperature was 40 degrees C. The LOX showed the highest reactivity toward 18:2 followed by 18:3 and 20:4. A very low reaction rate was observed toward 20:5 and 22:6. On the basis of retention time in normal phase HPLC, the products of 18:2 or 18:3 catalyzed by purified LOX were hydroperoxyoctadecadienoic acid or hydroperoxyoctadecatrienoic acid. It seems that 9-LOX is the predominant enzyme in banana leaf. Banada leaf dried at 110 degrees C for 2 h developed algal aroma. Banana leaf extract stored at 10 degrees C for 12 h formed an oolong tea-like flavor. Banana leaf extract reacted with 18:2 or soybean oil pretreated with bacterial lipase produced green and melon-like aroma, whereas the same reaction with 18:3 produced a sweet, fruity, cucumber-like flavor note. PMID:16608245
Kuo, Jen-Min; Hwang, Ann; Yeh, Dong-Bor; Pan, Min-Hsiung; Tsai, Mei-Ling; Pan, Bonnie Sun
The GenK-catalyzed C-6? Methylation in the Biosynthesis of Gentamicin: Isolation and Characterization of a Cobalamin-dependent Radical SAM Enzyme
The existence of cobalamin (Cbl)-dependent enzymes that are members of the radical S-adenosyl-L-methionine (SAM) superfamily was previously predicted based on bioinformatic analysis. A number of these are Cbl-dependent methyltransferases but the details surrounding their reaction mechanisms have remained unclear. In this report we demonstrate the in vitro activity of GenK, a Cbl-dependent radical SAM enzyme that methylates an unactivated sp3 carbon during the biosynthesis of gentamicin, an aminoglycoside antibiotic. Experiments to investigate the stoichiometry of the GenK reaction revealed that one equivalent each of 5?-deoxyadenosine and S-adenosyl-homocysteine are produced for each methylation reaction catalyzed by GenK. Furthermore, isotope-labeling experiments demonstrate that the S-methyl group from SAM is transferred to Cbl and the aminoglycoside product during the course of the reaction. Based on these results, one mechanistic possibility for the GenK reaction can be ruled out and further questions regarding the mechanisms of Cbl-dependent radical SAM methyltransferases, in general, are discussed.
Kim, Hak Joong; McCarty, Reid M.; Ogasawara, Yasushi; Liu, Yung-nan; Mansoorabadi, Steven O.; LeVieux, Jake; Liu, Hung-wen
Palladium-catalyzed/norbornene-mediated c?h activation/ N-tosylhydrazone insertion reaction: a route to highly functionalized vinylarenes.
A straightforward method for the synthesis of highly functionalized vinylarenes through palladium-catalyzed, norbornene-mediated C?H activation/carbene migratory insertion is described. Extension to a one-pot procedure is also developed. Furthermore, this method can also be used to generate polysubstituted bicyclic molecules. The reaction proceeds under mild conditions to give the products in satisfactory yields using readily available starting materials. This is a Catellani-Lautens reaction that incorporates different types of coupling partners. Additionally, this reaction is the first to demonstrate the possibility of combining Pd-catalyzed insertion of diazo compounds and Pd-catalyzed C?H activation. PMID:24771707
Zhou, Ping-Xin; Zheng, Lan; Ma, Jun-Wei; Ye, Yu-Ying; Liu, Xue-Yuan; Xu, Peng-Fei; Liang, Yong-Min
The rapid and enhanced reduction of graphene oxide by microwave assisted acid catalyzed reaction.
We report a novel synthetic route to fabricate reduced graphene oxide (rGO) from graphene oxide (GO) using a microwave assisted acid catalyzed reaction in organic solvent. The obtained rGO in this study exhibited 4 times higher electrical conductivity, less oxygen content and better ordered structure than that of conventional solvothermally fabricated ones. By using microwave irradiation, high quality rGO can be obtained in several minutes. PMID:24245202
Tien, Huynh Ngoc; Luan, Van Hoang; Hoa, Le Thuy; Lee, Tae Kyu; Kong, Byung-Seon; Chung, Jin Suk; Kim, Eui Jung; Hur, Seung Hyun
Evaluation of catalyst acidity and substrate electronic effects in a hydrogen bond-catalyzed enantioselective reaction.
A modular catalyst structure was applied to evaluate the effects of catalyst acidity in a hydrogen bond-catalyzed hetero Diels-Alder reaction. Linear free energy relationships between catalyst acidity and both rate and enantioselectivity were observed, where greater catalyst acidity leads to increased activity and enantioselectivity. A relationship between reactant electronic nature and rate was also observed, although there is no such correlation to enantioselectivity, indicating the system is under catalyst control. PMID:20919686
Jensen, Katrina H; Sigman, Matthew S
Isotope Effects and Mechanism of the Asymmetric BOROX Br?nsted Acid Catalyzed Aziridination Reaction
The mechanism of the chiral VANOL-BOROX Br°nsted acid catalyzed aziridination reaction of imines and ethyldiazoacetate has been studied using a combination of experimental kinetic isotope effects and theoretical calculations. A stepwise mechanism where reversible formation of a diazonium ion intermediate precedes rate-limiting ring-closure to form the cis-aziridine is implicated. A revised model for the origin of enantio- and diastereoselectivity is proposed based on relative energies of the ring closing transition structures.
Vetticatt, Mathew J.; Desai, Aman A.; Wulff, William D.
Dehydrogenative Meyer-Schuster-like rearrangement: a gold-catalyzed reaction generating an alkyne.
Easily accessible propargylic esters are converted to the inverted alkynyl ketones in an oxidative gold-catalyzed reaction. Gagosz's catalyst in combination with PhI(OAc)2 is the best system for this conversion and 18 examples with yields up to 80?% are reported. The results indicate that the triple bond in the product is formed by elimination from a vinylgold intermediate. In a formal sense the new conversion overall is a dehydrogenative Meyer-Schuster rearrangement. PMID:24338996
Yu, Yang; Yang, Weibo; Pflõsterer, Daniel; Hashmi, A Stephen K
REtools: A laboratory program for restriction enzyme work: enzyme selection and reaction condition assistance
Background Restriction enzymes are one of the everyday tools used in molecular biology. The continuously expanding panel of known restriction enzymes (several thousands) renders their optimal use virtually impossible without computerized assistance. Several manufacturers propose on-line sites that assist scientists in their restriction enzyme work, however, none of these sites meet all the actual needs of laboratory workers, and they do not take into account the enzymes actually present in one's own laboratory. Results Using FileMaker Pro, we developed a stand-alone application which can run on both PCs and Macintoshes. We called it REtools, for Restriction Enzyme tools. This program, which references all currently known enzymes (>3500), permits the creation and update of a personalized list of restriction enzymes actually available in one's own laboratory. Upon opening the program, scientists will be presented with a user friendly interface that will direct them to different menus, each one corresponding to different situations that restriction enzyme users commonly encounter. We particularly emphasized the ease of use to make REtools a solution that laboratory members would actually want to use. Conclusion REtools, a user friendly and easily customized program to organize any laboratory enzyme stock, brings a software solution that will make restriction enzyme use and reaction condition determination straightforward and efficient. The usually unexplored potential of isoschizomers also becomes accessible to all, since REtools proposes all possible enzymes similar to the one(s) chosen by the user. Finally, many of the commonly overlooked subtleties of restriction enzyme work, such as methylation requirement, unusual reaction conditions, or the number of flanking bases required for cleavage, are automatically provided by REtools.
Martin, Patrick; Boulukos, Kim E; Pognonec, Philippe
Iron- and bismuth-catalyzed asymmetric Mukaiyama aldol reactions in aqueous media.
We have developed asymmetric Mukaiyama aldol reactions of silicon enolates with aldehydes catalyzed by chiral Fe(II) and Bi(III) complexes. Although previous reactions often required relatively harsh conditions, such as strictly anhydrous conditions, very low temperatures (-78 ░C), etc., the reactions reported herein proceeded in the presence of water at 0 ░C. To find appropriate chiral water-compatible Lewis acids for the Mukaiyama aldol reaction, many Lewis acids were screened in combination with chiral bipyridine L1, which had previously been found to be a suitable chiral ligand in aqueous media. Three types of chiral catalysts that consisted of a Fe(II) or Bi(III) metal salt, a chiral ligand (L1), and an additive have been discovered and a wide variety of substrates (silicon enolates and aldehydes) reacted to afford the desired aldol products in high yields with high diastereo- and enantioselectivities through an appropriate selection of one of the three catalytic systems. Mechanistic studies elucidated the coordination environments around the Fe(II) and Bi(III) centers and the effect of additives on the chiral catalysis. Notably, both Br°nsted acids and bases worked as efficient additives in the Fe(II) -catalyzed reactions. The assumed catalytic cycle and transition states indicated important roles of water in these efficient asymmetric Mukaiyama aldol reactions in aqueous media with the broadly applicable and versatile catalytic systems. PMID:24101589
Kitanosono, Taku; Ollevier, Thierry; Kobayashi, Sh?
Kinetics of enzyme-catalyzed alcoholysis of soybean oil in n-hexane.
This work investigated the production of fatty acid ethyl esters (FAEEs) from soybean oil using n-hexane as solvent and two commercial lipases as catalysts, Novozym 435 and Lipozyme IM. A Taguchi experimental design was adopted considering the variables temperature (35-65 degrees C), addition of water (0-10 wt/wt%), enzyme (5-20 wt/wt%) concentration, and oil-to-ethanol molar ratio (1:3-1:10). It is shown that complete conversion in FAEE is achieved for some experimental conditions. The effects of process variables on reaction conversion and kinetics of the enzymatic reactions are presented for all experimental conditions investigated in the factorial design. PMID:15917602
de Oliveira, Dķbora; do Nascimento Filho, Irajß; Di Luccio, Marco; Faccio, Carina; Dalla Rosa, Clarissa; Bender, JoŃo Paulo; Lipke, Nßdia; Amroginski, Cristiana; Dariva, Clßudio; de Oliveira, Josķ Vladimir
Enzyme-Catalyzed Oxidation of 5-Hydroxymethylfurfural to Furan-2,5-dicarboxylic Acid.
Furan-2,5-dicarboxylic acid (FDCA) is a biobased platform chemical for the production of polymers. In the past few years, numerous multistep chemical routes have been reported on the synthesis of FDCA by oxidation of 5-hydroxymethylfurfural (HMF). Recently we identified an FAD-dependent enzyme which is active towards HMF and related compounds. This oxidase has the remarkable capability of oxidizing [5-(hydroxymethyl)furan-2-yl]methanol to FDCA, a reaction involving four consecutive oxidations. The oxidase can produce FDCA from HMF with high yield at ambient temperature and pressure. Examination of the underlying mechanism shows that the oxidase acts on alcohol groups only and depends on the hydration of aldehydes for the oxidation reaction required to form FDCA. PMID:24802551
Dijkman, Willem P; Groothuis, Daphne E; Fraaije, Marco W
Theoretical investigation for the reaction of NO 2 with CO catalyzed by Sc +
The mechanism of the reaction NO(2A)+CO(1?+)?NO(2?)+CO(1?g+) catalyzed by Sc + has been investigated by means of UB3LYP/6-311+G(2d) level. Our calculated results strongly indicate that both the reactions NO 2( 2A 1) + Sc +(X 3D) ? NO( 2?) + ScO +(X 1? +) and ScO(X1?+)+CO(1?+)?Sc(XD)+CO(1?g+) are spin-forbidden reactions. The crossing points (CPs) that are involved and the possible spin inversion processes are discussed using the intrinsic reaction coordinate (IRC) approach. On the basis of Hammond postulate, they are typical 'two-state reactivity' (TSR) reactions. And the O-atom affinities (OA) testified that the argumentation is thermodynamically allowed.
Wang, Yong-Cheng; Zhang, Jian-Hui; Geng, Zhi-Yuan; Chen, Dong-Ping; Liu, Ze-Yu; Yang, Xiao-Yan
Differential selectivity of the Escherichia coli cell membrane shifts the equilibrium for the enzyme-catalyzed isomerization of galactose to tagatose.
An Escherichia coli galactose kinase gene knockout (DeltagalK) strain, which contains the l-arabinose isomerase gene (araA) to isomerize d-galactose to d-tagatose, showed a high conversion yield of tagatose compared with the original galK strain because galactose was not metabolized by endogenous galactose kinase. In whole cells of the DeltagalK strain, the isomerase-catalyzed reaction exhibited an equilibrium shift toward tagatose, producing a tagatose fraction of 68% at 37 degrees C, whereas the purified l-arabinose isomerase gave a tagatose equilibrium fraction of 36%. These equilibrium fractions are close to those predicted from the measured equilibrium constants of the isomerization reaction catalyzed in whole cells and by the purified enzyme. The equilibrium shift in these cells resulted from the higher uptake and lower release rates for galactose, which is a common sugar substrate, than for tagatose, which is a rare sugar product. A DeltamglB mutant had decreased uptake rates for galactose and tagatose, indicating that a methylgalactoside transport system, MglABC, is the primary contributing transporter for the sugars. In the present study, whole-cell conversion using differential selectivity of the cell membrane was proposed as a method for shifting the equilibrium in sugar isomerization reactions. PMID:18263746
Kim, Jin-Ha; Lim, Byung-Chul; Yeom, Soo-Jin; Kim, Yeong-Su; Kim, Hye-Jung; Lee, Jung-Kul; Lee, Sook-Hee; Kim, Seon-Won; Oh, Deok-Kun
Beta-lactamase-catalyzed aminolysis of depsipeptides: Proof of the nonexistence of a specific D-phenylalanine/enzyme complex by double-label isotope trapping
The steady-state kinetics of the Enterobacter cloacae P99 beta-lactamase-catalyzed aminolysis of the depsipeptide m-(((phenylacetyl)glycyl)oxy)benzoic acid by D-phenylalanine were consistent with an ordered sequential mechanism with D-phenylalanine binding first. In terms of this mechanism, the kinetics data required that in 20 mM MOPS buffer, pH 7.5, the dissociation constant of the initially formed enzyme/D-phenylalanine complex be around 1.3 mM; at pH 9.0 in 0.1 M carbonate buffer, the complex should be somewhat more stable. Attempts to detect this complex in a binary mixture by spectroscopic methods (fluorescence, circular dichroic, and nuclear magnetic resonance spectra) failed. Kinetic methods were also unsuccessful--the presence of 20 mM D-phenylalanine did not appear to affect beta-lactamase activity nor inhibition of the enzyme by phenylmethanesulfonyl fluoride, phenylboronic acid, or (3-dansylamidophenyl)boronic acid. Equilibrium dialysis experiments appeared to indicate that the dissociation constant of any binary enzyme/D-phenylalanine complex must be somewhat higher than the kinetics allowed (greater than 2 mM). Since the kinetics also required that, at high depsipeptide concentrations, and again with the assumption of the ordered sequential mechanism, the reaction of the enzyme/D-phenylalanine complex to aminolysis products be faster than its reversion to enzyme and D-phenylalanine, a double-label isotope-trapping experiment was performed.
Pazhanisamy, S.; Pratt, R.F. (Wesleyan Univ., Middletown, CT (USA))
Big-Bang Nucleosynthesis Reactions Catalyzed by a Long-Lived Negatively Charged Leptonic Particle
An accurate quantum three-body calculation is performed for the new type of big-bang nucleosynthesis (BBN) reactions that are catalyzed by a hypothetical long-lived negatively charged, massive leptonic particle (called X^-) such as the supersymmetric (SUSY) particle stau, the scalar partner of the tau lepton. It is known that if the X^- particle has a lifetime ?_X ? 10^3 s, it can capture a light element previously synthesized in standard BBN and form a Coulombic bound state, for example, (^7Be X^-) at temperature T_9 ? 0.4 (in units of 10^9 K), (? X^-) at T_9 ? 0.1 and (p X^-) at T_9 ? 0.01. The bound state, an exotic atom, is expected to induce the following reactions in which X^- acts as a catalyst: i) ?-transfer reactions such as (? X^-)+d to ^6Li + X, ii) radiative capture reactions such as (^7Be X^-) + p to (^8B X^-) + ?, iii) three-body breakup reactions such as (^7Li X^-) + p to ? + ? + X^-, iv) charge-exchange reactions such as (p X^-) + ? to (? X^-) +p and v) neutron induced reactions such as (^8Be X^-) + n to ^9Be + X^-. In recent papers it has been claimed that some of these X^-catalyzed reactions have significantly large cross sections so that the inclusion of the reactions into the BBN network calculation can markedly change the abundances of some elements, giving not only a solution to the ^6Li-^7Li problem (the calculated underproduction of ^6Li by a factor of ś 1000 and overproduction of ^7Li+$^7Be by a factor of ś 3) but also a constraint on the lifetime and primordial abundance of the elementary particle X^-. However, most of these calculations of the reaction cross sections in the literature were performed assuming too naive models or approximations that are unsuitable for these complicated low-energy nuclear reactions. We use a high-accuracy few-body calculation method developed by the authors and provide precise cross sections and rates of these catalyzed BBN reactions for use in the BBN network calculation.
Kamimura, M.; Kino, Y.; Hiyama, E.
Computational analysis of cyclophane-based bisthiourea-catalyzed Henry reactions.
The Henry reaction between benzaldehyde and nitromethane catalyzed by a cyclophane-based bisthiourea has been studied with density functional theory [M06-2X-D3/def2-TZVPP/IEFPCM//TPSS-D2/6-31G(d)/IEFPCM]. The results of our study reveal that the transformation involves the reaction of a thiourea-nitronate complex with the uncoordinated aldehyde. On the basis of our calculations, the formation of the major stereoisomer is kinetically preferred. Employing smaller model systems, we show that the observed stereoselectivity arises primarily from differences in hydrogen bonding in diastereomeric transition states. PMID:24927014
Breugst, Martin; Houk, K N
Polystyrenesulfonate-catalyzed synthesis of novel pyrroles through Paal-Knorr reaction
Background The classical Paal-Knorr reaction is one of the simplest and most economical methods for the synthesis of biologically important and pharmacologically useful pyrrole derivatives. Results Polystyrenesulfonate-catalyzed simple synthesis of substituted pyrroles following Paal-Knorr reaction has been accomplished with an excellent yield in aqueous solution. This method also produces pyrroles with multicyclic polyaromatic amines. Conclusions The present procedure for the synthesis of N-polyaromatic substituted pyrroles will find application in the synthesis of potent biologically active molecules.
The Allyl Intermediate in Regioselective and Enantioselective Iridium-Catalyzed Asymmetric Allylic Substitution Reactions
The isolation and structural characterization of metallacyclic allyl (2a) and crotyl (2b) iridium complexes are reported. Complexes 2a and 2b are rare examples of iriduim allyl complexes that undergo nucleophilic attack at terminal position, rather than the central position, of the allyl unit. Structures of 2a and 2b were obtained by X-ray diffraction. Nucleophilic attack was observed at the carbon that is bound to iridium trans to phosphorus through a longer Ir-C bond. However, the effect of the trans phosphine ligand on the Ir-C bond lengths was smaller than the effect of the substituent on the allyl group in 2b. The competence of complexes 2a and 2b to be intermediates in the catalytic asymmetric allylic substitutions was evaluated by studying their reactivity towards stabilized carbon and heteroatom nucleophiles and comparing the rates and selectivities to those of the catalytic reactions. The stereoselectivity and regioselectivity of stoichiometric reactions of 2b were similar to those of reactions catalyzed by the previously reported iridium catalysts, supporting their intermediacy in the catalytic reactions. Based on the structural data, a model is proposed for the origin of stereoselectivity in iridium-catalyzed asymmetric allylic substitution reactions.
Madrahimov, Sherzod T.; Markovic, Dean; Hartwig., John F.
The mechanism of the NHC catalyzed aza-Morita-Baylis-Hillman reaction: insights into a new substrate-catalyzed bimolecular pathway.
The first mechanistic study on the NHC-catalyzed aza-MBH reaction between cyclopentenone and N-mesylbenzaldimine using density functional theory reveals that a bimolecular mechanism, involving two molecules of benzaldimine in the proton transfer, is energetically more preferred over the conventional direct proton transfer. PMID:24569854
Verma, Pritha; Verma, Pragya; Sunoj, Raghavan B
Copper-catalyzed intramolecular tandem reaction of (2-halogenphenyl)(3-phenyloxiran-2-yl)methanones: synthesis of (Z)-aurones.
A convenient and efficient method for the copper-catalyzed synthesis of (Z)-aurones via intramolecular tandem reaction of (2-halogenphenyl)(3-phenyloxiran-2-yl)methanones is reported. Moreover, a plausible mechanism for the formation of (Z)-aurones is proposed. This is the first report on the synthesis of (Z)-aurones through copper-catalyzed Ullmann coupling reaction employing epoxides as substrates. PMID:24735197
Weng, Yiyi; Chen, Qixu; Su, Weike
RNase P enzymes: divergent scaffolds for a conserved biological reaction.
Ribonuclease P (RNase P) catalyzes the maturation of the 5' end of precursor-tRNAs (pre-tRNA) and is conserved in all domains of life. However, the composition of RNase P varies from bacteria to archaea and eukarya, making RNase P one of the most diverse enzymes characterized. Most known RNase P enzymes contain a large catalytic RNA subunit that associates with one to 10 proteins. Recently, a protein-only form of RNase P was discovered in mitochondria and chloroplasts of many higher eukaryotes. This proteinaceous RNase P (PRORP) represents a new class of metallonucleases. Here we discuss our recent crystal structure of PRORP1 from Arabidopsis thaliana and speculate on the reasons for the replacement of catalytic RNA by a protein catalyst. We conclude, based on an analysis of the catalytic efficiencies of ribonucleoprotein (RNP) and PRORP enzymes, that the need for greater catalytic efficiency is most likely not the driving force behind the replacement of the RNA with a protein catalyst. The emergence of a protein-based RNase P more likely reflects the increasing complexity of the biological system, including difficulties in importation into organelles and vulnerability of organellar RNAs to cleavage. PMID:23595059
Howard, Michael J; Liu, Xin; Lim, Wan Hsin; Klemm, Bradely P; Fierke, Carol A; Koutmos, Markos; Engelke, David R
Spontaneous high-yield hydrogen production from cellulosic materials and water catalyzed by enzyme cocktail
Carbon-neutral hydrogen gas is a compelling energy carrier, especially for the transportation section. Low-cost hydrogen can be produced from abundant renewable lignocellulosic biomass through a number of methods employing chemical catalysis, biocatalysis or a combination of both, but these technologies suffer from low hydrogen yields (well below the theoretical yield of 12 H2 per glucose), undesired side-products and/or required severe reaction conditions. Here we present a novel in vitro synthetic biology approach for producing near theoretical hydrogen yields from cellulosic materials (cellodextrins) and water at 32oC and 1 atm. These non-natural catabolic pathways containing up to 14 enzymes and one coenzyme degrade cellodextrins initially to glucose-1-phosphate and eventually to CO2, split water and finally release the chemical energy in the form of hydrogen gas. Up to 11.2 H2 per anhydroglucose was produced in a batch reaction. This spontaneous endothermic reaction is driven by entropy gain, suggesting that the thermal energy is adsorbed for generating more chemical energy (hydrogen gas) than that in cellodextrins, i.e., output/input of chemical energy > 1, with an input of ambient-temperature thermal energy.
Ye, Xinhao [Virginia Polytechnic Institute and State University (Virginia Tech); Wang, Yiran [Virginia Polytechnic Institute and State University (Virginia Tech); Hopkins, Robert C. [University of Georgia, Athens, GA; Adams, Michael W. W. [University of Georgia, Athens, GA; Evans, Barbara R [ORNL; Mielenz, Jonathan R [ORNL; Zhang, Y.-H. Percival [Virginia Polytechnic Institute and State University (Virginia Tech)
B-d-Xylosidase from Selenomonas ruminantium: Catalyzed Reactions with Natural and Artificial Substrates
Catalytically efficient ?-d-xylosidase from Selenomonas ruminantium (SXA) exhibits pK as 5 and 7 (assigned to catalytic base, D14, and catalytic acid, E186) for k cat/K m with substrates 1,4-?-d-xylobiose (X2) and 1,4-?-d-xylotriose (X3). Catalytically inactive, dianionic SXA (D14-E186-) has threefold lower affinity than catalytically active, monoanionic SXA (D14-E186H) for X2 and X3, whereas D14-E186- has twofold higher affinity than D14-E186H for 4-nitrophenyl-?-d-xylopyranoside (4NPX), and D14-E186- has no affinity for 4-nitrophenyl-?-l-arabinofuranoside. Anomeric isomers, ?-d-xylose and ?-d-xylose, have similar affinity for SXA. 4-Nitrophenol competitively inhibits SXA-catalyzed hydrolysis of 4NPX. SXA steady-state kinetic parameters account for complete progress curves of SXA-catalyzed hydrolysis reactions.
Jordan, Douglas B.
Asymmetric Br?nsted acid-catalyzed aza-Diels-Alder reaction of cyclic C-acylimines with cyclopentadiene
Summary A new chiral Br°nsted acid-catalyzed aza-Diels¢Alder reaction of cyclic C-acylimines with cyclopentadiene has been developed. The reaction provides optically active aza-tetracycles in good yields with high diastereo- and enantioselectivities under mild reaction conditions.
Raja, Sadiya
Silver-Catalyzed Formal Inverse Electron-Demand Diels-Alder Reaction of 1,2-Diazines and Siloxy Alkynes
A highly effective silver-catalyzed formal inverse electron-demand Diels-Alder reaction of 1,2-diazines and siloxy alkynes has been developed. The reactions provide ready access to a wide range of siloxy naphthalenes and anthracenes, which are formed in good to high yields, under mild reaction conditions, using low catalyst loadings.
Turkmen, Yunus E.; Montavon, Timothy J.; Kozmin, Sergey A.; Rawal, Viresh H.
Enzyme Catalysis and the Gibbs Energy
Gibbs-energy profiles are often introduced during the first semester of organic chemistry, but are less often presented in connection with enzyme-catalyzed reactions. In this article I show how the Gibbs-energy profile corresponds to the characteristic kinetics of a simple enzyme-catalyzed reaction. (Contains 1 figure and 1 note.)
1+1 = 3: a fusion of 2 enzymes in the methionine salvage pathway of Tetrahymena thermophila creates a trifunctional enzyme that catalyzes 3 steps in the pathway.
The methionine salvage pathway is responsible for regenerating methionine from its derivative, methylthioadenosine. The complete set of enzymes of the methionine pathway has been previously described in bacteria. Despite its importance, the pathway has only been fully described in one eukaryotic organism, yeast. Here we use a computational approach to identify the enzymes of the methionine salvage pathway in another eukaryote, Tetrahymena thermophila. In this organism, the pathway has two fused genes, MTNAK and MTNBD. Each of these fusions involves two different genes whose products catalyze two different single steps of the pathway in other organisms. One of the fusion proteins, mtnBD, is formed by enzymes that catalyze non-consecutive steps in the pathway, mtnB and mtnD. Interestingly the gene that codes for the intervening enzyme in the pathway, mtnC, is missing from the genome of Tetrahymena. We used complementation tests in yeast to show that the fusion of mtnB and mtnD from Tetrahymena is able to do in one step what yeast does in three, since it can rescue yeast knockouts of mtnB, mtnC, or mtnD. Fusion genes have proved to be very useful in aiding phylogenetic reconstructions and in the functional characterization of genes. Our results highlight another characteristic of fusion proteins, namely that these proteins can serve as biochemical shortcuts, allowing organisms to completely bypass steps in biochemical pathways. PMID:19851454
Salim, Hannah M W; Negritto, Maria Cristina; Cavalcanti, Andre R O
1+1 = 3: A Fusion of 2 Enzymes in the Methionine Salvage Pathway of Tetrahymena thermophila Creates a Trifunctional Enzyme That Catalyzes 3 Steps in the Pathway
The methionine salvage pathway is responsible for regenerating methionine from its derivative, methylthioadenosine. The complete set of enzymes of the methionine pathway has been previously described in bacteria. Despite its importance, the pathway has only been fully described in one eukaryotic organism, yeast. Here we use a computational approach to identify the enzymes of the methionine salvage pathway in another eukaryote, Tetrahymena thermophila. In this organism, the pathway has two fused genes, MTNAK and MTNBD. Each of these fusions involves two different genes whose products catalyze two different single steps of the pathway in other organisms. One of the fusion proteins, mtnBD, is formed by enzymes that catalyze non-consecutive steps in the pathway, mtnB and mtnD. Interestingly the gene that codes for the intervening enzyme in the pathway, mtnC, is missing from the genome of Tetrahymena. We used complementation tests in yeast to show that the fusion of mtnB and mtnD from Tetrahymena is able to do in one step what yeast does in three, since it can rescue yeast knockouts of mtnB, mtnC, or mtnD. Fusion genes have proved to be very useful in aiding phylogenetic reconstructions and in the functional characterization of genes. Our results highlight another characteristic of fusion proteins, namely that these proteins can serve as biochemical shortcuts, allowing organisms to completely bypass steps in biochemical pathways.
Salim, Hannah M. W.; Negritto, Maria Cristina; Cavalcanti, Andre R. O.
?,?-Unsaturated Acyl Azoliums from N-Heterocyclic Carbene Catalyzed Reactions: Observation and Mechanistic Investigation**
Catalytically generated acyl azoliums I and their ?,?-unsaturated counterparts II are thought to be key reactive intermediates in a rapidly growing number of transformations promoted by N-heterocyclic carbene (NHC) catalysts.[1] Acyl azoliums are invoked in the postulated catalytic cycles of nearly all of the new NHC-catalyzed reactions of ?-functionalized aldehydes reported since 2004, in which they are generally assumed to possess the reactivity of an activated carboxylic acid, that is, analogous to an activated ester.[2] In NHC-catalyzed processes, they are most often obtained through internal redox reactions of functionalized aldehydes but have also been prepared by oxidations of the Breslow intermediates[3] or additions to ketenes.[4] Acyl azoliums I are important intermediates in thiamine pyrophosphate (ThPP) dependent enzymatic reactions.[5] Townsend et al. have recently proposed that unsaturated acyl azolium III is the key intermediate in clavulanic acid biosynthesis;[6] despite careful efforts, III or its analogues II have never been characterized or independently synthesized. Here, we document the observation and characterization of ?,?-unsaturated acyl azoliums 1 and 2 (Scheme 1) and demonstrate that their corresponding hemiacetals (1? and 2ö) are the kinetically important intermediates in both their acylation and annulation reactions.
Mahatthananchai, Jessada; Zheng, Pinguan; Bode, Jeffrey W.
Diastereoselectivity in Lewis-Acid Catalyzed Mukaiyama Aldol Reactions: A DFT Study
The basis for diastereoselectivity in Lewis acid-catalyzed Mukaiyama aldol reactions was studied using density functional theory. By exploring the conformations of the transition structures for the diastereodifferentiating step of seven different reactions, simple models were generated. The effects of varying the substituents on the enol carbon and the ?-carbon of the silyl enol ether from methyl to tert-butyl groups and the substituent on the aldehyde between methyl and phenyl groups were investigated by comparison of the transition structures for different reactions. Expanding on the previous qualitative models by Heathcock and Denmark, we found that while the pro-anti pathways takes place via antiperiplanar transition structures, the pro-syn pathways prefer synclinal transition structures. The relative steric effects of the Lewis acid and trimethyl silyl groups and the influence of E/Z isomerism on the aldol transition state were investigated. By calculating 36 transition structures at the M06/6-311G*//B3LYP/6-31G* level of theory and employing the IEFPCM polarizable continuum model for solvation effects, this study expands the mechanistic knowledge and provides a model for understanding the diastereoselectivity in Lewis acid-catalyzed Mukaiyama aldol reactions.
Lee, Joshua M.; Helquist, Paul; Wiest, Olaf
Comparison between electrochemistry/mass spectrometry and cytochrome P450 catalyzed oxidation reactions.
The extent to which electrochemistry on-line with electrospray mass spectrometry can be used to mimic cytochrome P450 catalyzed oxidations has been investigated. Comparisons on the mechanistic level have been made for most reactions in an effort to explain why certain reactions can, and some cannot, be mimicked by electrochemical oxidations. The EC/MS/MS system used successfully mimics in cases where the P450 catalyzed reactions are supposed to proceed via a mechanism initiated by a one-electron oxidation, such as N-dealkylation, S-oxidation, P-oxidation, alcohol oxidation and dehydrogenation. The P450 catalyzed reactions initiated via direct hydrogen atom abstraction, such as O-dealkylation and hydroxylation of unsubstituted aromatic rings, generally had a too high oxidation potential to be electrochemically oxidized below the oxidation potential limit of water, and were not mimicked by the EC/MS/MS system. Even though the EC/MS/MS system is not able to mimic all oxidations performed by cytochrome P450, valuable information can be obtained concerning the sensitivity of the substrate towards oxidation and in which position of the molecule oxidations are likely to take place. For small-scale electrochemical synthesis of metabolites, starting from the drug, the EC/MS/MS system should be very useful for quick optimization of the electrochemical conditions. The simplicity of the system, and the ease and speed with which it can be applied to a large number of compounds, make it a useful tool in drug metabolism research. PMID:12672134
Jurva, Ulrik; Wikstr÷m, HÕkan V; Weidolf, Lars; Bruins, Andries P
Fundamental Reaction Pathway and Free Energy Profile for Hydrolysis of Intracellular Second Messenger Adenosine 3',5'-Cyclic Monophosphate (cAMP) Catalyzed by Phosphodiesterase-4
As important drug targets for a variety of human diseases, cyclic nucleotide phosphodiesterases (PDEs) are a superfamily of enzymes sharing a similar catalytic site. We have performed pseudobond first-principles quantum mechanical/molecular mechanical-free energy perturbation (QM/MM-FE) and QM/MM-Poisson-Boltzmann surface area (PBSA) calculations to uncover the detailed reaction mechanism for PDE4-catalyzed hydrolysis of adenosine 3',5'-cyclic monophosphate (cAMP). This is the first report on QM/MM reaction-coordinate calculations including the protein environment of any PDE-catalyzed reaction system, demonstrating a unique catalytic reaction mechanism. The QM/MM-FE and QM/MM-PBSA calculations revealed that the PDE4-catalyzed hydrolysis of cAMP consists of two reaction stages: cAMP hydrolysis (stage 1) and bridging hydroxide ion regeneration (stage 2). The stage 1 includes the binding of cAMP in the active site, nucleophilic attack of the bridging hydroxide ion on the phosphorous atom of cAMP, cleavage of O3'-P phosphoesteric bond of cAMP, protonation of the departing O3' atom, and dissociation of hydrolysis product (AMP). The stage 2 includes the binding of solvent water molecules with the metal ions in the active site and regeneration of the bridging hydroxide ion. The dissociation of the hydrolysis product is found to be rate-determining for the enzymatic reaction process. The calculated activation Gibbs free energy of ?16.0 and reaction free energy of -11.1 kcal/mol are in good agreement with the experimentally derived activation free energy of 16.6 kcal/mol and reaction free energy of -11.5 kcal/mol, suggesting that the catalytic mechanism obtained from this study is reliable and provides a solid base for future rational drug design.
Chen, Xi; Zhao, Xinyun; Xiong, Ying; Liu, Junjun; Zhan, Chang-Guo
Target-catalyzed dynamic assembly-based pyrene excimer switching for enzyme-free nucleic acid amplified detection.
Because of the intrinsic importance of nucleic acid as biotargets, the simple and sensitive detection of nucleic acid is very essential for biological studies and medical diagnostics. Herein, a new strategy for enzyme-free nucleic acid amplified detection has been opened up by combining the signal-amplification capability of target-catalyzed dynamic assembly with the spatially sensitive fluorescent signal of the pyrene excimer. In this strategy, three metastable pyrene-labeled hairpin DNA probes were designed as assembly components, which were kinetically handicapped from cross-opening in the absence of the target DNA. However, in the presence of the target, the dynamic assembly of branched junctions was circularly catalyzed and accompanied by the switching of the pyrene excimer which emits at ~488 nm. Thus, the target DNA could be detected by this simple mix-and-detect amplification method, without expensive and perishable protein enzymes. A good detection capability exhibited with a detectable minimum target concentration of 10 pM, which was comparable to or even better than some reported enzyme-dependent amplification methods, and the potential for the target detection from complex fluids was verified. In addition, as a novel transformation of dynamic DNA assembly technology into enzyme-free signal-amplification analytical application, we infer that the proposed strategy will hold promising potential for application in a wider range of fields, including aptamer-based non-nucleic acid target sensing, biomedicine, and bioimaging. PMID:24749630
Qing, Zhihe; He, Xiaoxiao; Huang, Jin; Wang, Kemin; Zou, Zhen; Qing, Taiping; Mao, Zhengui; Shi, Hui; He, Dinggeng
Water-dependent reaction pathways: an essential factor for the catalysis in HEPD enzyme.
The hydroxyethylphosphonate dioxygenase (HEPD) catalyzes the critical carbon-carbon bond cleavage step in the phosphinothricin (PT) biosynthetic pathway. The experimental research suggests that water molecules play an important role in the catalytic reaction process of HEPD. This work proposes a water involved reaction mechanism where water molecules serve as an oxygen source in the generation of mononuclear nonheme iron oxo complexes. These molecules can take part in the catalytic cycle before the carbon-carbon bond cleavage process. The properties of trapped water molecules are also discussed. Meanwhile, water molecules seem to be responsible for converting the reactive hydroxyl radical group ((-)OH) to the ferric hydroxide (Fe(III)-OH) in a specific way. This converting reaction may prevent the enzyme from damages caused by the hydroxyl radical groups. So, water molecules may serve as biological catalysts just like the work in the heme enzyme P450 StaP. This work could provide a better interpretation on how the intermediates interact with water molecules and a further understanding on the O(18) label experimental evidence in which only a relatively smaller ratio of oxygen atoms in water molecules (?40%) are incorporated into the final product HMP. PMID:22950439
Du, Likai; Gao, Jun; Liu, Yongjun; Liu, Chengbu
Exploiting Acyl and Enol Azolium Intermediates via NHeterocyclic Carbene Catalyzed Reactions of Alpha-Reducible Aldehydes
N-heterocyclic carbenes are well known for their role in catalyzing benzoin and Stetter reactions: the generation of acyl anion equivalents from simple aldehydes to react with a variety of electrophiles. However, when an aldehyde bearing a leaving group or unsaturation adjacent to the acyl anion equivalent is subjected to an NHC, a new avenue of reactivity is unlocked, leading to a number of novel transformations which can generate highly complex products from simple starting materials, many of which are assembled through unconventional bond disconnections. The field of these new reactions - those utilizing ?-reducible aldehydes to access previously unexplored catalytic intermediates ¢ has expanded rapidly in the past eight years. This review aims to provide the reader with a historical perspective on the underlying discoveries that led to the current state of the art, a mechanistic description of these reactions, and a summary of the recent advances in this area.
Vora, Harit U.; Wheeler, Philip
Theoretical (DFT) insights into the mechanism of copper-catalyzed cyclopropanation reactions. Implications for enantioselective catalysis.
The mechanism of the copper(I)-catalyzed cyclopropanation reaction has been extensively investigated for a medium-size reaction model by means of B3LYP/6-31G(d) calculations. The starting ethylene complex of the N,N'-dimethylmalonaldiimine--copper (I) catalyst undergoes a ligand exchange with methyl diazoacetate to yield a reaction intermediate, which subsequently undergoes nitrogen extrusion to generate a copper--carbene complex. The cyclopropanation step takes place through a direct carbene insertion of the metal--carbene species to yield a catalyst--product complex, which can finally regenerate the starting complex. The stereochemical predictions of a more realistic model (by considering a chiral bis(oxazoline)--copper (I) catalyst) have been rationalized in terms of steric repulsions, showing good agreement with experimental data. PMID:11480983
Fraile, J M; GarcĒa, J I; MartĒnez-Merino, V; Mayoral, J A; Salvatella, L
Guerbet reaction of primary alcohols leading to beta-alkylated dimer alcohols catalyzed by iridium complexes.
[IrCl(cod)]2 and [Cp*IrCl2]2 complexes catalyzed efficiently the Guerbet reaction of primary alcohols to beta-alkylated dimer alcohols in good yields. For instance, the reaction of 1-butanol in the presence of [Cp*IrCl2]2 (1 mol %), t-BuOK (40 mol %), and 1,7-octadiene (10 mol %) produced 2-ethyl-1-hexanol in 93% yield. Various primary alcohols undergo the Guerbet reaction under the influence of Ir complexes to give the corresponding dimer alcohols in good yields. This method provides an alternative direct route to beta-alkylated primary alcohols which are prepared by aldol condensation of aldehydes followed by hydrogenation. PMID:17025333
Matsu-ura, Toyomi; Sakaguchi, Satoshi; Obora, Yasushi; Ishii, Yasutaka
Reaction of allylsilanes and allylstannanes with alkynes catalyzed by electrophilic late transition metal chlorides.
The intramolecular reaction of allylsilanes and allylstannanes with alkynes proceeds catalytically in the presence of Pt(II), Pd(II), Ru(II), and Au(III) chlorides. Although more limited, AgOTf also catalyzes the cyclization. Usually, PtCl2 as the catalyst in methanol or acetone gives the best results. The reaction proceeds by exo attack of the allyl nucleophile on the alkyne to form five- or six-membered ring carbocycles. The reaction generally proceeds with anti stereoselectivity. However, a terminally substituted trimethylsilyl derivative reacts by a syn-type addition. The intermediate alkenylpalladium complex has been trapped with allyl chloride to form an allylated derivative with an additional carbon-carbon bond. PMID:12126406
Fernßndez-Rivas, Carolina; Mķndez, MarĒa; Nieto-Oberhuber, Cristina; Echavarren, Antonio M
Deuterium isotope effect on the induction period of the cerium catalyzed Belousov-Zhabotinsky reaction
In this work we present results about the deuterium isotopic effect on the global kinetics of a cerium catalyzed Belousov-Zhabotinsky reaction. A nonlinear dependence of the induction period upon the percentage of deuterated reactants was found in batch conditions. In order to understand this result, we investigated two reaction pathways responsible for the length of the induction period, namely: (a) the reaction between the enolic form of the malonic acid with molecular bromine and (b) the oxidation of malonic acid by the Ce(IV) ion. In both cases we obtained a linear dependence of the kinetic constants on the percentage of deuterated reactants. Nevertheless, by inserting the experimental values in the MBM (Marburg-Budapest-Missoula) model, we were able to qualitatively simulate the observed trend of the induction period.
Rossi, Federico; Simoncini, Eugenio; Marchettini, Nadia; Tiezzi, Enzo
Imparting Catalyst-Control upon Classical Palladium-Catalyzed Alkenyl C-H Bond Functionalization Reactions
Conspectus The functional group transformations carried out by the palladium-catalyzed Wacker and Heck reactions are radically different, but they are both alkenyl C-H bond functionalization reactions that have found extensive use in organic synthesis. The synthetic community depends heavily on these important reactions, but selectivity issues arising from control by the substrate, rather than control by the catalyst, have prevented the realization of their full potential. Because of important similarities in the respective selectivity-determining nucleopalladation and ?-hydride elimination steps of these processes, we posit that the mechanistic insight garnered through the development of one of these catalytic reactions may be applied to the other. In this Account, we detail our efforts to develop catalyst-controlled variants of both the Wacker oxidation and the Heck reaction to address synthetic limitations and provide mechanistic insight into the underlying organometallic processes of these reactions. In contrast to previous reports, we discovered that electrophilic palladium catalysts with non-coordinating counterions allowed for the use of a Lewis basic ligand to efficiently promote TBHP-mediated Wacker oxidation reactions of styrenes. This discovery led to the mechanistically guided development of a Wacker reaction catalyzed by a palladium complex with a bidentate ligand. This ligation may prohibit coordination of allylic heteroatoms, thereby allowing for the application of the Wacker oxidation to substrates that were poorly behaved under classical conditions. Likewise, we unexpectedly discovered that electrophilic Pd-?-alkyl intermediates are capable of distinguishing between electronically inequivalent C¢H bonds during ?-hydride elimination. As a result, we have developed E-styrenyl selective oxidative Heck reactions of previously unsuccessful electronically non-biased alkene substrates using arylboronic acid derivatives. The mechanistic insight gained from the development of this chemistry allowed for the rational design of a similarly E-styrenyl selective classical Heck reaction using aryldiazonium salts and a broad range of alkene substrates. The key mechanistic findings from the development of these reactions provide new insight into how to predictably impart catalyst control in organometallic processes that would otherwise afford complex product mixtures. Given our new understanding, we are optimistic that reactions that introduce increased complexity relative to simple classical processes may now be developed based on our ability to predict the selectivity-determining nucleopalladation and ?-hydride elimination steps through catalyst design.
Sigman, Matthew S.; Werner, Erik W.
Site-Specific Bioconjugation of a Murine Dihydrofolate Reductase Enzyme by Copper(I)-Catalyzed Azide-Alkyne Cycloaddition with Retained Activity
Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) is an efficient reaction linking an azido and an alkynyl group in the presence of copper catalyst. Incorporation of a non-natural amino acid (NAA) containing either an azido or an alkynyl group into a protein allows site-specific bioconjugation in mild conditions via CuAAC. Despite its great potential, bioconjugation of an enzyme has been hampered by several issues including low yield, poor solubility of a ligand, and protein structural/functional perturbation by CuAAC components. In the present study, we incorporated an alkyne-bearing NAA into an enzyme, murine dihydrofolate reductase (mDHFR), in high cell density cultivation of Escherichia coli, and performed CuAAC conjugation with fluorescent azide dyes to evaluate enzyme compatibility of various CuAAC conditions comprising combination of commercially available Cu(I)-chelating ligands and reductants. The condensed culture improves the protein yield 19-fold based on the same amount of non-natural amino acid, and the enzyme incubation under the optimized reaction condition did not lead to any activity loss but allowed a fast and high-yield bioconjugation. Using the established conditions, a biotin-azide spacer was efficiently conjugated to mDHFR with retained activity leading to the site-specific immobilization of the biotin-conjugated mDHFR on a streptavidin-coated plate. These results demonstrate that the combination of reactive non-natural amino acid incorporation and the optimized CuAAC can be used to bioconjugate enzymes with retained enzymatic activity.
Lim, Sung In; Mizuta, Yukina; Takasu, Akinori; Kim, Yong Hwan; Kwon, Inchan
Highly Sensitive Electrochemical Aptasensor Based on a Ligase-Assisted Exonuclease III-Catalyzed Degradation Reaction.
In this paper, we have proposed a new electrochemical aptasensor based on a novel ligase-assisted Exo III-catalyzed degradation reaction (LAECDR), which consists of DNA ligase-catalyzed ligation of thrombin-binding aptamer (TBA) with an extension strand (E-strand) and Exo III-catalyzed selective degradation of probe DNA, by using an improved target-induced strand displacement strategy. As a result of LAECDR, methylene blue (MB)-labeled mononucleotides can be released from the 3'-terminal of probe DNA and captured by cucurbit[7]uril-functionalized electrode to induce noticeable electrochemical response. Nevertheless, in the presence of the target protein, thrombin, the TBA that is partially complementary to probe DNA is preferentially binding with the target protein, thereby inhibiting LAECDR from taking place. The remaining intact probe DNA will prevent the terminal-attached MB from approaching to the electrode surface due to strong electrostatic repulsion, so the electrochemical response will be changed by thrombin. By tracing the electrochemical response of adsorbed MB, our aptasensor can exhibit high sensitivity for thrombin detection with a wide linear range from 100 fM to 1 nM and an extremely low detection limit of 33 fM, which can also easily distinguish thrombin in the complex serum samples with high specificity. Therefore, our aptasensor might have great potential in clinical applications in the future. PMID:24786305
Zhao, Jing; Hu, Suisui; Zhong, Weidong; Wu, Jiguang; Shen, Zhongming; Chen, Zhong; Li, Genxi
High performance catalyzed-reaction layer for medium temperature operating solid oxide fuel cells
New concepts for a high performance catalyzed-reaction layer for medium temperature operating solid oxide fuel cells were proposed. Mixed conducting oxide particles, samaria-doped ceria (SDC), were employed as the anode material utilizing highly dispersed noble metal catalysts on their surface. As the cathode material, Sr-doped LaMnO[sub 3] (LSM) particles catalyzed with microcrystalline Pt were employed. Performances of the anode or cathode were examined in the cell using yttria-stabilized zirconia electrolyte at a series of operating temperatures. It was found that the anodic polarization resistance and its activation energy were greatly decreased by loading only a small amount of the catalysts (such as Ru, Rh, and Pt) onto the SDC particles. The polarization loss at the anode showed a minimum value by using the SDC particles with a mean diameter of 1.5 to 2.0 [mu]m. A large depolarizing effect was also observed with a Pt-catalyzed LSM cathode, especially at high current densities.
Watanabe, M.; Uchida, H.; Shibata, M.; Mochizuki, N.; Amikura, K. (Yamanashi Univ., Kofu (Japan). Lab. of Electrochemical Energy Conversion)
Density functional theory study of the mechanism of the proline-catalyzed intermolecular aldol reaction
.ĀĀ Transition structures associated with the C-C bond-formation step of the proline-catalyzed intermolecular aldol reaction\\u000a between acetone and isobutyraldehyde have been studies using density functional theory methods at the B3LYP\\/6-31G** computational\\u000a level. A continuum model has been selected to represent solvent effects. For this step, which is the stereocontrolling and\\u000a rate-determining step, four reactive channels corresponding to the syn and
Manuel Arn¾; Luis R. Domingo
How does Pin1 catalyze the cis-trans prolyl peptide bond isomerization? A QM/MM and mean reaction force study.
Pin1 represents an enzyme that specifically catalyzes the isomerization of peptide bonds between phosphorylated threonine or serine residues and proline. Despite its relevance as molecular timer in a number of biological processes related to cancer and Alzheimer disease, a detailed understanding of the factors contributing to the catalysis is still missing. In this study, we employ extensive QM/MM molecular dynamics simulations in combination with the mean reaction force (MRF) to discern the influence of the enzyme on the reaction mechanism and the origin of the catalysis. As a recently introduced method, the MRF separates the activation free energy barrier to reach the transition state into structural and electronic contributions providing a more detailed description of the enzyme's function. As a reference, we first study the isomerization starting from the cis form in solution and obtain a free energy barrier and a reaction free energy, which are in agreement with previous studies and experiment. With the new mean reaction force method, intramolecular hydrogen bonds in the peptide were identified that stabilize the transition state and reduce the electronic contribution to the free energy barrier. To elucidate the mechanism of catalysis of Pin1, the reaction in solution and in the catalytic cavity of the enzyme were compared. Both yield the same free energy barrier for the isomerization of the cis form, but with different decomposition in structural and electronic contributions by the mean reaction force. The enzyme reduces the energy required for structural rearrangements to reach the transition state, pointing to a destabilization of the reactant, but increases the electronic contribution to the barrier through specific enzyme-peptide hydrogen bonds. In the reverse reaction, the isomerization of the trans form, the enzyme alters the energetics and the mechanism of the reaction considerably. Unfavorable enzyme-peptide interactions in the catalytic cavity during the isomerization change the reaction coordinate, resulting in two minima with small energy differences to the transition state. These small free energy barriers should in principle make the reaction feasible at room temperature once the conformer is bound in the right conformation. PMID:23030417
V÷hringer-Martinez, Esteban; Duarte, Fernanda; Toro-Labbķ, Alejandro
Effect of tritium on luminous marine bacteria and enzyme reactions.
The paper studies chronic effect of tritiated water, HTO, (0.0002-200 MBq/L) on bioluminescent assay systems: marine bacteria Photobacterium phosphoreum (intact and lyophilized) and coupled enzyme reactions. Bioluminescence intensity serves as a marker of physiological activity. Linear dependencies of bioluminescent intensity on exposure time or radioactivity were not revealed. Three successive stages in bacterial bioluminescence response to HTO were found: (1) absence of the effect, (2) activation, and (3) inhibition. They were interpreted in terms of reaction of organisms to stress-factor i.e. stress recognition, adaptive response/syndrome, and suppression of physiological function. In enzyme system, in contrast, the kinetic stages mentioned above were not revealed, but the dependence of bioluminescence intensity on HTO specific radioactivity was found. Damage of bacteria cells in HTO (100 MBq/L) was visualized by electron microscopy. Time of bioluminescence inhibition is suggested as a parameter to evaluate the bacterial sensitivity to ionizing radiation. PMID:23410594
Selivanova, M A; Mogilnaya, O A; Badun, G A; Vydryakova, G A; Kuznetsov, A M; Kudryasheva, N S
ZnS quantum dots as pH probes for study of enzyme reaction kinetics.
Water soluble ZnS quantum dots (QDs) modified by mercaptoacetic acid (MAA) were used to determinate proton concentration in aqueous solutions by fluorescence spectroscopic technique. The results showed that the fluorescence of the water-soluble QDs could be quenched by proton concentration and the fluorescence intensity of the water-soluble QDs decreased linearly as the pH varied from 4.5 to 7.0. Based on this phenomenon, a convenient, rapid and specific method to determine of enzyme reaction kinetics was proposed. The modified ZnS QDs were successfully used as pH probes in monitoring the hydrolysis of glycidyl butyrate catalyzed by porcine pancreatic lipase (PPL). The proposed method was found to improve stability, sensitivity and a monitoring range for determination proton concentration as compared to the already described analytical methods based on p-Nitrophenoxide (PNP). PMID:22579390
Wu, Dudu; Chen, Zhi
Transition-metal-catalyzed Suzuki-Miyaura cross-coupling reactions: a remarkable advance from palladium to nickel catalysts.
In the transition-metal-catalyzed cross-coupling reactions, the use of the first row transition metals as catalysts is much more appealing than the precious metals owing to the apparent advantages such as cheapness and earth abundance. Within the last two decades, particularly the last five years, explosive interests have been focused on the nickel-catalyzed Suzuki-Miyaura reactions. This has greatly advanced the chemistry of transition-metal-catalyzed cross-coupling reactions. Most notably, a broad range of aryl electrophiles such as phenols, aryl ethers, esters, carbonates, carbamates, sulfamates, phosphates, phosphoramides, phosphonium salts, and fluorides, as well as various alkyl electrophiles, which are conventionally challenging, by applying palladium catalysts can now be coupled efficiently with boron reagents in the presence of nickel catalysts. In this review, we would like to summarize the progress in this reaction. PMID:23460083
Han, Fu-She
Determination of adsorption and kinetic parameters for methyl acetate esterification and hydrolysis reaction catalyzed by Amberlyst 15
In this paper, the adsorption equilibrium constants, dispersion coefficients, and kinetic parameters were obtained for the liquid phase reversible reaction of methanol with acetic acid catalyzed by Amberlyst 15. The adsorption and kinetic parameters are determined corresponding to two different mobile phases, methanol and water. Such parameters are required for three different applications of the model reaction: namely, synthesis of
Weifang Yu; K. Hidajat; Ajay K. Ray
Rhodium(III)-Catalyzed Alkenylation Reactions of 8-Methylquinolines with Alkynes by C(sp(3) )?H Activation.
The alkenylation reactions of 8-methylquinolines with alkynes, catalyzed by [{Cp*RhCl2 }2 ], proceeds efficiently to give 8-allylquinolines in good yields by C(sp(3) )?H bond activation. These reactions are highly regio- and stereoselective. A catalytically competent five-membered rhodacycle has been structurally characterized, thus revealing a key intermediate in the catalytic cycle. PMID:24623676
Liu, Bingxian; Zhou, Tao; Li, Bin; Xu, Shansheng; Song, Haibin; Wang, Baiquan
Chiral gold complex-catalyzed hetero-Diels-Alder reaction of diazenes: highly enantioselective and general for dienes.
A chiral gold(I) complex-catalyzed highly regio- and enantioselective azo hetero-Diels-Alder reaction has been developed. The chiral gold(I) complex acting as a Lewis acid exhibits high efficiency in the activation of urea-based diazene dienophiles. Moreover, this chiral gold catalyst also rendered a cascade intramolecular enyne cycloisomerization/asymmetric azo-HDA reaction. PMID:23421493
Liu, Bin; Li, Kang-Nan; Luo, Shi-Wei; Huang, Jian-Zhou; Pang, Huan; Gong, Liu-Zhu
Rapid Access to Spirocyclized Indolenines via Palladium-Catalyzed Cascade Reactions of Tryptamine Derivatives and Propargyl Carbonate.
We report the intermolecular palladium-catalyzed reaction of tert-butyl propargyl carbonate with tryptamine derivatives or other indole-containing bis-nucleophiles. The reaction proceeds under mild conditions and with low catalyst loadings to afford novel spiroindolenine products in good to high yields. PMID:24964382
Montgomery, Thomas D; Nibbs, Antoinette E; Zhu, Ye; Rawal, Viresh H
The Palladium-Catalyzed Cross-Coupling Reaction of Phenylboronic Acid with Haloarenes in the Presence of Bases
The transition metal-catalyzed reactions of organometallics with organic halides have been extensively studied to prove a new approach to selective formation of carbon-carbon bonds. Recently, such coupling reactions of haloarenes with aryl magnesium and zinc compounds in the presence of palladium or nickel complexes have been reported for the synthesis of biaryls. Davidson and Triggs have previously reported that arylboronic
N. Miyaura; T. Yanagi; A. Suzuki
Car--Parrinello Molecular Dynamics Study of Base-Catalyzed Hydrolysis Reactions
We apply the first principles metadynamics simulation technique implemented in the Car-Parrinello molecular dynamics package to study the base-catalyzed hydrolysis of N-methylacetamide in aqueous solution. Our calculations are carried out in the framework of density functional theory combined with the hybrid BLYP exchange-correlation functional The free energy surfaces and hydrolysis reaction pathways for N-methylacetamide are examined in the presence of a hydroxide ion, and 4, 32, and 64 water molecules. We find that at least 32 water molecules must be explicitly included in metadynamics simulations to accurately describe the mechanism of the hydrolysis reaction of N-Methylacetamide. Our theoretical estimate for the dissociation energy of N-Methylacetamide is in good agreement with the results of previous experimental and theoretical studies.
Alnemrat, Sufian; Vasiliev, Igor; Wang, Haobin
Alkali-Stabilized Pt-OHx Species Catalyze Low-Temperature Water-Gas Shift Reactions
We report that alkali ions (sodium or potassium) added in small amounts activate platinum adsorbed on alumina or silica for the low-temperature water-gas shift (WGS) reaction (H{sub 2}O + CO {yields} H{sub 2} + CO{sub 2}) used for producing H{sub 2}. The alkali ion-associated surface OH groups are activated by CO at low temperatures ({approx}100 C) in the presence of atomically dispersed platinum. Both experimental evidence and density functional theory calculations suggest that a partially oxidized Pt-alkali-O{sub x}(OH){sub y} species is the active site for the low-temperature Pt-catalyzed WGS reaction. These findings are useful for the design of highly active and stable WGS catalysts that contain only trace amounts of a precious metal without the need for a reducible oxide support such as ceria.
Zhai, Y.; Pierre, D; Si, R; Deng, W; Ferrin, P; Nilekar, A; Peng, G; Herron, J; Bell, D; et. al.
Surface-catalyzed air oxidation reactions of hydrazines: Tubular reactor studies
The surface-catalyzed air oxidation reactions of hydrazine, monomethylhydrazine, unsymmetrical dimethylhydrazine, symmetrical dimethylhydrazine, trimethylhydrazine and tetramethylhydrazine were investigated in a metal-powder packed turbular flow reactor at 55 plus or minus 3 C. Hydrazine was completely reacted on all surfaces studied. The major products of monomethylhydrazine (MMH) oxidation were methanol, methane and methyldiazene. The di-, tri- and tetra-methyl hydrazines were essentially unreactive under these conditions. The relative catalytic reactivities toward MMH are: Fe greater than Al2O3 greater than Ti greater than Zn greater than 316 SS greater than Cr greater than Ni greater than Al greater than 304L SS. A kinetic scheme and mechanism involving adsorption, oxidative dehydrogenation and reductive elimination reactions on a metal oxide surface are proposed.
Kilduff, Jan E.; Davis, Dennis D.; Koontz, Steven L.
Secondary sup 15 N isotope effects on the reactions catalyzed by alcohol and formate dehydrogenases
Secondary {sup 15}N isotope effects at the N-1 position of 3-acetylpyridine adenine dinucleotide have been determined, by using the internal competition technique, for horse liver alcohol dehydrogenase (LADH) with cyclohexanol as a substrate and yeast formate dehydrogenase (FDH) with formate as a substrate. On the basis of less precise previous measurements of these {sup 15}N isotope effects, the nicotinamide ring of NAD has been suggested to adopt a boat conformation with carbonium ion character at C-4 during hydride transfer. If this mechanism were valid, as N-1 becomes pyramidal an {sup 15}N isotope effect for the reaction catalyzed by LADH was measured. These values suggest that a significant {sup 15}N kinetic isotope effect is not associated with hydride transfer for LADH and FDH. Thus, in contrast with the deformation mechanism previously postulated, the pyridine ring of the nucleotide apparently remains planar during these dehydrogenase reactions.
Rotberg, N.S.; Cleland, W.W. (Univ. of Wisconsin, Madison (USA))
Mixed-ligand catalysts: a powerful tool in transition-metal- catalyzed cross-coupling reactions.
Transition-metal-catalyzed cross-coupling reactions have fundamentally revolutionized organic synthesis, empowering the otherwise difficult to achieve products with rapid and convenient accesses alongside excellent yields. Within these reactions, ligands often play a critical role in specifically and effectively advocating the corresponding catalysis. Consequently, a myriad of ligands have been created and applied to make a fine tuning of electronic and steric effect of catalysts, remarkably promoting catalytic efficiency and applicability. The "mixed-ligand" concept has recently emerged; by combining and capitalizing on the superiority of each individual ligand already available, an expedient way can be achieved to reach a larger extent of catalytic diversity and efficacy. Given the availability of a wealth of ligands, it is reasonable to have great expectations for the original application of mixed-ligand catalytic systems and their important value in organic synthesis. PMID:24677584
Fan, Yuting; Cong, Mei; Peng, Ling
Hydroxylation reaction catalyzed by the Burkholderia cepacia AC1100 bacterial strain. Involvement of the chlorophenol-4-monooxygenase.
The Burkholderia cepacia AC1100 strain, known to degrade the herbicide, 2,4,5-Trichlorophenoxyacetic acid (2,4,5-T), is able to metabolize 4-hydroxyarylaldehyde, not only into the corresponding acid, but also into a new hydroquinone, 2,5-dihydroxyarylaldehyde. When incubated with resting AC1100 cells or cell-free extracts, syringaldehyde and 3,5-dimethoxy-4-hydroxybenzaldehyde were converted into such metabolites, identified by comparison of their mass and 1H-NMR spectra with those of authentic chemically synthesized samples. With 5-bromovanillin, only one metabolite was formed, the structure of which was identified as 2, 5-dihydroxy-4-methoxy-6-bromobenzaldehyde through 1H-NMR two-dimensional NOESY experiments. All these products result formally from a para hydroxylation of the phenol followed by the cis migration of the aldehyde. This reaction is the only one to be associated with the 2,4,5-T degradation pathway, as the acid formation was retained when the AC1100 strain had lost its degradation ability. Through competitive experiments with halophenols and methimazole, an alternative substrate of flavin monooxygenase, the chlorophenol-4-monooxygenase was recognized to be the enzyme involved in the hydroxylation of 4-hydroxyarylaldehyde. The purified enzyme, previously reported to catalyze the para hydroxylation or dehalogenating hydroxylation of chlorophenols, also promotes this hydroxylation reaction in the presence of NADH and FAD. The kcat value determined for the best substrate, syringaldehyde, 0. 08 s-1, was about 20% of that obtained for 2,6-dichlorophenol hydroxylation (0.38 s-1). PMID:10215866
Martin, G; Dijols, S; Capeillere-Blandin, C; Artaud, I
Summary Hydrolytic reactions of oligopeptide 4-nitroanilides catalyzed by human-?-thrombin, human activated protein C and human factor Xa were studied at pH 8.0¢8.4 and 25.0 ▒ 0.1 ░C by the progress curve method and individual rate constants were calculated mostly within 10% internal error using DYNAFITV. A systematic strategy has been developed for fitting a three-step consecutive mechanism to eighteen hundred to six thousand time-course data points polled from two to four independent kinetic experiments. Enzyme and substrate concentrations were also calculated. Individual rate constants well reproduce published values obtained under comparable conditions and the Michaelis-Menten kinetic parameters calculated from these elementary rate constants are also within reasonable limits of published values. For comparison, the integrated Michaelis-Menten equation was also fitted to data from twelve sets. Both the kcat and kcat/Km values are within 15% agreement with those calculated using the elementary rate constants obtained with DYNAFITV. Rate constants for the second and third consecutive steps are within 3¢4 fold indicating that both determine the overall rate. The Factor Xa-catalyzed hydrolysis of N?-Z-D-Arg-Gly-Arg-pNAĘ2HCl at pH 8.4 in a series of buffers containing increasing fractions of deuterium at 25.0 ▒ 0.1 ░C shows a very strong dependence of k3 and a moderate dependence of k2 on D content in the buffer: the fractionation factors are: 0.49 ▒ 0.03 for K1, 0.70 ▒ 0.05 for k2, and (0.32 ▒ 0.03)2 for k3.
Zhang, Daoning; Kovach, Ildiko M.; Sheehy, John Paul
Crystal structure of the yeast His6 enzyme suggests a reaction mechanism
The Saccharomyces cerevisiae His6 gene codes for the enzyme phosphoribosyl-5-amino-1-phosphoribosyl-4-imidazolecarboxamide isomerase, catalyzing the fourth step in histidine biosynthesis. To get an insight into the structure and function of this enzyme, we determined its X-ray structure at a resolution of 1.30 ┼ using the anomalous diffraction signal of the protein's sulphur atoms at 1.77 ┼ wavelength. His6 folds in an (?/?)8 barrel similar to HisA, which performs the same function in bacteria and archaea. We found a citrate molecule from the buffer bound in a pocket near the expected position of the active site and used it to model the open form of the substrate (phosphoribulosyl moiety), which is a reaction intermediate. This model enables us to identify catalytic residues and to propose a reaction mechanism where two aspartates act as acid/base catalysts: Asp134 as a proton donor for ring opening, and Asp9 as a proton acceptor and donor during enolization of the aminoaldose. Asp9 is conserved in yeast His6 and bacterial or archaeal HisA sequences, and Asp134 has equivalents in both HisA and TrpF, but they occur at a different position in the protein sequence.
Quevillon-Cheruel, Sophie; Leulliot, Nicolas; Graille, Marc; Blondeau, Karine; Janin, Joel; Tilbeurgh, Herman Van
Palladium-Catalyzed Cross-Coupling Reactions of Organosilanols and their Salts
Conspectus In the panoply of modern synthetic methods for forming carbon-carbon and carbon-heteroatom bonds, the transition metal-catalyzed cross coupling of organometallic nucleophiles with organic electrophiles enjoys a preeminent status. The preparative utility of these reactions is, in large measure, a consequence of the wide variety of organometallic donors that have been conscripted into service. The most common of these reagents are organic derivatives of tin, boron, and zinc, which each possess unique advantages and shortcomings. Because of their low cost, low toxicity, and high chemical stability, organosilanes have emerged as viable alternatives to the conventional reagents in recent years. However, unlike the tin- and zinc-based reactions that require no activation or the boron-based reactions that require only heating with mild bases, silicon-based cross-coupling reactions often require heating in the presence of a fluoride source; this has significantly hampered the widespread acceptance of organosilanes. To address the ōfluoride problemö, we have introduced a new paradigm for palladium-catalyzed, silicon-based cross-coupling reactions that employs organosilanols, a previously underutilized class of silicon reagents. The use of organosilanols either in the presence of Br°nsted bases or as their silanolate salts represents a simple and mild alternative to the classic fluoride-based activation method. Organosilanols are easily available by many well-established methods for introducing carbon-silicon bonds onto alkenes, alkynes and arenes, and heteroarenes. Moreover, we have developed four different protocols for the generation of alkali metal salts of, vinyl-, alkenyl-, alkynyl-, aryl-, and heteroarylsilanolates: (1) reversible deprotonation with weak Br°nsted bases, (2) irreversible deprotonation with strong Br°nsted bases, (3) isolation of the salts from irreversible deprotonation, and (4) silanolate exchange with disiloxanes. We have demonstrated the advantages of each of these methods for a number of different coupling classes. The defining feature of this new process is the formation of a covalently linked palladium silanolate species that facilitates the critical transmetalation step. We have verified the intermediacy of a critical species that contains the key Si-O-Pd linkage by its identification as the resting state in reaction mixtures, by X-ray analysis, and by demonstrating its competence in thermal cross-coupling with no additives. Our conclusions contradict the long-standing dogma that silicon-based cross-coupling reactions require the generation of a pentacoordinate siliconate prior to transmetalation. This revelation has opened a new vista for discovery of new reactions that involve this critical process.
Denmark, Scott E.; Regens, Christopher S.
Chemical reactions in the interstellar medium: The HOC+ ? HCO+ Isomerization Reaction catalyzed by H2
The present work studies the catalytic effect of molecular hydrogen on the hydrogen transfer from O bounded to C bounded in HOC+ . For this purpose, the reactions with and without hydrogen assistance were studied. The potential energy surface of this reaction was studied using Density Functional Theory methods (PBE/TVZP). The energy barrier was found to be significantly lower than that of the isolated system: An energy profile in function of the intrinsic reaction coordinate was obtained and used to get the reaction force profile and reaction work, which in turn is used to characterize the reaction mechanism. The main contribution to the activation barrier in the uncatalyzed isomerization is W1= 24,42 kcal/mol and can be attributed to structural changes, which the system suffers in order to reach the transition state. This fact is not modified by the introduction of H2, where the main contribution again is W 1 = 8.38 kcal/mol.This shows that the hydrogen catalyst has no special effect over a specific region, but homogenously lowers W1 and W2.
Vogt-Geisse, S.; Toro-Labbe, A.
Alkyne-azide click reaction catalyzed by metallic copper under ultrasound.
This protocol is for the ultrasound (US)-assisted 1,3-dipolar cycloaddition reaction of azides and alkynes using metallic copper (Cu) as the catalyst. The azido group is a willing participant in this kind of organic reaction and its coupling with alkynes is substantially improved in the presence of Cu(I). This protocol does not require additional ligands and proceeds with excellent yields. The Cu-catalyzed azide-alkyne cycloaddition (CuAAC) is generally recognized as the most striking example of 'click chemistry'. Reactions involving metals represent the favorite domain of sonochemistry because US favors mechanical depassivation and enhances both mass transfer and electron transfer from the metal to the organic acceptor. The reaction rate increases still further when simultaneous US and microwave irradiation are applied. The US-assisted click synthesis has been applied for the preparation of a wide range of 1,4-disubstituted 1,2,3-triazole derivatives starting both from small molecules and oligomers such as cyclodextrins (CDs). Using this efficient and greener protocol, all the adducts can be synthesized in 2-4 h (including work-up and excluding characterization). Click chemistry has been shown to be able to directly link chemistry to biology, thus becoming a true interdisciplinary reaction with extremely wide applicability. PMID:20203675
Cintas, Pedro; Barge, Alessandro; Tagliapietra, Silvia; Boffa, Luisa; Cravotto, Giancarlo
Mesoscopic statistical properties of multistep enzyme-mediated reactions.
Enzyme-mediated reactions may proceed through multiple intermediate conformational states before creating a final product molecule, and one often wishes to identify such intermediate structures from observations of the product creation. In this study, the authors address this problem by solving the chemical master equations for various enzymatic reactions. A perturbation theory analogous to that used in quantum mechanics allows the determination of the first (n) and the second (?2) cumulants of the distribution of created product molecules as a function of the substrate concentration and the kinetic rates of the intermediate processes. The mean product flux V=d(n)/dt (or 'dose-response' curve) and the Fano factor F= ?2/(n) are both realistically measurable quantities, and whereas the mean flux can often appear the same for different reaction types, the Fano factor can be quite different. This suggests both qualitative and quantitative ways to discriminate between different reaction schemes, and the authors explore this possibility in the context of four sample multistep enzymatic reactions. Measuring both the mean flux and the Fano factor can not only discriminate between reaction types, but can also provide some detailed information about the internal, unobserved kinetic rates, and this can be done without measuring single-molecule transition events. PMID:21028932
de Ronde, W H; Daniels, B C; Mugler, A; Sinitsyn, N A; Nemenman, I
Statistical properties of multistep enzyme-mediated reactions
Enzyme-mediated reactions may proceed through multiple intermediate conformational states before creating a final product molecule, and one often wishes to identify such intermediate structures from observations of the product creation. In this paper, we address this problem by solving the chemical master equations for various enzymatic reactions. We devise a perturbation theory analogous to that used in quantum mechanics that allows us to determine the first () and the second (variance) cumulants of the distribution of created product molecules as a function of the substrate concentration and the kinetic rates of the intermediate processes. The mean product flux V=d/dt (or 'dose-response' curve) and the Fano factor F=variance/ are both realistically measurable quantities, and while the mean flux can often appear the same for different reaction types, the Fano factor can be quite different. This suggests both qualitative and quantitative ways to discriminate between different reaction schemes, and we explore this possibility in the context of four sample multistep enzymatic reactions. We argue that measuring both the mean flux and the Fano factor can not only discriminate between reaction types, but can also provide some detailed information about the internal, unobserved kinetic rates, and this can be done without measuring single-molecule transition events.
Nemenman, Ilya [Los Alamos National Laboratory; Sinitsyn, Nikolai A [Los Alamos National Laboratory; De Ronde, Wiet H [AMOLF; Daniels, Bryan C [CORNELL; Mugler, Andrew [COLUMBIA
Optimal distribution of immobilized enzyme in a pellet for a substrate-inhibited reaction
This article sets out to show how the enzyme should be distributed within a porous pellet so that the enzyme effectiveness is maximized, given a fixed total amount of enzyme and a set of diffusion and reaction parameters. The general behaviour of substrate-inhibited reactions and application and function of the optimal enzyme distribution is discussed.
Morbidelli, M.; Servida, A.; Varma, A.
MuteinDB: the mutein database linking substrates, products and enzymatic reactions directly with genetic variants of enzymes
Mutational events as well as the selection of the optimal variant are essential steps in the evolution of living organisms. The same principle is used in laboratory to extend the natural biodiversity to obtain better catalysts for applications in biomanufacturing or for improved biopharmaceuticals. Furthermore, single mutation in genes of drug-metabolizing enzymes can also result in dramatic changes in pharmacokinetics. These changes are a major cause of patient-specific drug responses and are, therefore, the molecular basis for personalized medicine. MuteinDB systematically links laboratory-generated enzyme variants (muteins) and natural isoforms with their biochemical properties including kinetic data of catalyzed reactions. Detailed information about kinetic characteristics of muteins is available in a systematic way and searchable for known mutations and catalyzed reactions as well as their substrates and known products. MuteinDB is broadly applicable to any known protein and their variants and makes mutagenesis and biochemical data searchable and comparable in a simple and easy-to-use manner. For the import of new mutein data, a simple, standardized, spreadsheet-based data format has been defined. To demonstrate the broad applicability of the MuteinDB, first data sets have been incorporated for selected cytochrome P450 enzymes as well as for nitrilases and peroxidases. Database URL: http://www.MuteinDB.org
Braun, Andreas; Halwachs, Bettina; Geier, Martina; Weinhandl, Katrin; Guggemos, Michael; Marienhagen, Jan; Ruff, Anna J.; Schwaneberg, Ulrich; Rabin, Vincent; Torres Pazmino, Daniel E.; Thallinger, Gerhard G.; Glieder, Anton
The Effect of Osmolytes on Protein Dynamics in the LDH-Catalyzed Reactionå
Laser induced temperature jump relaxation spectroscopy was used to probe the effect of osmolytes on the microscopic rate constants of the LDH-catalyzed reaction. NADH fluorescence and absorption relaxation kinetics were measured for the LDH reaction system in presence of varying amounts of trimethylamine-N-oxide (TMAO), a protein stabilizing osmolyte, or urea, a protein destabilizing osmolyte. TMAO in 1 M concentration strongly increases the rate of hydride transfer, nearly nullifies its activation energy, and also slightly increases the enthalpy of hydride transfer. In 1 M urea the hydride transfer enthalpy is almost nullified, but activation energy of the step is not affected significantly. TMAO increases preference of closed conformation of the active site loop in LDHĢNAD+Ģlactate complex; urea decreases it. The loop-opening rate in LDHĢNADHĢpyruvate complex changes its temperature dependence to inverse-Arrhenius with TMAO. In this complex, urea speeds up the loop motion, without changing the loop opening enthalpy. A strong, non-Arrhenius drop in pyruvate binding rate in presence of TMAO offers a decrease in the fraction of the open-loop, pyruvate-binding competent form at higher temperatures. Pyruvate off-rate is not affected by urea, but decreases with TMAO. Thus, the osmolytes strongly affect the rates and thermodynamics of specific events along the LDH-catalyzed reaction: binding of substrates, loop closure, and the chemical event. Qualitatively, these results can be understood as an osmolyte-induced change in the energy landscape of the protein complexes, shifting the conformational nature of functional sub-states within the protein ensemble.
Zhadin, Nickolay; Callender, Robert
Chemoselective N-heterocyclic carbene-catalyzed cross-benzoin reactions: importance of the fused ring in triazolium salts.
Morpholinone- and piperidinone-derived triazolium salts are shown to catalyze highly chemoselective cross-benzoin reactions between aliphatic and aromatic aldehydes. The reaction scope includes ortho-, meta-, and para-substituted benzaldehyde derivatives with a range of electron-donating and -withdrawing groups as well as branched and unbranched aliphatic aldehydes. Catalytic loadings as low as 5 mol % give excellent yields in these reactions (up to 99%). PMID:24809936
Langdon, Steven M; Wilde, Myron M D; Thai, Karen; Gravel, Michel
Hydrophobic Vitamin B12. VII. Ring-Expansion Reactions Catalyzed by Hydrophobic Vitamin B12 in Octopus Azaparacyclophane
Ring-expansion reactions of alkyl ligands bound to heptapropyl cobyrinate at the axial site of the nuclear cobalt were found to be markedly favoured in the hydrophobic cavity of an octopus azaparacyclophane, relative to reactions in methanol and benzene, under anaerobic photolysis conditions at 20.0░C. Heptapropyl cobyrinate perchlorate catalyzed the same ring-expansion reactions, which convert 2-methyl-1,3-cyclopentanedione and 3-methyl-2-pyrrolidinone into 1,4-cyclohexanedione and
Yukito Murakami; Yoshio Hisaeda; Teruhisa Ohno
Efficient approach to 4-sulfonamidoquinolines via copper(I)-catalyzed cascade reaction of sulfonyl azides with alkynyl imines.
A novel and efficient approach to 4-sulfonamidoquinolines via copper-catalyzed cascade reaction of sulfonyl azides with alkynyl imines has been developed in which a 1,3-dipole cycloaddition/ketenimine formation/6?-electrocyclization/[1,3]-H shift cascade reaction was involved. Various 4-sulfonamidoquinolines were afforded in up to 84% yield for 19 examples. This synthetic strategy features with atom economy, concise steps, easy operation, and mild reaction conditions. PMID:23521106
Cheng, Guolin; Cui, Xiuling
Palladium-catalyzed Suzuki-Miyaura cross-coupling reactions employing dialkylbiaryl phosphine ligands.
The cores of many types of polymers, ligands, natural products, and pharmaceuticals contain biaryl or substituted aromatic structures, and efficient methods of synthesizing these structures are crucial to the work of a broad spectrum of organic chemists. Recently, Pd-catalyzed carbon-carbon bond-forming processes, particularly the Suzuki-Miyaura cross-coupling reaction (SMC), have risen in popularity for this purpose. The SMC has many advantages over other methods for constructing these moieties, including mild conditions, high tolerance toward functional groups, the commercial availability and stability of its reagents, and the ease of handling and separating byproducts from its reaction mixtures. Until 1998, most catalysts for the SMC employed triarylphosphine ligands. More recently, new bulky and electron-rich phosphine ligands, which can dramatically improve the efficiency and selectivity of such cross-coupling reactions, have been introduced. In the course of our studies on carbon-nitrogen bond-forming reactions, we found that the use of electron-rich and bulky phosphines enhanced the rate of both the oxidative addition and reductive elimination processes; this was the beginning of our development of a new family of ligands, the dialkylbiarylphosphines L1-L12. These ligands can be used for a wide variety of palladium-catalyzed carbon-carbon, carbon-nitrogen, and carbon-oxygen bond-forming processes as well as serving as supporting ligands for a number of other reactions. The enhanced reactivity of these catalysts has expanded the scope of cross-coupling partners that can be employed in the SMC. With use of such dialkylbiarylphosphine ligands, the coupling of unactivated aryl chlorides, aryl tosylates, heteroaryl systems, and very hindered substrate combinations have become routine. The utility of these ligands has been successfully demonstrated in a wide number of synthetic applications, including industrially relevant processes. In this Account, we provide an overview of the use and impact of dialkylbiarylphosphine ligands in the SMC. We discuss our studies on the mechanistic framework of the reaction, which have allowed us to rationally modify the ligand structures in order to tune their properties. We also describe selected applications in the synthesis of natural products and new materials to illustrate the utility of these dialkylbiarylphosphine ligands in various "real-world" synthetic applications. PMID:18620434
Martin, Ruben; Buchwald, Stephen L
Catalytic c?h amination: a reaction now accessible to engineered natural enzymes.
Catalytic C?H aminations with natural enzymes have not been reported thus far. However, when a cytochrome P450 enzyme is modified by switching from an iron(III) to an iron(II) center and by mutating amino acids that are critical for the catalytic activity of this monooxygenase, this modified enzyme catalyzes the intramolecular C?H amination of benzenesulfonyl azides. PMID:24895319
Mahy, Jean-Pierre; Ciesielski, Jennifer; Dauban, Philippe
Desaturation, dioxygenation, and monooxygenation reactions catalyzed by naphthalene dioxygenase from Pseudomonas sp. strain 9816-4.
The stereospecific oxidation of indan and indene was examined with mutant and recombinant strains expressing naphthalene dioxygenase of Pseudomonas sp. strain 9816-4. Pseudomonas sp. strain 9816/11 and Escherichia coli JM109(DE3)[pDTG141] oxidized indan to (+)-(1S)-indanol, (+)-cis-(1R,2S)-indandiol, (+)-(1S)-indenol, and 1-indanone. The same strains oxidized indene to (+)-cis-(1R,2S)-indandiol and (+)-(1S)-indenol. Purified naphthalene dioxygenase oxidized indan to the same four products formed by strains 9816/11 and JM109(DE3)[pDTG141]. In addition, indene was identified as an intermediate in indan oxidation. The major products formed from indene by purified naphthalene dioxygenase were (+)-(1S)-indenol and (+)-(1R,2S)-indandiol. The results show that naphthalene dioxygenase catalyzes the enantiospecific monooxygenation of indan to (+)-(1S)-indanol and the desaturation of indan to indene, which then serves as a substrate for the formation of (+)-(1R,2S)-indandiol and (+)-(1S)-indenol. The relationship of the desaturase, monooxygenase, and dioxygenase activities of naphthalene dioxygenase is discussed with reference to reactions catalyzed by toluene dioxygenase, plant desaturases, cytochrome P-450, methane monooxygenase, and other bacterial monooxygenases.
Gibson, D T; Resnick, S M; Lee, K; Brand, J M; Torok, D S; Wackett, L P; Schocken, M J; Haigler, B E
D-Serine inhibits serine palmitoyltransferase, the enzyme catalyzing the initial step of sphingolipid biosynthesis
Serine palmitoyltransferase (SPT), responsible for the initial step of sphingolipid biosynthesis, catalyzes condensation of palmitoyl coenzyme A and L-serine to produce 3-ketodihydrosphingosine (KDS). For determination of the stereochemical specificity of the amino acid substrate, a competition analysis of the production of [3H]KDS from L-[3H]serine was performed using purified SPT. D-Serine inhibited [3H]KDS production as effectively as non-radioactive L-serine, whereas neither
Kentaro Hanada; Tomoko Hara; Masahiro Nishijima
Asymmetric Cascade Reaction to Allylic Sulfonamides from Allylic Alcohols by Palladium(II)/Base-Catalyzed Rearrangement of Allylic Carbamates.
A regio- and enantioselective tandem reaction is reported capable of directly transforming readily accessible achiral allylic alcohols into chiral sulfonyl-protected allylic amines. The reaction is catalyzed by the cooperative action of a chiral ferrocene palladacycle and a tertiary amine base and combines high step-economy with operational simplicity (e.g. no need for inert-gas atmosphere or catalyst activation). Mechanistic studies support a Pd(II) -catalyzed [3,3] rearrangement of allylic carbamates-generated in situ from the allylic alcohol and an isocyanate-as the key step, which is followed by a decarboxylation. PMID:24898109
Bauer, Johannes Moritz; Frey, Wolfgang; Peters, Renķ
Stochastic theory of large-scale enzyme-reaction networks: Finite copy number corrections to rate equation models
Chemical reactions inside cells occur in compartment volumes in the range of atto- to femtoliters. Physiological concentrations realized in such small volumes imply low copy numbers of interacting molecules with the consequence of considerable fluctuations in the concentrations. In contrast, rate equation models are based on the implicit assumption of infinitely large numbers of interacting molecules, or equivalently, that reactions occur in infinite volumes at constant macroscopic concentrations. In this article we compute the finite-volume corrections (or equivalently the finite copy number corrections) to the solutions of the rate equations for chemical reaction networks composed of arbitrarily large numbers of enzyme-catalyzed reactions which are confined inside a small subcellular compartment. This is achieved by applying a mesoscopic version of the quasisteady-state assumption to the exact Fokker-Planck equation associated with the Poisson representation of the chemical master equation. The procedure yields impressively simple and compact expressions for the finite-volume corrections. We prove that the predictions of the rate equations will always underestimate the actual steady-state substrate concentrations for an enzyme-reaction network confined in a small volume. In particular we show that the finite-volume corrections increase with decreasing subcellular volume, decreasing Michaelis-Menten constants, and increasing enzyme saturation. The magnitude of the corrections depends sensitively on the topology of the network. The predictions of the theory are shown to be in excellent agreement with stochastic simulations for two types of networks typically associated with protein methylation and metabolism.
Thomas, Philipp; Straube, Arthur V.; Grima, Ramon
The mechanism of enzyme-inhibitor-substrate reactions has been analyzed from a theoretical standpoint and illustrated by data from the system cholinesterase-physostigmine-acetylcholine. This treatment is by no means limited to a single system but should be generally applicable to others of similar type. Competitive enzyme-inhibitor-substrate systems show the same characteristic "zones of behavior" already demonstrated for non-competitive systems by Straus and Goldstein. These zones, three in number, determine the mathematical function which relates activity of an enzyme to concentration of an added substrate or inhibitor or both. The effects of suboptimal substrate concentration in such systems have been considered, and the errors arising from various common simplifications of the descriptive equations have been pointed out. The zone behavior phenomenon has been shown to be useful in determining the number of molecules of substrate or inhibitor combining reversibly with a single enzyme center. The kinetics of competitive inhibition, dilution effect, combination of inhibitor or substrate with enzyme, and destruction of inhibitor or substrate by enzyme have been analyzed and experimentally verified, and absolute velocity constants have been determined. Theoretical conclusions have been discussed from the standpoint of their physiological significance. Specifically, it has been shown that: 1. The inhibition of cholinesterase by physostigmine is competitive. A single molecule of physostigmine or acetylcholine combines with one center of cholinesteraseŚn = 1; and the mechanism n = 2 has been. excluded. Numerical values of the constants for this system are as follows: KI = 3.11 x 10¢8 k1 (combination) = 8.3 x 105 k2 (dissociation) = 0.026 KS = 1.25 x 10¢3 k3 (combination) = 260 k4 (dissociation) = 0.32 2. No definitive value can be assigned to E, the molar concentration of enzyme centers, but in 4.54 per cent dog serum, E < 1.8 x 10¢8 (EI' < 0.58). The system therefore operates in (or nearly in) zone A at this concentration. 3. Competitive displacement of inhibitor by substrate and vice versa introduces considerable error in the usual 20 minute determination of the activity of an inhibited enzyme, unless properly corrected for. 4. Dissociation of the enzyme-inhibitor complex on dilution proceeds moderately slowly so that the full corrections for dilution cannot be applied unless time has been allowed for full dissociation. 5. Combination of physostigmine with cholinesterase is slow at all but large concentrations of inhibitor. 6. The destruction of physostigmine or acetylcholine by cholinesterase follows the predicted curve; kD for the destruction of physostigmine is found to be > 0.00182; kD for acetylcholine destruction is > 3500. There is no reason to assume inhibition of destruction by excess substrate or inhibitor. 7. The common assumption that enzymatic activity follows (or nearly follows) a monomolecular course is true only under limited conditions, which have been here defined. It is not valid, as a rule, for the enzymatic destruction of an inhibitor (e.g., physostigmine) and its application to such a case may lead to erroneous conclusions about the reaction mechanism.
Goldstein, Avram
Multiple mechanisms in Pd(II)-catalyzed S(N)2' reactions of allylic alcohols.
Density functional calculations and experiments were used to examine mechanisms of Pd(II) catalyzed intramolecular cyclization and dehydration in acyclic and bicyclic monoallylic diols, a formal S(N)2' reaction. In contrast to the previously proposed syn-oxypalladation mechanism for acyclic monoallylic diols, calculations and experiments strongly suggest that hydrogen bonding templates a hydroxyl group and Pd addition across the alkene and provides a low energy pathway via anti-addition (anti-oxypalladation) followed by intramolecular proton transfer and anti-elimination of water. This anti-addition, anti-elimination pathway also provides a simple rationale for the observed stereospecificity. For bicyclic monoallylic diol compounds, Pd(II) is capable of promoting either anti- or syn-addition. In addition, palladium chloride ligands can mediate proton transfer to promote dehydration when direct intramolecular proton transfer between diol groups is impossible. PMID:23862564
Ghebreghiorgis, Thomas; Kirk, Brian H; Aponick, Aaron; Ess, Daniel H
Chiral phosphine-olefin ligands in the rhodium-catalyzed asymmetric 1,4-addition reactions.
A full overview on the use of chiral phosphine-olefin ligands 1 in the rhodium-catalyzed asymmetric 1,4-addition of arylboronic acids to alpha,beta-unsaturated carbonyl compounds is described. Effective chiral environment of a Rh/1 complex was shown to resemble that of a Rh/(R,R)-Ph-bod* complex by comparing the experimental results as well as the X-ray crystal structures. High catalytic activity of a Rh/1 complex was disclosed and the catalytic cycle involving a trimer-monomer equilibrium was established through mechanistic studies using a reaction calorimeter and (31)P NMR spectroscopy. A negative nonlinear effect derived from an inactive trimer-active monomer equilibrium of the catalyst was also successfully observed. PMID:17249670
Duan, Wei-Liang; Iwamura, Hiroshi; Shintani, Ryo; Hayashi, Tamio
Comparison Of Reaction Barriers In Energy And Free Energy For Enzyme Catalysis
Reaction paths on potential energy surfaces obtained from QM/MM calculations of enzymatic or solution reactions depend on the starting structure employed for the path calculations. The free energies associated with these paths should be more reliable for studying reaction mechanisms, because statistical averages are used. To investigate this, the role of enzyme environment fluctuations on reaction paths has been studied with an ab initio QM/MM method for the first step of the reaction catalyzed by 4-oxalocrotonate tautomerase (4OT). Four minimum energy paths (MEPs) are compared, which have been determined with two different methods. The first path (path A) has been determined with a procedure that combines the nudged elastic band (NEB) method and a second order parallel path optimizer recently developed in our group. The second path (path B) has also been determined by the combined procedure, however, the enzyme environment has been relaxed by molecular dynamics (MD) simulations. The third path (path C) has been determined with the coordinate driving (CD) method, using the enzyme environment from path B. We compare these three paths to a previously determined path (path D) determined with the CD method. In all four cases the QM/MM-FE method (Y. Zhang et al., JCP, 112, 3483) was employed to obtain the free energy barriers for all four paths. In the case of the combined procedure, the reaction path is approximated by a small number of images which are optimized to the MEP in parallel, which results in a reduced computational cost. However, this does not allow the FEP calculation on the MEP. In order to perform FEP calculations on these paths, we introduce a modification to the NEB method that enables the addition of as many extra images to the path as needed for the FEP calculations. The calculated potential energy barriers show differences in the activation barrier between the calculated paths of as much as 5.17 kcal/mol. However, the largest free energy barrier difference is 1.58 kcal/mol. These results show the importance of the inclusion of the environment fluctuation in the calculation of enzymatic activation barriers
Andrķs Cisneros, G.; Yang, Weitao
Transition-metal-catalyzed carbonylation reactions of olefins and alkynes: a personal account.
Carbon monoxide was discovered and identified in the 18th century. Since the first applications in industry 80 years ago, academic and industrial laboratories have broadly explored CO's use in chemical reactions. Today organic chemists routinely employ CO in organic chemistry to synthesize all kinds of carbonyl compounds. Despite all these achievements and a century of carbonylation catalysis, many important research questions and challenges remain. Notably, apart from academic developments, industry applies carbonylation reactions with CO on bulk scale. In fact, today the largest applications of homogeneous catalysis (regarding scale) are carbonylation reactions, especially hydroformylations. In addition, the vast majority of acetic acid is produced via carbonylation of methanol (Monsanto or Cativa process). The carbonylation of olefins/alkynes with nucleophiles, such as alcohols and amines, represent another important type of such reactions. In this Account, we discuss our work on various carbonylations of unsaturated compounds and related reactions. Rhodium-catalyzed isomerization and hydroformylation reactions of internal olefins provide straightforward access to higher value aldehydes. Catalytic hydroaminomethylations offer an ideal way to synthesize substituted amines and even heterocycles directly. More recently, our group has also developed so-called alternative metal catalysts based on iridium, ruthenium, and iron. What about the future of carbonylation reactions? CO is already one of the most versatile C1 building blocks for organic synthesis and is widely used in industry. However, because of CO's high toxicity and gaseous nature, organic chemists are often reluctant to apply carbonylations more frequently. In addition, new regulations have recently made the transportation of carbon monoxide more difficult. Hence, researchers will need to develop and more frequently use practical and benign CO-generating reagents. Apart from formates, alcohols, and metal carbonyls, carbon dioxide also offers interesting options. Industrial chemists seek easy to prepare catalysts and patent-free ligands/complexes. In addition, non-noble metal complexes will interest both academic and industrial researchers. The novel Lucite process for methyl methacrylate is an important example of an improved catalyst. This reaction makes use of a specific palladium/bisphosphine catalyst, which led to the successful implementation of the technology. More active and productive catalysts for related carbonylations of less reactive olefins would allow for other large scale applications of this methodology. From an academic point of view, researchers continue to look for selective reactions with more functionalized olefins. Finally, because of the volatility of simple metal carbonyl complexes, carbonylation reactions today remain a domain of homogeneous catalysis. The invention of more stable and recyclable heterogeneous catalysts or metal-free carbonylations (radical carbonylations) will be difficult, but could offer interesting challenges for young chemists. PMID:24564478
Wu, Xiao-Feng; Fang, Xianjie; Wu, Lipeng; Jackstell, Ralf; Neumann, Helfried; Beller, Matthias
Transpeptidation reactions of a specific substrate catalyzed by the streptomyces R61 DD-peptidase: characterization of a chromogenic substrate and acyl acceptor design.
The Streptomyces R61 dd-peptidase, a functional model for penicillin-binding proteins, catalyzes the hydrolysis and aminolysis of d-alanyl-d-alanine-terminating peptides by specific amines. In vivo, this reaction completes bacterial cell wall biosynthesis. For in vitro studies of this enzyme to date, various nonspecific acyl-donor substrates have been employed. Recently, however, a peptidoglycan-mimetic peptide substrate, glycyl-l-alpha-amino-epsilon-pimelyl-d-alanyl-d-alanine, has been described that is much more specific for this enzyme. In this paper, we describe the synthesis and kinetic characterization of an analogous thiolester substrate, 3-(N-glycyl-l-cysteinyl)-propanoyl-d-alanyl-d-thiolactate, that the enzyme hydrolyzes and aminolyzes very efficiently (k(cat)/K(m) = 1.0 x 10(7) s(-)(1) M(-)(1)). Direct or indirect, by means of a thiol trap, spectrophotometric monitoring of the reactions of this substrate is readily achieved. Deacylation of the enzyme is rate-determining under substrate saturation conditions, and therefore the aminolysis reaction can be directly studied. The results show that d-amino acids and certain Gly-l-Xaa dipeptides and tripeptides may act as acyl acceptors at the active site of the enzyme. d-Phenylalanine and Gly-l-Phe were the most effective d-amino acid and dipeptide acceptors, respectively. On the basis of the dual specificity of the active site for acceptors (d-amino acids and Gly-l-Xaa peptides), "dual function" acceptors were designed and synthesized. Two of these, aminomalon-(N-ethyl)amide and aminomalon-(N-phenethyl)amide, were particularly effective. It did seem, however, that the observed rates of reaction of these very effective acceptors may be limited by some common, possibly physical, step. More extended, peptidoglycan-like, acceptors were found to be essentially unreactive. The reasons for this counterintuitive behavior are discussed. PMID:16042374
Kumar, Ish; Pratt, R F
Gold (I)-Catalyzed Diastereo- and Enantioselective 1,3-Dipolar Cycloaddition and Mannich Reactions of Azlactones
Azlactones participate in stereoselective reactions with electron-deficient alkenes and N-sulfonyl aldimines to give products of 1,3-dipolar cycloaddition and Mannich addition reactions respectively. Both of these reactions proceed with good to excellent diastereo- and enantioselectivity using a single class of gold-catalysts, namely C2-symmetric bis(phosphinegold(I) carboxylate)complexes. The development of the azlactone Mannich reaction to provide fully protected anti-?,?-diamino acid derivatives is described. 1,3-Dipolar cycloaddition reactions of several acyclic 1,2-disubstituted alkenes, and the chemistry of the resultant cycloadducts, are examined to probe the stereochemical course of this reaction. Reaction kinetics and tandem MS studies of both the cycloaddition and Mannich reactions are reported. These studies support a mechanism in which the gold complexes catalyze addition reactions through nucleophile activation rather than the more typical activation of the electrophilic reaction component.
Melhado, Asa D.; Amarante, Giovanni W.; Wang, Z. Jane; Luparia, Marco; Toste, F. Dean
Cobalamin- and Corrinoid-Dependent Enzymes
This chapter will review the literature on cobalamin- and corrinoid-containing enzymes. These enzymes fall into two broad classes, those using methylcobalamin or related methylcorrinoids as prosthetic groups and catalyzing methyltransfer reactions, and those using adenosylcobalamin as the prosthetic group and catalyzing the generation of substrate radicals that in turn undergo rearrangements and/or eliminations.
Matthews, Rowena G.
A preliminary investigation of acid-catalyzed polymerization reactions of shale oil distillates
Sinor (1989) reported that a major specialty market may exist for shale oil as an asphalt blending material. Shale oil can be converted to an asphalt blending material by acid catalyzed condensation and polymerization reactions of the many molecular species comprising the composition of shale oil. To simplify the investigation, crude shale oil was separated by distillation into three distillates of different hydrocarbon and heteroaromatic compositions. These distillates were then treated with two different types of acids to determine the effect of acid type on the end products. Three western shale oil distillates, a naphtha, a middle distillate, and an atmospheric gas oil, were reacted with anhydrous AlCl{sub 3} and 85% H{sub 2}SO{sub 4} under low-severity conditions. At relatively low temperatures, little change in the hydrocarbon composition was noted for the AlCl{sub 3} reactions. AlCl{sub 3}{center_dot} (a polymerized product and/or complex) was formed. However, it is assumed that the sludge was mainly the result of heteroaromatic-AlCl{sub 3} reactions.
Netzel, D.A.
Sinor (1989) reported that a major specialty market may exist for shale oil as an asphalt blending material. Shale oil can be converted to an asphalt blending material by acid catalyzed condensation and polymerization reactions of the many molecular species comprising the composition of shale oil. To simplify the investigation, crude shale oil was separated by distillation into three distillates of different hydrocarbon and heteroaromatic compositions. These distillates were then treated with two different types of acids to determine the effect of acid type on the end products. Three western shale oil distillates, a naphtha, a middle distillate, and an atmospheric gas oil, were reacted with anhydrous AlCl{sub 3} and 85% H{sub 2}SO{sub 4} under low-severity conditions. At relatively low temperatures, little change in the hydrocarbon composition was noted for the AlCl{sub 3} reactions. AlCl{sub 3}{center dot} (a polymerized product and/or complex) was formed. However, it is assumed that the sludge was mainly the result of heteroaromatic-AlCl{sub 3} reactions.
Identification of a suitable and selective inhibitor towards aldehyde oxidase catalyzed reactions.
1.?Aldehyde oxidase (AO) is a liver cytosolic molybdoflavoprotein enzyme whose importance in drug metabolism is gaining in the recent. The objective of this work is to find a potent and selective inhibitor for AO activity using phthalazine oxidation as a marker reaction. 2.?Among organic solvents tested, it was identified that methanol was not a suitable choice for AO activity even at concentrations less than 0.2% v/v. Acetonitrile and DMSO did not show any effect till 0.5% v/v but thereafter activites tend to decrease. 3.?For selectivity, 23 compounds were selected and evaluated for their effects on AO and nine CYP450 enzymes. Among the tested compounds chlorpromazine, estradiol, hydralazine, quetiapine and raloxifene were selected based on their potency of inhibition towards AO activity. 4.?Raloxifene was found to be a non-specific inhibitor of all major tested CYP450 enzymes and was excluded as a selective inhibitor for AO. Quetiapine also showed a degree of inhibition towards the major CYP450 tested. Hydralazine used as a specific inhibitor during the past for AO activity demonstrated a stimulation of AO activity at high and low concentrations respectively and the inhibition noted to be time dependent while inhibiting other enzymes like monoamine oxidase. 5.?Estradiol showed no inhibition towards the tested CYP450 enzymes and thus proved to be a selective and specific inhibitor for AO activity with an uncompetitive mode of inhibition. PMID:24156774
Nirogi, Ramakrishna; Kandikere, Vishwottam; Palacharla, Raghava Choudary; Bhyrapuneni, Gopinadh; Kanamarlapudi, Vijaya Bhargava; Ponnamaneni, Ranjith Kumar; Manoharan, Arun Kumar
Diphtheria toxin catalyzed hydrolysis of NAD(+): molecular dynamics study of enzyme-bound substrate, transition state, and inhibitor.
The mechanism of the diphtheria toxin-catalyzed hydrolysis of NAD(+) was investigated by quantum chemical calculations and molecular dynamics simulations. Several effects that could explain the 6000-fold rate acceleration (Delta Delta G(++) approximately 5 kcal/mol) by the enzyme were considered. First, the carboxamide arm of the enzyme-bound NAD(+) adopts a trans conformation while the most stable conformation is cis. The most stable conformation for the nicotinamide product has the amide carbonyl trans. The activation energy for the cleavage of the ribosidic bond is reduced by 2 kcal/mol due to the relaxation of this ground state conformational stress in the transition state. Second, molecular dynamics simulations to the nanosecond time range revealed that the carboxylate of Glu148 forms a hydrogen bond to the substrate's 2' hydroxyl group in E.S (approximately 17% of the time) and E.TS (approximately 57% of the time) complexes. This interaction is not seen in crystal structures. The ApUp inhibitor is held more tightly by the enzyme than the transition state and the substrate. Analysis of correlated motions reveals differences in the pattern of anticorrelated motions for protein backbone atoms when the transition state occupies the active site as compared to the E.NAD(+) complex. PMID:11724604
Kahn, K; Bruice, T C
Nafion«-catalyzed microwave-assisted Ritter reaction: An atom-economic solvent-free synthesis of amides
An atom-economic solvent-free synthesis of amides by the Ritter reaction of alcohols and nitriles under microwave irradiation is reported. This green protocol is catalyzed by solid supported Nafion«NR50 with improved efficiency and reduced waste production....
Phosphine-catalyzed Rauhut-Currier domino reaction: a facile strategy for the construction of carbocyclic spirooxindoles skeletons.
Push-over: A novel domino reaction of activated conjugated dienes and methyleneindolinones incorporates a phosphine-catalyzed intermolecular Rauhut-Currier to form two C-C bonds and a quaternary carbon center. This method can be used to synthesize spirocyclopenteneoxindoles skeletons, which are potential building blocks for biologically active compounds. PMID:23813882
Hu, Chongchong; Zhang, Qinglong; Huang, You
Pd-Catalyzed Suzuki-Miyaura Cross-Coupling Reactions Between Sulfamates and Potassium Boc-Protected Aminomethyltrifluoroborates
Sulfamates were studied as the electrophilic partners in the palladium-catalyzed Suzuki¢Miyaura cross-coupling reaction with potassium Boc-protected primary and secondary aminomethyltrifluoroborates. A broad range of substrates was successfully coupled to provide the desired products. Complex molecules containing a new carbon-carbon bond and an aminomethyl moiety could be prepared through this developed method.
Molander, Gary A.; Shin, Inji
Direct assembly of 3,4-difunctionalized benzofurans and polycyclic benzofurans by phenol dearomatization and palladium-catalyzed domino reaction.
A method to directly convert 2-alkynylphenols to 3,4-difunctionalized benzofurans and polycyclic benzofurans was developed. This protocol involves a hypervalent-iodine-mediated oxidative dearomatization to break the aromaticity of 2-alkynylphenols, and a palladium-catalyzed domino reaction to install two functional groups at the C3 and the C4 positions and restore the aromaticity of benzofurans. PMID:24845520
Han, Zhaomeng; Zhang, Liang; Li, Zhiming; Fan, Renhua
Intramolecular Diels¢Alder reaction of 1,7,9-decatrienoates catalyzed by indium(III) trifluoromethanesulfonate in aqueous media
The intramolecular Diels¢Alder reaction of ester-tethered 1,7,9-decatrienoate derivatives in a mixture of water and 2-propanol was catalyzed by indium(III) triflate to give the cycloadducts in good yield with perfect endo-selectivity.
Hikaru Yanai; Akio Saito; Takeo Taguchi
Phosphine-catalyzed sequential annulation domino reaction: rapid construction of bicyclo[4.1.0]heptene skeletons.
A convenient and efficient phosphine-catalyzed sequential annulation domino reaction between dienic sulfones and MBH carbonates has been developed. In the presence of 20 mol% of tris(4-fluorophenyl)phosphine, functionalized bicyclo[4.1.0]heptenes were prepared in excellent yields and stereoselectivities under mild conditions. PMID:24733288
Zheng, Jie; Huang, You; Li, Zhengming
Establishment of broadly applicable reaction conditions for the palladium-catalyzed direct arylation of heteroatom-containing aromatic compounds.
Conditions for the palladium-catalyzed direct arylation of a wide range of heterocycles with aryl bromides are reported. Those conditions employ a stoichiometric ratio of both coupling partners, as well as a substoichiometric quantity of pivalic acid, which results in significantly faster reactions. An evaluation of the influence of the nature of the aryl halide has also been carried out. PMID:19206211
Liķgault, BenoŅt; Lapointe, David; Caron, Laurence; Vlassova, Anna; Fagnou, Keith
Diazo compounds and N-tosylhydrazones: novel cross-coupling partners in transition-metal-catalyzed reactions.
Transition-metal-catalyzed carbene transformations and cross-couplings represent two major reaction types in organometallic chemistry and organic synthesis. However, for a long period of time, these two important areas have evolved separately, with essentially no overlap or integration. Thus, an intriguing question has emerged: can cross-coupling and metal carbene transformations be merged into a single reaction cycle? Such a combination could facilitate the development of novel carbon-carbon bond-forming methodologies. Although this concept was first explored about 10 years ago, rapid developments inthis area have been achieved recently. Palladium catalysts can be used to couple diazo compounds with a wide variety of organic halides. Under oxidative coupling conditions, diazo compounds can also react with arylboronic acids and terminal alkynes. Both of these coupling reactions form carbon-carbon double bonds. As the key step in these catalytic processes, Pd carbene migratory insertion plays a vital role in merging the elementary steps of Pd intermediates, leading to novel carbon-carbon bond formations. Because the diazo substrates can be generated in situ from N-tosylhydrazones in the presence of base, the N-tosylhydrazones can be used as reaction partners, making this type of cross-coupling reaction practical in organic synthesis. N-Tosylhydrazones are easily derived from the corresponding aldehydes or ketones. The Pd-catalyzed cross-coupling of N-tosylhydrazones is considered a complementary reaction to the classic Shapiro reaction for converting carbonyl functionalities into carbon-carbon double bonds. It can also serve as an alternative approach for the Pd-catalyzed cross-coupling of carbonyl compounds, which is usually achieved via triflates. The combination of carbene formation and cross-coupling in a single catalytic cycle is not limited to Pd-catalyzed reactions. Recent studies of Cu-, Rh-, Ni-, and Co-catalyzed cross-coupling reactions with diazo compounds or N-tosylhydrazones show that these transformations also work with other transition metals, demonstrating the generality of the diazo compounds as new cross-coupling partners in transition-metal-catalyzed coupling reactions. PMID:23013153
Xiao, Qing; Zhang, Yan; Wang, Jianbo
Enantioselective Synthesis of anti- and syn-homopropargyl alcohols via Chiral Br?nsted Acid Catalyzed asymmetric Allenylboration reactions
Chiral Br°nsted acid catalyzed asymmetric allenylboration reactions are described. Under optimized conditions, anti-homopropargyl alcohols 2 are obtained in high yields with excellent diastereo- and enantioselectivities from stereochemically matched aldehyde allenylboration reactions with (M)-1 catalyzed by the chiral phosphoric acid (S)-4. The syn-isomers 3 can also be obtained in good diastereoselectivities and excellent enantioselectivities from the mismatched allenylboration reactions of aromatic aldehydes using (M)-1 in the presence of the enantiomeric phosphoric acid (R)-4. The stereochemistry of the methyl group introduced into 2 and 3 is controlled by the chirality of the allenylboronate (M)-1, whereas the configuration of the new hydroxyl stereocenter is controlled by the enantioselectivity of the chiral phosphoric acid catalyst used in these reactions. The synthetic utility of this methodology was further demonstrated in triple asymmetric syntheses of a variety of anti,anti-stereotriads, the direct synthesis of which has constituted a significant challenge using previous generations of aldol and crotylmetal reagents.
Chen, Ming; Roush, William R.
Selectivity of montmorillonite catalyzed prebiotic reactions of D, L-nucleotides
The montmorillonite-catalyzed reactions of the 5?-phosphorimidazolides of D, L-adenosine (D, L-ImpA) (Figure 1a. N = A, R = H) and D, L-uridine (Figure 1a., N = U, R = H) yields oligomers that were as long as 7 mers and 6 mers, respectively. The reactions of dilute solutions of D-ImpA and D-ImpU under the same conditions gave oligomers as long as 9 and 8 mers respectively. This demonstrated that oligomer formation is only partially inhibited by incorporation of both the D- and L-enantiomers. The structures of the dimers, trimers and tetramer fractions formed from D, L-ImpA was investigated by selective enzymatic hydrolysis, comparison with authentic samples and mass spectrometry. Homochiral products were present in greater amounts than would be expected if theoretical amounts of each were formed. The ratio of the proportion of homochiral products to that of the amount of each expected for the dimers (cyclic and linear), trimers and tetramers, was 1.3, 1.6, and 2.1, respectively. In the D, L-ImpU reaction homochiral products did not predominate with ratios of dimers (cyclic and linear), trimers and tetramers 0.8, 0.44, and 1.4, respectively. The proportions of cyclic dimers in the dimer fraction were 52 66% with D, L-ImpA and 44 69% with D, L-ImpU. No cyclic dimers were formed in the absence of montmorillonite. The differences in the reaction products of D, L-ImpA and D, L-ImpU are likely to be due to the difference in the orientations of the activated monomers when bound to the catalytic sites on montmorillonite. The consequences of the selectivity of montmorillonite as a prebiotic catalyst are discussed.
Joshi, Prakash C.; Pitsch, Stefan; Ferris, James P.
Fluorogenic probes using 4-substituted-2-nitrobenzenesulfonyl derivatives as caging groups for the analysis of human glutathione transferase catalyzed reactions.
We have synthesized a series of 4-substituted-2-nitrobenzene-sulfonyl compounds for caged fluorogenic probes and conducted a Hammett plot analysis using the steady-state kinetic parameters. The results revealed that the glutathione transferase (GST) alpha catalyzed reaction was dependent on the ? value in the same way as the non-enzymatic reaction, whereas the dependence of the ? value of the GST mu and pi was not as pronounced as that of GST alpha. PMID:24151635
Shibata, Aya; Nakano, Yukiko; Ito, Mika; Araki, Mika; Zhang, Jie; Yoshida, Yasuhiko; Shuto, Satoshi; Mannervik, Bengt; Mogenstern, Ralf; Ito, Yoshihiro; Abe, Hiroshi
On indium(III) chloride-catalyzed aldol reactions of silyl enol ethers with aldehydes in water
Contrary to previous reports, it was found that hydrolysis of silyl enol ethers is superior to the desired condensation in InCl3-catalyzed aldol reactions of silyl enol ethers with aldehydes in water. The reactions were found to proceed in certain amounts in the presence of a catalytic amount of a Lewis acid under neat (solvent-free) conditions, while substrate limitation was observed
Sh? Kobayashi; Tsuyoshi Busujima; Satoshi Nagayama
Photoacoustic investigations of CO 2¢CH 4 reaction catalyzed by nickel particles embedded into SBA15 mesopores
A photoacoustic spectroscopy technique was employed to the kinetic study of the CO2\\/CH4 reaction catalyzed by Ni particles embedded into the mesochannels of SBA15. The catalytic CO2\\/CH4 reaction was performed in a closed-circulating reactor system at various partial pressures of CO2 and CH4 (40Torr total pressure) in the temperature range of 500¢700░C. The CO2 photoacoustic signal that varied with the
Hun Jung; Ji-Woong Kim; Young-Gil Cho; Jin-Seung Jung; Sung-Han Lee; Joong-Gill Choi
Reaction Pathways and Energetics of Etheric C?O Bond Cleavage Catalyzed by Lanthanide Triflates
Efficient and selective cleavage of etheric C?O bonds is crucial for converting biomass into platform chemicals and liquid transportation fuels. In this contribution, computational methods at the DFT B3LYP level of theory are employed to understand the efficacy of lanthanide triflate catalysts (Ln(OTf)3, Ln = La, Ce, Sm, Gd, Yb, and Lu) in cleaving etheric C?O bonds. In agreement with experiment, the calculations indicate that the reaction pathway for C?O cleavage occurs via a C?H ? O?H proton transfer in concert with weakening of the C?O bond of the coordinated ether substrate to ultimately yield a coordinated alkenol. The activation energy for this process falls as the lanthanide ionic radius decreases, reflecting enhanced metal ion electrophilicity. Details of the reaction mechanism for Yb(OTf)3-catalyzed ring opening are explored in depth, and for 1-methyl-d3-butyl phenyl ether, the computed primary kinetic isotope effect of 2.4 is in excellent agreement with experiment (2.7), confirming that etheric ring-opening pathway involves proton transfer from the methyl group alpha to the etheric oxygen atom, which is activated by the electrophilic lanthanide ion. Calculations of the catalytic pathway using eight different ether substrates indicate that the more rapid cleavage of acyclic versus cyclic ethers is largely due to entropic effects, with the former C?O bond scission processes increasing the degrees of freedom/particles as the transition state is approached.
Assary, Rajeev S.; Atesin, Abdurrahman C.; Li, Zhi; Curtiss, Larry A.; Marks, Tobin J.
Molecular dynamics simulations of the first steps of the reaction catalyzed by HIV-1 protease.
The mechanism of the first steps of the reaction catalyzed by HIV-1 protease was studied through molecular dynamics simulations. The potential energy surface in the active site was generated using the approximate valence bond method. The approximate valence bond (AVB) method was parameterized based on density functional calculations. The surrounding protein and explicit water environment was modeled with conventional, classical force field. The calculations were performed based on HIV-1 protease complexed with the MVT-101 inhibitor that was modified to a model substrate. The protonation state of the catalytic aspartates was determined theoretically. Possible reaction mechanisms involving the lytic water molecule are accounted for in this study. The modeled steps include the dissociation of the lytic water molecule and proton transfer onto Asp-125, the nucleophilic attack followed by a proton transfer onto peptide nitrogen. The simulations show that in the active site most preferable energetically are structures consisting of ionized or polarized molecular fragments that are not accounted for in conventional molecular dynamics. The mobility of the lytic water molecule, the dynamics of the hydrogen bond network, and the conformation of the aspartates in the active center were analyzed.
Trylska, Joanna; Bala, Piotr; Geller, Maciej; Grochowski, Pawel
Kinetic resolution of racemic 1-phenyl 1-propanol by lipase catalyzed enantioselective esterification reaction.
In this study, resolution of (R,S)-1-phenyl 1-propanol by lipase-catalyzed enantioselective esterification was achieved. To investigate the effect of lipase type on enantiomeric excess, three different lipases were used. Novozym 435 exhibited the highest enantioselectivity for resolution of (R,S)-1-phenyl 1-propanol. The effects of carbon length of fatty acids from C12 to C16, which were used as acyl donor, organic solvents with Log P values from 0.5 to 4.5, acyl donor/alcohol molar ratio (1:1, 3:2, 2:1, 3:1), amount of added molecular sieves (0-133.2 kg/m(3)), and temperature (10-60░ C) on the enantioselectivity were investigated. The best reaction conditions were comprised of using toluene (Log P= 2.5) as solvent, lauric acid (12C) as acyl donor, 133.2 kg/m(3) molecular sieves at 50░ C and acyl donor/alcohol molar ratio as 1:1. Under these conditions, the enantiomeric excess of S enantiomer ee (S) was obtained as 95% for a reaction time of 2.5 hours. PMID:20831353
Karadeniz, Fatma; Bayraktar, Emine; Mehmetoglu, Ulk³
Metal ion-catalyzed cycloaddition vs hydride transfer reactions of NADH analogues with p-benzoquinones.
1-Benzyl-4-tert-butyl-1,4-dihydronicotinamide (t-BuBNAH) reacts efficiently with p-benzoquinone (Q) to yield a [2+3] cycloadduct (1) in the presence of Sc(OTf)(3) (OTf = OSO(2)CF(3)) in deaerated acetonitrile (MeCN) at room temperature, while no reaction occurs in the absence of Sc(3+). The crystal structure of 1 has been determined by the X-ray crystal analysis. When t-BuBNAH is replaced by 1-benzyl-1,4-dihydronicotinamide (BNAH), the Sc(3+)-catalyzed cycloaddition reaction of BNAH with Q also occurs to yield the [2+3] cycloadduct. Sc(3+) forms 1:4 complexes with t-BuBNAH and BNAH in MeCN, whereas there is no interaction between Sc(3+) and Q. The observed second-order rate constant (k(obs)) shows a first-order dependence on [Sc(3+)] at low concentrations and a second-order dependence at higher concentrations. The first-order and the second-order dependence of the rate constant (k(et)) on [Sc(3+)] was also observed for the Sc(3+)-promoted electron transfer from CoTPP (TPP = tetraphenylporphyrin dianion) to Q. Such dependence of k(et) on [Sc(3+)] is ascribed to formation of 1:1 and 1:2 complexes between Q(*)(-) and Sc(3+) at the low and high concentrations of Sc(3+), respectively, which results in acceleration of the rate of electron transfer. The formation constants for the 1:2 complex (K(2)) between the radical anions of a series of p-benzoquinone derivatives (X-Q(*)(-)) and Sc(3+) are determined from the dependence of k(et) on [Sc(3+)]. The K(2) values agree well with those determined from the dependence of k(obs) on [Sc(3+)] for the Sc(3+)-catalyzed addition reaction of t-BuBNAH and BNAH with X-Q. Such an agreement together with the absence of the deuterium kinetic isotope effects indicates that the addition proceeds via the Sc(3+)-promoted electron transfer from t-BuBNAH and BNAH to Q. When Sc(OTf)(3) is replaced by weaker Lewis acids such as Lu(OTf)(3), Y(OTf)(3), and Mg(ClO(4))(2), the hydride transfer reaction from BNAH to Q also occurs besides the cycloaddition reaction and the k(obs) value decreases with decreasing the Lewis acidity of the metal ion. Such a change in the type of reaction from a cycloaddition to a hydride transfer depending on the Lewis acidity of metal ions employed as a catalyst is well accommodated by the common reaction mechanism featuring the metal-ion promoted electron transfer from BNAH to Q. PMID:11603968
Fukuzumi, S; Fujii, Y; Suenobu, T
Sarcoidosis patient: an unexpected reaction to carbonic anhydrase enzyme inhibitor.
Ocular diseases are very common in many of the systemic diseases such as sarcoidosis, and may sometimes be the presenting symptom of the disease. In this case report, we present an unusual reaction of the sarcoid granuloma to carbonic anhydrase enzyme inhibitors (CAIs), which was encountered in a patient with ocular sarcoidosis. This observation was taken after a 2-week interval between a CT scan orbits and an MRI orbits which showed a decrease in size from 4ū3ū4 cm to 2.5ū2.5ū2 cm, respectively. We suspected the dorzolamide CAI to have had a significant role in the reduction in size. It is suggested that acidotic changes that occur due to the effect of the carbonic anhydrase inhibitor causes electrolyte imbalance, intracellular as well as extracellular, which lead to the reduction in the size of the granuloma. PMID:23893285
Khedr, Yahya A H; Khedr, Abdulla H
Bacteroides thetaiotaomicron VPI-5482 glycoside hydrolase family 66 homolog catalyzes dextranolytic and cyclization reactions.
Bacteroides thetaiotaomicron VPI-5482 harbors a gene encoding a putative cycloisomaltooligosaccharide glucanotransferase (BT3087) belonging to glycoside hydrolase family 66. The goal of the present study was to characterize the catalytic properties of this enzyme. Therefore, we expressed BT3087 (recombinant endo-dextranase from Bacteroides thetaiotaomicron VPI-5482) in Escherichia?coli and determined that recombinant endo-dextranase from Bacteroides thetaiotaomicron VPI-5482 preferentially synthesized isomaltotetraose and isomaltooligosaccharides (degree of polymerization > 4) from dextran. The enzyme also generated large cyclic isomaltooligosaccharides early in the reaction. We conclude that members of the glycoside hydrolase 66 family may be classified into three types: (a) endo-dextranases, (b) dextranases possessing weak cycloisomaltooligosaccharide glucanotransferase activity, and (c) cycloisomaltooligosaccharide glucanotransferases. PMID:22776355
Kim, Young-Min; Yamamoto, Eiji; Kang, Min-Sun; Nakai, Hiroyuki; Saburi, Wataru; Okuyama, Masayuki; Mori, Haruhide; Funane, Kazumi; Momma, Mitsuru; Fujimoto, Zui; Kobayashi, Mikihiko; Kim, Doman; Kimura, Atsuo
Highly Divergent Methyltransferases Catalyze a Conserved Reaction in Tocopherol and Plastoquinone Synthesis in Cyanobacteria and Photosynthetic Eukaryotes
Tocopherols are lipid-soluble compounds synthesized only by photosynthetic eukaryotes and oxygenic cyanobacteria. The path- way and enzymes for tocopherol synthesis are homologous in cyanobacteria and plants except for 2-methyl-6-phytyl-1,4-benzo- quinone\\/2-methyl-6-solanyl-1,4-benzoquinone methyltransferase (MPBQ\\/MSBQ MT), which catalyzes a key methylation step in both tocopherol and plastoquinone (PQ) synthesis. Using a combined genomic, genetic, and biochemical approach, we isolated and characterized the VTE3
Zigang Cheng; Scott Sattler; Hiroshi Maeda; Yumiko Sakuragi; Donald A. Bryant; Dean DellaPenna
Light-Induced Ruthenium-Catalyzed Nitrene Transfer Reactions: A Photochemical Approach towards N-Acyl Sulfimides and Sulfoximines.
1,4,2-Dioxazol-5-ones are five-membered heterocycles known to decarboxylate under thermal or photochemical conditions, thus yielding N-acyl nitrenes. Described herein is a light-induced ruthenium-catalyzed N-acyl nitrene transfer to sulfides and sulfoxides by decarboxylation of 1,4,2-dioxazol-5-ones at room temperature, thus providing direct access to N-acyl sulfimides and sulfoximines under mild reaction conditions. In addition, a one-pot sulfur imidation/oxidation sequence catalyzed by a single ruthenium complex is reported. PMID:24719367
Bizet, Vincent; Buglioni, Laura; Bolm, Carsten
Evidence that the CysG protein catalyzes the first reaction specific to B12 synthesis in Salmonella typhimurium, insertion of cobalt.
The cysG gene of Salmonella typhimurium is involved in synthesis of both cobalamin (B12) and siroheme (a cofactor required for SO3(2-) and NO2(2-) reductases). The failure to reduce SO3(2-) leads to cysteine auxotrophy, for which the enzyme is named. Although Escherichia coli does not synthesize B12 de novo, it possesses a very similar CysG enzyme which has been shown to catalyze two methylations (uroporphyrinogen III to precorrin-2), ring oxidation (precorrin-2 to factor II), and iron insertion (factor II to siroheme). In S. typhimurium, precorrin-2 is a precursor of both siroheme and B12. All previously known Salmonella cysG mutants are defective in the synthesis of both siroheme and cobalamin. We describe two new classes of cysG mutants that cannot synthesize B12 but still make siroheme. For class I mutants, exogenous cobalt corrects the B12 defect but inhibits ability to make siroheme; B12 synthesis is inhibited by added iron. Class II mutants are unaffected by exogenous cobalt, but their B12 defect is corrected by derepression of the B12 biosynthetic genes (cob). We propose that all mutants are defective in insertion of cobalt into factor II and that the Salmonella CysG enzyme normally catalyzes this insertion-the first reaction dedicated to cobalamin synthesis. Although E. coli does not make B12, its CysG enzyme has been shown in vitro to insert cobalt into factor II and may have evolved to support B12 synthesis in some ancestor common to Salmonella species and E. coli.
Fazzio, T G; Roth, J R
Degradation of phenolic compounds with hydrogen peroxide catalyzed by enzyme from Serratia marcescens AB 90027.
In this paper, the degradation of phenolic compounds using hydrogen peroxide as oxidizer and the enzyme extract from Serratia marcescens AB 90027 as catalyst was reported. With such an enzyme/H2O2 combination treatment, a high chemical oxygen demand (COD) removal efficiency was achieved, e.g., degradation of hydroquinone exceeded 96%. From UV-visible and IR spectra, the degradation mechanisms were judged as a process of phenyl ring cleavage. HPLC analysis shows that in the degradation p-benzoquinone, maleic acid and oxalic acid were formed as intermediates and that they were ultimately converted to CO2 and H2O. With the enzyme/H2O2 treatment, vanillin, hydroquinone, catechol, o-aminophenol, p-aminophenol, phloroglucinol and p-hydroxybenzaldehyde were readily degraded, whereas the degradation of phenol, salicylic acid, resorcinol, p-cholorophenol and p-nitrophenol were limited. Their degradability was closely related to the properties and positions of their side chain groups. Electron-donating groups, such as -OH, -NH2 and -OCH3 enhanced the degradation, whereas electron-withdrawing groups, such as -NO2, -Cl and -COOH, had a negative effect on the degradation of these compounds in the presence of enzyme/H2O2. Compounds with -OH at ortho and para positions were more readily degraded than those with -OH at meta positions. PMID:16890975
Yao, Ri-Sheng; Sun, Min; Wang, Chun-Ling; Deng, Sheng-Song
The NADH oxidation domain of complex I: do bacterial and mitochondrial enzymes catalyze ferricyanide reduction similarly?
The hexammineruthenium (HAR) and ferricyanide reductase activities of Complex I (H+-translocating NADH:ubiquinone reductase) from Paracoccus denitrificans and bovine heart mitochondria were studied. The rates of HAR reduction are high, and its steady-state kinetics is similar in both P. denitrificans and bovine Complex I. The deamino-NADH:HAR reductase activity of Complex I from both sources is significantly higher than the respective activity in the presence of NADH. The HAR reductase activity of the bacterial and mitochondrial Complex I is similarly and strongly pH dependent. The pK(a) of this activity could not be determined, however, due to low stability of the enzymes at pH values above 8.0. In contrast to the high similarity between bovine and P. denitrificans Complex I as far as HAR reduction is concerned, the ferricyanide reductase activity of the bacterial enzyme is much lower than in mitochondria. Moreover, ferricyanide reduction in P. denitrificans, but not bovine mitochondria, is partially sensitive to dicyclohexylcarbodiimide (T. Yagi, Biochemistry 26 (1987) 2822-2828). On the other hand, the inhibition of ferricyanide reduction by high concentration of NADH, a typical phenomenon in bovine Complex I, is much weaker in the bacterial enzyme. The functional differences between the two enzymes might be linked to the properties of their binuclear Fe-S clusters. PMID:10924899
Zickermann, V; Kurki, S; Kervinen, M; Hassinen, I; Finel, M
Reaction of enzymes with starch granules: kinetics and products of the reaction with glucoamylase
The reaction of glucoamylase with starch granules from seven botanical sources (waxy maize, maize, barley, tapioca, amylomaize-7, shoti, and potato) and with four potato starches modified with acid in four types of alcohols (methanol, ethanol, 2-propanol, and 1-butanol) were studied using three concentrations of enzyme (2, 20, and 200 units mL?1). The kinetics of the formation of d-glucose were followed
Atsuo Kimura; John F. Robyt
Gene Cloning and Molecular Characterization of a Two-Enzyme System Catalyzing the Oxidative Detoxification of ?-Endosulfan
The gram-positive bacterium Mycobacterium sp. strain ESD is able to use the cyclodiene insecticide endosulfan as a source of sulfur for growth. This activity is dependent on the absence of sulfite or sulfate in the growth medium. A cosmid library of strain ESD DNA was constructed in a Mycobacterium-Escherichia coli shuttle vector and screened for endosulfan-degrading activity in Mycobacterium smegmatis, a species that does not degrade endosulfan. Using this method, we identified a single cosmid that conferred sulfur-dependent endosulfan-degrading activity on the host strain. An open reading frame (esd) was identified within this cosmid that, when expressed behind a constitutive promoter in a mycobacterial expression vector, conferred sulfite- and sulfate-independent ?-endosulfan degradation activity on the recombinant strain. The translation product of this gene (Esd) had up to 50% sequence identity with an unusual family of monooxygenase enzymes that use reduced flavins, provided by a separate flavin reductase enzyme, as cosubstrates. An additional partial open reading frame was located upstream of the Esd gene that had sequence homology to the same monooxygenase family. A flavin reductase gene, identified in the M. smegmatis genome, was cloned, expressed, and used to provide reduced flavin mononucleotide for Esd in enzyme assays. Thin-layer chromatography and gas chromatography analyses of the enzyme assay mixtures revealed the disappearance of ?-endosulfan and the appearance of the endosulfan metabolites, endosulfan monoaldehyde and endosulfan hydroxyether. This suggests that Esd catalyzes the oxygenation of ?-endosulfan to endosulfan monoaldehyde and endosulfan hydroxyether. Esd did not degrade either ?-endosulfan or the metabolite of endosulfan, endosulfan sulfate.
Sutherland, Tara D.; Horne, Irene; Russell, Robyn J.; Oakeshott, John G.
Dissecting the component reactions catalyzed by the actinorhodin minimal polyketide synthase.
The actinorhodin (act) minimal polyketide synthase (PKS) from Streptomyces coelicolor consists of three proteins: an acyl carrier protein (ACP) and two beta-ketoacyl ACP synthase components known as KSalpha and KSbeta. The act minimal PKS catalyzes at least 18 separate reactions which can be divided into loading, initiation, extension, and cyclization and release phases. Two quantitative kinetic assays were developed and used to measure individual rate and Michaelis constants for loading, initiation and extension steps. In the minimal PKS, the reaction between malonyl CoA and ACP to form malonyl ACP (loading) is the rate-limiting step (kcat = 0.49 min-1, KM = 207 microM). This reaction increases 5-fold in rate in the presence of KSalphaKSbeta (kcat = 2.3 min-1, KM = 215 microM). In the presence of S. coelicolor malonyl CoA:ACP transacylase (MCAT), the rate of loading increases and the kinetic parameters of malonyl-ACP as a substrate of KSalphaKSbeta can be measured (kcat = 20.6 min-1, KM = 2.4 microM). Under these conditions, it appears that decarboxylation of malonyl-ACP to form acetyl-ACP (initiation) is the rate-limiting step. When an excess of acetyl ACP is supplied, either chain extension, cyclization, or release steps become rate limiting (k approximately 60 min-1). No ACP-bound intermediates could be observed, suggesting that partially or fully extended chains do not accumulate because chain extension is rate limiting under these conditions and that cyclization and release are fast. apo-ACP acts as a mixed inhibitor of malonyl ACP binding to KSalpha/KSbeta (Kic = 50 microM, Kiu = 137 microM), but apo-ACP does not appear to inhibit MCAT. PMID:18034463
Beltran-Alvarez, Pedro; Cox, Russell J; Crosby, John; Simpson, Thomas J
Mechanistic Study of Chemoselectivity in Ni-Catalyzed Coupling Reactions between Azoles and Aryl Carboxylates.
Itami et al. recently reported the C-O electrophile-controlled chemoselectivity of Ni-catalyzed coupling reactions between azoles and esters: the decarbonylative C-H coupling product was generated with the aryl ester substrates, while C-H/C-O coupling product was generated with the phenol derivative substrates (such as phenyl pivalate). With the aid of DFT calculations (M06L/6-311+G(2d,p)-SDD//B3LYP/6-31G(d)-LANL2DZ), the present study systematically investigated the mechanism of the aforementioned chemoselective reactions. The decarbonylative C-H coupling mechanism involves oxidative addition of C(acyl)-O bond, base-promoted C-H activation of azole, CO migration, and reductive elimination steps (C-H/Decar mechanism). This mechanism is partially different from Itami's previous proposal (Decar/C-H mechanism) because the C-H activation step is unlikely to occur after the CO migration step. Meanwhile, C-H/C-O coupling reaction proceeds through oxidative addition of C(phenyl)-O bond, base-promoted C-H activation, and reductive elimination steps. It was found that the C-O electrophile significantly influences the overall energy demand of the decarbonylative C-H coupling mechanism, because the rate-determining step (i.e., CO migration) is sensitive to the steric effect of the acyl substituent. In contrast, in the C-H/C-O coupling mechanism, the release of the carboxylates occurs before the rate-determining step (i.e., base-promoted C-H activation), and thus the overall energy demand is almost independent of the acyl substituent. Accordingly, the decarbonylative C-H coupling product is favored for less-bulky group substituted C-O electrophiles (such as aryl ester), while C-H/C-O coupling product is predominant for bulky group substituted C-O electrophiles (such as phenyl pivalate). PMID:24823646
Lu, Qianqian; Yu, Haizhu; Fu, Yao
Rescue of K12G Triosephosphate Isomerase by Ammonium Cations: The Reaction of an Enzyme in Pieces
The K12G mutation at yeast triosephosphate isomerase (TIM) results in a 5.5 ū 105-fold decrease in kcat/Km for isomerization of glyceraldehyde 3-phosphate, and the activity of this mutant can be successfully ōrescuedö by NH4+ and primary alkylammonium cations. The transition state for the K12G mutant TIM-catalyzed reaction is stabilized by 1.5 kcal/mol by interaction with NH4+. The larger 3.9 kcal/mol stabilization by CH3CH2CH2CH2NH3+ is due to hydrophobic interactions between the mutant enzyme and the butyl side chain of the cation activator. There is no significant transfer of a proton from alkylammonium cations to GAP at the transition state for the K12G mutant TIM-catalyzed reaction, because activation by a series of RNH3+ shows little or no dependence on the pKa of RNH3+. A comparison of kcat/Km = 6.6 ū 106 M?1 s?1 for the wildtype TIM-catalyzed isomerization of GAP and the third-order rate constant of 150 M?2 s?1 for activation by NH4+ of the K12G mutant TIM-catalyzed isomerization shows that stabilization of the bound transition state by the effectively intramolecular interaction of the cationic side chain of Lys-12 at wildtype TIM is 6.3 kcal/mol greater than for the corresponding intermolecular interaction of NH4+ at K12G mutant TIM.
Go, Maybelle K.; Amyes, Tina L.; Richard, John P.
Pd(II)-Catalyzed C-H Activation/C-C Cross-Coupling Reactions: Versatility and Practicality
In the past decade, palladium-catalyzed C¢H activation/C¢C bond forming reactions have emerged as promising new catalytic transformations; however, development in this field is still at an early stage compared to the state of the art in cross-coupling reactions using aryl and alkyl halides. This Review begins with a brief introduction of four extensively investigated modes of catalysis for forming C¢C bonds from C¢H bonds: Pd(II)/Pd(0), Pd(II)/Pd(IV), Pd(0)/Pd(II)/Pd(IV) and Pd(0)/Pd(II) catalysis. More detailed discussion is then directed towards the recent development of Pd(II)-catalyzed coupling of C¢H bonds with organometallic reagents through a Pd(II)/Pd(0) catalytic cycle. Despite much progress made to date, improving the versatility and practicality of this new reaction remains a tremendous challenge.
Chen, Xiao; Engle, Keary M.; Wang, Dong-Hui; Yu, Jin-Quan
Reactions of biological antioxidants: II. Fe(III)-catalyzed reactions of methyl linoleate hydroperoxides with derivatives of coenzymes Q and vitamin E
Lipid free-radical oxidations of ubiquinol-6, ubichromenol-6, ubichromenol-10, and ?-tocopherol hydroquinone were kinetically\\u000a examined in the presence of Fe(III)-catalyzed dissociations of preformed methyl linoleate hydroperoxides. The rates of oxidation\\u000a of the chromenols increased more than those of the hydroquinones as reaction acidity was increased. Differences in thermal\\u000a effects upon rates were influenced by the levels of water in the reactions. The
E. H. Gruger; A. L. Tappel
Choline Monooxygenase, an Unusual Iron-Sulfur Enzyme Catalyzing the First Step of Glycine Betaine Synthesis in Plants: Prosthetic Group Characterization and cDNA Cloning
Plants synthesize the osmoprotectant glycine betaine via the route choline --> betaine aldehyde --> glycine betaine. In spinach, the first step is catalyzed by choline monooxygenase (CMO), a ferredoxin-dependent stromal enzyme that has been hypothesized to be an oligomer of identical subunits and to be an Fe-S protein. Analysis by HPLC and matrix-assisted laser desorption ionization MS confirmed that native
Bala Rathinasabapathi; Michael Burnet; Brenda L. Russell; Douglas A. Gage; Pao-Chi Liao; Gordon J. Nye; Paul Scott; John H. Golbeck; Andrew D. Hanson
Independent evolutionary origins of functional polyamine biosynthetic enzyme fusions catalyzing de novo diamine to triamine formation
Summary We have identified gene fusions of polyamine biosynthetic enzymes S-adenosylmethionine decarboxylase (AdoMetDC, speD) and aminopropyltransferase (speE) orthologues in diverse bacterial phyla. Both domains are functionally active and we demonstrate the novel de novo synthesis of the triamine spermidine from the diamine putrescine by fusion enzymes from ?-proteobacterium Delftia acidovorans and ?-proteobacterium Syntrophus aciditrophicus, in a ?speDE gene deletion strain of Salmonella enterica sv. Typhimurium. Fusion proteins from marine ?-proteobacterium Candidatus Pelagibacter ubique, actinobacterium Nocardia farcinica, chlorobi species Chloroherpeton thalassium, and ?-proteobacterium Delftia acidovorans each produce a different profile of non-native polyamines including sym-norspermidine when expressed in Escherichia coli. The different aminopropyltransferase activities together with phylogenetic analysis confirm independent evolutionary origins for some fusions. Comparative genomic analysis strongly indicates that gene fusions arose by merger of adjacent open reading frames. Independent fusion events, and horizontal and vertical gene transfer contributed to the scattered phyletic distribution of the gene fusions. Surprisingly, expression of fusion genes in E. coli and S. Typhimurium revealed novel latent spermidine catabolic activity producing non-native 1,3-diaminopropane in these species. We have also identified fusions of polyamine biosynthetic enzymes agmatine deiminase and N-carbamoylputrescine amidohydrolase in archaea, and of S-adenosylmethionine decarboxylase and ornithine decarboxylase in the single-celled green alga Micromonas.
Green, Robert; Hanfrey, Colin C.; Elliott, Katherine A.; McCloskey, Diane E.; Wang, Xiaojing; Kanugula, Sreenivas; Pegg, Anthony E.; Michael, Anthony J.
Semisynthesis of human growth hormone-releasing factors by alpha-amidating enzyme catalyzed oxidation of glycine-extended precursors.
Recombinant alpha-amidating enzyme was used in the semisynthesis (1-5 mg scale) of human growth hormone-releasing factor, GRF(1-44)-NH2, by in vitro enzymatic oxidation of the glycine-extended precursor, GRF(1-44)-Gly-OH, prepared by solid-phase synthesis. The equipotent analog, GRF(1-29)-NH2, and the superactive analog, [Ala15]-GRF(1-29)-NH2, were also prepared by this route and were fully characterized. Isolated yields of about 75% were obtained, and the products each possessed full potency in an in vitro rat pituitary bioassay and full receptor-binding affinity. Methods to monitor the amidation of polypeptide substrates and analyze the final products are described, including the use of capillary zone electrophoresis. A transient alpha-hydroxyglycine intermediate, [Ala15]-GRF(1-29)-Gly(alpha-OH)-OH, was isolated and characterized. Kinetic studies with this intermediate demonstrate that the rat alpha-amidating enzyme from recombinant mouse C127 cells possesses both the monooxygenase and lyase activities needed to catalyze both steps of the amidation process. PMID:1421807
Bongers, J; Felix, A M; Campbell, R M; Lee, Y; Merkler, D J; Heimer, E P
High temporal resolution monitoring of enzyme reaction and inhibition using optically gated vacancy capillary electrophoresis and immobilized enzyme
A novel method for monitoring of enzyme reaction and inhibition with high temporal resolution was developed by using optically gated vacancy capillary electrophoresis (OGVCE) with laser-induced fluorescence (LIF) detection and immobilized enzyme. Trypsin cleavage reaction and inhibition were investigated by the presented OGVCE-LIF assay, using carboxyfluorescein (FAM) end-labeled Angiotensin as the substrate and commercially available immobilized trypsin. The substrate and
Li Yang; Chunyang Chen; Yuanfang Chen; Jing Shi; Sidong Liu; Liping Guo; Haifeng Xu
Transglycosylation reaction catalyzed by a class V chitinase from cycad, Cycas revoluta: a study involving site-directed mutagenesis, HPLC, and real-time ESI-MS.
Class V chitinase from cycad, Cycas revoluta, (CrChi-A) is the first plant chitinase that has been found to possess transglycosylation activity. To identify the structural determinants that bring about transglycosylation activity, we mutated two aromatic residues, Phe166 and Trp197, which are likely located in the acceptor binding site, and the mutated enzymes (F166A, W197A) were characterized. When the time-courses of the enzymatic reaction toward chitin oligosaccharides were monitored by HPLC, the specific activity was decreased to about 5-10% of that of the wild type and the amounts of transglycosylation products were significantly reduced by the individual mutations. From comparison between the reaction time-courses obtained by HPLC and real-time ESI-MS, we found that the transglycosylation reaction takes place under the conditions used for HPLC but not under the ESI-MS conditions. The higher substrate concentration (5 mM) used for the HPLC determination is likely to bring about chitinase-catalyzed transglycosylation. Kinetic analysis of the time-courses obtained by HPLC indicated that the sugar residue affinity of +1 subsite was strongly reduced in both mutated enzymes, as compared with that of the wild type. The IC(50) value for the inhibitor allosamidin determined by real-time ESI-MS was not significantly affected by the individual mutations, indicating that the state of the allosamidin binding site (from -3 to -1 subsites) was not changed in the mutated enzymes. We concluded that the aromatic side chains of Phe166 and Trp197 in CrChi-A participate in the transglycosylation acceptor binding, thus controlling the transglycosylation activity of the enzyme. PMID:19879383
Taira, Toki; Fujiwara, Maho; Dennhart, Nicole; Hayashi, Hiroko; Onaga, Shoko; Ohnuma, Takayuki; Letzel, Thomas; Sakuda, Shohei; Fukamizo, Tamo
Theoretical insights into the role of a counterion in copper-catalyzed enantioselective cyclopropanation reactions.
The effect of a coordinating counteranion on the mechanism of Cu(I)-catalyzed cyclopropanation has been investigated extensively for a medium-sized reaction model by means of theoretical calculations at the B3LYP/6-31G(d) level. The main mechanistic features are similar to those found for the cationic (without a counteranion) mechanism, the rate-limiting step being nitrogen extrusion from a catalyst-diazoester complex to generate a copper-carbene intermediate. The cyclopropanation step takes place through a direct carbene insertion of the metal-carbene species to yield a catalyst-product complex, which can finally regenerate the starting complex. However, the presence of the counteranion has a noticeable influence on the calculated geometries of all the intermediates and transition structures. Furthermore, the existence of a preequilibrium with a dimeric form of the catalyst, together with a higher activation barrier in the insertion step, explains the lower yield of cyclopropane products observed experimentally in the presence of chloride counterion. The stereochemical predictions of a more realistic model (made by considering a chiral bis(oxazoline)-copper(i) catalyst) have been rationalized in terms of the lack of significant steric repulsions, and the model shows good agreement with the low enantioselectivities observed experimentally for these kinds of catalytic systems. PMID:14767941
Fraile, Josķ M; GarcĒa, Josķ I; Gil, MarĒa J; MartĒnez-Merino, VĒctor; Mayoral, Josķ A; Salvatella, Luis
Acid-catalyzed conversion of xylose, xylan and straw into furfural by microwave-assisted reaction.
Furfural is a biomass derived-chemical that can be used to replace petrochemicals. In this study, the acid-catalyzed conversion of xylose and xylan to furfural by microwave-assisted reaction was investigated at selected ranges of temperature (140-190░C), time (1-30 min), substrate concentration (1:5-1:200 solid:liquid ratio), and pH (2-0.13). We found that a temperature of 180░C, a solid:liquid ratio of 1:200, a residence time of 20 min, and a pH of 1.12 gave the best furfural yields. The effect of different Br°nsted acids on the conversion efficiency of xylose and xylan was also evaluated, with hydrochloric acid being found to be the most effective catalyst. The microwave-assisted process provides highly efficient conversion: furfural yields obtained from wheat straw, triticale straw, and flax shives were 48.4%, 45.7%, and 72.1%, respectively. PMID:21620690
Yemi?, Oktay; Mazza, Giuseppe
Nickel-based Enzyme Systems*
Of the eight known nickel enzymes, all but glyoxylase I catalyze the use and/or production of gases central to the global carbon, nitrogen, and oxygen cycles. Nickel appears to have been selected for its plasticity in coordination and redox chemistry and is able to cycle through three redox states (1+, 2+, 3+) and to catalyze reactions spanning ?1.5 V. This minireview focuses on the catalytic mechanisms of nickel enzymes, with an emphasis on the role(s) of the metal center. The metal centers vary from mononuclear to complex metal clusters and catalyze simple hydrolytic to multistep redox reactions.
Ragsdale, Stephen W.
Zn(II)- or Ag(I)-catalyzed 1,4-metathesis reactions between 3-En-1-ynamides and nitrosoarenes.
Catalyst-dependent metathesis reactions between 3-en-1-ynamides and nitrosoarenes are described. Particularly notable are the unprecedented 1,4-metathesis reactions catalyzed by Ag(I) or Zn(II) to give 2-propynimidamides and benzaldehyde derivatives. With 3-en-1-ynamides bearing a cycloalkenyl group, 1,4-oxoimination products were produced efficiently. We have developed metathesis/alkynation cascades for unsubstituted 2-propynimidamides and benzaldehyde species generated in situ, to manifest 1,4-hydroxyimination reactions of 3-en-1-ynes. Both 1,4-oxoiminations and 1,4-hydroxyiminations increase the molecular complexity of products. PMID:24521211
Gawade, Sagar Ashok; Huple, Deepak B; Liu, Rai-Shung
Molecular cloning and characterization of norcoclaurine synthase, an enzyme catalyzing the first committed step in benzylisoquinoline alkaloid biosynthesis.
(S)-Norcoclaurine synthase (NCS) (EC 18.104.22.168) catalyzes the condensation of 3,4-dihydroxyphenylethylamine (dopamine) and 4-hydroxyphenylacetaldehyde (4-HPAA) as the first committed step in the biosynthesis of benzylisoquinoline alkaloids such as morphine, sanguinarine, and berberine, in plants. A molecular clone encoding NCS was isolated from a meadow rue (Thalictrum flavum ssp. glaucum) cell suspension culture cDNA library. Heterologous expression of the NCS cDNA, truncated to remove a putative signal peptide, produced a recombinant protein with NCS activity. Recombinant NCS showed sigmoidal saturation kinetics for dopamine (Hill coefficient=1.98), hyperbolic saturation kinetics for 4-HPAA (Km of 700 microm), and pH and temperature optima of 7.0 and 40 degrees C, respectively, all similar to the purified, plant-derived enzyme. NCS exhibits 28-38% identity, and putative structural homology, with the Bet v 1 allergen and pathogenesis-related (PR)10 protein families. NCS also displays 35% identity with the enzyme (HYP1) responsible for hypericin biosynthesis in St John's wort (Hypericum perforatum). The novel catalytic functions of NCS and HYP1 define a new class of plant secondary metabolic enzymes within the Bet v 1 and PR10 protein families. Weaker homology was also detected between NCS and proteins identified in the latex of Papaver somniferum (opium poppy), and in Arabidopsis thaliana. A family of three to five NCS genes is abundantly expressed in the rhizome, followed by petioles and roots of T. flavum. NCS transcripts were localized to the immature endodermis and pericycle in roots, and the protoderm of leaf primordia in rhizomes; thus, the sites of NCS gene expression and berberine accumulation are temporally and spatially separated in roots and rhizomes respectively. PMID:15447655
Samanani, Nailish; Liscombe, David K; Facchini, Peter J
Kinetics, mechanism, and computational studies of rhenium-catalyzed desulfurization reactions of thiiranes (thioepoxides).
The oxorhenium(V) dimer {MeReO(edt)}2 (1; where edt = 1,2-ethanedithiolate) catalyzes S atom transfer from thiiranes to triarylphosphines and triarylarsines. Despite the fact that phosphines are more nucleophilic than arsines, phosphines are less effective because they rapidly convert the dimer catalyst to the much less reactive catalyst [MeReO(edt)(PAr3)] (2). With AsAr3, which does not yield the monomer, the rate law is given by v = k[thiirane][1], independent of the arsine concentration. The values of k at 25.0 degrees C in CDCl3 are 5.58 +/- 0.08 L mol(-1) s(-1) for cyclohexene sulfide and ca. 2 L mol(-1) s(-1) for propylene sulfide. The activation parameters for cyclohexene sulfide are deltaH(double dagger) = 10.0 +/- 0.9 kcal mol(-1) and deltaS(double dagger) = -21 +/- 3 cal K(-1) mol(-1). Arsine enters the catalytic cycle after the rate-controlling release of alkene, undergoing a reaction with the Re(VII)(O)(S) intermediate that is so rapid in comparison that it cannot be studied directly. The use of a kinetic competition method provided relative rate constants and a Hammett reaction constant, rho = -1.0. Computations showed that there is little thermodynamic selectivity for arsine attack at O or S of the intermediate. There is, however, a large kinetic selectivity in favor of Ar3AsS formation: the calculated values of deltaH(double dagger) for attack of AsAr3 at Re=O vs Re=S in Re(VII)(O)(S) are 23.2 and 1.1 kcal mol(-1), respectively. PMID:16813398
Ibdah, Abdellatif; Jenks, William S; Espenson, James H
An Improved Method for Studying the Enzyme-Catalyzed Oxidation of Glucose Using Luminescent Probes
A new method is presented for measuring the rate of the oxidation of glucose in the presence of glucose oxidase. The improved method employs luminescence measurements to directly determine the concentration of oxygen in real time, thus obviating complicated reaction schemes employed in previous methods. Our method has been used to determineģ
Bare, William D.; Pham, Chi V.; Cuber, Matthew; Demas, J. N.
An acyl group makes a difference in the reactivity patterns of cytochrome P450 catalyzed N-demethylation of substituted N,N-dimethylbenzamides-high spin selective reactions.
This paper addresses the experimentally observed mechanistic differences between the cytochrome P450-catalyzed N-demethylation of substituted N,N-dimethylanilines (DMA) and of N,N-dimethylbenzamides (DMBA). The two reactions of these substrates are initiated by C-H activation of the methyl groups on the nitrogen. Thus, the DMA reactions exhibit small deuterium kinetic isotope effects (KIEs), and these KIEs and the corresponding reaction rates exhibit a linear response to the electronic nature of the para substituent. By contrast, the DMBA reactions exhibit large KIEs; the KIEs and reaction rates do not at all respond to the nature of the para substituent. Accordingly, the present paper uses density functional theoretical calculations to address these reactivity patterns in para-substituted DMBA and compare these results to those obtained for the DMA reactions previously (Wang, Y.; Kumar, D.; Yang, C. L.; Han, K. L.; Shaik, S. J. Phys. Chem. B 2007, 111, 7700). The theoretical calculations reproduce the experimental trends of narrow variations in rates and KIEs. It is shown that the above mechanistic differences between the two reaction series of DMA and DMBA are caused by the ability of the para substituent to maintain a conjugation path between the C-H reaction center and the aryl moiety. Furthermore, the computational results show a new feature of reactivity, namely, that the N-demethylation of DMBA proceeds by a spin-selective reaction via the high spin state of the active species of the enzyme. This conclusion is reinforced by the match of the calculated and experimental KIE values. PMID:20146528
Wang, Yong; Li, Dongmei; Han, Keli; Shaik, Sason
Kinetic analysis of the reactions catalyzed by histidine and phenylalanine ammonia lyases.
Although both the structures and the reactions of histidine and phenylalanine ammonia lyases (HAL and PAL) are very similar, the former shows a primary kinetic deuterium (D) isotope effect, while the latter does not. In the HAL reaction, the release of ammonia is partially rate-determining and is slower than the release of the product (E)-urocanate (4), whereas in the PAL reaction, the release of (E)-cinnamate (2) is the rate-limiting step. With (2S,3S)-[3-(2)H1]phenylalanine (1a), we determined the kinetic D isotope effects with the PAL mutants Q487A, Y350F, L137 H, and the double mutant L137 H/Q487E. The kH/kD values for the former two were of the same magnitude as with wild-type PAL (1.20+/-0.07), while the exchange of L137 to H almost doubled the effect (kH/kD=2.32+/-0.01). We conclude that L137 is part of the hydrophobic pocket harboring the phenyl group of the substrate/product and is responsible for its strong binding. The stability of the HAL ammonia complex was demonstrated 40 years ago. Here, we show that, in contrast to the former assumption, ammonia in the complex is not covalently bound to the prosthetic electrophile, 3,5-dihydro-5-methylidene-4H-imidazol-4-one (MIO; 5). We carried out experiments with a mutant enzyme lacking MIO and exhibiting ca. 10(3) times less activity. Nevertheless, the enzyme-ammonia complex was formed, and the mutant behaved upon addition of (E)-[14C]urocanate (4a) like wild-type HAL. We conclude, therefore, that ammonia is bound in the complex by Coulomb forces as ammonium ion and can be released only after (E)-urocanate (4). PMID:17191848
Viergutz, Sandra; Rķtey, Jßnos
A novel ortho-dehalogenation reaction of 2-chlorocinnamic acid catalyzed by the pink yeast Rhodotorula rubra Y-1529.
In the present study, a resting cells suspension of Rhodotorula rubra Y-1529 was shown to have the capacity to perform an ortho-dehalogenation reaction on 2-chlorocinnamic acid. The results from the biodegradation of U-[14C]benzoic acid, cinnamic acid, 3-chlorocinnamic acid and 4-chlorocinnamic acid suggest that the first step of the ortho-dehalogenation reaction occurred during the oxidation of the unsaturated C3 side chain of 2-chlorocinnamic acid to 2-chlorobenzoic acid. None of the 2-chlorobenzoic acid was found in the biodegradation system, suggesting that this step was a highly regulated step. After the side-chain oxidation reaction, the hydroxylation of the benzene ring was determined to be at the para-position first, followed by the meta-position. The occurrence of 3:4-position ring fission reactions and the production of the final product, CO2, was proven by the biodegradation of U-[14C] benzoic acid. This oxidative dehalogenation reaction catalyzed by R. rubra was found to be regiospecific for 2-chlorocinnamic acid; the chloride ion was probably removed after the ring fission reaction. A pathway of the ortho-dehalogenation reaction of 2-chlorocinnamic acid catalyzed by R. rubra was proposed based on these data. PMID:10789983
Sun, F M; Wang, J S; Traxler, R W
Complementary and synergistic roles in enzyme-catalyzed regioselective and complete hydrolytic deprotection of O-acetylated ?-D-glucopyranosides of N-arylacetohydroxamic acids.
An efficient chemoenzymatic synthesis of ?-D-glucopyranosides of N-arylacetohydroxamic acids 3a-c was achieved by the chemoselective O-deacetylation of 1a-c under mild, neutral conditions, with no accompanying N-deacetylation. Lipase AS Amano from Aspergillus niger (LAS) and carboxylesterase from Streptomyces rochei (CSR) played complementary, synergistic roles in the O-deacetylation of 1a and its partially O-deacetylated intermediates. An intramolecular O-acetyl migration, which proceeded simultaneously, also accelerated the overall reaction rate. Under weakly acidic conditions at pH 5.0, where the intramolecular O-acetyl migration is markedly slower, LAS, CSR, and porcine liver esterase (PLE) exhibited different regioselective O-deacetylation activities. LAS and PLE showed regioselective 3-O-deacetylation and 2-O-deacetylation activity, respectively, for 1a and its tri-O-acetyl derivatives (4-7). CSR showed marked preferences for 3-O-deacetylation of 2,3,6-tri-O-acetyl intermediate 5 and 4-O-deacetylation of 2,4,6-tri-O-acetyl intermediate 6. In contrast, CSR showed almost no O-deacetylation activity toward the other tri-O-acetyl intermediates 4 and 7, which were efficiently O-deacetylated by LAS in a complementary manner. Using these enzyme-catalyzed regioselective O-deacetylation as well as chemical methods, we could synthesize all 14 partially O-acetylated intermediates (4-17) derived from 1a. PMID:22283641
Baba, Akiko; Yoshioka, Tadao
Factors that Affect Oxygen Activation and Coupling of the Two Redox Cycles in the Aromatization Reaction Catalyzed by NikD, an Unusual Amino Acid Oxidaseåć
NikD is a flavoprotein oxidase that catalyzes the oxidation of piperideine-2-carboxylate (P2C) to picolinate in a remarkable aromatization reaction comprising two redox cycles and at least one isomerization step. Tyr258 forms part of an "aromatic cage" that surrounds the ring in picolinate and its precursors. Mutation of Tyr258 to Phe does not perturb the structure of nikD but does affect the coupling of the two redox cycles and causes a 10-fold decrease in turnover rate. Tyr258Phe catalyzes a quantitative 2-electron oxidation of P2C but only 60% of the resulting dihydropicolinate intermediate undergoes a second redox cycle to produce picolinate. The mutation does not affect product yield with an alternate substrate (3,4-dehydro-L-proline) that is aromatized in a single 2-electron oxidation step. Wild-type and mutant enzyme exhibit identical rate constants for P2C oxidation to dihydropicolinate and isomerization of a reduced enzymeĢdihydropicolinate complex. The observed rates are 200- and 10-fold faster, respectively, than the mutant turnover rate. Picolinate release from Tyr258Phe is 100-fold faster than turnover. The presence of bound substrate or product is a key factor in oxygen activation by wild-type nikD, as judged by the 10- to 75-fold faster rates observed for complexes of the reduced enzyme with picolinate, benzoate or 1-cyclohexenoate, a 1-deaza P2C analog. The reduced Tyr258PheĢ1-cyclohexenoate complex is 25-fold less reactive with oxygen than the wild-type complex. We postulate that mutation of Tyr258 causes subtle changes in active site dynamics that promote release of the reactive dihydropicolinate intermediate and disrupt the efficient synchronization of oxygen activation observed with wild-type nikD.
Kommoju, Phaneeswara-Rao; Bruckner, Robert C.; Ferreira, Patricia; Carrell, Christopher J.; Mathews, F. Scott; Jorns, Marilyn Schuman
Advanced Low Energy Enzyme Catalyzed Solvent for CO{sub 2} Capture
A proof-of-concept biocatalyst enhanced solvent process was developed and demonstrated in an integrated bench-scale system using coal post combustion flue gas. The biocatalyst was deployed as a coating on M500X structured packing. Rate enhancement was evaluated using a non-volatile and non- toxic 20 wt% potassium carbonate solution. Greater than 500-fold volumetric scale-up from laboratory to bench scale was demonstrated in this project. Key technical achievements included: 10-fold mass transfer enhancement demonstrated in laboratory testing relative to blank potassium carbonate at 45░C; ~ 7-fold enhancement over blank in bench-scale field testing at National Carbon Capture Center; aerosol emissions were below detection limits (< 0.8 ppm); 90% capture was demonstrated at ~19.5 Nm{sup 3}/hr (dry basis); and ~ 80% CO{sub 2} capture was demonstrated at ~ 30 Nm{sup 3}/hr (dry basis) for more than 2800-hrs on flue gas with minimal detectible decline in activity. The regeneration energy requirement was 3.5 GJ/t CO{sub 2} for this solvent, which was below the target of <2.1 GJ/t CO{sub 2}. Bench unit testing revealed kinetic limitations in the un-catalyzed stripper at around 85░C, but process modeling based on bench unit data showed that equivalent work of less than 300 kWh/t CO{sub 2} including all CO{sub 2} compression can be achieved at lower temperature stripping conditions. Cost analysis showed that 20% potassium carbonate in a basic solvent flow sheet with biocatalyst coated packing has economic performance comparable to the reference NETL Case-12, 30% MEA. A detailed techno-economic analysis indicated that addition of catalyst in the stripper could reduce the cost of capture by ~6% and cost of avoided CO{sub 2} by ~10% below reference NETL Case-12. Based on these results, a directional plan was identified to reduce the cost of CO{sub 2} capture in future work.
Zaks, Alex; Reardon, John
Atomically dispersed Au-(OH)x species bound on titania catalyze the low-temperature water-gas shift reaction.
We report a new method for stabilizing appreciable loadings (~1 wt %) of isolated gold atoms on titania and show that these catalyze the low-temperature water-gas shift reaction. The method combines a typical gold deposition/precipitation method with UV irradiation of the titania support suspended in ethanol. Dissociation of H2O on the thus-created Au-O-TiO(x) sites is facile. At higher gold loadings, nanoparticles are formed, but they were shown to add no further activity to the atomically bound gold on titania. Removal of this "excess" gold by sodium cyanide leaching leaves the activity intact and the atomically dispersed gold still bound on titania. The new materials may catalyze a number of other reactions that require oxidized active metal sites. PMID:23437858
Yang, Ming; Allard, Lawrence F; Flytzani-Stephanopoulos, Maria
Microwave-assisted, rhodium(III)-catalyzed N-annulation reactions of aryl and ?,?-unsaturated ketones with alkynes.
New Rh(III)-catalyzed, one-pot N-annulation reactions of aryl and ?,?-unsaturated ketones with alkynes in the presence of ammonium acetate have been developed. Under microwave irradiation conditions, the processes lead to rapid formation of the respective isoquinoline and pyridine derivatives with efficiencies that are strongly dependent on the steric nature of the aryl ring and enone substituents. By employing this protocol, a variety of isoquinoline and pyridine derivatives were prepared in high yields. In addition, a new one-pot approach to the synthesis of pyridines, involving four-component reactions of ketones, formaldehyde, NH(4)OAc, and alkynes, has been uncovered. This process takes place through a route involving initial aldol condensation of the ketone with formaldehyde to generate a branched ?,?-unsaturated ketone that then undergoes Rh(III)-catalyzed N-annulation with NH(4)OAc and the alkyne PMID:24516891
Lee, Hyejeong; Sim, Yong-Kyun; Park, Jung-Woo; Jun, Chul-Ho
Palladium(0)-catalyzed suzuki-miyaura cross-coupling reactions of potassium aryl- and heteroaryltrifluoroborates with alkenyl bromides.
Efficient palladium(0)-catalyzed Suzuki-Miyaura cross-couplings are described. The reactions involving potassium aryl- and heteroaryltrifluoroborates with alkenyl bromides can generally be carried out using < or =2 mol % of palladium catalyst and 3 equiv of base in toluene/H2O. When stereodefined alkenyl bromides are employed, the resulting styrene derivatives are accessed stereospecifically. A variety of functional groups are tolerated in both coupling partners. PMID:16839157
Molander, Gary A; Fumagalli, Tiziano
Rare earth perfluorooctanoate [RE(PFO) 3] catalyzed one-pot Mannich reaction: three component synthesis of ?-amino carbonyl compounds
Mannich reaction of acetophenone, aldehydes and aromatic amines catalyzed efficiently by RE(PFO)3 was described firstly, which carried out smoothly in high yields with three component one-pot method. Furthermore, it was found these catalysts were completely recovered and reused without loss of their catalytic activities and are thus environmentally conscious, and this procedure is a new choice to synthesis ?-aminocarbonyl compounds.
Limin Wang; Jianwei Han; Jia Sheng; He Tian; Zhaoyu Fan
Process optimization of enzyme catalyzed production of dietary diacylglycerol (DAG) using TLIM as biocatalyst.
Diacylglycerol (DAG)-rich sunflower oil was prepared and the optimal conditions for synthesis of DAG-rich oil by glycerolysis using biocatalyst TLIM was determined. A maximum production of 59.8% DAG was obtained after 5 h of constant reaction under vacuum (756 mm of Hg). The optimum temperature for glycerolysis was found to be 50░C, while stoichiometric molar ratio of sunflower oil:glycerol was 2:1 for this reaction. A minimum acid value of 0.48 mg of KOH.g(-1) of oil was observed under these conditions. The fatty acid composition of DAG-rich oil was found to be similar to the original TAG-rich sunflower oil used in the work. The lipase catalysed glycerolysis using 1,3 specific lipase was used to promote the formation of 1,3 isoform of DAG as this isoform is known to possess anti-obesity effect. DAG content was determined by HPTLC and GCMS. The DAG-rich oil contained 59.75% DAG of which 63.34% was found as 1,3-DAG and 36.65% was 1,2-DAG/2,3-DAG. PMID:24500104
Dhara, Rupali; Singhal, Rekha S
9-Mercaptodethiobiotin is Generated as a Ligand to the [2Fe-2S]+ Cluster During the Reaction Catalyzed by Biotin Synthase from Escherichia coli
Biotin synthase catalyzes formation of the thiophane ring through stepwise substitution of a sulfur atom for hydrogen atoms at the C9 and C6 positions of dethiobiotin. Biotin synthase is a Radical SAM enzyme that reductively cleaves S-adenosylmethionine, generating 5?-deoxyadenosyl radicals that initially abstract a hydrogen atom from the C9 position of dethiobiotin. We have proposed that the resulting dethiobiotinyl radical is quenched by the ?-sulfide of the nearby [2Fe-2S]2+ cluster, resulting in coupled formation of 9-mercaptodethiobiotin and a reduced [2Fe-2S]+ cluster. This reduced FeS cluster is observed by electron paramagnetic resonance spectroscopy as a mixture of two orthorhombic spin systems. In the present work, we use isotopically labeled 9-mercaptodethiobiotin and enzyme to probe the ligand environment of the [2Fe-2S]+ cluster in this reaction intermediate. HYSCORE spectra exhibit strong cross-peaks demonstrating strong isotropic coupling of the nuclear spin with the paramagnetic center. The hyperfine coupling constants are consistent with a structural model for the reaction intermediate in which 9-mercaptodethiobiotin is covalently coordinated to the remnant [2Fe-2S]+ cluster.
Fugate, Corey J.; Stich, Troy A.; Kim, Esther G.; Myers, William K.; Britt, R. David; Jarrett, Joseph T.
9-Mercaptodethiobiotin is generated as a ligand to the [2Fe-2S]+ cluster during the reaction catalyzed by biotin synthase from Escherichia coli.
Biotin synthase catalyzes formation of the thiophane ring through stepwise substitution of a sulfur atom for hydrogen atoms at the C9 and C6 positions of dethiobiotin. Biotin synthase is a radical S-adenosylmethionine (SAM) enzyme that reductively cleaves S-adenosylmethionine, generating 5'-deoxyadenosyl radicals that initially abstract a hydrogen atom from the C9 position of dethiobiotin. We have proposed that the resulting dethiobiotinyl radical is quenched by the ?-sulfide of the nearby [2Fe-2S](2+) cluster, resulting in coupled formation of 9-mercaptodethiobiotin and a reduced [2Fe-2S](+) cluster. This reduced FeS cluster is observed by electron paramagnetic resonance spectroscopy as a mixture of two orthorhombic spin systems. In the present work, we use isotopically labeled 9-mercaptodethiobiotin and enzyme to probe the ligand environment of the [2Fe-2S](+) cluster in this reaction intermediate. Hyperfine sublevel correlation spectroscopy (HYSCORE) spectra exhibit strong cross-peaks demonstrating strong isotropic coupling of the nuclear spin with the paramagnetic center. The hyperfine coupling constants are consistent with a structural model for the reaction intermediate in which 9-mercaptodethiobiotin is covalently coordinated to the remnant [2Fe-2S](+) cluster. PMID:22607542
Fugate, Corey J; Stich, Troy A; Kim, Esther G; Myers, William K; Britt, R David; Jarrett, Joseph T
Isomerization, but not oxidation, is suppressed by a single point mutation, E361Q, in the reaction catalyzed by cholesterol oxidase
The putative active site base of cholesterol oxidase from Streptomyces has been removed by site-directed mutagenesis and the mutant enzyme characterized. When glutamate-361 is mutated to a glutamine, the isomerization chemistry catalyzed by cholesterol oxidase is suppressed and the intermediate cholest-5-ene-3-one is isolated. The specific activity for oxidation is 20-fold slower than the wild-type reaction, though the specific activity for isomerization is 10,000-fold slower. Furthermore, incubation of cholest-5-ene-3-one with the E361Q cholesterol oxidase resulted in the production of cholest-4-ene-6{beta}-hydroperoxy-3-one (6%), cholest-4-ene-3,6-dione (32%), cholest-4-ene-6{beta}-ol-3-one (36%), and cholest-4-ene-6{alpha}-hydroperoxy-3-one/ cholest-4-ene-6{alpha}-ol-3-one (13%), in addition to cholest-4-ene-3-one (13%). Measurement of reaction stoichiometry eliminated the possibility that H{sub 2}O{sub 2} or the C4a-hydroperoxy flavin was the oxygenation agent. It is proposed that cholest-4-ene-6-hydroperoxy-3-one is the product of radical chain autoxidation and that cholest-4-ene-3,6-dione and cholest-4-ene-6-ol-3-one are decomposition products of the hydroperoxy steroid radical. The characterization of the E361Q mutant chemistry has illuminated the importance of intermediate sequestration in enzyme catalysis. 42 refs., 5 figs., 2 tabs.
Sampson, N.S.; Kass, I.J. [State Univ. of New York, Stony Brook, NY (United States)] [State Univ. of New York, Stony Brook, NY (United States)
Unification of reaction pathway and kinetic scheme for N2 reduction catalyzed by nitrogenase
Nitrogenase catalyzes the reduction of N2 and protons to yield two NH3 and one H2. Substrate binding occurs at a complex organo-metallocluster called FeMo-cofactor (FeMo-co). Each catalytic cycle involves the sequential delivery of eight electrons/protons to this cluster, and this process has been framed within a kinetic scheme developed by Lowe and Thorneley. Rapid freezing of a modified nitrogenase under turnover conditions using diazene, methyldiazene (HNĀ=ĀN-CH3), or hydrazine as substrate recently was shown to trap a common intermediate, designated I. It was further concluded that the two N-atoms of N2 are hydrogenated alternately (ōAlternatingö (A) pathway). In the present work, Q-band CW EPR and 95Mo ESEEM spectroscopy reveal such samples also contain a common intermediate with FeMo-co in an integer-spin state having a ground-state ōnon-Kramersö doublet. This species, designated H, has been characterized by ESEEM spectroscopy using a combination of 14,15N isotopologs plus 1,2H isotopologs of methyldiazene. It is concluded that: H has NH2 bound to FeMo-co and corresponds to the penultimate intermediate of N2 hydrogenation, the state formed after the accumulation of seven electrons/protons and the release of the first NH3; I corresponds to the final intermediate in N2 reduction, the state formed after accumulation of eight electrons/protons, with NH3 still bound to FeMo-co prior to release and regeneration of resting-state FeMo-co. A proposed unification of the Lowe-Thorneley kinetic model with the ōpromptö alternating reaction pathway represents a draft mechanism for N2 reduction by nitrogenase.
Lukoyanov, Dmitriy; Yang, Zhi-Yong; Barney, Brett M.; Dean, Dennis R.; Seefeldt, Lance C.; Hoffman, Brian M.
Evidence of Kinetic Control of Ligand Binding and Staged Product Release in MurA (enolpyruvyl UDP-GlcNAc synthase)-catalyzed Reactions
MurA (enolpyruvyl UDP-GlcNAc synthase) catalyzes the first committed step in peptidoglycan biosynthesis. In this study, MurA-catalyzed breakdown of its tetrahedral intermediate (THI), with a k{sub cat}/K{sub M} of 520 M{sup -1} s{sup -1}, was far slower than the normal reaction, and 3 x 10{sup 5}-fold slower than the homologous enzyme, AroA, reacting with its THI. This provided kinetic evidence of slow binding and a conformationally constrained active site. The MurA cocrystal structure with UDP-N-acetylmuramic acid (UDP-MurNAc), a potent inhibitor, and phosphite revealed a new 'staged' MurA conformation in which the Arg397 side chain tracked phosphite out of the catalytic site. The closed-to-staged transition involved breaking eight MurA {center_dot} ligand ion pairs, and three intraprotein hydrogen bonds helping hold the active site loop closed. These were replaced with only two MurA {center_dot} UDP-MurNAc ion pairs, two with phosphite, and seven new intraprotein ion pairs or hydrogen bonds. Cys115 appears to have an important role in forming the staged conformation. The staged conformation appears to be one step in a complex choreography of release of the product from MurA.
Jackson, S.; Zhang, F; Chindemi, P; Junop, M; Berti, P
Hybrid quantum/classical molecular dynamics simulations of the proton transfer reactions catalyzed by ketosteroid isomerase: analysis of hydrogen bonding, conformational motions, and electrostatics.
Hybrid quantum/classical molecular dynamics simulations of the two proton transfer reactions catalyzed by ketosteroid isomerase are presented. The potential energy surfaces for the proton transfer reactions are described with the empirical valence bond method. Nuclear quantum effects of the transferring hydrogen increase the rates by a factor of approximately 8, and dynamical barrier recrossings decrease the rates by a factor of 3-4. For both proton transfer reactions, the donor-acceptor distance decreases substantially at the transition state. The carboxylate group of the Asp38 side chain, which serves as the proton acceptor and donor in the first and second steps, respectively, rotates significantly between the two proton transfer reactions. The hydrogen-bonding interactions within the active site are consistent with the hydrogen bonding of both Asp99 and Tyr14 to the substrate. The simulations suggest that a hydrogen bond between Asp99 and the substrate is present from the beginning of the first proton transfer step, whereas the hydrogen bond between Tyr14 and the substrate is virtually absent in the first part of this step but forms nearly concurrently with the formation of the transition state. Both hydrogen bonds are present throughout the second proton transfer step until partial dissociation of the product. The hydrogen bond between Tyr14 and Tyr55 is present throughout both proton transfer steps. The active site residues are more mobile during the first step than during the second step. The van der Waals interaction energy between the substrate and the enzyme remains virtually constant along the reaction pathway, but the electrostatic interaction energy is significantly stronger for the dienolate intermediate than for the reactant and product. Mobile loop regions distal to the active site exhibit significant structural rearrangements and, in some cases, qualitative changes in the electrostatic potential during the catalytic reaction. These results suggest that relatively small conformational changes of the enzyme active site and substrate strengthen the hydrogen bonds that stabilize the intermediate, thereby facilitating the proton transfer reactions. Moreover, the conformational and electrostatic changes associated with these reactions are not limited to the active site but rather extend throughout the entire enzyme. PMID:19799395
Chakravorty, Dhruva K; Soudackov, Alexander V; Hammes-Schiffer, Sharon
The molybdenum oxotransferases and related enzymes.
A perspective is provided of recent advances in our understanding of molybdenum-containing enzymes other than nitrogenase, a large and diverse group of enzymes that usually (but not always) catalyze oxygen atom transfer to or from a substrate, utilizing a Mo=O group as donor or acceptor. An emphasis is placed on the diversity of protein structure and reaction catalyzed by each of the three major families of these enzymes. PMID:23318732
Hille, Russ
Functional Group Tolerant Nickel-Catalyzed Cross-Coupling Reaction for Enantioselective Construction of 30 Methyl-Bearing Stereocenters
The first Negishi nickel-catalyzed stereospecific cross-coupling reaction of secondary benzylic esters is reported. A series of traceless directing groups are evaluated for ability to promote cross-coupling with dimethylzinc. Esters with a chelating thioether derived from commercially-available 2-(methylthio)acetic acid are most effective. The products are formed in high yield and with excellent stereospecificity. A variety of functional groups are tolerated in the reaction including alkenes, alkynes, esters, amines, imides, and O-, S-, and N-heterocycles. The utility of this transformation is highlighted in the enantioselective synthesis of a retinoic acid receptor (RAR) agonist and a fatty acid amide hydrolase (FAAH) inhibitor.
Wisniewska, Hanna M.; Swift, Elizabeth C.; Jarvo, Elizabeth R.
Gold-catalyzed oxidative reactions of propargylic carbonates involving 1,2-carbonate migration: stereoselective synthesis of functionalized alkenes.
A gold-catalyzed oxidative reaction of propargylic carbonates or acetates using 3,5-dichloropyridine as the oxidant has been developed. The reaction provides efficient access to ?-functionalized-?,?-unsaturated ketones with excellent regio- and diastereocontrol via a regioselective attack of the N-oxide to the gold-activated alkyne followed by a 1,2-carbonate migration. In addition, the alkene products could be further transformed into the valuable 5-hydroxycyclopent-2-enones via cyclocondensation with acetone or cyclodimerization under basic conditions. PMID:24731195
Sun, Ning; Chen, Ming; Liu, Yuanhong
Palladium-catalyzed tandem reaction of 2-hydroxyarylacetonitriles with sodium sulfinates: one-pot synthesis of 2-arylbenzofurans.
The first example of the palladium-catalyzed one-pot synthesis of 2-arylbenzofurans in moderate to excellent yields via a tandem reaction of 2-hydroxyarylacetonitriles with sodium sulfinates is reported. A plausible mechanism for the formation of 2-arylbenzofurans involving desulfinative addition and intramolecular annulation reactions is proposed. Moreover, the present synthetic route to benzofurans could be readily scaled up to the gram quantity without any difficulty. Thus, the method represents a convenient and practical strategy for synthesis of benzofuran derivatives. PMID:24824918
Chen, Jiuxi; Li, Jianjun; Su, Weike
A general suzuki cross-coupling reaction of heteroaromatics catalyzed by nanopalladium on amino-functionalized siliceous mesocellular foam.
Suzuki-Miyaura cross-coupling reactions of heteroaromatics catalyzed by palladium supported in the cavities of amino-functionalized siliceous mesocellular foam are presented. The nanopalladium catalyst effectively couples not only heteroaryl halides with boronic acids but also heteroaryl halides with boronate esters, potassium trifluoroborates, MIDA boronates, and triolborates, producing a wide range of heterobiaryls in good to excellent yields. Furthermore, the heterogeneous palladium nanocatalyst can easily be removed from the reaction mixture by filtration and recycled several times with minimal loss in activity. This catalyst provides an alternative, environmentally friendly, low-leaching process for the preparation of heterobiaryls. PMID:24673451
Bratt, Emma; Verho, Oscar; Johansson, Magnus J; Bõckvall, Jan-Erling
Operation conditions affecting the performance of airlift reactors for immobilized enzyme reactions
The applicability of concentric airlift reactors for immobilized enzyme reaction has been studied. Because of simple mechanical structure, good mixing, relatively low shear stress, and lower power consumption, the airlift reactor is apealing for immobilized enzyme reaction. The operation conditions can be optimized by manipulating aeration rate, top clearance space, and solid content.
Chun-Min Chang; Wen Jang Lu; Ku Song Own; Shyh-Jye Hwang
Stereo-specificity for pro-(R) hydrogen of NAD(P)H during enzyme-catalyzed hydride transfer to CL-20.
A dehydrogenase from Clostridium sp. EDB2 and a diaphorase from Clostridium kluyveri were reacted with CL-20 to gain insights into the enzyme-catalyzed hydride transfer to CL-20, and the enzyme's stereo-specificity for either pro-R or pro-S hydrogens of NAD(P)H. Both enzymes biotransformed CL-20 at rates of 18.5 and 24nmol/h/mg protein, using NADH and NADPH as hydride-source, respectively, to produce a N-denitrohydrogenated product with a molecular weight of 393Da. In enzyme kinetics studies using reduced deuterated pyridine nucleotides, we found a kinetic deuterium isotopic effect of 2-fold on CL-20 biotransformation rate using dehydrogenase enzyme against (R)NADD as a hydride-source compared to either (S)NADD or NADH. Whereas, in case of diaphorase, the kinetic deuterium isotopic effect of about 1.5-fold was observed on CL-20 biotransformation rate using (R)NADPD as hydride-source. In a comparative study with LC-MS, using deuterated and non-deuterated NAD(P)H, we found a positive mass-shift of 1Da in the N-denitrohydrogenated product suggesting the involvement of a deuteride (D(-)) transfer from NAD(P)D. The present study thus revealed that both dehydrogenase and diaphorase enzymes from the two Clostridium species catalyzed a hydride transfer to CL-20 and showed stereo-specificity for pro-R hydrogen of NAD(P)H. PMID:16225844
Bhushan, Bharat; Halasz, Annamaria; Hawari, Jalal
Stereo-specificity for pro-(R) hydrogen of NAD(P)H during enzyme-catalyzed hydride transfer to CL-20
A dehydrogenase from Clostridium sp. EDB2 and a diaphorase from Clostridium kluyveri were reacted with CL-20 to gain insights into the enzyme-catalyzed hydride transfer to CL-20, and the enzyme's stereo-specificity for either pro-R or pro-S hydrogens of NAD(P)H. Both enzymes biotransformed CL-20 at rates of 18.5 and 24 nmol/h/mg protein, using NADH and NADPH as hydride-source, respectively, to produce a N-denitrohydrogenated product with a molecular weight of 393 Da. In enzyme kinetics studies using reduced deuterated pyridine nucleotides, we found a kinetic deuterium isotopic effect of 2-fold on CL-20 biotransformation rate using dehydrogenase enzyme against (R)NADD as a hydride-source compared to either (S)NADD or NADH. Whereas, in case of diaphorase, the kinetic deuterium isotopic effect of about 1.5-fold was observed on CL-20 biotransformation rate using (R)NADPD as hydride-source. In a comparative study with LC-MS, using deuterated and non-deuterated NAD(P)H, we found a positive mass-shift of 1 Da in the N-denitrohydrogenated product suggesting the involvement of a deuteride (D{sup -}) transfer from NAD(P)D. The present study thus revealed that both dehydrogenase and diaphorase enzymes from the two Clostridium species catalyzed a hydride transfer to CL-20 and showed stereo-specificity for pro-R hydrogen of NAD(P)H.
Bhushan, Bharat [Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Avenue, Montreal, Que., H4P 2R2 (Canada); Halasz, Annamaria [Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Avenue, Montreal, Que., H4P 2R2 (Canada); Hawari, Jalal [Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Avenue, Montreal, Que., H4P 2R2 (Canada)]. E-mail: firstname.lastname@example.com
Palladium-catalyzed coupling reactions of bromothiophenes at the C-H bond adjacent to the sulfur atom with a new activator system, AgNO3/KF.
[reaction: see text] Bromothiophene derivatives react with aryl iodides catalyzed by a palladium complex in the presence of a silver(I) nitrate/potassium fluoride system to induce coupling at the C-H bond, while the carbon-bromine bond is intact. The produced coupling product bearing the C-Br bond allows further palladium-catalyzed C-C bond-forming reactions in reasonable yields. PMID:16235963
Kobayashi, Kei; Sugie, Atsushi; Takahashi, Masabumi; Masui, Kentaro; Mori, Atsunori
Regioselective synthesis of 1,2-dihydroquinolines by a solvent-free MgBr2-catalyzed multicomponent reaction.
A highly efficient and regioselective synthesis of 1,2-dihydroquinolines via a multicomponent reaction between an aniline and two ketones is described. This reaction was catalyzed by magnesium bromide and carried out under solvent-free conditions. When the reaction was performed by using 3-substituted anilines and nonsymmetrically substituted ketones, principally a single product was found among the four expected regioisomers. A variety of anilines and ketones, including cyclic ketones, were evaluated providing a series of 1,2-dihydroquinolines with diverse substitution patterns. A study of the mechanism is discussed. There is evidence of the in situ formation of the imine as a result of the reaction between the aniline and one of the ketones, before annulation to the heterocyclic ring. PMID:24044723
Gutiķrrez, Rsuini U; Correa, Hans C; Bautista, Rafael; Vargas, Josķ Luis; Jerezano, Alberto V; Delgado, Francisco; Tamariz, JoaquĒn
Understanding the mechanism of stereoselective synthesis of cyclopentenes via N-heterocyclic carbene catalyzed reactions of enals with enones.
The N-heterocyclic carbene (NHC) catalyzed addition of enals to enones to yield trans-cyclopentenes has been investigated using DFT methods at B3LYP/6-31G** computational level. This NHC catalyzed reaction comprises several steps. The first one is the formation of a Breslow intermediate, which nucleophilically attacks to the conjugated position of the enone to yield an enol-enolate. This second step is responsible for the trans relationship at the final cyclopentene. An intramolecular aldolic condensation allows for the formation of the alkoxy cyclopentane intermediate, that by intramolecular nucleophilic attack on the carbonyl group yields a bicyclic ether. The extrusion of the NHC catalyst affords a bicyclic lactone, yielding by CO(2) elimination, the final trans-cyclopentene. PMID:20740249
Domingo, Luis R; Zaragozß, Ram¾n J; Arn¾, Manuel
Calix[6]arene derivatives bearing sulfonate and alkyl groups as surfactants in Sc(OTf) 3-catalyzed Mukaiyama aldol reactions in water
Amphiphilic calix[6]arene derivatives 1a¢b were found to be efficient surfactants for Sc(OTf)3-catalyzed Mukaiyama aldol reaction of silyl enol ethers with aldehydes in water. The results indicated that a hydrophobic microenvironment was formed in the reaction system, which is favorable to stabilize some labile silyl enol ethers and thus promotes the reactions.
Hong-Yu Tian; Yong-Jun Chen; Dong Wang; Cheng-Chu Zeng; Chao-Jun Li
Spectroscopic analyses of the biofuels-critical phytochemical coniferyl alcohol and its enzyme-catalyzed oxidation products.
Lignin composition (monolignol types of coniferyl, sinapyl or p-coumaryl alcohol) is causally related to biomass recalcitrance. We describe multiwavelength (220, 228, 240, 250, 260, 290, 295, 300, 310 or 320 nm) absorption spectroscopy of coniferyl alcohol and its laccase- or peroxidase-catalyzed products during real time kinetic, pseudokinetic and endpoint analyses, in optical turn on or turn off modes, under acidic or basic conditions. Reactions in microwell plates and 100 microL volumes demonstrated assay miniaturization and high throughput screening capabilities. Bathochromic and hypsochromic shifts along with hyperchromicity or hypochromicity accompanied enzymatic oxidations by laccase or peroxidase. The limits of detection and quantitation of coniferyl alcohol averaged 2.4 and 7.1 muM respectively, with linear trend lines over 3 to 4 orders of magnitude. Coniferyl alcohol oxidation was evident within 10 minutes or with 0.01 microg/mL laccase and 2 minutes or 0.001 microg/mL peroxidase. Detection limit improved to 1.0 microM coniferyl alcohol with Km of 978.7 +/- 150.7 microM when examined at 260 nm following 30 minutes oxidation with 1.0 microg/mL laccase. Our assays utilized the intrinsic spectroscopic properties of coniferyl alcohol or its oxidation products for enabling detection, without requiring chemical synthesis or modification of the substrate or product(s). These studies facilitate lignin compositional analyses and augment pretreatment strategies for reducing biomass recalcitrance. PMID:19935474
Achyuthan, Komandoor Elayavalli; Adams, Paul David; Simmons, Blake Alexander; Singh, Anup Kumar
Three-Component Ag-Catalyzed Enantioselective Vinylogous Mannich and Aza-Diels-Alder Reactions with Alkyl-Substituted Aldehydes
Efficient protocols for three-component catalytic enantioselective vinylogous Mannich (VM) reactions of alkyl-substituted aldimines (including those bearing heteroatom-containing substituents) and readily available siloxyfurans are presented. High efficiency and stereoselectivity is achieved through the use of o-thiomethyl-p-methoxyaniline-derived aldimines. Reactions, performed under an atmosphere of air and in undistilled THF, can be promoted in the presence of as little as 1 mol % of easily accessible amino acid-based chiral ligands and commercially available AgOAc. The desired products are obtained in 44% to 92% yield, and in up to >98:<2 diastereomer and >99:<1 enantiomer ratio (>98% ee). Removal of the N-activating group is performed through a one-vessel oxidation/hydrolysis operation, which proceeds via a stable aza-quinone (characterized by X-ray crystallography). Evidence is presented indicating that reactions with chiral non-racemic aldehydes are subject to catalyst control: both substrate enantiomers react to afford the desired product diastereomers in high stereoselectivity. Aryl- and alkynyl-substituted o-thiomethyl-p-methoxyaniline-derived aldimines undergo Ag-catalyzed enantioselective VM more efficiently and with higher selectivity than the corresponding o-anisidyl substrates. Additionally, Ag-catalyzed aza-Diels-Alder reactions of the alkyl-substituted aldimines bearing the structurally modified N-aryl unit afford enantiomerically enriched (up to 95% ee) products in up to 88% yield.
Mandai, Hiroki; Mandai, Kyoko
Structural evidence for a 1,2-enediolate intermediate in the reaction catalyzed by 3-keto-L-gulonate 6-phosphate decarboxylase, a member of the orotidine 5'-monophosphate decarboxylase suprafamily.
3-Keto-L-gulonate 6-phosphate decarboxylase (KGPDC) and orotidine 5'-phosphate decarboxylase (OMPDC) are members of an enzyme suprafamily, the OMPDC suprafamily, because they are homologous enzymes that catalyze mechanistically distinct reactions using different substrates. KGPDC catalyzes the Mg(2+) ion-dependent decarboxylation of 3-keto-L-gulonate 6-phosphate to yield L-xylulose 5-phosphate and CO(2); OMPDC catalyzes the metal ion-independent decarboxylation of OMP to UMP and CO(2). Structural studies have shown that KGPDC and OMPDC share several strictly conserved active site residues that are used differently by each enzyme to catalyze their mechanistically distinct reactions. Although the mechanism of the KGPDC-catalyzed reaction has yet to be elucidated, it is thought to proceed via a Mg(2+) ion-stabilized 1,2-enediolate intermediate. Here we report the crystal structures of KGPDC complexed with L-gulonate 6-phosphate, L-threonohydroxamate 4-phosphate, and L-xylitol 5-phosphate, analogues of the substrate, enediolate intermediate, and product, as well as with the product, L-xylulose 5-phosphate, at 1.2, 1.8, 1.7, and 1.8 A resolution, respectively. These structures support a mechanism that involves the formation of a cis-1,2-enediolate intermediate. Contrary to expectations, the geometry of the intermediate does not involve bidentate coordination of both enediolate oxygen atoms to the Mg(2+) ion but rather involves only the coordination of the oxygen on C2 to the Mg(2+) ion. The oxygen atom on C1 instead forms hydrogen bonds to both Lys64 and Asp67, two strictly conserved active site residues. Lys64 also interacts with the oxygen on C2 and may serve to stabilize a cis conformation of the 1,2-enediolate. These structures also implicate His136 to be the general acid that protonates the 1,2-enediolate intermediate. This study further demonstrates that multiple unrelated enzyme functions can evolve from a single active site architecture without regard for substrate binding affinity or mechanism. PMID:14567674
Wise, Eric L; Yew, Wen Shan; Gerlt, John A; Rayment, Ivan
Computer program for the kinetic equations of enzyme reactions. The case in which more than one enzyme species is present at the onset of the reaction.
This paper presents an extension of the program developed by Var¾n, Havsteen, GarcĒa, GarcĒa-Cßnovas & Tudela [(1990) Biochem. J. 270, 825-828] for the expression of the transient-phase and steady-state kinetic equations of a general enzyme system in which the only enzyme species present at the onset of the reaction is the free enzyme. The program has been extended to situations in which more than one enzyme species may be present at the onset of the reaction. The program is given in Supplementary Publication SUP50165 (5 pages), which has been deposited at the British Library Document Supply Centre, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1991) 273, 5.
Varon, R; Havsteen, B H; Garcia, M; Garcia-Canovas, F; Tudela, J
Probing the specificity of gamma-glutamylamine cyclotransferase: an enzyme involved in the metabolism of transglutaminase-catalyzed protein crosslinks.
?-Glutamylamine cyclotransferase (gGACT) catalyzes the intramolecular cyclization of a variety of L-?-glutamylamines producing 5-oxo-L-proline and free amines. Its substrate specificity implicates it in the downstream metabolism of transglutaminase products, and is distinct from that of ?-glutamyl cyclotransferase which acts on L-?-glutamyl amino acids. To elucidate the mechanism by which gGACT distinguishes between L-?-glutamylamine and amino acid substrates, the specificity of the rabbit kidney enzyme for the amide region of substrates was probed through the kinetic analysis of a series of L-?-glutamylamines. The isodipeptide N(?)-(L-?-glutamyl)-L-lysine 1 was used as a reference. The kinetic constants of the L-?-glutamyl derivative of n-butylamine 7, were nearly identical to those of 1. Introduction of a methyl or carboxylate group on the carbon adjacent to the side-chain amide nitrogen in L-?-glutamylamine substrates resulted in a dramatic decrease in substrate properties for gGACT thus providing an explanation of why gGACT does not act on L-?-glutamyl amino acids except for L-?-glutamylglycine. Placement of substituents on carbons further removed from the side-chain amide nitrogen in L-?-glutamylamines restored activity for gGACT, and L-?-glutamylneohexylamine 19 had a higher specificity constant (k(cat) /K(m)) than 1. gGACT did not exhibit any stereospecificity in the amide region of L-?-glutamylamine substrates. In addition, analogues (26-30) with heteroatom substitutions for the ? methylene position of the L-?-glutamyl moiety were examined. Several thiocarbamoyl derivatives of L-cysteine (28-30) were excellent substrates for gGACT. PMID:22120669
Bowser, Todd E; Trawick, Mary Lynn
Mechanistic studies of the radical S-adenosyl-L-methionine enzyme DesII: EPR characterization of a radical intermediate generated during its catalyzed dehydrogenation of TDP-D-quinovose.
DesII, a radical S-adenosyl-l-methionine (SAM) enzyme from Streptomyces venezuelae, catalyzes the deamination of TDP-4-amino-4,6-dideoxy-D-glucose to TDP-3-keto-4,6-dideoxy-D-glucose in the desosamine biosynthetic pathway. DesII can also catalyze the dehydrogenation of TDP-D-quinovose to the corresponding 3-keto sugar. Similar to other radical SAM enzymes, DesII catalysis has been proposed to proceed via a radical mechanism. This hypothesis is now confirmed by EPR spectroscopy with the detection of a TDP-D-quinovose radical intermediate having a g-value of 2.0025 with hyperfine coupling to two spin 1/2 nuclei, each with a splitting constant of 33.6 G. A significant decrease in the EPR line width is observed when the radical is generated in reactions conducted in D(2)O versus H(2)O. These results are consistent with a C3 ?-hydroxyalkyl radical in which the p-orbital harboring the unpaired electron spin at C3 is periplanar with the C-H bonds at both C2 and C4. PMID:21513273
Ruszczycky, Mark W; Choi, Sei-hyun; Mansoorabadi, Steven O; Liu, Hung-wen
Investigation of the complex reaction coordinate of acid catalyzed amide hydrolysis from molecular dynamics simulations
The rate-determining step of acid catalyzed peptide hydrolysis is the nucleophilic attack of a water molecule to the carbon atom of the amide group. Therein the addition of the hydroxyl group to the amide carbon atom involves the association of a water molecule transferring one of its protons to an adjacent water molecule. The protonation of the amide nitrogen atom
Dirk Zahn
Synthesis of Saturated 1,4-Benzodiazepines via Pd-Catalyzed Carboamination Reactions
A new synthesis of 1,4-benzodiazepines and 1,4-benzodiazepin-5-ones is reported. The Pd-catalyzed coupling ofN-allyl-2-aminobenzylamine derivatives with aryl bromides affords the heterocyclic products in good yield, and substrates bearing allylic methyl groups are transformed toc is-2,3-disubstituted products with >20:1 dr.
Neukom, Joshua D.; Aquino, Alvin S.; Wolfe, John P.
Synthesis of saturated 1,4-benzodiazepines via Pd-catalyzed carboamination reactions.
A new synthesis of 1,4-benzodiazepines and 1,4-benzodiazepin-5-ones is reported. The Pd-catalyzed coupling of N-allyl-2-aminobenzylamine derivatives with aryl bromides affords the heterocyclic products in good yield, and substrates bearing allylic methyl groups are transformed to cis-2,3-disubstituted products with >20:1 dr. PMID:21446677
Neukom, Joshua D; Aquino, Alvin S; Wolfe, John P
Palladium-catalyzed desulfitative cross-coupling reaction of sodium sulfinates with benzyl chlorides.
A palladium-catalyzed approach for the synthesis of diarylmethanes from sodium sulfinates and benzyl chlorides is described. Various aromatic sodium sulfinates were used as aryl sources via extrusion of SO2 and gave the diarylmethanes in moderate to good yields. PMID:23556515
Zhao, Feng; Tan, Qi; Xiao, Fuhong; Zhang, Shufeng; Deng, Guo-Jun
Faox enzymes inhibited Maillard reaction development during storage both in protein glucose model system and low lactose UHT milk.
Fructosamines, also known as Amadori products, are formed by the condensation of glucose with the amino group of amino acids or proteins. These compounds are precursors of advanced glycation end products (AGEs) that can be formed either endogenously during aging and diabetes, and exogenously in heat-processed food. The negative effects of dietary AGEs on human health as well as their negative impact on the quality of dairy products have been widely described, therefore specific tools able to prevent the formation of glycation products are needed. Two fructosamine oxidase enzymes isolated from Aspergillus sp. namely, Faox I and Faox II catalyze the oxidative deglycation of Amadori products representing a potential tool for inhibiting the Maillard reaction in dairy products. In this paper, the ability of recombinant Faox I and II in limiting the formation of carboxy-methyl lysine (CML) and protein-bound hydroxymethyl furfurol (b-HMF) in a commercial UHT low lactose milk and a beta-lactoglobulin (?-LG) glucose model system was investigated. Results show a consistent reduction of CML and b-HMF under all conditions. Faox effects were particularly evident on b-HMF formation in low lactose commercial milk. Peptide analysis of the ?-LG glucose system identified some peptides, derived from cyanogen bromide hydrolysis, as suitable candidates to monitor Faox action in milk-based products. All in all data suggested that non-enzymatic reactions in dairy products might be strongly reduced by implementing Faox enzymes. PMID:23604465
Troise, Antonio Dario; Dathan, Nina A; Fiore, Alberto; Roviello, Giovanni; Di Fiore, Anna; Caira, Simonetta; Cuollo, Marina; De Simone, Giuseppina; Fogliano, Vincenzo; Monti, Simona M
A Novel Glucosylation Reaction on Anthocyanins Catalyzed by Acyl-Glucose-Dependent Glucosyltransferase in the Petals of Carnation and Delphinium[C][W
Glucosylation of anthocyanin in carnations (Dianthus caryophyllus) and delphiniums (Delphinium grandiflorum) involves novel sugar donors, aromatic acyl-glucoses, in a reaction catalyzed by the enzymes acyl-glucose¢dependent anthocyanin 5(7)-O-glucosyltransferase (AA5GT and AA7GT). The AA5GT enzyme was purified from carnation petals, and cDNAs encoding carnation Dc AA5GT and the delphinium homolog Dg AA7GT were isolated. Recombinant Dc AA5GT and Dg AA7GT proteins showed AA5GT and AA7GT activities in vitro. Although expression of Dc AA5GT in developing carnation petals was highest at early stages, AA5GT activity and anthocyanin accumulation continued to increase during later stages. Neither Dc AA5GT expression nor AA5GT activity was observed in the petals of mutant carnations; these petals accumulated anthocyanin lacking the glucosyl moiety at the 5 position. Transient expression of Dc AA5GT in petal cells of mutant carnations is expected to result in the transfer of a glucose moiety to the 5 position of anthocyanin. The amino acid sequences of Dc AA5GT and Dg AA7GT showed high similarity to glycoside hydrolase family 1 proteins, which typically act as ?-glycosidases. A phylogenetic analysis of the amino acid sequences suggested that other plant species are likely to have similar acyl-glucose¢dependent glucosyltransferases.
Matsuba, Yuki; Sasaki, Nobuhiro; Tera, Masayuki; Okamura, Masachika; Abe, Yutaka; Okamoto, Emi; Nakamura, Haruka; Funabashi, Hisakage; Takatsu, Makoto; Saito, Mikako; Matsuoka, Hideaki; Nagasawa, Kazuo; Ozeki, Yoshihiro
Fully Diastereoselective Synthesis of Polysubstituted, Functionalized Piperidines and Decahydroquinolines Based on Multicomponent Reactions Catalyzed by Cerium(IV) Ammonium Nitrate.
The cerium(IV) ammonium nitrate (CAN)-catalyzed, three-component reaction between primary amines, ?-dicarbonyl compounds, and ?,?-unsaturated aldehydes in ethanol heated to reflux, constitutes a general, one-pot synthesis of 1,4-dihydropyridines. Their reduction with sodium triacetoxyborohydride furnished piperidine derivatives bearing up to five substituents with full diastereoselectivity in a hitherto inaccessible stereochemical arrangement. The reaction proceeded with no significant loss of enantiomeric purity under mild reduction conditions that are compatible with several functional groups that are normally sensitive to reduction. Octahydroquinolin-5-one derivatives, which were prepared by a modified version of the initial multicomponent reaction, were not suitable substrates for the sodium triacetoxyborohydride mediated reduction, but they were transformed into the corresponding decahydroquinolines, including a precursor of the amphibian alkaloid pumiliotoxin?C, by catalytic hydrogenation under a variety of conditions. PMID:24909665
Suryavanshi, Padmakar A; Sridharan, Vellaisamy; Maiti, Swarupananda; Menķndez, J Carlos
Ligand spheres in asymmetric hetero Diels-Alder reactions catalyzed by Cu(II) box complexes: experiment and modeling.
The stereoselective hetero Diels-Alder reaction between ethyl glyoxylate and cyclohexadiene catalyzed by [Cu(ii)t-Bu-(box)](OTf)2 was investigated. The reaction was performed step-by-step and the geometry of the Cu(ii) complexes formed in the course of the catalysis was analysed by EPR spectroscopy, advanced pulsed EPR methods (ENDOR, and HYSCORE) and DFT calculations. Our results show that one triflate counterion is directly coordinated to Cu(ii) during the catalytic process (axial position). This leads to penta-coordinated Cu(ii) complexes. Solvent molecules are able to alter the geometry of the Cu(ii) complexes although their coordination is weak. These findings provide an explanation for the solvent and counterion effects observed in many catalytic reactions. PMID:24146076
Umamaheswari, V; Cias, Pawel; P÷ppl, Andreas; Kaupp, Martin; Gescheidt, Georg
Tight Gas Sands Research Program: Field Operations and Analysis. Degradation of Hydroxypropyl Guar Fracturing Fluids by Enzyme, Oxidative, and Catalyzed Oxidative Breakers. Part 1. Linear Hydroxypropyl Guar Solutions. Topical Report, February 1991-December 1991.
The research was designed to accomplish the following objectives: Determine the effects of pH, temperature, and polymer concentration on HPG solution degradation by enzyme, oxidative (ammonium persulfate), and catalyzed oxidative breakers (ammonium persul...
D. Craig S. A. Holditch
Role of MgO and CaO promoters in Ni-catalyzed hydrogenation reactions of CO and carbon
The roles of Mg and Ca promoters in Ni-catalyzed hydrogasification of carbon were investigated with emphasis on nickel dispersion and nickel-carbon interactions during gasification. The dispersion of nickel on carbon, which was estimated by means of XRD, H{sub 2}-TPD, and CO methanation test, was (Ni + Mg){much gt}(Ni + Ca)>Ni. The increased dispersions of nickel by the Mg and Ca added were found to result in the enhanced Ni-C interaction, which was monitored through the desorption of CO from oxygen remaining on carbon, and, therefore, in the promotions of Ni-catalyzed lower-temperature gasification at 400-700 C. The Ca promoter was likely to give surface CaO(COO) species upon heating up to 550 C and release CO{sub 2} above {approximately} 650 C. The CO{sub 2} released is efficiently converted by the nickel adjacent to CaO into CO to create Ni-(O)-C species above 700 C, resulting in acceleration of Ni-catalyzed gasification above 700 C. In situ oxygen transfer to Ni/C during reaction is the most important role played by the Ca promoter.
Haga, Tetsuya; Ozaki, Junichi; Suzuki, Kyosuke; Nishiyama, Yoshiyuki ( Tohoku Univ., Sendai (Japan))
Bulk gold catalyzed oxidation reactions of amines and isocyanides and iron porphyrin catalyzed N-H and O-H bond insertion/cyclization reactions of diamines and aminoalcohols
This work involves two projects. The first project entails the study of bulk gold as a catalyst in oxidation reactions of isocyanides and amines. The main goal of this project was to study the activation and reactions of molecules at metal surfaces in order to assess how organometallic principles for homogeneous processes apply to heterogeneous catalysis. Since previous work had used oxygen as an oxidant in bulk gold catalyzed reactions, the generality of gold catalysis with other oxidants was examined. Amine N-oxides were chosen for study, due to their properties and use in the oxidation of carbonyl ligands in organometallic complexes. When amine N-oxides were used as an oxidant in the reaction of isocyanides with amines, the system was able to produce ureas from a variety of isocyanides, amines, and amine N-oxides. In addition, the rate was found to generally increase as the amine N-oxide concentration increased, and decrease with increased concentrations of the amine. Mechanistic studies revealed that the reaction likely involves transfer of an oxygen atom from the amine N-oxide to the adsorbed isocyanide to generate an isocyanate intermediate. Subsequent nucleophilic attack by the amine yields the urea. This is in contrast to the bulk gold-catalyzed reaction mechanism of isocyanides with amines and oxygen. Formation of urea in this case was proposed to proceed through a diaminocarbene intermediate. Moreover, formation of the proposed isocyanate intermediate is consistent with the reactions of metal carbonyl ligands, which are isoelectronic to isocyanides. Nucleophilic attack at coordinated CO by amine N-oxides produces CO{sub 2} and is analogous to the production of an isocyanate in this gold system. When the bulk gold-catalyzed oxidative dehydrogenation of amines was examined with amine N-oxides, the same products were afforded as when O{sub 2} was used as the oxidant. When the two types of oxidants were directly compared using the same reaction system and conditions, it was found that the oxidative dehydrogenation of dibenzylamine to Nbenzylidenebenzylamine, with N-methylmorpholine N-oxide (NMMO), was nearly quantitative (96%) within 24 h. However, the reaction with oxygen was much slower, with only a 52% yield of imine product over the same time period. Moreover, the rate of reaction was found to be influenced by the nature of the amine N-oxide. For example, the use of the weakly basic pyridine N-oxide (PyNO) led to an imine yield of only 6% after 24 h. A comparison of amine N-oxide and O2 was also examined in the oxidation of PhCH{sub 2}OH to PhCHO catalyzed by bulk gold. In this reaction, a 52% yield of the aldehyde was achieved when NMMO was used, while only a 7% product yield was afforded when O{sub 2} was the oxidant after 48 h. The bulk gold-catalyzed oxidative dehydrogenation of cyclic amines generates amidines, which upon treatment with Aerosil and water were found to undergo hydrolysis to produce lactams. Moreover, 5-, 6-, and 7-membered lactams could be prepared through a one-pot reaction of cyclic amines by treatment with oxygen, water, bulk gold, and Aerosil. This method is much more atom economical than industrial processes, does not require corrosive acids, and does not generate undesired byproducts. Additionally, the gold and Aerosil catalysts can be readily separated from the reaction mixture. The second project involved studying iron(III) tetraphenylporphyrin chloride, Fe(TPP)Cl, as a homogeneous catalyst for the generation of carbenes from diazo reagents and their reaction with heteroatom compounds. Fe(TPP)Cl, efficiently catalyzed the insertion of carbenes derived from methyl 2-phenyldiazoacetates into O-H bonds of aliphatic and aromatic alcohols. Fe(TPP)Cl was also found to be an effective catalyst for tandem N-H and O-H insertion/cyclization reactions when 1,2-diamines and 1,2-alcoholamines were treated with diazo reagents. This approach provides a one-pot process for synthesizing piperazinones and morpholinones and related analogues such as quinoxalinones and benzoxazin-2-ones.
Klobukowski, Erik
Chemical syntheses of inhibitory substrates of the RNA-RNA ligation reaction catalyzed by the hairpin ribozyme
The chemical syntheses of RNA oligomers containing modifications on the 5?-carbon of the 5?-terminal nucleoside for crystallographic and mechanistic studies of the hairpin ribozyme are reported. Phosphoramidites 4 and 8 were prepared and used in solid phase syntheses of RNA oligomers containing the sequence 5?-N?UCCUCUCC, where N? indicates either 5?-chloro-5?-deoxyguanosine or 5?-amino-5?-deoxyguanosine, respectively. A ribozyme ligation assay with the 5?-chloro- and 5?-amino-modified RNA oligomers demonstrated their inhibition of the hairpin-catalyzed RNA¢RNA ligation reaction.
Massey, Archna P.; Sigurdsson, Snorri Th.
Stereospecific synthesis of cyclobutylboronates through copper(I)-catalyzed reaction of homoallylic sulfonates and a diboron derivative.
A copper(I)-catalyzed stereospecific reaction for the preparation of cis- and trans-1-silyl-2-borylcyclobutanes as well as 1-phenyl-2-borylcyclobutanes is reported. (Z)- and (E)-Homoallylic methanesulfonates were converted to the corresponding trans- and cis-cyclobutane derivatives, respectively, in the presence of a CuCl/dppp catalyst, bis(pinacolato)diboron, and K(O-t-Bu)/THF. Stereospecific derivatizations of the cis- and trans-borylcyclobutanes were carried out to demonstrate the utility of the borylcyclobutanes. PMID:20384300
Ito, Hajime; Toyoda, Takashi; Sawamura, Masaya
Sequential Reactions of Surface-Tethered Glycolytic Enzymes
SUMMARY The development of complex hybrid organic-inorganic devices faces several challenges, including how they can generate energy. Cells face similar challenges regarding local energy production. Mammalian sperm solve this problem by generating ATP down the flagellar principal piece by means of glycolytic enzymes, several of which are tethered to a cytoskeletal support via germ cell-specific targeting domains. Inspired by this design, we have produced recombinant hexokinase type 1 and glucose-6-phosphate isomerase capable of oriented immobilization on a nickel-nitrilotriacetic acid modified surface. Specific activities of enzymes tethered via this strategy were substantially higher than when randomly adsorbed. Furthermore, these enzymes showed sequential activities when tethered onto the same surface. This is the first demonstration of surface-tethered pathway components showing sequential enzymatic activities, and it provides a first step toward reconstitution of glycolysis on engineered hybrid devices.
Mukai, Chinatsu; Bergkvist, Magnus; Nelson, Jacquelyn L.; Travis, Alexander J.
The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...
Inversion of product selectivity in an enzyme-inspired metallosupramolecular tweezer catalyzed epoxidation reactionå
This study describes a heteroligated, hemilabile PtII¢P,S tweezer coordination complex that combines a chiral Jacobsen¢Katsuki MnIII-salen epoxidation catalyst with an amidopyridine receptor, which leads to an inversion of the major epoxide product compared to catalysts without a recognition group.
Ulmann, Pirmin A.; Braunschweig, Adam B.; Lee, One-Sun; Wiester, Michael J.
Identification in Haloferax volcanii of phosphomevalonate decarboxylase and isopentenyl phosphate kinase as catalysts of the terminal enzyme reactions in an archaeal alternate mevalonate pathway.
Mevalonate (MVA) metabolism provides the isoprenoids used in archaeal lipid biosynthesis. In synthesis of isopentenyl diphosphate, the classical MVA pathway involves decarboxylation of mevalonate diphosphate, while an alternate pathway has been proposed to involve decarboxylation of mevalonate monophosphate. To identify the enzymes responsible for metabolism of mevalonate 5-phosphate to isopentenyl diphosphate in Haloferax volcanii, two open reading frames (HVO_2762 and HVO_1412) were selected for expression and characterization. Characterization of these proteins indicated that one enzyme is an isopentenyl phosphate kinase that forms isopentenyl diphosphate (in a reaction analogous to that of Methanococcus jannaschii MJ0044). The second enzyme exhibits a decarboxylase activity that has never been directly attributed to this protein or any homologous protein. It catalyzes the synthesis of isopentenyl phosphate from mevalonate monophosphate, a reaction that has been proposed but never demonstrated by direct experimental proof, which is provided in this account. This enzyme, phosphomevalonate decarboxylase (PMD), exhibits strong inhibition by 6-fluoromevalonate monophosphate but negligible inhibition by 6-fluoromevalonate diphosphate (a potent inhibitor of the classical mevalonate pathway), reinforcing its selectivity for monophosphorylated ligands. Inhibition by the fluorinated analog also suggests that the PMD utilizes a reaction mechanism similar to that demonstrated for the classical MVA pathway decarboxylase. These observations represent the first experimental demonstration in H. volcanii of both the phosphomevalonate decarboxylase and isopentenyl phosphate kinase reactions that are required for an alternate mevalonate pathway in an archaeon. These results also represent, to our knowledge, the first identification and characterization of any phosphomevalonate decarboxylase. PMID:24375100
Vannice, John C; Skaff, D Andrew; Keightley, Andrew; Addo, James K; Wyckoff, Gerald J; Miziorko, Henry M
Rapid-Equilibrium Enzyme Kinetics
Rapid-equilibrium rate equations for enzyme-catalyzed reactions are especially useful because if experimental data can be fit by these simpler rate equations, the Michaelis constants can be interpreted as equilibrium constants. However, for some reactions it is necessary to use the more complicated steady-state rate equations. Thermodynamics isģ
Alberty, Robert A.
Enzyme catalytic efficiency: a function of bio-nano interface reactions.
Biocatalyst immobilization onto carbon-based nanosupports has been implemented in a variety of applications ranging from biosensing to biotransformation and from decontamination to energy storage. However, retaining enzyme functionality at carbon-based nanosupports was challenged by the non-specific attachment of the enzyme as well as by the enzyme-enzyme interactions at this interface shown to lead to loss of enzyme activity. Herein, we present a systematic study of the interplay reactions that take place upon immobilization of three pure enzymes namely soybean peroxidase, chloroperoxidase, and glucose oxidase at carbon-based nanosupport interfaces. The immobilization conditions involved both single and multipoint single-type enzyme attachment onto single and multi-walled carbon nanotubes and graphene oxide nanomaterials with properties determined by Fourier transform infrared spectroscopy (FTIR), energy dispersive X-ray analysis (EDX), scanning electron microscopy (SEM), and atomic force microscopy (AFM). Our analysis showed that the different surface properties of the enzymes as determined by their molecular mapping and size work synergistically with the carbon-based nanosupports physico-chemical properties (i.e., surface chemistry, charge and aspect ratios) to influence enzyme catalytic behavior and activity at nanointerfaces. Knowledge gained from these studies can be used to optimize enzyme-nanosupport symbiotic reactions to provide robust enzyme-based systems with optimum functionality to be used for fermentation, biosensors, or biofuel applications. PMID:24666280
Campbell, Alan S; Dong, Chenbo; Meng, Fanke; Hardinger, Jeremy; Perhinschi, Gabriela; Wu, Nianqiang; Dinu, Cerasela Zoica
Method of reduction of nitroaromatics by enzymatic reaction with redox enzymes
A method for the controlled reduction of nitroaromatic compounds such as nitrobenzene and 2,4,6-trinitrotoluene by enzymatic reaction with redox enzymes, such as Oxyrase (Trademark of Oxyrase, Inc., Mansfield, Ohio).
Shah, Manish M. (Richland, WA)
Method of controlled reduction of nitroaromatics by enzymatic reaction with oxygen sensitive nitroreductase enzymes
A method is described for the controlled reduction of nitroaromatic compounds such as nitrobenzene and 2,4,6-trinitrotoluene by enzymatic reaction with oxygen sensitive nitroreductase enzymes, such as ferredoxin NADP oxidoreductase. 6 figs.
Shah, M.M.; Campbell, J.A.
A method for the controlled reduction of nitroaromatic compounds such as nitrobenzene and 2,4,6-trinitrotoluene by enzymatic reaction with oxygen sensitive nitroreductase enzymes, such as ferredoxin NADP oxidoreductase.
Shah, Manish M. (Richland, WA); Campbell, James A. (Pasco, WA)
Synthesis of (▒)-cis-clavicipitic acid by a Rh(I)-catalyzed intramolecular imine reaction.
A new and short synthesis of racemic cis-clavicipitic acid was achieved by taking advantage of the double nucleophilic character of indole-4-pinacolboronic ester. Key to the success of the synthesis were an efficient and selective C-3 indole Friedel-Crafts alkylation and the development of an unprecedented intramolecular rhodium-catalyzed 1,2-addition of an aryl pinacolboronic ester to an unactivated imine. PMID:24605802
Bartoccini, Francesca; Casoli, Mariangela; Mari, Michele; Piersanti, Giovanni
A copper-free palladium catalyzed cross coupling reaction of vinyl tosylates with terminal acetylenes
A copper-free palladium-catalyzed cross coupling of vinyl tosylate (2) and terminal acetylenes was investigated, affording a convenient and efficient method for construction of an sp¢sp2 carbon?carbon bond. The tosylate (2) derived from 1,3-cyclohexanedione was reacted with terminal acetylene under the copper-free conditions at ambient temperature, in the presence of palladium acetate and triphenylphosphine, to provide the conjugated en-yn-one products in
Xiaoyong Fu; Shuyi Zhang; Jianguo Yin; Doris P. Schumacher