what type of rna has an amino acid attached and is used in the formation of a peptide chain
tRNA
3027582
amino acid from the tRNA onto a growing peptide, according to the genetic code. Aminoacyl tRNA therefore plays an important role in RNA translation, the expression of genes to create proteins. As genetic efficiency evolved in higher organisms, 13 new domains with no obvious association with the catalytic activity of aaRSs genes have been added. The synthetase first binds ATP and the corresponding amino acid (or its precursor) to form an aminoacyl-adenylate, releasing inorganic pyrophosphate (PP). The adenylate-aaRS complex then binds the appropriate tRNA molecule's D arm, and the amino acid is transferred from the aa-AMP to either the 2'-
Aminoacyl tRNA synthetase
7276722
chain by the formation of peptide bonds. The genetic code is read three nucleotides at a time, in units called codons, via interactions with specialized RNA molecules called transfer RNA (tRNA). Each tRNA has three unpaired bases known as the anticodon that are complementary to the codon it reads on the mRNA. The tRNA is also covalently attached to the amino acid specified by the complementary codon. When the tRNA binds to its complementary codon in an mRNA strand, the ribosome attaches its amino acid cargo to the new polypeptide chain, which is synthesized from amino terminus to carboxyl terminus.
Gene
303207
genes into the amino acid sequences of proteins. The three universal types of RNA include transfer RNA (tRNA), messenger RNA (mRNA), and ribosomal RNA (rRNA). Messenger RNA acts to carry genetic sequence information between DNA and ribosomes, directing protein synthesis. Ribosomal RNA is a major component of the ribosome, and catalyzes peptide bond formation. Transfer RNA serves as the carrier molecule for amino acids to be used in protein synthesis, and is responsible for decoding the mRNA. In addition, many other classes of RNA are now known. Artificial nucleic acid analogues have been designed and synthesized by chemists, and include
Nucleic acid
6557141
small GTPase. For fast and accurate recognition of the appropriate tRNA, the ribosome utilizes large conformational changes (conformational proofreading). Now the P site contains the beginning of the peptide chain of the protein to be encoded and the A site has the next amino acid to be added to the peptide chain. The growing polypeptide connected to the tRNA in the P site is detached from the tRNA in the P site and a peptide bond is formed between the last amino acids of the polypeptide and the amino acid still attached to the tRNA in the A site. This
Prokaryotic translation
1606837
upstream of the first gene of amino acid biosynthetic operons. These RNA elements form one of two possible structures in regions encoding very short peptide sequences that are rich in the end product amino acid of the operon. A terminator structure forms when there is an excess of the regulatory amino acid and ribosome movement over the leader transcript is not impeded. When there is a deficiency of the charged tRNA of the regulatory amino acid the ribosome translating the leader peptide stalls and the antiterminator structure forms. This allows RNA polymerase to transcribe the operon. Known RNA leaders are
Non-coding RNA
2819911
peptide bond to be formed to its attached amino acid. The peptidyl-tRNA, which transfers the growing polypeptide to the aminoacyl-tRNA bound in the A/A site, is bound in the P/P site. Once the peptide bond is formed, the tRNA in the P/P site is deacylated, or has a free 3’ end, and the tRNA in the A/A site carries the growing polypeptide chain. To allow for the next elongation cycle, the tRNAs then move through hybrid A/P and P/E binding sites, before completing the cycle and residing in the P/P and E/E sites. Once the A/A and P/P tRNAs have
Transfer RNA
6557142
process, known as "peptide bond formation", is catalyzed by a ribozyme (the 23S ribosomal RNA in the 50S ribosomal subunit). Now, the A site has the newly formed peptide, while the P site has an uncharged tRNA (tRNA with no amino acids). The newly formed peptide in the A site tRNA is known as "dipeptide" and the whole assembly is called "dipeptidyl-tRNA". The tRNA in the P site minus the amino acid is known to be "deacylated". In the final stage of elongation, called "translocation", the "deacylated" tRNA (in the P site) and the "dipeptidyl-tRNA" (in the A site) along
Prokaryotic translation
2819901
a covalent attachment to the amino acid that corresponds to the anticodon sequence. Each type of tRNA molecule can be attached to only one type of amino acid, so each organism has many types of tRNA. Because the genetic code contains multiple codons that specify the same amino acid, there are several tRNA molecules bearing different anticodons which carry the same amino acid. The covalent attachment to the tRNA 3’ end is catalyzed by enzymes called aminoacyl tRNA synthetases. During protein synthesis, tRNAs with attached amino acids are delivered to the ribosome by proteins called elongation factors, which aid in
Transfer RNA
278178
Amino acids are made into proteins by being joined together in a chain of peptide bonds. Each different protein has a unique sequence of amino acid residues: this is its primary structure. Just as the letters of the alphabet can be combined to form an almost endless variety of words, amino acids can be linked in varying sequences to form a huge variety of proteins. Proteins are made from amino acids that have been activated by attachment to a transfer RNA molecule through an ester bond. This aminoacyl-tRNA precursor is produced in an ATP-dependent reaction carried out by an aminoacyl
Metabolism
12734
and carboxylic acid groups of amino acids can react to form amide bonds, one amino acid molecule can react with another and become joined through an amide linkage. This polymerization of amino acids is what creates proteins. This condensation reaction yields the newly formed peptide bond and a molecule of water. In cells, this reaction does not occur directly; instead, the amino acid is first activated by attachment to a transfer RNA molecule through an ester bond. This aminoacyl-tRNA is produced in an ATP-dependent reaction carried out by an aminoacyl tRNA synthetase. This aminoacyl-tRNA is then a substrate for the
Amino acid
14069946
Amino acid activation Amino acid activation (also known as aminoacylation or tRNA charging) refers to the attachment of an amino acid to its Transfer RNA (tRNA). During amino acid activation the amino acids (aa) are attached to their corresponding tRNA. The coupling reactions are catalysed by a group of enzymes called aminoacyl-tRNA synthetases (named after the reaction product aminoacyl-tRNA or aa-tRNA). The coupling reaction proceeds in two steps: The amino acid is coupled to the penultimate nucleotide at the 3’-end of the tRNA (the A in the sequence CCA) via an ester bond. The formation of the ester bond conserves
Amino acid activation
10295111
polymerase and the operon is not transcribed. This structure forms when the cell has an excess of the regulatory amino acid and ribosome movement over the leader transcript is not impeded. When there is a deficiency of the charged tRNA of the regulatory amino acid the ribosome translating the leader peptide stalls and the antiterminator structure can form. This allows RNA polymerase to transcribe the operon. Histidine operon leader The Histidine operon leader is an RNA element found in the bacterial histidine operon. At least 6 amino acid operons are known to be regulated by attenuation. In each a leader
Histidine operon leader
4008747
occur to ensure the correct addition of amino acids: 1. The binding of the correct tRNA into the A site of the ribosome 2. The formation of a peptide bond between the tRNA in the A site and the polypeptide chain attached to the tRNA in the P site 3. Translocation or advancement of the tRNA-mRNA complex by three nucleotides Translocation "kicks off" the tRNA at the E site and shifts the tRNA from the A site into the P site, leaving the A site free for an incoming tRNA to add another amino acid. The last stage of translation
Biosynthesis
10295442
the operon is not transcribed. This structure forms when the cell has an excess of the regulatory amino acid and ribosome movement over the leader transcript is not impeded. When there is a deficiency of the charged tRNA of the regulatory amino acid the ribosome translating the leader peptide stalls and the antiterminator structure can form. This allows RNA polymerase to transcribe the operon. Threonine operon leader The threonine operon leader is an RNA element. Threonine is one of at least 6 amino acid operons are known to be regulated by attenuation. In each a leader sequence of 150-200 bp
Threonine operon leader
348236
component nucleotides with the assistance of ribonucleases. Transfer RNA (tRNA) is a small RNA chain of about 80 nucleotides that transfers a specific amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis during translation. It has sites for amino acid attachment and an anticodon region for codon recognition that binds to a specific sequence on the messenger RNA chain through hydrogen bonding. Ribosomal RNA (rRNA) is the catalytic component of the ribosomes. Eukaryotic ribosomes contain four different rRNA molecules: 18S, 5.8S, 28S and 5S rRNA. Three of the rRNA molecules are synthesized in the nucleolus,
RNA
348385
which encodes the sequence of the amino acids in a protein, is copied into a messenger RNA chain. It may be copied many times into RNA chains. Ribosomes can bind to a messenger RNA chain and use its sequence for determining the correct sequence of amino acids for generating a given protein. Amino acids are selected, collected, and carried to the ribosome by transfer RNA (tRNA) molecules, which enter one part of the ribosome and bind to the messenger RNA chain. It is during this binding that the correct translation of nucleic acid sequence to amino acid sequence occurs. For
Ribosome
10294465
the charged leucyl tRNA the ribosome translating the leader peptide stalls and the antiterminator structure can form. This allows RNA polymerase to transcribe the operon. At least 6 amino acid operons are known to be regulated by attenuation. Leucine operon leader The Leucine operon leader is an RNA element found upstream of the first gene in the Leucine biosynthetic operon. The leader sequence can assume two different secondary structures known as the terminator and the anti-terminator structure. The leader also codes for very short peptide sequence that is rich in leucine amino acid. The terminator structure is recognised as a
Leucine operon leader
278179
tRNA synthetase. This aminoacyl-tRNA is then a substrate for the ribosome, which joins the amino acid onto the elongating protein chain, using the sequence information in a messenger RNA. Nucleotides are made from amino acids, carbon dioxide and formic acid in pathways that require large amounts of metabolic energy. Consequently, most organisms have efficient systems to salvage preformed nucleotides. Purines are synthesized as nucleosides (bases attached to ribose). Both adenine and guanine are made from the precursor nucleoside inosine monophosphate, which is synthesized using atoms from the amino acids glycine, glutamine, and aspartic acid, as well as formate transferred from
Metabolism
496441
gives proline an exceptional conformational rigidity compared to other amino acids. It also affects the rate of peptide bond formation between proline and other amino acids. When proline is bound as an amide in a peptide bond, its nitrogen is not bound to any hydrogen, meaning it cannot act as a hydrogen bond donor, but can be a hydrogen bond acceptor. Peptide bond formation with incoming Pro-tRNA is considerably slower than with any other tRNAs, which is a general feature of N-alkylamino acids. Peptide bond formation is also slow between an incoming tRNA and a chain ending in proline; with
Proline
14069947
a considerable part of the energy from the activation reaction. This stored energy provides the majority of the energy needed for peptide bond formation during translation. Each of the 20 amino acids are recognized by its specific aminoacyl-tRNA synthetase. The synthetases are usually composed of one to four protein subunits. The enzymes vary considerably in structure although they all perform the same type of reaction by binding ATP, one specific amino acid and its corresponding tRNA. The specificity of the amino acid activation is as critical for the translational accuracy as the correct matching of the codon with the anticodon.
Amino acid activation
15099071
where the amino-acid-bearing ends of tRNA bind, and where no proteins are present. These studies led to the conclusion that the ribosome is a ribozyme. The rRNA sequences that make up the ribosomal active site represent some of the most highly conserved sequences in the biological world. Together, these observations indicate that peptide bond formation catalyzed by RNA was a feature of the last common ancestor of all known forms of life. Experimental methods were invented that allowed investigators to use large, diverse populations of RNA molecules to carry out in vitro molecular experiments that utilized powerful selective replication strategies
History of RNA biology
323434
Peptide bond A peptide bond is an amide type of covalent chemical bond linking two consecutive alpha-amino acids from C1 (carbon number one) of one alpha-amino acid and N2 (nitrogen number two) of another along a peptide or protein chain. It can also be called an eupeptide bond to separate it from an isopeptide bond, a different type of amide bond between two amino acids. When two amino acids form a "dipeptide" through a "peptide bond" it is type of condensation reaction. In this kind of condensation, two amino acids approach each other, with the non-side chain (C1) carboxylic acid
Peptide bond
2927344
direction (because when a protein is translated from messenger RNA, it is created from N-terminus to C-terminus - amino acids are added to the carbonyl end). Each amino acid has an amine group and a carboxylic group. Amino acids link to one another by peptide bonds which form through a dehydration reaction that joins the carboxyl group of one amino acid to the amine group of the next in a head-to-tail manner to form a polypeptide chain. The chain has two ends – an amine group, the N-terminus, and an unbound carboxyl group, the C-terminus. When a protein is translated
N-terminus
1300710
amino acid through the amide bond formation at the contact sites of the activating domains. Each module typically consists of an adenylation (A) domain, a peptidyl carrier protein (PCP) domain, and a condensation (C) or elongation domain. In the A domain, the specific amino acid is activated by converting into an aminoacyl adenylate enzyme complex attached to a 4'phosphopantetheine cofactor by thioesterification The complex is then transferred to the PCP domain with the expulsion of AMP. The PCP domain uses the attached 4'-phosphopantethein prosthetic group to load the growing peptide chain and their precursors. The organization of the modules necessary
Vancomycin
12736
a peptide bond formed between the side chain carboxyl of the glutamate (the gamma carbon of this side chain) and the amino group of the cysteine. This dipeptide is then condensed with glycine by glutathione synthetase to form glutathione. In chemistry, peptides are synthesized by a variety of reactions. One of the most-used in solid-phase peptide synthesis uses the aromatic oxime derivatives of amino acids as activated units. These are added in sequence onto the growing peptide chain, which is attached to a solid resin support. The ability to easily synthesize vast numbers of different peptides by varying the types
Amino acid
8999741
bond formation requires the presence of another residue, glutamic acid, which catalyzes bond formation in a proximity induced manner. An example of a small peptide containing an isopeptide bond is glutathione, which has a bond between the side chain of a glutamate residue and the amino group of a cysteine residue. An example of a protein involved in isopeptide bonding is ubiquitin, which gets attached to other proteins with a bond between the C-terminal glycine residue of ubiquitin and a lysine side chain of the substrate protein. The function of enzyme generated isopeptide bonds can be roughly divided into two
Isopeptide bond
4241293
chain protection. The allyloxycarbonyl (alloc) protecting group is sometimes used to protect an amino group (or carboxylic acid or alcohol group) when an orthogonal deprotection scheme is required. It is also sometimes used when conducting on-resin cyclic peptide formation, where the peptide is linked to the resin by a side-chain functional group. The Alloc group can be removed using tetrakis(triphenylphosphine)palladium(0). For special applications like synthetic steps involving protein microarrays, protecting groups sometimes termed "lithographic" are used, which are amenable to photochemistry at a particular wavelength of light, and so which can be removed during lithographic types of operations. The formation
Peptide synthesis
4973469
of neprilysin inhibitors and angiotensin receptor blockers has been shown to be advantageous to ACE inhibitors, the current first-line therapy, in multiple settings. Other terms for BNP include "B-type natriuretic peptide, ventricular natriuretic peptide and natriuretic peptide B"') Brain natriuretic peptide Brain natriuretic peptide (BNP), also known as B-type natriuretic peptide, is a hormone secreted by cardiomyocytes in the heart ventricles in response to stretching caused by increased ventricular blood volume. BNP is named as such because it was originally identified in extracts of pig brain. The 32-amino acid polypeptide BNP is secreted attached to a 76–amino acid N-terminal fragment
Brain natriuretic peptide
10691590
the transcript is then degraded. The trans-translation procedure is a bacterial mechanism to resolve stalled ribosomes. It consists of the hybrid transfer RNA and messenger RNA (tm-RNA) with the small protein SmpB. When the ribosome stalls at the 3'end of mRNA the tm-RNA is joined to the ribosome from the A site which has amino acid attached to it (11-amino acid tag). Then, the amino acid binds to the polypeptide chain. Then the normal translation will translate the tm-RNA codons sequence that will provide a particular tag which signifies that the protein is incomplete. Ultimately, liberated that stalled ribosome. Many
Non-stop decay
2927339
C-terminus The C-terminus (also known as the carboxyl-terminus, carboxy-terminus, C-terminal tail, C-terminal end, or COOH-terminus) is the end of an amino acid chain (protein or polypeptide), terminated by a free carboxyl group (-COOH). When the protein is translated from messenger RNA, it is created from N-terminus to C-terminus. The convention for writing peptide sequences is to put the C-terminal end on the right and write the sequence from N- to C-terminus. Each amino acid has a carboxyl group and an amine group. Amino acids link to one another to form a chain by a dehydration reaction which joins the amine
C-terminus
4241277
allows the rapid assembly of a peptide chain through successive reactions of amino acid derivatives on an insoluble porous support. The solid support consists of small, polymeric resin beads functionalized with reactive groups (such as amine or hydroxyl groups) that link to the nascent peptide chain. Since the peptide remains covalently attached to the support throughout the synthesis, excess reagents and side products can be removed by washing and filtration. This approach circumvents the comparatively time-consuming isolation of the product peptide from solution after each reaction step, which would be required when using conventional solution-phase synthesis. Each amino acid to
Peptide synthesis
14419100
Isoglutamine Isoglutamine or α-glutamine is a gamma amino acid derived from glutamic acid by substituting the carboxyl group in position 1 with an amide group. This is in contrast to the proteinogenic amino acid glutamine, which is the 5-amide of glutamic acid. Isoglutamine can form the C-terminus of a peptide chain, as in muramyl dipeptide (MDP), a constituent of bacterial cell walls. It can also occur inside a peptide chain, in which case the chain is continued at the carboxyl group and isoglutamine behaves as a γ-amino acid, as in mifamurtide, a synthetic derivative of MDP used to treat osteosarcoma.
Isoglutamine
3198708
observed ninhydrin's reaction with amino acids. In 1954, Swedish investigators Oden and von Hofsten proposed that ninhydrin could be used to develop latent fingerprints. Ninhydrin can also be used to monitor deprotection in solid phase peptide synthesis (Kaiser Test). The chain is linked via its C-terminus to the solid support, with the N-terminus extending off it. When that nitrogen is deprotected, a ninhydrin test yields blue. Amino-acid residues are attached with their N-terminus protected, so if the next residue has been successfully coupled onto the chain, the test gives a colorless or yellow result. Ninhydrin is also used in amino
Ninhydrin
334929
Peptidoglycan Peptidoglycan, also known as murein, is a polymer consisting of sugars and amino acids that forms a mesh-like layer outside the plasma membrane of most bacteria, forming the cell wall. The sugar component consists of alternating residues of β-(1,4) linked "N"-acetylglucosamine (NAG) and "N"-acetylmuramic acid (NAM) . Attached to the "N"-acetylmuramic acid is a peptide chain of three to five amino acids. The peptide chain can be cross-linked to the peptide chain of another strand forming the 3D mesh-like layer. Peptidoglycan serves a structural role in the bacterial cell wall, giving structural strength, as well as counteracting the osmotic
Peptidoglycan
4241278
be coupled to the peptide chain N-terminus must be protected on its N-terminus and side chain using appropriate protecting groups such as Boc (acid-labile) or Fmoc (base-labile), depending on the side chain and the protection strategy used (see below). The general SPPS procedure is one of repeated cycles of alternate N-terminal deprotection and coupling reactions. The resin can be washed between each steps. First an amino acid is coupled to the resin. Subsequently, the amine is deprotected, and then coupled with the free acid of the second amino acid. This cycle repeats until the desired sequence has been synthesized. SPPS
Peptide synthesis
18041615
Nonribosomal Code The nonribosomal code refers to key amino acid residues and their positions within the primary sequence of an adenylation domain of a nonribosomal peptide synthetase used to predict substrate specificity and thus (partially) the final product. Analogous to the nonribosomal code is prediction of peptide composition by DNA/RNA codon reading, which is well supported by the central dogma of molecular biology and accomplished using the genetic code simply by following the DNA codon table or RNA codon table. However, prediction of natural product/secondary metabolites by the nonribosomal code is not as concrete as DNA/RNA codon-to-amino acid and much
Nonribosomal Code
14361109
common to each peptide spot. This 3 amino acid segment is used as the linker by which the 17 amino acid chain ("17-mer") is attached to the slide. The 17-mer is the "random peptide", with a random sequence selected by the use of a random number generator. This randomness makes the immunosignature technology different from existing technology to identify disease states via biomarkers, because the 10,000 unique, random peptides per slide are not specifically selected for containing particular sequences. The random sequences are not selected for containing known epitopes, or antibody binding sites, of pathogens. When a sample of diluted
Immunosignature
9701352
process by which peptide bonds are hydrolyzed to amino acids. Unnatural acid insertion in the peptide chain has multiple advantages. It facilitates the formation of stable foldamers with distinct secondary structure. β-Peptides are conformationally more stable in aqueous solution than naturally occurring peptides, especially for small chains. The secondary structure is reinforced by the presence of a rigid β-amino acid, which contains cyclohexane or cyclopentane fragments. These fragments generate a more rigid structure and influence the opening angle of the foldamer. These features are very important for new peptide design. Helical β-peptides mimic antimicrobial activities of host defense peptides. A
Cell-penetrating peptide
2514281
unusual amino acid-like substrate. Following addition of phenylalaninol the completed peptide chain is cleaved by the thioesterase domain, cleaving the thioester bond and leaving an alcohol. Alamethicin Alamethicin is a channel-forming peptide antibiotic, produced by the fungus "Trichoderma viride". It belongs to peptaibol peptides which contain the non-proteinogenic amino acid residue Aib (2-aminoisobutyric acid). This residue strongly induces formation of alpha-helical structure. The peptide sequence is: Ac-Aib-Pro-Aib-Ala-Aib-Ala-Gln-Aib-Val-Aib-Gly-Leu-Aib-Pro-Val-Aib-Aib-Glu-Gln-Phl In cell membranes, it forms voltage-dependent ion channels by aggregation of four to six molecules. Alamethicin biosynthesis is hypothesized to be catalyzed by alamethicin synthase, a Nonribosomal peptide synthase (NRPS) first isolated in
Alamethicin
11112602
RNA ribozymes; As a tool with resistance to RNA hydrolysis; Investigation of the mechanisms used by enzyme; Investigation of the structural features of nucleic acids. To overcome the fact that ribose's 2' hydroxy group that reacts with the phosphate linked 3' hydroxy group (RNA is too unstable to be used or synthesized reliably), a ribose analogue is used. The most common RNA analogues are 2'-O-methyl-substituted RNA, locked nucleic acid (LNA) or bridged nucleic acid (BNA), morpholino, and peptide nucleic acid (PNA). Although these oligonucleotides have a different backbone sugar or, in the case of PNA, an amino acid residue in
Nucleic acid analogue
14037184
cells appears to preserve some 'molecular fossils' from this RNA world. These RNA fossils include the ribosome itself (in which RNA catalyses peptide-bond formation), the modern ribozyme catalyst RNase P, and tRNAs. The nearly universal genetic code preserves some evidence for the RNA world. For instance, recent studies of transfer RNAs, the enzymes that charge them with amino acids (the first step in protein synthesis) and the way these components recognise and exploit the genetic code, have been used to suggest that the universal genetic code emerged before the evolution of the modern amino acid activation method for protein synthesis.
Evolution of cells
10512796
include: in the Fischer peptide synthesis (Emil Fischer, 1903) an α-chloro acid chloride is condensed with the ester of an amino acid. The ester is then hydrolyzed and the acid converted to the acid chloride enabling the extension of the peptide chain by another unit. In a final step the chloride atom is replaced by an amino group completing the peptide synthesis. Schotten–Baumann reaction The Schotten–Baumann reaction is a method to synthesise amides from amines and acid chlorides: Sometimes the name for this reaction is also used to indicate the reaction between an acid chloride and an alcohol to form
Schotten–Baumann reaction
7260586
2 to form the 1-2 structure prevents the formation of the 2-3 structure, while the formation of 2-3 prevents the formation of 3-4. The 3-4 structure is a transcription termination sequence, once it forms RNA polymerase will disassociate from the DNA and transcription of the structural genes of the operon will not occur. Part of the leader transcript codes for a short polypeptide of 14 amino acids, termed the leader peptide. This peptide contains two adjacent tryptophan residues, which is unusual, since tryptophan is a fairly uncommon amino acid (about one in a hundred residues in a typical E. coli
Attenuator (genetics)
4241281
important feature that has enabled the broad application of SPPS is the generation of extremely high yields in the coupling step. Highly efficient amide bond-formation conditions are required. and adding an excess of each amino acid (between 2- and 10-fold). The minimization of amino acid racemization during coupling is also of vital importance to avoid epimerization in the final peptide product. Amide bond formation between an amine and carboxylic acid is slow, and as such usually requires 'coupling reagents' or 'activators'. Activation of the carboxyl group generally involves the formation of an 'active ester' "in situ". A selection of peptide
Peptide synthesis
8366483
Metalloexopeptidase A metalloexopeptidase is a type of enzyme that acts as a metalloproteinase exopeptidase. These enzymes have a catalytic mechanism involving a metal, often zinc. They function in molecular biology as agents that cut the terminal (or penultimate) peptide bonds ending peptide chains. Analogous to slicing the end off a loaf of bread, the process releases a single amino acid (or dipeptide) for use. The terms "metallo carboxypeptidase", "metallo-carboxypeptidase" and "metallocarboxypeptidase" are used to describe a metalloexopeptidase carboxypeptidase. These peptidases specifically target the C-terminus, the unbound carboxyl group (-COOH) at one distinct end of the amino acid chain (cutting one
Metalloexopeptidase
4973460
Brain natriuretic peptide Brain natriuretic peptide (BNP), also known as B-type natriuretic peptide, is a hormone secreted by cardiomyocytes in the heart ventricles in response to stretching caused by increased ventricular blood volume. BNP is named as such because it was originally identified in extracts of pig brain. The 32-amino acid polypeptide BNP is secreted attached to a 76–amino acid N-terminal fragment in the prohormone called NT-proBNP (BNPT), which is biologically inactive. Once released, BNP binds to and activates the atrial natriuretic factor receptor NPRA, and to a lesser extent NPRB, in a fashion similar to atrial natriuretic peptide (ANP)
Brain natriuretic peptide
14829058
with Type 1 toxin-antitoxin systems. LdrD-RdlD toxin-antitoxin system RdlD RNA (regulator detected in LDR-D) is a family of small non-coding RNAs which repress the protein LdrD in a type I toxin-antitoxin system. It was discovered in "Escherichia coli" strain K-12 in a long direct repeat (LDR) named LDR-D. This locus encodes two products: a 35 amino acid peptide toxin (ldrD) and a 60 nucleotide RNA antitoxin. The 374nt toxin mRNA has a half-life of around 30 minutes while rdlD RNA has a half-life of only 2 minutes. This is in keeping with other type I toxin-antitoxin systems. Northern blots showed
LdrD-RdlD toxin-antitoxin system
318742
combined effect of all of the amino acid side chains in a protein that ultimately determines its three-dimensional structure and its chemical reactivity. The amino acids in a polypeptide chain are linked by peptide bonds. Once linked in the protein chain, an individual amino acid is called a "residue," and the linked series of carbon, nitrogen, and oxygen atoms are known as the "main chain" or "protein backbone." The peptide bond has two resonance forms that contribute some double-bond character and inhibit rotation around its axis, so that the alpha carbons are roughly coplanar. The other two dihedral angles in
Protein
10171712
process, each of the peptides in the cycle are connected to one another one at a time by coupling reactions. In this case, first a valine residue is protected by the Fmoc protecting group to protect the amine group in the amino acid. The peptide is then coupled to an OICh (cholestene) group. OICh is a protecting group used to protect the carboxyl group in the amino acid. Next, the Fmoc group is removed to make an amine by using diethyl amine (Et2N). The next amino acid in the peptide chain is then added to the amine in the same
Antamanide
4969275
carboxylic end of the peptide. Exopeptidase An exopeptidase is any peptidase that catalyzes the cleavage of the terminal (or the penultimate) peptide bond; the process releases a single amino acid or dipeptide from the peptide chain. Depending on whether the amino acid is released from the amino or the carboxy terminal, an exopeptidase is further classified as an aminopeptidase or a carboxypeptidase, respectively. Thus, an aminopeptidase, an enzyme in the brush border of the small intestine, will cleave a single amino acid from the amino terminal, whereas carboxypeptidase, which is a digestive enzyme present in pancreatic juice, will cleave a
Exopeptidase
14814595
Norvaline Norvaline (abbreviated as Nva) is an amino acid with the formula CH(CH)CH(NH)COH. The compound is an isomer of the more common amino acid valine. Like most other α-amino acids, norvaline is chiral. It is a white, water-soluble solid. Norvaline is a non-proteinogenic unbranched-chain amino acid. It has previously been reported to be a natural component of an antifungal peptide of "Bacillus subtilis". Norvaline and other modified unbranched chain amino acids have received attention because they appear to be incorporated in some recombinant proteins found in "E. coli". Its biosynthesis has been examined. The incorporation of Nva into peptides reflects
Norvaline
2835842
Bradykinin Bradykinin is an inflammatory mediator. It is a peptide that causes blood vessels to dilate (enlarge), and therefore causes blood pressure to fall. A class of drugs called ACE inhibitors, which are used to lower blood pressure, increase bradykinin (by inhibiting its degradation), further lowering blood pressure. Bradykinin dilates blood vessels via the release of prostacyclin, nitric oxide, and Endothelium-Derived Hyperpolarizing Factor. Bradykinin is a physiologically and pharmacologically active peptide of the kinin group of proteins, consisting of nine amino acids. Bradykinin is a 9-amino acid peptide chain. The amino acid sequence of bradykinin is: Arg-Pro-Pro-Gly-Phe-Ser-Pro-Phe-Arg (RPPGFSPFR). Its empirical
Bradykinin
4969274
Exopeptidase An exopeptidase is any peptidase that catalyzes the cleavage of the terminal (or the penultimate) peptide bond; the process releases a single amino acid or dipeptide from the peptide chain. Depending on whether the amino acid is released from the amino or the carboxy terminal, an exopeptidase is further classified as an aminopeptidase or a carboxypeptidase, respectively. Thus, an aminopeptidase, an enzyme in the brush border of the small intestine, will cleave a single amino acid from the amino terminal, whereas carboxypeptidase, which is a digestive enzyme present in pancreatic juice, will cleave a single amino acid from the
Exopeptidase
14829055
LdrD-RdlD toxin-antitoxin system RdlD RNA (regulator detected in LDR-D) is a family of small non-coding RNAs which repress the protein LdrD in a type I toxin-antitoxin system. It was discovered in "Escherichia coli" strain K-12 in a long direct repeat (LDR) named LDR-D. This locus encodes two products: a 35 amino acid peptide toxin (ldrD) and a 60 nucleotide RNA antitoxin. The 374nt toxin mRNA has a half-life of around 30 minutes while rdlD RNA has a half-life of only 2 minutes. This is in keeping with other type I toxin-antitoxin systems. Northern blots showed that "ldrD" and "rdlD" are
LdrD-RdlD toxin-antitoxin system
9997804
ring are named Ser/Thr/Cys-(ψR1,R2 Pro). Due to the preference for a cis-amide bond with the preceding residue of C2-substituted pseudoprolines, their incorporation results in a kink conformation of the peptide backbone, thus preventing peptide aggregation, self-association, or β-structure formation. Hence, pseudoprolines fulfill two functions simultaneously: they serve (1) as temporary side-chain protection for Ser, Thr, and Cys and (2) as solubilizing building blocks to increase solvation and coupling rates during peptide synthesis and in subsequent chain assembly. Pseudoprolines are obtained by reacting the free amino acids with aldehydes or ketone. The coupling of amino acid derivatives to a growing peptide
Pseudoproline
10244591
the ribosome translating the leader peptide stalls and the antiterminator structure can form. This allows RNA polymerase to transcribe the operon. At least 6 different amino acid operons are known to be regulated by this attenuation. The formation of the anti-terminator requires the trp RNA-binding attenuation protein (TRAP protein) in species of "Bacillus" and related bacteria. This protein is encoded by the MtrB gene. TRAP protein forms an oligomer of 11 subunits, in the presence of tryptophan this binds to section of RNA containing 11 (G/U)AG repeats. This sequence overlaps the anti-terminator loop, thus TRAP-binding preventing formation of the anti-termintor
Tryptophan operon leader
12715
by precipitation from water by adjusting the pH to the required isoelectric point. Amino acids are the structural units (monomers) that make up proteins. They join together to form short polymer chains called peptides or longer chains called either polypeptides or proteins. These polymers are linear and unbranched, with each amino acid within the chain attached to two neighboring amino acids. The process of making proteins encoded by DNA/RNA genetic material is called "translation" and involves the step-by-step addition of amino acids to a growing protein chain by a ribozyme that is called a ribosome. The order in which the
Amino acid
20013981
is an unusual derivative featuring cyclopropenium linked to a cyclopentadienide. Chloride salts of cyclopropenium esters are intermediates in the use of dichlorocyclopropenes for the conversion of carboxylic acids to acid chlorides: Related cyclopropenium cations are produced in the regeneration of the 1,1-dichlorocyclopropenes from the cyclopropenones. The cyclopropenium chlorides have been applied to peptide bond formation. For example, in the figure below, reacting a boc-protected amino acid with an unprotected amino acid in the presence of the cyclopropenium ion allows the formation of a peptide bond via acid chloride formation followed by nucleophilic substitution with the unprotected amino acid. This method
Cyclopropenium ion
19082731
Agelenin Agelenin, also called U-agatoxin-Aop1a, is an antagonist of the presynaptic P-type calcium channel in insects. This neurotoxic peptide consists of 35 amino acids and can be isolated from the venom of the spider "Allagelena opulenta". Agelenin - toxicologically named as U-agatoxin-Aop1a and abbreviated as U-AGTX-Aop1a - is an insecticidal toxin of the venom of the species "Allagelena opulenta". It was first discovered in 1990. Agelenin consists of a polypeptide chain of 35 amino acid residues. It has a short anti-parallel β-sheet connected by three disulfide bonds and four β-turns that form the compact core structure. The three amino acid
Agelenin
12711742
includes an mRNA encoding for a short, toxic peptide ("bsrE", "bsrG" and "bsrH" ) and an antitoxin that consists of an antisense RNA. Further studies established that the 294-nucleotide "bsrG" encodes a 39-amino-acid toxin, and the 180 nucleotide antisense sRNA called SR4 acts as the antitoxin (they overlap by 123 nucleotides). SR4 interaction with the 3'UTR of "bsrG" RNA promotes "bsrG" degradation and inhibits its translation. BsrG interferes with cell envelope biosynthesis, causes membrane invaginations and delocalisation of the cell wall synthesis and initiates autolysis. The 256 nucleotide "bsrE" RNA encodes 30 amino-acid toxin peptide. Its antitoxin gene, SR5 overlaps
Bacillus subtilis BSR sRNAs
2646751
C-peptide The connecting peptide, or C-peptide, is a short 31-amino-acid polypeptide that connects insulin's A-chain to its B-chain in the proinsulin molecule. In diabetes and other diseases a measurement of C-peptide blood serum levels can be used to distinguish between certain diseases with similar clinical features. In the insulin synthesis pathway, first preproinsulin is translocated into the endoplasmic reticulum of beta cells of the pancreas with an A-chain, a C-peptide, a B-chain, and a signal sequence. The signal sequence is cleaved from the N-terminus of the peptide by a signal peptidase, leaving proinsulin. After proinsulin is packaged into vesicles in
C-peptide
8063373
out. TycA is the smallest and activates a single amino acid from one module, TycB is intermediate in size and activates 3 amino acids with 3 modules, and TycC is the largest and activates 6 amino acids with 6 modules (See figure 3). Each module performs all the catalytic reactions necessary to incorporate a single amino acid onto the peptide chain. This is accomplished through the subdomains for adenylation (A), peptityl carrier protein (PCP), condensation (C), and depending on the amino acid position, an epimerization (E). The adenylation subdomain is used in activating the specific amino acid. Each module uses
Tyrocidine
17908826
There are for introns excised from ZC3H12B. ZC3H12B is a probable ribonuclease containing CCCH-type zinc finger domain and ribonuclease domains. The 836 amino acid protein has a predicted molecular weight of 94.2 kdal. It does not contain a signal peptide or a transmembrane region. PSORTII predicted 65.2% probability of nuclear location. CCCH-type zinc fingers and ribonucleases are presumably located in the nucleus for RNA cleaving and specifically, RNA hairpin cleaving (Boysen and Hearn 2008). The protein secondary structure is a mixture of alpha helices and beta strands. The two domains identified so far are the ribonuclease and CCCH-type zinc finger
ZC3H12B
4304430
synthesised in the opposite direction in cells. In peptide synthesis, an amino-protected amino acid is bound to a solid phase material (most commonly, low cross-linked polystyrene beads), forming a covalent bond between the carbonyl group and the resin, most often an amido or an ester bond. Then the amino group is deprotected and reacted with the carbonyl group of the next amino-protected amino acid. The solid phase now bears a dipeptide. This cycle is repeated to form the desired peptide chain. After all reactions are complete, the synthesised peptide is cleaved from the bead. The protecting groups for the amino
Solid-phase synthesis
8999739
Isopeptide bond An isopeptide bond is an amide bond that can form for example between the carboxyl group of one amino acid and the amino group of another. At least one of these joining groups is part of the side chain of one of these amino acids. This is unlike in a peptide bond which is sometimes called an "eupeptide" bond, especially when discussing about both of these bond types in the same context to make a distinction between the two. Lysine for example has an amino group on its side chain and glutamic acid has a carboxy group on
Isopeptide bond
6055668
formation of peptide bonds (with CO formation as a driving force). The proposed mechanism for the reaction between a carboxylic acid and CDI is presented below. In the realm of peptide synthesis, this product may be treated with an amine such as that found on an amino acid to release the imidazole group and couple the peptides. The side products, carbon dioxide and imidazole, are relatively innocuous. Racemization of the amino acids also tends to be minimal, reflecting the mild reaction conditions. CDI can also be used for esterification, although alcoholysis requires heat or the presence of a potent nucleophiles
Carbonyldiimidazole
3722985
Protein structure Protein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers specifically polypeptides formed from sequences of amino acids, the monomers of the polymer. A single amino acid monomer may also be called a residue indicating a repeating unit of a polymer. Proteins form by amino acids undergoing condensation reactions, in which the amino acids lose one water molecule per reaction in order to attach to one another with a peptide bond. By convention, a chain under 30 amino acids is often identified as a peptide, rather than a protein. To be able
Protein structure
13881450
small, simple building blocks. Essentially this approach is needed for nanoscale structure, as the top-down method of miniaturizing device using sophisticated lithography and etching techniques has reached a physical limit. Moreover, the top-down approach is applicable to mainly only silicon based technology, and is unable to be used for biological developments. The peptide structure is organized hierarchically into four levels. The primary structure of a peptide is the sequence of the amino acids on the peptide chain. Amino acids are monomer molecules that carries a carboxyl and an amine functional groups; a spectrum of other chemical groups are attached to
Self-assembling peptide
9009029
of epithelial injury. CCL28 has also been implicated in the migration of IgA-expressing cells to the mammary gland, salivary gland, intestine and other mucosal tissues. It has also been shown as a potential antimicrobial agent effective against certain pathogens, such as Gram negative and Gram positive bacteria and the fungus "Candida albicans". Human CCL28 is encoded by an RNA transcript of 373 nucleotides and a gene with four exons. The gene codes for a 127-amino acid CCL28 protein with a 22-amino acid N-terminal signal peptide. It shares 76% nucleic acid identity and 83% amino acid similarity to the equivalent molecule
CCL28
12425473
translation process and that small RNAs can catalyze all of the chemical groups and information transfers required for life. The structure of the ribosome has been called the "smoking gun," as it showed that the ribosome is a ribozyme, with a central core of RNA and no amino acid side chains within 18 angstroms of the active site where peptide bond formation is catalyzed. The concept of the RNA world was first proposed in 1962 by Alexander Rich, and the term was coined by Walter Gilbert in 1986. Possible precursors for the evolution of protein synthesis include a mechanism to
Abiogenesis
20753810
to release the heptapeptide from the NRPS complex. The growing peptide chain is passed through modules for each amino acid. The basic organization of each module is A-PCP-C. The A, or adenylation, region activates the domain’s amino acid to allow transfer to the PCP, or peptide carrying protein, region. The activated amino acid is transferred to a cysteine residue in the PCP region, which anchors the amino acid and prepares the amino acid to be added to the polypeptide. The C, or condensation, region attaches the amino acid to the polypeptide. In addition, modules 2, 4, and 5 have E
Chloroeremomycin
1729315
intestinal lining stimulates the pancreas after being transported via the bloodstream. They named this intestinal secretion "secretin". Secretin was the first such "chemical messenger" identified. This type of substance is now called a hormone, a term coined by Bayliss in 1905. Secretin is initially synthesized as a 120 amino acid precursor protein known as prosecretin. This precursor contains an N-terminal signal peptide, spacer, secretin itself (residues 28–54), and a 72-amino acid C-terminal peptide. The mature secretin peptide is a linear peptide hormone, which is composed of 27 amino acids and has a molecular weight of 3055. A helix is formed
Secretin
1434028
the lumen of the endoplasmic reticulum (ER). Both type 1 and type 2 RIPs are functionally active against ribosomes "in vitro"; however, only type 2 RIPs display cytotoxicity due to the lectin-like properties of the B chain. In order to display its ribosome-inactivating function, the ricin disulfide bond must be reductively cleaved. Ricin is synthesized in the endosperm of castor oil plant seeds. The ricin precursor protein is 576 amino acid residues in length and contains a signal peptide (residues 1–35), the ricin A chain (36–302), a linker peptide (303–314), and the ricin B chain (315–576). The N-terminal signal sequence
Ricin
13258633
and then the use of SPPS to attach the building block together. An outline of this approach is illustrated below. Several methods exist for the synthesis of monosaccharide amino acid building block as illustrated below. Provided the monosaccharide amino acid building block is stable to peptide coupling conditions, amine deprotection conditions and resin cleavage. Linear assembly remains a popular strategy for the synthesis of glycopeptides with many examples in the literature. In the convergent assembly strategy a peptide chain and glycan residue are first synthesis separately. Then the glycan is glycosylated onto a specific residue of the peptide chain. This
Glycopeptide
2076721
of peptide and nucleotide monomers determines the biological function of their polymers whereas common carbohydrate monomers have one general function such as for energy storage and delivery. Proteins are important biological molecules and play an integral role in the structure and function of viruses, bacteria, and eukaryotic cells. Their backbones are characterized by amide linkages formed by the polymerization between amino and carboxylic acid groups attached to the alpha carbon of each of the twenty amino acids. These amino acid sequences are translated from cellular mRNAs by ribosomes in the cytoplasm of the cell. The ribosomes have enzymatic activity which
Backbone chain
677348
respectively. The mechanism used to cleave a peptide bond involves making an amino acid residue that has the cysteine and threonine (proteases) or a water molecule (aspartic acid, metallo- and acid proteases) nucleophilic so that it can attack the peptide carboxyl group. One way to make a nucleophile is by a catalytic triad, where a histidine residue is used to activate serine, cysteine, or threonine as a nucleophile. This is not an evolutionary grouping, however, as the nucleophile types have evolved convergently in different superfamilies, and some superfamilies show divergent evolution to multiple different nucleophiles. A seventh catalytic type of
Protease
14853085
pyoverdine have been isolated and studied, they all have certain characteristics in common. Each pyoverdine molecule has three parts: a dihydroxyquinoline core, a 6-14 amino acid peptide that varies amongst strains, and a side chain (usually composed of a 4-5 carbon α-ketoacid from the Krebs/citric acid cycle). The core of pyoverdine is responsible for several of its properties, including its well-known yellowish color and fluorescence. The dihydroxyquinoline core is composed of (1S)-5-amino-2,3-dihydro- 8,9-dihydroxy-1H-pyrimido[1,2-a]quinoline-1-carboxylic acid. This portion of the molecule is invariant amongst all observed pyoverdine molecules. The core is modified by the addition of an amino acid chain of pyoverdine
Pyoverdine
1793092
metal ions. Hairpin ribozyme can also catalyze the self-cleavage of RNA without metal ions but the mechanism is still unclear. Ribozyme can also catalyze the formation of peptide bond between adjacent amino acid by lowing the activation entropy. Although most ribozymes are quite rare in the cell, their roles are sometimes essential to life. For example, the functional part of the ribosome, the molecular machine that translates RNA into proteins, is fundamentally a ribozyme, composed of RNA tertiary structural motifs that are often coordinated to metal ions such as Mg as cofactors. In a model system, there is no requirement
Ribozyme
7724639
Polyglutamic acid Polyglutamic acid (PGA) is a polymer of the amino acid glutamic acid (GA). Gamma PGA (Poly-γ-glutamic acid, γ-PGA) - the form where the peptide bonds are between the amino group of GA and the carboxyl group at the end of the GA side chain - is a major constituent of the Japanese food natto. Gamma PGA is formed by bacterial fermentation. Gamma PGA has a wide number of potential uses ranging from food and medicine to water treatment. The other isomer, poly-α-glutamic acid is being used as a drug delivery system in cancer treatment and research is underway
Polyglutamic acid
325974
Peptide Peptides (from Gr.: πεπτός, "peptós" "digested"; derived from πέσσειν, "péssein" "to digest") are short chains of amino acid monomers linked by peptide (amide) bonds. The covalent chemical bonds are formed when the carboxyl group of one amino acid reacts with the amino group of another. The shortest peptides are dipeptides, consisting of 2 amino acids joined by a single peptide bond, followed by tripeptides, tetrapeptides, etc. A polypeptide is a long, continuous, and unbranched peptide chain. Hence, peptides fall under the broad chemical classes of biological oligomers and polymers, alongside nucleic acids, oligosaccharides and polysaccharides, etc. Peptides are distinguished
Peptide
3014758
to control the experiment. They created synthetic RNA molecules outside the bacterium and introduced this RNA to the "E. coli" system. The experiment used 20 test tubes, each filled with a different amino acid. For each individual experiment, 19 amino acids were "cold", and one was radioactively tagged with C so they could detect the tagged amino acid later. They varied the "hot" amino acid in each round of the experiment, seeking to determine which amino acid would be incorporated into a protein following the addition of a particular type of synthetic RNA. In their experiments in late May 1961
Nirenberg and Matthaei experiment
8977419
signs of EDS have also been found to have COL3A1 mutations. The first single base mutation in the COL3A1 gene was reported in 1989 in a patient with vEDS and changing glycine amino acid to serine. Since then, over 600 different mutations have been characterized in the COL3A1 gene. About 2/3 of these mutations change a glycine amino acid to another amino acid in the triple-helical region of the protein chain. A large number of RNA splicing mutations have also been identified. It is difficult to predict the clinical severity based on the type and location of COL3A1 mutations. Several
Collagen, type III, alpha 1
3604080
a native peptide bond as in NCL. This reaction, which is called SEA Native Peptide Ligation, is a useful extension of Native Chemical Ligation. NCL has been proven to be a convenient method for the chemical synthesis of proteins well over 100 amino acids in length, as demonstrated on the 166-amino-acid polypeptide chain of the synthetic variant of erythropoietin and the 203 amino acid HIV-1 protease. Native chemical ligation Native chemical ligation or NCL is an important extension of the chemical ligation field, a concept for constructing a large polypeptide formed by the assembling of two or more unprotected peptides
Native chemical ligation
12698
formula HNCHRCOOH in most cases, where R is an organic substituent known as a "side chain"); often the term "amino acid" is used to refer specifically to these. They include the 22 proteinogenic ("protein-building") amino acids, which combine into peptide chains ("polypeptides") to form the building-blocks of a vast array of proteins. These are all -stereoisomers ("left-handed" isomers), although a few -amino acids ("right-handed") occur in bacterial envelopes, as a neuromodulator (-serine), and in some antibiotics. Twenty of the proteinogenic amino acids are encoded directly by triplet codons in the genetic code and are known as "standard" amino acids. The
Amino acid
4241292
is much larger than the Boc group. Accordingly, prices for Fmoc amino acids were high until the large-scale piloting of one of the first synthesized peptide drugs, enfuvirtide, began in the 1990s, when market demand adjusted the relative prices of Fmoc- vs Boc- amino acids. The (Z) group is another carbamate-type amine protecting group, first used by Max Bergmann in the synthesis of oligopeptides. It is removed under harsh conditions using HBr in acetic acid, or milder conditions of catalytic hydrogenation. While it has been used periodically for α-amine protection in peptide synthesis, it is almost exclusively used for side
Peptide synthesis
12703
yield amino acids after enzymatic digestion or acid hydrolysis. In 1902, Emil Fischer and Franz Hofmeister independently proposed that proteins are formed from many amino acids, whereby bonds are formed between the amino group of one amino acid with the carboxyl group of another, resulting in a linear structure that Fischer termed "peptide". In the structure shown at the top of the page, R represents a side chain specific to each amino acid. The carbon atom next to the carboxyl group (which is therefore numbered 2 in the carbon chain starting from that functional group) is called the α–carbon. Amino
Amino acid
29124
The “knobs” part is engineered by replacing a small amino acid with a larger one. It fits into the “hole”, which is engineered by replacing a large amino acid with a smaller one. What connects the “knobs” to the “holes” are the disulfide bonds between each chain. The “knobs-into-holes” shape facilitates antibody dependent cell mediated cytotoxicity. Single chain variable fragments (scFv) are connected to the variable domain of the heavy and light chain via a short linker peptide. The linker is rich in glycine, which gives it more flexibility, and serine/threonine, which gives it specificity. Two different scFv fragments can
Antibody
2454496
cells is an essential first step in the infection process for colonization and subsequent induction of mucosal infection. The RNA-binding protein Slr1 plays a role in instigating hyphal formation and virulence in "C. albicans". Candidalysin is a cytolytic 31-amino acid α-helical peptide toxin that is released during hyphal formation. It contributes to virulence during mucosal infections. Due to its nature as a model organism, being an important human pathogen and the alternative codon usage (CUG translated into serine rather than leucine), several specific projects and tools have been created to study "C. albicans". The diploid nature and the absence of
Candida albicans
2044528
and an inner loop. The outer loop is formed by peptide bonds between a carboxyl terminus of an amino acid to the subsequent amino terminus of the next residue. The inner loop is closed by a tryptathionine linkage between 6-hydroxy-tryptophan and cysteine. In addition, α-amanitin is decorated with modified amino acid side chains (2"S",3"R",4"R")-4,5-dihydroxy-isoleucine, "trans"-4-hydroxy-proline, which gives its high affinity for RNA polymerase II and III. Matinkhoo et al. devised strategies to surmount three synthetic hurdles to give α-amanitin in 2018. First, enantioselective synthesis of solid phase peptide synthesis-compatible (2"S",3"R",4"R")-4,5-dihydroxyisoleucine was afforded in 11 steps from 2-(benzyloxy)acetaldehyde. Two key stereochemistry-defining
Alpha-Amanitin
631864
will bind metals such as mercury, lead, and cadmium tightly. In the translation of messenger RNA molecules to produce polypeptides, cysteine is coded for by the UGU and UGC codons. Cysteine has traditionally been considered to be a hydrophilic amino acid, based largely on the chemical parallel between its sulfhydryl group and the hydroxyl groups in the side chains of other polar amino acids. However, the cysteine side chain has been shown to stabilize hydrophobic interactions in micelles to a greater degree than the side chain in the nonpolar amino acid glycine and the polar amino acid serine. In a
Cysteine
3919365
two reasons: to aid the ordering of individual peptide fragments' sequences into a whole chain, and because the first round of Edman degradation is often contaminated by impurities and therefore does not give an accurate determination of the "N"-terminal amino acid. A generalised method for "N"-terminal amino acid analysis follows: There are many different reagents which can be used to label terminal amino acids. They all react with amine groups and will therefore also bind to amine groups in the side chains of amino acids such as lysine - for this reason it is necessary to be careful in interpreting
Protein sequencing
8109990
with sugar phosphates, and sugar phosphates are one of the key molecules in metabolism, oxidative pentose phosphate pathways, gluconeogenesis, important intermediates in glycolysis. Sugar phosphates are not only involved in metabolic regulation and signaling but also involved in the synthesis of other phosphate compounds. Peptide nucleic acid (PNA) is a nucleic acid in which natural nucleic acid has been replaced by a synthetic peptide backbone formed from N-(2-amino-ethyl)-glycine units along with sugar phosphate backbone forming in an achiral and uncharged moiety that mimics RNA or DNA oligonucleotides. PNA cannot be degraded inside living cells but it is chemically stable and
Sugar phosphates
4944666
the liver involves hepatocyte nuclear factor 4 alpha (HNF4A) binding to a DR1 like cis element which then stimulate production. Competing with HNF4A at a third site on the promoter is PPARG-2 which reduces copying the gene to RNA. If HNF4A level is low then COUP-TF binds to the first site and turns off production of SHBG. Sex hormone-binding globulin is homodimeric, meaning it has two identical peptide chains making up its structure. The amino acid sequence is the same as for androgen-binding protein but that has different oligosaccharides attached and is produced in testes. SHBG has two two laminin
Sex hormone-binding globulin
20602288
square brackets. "Modifications" [#-Xaa,#-Xaa] The notation utilizes a prefix code of 3, 4 characters. Specifies the position and type of modified amino acid(s) in the peptide. Each modified amino acid is identified by its position in the core peptide sequence using abbreviations found in UniProt and IUPAC. A comma separates multiple post-translational modifications. "Taxonomic name abbreviation" -linus The first three letters of the genus name and first two letters of the species name are used to identify the origin of the orbitide. Based on the list of species maintained by UniProt (<nowiki>http://www.uniprot.org/docs/speclist</nowiki>). "Common suffix" (-orb) Short for orbitide. Amino acid
Linusorb
2646756
Peptides, Eli Lilly, and Cebix all had drug development programs for a C-peptide product. Cebix had the only ongoing program until it completed a Phase IIb trial in December 2014 that showed no difference between C-peptide and placebo, and it terminated its program and went out of business. C-peptide The connecting peptide, or C-peptide, is a short 31-amino-acid polypeptide that connects insulin's A-chain to its B-chain in the proinsulin molecule. In diabetes and other diseases a measurement of C-peptide blood serum levels can be used to distinguish between certain diseases with similar clinical features. In the insulin synthesis pathway, first
C-peptide
2835885
Alpha-Aminobutyric acid α-Aminobutyric acid (AABA), also known as homoalanine in biochemistry, is a non-proteinogenic alpha amino acid with chemical formula CHNO. The straight two carbon side chain is one carbon longer than alanine, hence the prefix homo-. Homoalaine is biosynthesised by transaminating oxobutyrate, a metabolite in isoleucine biosynthesis. It is used by nonribosomal peptide synthases. One example of a nonribosomal peptide containing homoalanine is ophthalmic acid, which was first isolated from calf lens. α-Aminobutyric acid is one of the three isomers of aminobutyric acid. The two other are the neurotransmitter γ-Aminobutyric acid (GABA) and β-Aminobutyric acid (BABA) which is known
Alpha-Aminobutyric acid
1346153
appear to be extensively studied. Cyclosporin is synthesized by a nonribosomal peptide synthetase, cyclosporin synthetase. The enzyme contains an adenylation domain, a thiolation domain, a condensation domain, and an N-methyltransferase domain. The adenylation domain is responsible for substrate recognition and activation, whereas the thiolation domain covalently binds the adenylated amino acids to phosphopantetheine, and the condensation domain elongates the peptide chain. Cyclosporin synthetase substrates include L-valine, L-leucine, L-alanine, glycine, 2-aminobutyric acid, 4-methylthreonine, and D-alanine, which is the starting amino acid in the biosynthetic process. With the adenylation domain, cyclosporin synthetase generates the acyl-adenylated amino acids, then covalently binds the amino
Ciclosporin
20507898
Pseudo K-tuple nucleotide composition The Pseudo K-tuple nucleotide composition or PseKNC, was extended from Chou’s Pseudo amino acid composition or PseAAC . Both PseAAC and PseKNC are of vector descriptor, but the former represents protein or peptide sequences while the latter represents DNA or RNA sequences. To avoid completely losing the sequence-order information for protein and peptide sequences, the pseudo amino acid composition or PseAAC was proposed by Kuo-Chen Chou. But how about for DNA and RNA sequences? To address this problem, the pseudo K-tuple nucleotide composition or PseKNC was proposed. For the convenience scientific community, a freely available web
Pseudo K-tuple nucleotide composition
19749690
which results in a potent anticoagulant effect. FXa is generated from FX by cleavage of a 52 amino acid activation peptide, as the "a" in factor Xa means activated. FXa consists of 254 amino acid catalytic domain and is also linked to a 142 amino acid light chain. The chain contains both GLA domain and two epidermal growth factor domains (EGF like domains). The active site of FXa is structured to catalyze the cleavage of physiological substrates and cleaves PhePheAsnProArg-ThrPhe and TyrIleAspGlyArg-IleVal in prothrombin. FXa has four so-called pockets which are targets for substrates to bind to factor Xa. These
Discovery and development of direct Xa inhibitors
2835886
for inducing plant disease resistance. Alpha-Aminobutyric acid α-Aminobutyric acid (AABA), also known as homoalanine in biochemistry, is a non-proteinogenic alpha amino acid with chemical formula CHNO. The straight two carbon side chain is one carbon longer than alanine, hence the prefix homo-. Homoalaine is biosynthesised by transaminating oxobutyrate, a metabolite in isoleucine biosynthesis. It is used by nonribosomal peptide synthases. One example of a nonribosomal peptide containing homoalanine is ophthalmic acid, which was first isolated from calf lens. α-Aminobutyric acid is one of the three isomers of aminobutyric acid. The two other are the neurotransmitter γ-Aminobutyric acid (GABA) and β-Aminobutyric
Alpha-Aminobutyric acid
15705374
There is an alpha-mode binding between the toxin and the channels. It has a lower activity towards Kv channels and it is predicted that it may prefer a type of SK channel with a narrower entryway as a specific receptor. BmKK2 toxin In molecular biology, the BmKK2 toxins are a family of scorpion toxins. They belong to the scorpion toxin subfamily alpha-KTx 14. They include a novel short-chain peptide from the Asian scorpion "Mesobuthus martensii" Karsch, a potassium channel blocker composed of 31 amino acid residues. The peptide adopts a classical alpha/beta-scaffold for alpha-KTxs. BmKK2 selectively inhibits the delayed rectifier
BmKK2 toxin