Nomenclature peptides

Fig. 24. Parallel arranged and antiparallel arranged (Pro-Ala-Gly) (n = 8,12,16). In accordance with the peptide nomenclature in which the amino terminal end, letters with mirror image were chosen in this figure (see top right). The parallel arrangement could be depicted only in this way...

The peptide nomenclature has been extended to include such analogues. The CO-NH bridge that has been replaced can be indicated by placing ip in square brackets before the name. The ip is placed between superscripts indicating the residues modified, and is followed by a comma and the replacing group, e.g., [3t/t4,CH2-S iupaciubin. 

I. Insect peptide nomenclature follows the rules prescribed in Raina and GSde, Insect Biochem, 1988,18,785-787. 

For the 14th Collective Index period, several revisions in CAS peptide nomenclature have been made, and further changes were made as part of the 2006 revisions. 

Standard three letter codes for amino acids are used throughout. Unless specifically noted, stereochemistry implies pure l amino acids. Peptides are consistently written from N to C terminus in standard peptide nomenclature. In a peptide, Gly corresponds the fragment HN-CH2-CO . For example, H-Gly-NH2 is the carboxamide of glycine (H2N-CH2-CONH2), Ac-Gly-Ala-OH is N-acetylated glycyl alanine. 

PEPTIDES Peptide Nomenclature Biological Functions of Peptides... 

Amino acid and peptide nomenclature conforms to lUPAC-IUB guidelines [1]. 

The lUBMB Commission on Nomenclature has issued a number of recommendations dealing with areas of a more biochemical nature (72), such as peptide hormones (86), conformation of polypeptide chains (87), abbreviations for nucleic acids and polynucleotides (88), iron—sulfur proteins (89), enzyme units (90), etc. The Commission has also produced rules and recommendations for naming enzymes (91,92). 

Figure 1.2 Proteins are built up by amino acids that are linked by peptide bonds to form a polypeptide chain, (a) Schematic diagram of an amino acid. Illustrating the nomenclature used in this book. A central carbon atom (Ca) is attached to an amino group (NH2), a carboxyl group (COOH), a hydrogen atom (H), and a side chain (R). (b) In a polypeptide chain the carboxyl group of amino acid n has formed a peptide bond, C-N, to the amino group of amino acid + 1. One water molecule is eliminated in this process. The repeating units, which are called residues, are divided into main-chain atoms and side chains. The main-chain part, which is identical in all residues, contains a central Ca atom attached to an NH group, a C =0 group, and an H atom. The side chain R, which is different for different residues, is bound to the Ca atom.

An exopeptidase that sequentially releases an amino from the C-terminus of a protein or peptide. Carbox-ypeptidases are classified in Enzyme Nomenclature according to catalytic type and are included in subsubclasses 3.4.16-3.4.18. 

An exopeptidase that sequentially releases a dipeptide from the N-terminus of a protein or peptide. Dipeptidy 1-peptidases are included in Enzyme Nomenclature subsubclass 3.4.14 along with tripeptidyl-peptidases. 

Michel MC, Beck-Sickinger AG, H Cox et al (1998) XVI. International Union of Pharmacology recommendations for the nomenclature of neuropeptide Y, peptide YY and pancreatic polypeptide receptors. Pharmacol Rev 50 143-150... 

Peptidases are enzymes that catalyse the hydrolysis of peptide bonds - the bonds between amino acids that are found in peptides and proteins. The terms protease , proteinase and proteolytic enzyme are synonymous, but strictly speaking can only be applied to peptidases that hydrolase bonds in proteins. Because there are many peptidases that act only on peptides, the term peptidase is recommended. Peptidases are included in subclass 3.4 of enzyme nomenclature [1,5]. 

An exopeptidase that does not cleave standard peptide bonds. An example is pyroglutamyl-peptidase I (MEROPS C15.010), which releases an N-terminal pyroglutamyl from hormones such as thyrotropinreleasing hormone and luteinizing hormone. Omega peptidases are included in Enzyme Nomenclature subsubclass 3.4.19. 

Table 5.5 Nomenclature of the ions formed in the mass spectral fragmentation of polypeptides. From Chapman, J. R. (Ed.), Protein and Peptide Analysis by Mass Spectrometry, Methods in Molecular Biology, Vol. 61, 1996. Reproduced by permission of Humana Press, Inc. 

A nomenclature was proposed by Seebach for the description of / -amino acids according to their substitution pattern, and for naming the resulting / -peptides [66, 67]. Enantiomerically pure / -amino acid derivatives with substituents in the 2-or 3-position are thus defined as - and / -amino acids, respectively (abbreviated to H-/ -HXaa-OH and H-/ -HXaa-OH). The corresponding /S-peptides built from these monomers will be named ff - and / -peptides. Similarly, /S -peptides consist of / -amino acid residues with substituents in both the 2- and 3-positions. Finally, peptides built from geminally disubsituted amino acids are referred to as and / -peptides (Fig. 2.6). 

Fig. 2.6 Nomenclature proposed by Seebach to name /9-peptides according to their substitution patterns [66, 67]...

Fig. 2.33 Classification of y-peptides according to their substitution patterns (Seebach s nomenclature) and folding propensity...

Another potentially paralytic conotoxin was recently described this was a peptide purified from Conus geographus venom, which like / -conotoxin appeared to target to voltage-sensitive Na channels. However, the structure of "conotoxin GS" [nomenclature of Yanagawa et al. (J7)] was less homologous to / -conotoxins than to the w-conotoxins, which are Ca channel blockers. The same peptide was purified and characterized using a different assay, the induction of highly aberrant behavior upon ic injection of mice (L. J. Cruz, unpublished data). 

These are a family of peptides which include substance P, isolated in 1931 but only sequenced in 1971. This peptide has been extensively studied since it was the first major peptide to be extracted from brain but only now are useful antagonists becoming available. Two closely related peptides were then isolated from mammalian tissues and can be added to a number of other tachykinins, many of which are found in amphibians. The name tachykinins originated from the vasoactive effects of substance P but the nomenclature has been resolved into calling the three major mammalian peptides substance P, neurokinin A (NKA) and neurokinin B (NKB) with the corresponding receptors being numbered 1 to 3. The order of potencies at the three receptors as follows ... 

---