Polypeptides, nomenclature

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.

Note The formal lUPAC-IUB Commission on Biochemical Nomenclature convention for the definition of the torsion angles polypeptide chain (Biochemistry 9 3471-3479, 1970) is different from that used here, where the atom serves as the point of reference for both rotations, but the result is the same. (Irving Gas)... 

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... 

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. 

It was earlier considered that all the amino acid-activating synthetases were derived from a single primeval synthetase , so that all synthetases would have similar structures. Surprisingly, however, this is not the case. When the primary sequences, and in part the secondary and tertiary structures, of all the synthetases had been determined, clear differences in their construction became obvious. The aminoacyl-tRNA synthetases consist either of one single polypeptide chain (a) or of two or four identical polypeptides (ot2 or 04). In addition, there are heterogeneously constructed species with two sets of two identical polypeptide chains (OC2P2). This nomenclature indicates that, for each synthetase, a or P refers to a primary structure. The number of amino acids can vary from 334 to more than 1,000. 

Keratins are alpha-type fibrous polypeptides with a diameter of 7 11 nm. They are important components of the cytoskeleton in almost all epithelial cells as well as in some nonepithelial cell types. Keratins are generally held to be the most ubiquitous markers of epithelial differentiation. So far, 20 distinct types numbered by Moll et al. (1982a, 1990, 1992) have been revealed. Keratins were earlier thought to be separable into hard and soft, or cytokeratins and other keratins, but these designations are now understood to be incorrect. In 2006, a new nomenclature (Schweizer et al. 2006) was adopted for describing keratins which takes this into account (Table 13.1). 

Hagenbuch, B. and Meier, P.J. (2004) Organic anion transporting polypeptides ofthe OATP/SLC21 family phylogenetic classification as OATP/SLCO superfamily, new nomenclature and molecular/functional properties. 

Fig. 5. A key to standard nomenclature for the atoms and the more important bond angles and dihedral angles along the polypeptide backbone. Atoms of the central residue are without subscripts.

Whereas the 3-pleated sheet provides a particularly nice and easily appreciated example of regular hydrogen bonding in polypeptide chains, the most common arrangement found in proteins is actually the a-helix (Figure 13.2). Do not worry about the a or P used in the nomenclature this merely signifies that the helical structure (a) was deduced earlier than that of the pleated sheet (P). 

AMINO ACIDS, PEPTIDES PROTEINS Recommended nomenclature and symbolism for amino acids and peptides J. Biol Chem. (1985) 260, 14-42 Biochemistry (1975) 14, 449-462 Abbreviations and symbols for the description of the conformation of polypeptide chains /. Biol Chem. (1970) 245, 6489-6497 Nomenclature of iron-sulfur proteins Eur. J. Biochem. (1979) 93, 427-430 Corrections Eur. J. Biochem. (1979) 102, 315 Nomenclature of peptide hormones J. Biol Chem. (1975) 250, 3215-3216 Nomenclature of human immunoglobulins Eur. J. Biochem. (1974) 45, 5-6 Recommended nomenclature of glycoproteins, glyco-peptides, and peptidoglycans /. Biol Chem. (1987) 262, 13-18 Recommended nomenclature of electron-transfer proteins... 

That part of a polypeptide chain(s) possessing catalytic function. The catalytic domain may comprise more than one structural domain and a multienzyme polypeptide contains at least two types of such domains. See Multienzyme Polypeptide Autonomous Catalytic Domain Nomenclature Committee, lUB (1989) Eur. J. Biochem. 185, 485. 

The subunit nomenclature for the A-ATPase is Kfor the proteolipid, I for the V- and F-ATPase a-subunit, and C for the V-ATPase subunit d. The small polypeptide called H in the A-ATPase is probably the homologue of the V-ATPase G-subunit. 

It is worthwhile to begin the discussion by first stating the conventions adopted for the description of polypeptide conformation. These conventions (Edsall et ah, 1966) were discussed at the 1965 Gordon Conference on Proteins some additional nomenclature was suggested at a workshop on protein conformation in Madras in January 1967. The whole subject is, at present, under consideration by the IUPAC-IUB Commission on Biochemical Nomenclature. 

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