Peptides nomenclature rules

Fig. 6.1. IUPAC-IUB Commission on Biochemical Nomenclature rules defining residues and peptide units in peptides. In the example shown, residue No. 2 contains the backbone atoms N2, C2, and C2. Peptide unit No. 2 contains the backbone atoms C2, C2, and Nf. Rj, R2, and R3 are the side chains of the amino acid residues (www.chem.qmul.ac.uk/iupac/AminoAcid/).

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

The abbreviations used for the amino acid residues are mainly those recommended in lUPAC-IUB Commission on Biochemical Nomenclature, Abbreviated Designation of Amino Acid Derivatives and Peptides, Tentative Rules [/. BioL Chem., 241, 527, 2491 (1966) Biochim, Biophys. Acta, 121, 1 (1966)]. Other abbreviations used are given in the list at the front of this book. 

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). 

The Commission on Biochemical Nomenclature (CBN) of the International Union of Pure and Applied Chemistry (IUPAC) and of the International Union of Biochemistry and Molecular Biology (IUBMB) has issued many recommendations and rules on peptides and amino acids. These recommendations and rules concern nomenclature, notations, abbreviations, symbols, etc. (see www.chem.qmul.ac.uk/iupac/AminoAcid/ and www.chem.qmul.ac.uk/iubmb/). 

Systematic substitutive nomenclature may be used to name all organic molecules. However, those that are of animal or vegetable origin have often received trivial names, such as cholesterol, oxytocin and glucose. Biochemical nomenclature is based upon such trivial names, which are either substitutively modified in accordance with the principles, rules and conventions described in Chapter 4, Section 4.5 (p. 70), or transformed and simplified into names of stereoparent hydrides, i.e. parent hydrides of a specific stereochemistry. These names are then modified by the rules of substitutive nomenclature. Three classes of compound will be discussed here to illustrate the basic approach carbohydrates amino acids and peptides and lipids. For details, see Biochemical Nomenclature and Related Documents, 2nd Edition, Portland Press, London (1992). 

The abbreviations and symbols for amino acids and peptides used in this article comply with the rules published by the IUPAC Commission for Biochemical Nomenclature see J. Biol. Chem. 245, 6489 (1970) ibid. 247, 977 (1972) ibid. 250, 3215 (1975) Biochem. J. 126, 773 (1972). The amino acids are in the L-configuration in the case of D-amino acids the abbreviations are prefixed by the letter D. 

Abbreviations used for amino acids and the designations of peptides follow the rules of the lUPAC-IUB Commision of Biochemical Nomenclature in J. Biol. Chem., 247 (1972) 977-983. The following additional abbreviations are used AGP, acyl carrier protein AM, aminomethyl (resin) Boc, tert.-butyloxycarbonyl BOP, benzotriazol-l-yl-oxy-tris(dimethylamino)phosphonium hexa-fluorophosphate Bu, -butyl DCC, N,N -di-cyclohexylcarbodiimide DEAE, diethyl-aminoethyl DIEA, N,N-diisopropylethyl-amine DIPCDI, N,N -diisopropylcarbodi-imide DMAP, 4-dimethylaminopyridine DMF, N,N-dimethylformamide Dts, dithia-succinoyl EtOAc, ethyl acetate EtOH, ethanol Fmoc, 9-fluorenylmethyloxycarbon-yl HOBt, 1-hydroxybenzotriazole HPLC, high-performance liquid chromatography IR, infrared IRAA, internal reference amino acid MBHA, 4-methylbenzhydrylamine (resin) Nle, norleucine NMR, nuclear mag-... 

Books and Review Articles - A number of book and review articles have appeared during the last year. Advances in the chemical synthesis of peptides were reviewed by Hardy, Katsoyannis and YoungJ. The description of the experimental details for the Merrifield method of peptide synthesis has been published by Stewart. It is also noted that the tentative rules for the abbreviated nomenclature of synthetic peptides have also been published. 

The nomenclature and abbreviations used are based mainly on the proposals of the lUPAC-IUB Commission on Biochemical Nomenclature, Tentative Rules, Biochemistry 6, 562 (1967)j of. also Peptides, Proc. 8th Europ. Peptide Symposium, Amsterdam 1967 p.xl. 

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