Nomenclature and Symbolism for Amino Acids and Peptides

INTRODUCTION

The traditional and well-known names of the common α-amino acids were, in general, given to them by their discoverers and bear no relationship to their chemical structures [1, 2]. The modification of these names to accommodate derivatives and to designate configuration was codified in 1947 [3] and revised in 1960 [4]. After proposals for the revision of the rules for naming α-amino acids with two centres of chirality had appeared in 1963 [5], a complete revision of the rules was made in 1974 [6] on the basis of a report by a committee convened by H. B. Vickery. Recommendations for symbols for amino-acid residues in peptide sequences made by Brand & Edsall (p. 224 in [8]) were revised in 1966 [9] and 1971 [10], and recommendations for a one-letter notation were approved in 1968 [11]. Recommendations for naming and symbolizing sequences derived from those of named peptides were made in 1966 [12].

The present revision combines all these documents. In Part I on nomenclature, the main changes are to propose names for particular ionic forms of residues (3AA-12.2) and to apply the stereochemical rules [13] more fully (3AA-3). Part 2 on symbolism introduces a few new symbols (3AA-15.2.7), simplifies the designation of ionized forms of peptides (3AA-19.3), explains the principles for giving symbols to reagents (3AA-18.2), presents a method for showing how parts of residues react (3AA-17.4), and describes the one-letter system for representing long sequences (3AA-20 and -21). Part 3, on the modification of named peptides, is extended to cover enantiomers and reversed sequences (3AA-22.7) and peptide analogues (3AA-22.8). Symbols for the twenty ribosomally incorporated (coded) amino acids are given in Table I, and symbols used in these recommendations for other amino acids are mostly listed in the Appendix, although a few others are given in 3AA-15.2. Substantially new recommendations are marked by triangles in the margins.

References

1. Vickery, H. B. & Schmidt, C. L. A. (1931) Chem. Rev. 9, 169-318.

2. Vickery, H. B. (1972) Adv. Protein Chem. 26, 81-171.

3. Vickery, H. B. (1947) J. Biol. Chem. 169, 237-245.

4. International Union of Pure and Applied Chemistry (IUPAC), Definitive Rules for the vNomenclature of Amino Acids (1960) J. Amer. Chem. Soc. 82, 5575-5577.

5. Vickery, H. B. (1963) J. Org. Chem. 28, 291-293.

6. IUPAC Commission on the Nomenclature of Organic Chemistry (CNOC) and IUPAC-IUB Commission on Biochemical Nomenclature (CBN), Nomenclature of α-Amino Acids, Recommendations 1974, Biochem. J. 149, 1-16 (1975); Biochemistry, 14, 449-462 (1975); Eur. J. Biochem. 53, 1-14 (1975); also pp. 64-77 in [7].

7. International Union of Biochemistry (1978) Biochemical Nomenclature and Related Documents, The Biochemical Society, London.

8. Brand, E. & Edsall, J. T. (1947) Annu. Rev. Biochem. 16, 223-272.

9. IUPAC-IUB Commission on Biochemical Nomenclature (CBN), Abbreviated Designation of Amino-Acid Derivatives and Peptides, Recommendations 1966, Arch. Biochem. Biophys. 121, 1-5 (1967); Biochem. J. 102, 23-27 (1967); Biochemistry, 5, 2485-2489 (1966); Biochim. Biophys. Acta, 121, 1-7 (1967); Bull. Soc. Chim. Biol. 49, 121-129 (1968) (in French); Eur. J. Biochem. 1, 375-378 (1967); Hoppe-Seyler's Z. Physiol. Chem. 348, 256-261 (1967) (in German); J. Biol. Chem. 241, 2491-2495 (1966); Mol. Biol. 2, 282-288 (1968) (in Russian).

10. IUPAC-IUB Commission on Biochemical Nomenclature (CBN), Symbols for Amino-Acid Derivatives and Peptides, Recommendations 1971, Arch. Biochem. Biophys. 150, 1-8 (1972); Biochem. J. 126, 773-780 (1972), corrected l35, 9 (1973); Biochemistry 11, 1726-1732 (1972); Biochim. Biophys. Acta, 263, 205-212 (1972); Eur. J. Biochem. 27, 201-207 (1972), corrected 45, 2 (1974); J. Biol. Chem. 247, 977-983 (1972); Pure Appl. Chem. 40, 315-331 (1974); also pp. 78-84 in [7].

11. IUPAC-IUB Commission on Biochemical Nomenclature (CBN), A One-Letter Notation for Amino Acid Sequences, 1968, Arch. Biochem. Biophys. 125(3), i-v (l968); Biochem. J. 113, 1-4 (1969); Biochemistry, 7, 2703-2705 (1968); Biochim. Biophys. Acta, 168, 6-10 (1968); Bull. Soc. Chim. Biol. 50, 1577-1582 (1968) (in French); Eur. J. Biochem. 5, 151-153 (1968); Hoppe-Seyler's Z. Physiol. Chem. 350, 793-797 (1969) (in German); J. Biol. Chem. 243, 3557-3559 (1968); Mol. Biol. 3, 473-477 (1969) (in Russian); Pure Appl. Chem. 31, 641-645 (1972), also pp. 91-93 in [7].

12. IUPAC-IUB Commission on Biochemical Nomenclature (CBN), Rules for Naming Synthetic Modifications of Natural Peptides, 1966, Arch. Biochem. Biophys. 121, 6-8 (1967); Biochem. J. 104, 17-19 (1967), corrected 135, 9 (1973); Biochemistry, 6, 362-364 (1967); Biochim. Biophys. Acta, 133, 1-5 (1967); Bull. Soc. Chim. Biol. 49, 325-330 (1967) (in French); Eur. J. Biochem. 1, 379-381 (1967), corrected 45, 3 (1974); Hoppe-Seyler's Z. Physiol. Chem. 348, 262-265 (1967) (in German); J. Biol. Chem. 242, 555-557 (1967); Mol. Biol. 2, 466-469 (1968) (in Russian; Pure Appl. Chem. 31, 647-653 (1972); also pp. 85-87 in [7].

13. IUPAC Commission on Nomenclature of Organic Chemistry (CNOC), Nomenclature of Organic Chemistry, Section E: Stereochemistry, Recommendations 1974, Pure Appl. Chem. 45, 11-30 (1976); also pp. 1-18 in [7] and pp. 473-490 in [14]. [See also Biochemical Nomenclature and Related Documents, 2nd edition, Portland Press, 1992, pages 1-18.]

14. International Union of Pure and Applied Chemistry (1979) Nomenclature of Organic Chemistry, Sections A, B, C, D, E, F and H, Pergamon Press, Oxford.

Continue in the next section with 3AA-1 and 3AA-2 of Amino Acids and Peptides.

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