Nomenclature and Symbolism for Amino Acids and Peptides

3AA-17

Continued from 3AA-14 to 3AA-16

Contents of 3AA-17

3AA-17 Substituted Amino Acids

References for 3AA-17

Continued in 3AA-18 and 3AA-19

3AA-17. SUBSTITUTED AMINO ACIDS

3AA-17.1. Substitutions in the 2-Amino and 1-Carboxyl Groups

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This follows logically from 3AA-16.1, 3AA-16.2 and 3AA-16.3 by using symbols for atoms or groups to represent the substituents. Examples (see also 3AA-18.2):

N-AcetylglycineAc-Gly
Glycine ethyl esterGly-OEt
N2-AcetyllysineAc-Lys
Serine methyl esterSer-OMe
O1-Ethyl N-acetylglutamate Ac-Glu-OEt
IsoglutamineGlu-NH2
O1-Methyl hydrogen aspartateAsp-OMe

A second substituent on N-2, when the first is shown with a line as above, may be represented with a second line to the left of the symbol for the substituted residue: . It may be convenient to print this as a vertical line joining the first: . Example: alanyl-N-methylvaline may be represented

See Addenda 1 and Addenda 4 for amide derivatives.

3AA-17.2. Substitutions on Side-Chain Functional Groups

Side-chain substituents may be portrayed above or below the amino-acid symbol (3AA-16.4) or by placing the symbol for the substituent in parentheses immediately after the amino-acid symbol. When the symbol for a substituent, such as an oligosaccharide, has a hyphen on its right-hand side to indicate the bond to the amino acid [22], then this symbol should be placed in parentheses before the amino-acid symbol rather than after it, e.g. -(Galβ1-4Xylβ1-)Ser- [22].

Symbols within parentheses written on one line should normally be used only in textual material and when the symbol for the substituent is short; otherwise the two-line symbols containing a vertical line will be clearer. Note that the substituents represented replace hydrogen except when the amino acid is aspartic acid or glutamic acid, when they replace the OH of the carboxyl group unless otherwise specified (3AA-16.4.2).

If a locant is required, it is placed beside the vertical line that represents side-chain substitution, or is joined to thc substituent symbol within the parentheses by a hyphen.

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ExamplesSymbolsNotes
O4-Methyl hydrogen aspartate (β-methyl aspartate)i
O5-Ethyl hydrogen N-acetylglutamate i
N6-Acetyllysine
O3-Acetylserine
O4-Sulfotyrosine (tyrosine O4-sulfate)
S-Ethylcysteine
3-Sulfenoalanineii
S-Sulfocysteine (S-cysteinesulfonic acid)ii, iii
S-Cyanocysteine
Cystine
D-Cystine
meso-Cystine
Methionine S-oxide (methionine oxide) ii, iv
Methionine S,S-dioxide (methionine dioxide)ii, iv
Phosphoserine (O3-phosphonoserine)v
Nτ-Methylhistidine (telemethylhistidine, see 3AA-2.2.4)

Notes

(i) Asp-OMe represents the O1-methyl ester of aspartic acid (C-1 modification by 3AA-16.3), whereas Asp(OMe) represents the O 4-methyl ester (side-chain modification by 3AA-16.4.2).

(ii) Names based on cysteine and symbols based on Cys already indicate sulfur in the molecule, and similarly with methionine and Met. Indication of modification of this sulfur should not suggest the addition of further sulfur. Hence calling 3-sulfenoalanine by the name cysteinesulfenic acid, 3-sulfinoalanine by the name cysteinesulfinic acid. methionine S-oxide by the name methionine sulfoxide, and methionine S,S-dioxide by the name methionine sulfone may be confusing and is not recommended.

(iii) Care should be taken with this symbol because readers who fail to realize that the symbol Cys contains the sulfur may confuse it with cysteic acid, now symbolized Cya (3AA-15.2.6). The earlier [10] symbol for cysteic acid has the disadvantage that the vertical line in it does not represent a single bond.

(iv) The vertical lines or parentheses previously [10] in the symbols for MetO and MetO2 are now omitted, because they wrongly implied removal of hydrogen.

(v) -P represents -PO3H2 [24].

3AA-17.3. Substitution on Side-Chain Skeleton

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This may use the same convention as 3AA-17.2, with the addition of locant numerals where necessary (see 3AA-16.4), e.g.

4-Carboxyglutamic acidas an alternative to Gla (3AA-15.2.6) if it is desired to emphasize carboxylation
2,3-Diaminopropanoic acid
(3-aminoalanine, see 3AA-15.2.5)
3,5-DiiodotyrosineTyr(I2) or Tyr(3,5-I2) if the context does not imply the locants.
3-Nitrotyrosine

3AA-17.4. The Use of Symbols in Representing Reactions of Side-Chains

The symbols are designed primarily to indicate sequence, and care must be taken to avoid confusion when they are adapted to other uses.

Although the conversion of a cysteine residue in a protein into an S-carboxymethylcysteine can be adequately represented as

-Cys- → -Cys(CH2-COOH)-

writers may wish to show the sulfur atom in order to indicate the chemistry of the reaction. Although it would be perfectly legitimate to write
-Ala(SH)- → -Ala(S-CH2-COOH)-

this would be confusing since the residue is thought of as cysteine rather than as modified alanine.

We therefore recommend putting the residue symbol into quotation marks if one of its groups is to be depicted separately (or, alternatively, using the symbol RXaa). Hence the thiol group of a cysteine residue may be shown as:


Terminal amino and carboxyl groups can be shown similarly, e.g. H2N-'Ala'- to show explicitly the amino group present in Ala- (in contrast with -Ala-NH2 which shows the amide of C-terminal alanine). This convention allows mechanisms to be drawn out, e.g.

with the quotation marks to alert readers to the fact that the symbol here does not include the sulfur atom. Sequences may also be shown, so that the acylation of a serine proteinase could be drawn as:

When this convention is used it should be described.

3AA-17.5. Modified Residue in Natural Peptides

If an unusual residue is to be symbolized within a particular context, it may be helpful to modify (e.g. with an asterisk) the symbol for the ribosomally incorporated residue, e.g. Ser* for 2-aminopropenoic acid (formed within a peptide chain by dehydration of a serine residue). Such an asterisk may be placed above the residue rather than after it to allow alignment with other 3-letter symbols. Symbols modified in this way should be defined when used.

3AA-17.6. Lack of Substitution

If it is desired to emphasize lack of substitution, H or OH may be added to the hyphen or vertical line that represents removal of one of these groups. Thus H-Ala may be contrasted with Ac-Ala, and Ala-OH with Ala-OMe.

References

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

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].

22. IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN). Abbreviated Terminology of Oligosaccharide Chains, Recommendations 1980, Eur. J. Biochem. 126, 433-437 (1982); J. Biol. Chem. 257, 3347-3351 (1982); Pure Appl. Chem. 54, 1517-1522 (1982).

24. IUPAC-IUB Commission on Biochemical Nomenclature (CBN), Nomenclature of phosphorus-containing compounds of biochemical importance, Recommendations 1976, Biochem. J. 171, 1-19 (1978); Eur. J. Biochem. 79, 1-9 (1977); Hoppe-Seyler's Z. Physiol. Chem. 358, 599-616 (1977); Proc. Natl Acad. Sci. USA, 74, 2222-2230 (1970); also pp. 203-311 in [7].

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