(1995; 53 pages)
14.1 In polypeptides, the linear sequence of amino acid residues is shown with the amino-terminal residue on the left and the carboxy-terminal residue on the right (followed by “-NH2” if it is carboxamide).
14.2 Oligopeptides produced by the condensation of fewer than about five amino acids are often depicted in their full form. Since several polypeptides of this type are used as drugs, the full structure may be useful for showing any chemical modifications present:
14.3 In the representation of polypeptides, amino acids are shown by means of the standard three-letter codes, peptide bonds being assumed to exist between C-1 and N-2 of adjacent residues. A code given without further qualification means that the amino acid concerned belongs to the L-series. If an amino acid belongs to the D-series, the letter “D” precedes the three-letter code and is joined to it by a hyphen. Unusual residues are shown in full. If a polypeptide occupies more than one line, a hyphen is placed at the end of each successive line until the formula has been completed.
14.4 Disulfide bridges are drawn as lines attaching the S atoms to the “Cys” units but without showing those atoms. The lines must be drawn vertically and appear to pass through the letter “y”. They may be placed above or below the unit chain, according to requirements. Either of the forms shown below is acceptable:
Sometimes a mixture of the two styles will be needed so as to ensure that the bridges do not cross over one another.
14.5 If an amino acid residue is substituted on the N-2 atom, the symbol for the substituent is placed before the three-letter code. If a side-chain modification occurs, the substituent may be depicted either in full or by means of its conventional symbol placed above or below the three-letter code and joined to it by a vertical line passing through the central letter. If necessary, a locant is placed beside the vertical line that represents side-chain substitution:
14.6 In cyclic peptides, the amino acid sequence is formulated in the usual manner but the residues at each end of the line are joined by a lengthened bond. If the residues are written on two lines, the sequence is reversed on one of them; hence the CO to NH direction within the peptide bond must be indicated by arrows:
14.7 Cyclic esters are shown by means of a lengthened bond starting from the carbonyl end of the sequence and ending at the symbol of the hydroxy amino acid:
14.8. If part of the molecule is not polypeptide, it can be represented in accordance with the rules for acyclic or cyclic compounds:
14.9 In showing polypeptides produced by the condensation of a large number of amino acids, one-letter codes rather than three-letter codes can be used to save space and facilitate computer processing. The one-letter codes are arranged in sets of ten letters separated by a space. For purposes of sequential numbering, the numbers of individual amino acids are generally placed below the codes. As an example, the polypeptide sequence of epoetin alfa:
becomes in abbreviated form: