Predicting Amino Acid Sequences of the Antibody Human VHChains from Its First Several Residues

• Published in: Proceedings of the National Academy of Sciences - PNAS 1998-04, Vol.95 (9), p.5193-5198
• Main Authors: Galitsky, Boris A., Gelfand, Israel M., Kister, Alexander E.
• Format: Article
• Language: English
• Subjects: Amino acids; Antibodies; Atoms; Coordinate systems; Immunology; Keywords; Molecular chains; Molecules; Nucleotides
• ISSN: 0027-8424

A new method for classification of Ig sequences is suggested. The defining characteristic of a class is presence of particular residues at several class-determining positions. Sequences within a class follow the same amino acid pattern, i.e., residues at identical positions are, in an over-whelming majority of sequences of that class, identical or chemically related. Thus, once the class of a sequence is determined, one can predict the residue(s) at almost any position in the sequence. In this paper, results of analysis of 1,172 human heavy chains are presented. It was shown that a sequence can be assigned to one of six classes depending on which residues are found at its positions 1, 3, 5, 6, 7, 9, 10, 12, and 13. It is important to note that it is possible to achieve same six-class classification of the human heavy chains on the basis of a different set of positions found not at the beginning but near the end of the sequence (around position 80). For every class, an amino acid pattern of an entire sequence (complementarity determining regions excepting) has been determined. Our approach allowed us to reconstruct the incomplete human heavy chains in which residues at certain positions at the beginning or end of the chain are known. We developed a software tool for analysis, classification, and prediction of residues in sequences of the Ig family.