FACTORS DETERMINING SECONDARY STRUCTURE IN GLOBULAR-PROTEINS

An approach to the analysis of amino acid features determining the formation of alpha-helices, beta-structures, and beta-turns is proposed; the method is based on determinant analysis of a set of conformations of different regions of the polypeptide chain. Each amino acid position corresponds to a set of values for parameters characterizing distant, intermediate, and local interactions. Assignment of an amino acid residue to one of the pairs of alternative classes of secondary structures was carried out using Fisher's linear discriminant function. The selection of the most informative parameters was made on the basis of F-inclusion statistics. Characteristics identifying regions of alpha-helix, beta-structure, and beta-turns were identified. Values of Mahalonobis D2 distances were used to evaluate their relative significance in the formation of secondary structures. The formation of alpha-helices and beta-structures were found to be affected by features of internal regions (such as the Chou and Fasman coefficients, doublet preference, hydrophobic moment), as well as by the amino acid composition at the N- and C-termini and that of adjacent regions. The Chou-Fasman positional coefficient made the greatest contribution to beta-turn structures after doublet preferences.