Correlations of nucleotide substitution rates and base composition of mammalian coding sequences with protein structure

We investigated the relationships between the nucleotide substitution rates and the predicted secondary structures in the three states representation (alpha-helix, beta-sheet, and coil). The analysis was carried out on 34 ali gnments, each of which comprised sequences belonging to at least four diffe rent mammalian orders. The rates of synonymous substitution were found to b e significantly different in regions predicted to be alpha-helix, beta-shee t, or coil. Likewise, the nonsynonymous rates also differ, although expecte dly at a lower extent, in the three types of secondary structure, suggestin g that different selective constraints associated with the different struct ures are affecting in a similar way the synonymous and nonsynonymous rates. Moreover, the base composition of the third codon positions is different i n coding sequence regions corresponding to different secondary structures o f proteins. (C) 1999 Elsevier Science B.V. All rights reserved.