A novel approach to molecular evolution study

Abstract

Evolution of species is one of the major problems in biology and great effort has been devoted to its study along the years. The enormous number of macromolecular sequences now available has allowed the development of molecular evolution, since homologous molecules can be compared and phylogenetic trees are deduced from this analysis. Up to now, molecular evolution has been studied estimating the punctual mutations in the nucleic acid or amino acid sequences. Here we present a different scheme, analyzing changes in the secondary structure of a given protein along species. Since the principal features of a protein (function, adaptability, interactions with its medium and with other molecules, etc.) are determined by its spatial configuration, we can also think that changes in this conformation are correlated with the evolutionary pathway. Phylogenetic trees, then, will be principally based on physical processes, since conformation is essential for interactions and many changes of the sequence unrelated to variations in protein structure will not be considered in our scheme. We have first developed a method (Figureau et al., 1995) in order to discriminate definite substructures (~ helices, 13 sheets) in proteins from the primary sequence. These structures are correctly predicted, since the success rate for 3 states (~, [3, else) is about 80% (Soto et al, 1996). The algorithm is then sufficiently reliable to be applied to the evolution problem. As a first example, we have chosen the cytochrome c molecule, analyzing, in this case, changes in the location of c~ helices for 35 of these molecules corresponding to different species. The relevance of a given molecular conformation in the cytochrome c molecule is emphasized.