COMPARISON OF CONFORMATIONAL CHARACTERISTICS IN STRUCTURALLY SIMILAR PROTEIN PAIRS

Although it is known that three-dimensional structure is well conserve d during the evolutionary development of proteins, there have been few studies that consider other parameters apart from divergence of the m ain-chain coordinates. In this study, we align the structures of 90 pa irs of homologous proteins having sequence identities ranging from 5 t o 100%. Their structures are compared as a function of sequence identi ty, including not only consideration of Calpha coordinates but also ac cessibility, Ooi numbers, secondary structure, and side-chain angles. We discuss how these properties change as the sequences become less si milar. This will be of practical use in homology modeling, especially for modeling very distantly related or analogous proteins. We also con sider how the average size and number of insertions and deletions vary as sequences diverge. This study presents further quantitative eviden ce that structure is remarkably well conserved in detail, as well as a t the topological level, even when the sequences do not show similarit y that is significant statistically.