Inferring functional constraints and divergence in protein families using 3D mapping of phylogenetic information.

ABSTRACT: Comparative sequence analysis has been used to study specific questions about the structure and function of proteins for many years. Here we propose a knowledge-based framework in which the maximum likelihood rate of evolution is used to quantify the level of constraint on the identity of a site. We demonstrate that site-rate mapping on 3D structures using datasets of rhodopsin-like G-protein receptors and alpha- and beta-tubulins provides an excellent tool for pinpointing the functional features shared between orthologous and paralogous proteins. In addition, functional divergence within protein families can be inferred by examining the differences in the site rates, the differences in the chemical properties of the side chains or amino acid usage between aligned sites. Two novel analytic

SUBMITTER: Blouin C 

PROVIDER: S-EPMC140515 | biostudies-literature | 2003 Jan

REPOSITORIES: biostudies-literature