Divergent evolution within protein superfolds inferred from profile-based phylogenetics.

ABSTRACT: Many dissimilar protein sequences fold into similar structures. A central and persistent challenge facing protein structural analysis is the discrimination between homology and convergence for structurally similar domains that lack significant sequence similarity. Classic examples are the OB-fold and SH3 domains, both small, modular beta-barrel protein superfolds. The similarities among these domains have variously been attributed to common descent or to convergent evolution. Using a sequence profile-based phylogenetic technique, we analyzed all structurally characterized OB-fold, SH3, and PDZ domains with less than 40% mutual sequence identity. An all-against-all, profile-versus-profile analysis of these domains revealed many previously undetectable significant interrelationships. The mat

SUBMITTER: Theobald DL 

PROVIDER: S-EPMC1769326 | biostudies-literature | 2005 Dec

REPOSITORIES: biostudies-literature