title: Estimation of evolutionary distances from protein spatial structures.
abstract: New equations are derived to estimate the number of amino acid substitutions per site between two homologous proteins from the root mean square (RMS) deviation between two spatial structures and from the fraction of identical residues between two sequences. The equations are based on evolutionary models, analyzing predominantly structural changes and not sequence changes. Evolution of spatial structure is treated as a diffusion in an elastic force field. Diffusion accounts for structural changes caused by amino acid substitutions, and elastic force reflects selection, which preserves protein fold. Obtained equations are supported by analysis of protein spatial structures.
authors.affiliation: Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas 75235-9041, USA.
authors.forename: N V
authors.initials: NV
authors.lastname: Grishin
mesh_terms: D000595:Amino Acid Sequence; D019143:Evolution, Molecular; D008433:Mathematics; D008957:Models, Genetic; D011506:Proteins / Q000737:chemistry* / Q000235:genetics*; D017386:Sequence Homology, Amino Acid
chemical_list: D011506:Proteins