title: Robust signals of coevolution of interacting residues in mammalian proteomes identified by phylogeny-aided structural analysis.
abstract: The structure of a protein depends critically on the complex interactions among its amino acid residues. It has long been hypothesized that interacting residues might tend to coevolve, but it is not known whether such coevolution is a general phenomenon across the proteome. Here, we describe a novel methodology called phylogeny-aided structural analysis, which uncovers robust signals of interacting-residue coevolution in mammalian proteomes. Furthermore, this new method allows the magnitude of coevolution to be quantified. Finally, it facilitates a comprehensive evaluation of various factors that affect interacting-residue coevolution, such as the physicochemical properties of the interactions between residues, solvent accessibility of the residues and their secondary structure context.
authors.affiliation: Howard Hughes Medical Institute, Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA.
authors.forename: Sun Shim
authors.initials: SS
authors.lastname: Choi
authors.forename: Weimin
authors.initials: W
authors.lastname: Li
authors.forename: Bruce T
authors.initials: BT
authors.lastname: Lahn
mesh_terms: D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry; D000818:Animals; D004285:Dogs; D019143:Evolution, Molecular; D006801:Humans; D051379:Mice; D010802:Phylogeny; D011506:Proteins / Q000737:chemistry; D020543:Proteome / Q000737:chemistry*; D040901:Proteomics / Q000379:methods*; D051381:Rats
chemical_list: D000596:Amino Acids; D011506:Proteins; D020543:Proteome