title: Substitution rates in alpha-helical transmembrane proteins.
abstract: It has been shown previously that some membrane proteins have a conserved core of amino acid residues. This idea not only serves to orient helices during model building exercises but may also provide insight into the structural role of residues mediating helix-helix interactions. Using experimentally determined high-resolution structures of alpha-helical transmembrane proteins we show that, of the residues within the hydrophobic transmembrane spans, the residues at lipid and subunit interfaces are more evolutionarily variable than those within the lipid-inaccessible core of a polypeptide's transmembrane domain. This supports the idea that helix-helix interactions within the same polypeptide chain and those at the interface between different polypeptide chains may arise in distinct ways. To show this, we use a new method to estimate the substitution rate of an amino acid residue given an alignment and phylogenetic tree of closely related proteins. This method gives better sensitivity in the otherwise-conserved transmembrane domains than a conventional similarity analysis and is relatively insensitive to the sequences used.
authors.affiliation: Cambridge Center for Molecular Recognition, Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, United Kingdom.
authors.forename: T J
authors.initials: TJ
authors.lastname: Stevens
authors.forename: I T
authors.initials: IT
authors.lastname: Arkin
mesh_terms: D000596:Amino Acids / Q000737:chemistry; D000818:Animals; D002462:Cell Membrane / Q000737:chemistry*; D019992:Databases as Topic; D003576:Electron Transport Complex IV / Q000737:chemistry; D019143:Evolution, Molecular; D006801:Humans; D050356:Lipid Metabolism; D008958:Models, Molecular; D008962:Models, Theoretical; D010802:Phylogeny; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry
chemical_list: D000596:Amino Acids; D011506:Proteins; D003576:Electron Transport Complex IV