title: Phylogenetic and structural analysis of mitochondrial complex I proteins.
abstract: Our understanding of the evolutionary process would benefit from a better understanding of protein structural changes during evolution. I report that combining phylogenetic and structural analyses of the mitochondrial protein sequences allow to identify important differences between protostomes and deuterostomes mitochondrial proteins: (1) ND5, and with less intensity, ND1, ND2 and ND4, have significantly lower hydrophobicity in deuterostomes than in proterostomes; (2) the C-terminal half portion of ND5 has lower hydrophobicity than the N-terminal half portion, suggesting the presence of larger extra-membrane hydrophilic loops in deuterostomes with respect to protostomes; (3) substitution matrices generated from different complex I proteins show different patterns of amino acid substitutions, suggesting that mitochondrial proteins have different evolutionary dynamics. I hypothesise that the better performances in phylogenetic inference of ND5 with respect to other mitochondrial proteins may be related to its position inside the complex I.
authors.affiliation: Computer Laboratory, University of Cambridge, 15 JJ Thomson Avenue, Cambridge, UK. pietro.lio@cl.cam.ac.uk
authors.forename: Pietro
authors.initials: P
authors.lastname: Liò
mesh_terms: D019943:Amino Acid Substitution / Q000235:genetics; D000596:Amino Acids / Q000737:chemistry / Q000235:genetics; D000818:Animals; D042967:Electron Transport Complex I / Q000737:chemistry / Q000235:genetics*; D019143:Evolution, Molecular; D006801:Humans; D057927:Hydrophobic and Hydrophilic Interactions; D024101:Mitochondrial Proteins / Q000737:chemistry / Q000235:genetics; D010802:Phylogeny
chemical_list: D000596:Amino Acids; D024101:Mitochondrial Proteins; D042967:Electron Transport Complex I