Phylogenetic and structural analysis of mitochondrial complex I proteins

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.