Using protein structural information in evolutionary inference: Transmembrane proteins

We present a model of amino acid sequence evolution based on a hidden Marko v model that extends to transmembrane proteins previous methods that incorp orate protein structural information into phylogenetics. Our model aims to give a better understanding of processes of molecular evolution and to extr act structural information from multiple alignments of transmembrane sequen ces and use such information to improve phylogenetic analyses. This should be of value in phylogenetic studies of transmembrane proteins: for example, mitochondrial proteins have acquired a special importance in phylogenetics and are mostly transmembrane proteins. The improvement in fit to example d ata sets of our new model relative to less complex models of amino acid seq uence evolution is statistically tested. To further illustrate the potentia l utility of our method, phylogeny estimation is performed on primate CCR5 receptor sequences, sequences of l and m subunits of the light reaction cen ter in purple bacteria, guinea pig sequences with respect to lagomorph and rodent sequences of calcitonin receptor and K-substance receptor, and cetac ean sequences of cytochrome b.