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MBE Advance Access published online on January 12, 2005
Molecular Biology and Evolution, doi:10.1093/molbev/msi081
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Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2005; all rights reserved.
Accepted December 20, 2004

Research Article

Protein Structural Influences in Rhodopsin Evolution

Lorraine Marsh 1* and Carole S. Griffiths 2

1 Department of Biology, Long Island University, Brooklyn, NY 11201
2 Department of Biology, Long Island University, Brooklyn, NY 11201; Ornithology Department, American Museum of Natural History, New York, NY 10024

* To whom correspondence should be addressed.
Lorraine Marsh, E-mail: Lorraine.Marsh{at}liu.edu


  Abstract

Incorporating specific structural information can be important for developing a realistic model of evolution for phylogenetic reconstruction of protein-coding genes. We analyzed 62 sequences of vertebrate rhodopsin. The bovine rhodopsin structure was used to label residue sites by surface accessibility, secondary structure and transmembrane location. Residue sites with amino acid differences were identified; using maximum parsimony, homoplasious residues were identified. Residues were analyzed for patterns that would indicate correlation of rate with secondary structure, surface accessibility or position relative to the lipid bilayer. Surface residues, especially those residing in one of the 7 transmembrane helices were significantly correlated with high rates of amino acid substitution. This category of residues defined solely by protein structural characteristics potentially defined a class enriched in homoplasious residues. Maximum parsimony analysis using all sites led to a tree with anomalies in the relationships of amphibian, mammalian, bird and alligator species. Analysis excluding the structurally defined residue class recovered a more accurate phylogeny. A model is presented for including structural influences on rate in phylogenetic inference.

Keywords: protein structure; substitution rate; rhodopsin; homoplasy; extra steps.
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