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Coevolutionary Patterns in Cytochrome c Oxidase Subunit I Depend on Structural and Functional Context

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Abstract

The strength and pattern of coevolution between amino acid residues vary depending on their structural and functional environment. This context dependence, along with differences in analytical technique, is responsible for the different results among coevolutionary analyses of different proteins. It is thus important to perform detailed study of individual proteins to gain better insight into how context dependence can affect coevolutionary patterns even within individual proteins, and to unravel the details of context dependence with respect to structure and function. Here we extend our previous study by presenting further analysis of residue coevolution in cytochrome c oxidase subunit I sequences from 231 vertebrates using a statistically robust phylogeny-based maximum likelihood ratio method. As in previous studies, a strong overall coevolutionary signal was detected, and coevolution within structural regions was significantly related to the Cα distances between residues. While the strong selection for adjacent residues among predicted coevolving pairs in the surface region indicates that the statistical method is highly selective for biologically relevant interactions, the coevolutionary signal was strongest in the transmembrane region, although the distances between coevolving residues were greater. This indicates that coevolution may act to maintain more global structural and functional constraints in the transmembrane region. In the transmembrane region, sites that coevolved according to polarity and hydrophobicity rather than volume had a greater tendency to colocalize with just one of the predicted proton channels (channel H). Thus, the details of coevolution in cytochrome c oxidase subunit I depend greatly on domain structure and residue physicochemical characteristics, but proximity to function appears to play a critical role. We hypothesize that coevolution is indicative of a more important functional role for this channel.

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Acknowledgments

We thank Judith Beekman for useful comments on the manuscript and Matt Reynolds for contributions to the EGenBio database. This work was supported by grants from the National Institutes of Health (GM065612 and GM065580), the National Science Foundation (through Louisiana EPSCOR and the Center for Biomodular Multi-scale Systems), and the State of Louisiana Board of Regents (Research Competitiveness Subprogram LEQSF 2001-04-RD-A-08 and the Millennium Research Program’s Biological Computation and Visualization Center) and Governor’s Biotechn ology Initiative.

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Authors and Affiliations

  1. Department of Biological Sciences and Biological Computing and Visualization Center, Louisiana State University, Baton Rouge, LA, 70803, USA

    Zhengyuan O. Wang & David D. Pollock

  2. Genome Sequencing Center, Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63108, USA

    Zhengyuan O. Wang

  3. Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, 80045, USA

    David D. Pollock

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  1. Zhengyuan O. Wang
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Correspondence to David D. Pollock.

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Wang, Z.O., Pollock, D.D. Coevolutionary Patterns in Cytochrome c Oxidase Subunit I Depend on Structural and Functional Context. J Mol Evol 65, 485–495 (2007). https://doi.org/10.1007/s00239-007-9018-8

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