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MBE Advance Access published online on February 20, 2009
Molecular Biology and Evolution, doi:10.1093/molbev/msp031
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© The Author 2009. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Article

Solvent exposure imparts similar selective pressures across a range of yeast proteins

Gavin C. Conant1,* and Peter F. Stadler2,3,4,5

1 Division of Animal Sciences, University of Missouri-Columbia, Columbia MO, U.S.A
2 Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
3 RNomics Group, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
4 Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria
5 Santa Fe Institute, Santa Fe NM, U.S.A

* Corresponding author information: Gavin Conant, Division of Animal Sciences, University of Missouri-Columbia, Columbia, MO 65211, USA Email: conantg{at}missouri.edu

Received for publication December 15, 2008. Revision received February 12, 2009. Accepted for publication February 16, 2009.

We study how an amino acid residue's solvent exposure influences its propensity for substitution by analyzing multiple alignments of 61 yeast genes for which the crystal structure is known. We find that the selective constraint on the interior residues is on average ten times that of residues on the surface. Surprisingly, there is no correlation between the overall selective constraint observed for a protein alignment and the ratio of constraints on interior and surface residues. By modeling the selective constraint on several amino acid properties, we show that while residue volume and hydropathy are strongly conserved across most alignments, there is little variation in interior versus surface conservation for these two properties. By contrast, residue charge (iso-electric point) is less generally conserved when considering the protein as a whole, but shows a strong constraint against the introduction of charged residues into the protein interior.

Key Words: Amino acid substitution • evolutionary models • protein structure


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