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MBE Advance Access published online on June 16, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msl040
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© The Author 2006. 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
Accepted June 13, 2006

Research Article

Structural Determinants of the Rate of Protein Evolution in Yeast

Jesse D. Bloom 1, D. Allan Drummond 2, Frances H. Arnold 1, and Claus O. Wilke 3 *

1 Division of Chemistry and Chemical Engineering, Mail Code 210-41, California Institute of Technology, Pasadena, California 91125, USA
2 Program in Computation and Neural Systems, Mail Code 210-41, California Institute of Technology, Pasadena, California 91125, USA
3 Section of Integrative Biology and Center for Computational Biology and Bioinformatics, University of Texas at Austin, Austin, TX 78731

* To whom correspondence should be addressed.
Claus O. Wilke, E-mail: cwilke{at}mail.utexas.edu


  Abstract

We investigate how a protein's structure inuences the rate at which its sequence evolves. Our basic hypothesis is that proteins with highly designable structures (structures that are encoded by many sequences) will evolve more rapidly. Recent theoretical advances argue that structures with a higher density of inter-residue contacts are more designable, and we show that high contact density is correlated with an increased rate of sequence evolution in yeast. In addition, we investigate the correlations between the rate of sequence evolution and several other structural descriptors, carefully controlling for the strong effect of expression level on evolutionary rate. Overall, we find that the structural descriptors that we consider appear to explain roughly 10% of the variation in rates of protein evolution in yeast. We also show that despite the well-known trend for buried residues to be more conserved, proteins with a higher fraction of buried residues nonetheless tend to evolve their sequences more rapidly. We suggest that this effect is due to the increased designability of structures with more buried residues. Our results provide evidence that protein structure plays an important role in shaping the rate of sequence evolution, and provides evidence to support recent theoretical advances linking structural designability to contact density.

Keywords: designability; protein structure; evolutionary rate; protein evolution; principal component regression; yeast.
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