Skip Navigation



MBE Advance Access published online on May 23, 2007
Molecular Biology and Evolution, doi:10.1093/molbev/msm097
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow Supplementary Material
Right arrow All Versions of this Article:
24/8/1769    most recent
msm097v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Choi, S. C.
Right arrow Articles by Thorne, J. L.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Choi, S. C.
Right arrow Articles by Thorne, J. L.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2007. 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

Quantifying the Impact of Protein Tertiary Structure on Molecular Evolution

Sang Chul Choi1, Asger Hobolth1, Douglas M. Robinson1,2, Hirohisa Kishino3 and Jeffrey L. Thorne1,4

1 Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27606, USA
2 Current Address: Statistical Genetics and Biomarkers Group, Bristol-Myers Squibb Co., 311 Pennington-Rocky Hill Road, Pennington, NJ 08534, USA
3 Laboratory of Biometrics, Graduate School of Agriculture and Life Sciences, University of Tokyo, 1-1-1 Yayoi Bunkyo-ku Tokyo 113-8657, Japan
4 Wissenschaftskolleg zu Berlin, Wallotstrasse 19, 14193 Berlin, Germany

Corresponding Author: Jeffrey L. Thorne (thorne{at}statgen.ncsu.edu)

Received for publication January 18, 2007. Revision received March 30, 2007. Accepted for publication May 11, 2007.

To investigate the evolutionary impact of protein structure, the experimentally determined tertiary structure and the protein-coding DNA sequence were collected for each of 1195 genes. These genes were studied via a model of sequence change that explicitly incorporates effects on evolutionary rates due to protein tertiary structure. In the model, these effects act via the solvent accessibility environments and pairwise amino acid interactions that are induced by tertiary structure. To compare the hypotheses that structure does and does not have a strong influence on evolution, Bayes factors were estimated for each of the 1195 sequences. Most of the Bayes factors strongly support the hypothesis that protein structure impacts protein evolution. Furthermore, both solvent accessibility and pairwise interactions among amino acids are inferred to have important roles in protein evolution. Our results also indicate that the strength of the relationship between tertiary structure and evolution has a weak but real correlation to the annotation information in the Gene Ontology database. Although their influences on rates of evolution vary among protein families, we find that the mean impacts of solvent accessibility and pairwise interactions are about the same.

Key Words: molecular evolution • protein structure impact • Gene Ontology • MCMC • Bayes factor


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Mol Biol EvolHome page
Z. Yang and R. Nielsen
Mutation-Selection Models of Codon Substitution and Their Use to Estimate Selective Strengths on Codon Usage
Mol. Biol. Evol., March 1, 2008; 25(3): 568 - 579.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.