Skip Navigation


MBE Advance Access originally published online on July 28, 2003
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (PDF) Freely available
Right arrow All Versions of this Article:
20/10/1692    most recent
msg184v1
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 ISI Web of Science
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 arrow Search for citing articles in:
ISI Web of Science (51)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Robinson, D. M.
Right arrow Articles by Thorne, J. L.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Robinson, D. M.
Right arrow Articles by Thorne, J. L.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Mol. Biol. Evol. 20(10):1692-1704. 2003
DOI: 10.1093/molbev/msg184
© 2003 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038

Protein Evolution with Dependence Among Codons Due to Tertiary Structure

Douglas M. Robinson*, David T. Jones{dagger}, Hirohisa Kishino{ddagger}, Nick Goldman§ and Jeffrey L. Thorne*,

* Bioinformatics Research Center, North Carolina State University
{dagger} Bioinformatics Unit, Department of Computer Science, University College London, London, United Kingdom
{ddagger} Laboratory of Biometrics, Graduate School of Agriculture and Life Sciences, University of Tokyo, Tokyo, Japan
§ European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom

E-mail: thorne{at}statgen.ncsu.edu.

Markovian models of protein evolution that relax the assumption of independent change among codons are considered. With this comparatively realistic framework, an evolutionary rate at a site can depend both on the state of the site and on the states of surrounding sites. By allowing a relatively general dependence structure among sites, models of evolution can reflect attributes of tertiary structure. To quantify the impact of protein structure on protein evolution, we analyze protein-coding DNA sequence pairs with an evolutionary model that incorporates effects of solvent accessibility and pairwise interactions among amino acid residues. By explicitly considering the relationship between nonsynonymous substitution rates and protein structure, this approach can lead to refined detection and characterization of positive selection. Analyses of simulated sequence pairs indicate that parameters in this evolutionary model can be well estimated. Analyses of lysozyme c and annexin V sequence pairs yield the biologically reasonable result that amino acid replacement rates are higher when the replacements lead to energetically favorable proteins than when they destabilize the proteins. Although the focus here is evolutionary dependence among codons that is associated with protein structure, the statistical approach is quite general and could be applied to diverse cases of evolutionary dependence where surrogates for sequence fitness can be measured or modeled.

Key Words: protein structure • evolution • Markov chain Monte Carlo • Bayesian


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
 Stat Methods Med ResHome page
I. Miklos, A. Novak, R. Satija, R. Lyngso, and J. Hein
Stochastic models of sequence evolution including insertion--deletion events
Statistical Methods in Medical Research, October 1, 2009; 18(5): 453 - 485.
[Abstract] [PDF]

Home page
 Syst BiolHome page
E. Susko
Bootstrap Support Is Not First-Order Correct
Syst Biol, July 1, 2009; (2009) syp016v1.
[Abstract] [Full Text] [PDF]

Home page
 Syst BiolHome page
T.-K. Seo and H. Kishino
Statistical Comparison of Nucleotide, Amino Acid, and Codon Substitution Models for Evolutionary Analysis of Protein-Coding Sequences
Syst Biol, June 29, 2009; (2009) syp015v1.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
M. Anisimova and C. Kosiol
Investigating Protein-Coding Sequence Evolution with Probabilistic Codon Substitution Models
Mol. Biol. Evol., February 1, 2009; 26(2): 255 - 271.
[Abstract] [Full Text] [PDF]

Home page
 Brief BioinformHome page
W. Delport, K. Scheffler, and C. Seoighe
Models of coding sequence evolution
Brief Bioinform, January 1, 2009; 10(1): 97 - 109.
[Abstract] [Full Text] [PDF]

Home page
 Phil Trans R Soc BHome page
S. C. Choi, B. D Redelings, and J. L Thorne
Basing population genetic inferences and models of molecular evolution upon desired stationary distributions of DNA or protein sequences
Phil Trans R Soc B, December 27, 2008; 363(1512): 3931 - 3939.
[Abstract] [Full Text] [PDF]

Home page
 Syst BiolHome page
G. Baele, Y. Van de Peer, and S. Vansteelandt
A Model-Based Approach to Study Nearest-Neighbor Influences Reveals Complex Substitution Patterns in Non-coding Sequences
Syst Biol, October 1, 2008; 57(5): 675 - 692.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
L. Bao, H. Gu, K. A. Dunn, and J. P. Bielawski
Likelihood-Based Clustering (LiBaC) for Codon Models, a Method for Grouping Sites according to Similarities in the Underlying Process of Evolution
Mol. Biol. Evol., September 1, 2008; 25(9): 1995 - 2007.
[Abstract] [Full Text] [PDF]

Home page
 Syst BiolHome page
T.-K. Seo and H. Kishino
Synonymous Substitutions Substantially Improve Evolutionary Inference from Highly Diverged Proteins
Syst Biol, June 1, 2008; 57(3): 367 - 377.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
S. Blanquart and N. Lartillot
A Site- and Time-Heterogeneous Model of Amino Acid Replacement
Mol. Biol. Evol., May 1, 2008; 25(5): 842 - 858.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
J. L. Thorne, S. C. Choi, J. Yu, P. G. Higgs, and H. Kishino
Population Genetics Without Intraspecific Data
Mol. Biol. Evol., August 1, 2007; 24(8): 1667 - 1677.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
T. Watabe, H. Kishino, L. de Oliveira Martins, and Y. Kitazoe
A Likelihood-based Index of Protein Protein Binding Affinities with Application to Influenza HA Escape from Antibodies
Mol. Biol. Evol., August 1, 2007; 24(8): 1627 - 1638.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
S. C. Choi, A. Hobolth, D. M. Robinson, H. Kishino, and J. L. Thorne
Quantifying the Impact of Protein Tertiary Structure on Molecular Evolution
Mol. Biol. Evol., August 1, 2007; 24(8): 1769 - 1782.
[Abstract] [Full Text] [PDF]

Home page
 Syst BiolHome page
N. Rodriguez-Ezpeleta, H. Brinkmann, B. Roure, N. Lartillot, B. F. Lang, and H. Philippe
Detecting and Overcoming Systematic Errors in Genome-Scale Phylogenies
Syst Biol, June 1, 2007; 56(3): 389 - 399.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
S. O. Sassi, E. L. Braun, and S. A. Benner
The Evolution of Seminal Ribonuclease: Pseudogene Reactivation or Multiple Gene Inactivation Events?
Mol. Biol. Evol., April 1, 2007; 24(4): 1012 - 1024.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
P. J. Waddell, H. Kishino, and R. Ota
Phylogenetic Methodology for Detecting Protein Interactions
Mol. Biol. Evol., March 1, 2007; 24(3): 650 - 659.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
A. Doron-Faigenboim and T. Pupko
A Combined Empirical and Mechanistic Codon Model
Mol. Biol. Evol., February 1, 2007; 24(2): 388 - 397.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
J. Yu and J. L. Thorne
Dependence among Sites in RNA Evolution
Mol. Biol. Evol., August 1, 2006; 23(8): 1525 - 1537.
[Abstract] [Full Text] [PDF]

Home page
 Syst BiolHome page
L. Mateiu and B. Rannala
Inferring Complex DNA Substitution Processes on Phylogenies Using Uniformization and Data Augmentation
Syst Biol, April 1, 2006; 55(2): 259 - 269.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
T. Gesell and A. von Haeseler
In silico sequence evolution with site-specific interactions along phylogenetic trees
Bioinformatics, March 15, 2006; 22(6): 716 - 722.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
Y. Y. Tseng and J. Liang
Estimation of Amino Acid Residue Substitution Rates at Local Spatial Regions and Application in Protein Function Inference: A Bayesian Monte Carlo Approach
Mol. Biol. Evol., February 1, 2006; 23(2): 421 - 436.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
A. Stern and T. Pupko
An Evolutionary Space-Time Model with Varying Among-Site Dependencies
Mol. Biol. Evol., February 1, 2006; 23(2): 392 - 400.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
T.-K. Seo, H. Kishino, and J. L. Thorne
Incorporating gene-specific variation when inferring and evaluating optimal evolutionary tree topologies from multilocus sequence data
PNAS, March 22, 2005; 102(12): 4436 - 4441.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
N. M. Krishnan, H. Seligmann, C.-B. Stewart, A. P. J. de Koning, and D. D. Pollock
Ancestral Sequence Reconstruction in Primate Mitochondrial DNA: Compositional Bias and Effect on Functional Inference
Mol. Biol. Evol., October 1, 2004; 21(10): 1871 - 1883.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
J. S. Pedersen, R. Forsberg, I. M. Meyer, and J. Hein
An Evolutionary Model for Protein-Coding Regions with Conserved RNA Structure
Mol. Biol. Evol., October 1, 2004; 21(10): 1913 - 1922.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
S. Whelan and N. Goldman
Estimating the Frequency of Events That Cause Multiple-Nucleotide Changes
Genetics, August 1, 2004; 167(4): 2027 - 2043.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
I. Miklos, G. A. Lunter, and I. Holmes
A "Long Indel" Model For Evolutionary Sequence Alignment
Mol. Biol. Evol., March 1, 2004; 21(3): 529 - 540.
[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.