Codep: Maximizing co‐evolutionary interdependencies to discover interacting proteins

Elisabeth R. M. Tillier; Laurence Biro; Ginny Li; Desiree Tillo

doi:10.1002/prot.20948

journal article Apr 21, 2006

Codep: Maximizing co‐evolutionary interdependencies to discover interacting proteins

Elisabeth R. M. Tillier Laurence Biro Ginny Li Desiree Tillo

Proteins: Structure, Function, and Bioinformatics Vol. 63 No. 4 pp. 822-831 · Wiley

View at Publisher Save 10.1002/prot.20948

Abstract

AbstractApproaches for the determination of interacting partners from different protein families (such as ligands and their receptors) have made use of the property that interacting proteins follow similar patterns and relative rates of evolution. Interacting protein partners can then be predicted from the similarity of their phylogenetic trees or evolutionary distances matrices. We present a novel method called Codep, for the determination of interacting protein partners by maximizing co‐evolutionary signals. The order of sequences in the multiple sequence alignments from two protein families is determined in such a manner as to maximize the similarity of substitution patterns at amino acid sites in the two alignments and, thus, phylogenetic congruency. This is achieved by maximizing the total number of interdependencies of amino acids sites between the alignments. Once ordered, the corresponding sequences in the two alignments indicate the predicted interacting partners. We demonstrate the efficacy of this approach with computer simulations and in analyses of several protein families. A program implementing our method, Codep, is freely available to academic users from our website: http://www.uhnresearch.ca/labs/tillier/. Proteins 2006. © 2006 Wiley‐Liss, Inc.

Topics

No keywords indexed for this article. Browse by subject →

References

42

[1]

10.1073/pnas.96.6.2896

[2]

10.1101/gr.10.8.1204

[3]

10.1016/s0968-0004(98)01274-2

[4]

10.1126/science.285.5428.751

[5]

10.1038/47056

[6]

Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles

Matteo Pellegrini, Edward M. Marcotte, Michael J. Thompson et al.

Proceedings of the National Academy of Sciences 10.1073/pnas.96.8.4285

[7]

In silico two‐hybrid system for the selection of physically interacting protein pairs

Florencio Pazos, Alfonso Valencia

Proteins: Structure, Function, and Bioinformatics 10.1002/prot.10074

[8]

10.1006/jmbi.2001.4920

[9]

10.1038/368251a0

[10]

10.1074/jbc.271.7.3619

[11]

Co-evolution of proteins with their interaction partners 1 1Edited by B. Honig

Chern-Sing Goh, Andrew A. Bogan, Marcin Joachimiak et al.

Journal of Molecular Biology 10.1006/jmbi.2000.3732

[12]

Similarity of phylogenetic trees as indicator of protein–protein interaction

Florencio Pazos, Alfonso Valencia

Protein Engineering, Design and Selection 10.1093/protein/14.9.609

[13]

The coevolution of gene family trees

Karl J. Fryxell

Trends in Genetics 10.1016/s0168-9525(96)80020-5

[14]

10.1093/bioinformatics/bth053

[15]

The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships

T. Sato, Y. Yamanishi, M. Kanehisa et al.

Bioinformatics 10.1093/bioinformatics/bti564

[16]

10.1016/s0022-2836(02)01038-0

[17]

Exploiting the Co-evolution of Interacting Proteins to Discover Interaction Specificity

Arun K. Ramani, Edward M. Marcotte

Journal of Molecular Biology 10.1016/s0022-2836(03)00114-1

[18]

10.1093/bioinformatics/btg278

[19]

Correlated mutations contain information about protein-protein interaction 1 1Edited by A. R. Fersht

Florencio Pazos, Manuela Helmer-Citterich, Gabriele Ausiello et al.

Journal of Molecular Biology 10.1006/jmbi.1997.1198

[20]

Using multiple interdependency to separate functional from phylogenetic correlations in protein alignments

Elisabeth R.M. Tillier, Thomas W.H. Lui

Bioinformatics 10.1093/bioinformatics/btg072

[21]

Ash RB (1965)

[22]

Felsenstein J (2004)

[23]

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

Julie D. Thompson, Desmond G. Higgins, Toby J. Gibson

Nucleic Acids Research 10.1093/nar/22.22.4673

[24]

Amino acid substitution matrices from protein blocks.

S Henikoff, Jorja G. Henikoff

Proceedings of the National Academy of Sciences 10.1073/pnas.89.22.10915

[25]

10.1089/106652703322756195

[26]

10.1145/368637.368660

[27]

Grassly NC "PSeq‐Gen: an application for the Monte Carlo simulation of protein sequence evolution along phylogenetic trees" Comput Appl Biosci (1997)

[28]

10.1016/s0014-5793(03)01019-6

[29]

The Protein Data Bank

H. M. Berman

Nucleic Acids Research 10.1093/nar/28.1.235

[30]

10.1093/nar/gkg095

[31]

10.1093/nar/gkh063

[32]

10.1038/nature03239

[33]

10.1111/j.1365-2958.1995.mmi_18030533.x

[34]

10.1128/jb.178.3.611-618.1996

[35]

10.1099/00221287-138-9-1949

[36]

10.1073/pnas.83.20.7850

[37]

Walker MS "Phosphorylation and dephosphorylation catalyzed in vitro by purified components of the nitrate sensing system, NarX and NarL" J Biol Chem (1993) 10.1016/s0021-9258(18)52884-2

[38]

10.1128/jb.178.2.396-402.1996

[39]

10.1093/nar/gki025

[40]

10.1016/s0022-1759(02)00414-3

[41]

10.1016/j.cytogfr.2003.10.004

[42]

Li W‐H. (1997)

Cited By

31

Graphical models of protein–protein interaction specificity from correlated mutations and interaction data

J. Thomas, Naren Ramakrishnan · 2009

Proteins: Structure, Function, and...

CAPS: coevolution analysis using protein sequences

Mario A. Fares, David McNally · 2006

Bioinformatics

Metrics

31

Citations

42

References

Details

Published: Apr 21, 2006
Vol/Issue: 63(4)
Pages: 822-831
License: View

Authors

E

Elisabeth R. M. Tillier

Cite This Article

Elisabeth R. M. Tillier, Laurence Biro, Ginny Li, et al. (2006). Codep: Maximizing co‐evolutionary interdependencies to discover interacting proteins. Proteins: Structure, Function, and Bioinformatics, 63(4), 822-831. https://doi.org/10.1002/prot.20948

Codep: Maximizing co‐evolutionary interdependencies to discover interacting proteins

You May Also Like