Codep: maximizing co-evolutionary interdependencies to discover interacting proteins

Proteins
Elisabeth R M TillierDesiree Tillo

Abstract

Approaches 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/.

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Citations

Mar 6, 2013·Nature Reviews. Genetics·David de JuanAlfonso Valencia
Sep 29, 2006·Bioinformatics·Mario A Fares, David McNally
Sep 8, 2011·Bioinformatics·Shu YangJunwen Wang
Aug 22, 2009·Genome Research·Elisabeth R M Tillier, Robert L Charlebois
Jan 25, 2008·BMC Bioinformatics·Jose M G IzarzugazaAlfonso Valencia
Jun 16, 2011·Algorithms for Molecular Biology : AMB·Alex RodionovElisabeth Rm Tillier
Feb 20, 2008·FEBS Letters·David JuanAlfonso Valencia
Sep 27, 2008·The EMBO Journal·Florencio Pazos, Alfonso Valencia
Nov 26, 2009·Evolution; International Journal of Organic Evolution·Xiaowei Jiang, Mario A Fares
Nov 5, 2014·Frontiers in Cell and Developmental Biology·David Ochoa, Florencio Pazos
Oct 9, 2009·Evolutionary Bioinformatics Online·Francisco ProsdocimiArlin Stoltzfus
Mar 9, 2012·Bioinformatics·Iman HajirasoulihaS Cenk Sahinalp
Apr 3, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Wan-Li ZhuJun Huang

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