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Nucleic Acids Research Advance Access originally published online on May 22, 2009
Nucleic Acids Research 2009 37(12):e88; doi:10.1093/nar/gkp414
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Nucleic Acids Research, 2009, Vol. 37, No. 12 e88
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Methods Online

A complex-centric view of protein network evolution

Nir Yosef1, Martin Kupiec2, Eytan Ruppin1,3 and Roded Sharan1,*

1The Blavatnik School of Computer Science, 2Department of Molecular Microbiology and Biotechnology and 3School of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel

*To whom correspondence should be addressed. Tel: +972-3-640-7139; Fax: +972-3-640-9357; Email: roded{at}tau.ac.il

Received November 10, 2008. Revised April 30, 2009. Accepted May 2, 2009.

The recent availability of protein–protein interaction networks for several species makes it possible to study protein complexes in an evolutionary context. In this article, we present a novel network-based framework for reconstructing the evolutionary history of protein complexes. Our analysis is based on generalizing evolutionary measures for single proteins to the level of whole subnetworks, comprehensively considering a broad set of computationally derived complexes and accounting for both sequence and interaction changes. Specifically, we compute sets of orthologous complexes across species, and use these to derive evolutionary rate and age measures for protein complexes. We observe significant correlations between the evolutionary properties of a complex and those of its member proteins, suggesting that protein complexes form early in evolution and evolve as coherent units. Additionally, our approach enables us to directly quantify the extent to which gene duplication has played a role in the evolution of complexes. We find that about one quarter of the sets of orthologous complexes have originated from evolutionary cores of homodimers that underwent duplication and divergence, testifying to the important role of gene duplication in protein complex evolution.


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