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Nucleic Acids Research 2005 33(11):3629-3635; doi:10.1093/nar/gki678
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Published online 27 June 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

Binding properties and evolution of homodimers in protein–protein interaction networks

Iaroslav Ispolatov*, Anton Yuryev, Ilya Mazo and Sergei Maslov1

Ariadne Genomics Inc. 9700 Great Seneca Highway, Suite 113, Rockville, MD 20850, USA 1Department of Physics, Brookhaven National Laboratory Upton, NY 11973, USA

*To whom correspondence should be addressed. Fax: +1 240 453 6208; Email: slava{at}ariadnegenomics.com

Received January 3, 2005. Revised June 9, 2005. Accepted June 9, 2005.

We demonstrate that protein–protein interaction networks in several eukaryotic organisms contain significantly more self-interacting proteins than expected if such homodimers randomly appeared in the course of the evolution. We also show that on average homodimers have twice as many interaction partners than non-self-interacting proteins. More specifically, the likelihood of a protein to physically interact with itself was found to be proportional to the total number of its binding partners. These properties of dimers are in agreement with a phenomenological model, in which individual proteins differ from each other by the degree of their ‘stickiness’ or general propensity toward interaction with other proteins including oneself. A duplication of self-interacting proteins creates a pair of paralogous proteins interacting with each other. We show that such pairs occur more frequently than could be explained by pure chance alone. Similar to homodimers, proteins involved in heterodimers with their paralogs on average have twice as many interacting partners than the rest of the network. The likelihood of a pair of paralogous proteins to interact with each other was also shown to decrease with their sequence similarity. This points to the conclusion that most of interactions between paralogs are inherited from ancestral homodimeric proteins, rather than established de novo after duplication. We finally discuss possible implications of our empirical observations from functional and evolutionary standpoints.

Correspondence may also be addressed to Sergei Maslov. Fax: +1 631 344 2918; Email: maslov{at}bnl.gov


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