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Bioinformatics Advance Access published online on January 19, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti167
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Bioinformatics © Oxford University Press 2004; all rights reserved.
Received September 6, 2004
Revised November 11, 2004
Accepted November 17, 2004

Discovery note

Topology of small-world networks of protein-protein complex structures

Antonio del Sol 1*, Hirotomo Fujihashi 1, and Paul O'Meara 1

1 Bioinformatics Research Project, Research and Development Division, Fujirebio Inc., 51 Komiya-cho, Hachioji-shi, Tokyo 192-0031, Japan

* To whom correspondence should be addressed.
Antonio del Sol, E-mail: ao-mesa{at}fujirebio.co.jp


  Abstract

The majority of real examples of small world networks exhibit a power law distribution of edges among the nodes, therefore not fitting into the wiring model proposed by Watts and Strogatz (1998). However, protein structures can be modeled as small world networks, with a distribution of the number of links decaying exponentially as in the case of this wiring model. We approach the protein-protein interaction mechanism by viewing it as a particular rewiring occurring in the system of two small world networks represented by the monomers, where a re-arrangement of links take place upon dimerization leaving the small world character in the dimer network. Due to this rewiring, the most central residues at the complex interfaces tend to form clusters, which are not homogenously distributed. We show that these highly central residues are strongly correlated with the presence of hot spots of binding free energy.

Supplementary information: http://www.fujirebio.co.jp/support/index.php (under construction).


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