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Bioinformatics Advance Access originally published online on January 31, 2007
Bioinformatics 2007 23(7):789-792; doi:10.1093/bioinformatics/btm018
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© 2007 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.

A simple shape characteristic of protein–protein recognition

George Nicola 1 and Ilya A. Vakser 2,*

1Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Rd, La Jolla, CA 92037, USA and 2Center for Bioinformatics and Department of Molecular Biosciences, The University of Kansas, 2030 Becker Drive, Lawrence, KS 66047, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: Observation of co-crystallized protein–protein complexes and low-resolution protein–protein docking studies suggest the existence of a binding-related anisotropic shape characteristic of protein–protein complexes.

Results: Our study systematically assessed the global shape of proteins in a non-redundant database of co-crystallized protein–protein complexes by measuring the distance of the surface residues to the protein's center of mass. The results show that on average the binding site residues are closer to the center of mass than the non-binding surface residues. Thus, the study directly detects an important and simple binding-related characteristic of protein shapes. The results provide an insight into one of the fundamental properties of protein structure and association.

Contact: vakser{at}ku.edu

Associate Editor: Anna Tramontano

Received on December 18, 2006; revised on January 15, 2007; accepted on January 17, 2007

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