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Association of putative concave protein-binding sites with the fluctuation behavior of residues

¹ Polymer Research Center and Chemical Engineering Department, Bogazici University, Bebek 34342, Istanbul, Turkey
² Basic Research Program, SAIC-Frederick, Inc. Center for Cancer Research Nanobiology Program NCI-Frederick, Frederick, Maryland 21702, USA
³ Sackler Institute of Molecular Medicine Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel

(RECEIVED August 29, 2005; FINAL REVISION July 18, 2006; ACCEPTED July 18, 2006)

Here, we propose a binding site prediction method based on the high frequency end of the spectrum in the native state of the protein structural dynamics. The spectrum is obtained using an elastic network model (GNM). High frequency vibrating (HFV) residues are determined from the fastest modes dynamics. HFV residue clusters and the associated surface patch residues are tested for their likelihood to locate at the binding interfaces using two different data sets, the Benchmark Set of mainly enzymes and antigen/antibodies and the Cluster Set of more diverse structures. The binding interface is identified to be within 7.5 Å of the HFV residue clusters in the Benchmark Set and Cluster Set, for 77% and 70% of the structures, respectively. The success rate increases to 88% and 84%, respectively, by using the surface patches. The results suggest that concave binding interfaces, typically those of enzyme-binding sites, are enriched by the HFV residues. Thus, we expect that the association of HFV residues with the interfaces is mostly for enzymes. If, however, a binding region has invaginations and cavities, as in some of the antigen/antibodies and in cases in the Cluster data set, we expect it would be detected there too. This implies that binding sites possess several (inter-related) properties such as cavities, high packing density, conservation, and disposition for hotspots at binding surfaces. It further suggests that the high frequency vibrating residue-based approach is a potential tool for identification of regions likely to serve as protein-binding sites. The software is available at http://www.prc.boun.edu.tr/PRC/software.html.

Keywords: binding sites; protein–protein interactions; GNM; structural dynamics; protein–protein interfaces

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