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1 Department of Chemistry, University of Massachusetts, Lowell, Lowell, Massachusetts 01887, USA
2 Biophysics Program, Institute for Physical Science and Technology, and 3 Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
(RECEIVED August 11, 2005; FINAL REVISION October 9, 2005; ACCEPTED October 9, 2005)
Allosteric interactions between residues that are spatially apart and well separated in sequence are important in the function of multimeric proteins as well as single-domain proteins. This observation suggests that, among the residues that are involved in long-range communications, mutation at one site should affect interactions at a distant site. By adopting a sequence-based approach, we present an automated approach that uses a generalization of the familiar sequence entropy in conjunction with a coupled two-way clustering algorithm, to predict the network of interactions that trigger allosteric interactions in proteins. We use the method to identify the subset of dynamically important residues in three families, namely, the small PDZ family, G protein–coupled receptors (GPCR), and the Lectins, which are cell-adhesion receptors that mediate the tethering and rolling of leukocytes on inflamed endothelium. For the PDZ and GPCR families, our procedure predicts, in agreement with previous studies, a network containing a small number of residues that are involved in their function. Application to the Lectin family reveals a network of residues interspersed throughout the C-terminal end of the structure that are responsible for binding to ligands. Based on our results and previous studies, we propose that functional robustness requires that only a small subset of distantly connected residues be involved in transmitting allosteric signals in proteins.
Keywords: structure; protein families; evolutionary relationships; proteomics
Article and publication are at http://www.proteinscience.org/cgi/doi/10.1110/ps.051767306.
Reprint requests to: D. Thirumalai, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA; e-mail: thirum{at}glue.umd.edu; fax: (301) 314-9404.
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