Conserved residue clusters at protein-protein interfaces and their use in binding site identification

Mainak Guharoy,Pinak Chakrabarti

doi:10.1186/1471-2105-11-286

Abstract

BackgroundBiological evolution conserves protein residues that are important for structure and function. Both protein stability and function often require a certain degree of structural co-operativity between spatially neighboring residues and it has previously been shown that conserved residues occur clustered together in protein tertiary structures, enzyme active sites and protein-DNA interfaces. Residues comprising protein interfaces are often more conserved compared to those occurring elsewhere on the protein surface. We investigate the extent to which conserved residues within protein-protein interfaces are clustered together in three-dimensions.ResultsOut of 121 and 392 interfaces in homodimers and heterocomplexes, 96.7 and 86.7%, respectively, have the conserved positions clustered within the overall interface region. The significance of this clustering was established in comparison to what is seen for the subsets of the same size of randomly selected residues from the interface. Conserved residues occurring in larger interfaces could often be sub-divided into two or more distinct sub-clusters. These structural cluster(s) comprising conserved residues indicate functionally important regions within the protein-protein interface that can be targeted for further structural and energetic analysis by experimental scanning mutagenesis. Almost 60% of experimental hot spot residues (with ΔΔG > 2 kcal/mol) were localized to these conserved residue clusters. An analysis of the residue types that are enriched within these conserved subsets compared to the overall interface showed that hydrophobic and aromatic residues are favored, but charged residues (both positive and negative) are less common. The potential use of this method for discriminating binding sites (interfaces) versus random surface patches was explored by comparing the clustering of conserved residues within each of these regions - in about 50% cases the true interface is ranked among the top 10% of all surface patches.ConclusionsProtein-protein interaction sites are much larger than small molecule biding sites, but still conserved residues are not randomly distributed over the whole interface and are distinctly clustered. The clustered nature of evolutionarily conserved residues within interfaces as compared to those within other surface patches not involved in binding has important implications for the identification of protein-protein binding sites and would have applications in docking studies.

Highlights

Biological evolution conserves protein residues that are important for structure and function
The question addressed in this paper is whether the subset of conserved residues in a protein-protein interface occurs scattered across the interface, or cluster together in three-dimension? It is possible that the conserved residues would form one or more localized clusters within the interface as it would enable the formation of "functional motifs"
Clustering of conserved residue positions in proteinprotein interfaces The first issue addressed is the relative spatial location of evolutionary conserved residues in protein-protein interfaces, if these are scattered throughout the interface or they form spatial clusters

Summary

Introduction

Biological evolution conserves protein residues that are important for structure and function. Spatial clustering of conserved residues yields information about the observed functional site in individual proteins and enables large-scale functional annotation by transfer of function from a characterised protein to a homologue of unknown activity [23]. Such clustering improved predictions in the case of enzyme active sites [24]. These conserved residue clusters may be analogous to modules containing conserved and highly cooperative groups of interface residues that characterize binding sites [27,28]

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