Sequence and structural features of binding site residues in protein-protein complexes: comparison with protein-nucleic acid complexes

M Gromiha,B Jayaram,N Saranya,Kazuhiko Fukui,S Selvaraj

doi:10.1186/1477-5956-9-s1-s13

Abstract

BackgroundProtein-protein interactions are important for several cellular processes. Understanding the mechanism of protein-protein recognition and predicting the binding sites in protein-protein complexes are long standing goals in molecular and computational biology.MethodsWe have developed an energy based approach for identifying the binding site residues in protein–protein complexes. The binding site residues have been analyzed with sequence and structure based parameters such as binding propensity, neighboring residues in the vicinity of binding sites, conservation score and conformational switching.ResultsWe observed that the binding propensities of amino acid residues are specific for protein-protein complexes. Further, typical dipeptides and tripeptides showed high preference for binding, which is unique to protein-protein complexes. Most of the binding site residues are highly conserved among homologous sequences. Our analysis showed that 7% of residues changed their conformations upon protein-protein complex formation and it is 9.2% and 6.6% in the binding and non-binding sites, respectively. Specifically, the residues Glu, Lys, Leu and Ser changed their conformation from coil to helix/strand and from helix to coil/strand. Leu, Ser, Thr and Val prefer to change their conformation from strand to coil/helix.ConclusionsThe results obtained in this study will be helpful for understanding and predicting the binding sites in protein-protein complexes.

Highlights

Protein-protein interactions are important for several cellular processes
We noticed that only 28% residues are common to each other and the percentage of binding site residues is a balance between those identified with different cutoff distances, indicating the importance of considering the energy between different atoms to define the binding residues
Conservation score for binding site residues in proteinprotein complexes We have computed the conservation score for all the residues and noticed that the binding residues are highly conserved in protein-protein complexes

Summary

Introduction

Protein-protein interactions are important for several cellular processes. Understanding the mechanism of protein-protein recognition and predicting the binding sites in protein-protein complexes are long standing goals in molecular and computational biology. Protein-protein interactions are important for most of the cellular processes in life. We have developed an energy based approach for defining the binding sites in protein-protein complexes [12]. We have analyzed the binding site residues based on sequence and structures of proteinprotein complexes. The results showed that the binding site residues have specific preferences at their vicinities and these residues are unique in protein-protein complexes. These binding site residues are more conserved than non-binding residues. The residues Glu, Lys and Ser play important roles to conformational switching

Methods

Results

Conclusion