Identification and Analysis of Binding Site Residues in Protein Complexes: Energy Based Approach

Abstract

Understanding the recognition mechanism of protein complexes is a challenging task in bioinformatics and computational biology. We have developed a novel energy based approach for identifying the binding site residues in protein–protein, protein-RNA and protein-DNA complexes. In protein-protein complexes, the residues and residue-pairs with charged and aromatic side chains are important for binding. These residues influence to form cation–π, electrostatic and aromatic interactions. In protein-RNA complexes, the positively charged, polar and aromatic residues are important for binding. These residues influence to form electrostatic, hydrogen bonding and stacking interactions. The positive charged and polar residues are preferred to bind with DNA in protein-DNA complexes. These results provide an overall view of binding in protein complexes. Our observations have been verified with the experimental binding specificity of protein-protein and protein-nucleic acid complexes and found good agreement with experiments.