Identification and Analysis of Binding Site Residues in Proteincarbohydrate Complexes using Energy Based Approach

M.   Michael   Gromiha; K.      Veluraja; Kazuhiko      Fukui

doi:10.2174/09298665113209990055

Abstract

Protein-carbohydrate interactions play important roles in several biological processes in living organisms. Understanding the recognition mechanism of protein-carbohydrate complexes is a challenging task in molecular and computational biology. In this work, we have developed an energy based approach for identifying the binding sites and important residues for binding in protein-carbohydrate complexes. Our method identified 3.3% of residues as binding sites in protein- carbohydrate complexes whereas the binding site residues in protein-protein, protein-RNA and protein-DNA complexes are 10.8%, 7.6% and 8.7%, respectively. In all these complexes, binding site residues are accommodated in singleresidue segments so that the neighboring residues are not involved in binding. Binding propensity analysis indicates the dominance of Trp to interact with carbohydrates through aromatic-aromatic interactions. Further, the preference of residue pairs and tripeptides interacting with carbohydrates has been delineated. The information gained in the present study will be beneficial for understanding the recognition mechanism of protein-carbohydrate complexes and for predicting the binding sites in carbohydrate binding proteins.

Keywords: Interaction energy, protein-carbohydrate complex, propensity, residue pair preference.

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