Identification and Analysis of Binding Site Residues in Proteincarbohydrate Complexes using Energy Based Approach
M. Michael Gromiha, K. Veluraja and Kazuhiko Fukui
Affiliation: Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036, Tamilnadu, India.
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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