Thermodynamics for Biological Systems : Classical and Statistical Aspect

Sanjib Senapati is a Professor in the Department of Biotechnology, Indian Institute of Technology Madras (IITM).His research group at I.I.T. Madras focuses on understanding the relationship between protein structure, function, and dynamics. Research is focused into two major sub-groups: 1) molecular modeling of enzyme-substrate/enzyme-inhibitor interactions and 2) structure-based drug designing. Studies are performed using computer simulation methods ranging from all-atom and coarse-grained molecular dynamics simulations, Monte Carlo simulations, protein-ligand and protein-protein docking. General properties that we address include change in protein structure and dynamics upon binding inhibitors and with mutations, ligand binding strength and specificity, and bound water structure. Our proteins of interest include: HIV-1 protease, Cyclin Dependent Kinases (CDKs), Cholesterylester transfer protein (CETP), Nicotinic Acetylcholine Receptor (nAChR) etc. Another thrust area includes the study of green solvents, ionic liquids and supercritical carbon dioxide. Here, our objective is to understand the molecular basis of increased/decreased stability of biomolecules and modulated kinetics of protein folding in these novel solvents. Subsequently, we attempt to validate our findings from computational studies usingspectroscopic and calorimetric 5 techniques. Also, with leads from our computational data we performinhibitor synthesis, enzymatic assays and drug designin our laboratory. Before joining IIT Madras in 2006, I have received my Ph.D. degree from I.I.T. Kanpur, India on Statistical Mechanics of liquids, where I had contributed on the understanding of liquid- membrane, liquid-solid interfaces, and also of liquids under confinement. Subsequently, I moved to University of North Carolina at Chapel Hill, USA to work on structure and dynamics of complex aqueous interfaces. Later I shifted to University of California San Diego (UCSD), USA, where I developed and applied a novel computational approach for drug designing, called the relaxed complex method, which allows for the direct accommodation of the receptors flexibility along with the ligands flexibility in protein-ligand docking.