Journal of Proteomics & Bioinformatics
Open Access

Role of waters in ligand binding

2^nd International Conference on Proteomics & Bioinformatics

July 2-4, 2012 Embassy Suites Las Vegas, USA

Art E. Cho

Accepted Abstracts: J Proteomics Bioinform

Abstract :

It is well known that the role of water molecules in the binding sites of proteins is critical to the protein-ligand binding phenomena. Some of these phenomena can be simulated with molecular dynamics (MD). Recent developments in the field of computational drug discovery, for example, track water movements in the binding sites of proteins to construct 3 dimensional mapping of chemical properties to aid in designing of drug compounds. In this talk, we will present our recent work on galactoseglucose binding protein (GGBP) and its mutants using MD simulations. Through close analyses of the movements of waters within the binding site, we were able to explain the previous experimental results which differentiate the binding affinities of GGBP mutants to 2 kinds of sugars. The analyses show that though the difference in structure can be subtle, movements of waters can be rather disparate leading to vastly different binding affinities. This particular example demonstrates that even without computing explicit thermodynamic quantities, MD simulations can help elucidate the involvement of waters in ligand binding.

Biography :

Art E. Cho is a professor in the department of bioinformatics and the chair of Nano-Bio-Info Technology Program at Korea University in Korea. He graduated from the University of California at Berkeley in 1988 with B.S. in physics and math. After completing the master?s program in mathematics at the University of Chicago, he went on to pursue Ph.D. in physics at Brown University. During his graduate work at Brown, he worked as a senior research scientist at supercomputing center of Samsung Advanced Institute of Technology, the job he undertook as a substitution of mandatory military service duty. After obtaining Ph.D. in physics in 2001, he worked as a postdoctoral scholar at Caltech and then as a research scientist at Columbia University. He also worked as an applications scientist at Schrodinger, Inc. Since 2007, he has been at Korea University. In 2010, while taking up a departmental duty as the Chairman, he started a consulting firm, named Quantum Bio Solutions, which caters to pharmaceutical industry utilizing his expertise in CADD (computer-aided drug design).