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Name Mr. Pancham Lal Gupta
Organization or Institution University of Florida
Presentation Type Poster
Topic Computational Chemistry

Study of pH-dependent ligand binding and cooperativity for E.coli glycinamide ribonucleotide transformylase


Pancham Lal Gupta, Adrian E. Roitberg

Author Institution(s)

Department of Chemistry, University of Florida, Gainesville, FL, 32611-7200, USA


Protein adopts the unique three-dimensional structure and its structure exhibits pockets for ligand binding. Ligand binding is an inherent factor in most of the proteins’ functions such as allostery, cooperativity and enzyme regulation. Hence, all these functions can be altered by the structural changes which depend upon the pH, temperature, pressure etc. In the present work, we focus on pH-dependent structural changes, ligand binding and cooperativity. The target enzyme in this work is E.coli glycinamide ribonucleotide transformylase (GAR Tfase). GAR Tfase acts as a regulatory enzyme in de novo purine biosynthesis so inhibition of this enzyme can prevent uncontrolled cell division. This makes GAR Tfase an anti-cancer target. Due to that, people are actively involved in designing the more potent and effective inhibitor molecules for GAR Tfase. Knowing hydrogen bonding network in the active site and the catalytic mechanism would be helpful in designing inhibitors. GAR Tfase exhibits pH-dependent conformational changes and catalytic activity and it has been shown in previous works that both are linked. To explore pH-effects in GAR Tfase, we are using the pH-replica exchange molecular dynamics (pH-REMD) simulations. Through simulation analyses, we found regions of structural changes in GAR Tfase which agrees well with experimental works. Besides that, we have computed pH-dependence of the relative free energy of ligand binding for both GAR and folate ligands. We have found that binding of one ligand stabilizes the binding of another ligand. This work helped in understanding the atomic level interactions responsible for ligand binding and mechanism for catalysis which will assist in optimizing the binding of drug inhibitor.