Dr. Deepa Rajamani

Dr. Deepa Rajamani

My research here focuses on studying the dynamics of protein surfaces to elucidate protein-protein interactions. Proteins have a dynamic surface and they still have recognizable motifs on their surface to bring about protein-protein interactions. We show that the mechanism for molecular recognition requires specific anchoring side chains on the surface of proteins to be structurally constrained lowering the flexibility of those side chains. These anchoring side chains form the ready-made recognition motifs for complex formation.

We run Molecular dynamics (MD) simulations on individually crystallized ligand proteins to determine the distributions of surface residues on a solvated protein and verify that the surface residues that bury largest solvent-accessible surface area upon complex formation are bound-like for most part of the MD simulation. From these studies we also determined the most probable conformations for the surface residues by looking at the most populated cluster from the MD derived distribution of residue conformations. These MD conformations are then used to redefine the protein surface for protein-protein docking studies. We find from our docking studies that the MD derived conformations improve docking results especially when the anchoring side chains which provide the recognition motifs are misplaced in the individually crystallized proteins that are used for docking studies.

We are also planning on extending the MD analysis of protein surfaces to protein-small molecule docking studies.

I have my undergraduate degree in pharmacy and a Masters' in Biotechnology. My interests have been in studying the molecular details of cellular function thereby understanding the pharmacological effects of therapeutic agents.