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Physics Colloquium - Friday, Dec. 5th, 2008, 4:00 P.M.


E300 Math/Science Center; Refreshments at 3:30 P.M. in Room E200

YEP student colloquium:
Gail Fanucci - Chemistry Department, University of Florida

Characterizing Flap Conformations in HIV-1 Protease: Combining Pulsed EPR and Computational Simulations

Human Immunodeficiency Virus Type 1 (HIV-1) protease is an enzyme required for viral replication, and as such represents a major drug target in the treatment of AIDS. HIV-1 PR is responsible for the cleavage of the viral polyproteins gag and gag-pol, and inhibition of this enzyme results in the formation of immature non-infectious virus particles. The structure and function of HIV-1 PR has been studied for over 20 years. However, questions regarding the conformations and motion of the hairpin turns (also known as flaps) that cover the active site cavity remain unanswered. We are utilizing distance measurements with pulsed electron paramagnetic resonance spectroscopy of a spin labeled construct of HIV-1 PR to characterize the flap conformations in inhibited and uninhibited samples. It is from the breadth of the distance distribution profiles obtained from analysis of the EPR data that insights regarding the flap conformations are gained. We also show that drug pressure induced mutations alter the average conformation of the flaps and the degree of opening of the flaps. Our EPR results are combined with molecular dynamic (MD) simulations from the Simmerling group (SUNY Stony Brook). Results from MD simulations successfully regenerate the experimentally determined distance distribution profiles, and more importantly, provide structural models needed to fully interpret the EPR results. By combining experiment and theory to under­stand the role that altered flap dynamics/conformations play in the mechanism of drug resistance, key insights are gained toward the rational development of new inhibitors of this important enzyme.