Transition states and dynamics of HIV-1 protease

Abstract

Enzyme-transition state (TS) interactions are key to enzymatic function and a common focus of inhibitor design. However, how enzymes reach the TS remains a hotly debated topic. Here we explore the TS of the reaction catalyzed by HIV-1 protease -- an established drug target for HIV/AIDS -- to understand drug resistance, improve inhibitor design, and, more broadly, explore details of how enzymes come to interact with the TS. We hypothesized that TS structures of native and drug-resistant HIV-1 protease would be chemically similar and provide a blueprint to design future inhibitors against drug resistant mutants. We have resolved the TS structure of the rate-limiting chemical step of the reaction catalyzed by HIV-1 protease by measuring kinetic isotope effects (KIEs) and matching them to calculated predictions. KIEs for the native and drug-resistant mutant are identical, as anticipated. An electrostatic potential map of the TS structure may serve as a guide for future inhibitor design. Next, we explored the role of dynamic motions of the enzyme in TS formation. Prior studies show that conformational motions on the microsecond to millisecond timescale are involved in catalysis, however, the chemical event of an enzymatic reaction occurs at 10-12 the rate of an enzymatic turnover. We hypothesized that enzyme motions on the same timescale as a chemical event (femtoseconds) promote TS crossing. Substituting all C, N, and non-exchangeable H's with their corresponding stable isotopes perturbed bond vibrational frequency, which was predicted to reduce catalytic rates. Indeed, rate reductions were observed in both steady-state and pre-steady-state kinetic analysis, supporting our hypothesis.