HIV-1 PROTEASE CLEAVAGE MECHANISM - A THEORETICAL INVESTIGATION BASEDON CLASSICAL MD SIMULATION AND REACTION-PATH CALCULATIONS USING A HYBRID QM MM POTENTIAL/

The cleavage mechanism of HIV-1 protease (HIV-PR) is investigated with classical molecular dynamics (MD) simulation and with methods incorpo rating a hybrid quantum mechanical and molecular mechanical (QM/MM) po tential function. An Xray structure of an HIV-PR/inhibitor complex was used to generate model HIV-PR/substrate and HIV-PR/intermediate compl exes. Analysis of the feasibility of reaction is based on three hypoth etical reaction mechanisms and a variety of possible starting conditio ns. The classical MD simulations were analyzed for conformations consi stent with reaction initiation, as reported previously. It was conclud ed that Asp125 is the general acid in the first reaction step and tran sfers a proton to the carbonyl oxygen. Simulations suggest that water 301 stabilizes productive reactant and intermediate conformations but does not participate directly in the reaction. A lytic water, when pre sent, is held very tightly in a position propitious for nucleophilic a ttack at the scissile carbon. For mechanisms consistent with the class ical simulations, reaction barriers were calculated using a QM/MM pote ntial. The QM/MM potential and a restrained energy minimization method for calculating reaction paths and barriers are described. Preliminar y results identify reasonable barrier heights and transition state con formations and predict that the first reaction step follows a predomin antly stepwise rather than concerted pathway. (C) 1998 Elsevier Scienc e B.V.