Reaction Mechanism of HIV-1 Protease by Hybrid Car-Parrinello/Classical MD Simulations

The authors present a QM/MM ab initio mol. dynamics study of the peptide hydrolysis reaction catalyzed by HIV-1 protease. The QM/MM calcns. are based on previous extensive classical MD simulations on the protein in complex with a model substrate. Gradient-cor. BLYP d. functional theory (DFT) describes the reactive part of the active site, and the AMBER force field describes the rest of the protein, the solvent, and the counterions. An unbiased enhanced sampling of the QM/MM free-energy surface is performed to identify a plausible reaction coordinate for the second step of the reaction. The enzymic reaction is characterized by two reaction free-energy barriers of .apprx.18 and .apprx.21 kcal mol-1 sepd. by a metastable gem-diol intermediate. In both steps, a proton transfer that involves the substrate and the two catalytic Asp mols. is obsd. The orientation and the flexibility of the reactants, governed by the surrounding protein frame, are the key factors in detg. the activation barrier. The calcd. value for the barrier of the second step is slightly larger than the value expected from exptl. data (.apprx.16 kcal mol-1). An extensive comparison with calcns. on gas-phase model systems at the Hartree-Fock, DFT-BP, DFT-BLYP, DFT-B3LYP, MP2, CCD, and QM/MM DFT-BLYP levels of theory suggests that the DFT-BLYP functional has the tendency to underestimate the energy of the gem-diol intermediate by .apprx.5-7 kcal mol-1. [on SciFinder (R)]