Conformational Diversity Induces Nanosecond-Timescale Chemical Disorder in the HIV-1 Protease Reaction Pathway
The role of conformational diversity on enzyme catalysis has been a matter of analysis on recent studies. Pre-organization of the active site has been pointed out as the major source for enzymes’ catalytic power. Within this line of thought, it is becoming clear that specific, instantaneous, non-rare enzyme conformations that make the active site perfectly pre-organized for the reaction, lead to the lowest activation barriers that mostly contribute to the macroscopic observed reaction rate. The present work is focused on exploring the relationship between structure and catalysis in HIV-1 protease (PR) with an adiabatic mapping method, starting from different initial structures, collected from a classical MD simulation. The first, rate-limiting step of HIV-1 PR catalytic mechanism was studied with the ONIOM QM/MM methodology (B3LYP/6-31G(d):ff99SB), with activation and reaction energies calculated at the M06-2X/6-311++G(2d,2p):ff99SB level of theory, in 19 different enzyme:substrate conformations. The results showed that the instantaneous enzyme conformations have two independent consequences on the enzyme’s chemistry: they influence the barrier height, something also observed in the past in other enzymes, but they also influence the specific reaction pathway, which is something unusual and unexpected, challenging the “one enzyme-one substrate-one reaction mechanism” paradigm. Two different reaction mechanisms, with similar reactants probabilities and barrier heights, lead to the same gem-diol intermediate, Subtle nanosecond-timescale rearrangements in the active site hydrogen bonding network were shown to determine which reaction the enzyme follows. We named this phenomenon as chemical disorder. The results make us to realize unexpected mechanistic consequences of conformational diversity in enzymatic reactivity.