cs5b00759_si_001.txt (687.71 kB)
Enzymatic Flexibility and Reaction Rate: A QM/MM Study of HIV‑1 Protease
dataset
posted on 2015-09-04, 00:00 authored by António
J. M. Ribeiro, Diogo Santos-Martins, Nino Russo, Maria J. Ramos, Pedro A. FernandesThe relevance of conformational fluctuations
on enzyme rates has
been a matter of debate for decades. Single molecule experiments have
detected variations on the catalytic rates between different enzyme
molecules, and within the same enzyme molecule, in a time scale larger
than turnover. Computational methods can detect different energy barriers,
induced by thermal conformational fluctuations, at a microscopic time
scale, several orders of magnitude faster than the turnover rate of
the fastest enzyme. Others have observed these barrier fluctuations,
but few computational studies have dissected them in detail and tried
to understand their origins and consequences. For this purpose, we
studied the first step of the reaction catalyzed by HIV-1 Protease,
starting from 40 different conformations. We found activation free
energies ranging from 14.5 to 51.3 kcal·mol–1. The calculated apparent barrier is 16.5 kcal·mol–1, which is very close to the experimental value of 15.9 kcal·mol–1 for product release. These fluctuations are determinant
to the overall rate, and these are correlated to specific structural
changes. The effect of each enzymatic conformation on the stabilization
of the transition state can be explained by the electrostatic interaction
of every protein residue with the flow of net electronic density (negative
charge) from the reactants to the transition state.