Dynamic and Electrostatic Effects on the Reaction Catalyzed by HIV-1 Protease

Abstract

HIV-1 Protease (HIV-1 PR) is one of the three enzymes essential for the replication process of HIV-1 virus, which explains why it has been the main target for design of drugs against acquired immunodeficiency syndrome (AIDS). This work is focused on exploring the proteolysis reaction catalyzed by HIV-1 PR, with special attention to the dynamic and electrostatic effects governing its catalytic power. Free energy surfaces for all possible mechanisms have been computed in terms of potentials of mean force (PMFs) within hybrid QM/MM potentials, with the QM sub-set of atoms described at semiempirical (AM1) and DFT (M06-2X) level. The results suggest that the most favorable reaction mechanism involves formation of a gem-diol intermediate, whose decomposition into the product complex would correspond to the rate-limiting step. The agreement between the activation free energy of this step with experimental data, as well as kinetic isotope effects (KIEs), supports this prediction. The role of the protein dynamic was studied by protein isotope labelling in the framework of the Variational Transition State Theory. The predicted enzyme KIEs, also very close to the values measured experimentally, reveal a measurable but small dynamic effect. Our calculations show how the contribution of dynamic effects to the effective activation free energy appears to be below 1 kcal·mol−1. On the contrary, the electric field created by the protein in the active site of the enzyme emerges as being critical for the electronic reorganization required during the reaction. These electrostatic properties of the active site could be used as a mould for future drug design.

Computational Optimization of Electric Fields for Improving Catalysis of a Designed Kemp Eliminase

“…Finally, Warshel and coworkers were the first to identify the preorganization of the electrostatic free energy as a key component of enzyme catalysis [26][27][28] ; in fact many groups have reported evidence for how electric fields contribute to the catalytic power of various natural enzymes. [29][30][31][32][33] (a) (b) (c) We have recently reported in two separate studies the effects of both side chain conformational entropy and mutual information 36 , as well as electrostatic stabilization 34 , for improving designed KE07 and KE70 enzymes during the LDE process. It was shown in the first study that improved variants used a combination of free energy destabilization of the reactant enzyme-ligand bound state (EL) (in agreement with Frushicheva et.…”

Temperature dependence of dynamic, tunnelling and kinetic isotope effects in formate dehydrogenase

“…One of these hypotheses suggests that the transition state (TS) stabilization relative to the reactant state is largely due to the preorganised electrostatic environment provided by the active site of the enzyme; 1-5 this proposal has been supported by many studies. [6][7][8][9][10][11][12][13][14][15][16][17][18][19][20] Nevertheless, it has also been proposed that protein motions contribute to reducing the energybarrier crossing through the TS toward the products. [21][22][23][24][25][26][27][28][29][30][31][32][33] In fact, the role of protein dynamics in enzymatic catalysis is one of the most controversial topics in modern enzymology, providing a hot debate among theoreticians and experimentalists.…”

Isotope Substitution of Promiscuous Alcohol Dehydrogenase Reveals the Origin of Substrate Preference in the Transition State

“…The difference in the rate constants measured with the “light” and “heavy” enzyme are caused by changes in the recrossing coefficients $\gamma$ 2b, 3b, 12. Indeed, because our simulations were carried out using an antisymmetric combination of the distances of the hydride to donor and the acceptor atoms as distinguished reaction coordinate, $\gamma$ incorporates the effect of the remaining degrees of freedom of both the protein and substrate, which accounts for the additional friction observed on the distinguished reaction coordinate.…”