Unraveling HIV protease flaps dynamics by Constant pH Molecular Dynamics simulations

Abstract

a b s t r a c tThe active site of HIV protease (HIV-PR) is covered by two flaps. These flaps are known to be essential for the catalytic activity of the HIV-PR, but their exact conformations at the different stages of the enzymatic pathway remain subject to debate. Understanding the correct functional dynamics of the flaps might aid the development of new HIV-PR inhibitors. It is known that, the HIV-PR catalytic efficiency is pHdependent, likely due to the influence of processes such as charge transfer and protonation/deprotonation of ionizable residues. Several Molecular Dynamics (MD) simulations have reported information about the HIV-PR flaps. However, in MD simulations the protonation of a residue is fixed and thus it is not possible to study the correlation between conformation and protonation state. To address this shortcoming, this work attempts to capture, through Constant pH Molecular Dynamics (CpHMD), the conformations of the apo, substrate-bound and inhibitor-bound HIV-PR, which differ drastically in their flap arrangements. The results show that the HIV-PR flaps conformations are defined by the protonation of the catalytic residues Asp25/Asp25 0 and that these residues are sensitive to pH changes. This study suggests that the catalytic aspartates can modulate the opening of the active site and substrate binding.

Dataset showing the impact of the protonation states on molecular dynamics of HIV protease

“… The data described here supports the research article “Unraveling HIV Protease Flaps Dynamics by Constant pH Molecular Dynamics Simulations” (Soares et al, 2016) [1] . The data involves both standard Molecular Dynamics (MD) and Constant pH Molecular Dynamics (CpHMD) to elucidate the effect of protonation states of catalytic dyad on the HIV-PR conformation.…”

“…The crystal structure 2HB4 was used as apo form of HIV-PR [8] . Before starting the simulation on the 1KJF structure, we performed the mutation N25D [1] .…”

Hybrid QM/MM free energy evaluation of drug-resistant mutational effect on binding of an inhibitor Indinavir to HIV-1 protease

“…Equilibrium MD simulations of IUS for 1 µs showed large conformational fluctuation of the flap region (Figure S14), although no distinct conformational transitions to the open or semi-open conformations observed by an X-ray crystallographic measurement and previous MD simulations [56,[92][93][94] were found during the simulation time, which may be a source of the slight overestimation of the increase of . We also performed the alchemical FEP calculations for IUS with different protonation states of the carboxylic acids of Asp25, i.e., the mono-protonated state and the di-protonated state, for comparison, and found that the difference in the protonation state moderately altered the free energy change upon the mutation by ~1 kcal/mol (Table S6).…”

“…X-ray crystallographic studies reported conformational changes of the protein upon mutations [13,19,20,94]. X-ray crystallographic structures of HIV-1 protease binding Indinavir exhibit large conformational changes of 80s loop comprised of amino acids 79-83 and the pyridyl group of Indinavir upon nine mutations including V82T [20] and two mutations including V82A [21],…”

Hybrid QM/MM free energy evaluation of drug-resistant mutational effect on binding of an inhibitor Indinavir to HIV protease

“…Equilibrium MD simulations of IUS for 1 µs showed large conformational fluctuation of the flap region (Figure S12), although no distinct conformational transitions to the open or semi-open conformations observed by an X-ray crystallographic measurement and previous MD simulations [86][87][88] were found during the simulation time, which may be a source of the slight overestimation of the increase of . We also performed the alchemical FEP calculations for IUS with different protonation states of the carboxylic acids of Asp25, i.e., the mono-protonated state and the di-protonated state, for comparison, and found that the difference in the protonation state moderately altered the free energy change upon the mutation by ~1 kcal/mol (Table S6).…”