Molecular dynamics simulation of HIV-1 protease in a crystalline environment and in solution. [Erratum to document cited in CA118(21):208404x]

Effect of an Electric Field on Surface Properties of Hydrophobic Particles during a Flotation Process in Salt Water

Under air flotation conditions, the effect of an electric field (EF) to the interfacial properties of hydrophobic particles in salt solution was investigated by using molecular dynamics simulation. The varieties of thickness of the hydrophobic layer on the surface of the hydrophobic particles, radial distribution function of Na⁺, diffusivity of CO₂ and H₂O, residence time of H₂O in the solvent shell of Na⁺, and the distribution of CO₂ near the graphene caused by the applied EF in different NaCl systems were calculated, and all those results were compared with those where there is no EF applied. The results reveal that the thickness of the hydrophobic layer near the hydrophobic particles is decreased under an EF. The coordination number and residence time of H₂O in the solvent shell of Na⁺ are also decreased, which indicates that the restraint of Na⁺ on surrounding H₂O is weakened, and the H₂O molecules are more mobile. Under an external EF, the diffusion coefficient of CO₂ and H₂O is increased, and the quantity of CO₂ near the surface of graphene is decreased according to the numerical results of the radial distribution of graphene-CO₂. All the results indicate that the EF will decrease the thickness of the hydrophobic layer near hydrophobic particles, which can therefore weaken the adsorption between the hydrophobic particles and the gas molecules. The simulation results in the present study can provide theoretical support for brine mineral flotation under an external EF.

Solution structure of HIV-1 protease flaps probed by comparison of molecular dynamics simulation ensembles and EPR experiments

The introduction of multidrug treatment regimens has dramatically prolonged the progression and survival of AIDS patients. However, the success of the long-term treatment has been hindered by strains of HIV that are increasingly resistant to inhibitors of targets such as HIV protease (HIV PR). Therefore, the need for a thorough understanding of the structure and dynamics of HIV PR and how these are altered in resistant mutants is crucial for the design of more effective treatments. Crystal structures of unbound HIV PR show significant heterogeneity and often have extensive crystal packing interactions. Recent site-directed spin labeling (SDSL) and double electron-electron resonance (DEER) spectroscopy studies characterized flap conformations in HIV-1 protease in an inhibited and uninhibited form and distinguished the extent of flap opening in an unbound form. However, the correlation between EPR-measured interspin distances and structural/dynamic features of the flaps has not been established. In this report, we link EPR-based data and 900 ns of MD simulation in explicit water to gain insight into the ensemble of conformations sampled by HIV PR flaps in solution, both in the presence and in the absence of an FDA-approved HIV PR inhibitor.