Hydration Structure and Dynamics of Inhibitor-Bound HIV-1 Protease.

ABSTRACT: Water is essential in many biological processes, and the hydration structure plays a critical role in facilitating protein folding, dynamics, and ligand binding. A variety of biophysical spectroscopic techniques have been used to probe the water solvating proteins, often complemented with molecular dynamics (MD) simulations to resolve the spatial and dynamic features of the hydration shell, but comparing relative water structure is challenging. In this study 1 μs MD simulations were performed to identify and characterize hydration sites around HIV-1 protease bound to an inhibitor, darunavir (DRV). The water density, hydration site occupancy, extent and anisotropy of fluctuations, coordinated water molecules, and hydrogen bonds were characterized and compared to the properties of bulk water

SUBMITTER: Leidner F 

PROVIDER: S-EPMC6219750 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature