Water structure in solution and crystal molecular dynamics simulations compared to protein crystal structures.

ABSTRACT: The function of proteins is influenced not only by the atomic structure but also by the detailed structure of the solvent surrounding it. Computational studies of protein structure also critically depend on the water structure around the protein. Herein we compare the water structure obtained from molecular dynamics (MD) simulations of galectin-3 in complex with two ligands to crystallographic water molecules observed in the corresponding crystal structures. We computed MD trajectories both in a water box, which mimics a protein in solution, and in a crystallographic unit cell, which mimics a protein in a crystal. The calculations were compared to crystal structures obtained at both cryogenic and room temperature. Two types of analyses of the MD simulations were performed. First, the posit

SUBMITTER: Caldararu O 

PROVIDER: S-EPMC9049968 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature