Simulations of a protein crystal with a high resolution X-ray structure: evaluation of force fields and water models.

ABSTRACT: We use classical molecular dynamics and 16 combinations of force fields and water models to simulate a protein crystal observed by room-temperature X-ray diffraction. The high resolution of the diffraction data (0.96 Å) and the simplicity of the crystallization solution (nearly pure water) make it possible to attribute any inconsistencies between the crystal structure and our simulations to artifacts of the models rather than inadequate representation of the crystal environment or uncertainty in the experiment. All simulations were extended for 100 ns of production dynamics, permitting some long-time scale artifacts of each model to emerge. The most noticeable effect of these artifacts is a model-dependent drift in the unit cell dimensions, which can become as large as 5% in certain force

SUBMITTER: Cerutti DS 

PROVIDER: S-EPMC2997720 | biostudies-literature | 2010 Oct

REPOSITORIES: biostudies-literature