Membrane protein dynamics and detergent interactions within a crystal: a simulation study of OmpA.

ABSTRACT: Molecular dynamics (MD) simulations are used to explore the dynamics of a membrane protein in its crystal environment. A 50-ns-duration simulation (at a temperature of 300 K) is performed for the crystallographic unit cell of the bacterial outer membrane protein OmpA. The unit cell contains four protein molecules, plus detergent molecules and water. An excellent correlation between simulated and experimental values of crystallographic B factors is observed. Effectively, 0.2 micros of protein trajectories are obtained, allowing a critical assessment of simulation quality. Some deficiency in conformational sampling is demonstrated, but averaging over multiple trajectories improves this limitation. The previously undescribed structure and dynamics of detergent molecules in a unit cell are rep

SUBMITTER: Bond PJ 

PROVIDER: S-EPMC1480439 | biostudies-literature | 2006 Jun

REPOSITORIES: biostudies-literature