期刊名称：Proceedings of the National Academy of Sciences
印刷版ISSN：0027-8424
电子版ISSN：1091-6490
出版年度：2006
卷号：103
期号：25
页码：9518-9523
DOI：10.1073/pnas.0600398103
语种：English
出版社：The National Academy of Sciences of the United States of America
摘要：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 {micro}s 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 reported here, providing insight into the interactions important in the formation and stabilization of the crystalline environment at room temperature. In particular, we show that at room temperature the detergent molecules form a dynamic, extended micellar structure spreading over adjacent OmpA monomers within the crystal.
关键词：molecular dynamics ; outer membrane protein ; conformational sampling
