Exploring transmembrane transport through alpha-hemolysin with grid-steered molecular dynamics.

ABSTRACT: The transport of biomolecules across cell boundaries is central to cellular function. While structures of many membrane channels are known, the permeation mechanism is known only for a select few. Molecular dynamics (MD) is a computational method that can provide an accurate description of permeation events at the atomic level, which is required for understanding the transport mechanism. However, due to the relatively short time scales accessible to this method, it is of limited utility. Here, we present a method for all-atom simulation of electric field-driven transport of large solutes through membrane channels, which in tens of nanoseconds can provide a realistic account of a permeation event that would require a millisecond simulation using conventional MD. In this method, the average

SUBMITTER: Wells DB 

PROVIDER: S-EPMC2888542 | biostudies-literature | 2007 Sep

REPOSITORIES: biostudies-literature