title: Computational observation of an ion permeation through a channel protein.
abstract: The ion permeation process, driven by a membrane potential through an outer membrane protein, OmpF porin of Escherichia coli, was simulated by molecular dynamics. A Na+ ion, initially placed in the solvent region at the outer side of the porin channel, moved along the electric field passing through the porin channel in a 1.3 nsec simulation; the permeation rate was consistent with the experimentally estimated channel activity (10(8)-10(9)/sec). It this simulation, it was indicated that the ion permeation through the porin channel proceeds by a "push-out" mechanism, and that Asp113 is an important residue for the channel activity.
authors.affiliation: Department of Biological Science and Technology, Science University of Tokyo, Chiba, Japan.
authors.forename: A
authors.initials: A
authors.lastname: Suenaga
authors.forename: Y
authors.initials: Y
authors.lastname: Komeiji
authors.forename: M
authors.initials: M
authors.lastname: Uebayasi
authors.forename: T
authors.initials: T
authors.lastname: Meguro
authors.forename: M
authors.initials: M
authors.lastname: Saito
authors.forename: I
authors.initials: I
authors.lastname: Yamato
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism*; D003198:Computer Simulation; D017136:Ion Transport; D008958:Models, Molecular; D018272:Porins / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; C109237:OmpF protein; D018272:Porins