Computational observation of an ion permeation through a channel protein.
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.
Suenaga
A
A
Department of Biological Science and Technology, Science University of Tokyo, Chiba, Japan.
Komeiji
Y
Y
Uebayasi
M
M
Meguro
T
T
Saito
M
M
Yamato
I
I
D001426:Bacterial Proteins / Q000378:metabolism*; D003198:Computer Simulation; D017136:Ion Transport; D008958:Models, Molecular; D018272:Porins / Q000378:metabolism*
D001426:Bacterial Proteins; C109237:OmpF protein; D018272:Porins