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 (108∼109/sec). In 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.