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.
Computational Observation of an Ion Permeation Through a Channel Protein
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Atushi Suenaga, Yuto Komeiji, Masami Uebayasi, Toshiyuki Meguro, Minoru Saito, Ichiro Yamato; Computational Observation of an Ion Permeation Through a Channel Protein. Biosci Rep 1 February 1998; 18 (1): 39–48. doi: https://doi.org/10.1023/A:1022292801256
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