Computational Observation of an Ion Permeation Through a Channel Protein |
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| Authors: | Atushi Suenaga Yuto Komeiji Masami Uebayasi Toshiyuki Meguro Minoru Saito Ichiro Yamato |
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| Affiliation: | (1) Department of Biological Science and Technology, Science University of Tokyo, 2641 Yamazaki, Noda-shi, Chiba, 278-8510, Japan;(2) Supermolecular Science Division, Electrotechnical Laboratory, 1-1-4 Umezono, Tsukuba-shi, Ibaraki, 305-0045, Japan;(3) Specific Metabolism Laboratory, National Institute of Bioscience and Human Technology, 1-1-3 Higashi, Tsukuba-shi, Ibaraki, 305-0046, Japan;(4) Parallel Application Laboratory, Real World Computing Partnership, 1-6-1 Takezono, Tsukuba-shi, Ibaraki, 305-0032, Japan |
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| 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 (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. |
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| Keywords: | Channel protein molecular dynamics ion permeation process channel activity |
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