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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机译：通过分子动力学模拟了由外膜蛋白OmpF孔蛋白的膜电位驱动的离子渗透过程。 Na +离子最初放置在孔洞通道外侧的溶剂区域中，在1.3 ns的模拟中沿着穿过孔洞通道的电场移动。渗透速率与实验估算的通道活性一致（108〜109 / sec）。在该模拟中，表明了通过“推出”机制使离子通过孔蛋白通道进行了渗透，并且Asp113是通道活性的重要残基。
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