In order to illustrate the ion transport mechanism of chloride channel (ClC) protein, a type of ClC protein, ClC-ec1, from Escherichia coli is embedded into an explicit membranewater system by using software VMD. Then a parallel molecular dynamics (MD) simulation is employed to equilibrate the ClC-ec1 structure for 27.5 ns at temperature 298.15 K. Based on this equilibrated structure, we compute the channel geometric size variation and electrostatic potential distribution along the channel. Meanwhile, Cl- transport process is simulated using oriented random walk method under variable external potential. The simulation result shows that Cl- transport velocity depends on the width of the narrowest channel region. Mutation of negative glutamate E148 can produce positive potential, which is beneficial for Cl- transport, around external Cl- binding region in the channel. The simulated current-voltage curves about Cl- transporting in ClC-ec1 protein agree with Jayaram’s experimental results.

中文翻译：

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复杂静电势下ClC型通道蛋白的离子迁移机理

为了说明氯离子通道蛋白（ClC）的离子迁移机理，通过使用VMD软件将一种来自大肠杆菌的ClC蛋白ClC-ec1嵌入到一个明确的膜水系统中。然后采用平行分子动力学（MD）模拟在298.15 K的温度下平衡ClC-ec1结构27.5 ns。基于此平衡结构，我们计算出通道的几何尺寸变化和沿通道的静电势分布。同时，利用定向随机游走法在可变外部电势下模拟了Cl-的运输过程。仿真结果表明，Cl-传输速度取决于最窄通道区域的宽度。负谷氨酸E148的突变可产生正电势，这对Cl转运是有利的，在通道中外部Cl-结合区域周围。关于ClC-ec1蛋白中Cl-转运的模拟电流-电压曲线与Jayaram的实验结果相符。