Carnegie Mellon-University of Pittsburgh Program in Computational Biology, Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
J Mol Biol. 2010 Feb 26;396(3):580-92. doi: 10.1016/j.jmb.2009.12.006. Epub 2009 Dec 11.
The voltage-dependent anion channel (VDAC) is the major pathway mediating the transfer of metabolites and ions across the mitochondrial outer membrane. Two hallmarks of the channel in the open state are high metabolite flux and anion selectivity, while the partially closed state blocks metabolites and is cation selective. Here we report the results from electrostatics calculations carried out on the recently determined high-resolution structure of murine VDAC1 (mVDAC1). Poisson-Boltzmann calculations show that the ion transfer free energy through the channel is favorable for anions, suggesting that mVDAC1 represents the open state. This claim is buttressed by Poisson-Nernst-Planck calculations that predict a high single-channel conductance indicative of the open state and an anion selectivity of 1.75--nearly a twofold selectivity for anions over cations. These calculations were repeated on mutant channels and gave selectivity changes in accord with experimental observations. We were then able to engineer an in silico mutant channel with three point mutations that converted mVDAC1 into a channel with a preference for cations. Finally, we investigated two proposals for how the channel gates between the open and the closed state. Both models involve the movement of the N-terminal helix, but neither motion produced the observed voltage sensitivity, nor did either model result in a cation-selective channel, which is observed experimentally. Thus, we were able to rule out certain models for channel gating, but the true motion has yet to be determined.
电压依赖性阴离子通道（VDAC）是介导代谢物和离子穿过线粒体外膜的主要途径。通道在开放状态下的两个特点是高代谢物通量和阴离子选择性，而部分关闭状态则阻止代谢物并具有阳离子选择性。在这里，我们报告了对最近确定的高分辨率鼠源 VDAC1（mVDAC1）结构进行静电计算的结果。泊松-玻尔兹曼计算表明，离子通过通道的转移自由能有利于阴离子，这表明 mVDAC1 代表开放状态。这一说法得到泊松-纳恩斯特-普朗克计算的支持，该计算预测了一个高单通道电导，表明处于开放状态，并且阴离子选择性为 1.75--阴离子对阳离子的选择性几乎是两倍。对突变通道进行了重复计算，并得到了与实验观察一致的选择性变化。然后，我们能够通过三个点突变在计算机上构建一个突变通道，使 mVDAC1 成为对阳离子有偏好的通道。最后，我们研究了通道在开放和关闭状态之间门控的两种方案。这两种模型都涉及到 N 端螺旋的运动，但这两种运动都没有产生观察到的电压敏感性，也没有产生实验观察到的阳离子选择性通道。因此，我们能够排除某些通道门控模型，但真实的运动仍有待确定。
