Mashl R J, Tang Y, Schnitzer J, Jakobsson E
Beckman Institute for Advanced Science and Technology, Department of Molecular and Integrative Physiology, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801, USA.
Biophys J. 2001 Nov;81(5):2473-83. doi: 10.1016/S0006-3495(01)75893-6.
A hierarchical computational strategy combining molecular modeling, electrostatics calculations, molecular dynamics, and Brownian dynamics simulations is developed and implemented to compute electrophysiologically measurable properties of the KcsA potassium channel. Models for a series of channels with different pore sizes are developed from the known x-ray structure, using insights into the gating conformational changes as suggested by a variety of published experiments. Information on the pH dependence of the channel gating is incorporated into the calculation of potential profiles for K(+) ions inside the channel, which are then combined with K(+) ion mobilities inside the channel, as computed by molecular dynamics simulations, to provide inputs into Brownian dynamics simulations for computing ion fluxes. The open model structure has a conductance of approximately 110 pS under symmetric 250 mM K(+) conditions, in reasonable agreement with experiments for the largest conducting substate. The dimensions of this channel are consistent with electrophysiologically determined size dependence of quaternary ammonium ion blocking from the intracellular end of this channel as well as with direct structural evidence that tetrabutylammonium ions can enter into the interior cavity of the channel. Realistic values of Ussing flux ratio exponents, distribution of ions within the channel, and shapes of the current-voltage and current-concentration curves are obtained. The Brownian dynamics calculations suggest passage of ions through the selectivity filter proceeds by a "knock-off" mechanism involving three ions, as has been previously inferred from functional and structural studies of barium ion blocking. These results suggest that the present calculations capture the essential nature of K(+) ion permeation in the KcsA channel and provide a proof-of-concept for the integrated microscopic/mesoscopic multitiered approach for predicting ion channel function from structure, which can be applied to other channel structures.
我们开发并实施了一种分层计算策略，该策略结合了分子建模、静电计算、分子动力学和布朗动力学模拟，以计算KcsA钾通道的电生理可测量特性。利用各种已发表实验所暗示的门控构象变化的见解，从已知的x射线结构出发，开发了一系列具有不同孔径的通道模型。通道门控对pH依赖性的信息被纳入通道内K(+)离子的电位分布计算中，然后将其与分子动力学模拟计算得到的通道内K(+)离子迁移率相结合，为计算离子通量的布朗动力学模拟提供输入。在对称的250 mM K(+)条件下，开放模型结构的电导率约为110 pS，与最大导电亚状态的实验结果合理一致。该通道的尺寸与从该通道细胞内端进行的季铵离子阻断的电生理确定的尺寸依赖性一致，也与四丁基铵离子可以进入通道内腔的直接结构证据一致。获得了Ussing通量比指数的实际值、通道内离子的分布以及电流-电压和电流-浓度曲线的形状。布朗动力学计算表明，离子通过选择性过滤器的过程是通过一种涉及三个离子的“敲除”机制进行的，这与先前从钡离子阻断的功能和结构研究中推断的一致。这些结果表明，目前的计算捕捉到了KcsA通道中K(+)离子渗透的本质，并为从结构预测离子通道功能的综合微观/介观多层方法提供了概念验证，该方法可应用于其他通道结构。
