Luzhkov V B, Aqvist J
Department of Cell and Molecular Biology, Uppsala University, BMC, Box 596, S-751 24, Uppsala, Sweden.
Biochim Biophys Acta. 2000 Sep 29;1481(2):360-70. doi: 10.1016/s0167-4838(00)00183-7.
We report results from microscopic molecular dynamics and free energy perturbation simulations of the KcsA potassium channel based on its experimental atomic structure. Conformational properties of selected amino acid residues as well as equilibrium positions of K(+) ions inside the selectivity filter and the internal water cavity are examined. Positions three and four (counting from the extracellular site) in the experimental structure correspond to distinctly separate binding sites for K(+) ions inside the selectivity filter. The protonation states of Glu71 and Asp80, which are close to each other and to the selectivity filter, as well as K(+) binding energies are determined using free energy perturbation calculations. The Glu71 residue which is buried inside a protein cavity is found to be most stable in the neutral form while the solvent exposed Asp80 is ionized. The channel altogether exothermically binds up to three ions, where two of them are located inside the selectivity filter and one in the internal water cavity. Ion permeation mechanisms are discussed in relation to these results.
我们基于KcsA钾通道的实验性原子结构，报告了其微观分子动力学和自由能微扰模拟的结果。研究了选定氨基酸残基的构象性质以及选择性过滤器和内部水腔中K⁺离子的平衡位置。实验结构中从细胞外侧开始计数的第三和第四位置对应于选择性过滤器内K⁺离子明显分开的结合位点。使用自由能微扰计算确定了彼此靠近且靠近选择性过滤器的Glu71和Asp80的质子化状态以及K⁺结合能。发现埋在蛋白质腔内的Glu71残基以中性形式最稳定，而暴露于溶剂中的Asp80则被电离。该通道总共放热结合多达三个离子，其中两个位于选择性过滤器内，一个位于内部水腔中。结合这些结果讨论了离子渗透机制。
