Im Wonpil, Roux Benoît
Department of Biochemistry, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10021, USA.
J Mol Biol. 2002 Jun 21;319(5):1177-97. doi: 10.1016/S0022-2836(02)00380-7.
A 5 ns all-atom molecular dynamics trajectory of Escherichia coli OmpF porin embedded in an explicit dimyristoyl-phosphatidylcholine (DMPC) bilayer bathed by a 1 M [KCl] aqueous salt solution is generated to explore the microscopic details of the mechanism of ion permeation. The atomic model includes the OmpF trimer, 124 DMPC, 13470 water molecules as well as 231 K+ and 201 Cl-, for a total of 70,693 atoms. The structural and dynamical results are in excellent agreement with the X-ray data. The global root-mean-square deviation of the backbone atoms relative to the X-ray structure is 1.4 A. A cluster of three fully charged arginine (Arg42, Arg82, and Arg132) facing two acidic residues (Asp113 and Glu117) on L3 in the narrowest part of the aqueous pore is observed to be very stable in the crystallographic conformation. In this region of the pore, the water molecules are markedly oriented perpendicular to the channel axis due to the strong transversal electrostatic field arising from those residues. On average the size of the pore is smaller during the simulation than in the X-ray structure, undergoing small fluctuations. No large movements of loop L3 leading to a gating of the pore are observed. Remarkably, it is observed that K+ and Cl- follow two well-separated average pathways spanning over nearly 40 A along the axis of the pore. In the center of the monomer, the two screw-like pathways have a left-handed twist, undergoing a counter-clockwise rotation of 180 degrees from the extracellular vestibule to the pore periplasmic side. In the pore, the dynamical diffusion constants of the ions are reduced by about 50% relative to their value in bulk solvent. Analysis of ion solvation across the channel reveals that the contributions from the water and the protein are complementary, keeping the total solvation number of both ions nearly constant. Unsurprisingly, K+ have a higher propensity to occupy the aqueous pore than Cl-, consistent with the cation selectivity of the channel. However, further analysis suggests that ion-ion pairs play an important role. In particular, it is observed that the passage of Cl- occurs only in the presence of K+ counterions, and isolated K+ can move through the channel and permeate on their own. The presence of K+ in the pore screens the negative electrostatic potential arising from OmpF to help the translocation of Cl- by formation of ion pairs.
生成了一个5纳秒的全原子分子动力学轨迹，该轨迹描述了嵌入在由1M [KCl]盐水溶液浸泡的明确的二肉豆蔻酰磷脂酰胆碱（DMPC）双层中的大肠杆菌外膜孔蛋白F（OmpF），以探索离子渗透机制的微观细节。原子模型包括OmpF三聚体、124个DMPC、13470个水分子以及231个K⁺和201个Cl⁻，总共70693个原子。结构和动力学结果与X射线数据高度吻合。主链原子相对于X射线结构的全局均方根偏差为1.4埃。在水孔最窄部分的L3上，观察到一组三个完全带正电的精氨酸（Arg42、Arg82和Arg132）面向两个酸性残基（Asp113和Glu117），在晶体学构象中非常稳定。在孔的这个区域，由于这些残基产生的强横向静电场，水分子明显垂直于通道轴取向。在模拟过程中，孔的平均尺寸比X射线结构中的小，且有小的波动。未观察到导致孔门控的L3环的大的移动。值得注意的是，观察到K⁺和Cl⁻沿着孔轴遵循两条明显分开的平均路径，跨度近40埃。在单体中心，两条螺旋状路径呈左旋扭曲，从细胞外前庭到孔周质侧逆时针旋转180度。在孔中，离子的动态扩散常数相对于它们在本体溶剂中的值降低了约50%。对跨通道离子溶剂化的分析表明，水和蛋白质的贡献是互补的，使两种离子的总溶剂化数几乎保持不变。不出所料，K⁺比Cl⁻更倾向于占据水孔，这与通道的阳离子选择性一致。然而，进一步分析表明离子对起着重要作用。特别是，观察到Cl⁻的通过仅在存在K⁺反离子的情况下发生，孤立的K⁺可以穿过通道并自行渗透。孔中K⁺的存在屏蔽了由OmpF产生的负静电势，通过形成离子对来帮助Cl⁻的转运。
