Kraszewski Sebastian, Yesylevskyy Semen O, Boiteux Céline, Ramseyer Christophe, Kharkyanen Valery N
Institut UTINAM, Laboratoire de Physique Moléculaire, UMR CNRS 6213, Faculté des Sciences et Techniques, Université de Franche-Comté, 16 route de Gray, 25030 Besançon Cedex, La Bouloie, France.
Phys Chem Chem Phys. 2008 Apr 28;10(16):2249-55. doi: 10.1039/b719512e. Epub 2008 Feb 28.
We performed in-depth analysis of the forces which act on the K(+) ions in the selectivity filter of the KcsA channel in order to estimate the relative importance of static and dynamic influence of the filter wall and water molecules on ion permeation and selectivity. The forces were computed using the trajectories of all-atom molecular dynamics simulations. It is shown that the dynamics of the selectivity filter contributes about 3% to the net force acting on the ions and can be neglected in the studies focused on the macroscopic properties of the channel, such as the current. Among the filter atoms, only the pore-forming carbonyl groups can be considered as dynamic in the studies of microscopic events of conduction, while the dynamic effects from all other atoms are negligible. We also show that the dynamics of the water molecules in the filter can not be neglected. The fluctuating forces from the water molecules can be as strong as net forces from the pore walls and can effectively drive the ions through the local energy barriers in the filter.
我们对作用于KcsA通道选择性过滤器中K⁺离子的力进行了深入分析，以评估过滤器壁和水分子对离子渗透和选择性的静态和动态影响的相对重要性。这些力是使用全原子分子动力学模拟的轨迹计算得出的。结果表明，选择性过滤器的动力学对作用于离子的净力贡献约3%，在专注于通道宏观特性（如电流）的研究中可忽略不计。在过滤器原子中，在传导微观事件的研究中，只有成孔羰基可被视为动态的，而所有其他原子的动态影响可忽略不计。我们还表明，过滤器中水分子的动力学不可忽略。水分子的波动作用力可与孔壁的净力一样强，并能有效地驱动离子通过过滤器中的局部能垒。
