Lee W K, Jordan P C
Biophys J. 1984 Dec;46(6):805-19. doi: 10.1016/S0006-3495(84)84079-5.
A model calculation is carried out to study the potential energy profile of a sodium ion with several water molecules inside a simplified model of the gramicidin ion channel. The sodium ion is treated as a Lennard-Jones sphere with a point charge at its center. The Barnes polarizable water model is used to mimic the water molecules. A polarizable and deformable gramicidinlike channel is constructed based on the model obtained by Koeppe and Kimura. Potential minima and saddle points are located and the static energy barriers are computed. The potential minima at the two mouths of the channel exhibit an aqueous solvation structure very different from that at any of the interior minima. These sites are approximately 23.6 and 24.4 A apart for binding of a sodium ion and a cesium ion, respectively. Ionic motion from these exterior sites to the first interior minimum requires substantial rearrangement of the waters of solvation; this rearrangement may be the hydration/dehydration step in ionic permeation through the channel. Based on these results, a mechanism by which the sodium ion moves from the exterior binding site to the interior of the channel is proposed. Our model channel accommodates about eight water molecules and the transport of the ion and water within the channel is found to be single file. Results of less extensive calculations for Cs+ and Li+ ions in a channel with or without water are also reported.
进行了模型计算，以研究在短杆菌肽离子通道的简化模型中，带有几个水分子的钠离子的势能分布。钠离子被视为一个 Lennard-Jones 球体，其中心带有一个点电荷。采用 Barnes 可极化水模型来模拟水分子。基于 Koeppe 和 Kimura 获得的模型构建了一个可极化且可变形的类短杆菌肽通道。确定了势能极小值和鞍点，并计算了静态能垒。通道两端的势能极小值处呈现出与任何内部极小值处截然不同的水合溶剂化结构。对于钠离子和铯离子的结合，这些位点分别相距约 23.6 和 24.4 Å。离子从这些外部位点移动到第一个内部极小值需要溶剂化水的大量重排；这种重排可能是离子通过通道渗透时的水合/脱水步骤。基于这些结果，提出了钠离子从外部结合位点移动到通道内部的机制。我们的模型通道容纳约八个水分子，并且发现离子和水在通道内的传输是单排的。还报告了在有水或无水通道中对 Cs+ 和 Li+ 离子进行的不太广泛的计算结果。
