Department of Physics & Astronomy, Johns Hopkins University, Baltimore, MD 21218.
Laboratory of Computational Biology, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892.
Proc Natl Acad Sci U S A. 2023 Jun 27;120(26):e2220343120. doi: 10.1073/pnas.2220343120. Epub 2023 Jun 20.
In bacterial voltage-gated sodium channels, the passage of ions through the pore is controlled by a selectivity filter (SF) composed of four glutamate residues. The mechanism of selectivity has been the subject of intense research, with suggested mechanisms based on steric effects, and ion-triggered conformational change. Here, we propose an alternative mechanism based on ion-triggered shifts in p values of SF glutamates. We study the NaMs channel for which the open channel structure is available. Our free-energy calculations based on molecular dynamics simulations suggest that p values of the four glutamates are higher in solution of K ions than in solution of Na ions. Higher p in the presence of K stems primarily from the higher population of dunked conformations of the protonated Glu sidechain, which exhibit a higher p shift. Since p values are close to the physiological pH, this results in predominant population of the fully deprotonated state of glutamates in Na solution, while protonated states are predominantly populated in K solution. Through molecular dynamics simulations we calculate that the deprotonated state is the most conductive, the singly protonated state is less conductive, and the doubly protonated state has significantly reduced conductance. Thus, we propose that a significant component of selectivity is achieved through ion-triggered shifts in the protonation state, which favors more conductive states for Na ions and less conductive states for K ions. This mechanism also suggests a strong pH dependence of selectivity, which has been experimentally observed in structurally similar NaChBac channels.
在细菌电压门控钠离子通道中，离子通过孔道的传输由由四个谷氨酸残基组成的选择性过滤器 (SF) 控制。选择性的机制一直是激烈研究的主题，提出的机制基于空间效应和离子触发的构象变化。在这里，我们提出了一种基于 SF 谷氨酸 p 值离子触发变化的替代机制。我们研究了 NaMs 通道，其开放通道结构是可用的。我们基于分子动力学模拟的自由能计算表明，在 K 离子溶液中，四个谷氨酸的 p 值高于在 Na 离子溶液中的 p 值。在 K 存在下，p 值较高主要是由于质子化 Glu 侧链的 dunked 构象的更高比例，其表现出更高的 p 值变化。由于 p 值接近生理 pH 值，这导致在 Na 溶液中谷氨酸主要处于完全去质子化状态，而在 K 溶液中主要处于质子化状态。通过分子动力学模拟，我们计算出去质子化状态是最具导电性的，单质子化状态的导电性较低，而双质子化状态的导电性显著降低。因此，我们提出，选择性的一个重要组成部分是通过质子化状态的离子触发变化来实现的，这有利于 Na 离子的更具导电性状态和 K 离子的导电性较低状态。这种机制还表明选择性具有很强的 pH 依赖性，这在结构相似的 NaChBac 通道中已经得到了实验观察。
