Catalysis of Na+ permeation in the bacterial sodium channel NaVAb
Catalysis of Na+ permeation in the bacterial sodium channel NaVAb
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DOI：
10.1073/pnas.1309452110
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发表时间：
2013-07-09
影响因子：
11.1
通讯作者：
Pomes, Regis
中科院分区：
文献类型：
--
作者：
Chakrabarti, Nilmadhab;Ing, Christopher;Pomes, Regis
电压门控钠通道NaVAb的高分辨率3D结构的确定为阐明离子电导和选择性的机制开辟了道路。为了检查Na+通过通道的选择性过滤器的渗透，我们进行了大规模的分子动力学模拟NaVAb在一个明确的，水合脂质双层在0 mV，在150 mM NaCl，为21.6 μ s的总模拟时间。虽然孔的细胞质端是封闭的，但在模拟过程中自发地发生了Na+通过选择性过滤器的可逆流入和流出，导致Na+在细胞外介质和通道的中心腔之间的平衡运动。Na+动力学分析揭示了离子渗透的撞击机制，其特征在于通道被2个和3个Na+离子交替占据，计算出的易位速率为（6 +/- 1）x 10（6）个离子.s（-1），与电生理学研究的预期一致。Na+的结合与选择性过滤器细胞外末端内衬的四个E177侧链的构象异构化密切相关。可变数目的Na+离子和羧酸根基团的相互协调导致它们缩合成可变电荷和空间排列的离子簇。这些离子簇的结构波动导致无数的离子结合模式，并促进高度简并，类液体的能量景观有利于Na+扩散。通过稳定多个离子占据状态，同时帮助Na+离子在选择性过滤器内扩散，E177侧链的构象灵活性支持Na+渗透的连锁机制。
Determination of a high-resolution 3D structure of voltage-gated sodium channel NaVAb opens the way to elucidating the mechanism of ion conductance and selectivity. To examine permeation of Na+ through the selectivity filter of the channel, we performed large-scale molecular dynamics simulations of NaVAb in an explicit, hydrated lipid bilayer at 0 mV in 150 mM NaCl, for a total simulation time of 21.6 mu s. Although the cytoplasmic end of the pore is closed, reversible influx and efflux of Na+ through the selectivity filter occurred spontaneously during simulations, leading to equilibrium movement of Na+ between the extracellular medium and the central cavity of the channel. Analysis of Na+ dynamics reveals a knock-on mechanism of ion permeation characterized by alternating occupancy of the channel by 2 and 3 Na+ ions, with a computed rate of translocation of (6 +/- 1) x 10(6) ions.s(-1) that is consistent with expectations from electrophysiological studies. The binding of Na+ is intimately coupled to conformational isomerization of the four E177 side chains lining the extracellular end of the selectivity filter. The reciprocal coordination of variable numbers of Na+ ions and carboxylate groups leads to their condensation into ionic clusters of variable charge and spatial arrangement. Structural fluctuations of these ionic clusters result in a myriad of ion binding modes and foster a highly degenerate, liquidlike energy landscape propitious to Na+ diffusion. By stabilizing multiple ionic occupancy states while helping Na+ ions diffuse within the selectivity filter, the conformational flexibility of E177 side chains underpins the knock-on mechanism of Na+ permeation.