Ion Bogdan F, Wells Marta M, Chen Qiang, Xu Yan, Tang Pei
Departments of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania.
Departments of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania.
Biophys J. 2017 Aug 8;113(3):605-612. doi: 10.1016/j.bpj.2017.06.041.
Ketamine inhibits pentameric ligand-gated ion channels (pLGICs), including the bacterial pLGIC from Gloeobacter violaceus (GLIC). The crystal structure of GLIC shows R-ketamine bound to an extracellular intersubunit cavity. Here, we performed molecular dynamics simulations of GLIC in the absence and presence of R- or S-ketamine. No stable binding of S-ketamine in the original cavity was observed in the simulations, largely due to its unfavorable access to residue D154, which provides important electrostatic interactions to stabilize R-ketamine binding. Contrary to the symmetric binding shown in the crystal structure, R-ketamine moved away from some of the binding sites and was bound to GLIC asymmetrically at the end of simulations. The asymmetric binding is consistent with the experimentally measured negative cooperativity of ketamine binding to GLIC. In the presence of R-ketamine, all subunits showed changes in structure and dynamics, irrespective of binding stability; the extracellular intersubunit cavity expanded and intersubunit electrostatic interactions involved in channel activation were altered. R-ketamine binding promoted a conformational shift toward closed GLIC. Conformational changes near the ketamine-binding site were propagated to the interface between the extracellular and transmembrane domains, and further to the pore-lining TM2 through two pathways: pre-TM1 and the β1-β2 loop. Both signaling pathways have been predicted previously using the perturbation-based Markovian transmission model. The study provides a structural and dynamics basis for the inhibitory modulation of ketamine on pLGICs.
氯胺酮可抑制五聚体配体门控离子通道（pLGICs），包括来自紫球藻（Gloeobacter violaceus, GLIC）的细菌pLGIC。GLIC的晶体结构显示R-氯胺酮与细胞外亚基间腔结合。在此，我们对不存在和存在R-或S-氯胺酮的情况下的GLIC进行了分子动力学模拟。在模拟中未观察到S-氯胺酮在原始腔中的稳定结合，这主要是由于其难以接近残基D154，而D154提供重要的静电相互作用以稳定R-氯胺酮的结合。与晶体结构中显示的对称结合相反，R-氯胺酮从一些结合位点移开，并在模拟结束时与GLIC不对称结合。这种不对称结合与实验测量的氯胺酮与GLIC结合的负协同性一致。在存在R-氯胺酮的情况下，所有亚基均显示出结构和动力学变化，而与结合稳定性无关；细胞外亚基间腔扩大，参与通道激活的亚基间静电相互作用发生改变。R-氯胺酮结合促进了向关闭的GLIC的构象转变。氯胺酮结合位点附近的构象变化通过两条途径传播到细胞外和跨膜结构域之间的界面，并进一步传播到孔衬里TM2：TM1前体和β1-β2环。这两条信号通路先前已使用基于微扰的马尔可夫传输模型进行了预测。该研究为氯胺酮对pLGICs的抑制性调节提供了结构和动力学基础。
