|
|
Simulating the ion permeation and ion selection for a eukaryotic voltage-gated sodium channel NaVPaS |
Juanrong Zhang1,2, Wenzhi Mao1,2, Yanhui Ren1,2, Rui-Ning Sun1,2, Nieng Yan2,3(), Haipeng Gong1,2() |
1. MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China 2. Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China 3. State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China |
|
|
|
Corresponding Author(s):
Nieng Yan,Haipeng Gong
|
Issue Date: 11 June 2018
|
|
1 |
Ahmed M, Hasani HJ, Ganesan A, Houghton M, Barakat K (2017) Modeling the human Nav1.5 sodium channel: structural and mechanistic insights of ion permeation and drug blockade. Drug Design Development & Therapy 11:2301–2324
https://doi.org/10.2147/DDDT.S133944
|
2 |
Carnevale V, Treptow W, Klein ML (2011) Sodium Ion Binding Sites and Hydration in the Lumen of a Bacterial Ion Channel from Molecular Dynamics Simulations. Journal of Physical Chemistry Letters 2:2504–2508
https://doi.org/10.1021/jz2011379
|
3 |
Li Y, Gong H (2015) Theoretical and simulation studies on voltagegated sodium channels. Protein Cell 6:413–422
https://doi.org/10.1007/s13238-015-0152-6
|
4 |
Lindeberg T (1998) Edge detection and ridge detection with automatic scale selection. International Journal of Computer Vision 30:117–156
https://doi.org/10.1023/A:1008097225773
|
5 |
Mahdavi S, Kuyucak S (2015) Mechanism of Ion Permeation in Mammalian Voltage-Gated Sodium Channels. Plos One 10: e0133000
https://doi.org/10.1371/journal.pone.0133000
|
6 |
Mccusker EC, Bagnéris C, Naylor CE, Cole AR, D’Avanzo N, Nichols CG, Wallace BA (2012) Structure of a bacterial voltagegated sodium channel pore reveals mechanisms of opening and closing. Nature Communications 3:1102
https://doi.org/10.1038/ncomms2077
|
7 |
Mishchenko Y (2009) Automation of 3D reconstruction of neural tissue from large volume of conventional serial section transmission electron micrographs. Journal of Neuroscience Methods 176:276–289
https://doi.org/10.1016/j.jneumeth.2008.09.006
|
8 |
Pan AC, Sezer D, Roux B (2008) Finding transition pathways using the string method with swarms of trajectories. Journal of Physical Chemistry B 112:3432–3440
https://doi.org/10.1021/jp0777059
|
9 |
Payandeh J, Scheuer T, Zheng N, Catterall WA (2011) The crystal structure of a voltage-gated sodium channel. Nature 475:353
https://doi.org/10.1038/nature10238
|
10 |
Schlief T, Schönherr R, Imoto K, Heinemann SH (1996) Pore properties of rat brain II sodium channels mutated in the selectivity filter domain. European Biophysics Journal 25:75–91
https://doi.org/10.1007/s002490050020
|
11 |
Shen H, Zhou Q, Pan X, Li Z, Wu J, Yan N (2017) Structure of a eukaryotic voltage-gated sodium channel at near-atomic resolution. Science 355:eaal4326
https://doi.org/10.1126/science.aal4326
|
12 |
Sun YM, Favre I, Schild L, Moczydlowski E (1997) On the structural basis for size-selective permeation of organic cations through the voltage-gated sodium channel : effect of alanine mutations at the DEKA locus on selectivity, inhibition by Ca2+ and H+, and molecular sieving. Journal of General Physiology 110:693–715
https://doi.org/10.1085/jgp.110.6.693
|
13 |
Xia M, Liu H, Li Y, Yan N, Gong H (2013) The mechanism of Na+/K+ selectivity in mammalian voltage-gated sodium channels based on molecular dynamics simulation. Biophysical Journal 104:2401
https://doi.org/10.1016/j.bpj.2013.04.035
|
14 |
Yan Z, Zhou Q, Wang L, Wu J, Zhao Y, Huang G, Peng W, Shen H, Lei J, Yan N (2017) Structure of the Nav1.4-β1 complex from electric eel. Cell 170:470
https://doi.org/10.1016/j.cell.2017.06.039
|
15 |
Zhang X, Ren W, Decaen P, Yan C, Tao X, Tang L, Wang J, Hasegawa K, Kumasaka T, He J (2012) Crystal structure of an orthologue of the NaChBac voltage-gated sodium channel. Nature 486:130–134
https://doi.org/10.1038/nature11054
|
|
Viewed |
|
|
|
Full text
|
|
|
|
|
Abstract
|
|
|
|
|
Cited |
|
|
|
|
|
Shared |
|
|
|
|
|
Discussed |
|
|
|
|