Simulating the ion permeation and ion selection for a eukaryotic voltage-gated sodium channel Na_VPaS

References

[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

[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

[3] Li Y, Gong H (2015) Theoretical and simulation studies on voltagegated sodium channels. Protein Cell 6:413–422

[4] Lindeberg T (1998) Edge detection and ridge detection with automatic scale selection. International Journal of Computer Vision 30:117–156

[5] Mahdavi S, Kuyucak S (2015) Mechanism of Ion Permeation in Mammalian Voltage-Gated Sodium Channels. Plos One 10: e0133000

[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

[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

[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

[9] Payandeh J, Scheuer T, Zheng N, Catterall WA (2011) The crystal structure of a voltage-gated sodium channel. Nature 475:353

[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

[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

[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

[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

[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

[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

RIGHTS & PERMISSIONS

2018 The Author(s) 2018