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For: Ke S, Timin EN, Stary-Weinzinger A. Different inward and outward conduction mechanisms in NaVMs suggested by molecular dynamics simulations. PLoS Comput Biol 2014;10:e1003746. [PMID: 25079564 PMCID: PMC4117422 DOI: 10.1371/journal.pcbi.1003746] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 06/13/2014] [Indexed: 01/03/2023]  Open
Number Cited by Other Article(s)
1
Chen AY, Brooks BR, Damjanovic A. Ion channel selectivity through ion-modulated changes of selectivity filter pKa values. Proc Natl Acad Sci U S A 2023;120:e2220343120. [PMID: 37339196 PMCID: PMC10293820 DOI: 10.1073/pnas.2220343120] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 04/26/2023] [Indexed: 06/22/2023]  Open
2
Ives CM, Thomson NJ, Zachariae U. A cooperative knock-on mechanism underpins Ca2+-selective cation permeation in TRPV channels. J Gen Physiol 2023;155:213957. [PMID: 36943243 PMCID: PMC10038842 DOI: 10.1085/jgp.202213226] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 11/15/2022] [Accepted: 02/28/2023] [Indexed: 03/23/2023]  Open
3
Alberini G, Alexis Paz S, Corradi B, Abrams CF, Benfenati F, Maragliano L. Molecular Dynamics Simulations of Ion Permeation in Human Voltage-Gated Sodium Channels. J Chem Theory Comput 2023;19:2953-2972. [PMID: 37116214 DOI: 10.1021/acs.jctc.2c00990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
4
Zhu Z, Deng Z, Wang Q, Wang Y, Zhang D, Xu R, Guo L, Wen H. Simulation and Machine Learning Methods for Ion-Channel Structure Determination, Mechanistic Studies and Drug Design. Front Pharmacol 2022;13:939555. [PMID: 35837274 PMCID: PMC9275593 DOI: 10.3389/fphar.2022.939555] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022]  Open
5
Chen AY, Brooks BR, Damjanovic A. Determinants of conductance of a bacterial voltage-gated sodium channel. Biophys J 2021;120:3050-3069. [PMID: 34214541 DOI: 10.1016/j.bpj.2021.06.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/22/2021] [Accepted: 06/08/2021] [Indexed: 10/21/2022]  Open
6
Kumar S, Singh SK, Rana B, Rana A. The regulatory function of mixed lineage kinase 3 in tumor and host immunity. Pharmacol Ther 2021;219:107704. [PMID: 33045253 PMCID: PMC7887016 DOI: 10.1016/j.pharmthera.2020.107704] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/02/2020] [Indexed: 12/26/2022]
7
Strong SE, Hestand NJ, Kananenka AA, Zanni MT, Skinner JL. IR Spectroscopy Can Reveal the Mechanism of K+ Transport in Ion Channels. Biophys J 2019;118:254-261. [PMID: 31812356 DOI: 10.1016/j.bpj.2019.11.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/28/2019] [Accepted: 11/12/2019] [Indexed: 01/18/2023]  Open
8
Wang Y, Finol-Urdaneta RK, Ngo VA, French RJ, Noskov SY. Bases of Bacterial Sodium Channel Selectivity Among Organic Cations. Sci Rep 2019;9:15260. [PMID: 31649292 PMCID: PMC6813354 DOI: 10.1038/s41598-019-51605-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 10/03/2019] [Indexed: 12/15/2022]  Open
9
Flood E, Boiteux C, Lev B, Vorobyov I, Allen TW. Atomistic Simulations of Membrane Ion Channel Conduction, Gating, and Modulation. Chem Rev 2019;119:7737-7832. [DOI: 10.1021/acs.chemrev.8b00630] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
10
Callahan KM, Roux B. Molecular Dynamics of Ion Conduction through the Selectivity Filter of the NaVAb Sodium Channel. J Phys Chem B 2018;122:10126-10142. [PMID: 30351118 DOI: 10.1021/acs.jpcb.8b09678] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
11
Ke S, Ulmschneider MB, Wallace BA, Ulmschneider JP. Role of the Interaction Motif in Maintaining the Open Gate of an Open Sodium Channel. Biophys J 2018;115:1920-1930. [PMID: 30366630 DOI: 10.1016/j.bpj.2018.10.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 09/27/2018] [Accepted: 10/01/2018] [Indexed: 01/09/2023]  Open
12
Flood E, Boiteux C, Allen TW. Selective ion permeation involves complexation with carboxylates and lysine in a model human sodium channel. PLoS Comput Biol 2018;14:e1006398. [PMID: 30208027 PMCID: PMC6152994 DOI: 10.1371/journal.pcbi.1006398] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 09/24/2018] [Accepted: 07/24/2018] [Indexed: 12/21/2022]  Open
13
Boiteux C, Flood E, Allen TW. Comparison of permeation mechanisms in sodium-selective ion channels. Neurosci Lett 2018;700:3-8. [PMID: 29807068 DOI: 10.1016/j.neulet.2018.05.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 05/24/2018] [Accepted: 05/25/2018] [Indexed: 12/27/2022]
14
Olesen K, Awasthi N, Bruhn DS, Pezeshkian W, Khandelia H. Faster Simulations with a 5 fs Time Step for Lipids in the CHARMM Force Field. J Chem Theory Comput 2018;14:3342-3350. [PMID: 29750867 DOI: 10.1021/acs.jctc.8b00267] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
15
Ion-triggered selectivity in bacterial sodium channels. Proc Natl Acad Sci U S A 2018;115:5450-5455. [PMID: 29735669 DOI: 10.1073/pnas.1722516115] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]  Open
16
Zhekova HR, Ngo V, da Silva MC, Salahub D, Noskov S. Selective ion binding and transport by membrane proteins – A computational perspective. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2017.03.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
17
Li Y, Sun R, Liu H, Gong H. Molecular dynamics study of ion transport through an open model of voltage-gated sodium channel. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017;1859:879-887. [DOI: 10.1016/j.bbamem.2017.02.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 01/12/2017] [Accepted: 02/05/2017] [Indexed: 12/30/2022]
18
Ahern CA, Payandeh J, Bosmans F, Chanda B. The hitchhiker's guide to the voltage-gated sodium channel galaxy. ACTA ACUST UNITED AC 2016;147:1-24. [PMID: 26712848 PMCID: PMC4692491 DOI: 10.1085/jgp.201511492] [Citation(s) in RCA: 252] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
19
Domene C, Barbini P, Furini S. Bias-Exchange Metadynamics Simulations: An Efficient Strategy for the Analysis of Conduction and Selectivity in Ion Channels. J Chem Theory Comput 2016;11:1896-906. [PMID: 26574394 DOI: 10.1021/ct501053x] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
20
Vien TN, DeCaen PG. Biophysical Adaptations of Prokaryotic Voltage-Gated Sodium Channels. CURRENT TOPICS IN MEMBRANES 2016;78:39-64. [PMID: 27586280 DOI: 10.1016/bs.ctm.2015.12.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
21
Patel D, Mahdavi S, Kuyucak S. Computational Study of Binding of μ-Conotoxin GIIIA to Bacterial Sodium Channels NaVAb and NaVRh. Biochemistry 2016;55:1929-38. [PMID: 26959170 DOI: 10.1021/acs.biochem.5b01324] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
22
Oakes V, Furini S, Domene C. Voltage-Gated Sodium Channels: Mechanistic Insights From Atomistic Molecular Dynamics Simulations. CURRENT TOPICS IN MEMBRANES 2016;78:183-214. [PMID: 27586285 DOI: 10.1016/bs.ctm.2015.12.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
23
Ngo V, Wang Y, Haas S, Noskov SY, Farley RA. K+ Block Is the Mechanism of Functional Asymmetry in Bacterial Na(v) Channels. PLoS Comput Biol 2016;12:e1004482. [PMID: 26727271 PMCID: PMC4700994 DOI: 10.1371/journal.pcbi.1004482] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 07/27/2015] [Indexed: 02/07/2023]  Open
24
Ing C, Pomès R. Simulation Studies of Ion Permeation and Selectivity in Voltage-Gated Sodium Channels. CURRENT TOPICS IN MEMBRANES 2016;78:215-60. [DOI: 10.1016/bs.ctm.2016.07.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
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