1
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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: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
The recent determination of cryo-EM structures of voltage-gated sodium (Nav) channels has revealed many details of these proteins. However, knowledge of ionic permeation through the Nav pore remains limited. In this work, we performed atomistic molecular dynamics (MD) simulations to study the structural features of various neuronal Nav channels based on homology modeling of the cryo-EM structure of the human Nav1.4 channel and, in addition, on the recently resolved configuration for Nav1.2. In particular, single Na+ permeation events during standard MD runs suggest that the ion resides in the inner part of the Nav selectivity filter (SF). On-the-fly free energy parametrization (OTFP) temperature-accelerated molecular dynamics (TAMD) was also used to calculate two-dimensional free energy surfaces (FESs) related to single/double Na+ translocation through the SF of the homology-based Nav1.2 model and the cryo-EM Nav1.2 structure, with different realizations of the DEKA filter domain. These additional simulations revealed distinct mechanisms for single and double Na+ permeation through the wild-type SF, which has a charged lysine in the DEKA ring. Moreover, the configurations of the ions in the SF corresponding to the metastable states of the FESs are specific for each SF motif. Overall, the description of these mechanisms gives us new insights into ion conduction in human Nav cryo-EM-based and cryo-EM configurations that could advance understanding of these systems and how they differ from potassium and bacterial Nav channels.
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Affiliation(s)
- Giulio Alberini
- Center for Synaptic Neuroscience and Technology (NSYN@UniGe), Istituto Italiano di Tecnologia, Largo Rosanna Benzi 10, 16132 Genova, Italy
- IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132 Genova, Italy
| | - Sergio Alexis Paz
- Departamento de Química Teórica y Computacional, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, X5000HUA Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Fisicoquímica de Córdoba (INFIQC), X5000HUA Córdoba, Argentina
| | - Beatrice Corradi
- Center for Synaptic Neuroscience and Technology (NSYN@UniGe), Istituto Italiano di Tecnologia, Largo Rosanna Benzi 10, 16132 Genova, Italy
- Department of Experimental Medicine, Università degli Studi di Genova, Viale Benedetto XV 3, 16132 Genova, Italy
| | - Cameron F Abrams
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Fabio Benfenati
- Center for Synaptic Neuroscience and Technology (NSYN@UniGe), Istituto Italiano di Tecnologia, Largo Rosanna Benzi 10, 16132 Genova, Italy
- IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132 Genova, Italy
| | - Luca Maragliano
- Center for Synaptic Neuroscience and Technology (NSYN@UniGe), Istituto Italiano di Tecnologia, Largo Rosanna Benzi 10, 16132 Genova, Italy
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
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2
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Groome JR. Historical Perspective of the Characterization of Conotoxins Targeting Voltage-Gated Sodium Channels. Mar Drugs 2023; 21:md21040209. [PMID: 37103349 PMCID: PMC10142487 DOI: 10.3390/md21040209] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/21/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023] Open
Abstract
Marine toxins have potent actions on diverse sodium ion channels regulated by transmembrane voltage (voltage-gated ion channels) or by neurotransmitters (nicotinic acetylcholine receptor channels). Studies of these toxins have focused on varied aspects of venom peptides ranging from evolutionary relationships of predator and prey, biological actions on excitable tissues, potential application as pharmacological intervention in disease therapy, and as part of multiple experimental approaches towards an understanding of the atomistic characterization of ion channel structure. This review examines the historical perspective of the study of conotoxin peptides active on sodium channels gated by transmembrane voltage, which has led to recent advances in ion channel research made possible with the exploitation of the diversity of these marine toxins.
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Affiliation(s)
- James R Groome
- Department of Biological Sciences, Idaho State University, Pocatello, ID 83209, USA
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3
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Li X, Jiang G, Jian M, Zhao C, Hou J, Thornton AW, Zhang X, Liu JZ, Freeman BD, Wang H, Jiang L, Zhang H. Construction of angstrom-scale ion channels with versatile pore configurations and sizes by metal-organic frameworks. Nat Commun 2023; 14:286. [PMID: 36653373 PMCID: PMC9849445 DOI: 10.1038/s41467-023-35970-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 01/11/2023] [Indexed: 01/19/2023] Open
Abstract
Controllable fabrication of angstrom-size channels has been long desired to mimic biological ion channels for the fundamental study of ion transport. Here we report a strategy for fabricating angstrom-scale ion channels with one-dimensional (1D) to three-dimensional (3D) pore structures by the growth of metal-organic frameworks (MOFs) into nanochannels. The 1D MIL-53 channels of flexible pore sizes around 5.2 × 8.9 Å can transport cations rapidly, with one to two orders of magnitude higher conductivities and mobilities than MOF channels of hybrid pore configurations and sizes, including Al-TCPP with 1D ~8 Å channels connected by 2D ~6 Å interlayers, and 3D UiO-66 channels of ~6 Å windows and 9 - 12 Å cavities. Furthermore, the 3D MOF channels exhibit better ion sieving properties than those of 1D and 2D MOF channels. Theoretical simulations reveal that ion transport through 2D and 3D MOF channels should undergo multiple dehydration-rehydration processes, resulting in higher energy barriers than pure 1D channels. These findings offer a platform for studying ion transport properties at angstrom-scale confinement and provide guidelines for improving the efficiency of ionic separations and nanofluidics.
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Affiliation(s)
- Xingya Li
- grid.1002.30000 0004 1936 7857Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800 Australia
| | - Gengping Jiang
- grid.412787.f0000 0000 9868 173XCollege of Science, Wuhan University of Science and Technology, Wuhan, 430072 China
| | - Meipeng Jian
- grid.1002.30000 0004 1936 7857Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800 Australia
| | - Chen Zhao
- grid.1017.70000 0001 2163 3550Chemical and Environmental Engineering, School of Engineering, RMIT University, Melbourne, VIC 3000 Australia
| | - Jue Hou
- grid.1017.70000 0001 2163 3550Chemical and Environmental Engineering, School of Engineering, RMIT University, Melbourne, VIC 3000 Australia
| | - Aaron W. Thornton
- grid.1016.60000 0001 2173 2719Manufacturing, CSIRO, Clayton, VIC 3168 Australia
| | - Xinyi Zhang
- grid.34418.3a0000 0001 0727 9022Hubei Key Laboratory of Ferro- & Piezoelectric Materials and Devices, Faculty of Physics & Electronic Science, Hubei University, Wuhan, 430062 China
| | - Jefferson Zhe Liu
- grid.1008.90000 0001 2179 088XDepartment of Mechanical Engineering, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Benny D. Freeman
- grid.1002.30000 0004 1936 7857Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800 Australia ,grid.89336.370000 0004 1936 9924Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712 USA
| | - Huanting Wang
- grid.1002.30000 0004 1936 7857Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800 Australia
| | - Lei Jiang
- grid.1002.30000 0004 1936 7857Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800 Australia
| | - Huacheng Zhang
- grid.1017.70000 0001 2163 3550Chemical and Environmental Engineering, School of Engineering, RMIT University, Melbourne, VIC 3000 Australia
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Ma L, Han X, Zhang S, Zeng Z, Song R, Chen X, Hou D, Wang L. Artificial Monovalent Metal Ion-Selective Fluidic Devices Based on Crown Ether@Metal-Organic Frameworks with Subnanochannels. ACS APPLIED MATERIALS & INTERFACES 2022; 14:13611-13621. [PMID: 35259870 DOI: 10.1021/acsami.1c24573] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Precise regulation of ion transport through nanoscale pores will profoundly impact diverse fields from separation to energy conversion but is still challenging to achieve in artificial ion channels. Herein, inspired by the exquisite ion selectivity of biological Na+ channels, we have successfully fabricated hierarchically grown metal-organic frameworks (MOFs) on an asymmetrical substrate assisted by atomically thin nanoporous graphene. Efficient separation of monovalent metal ions is realized by encapsulating 18-crown-6 into MOF crystals. The resulting 18-crown-6@ZIF-67/ZIF-8 device, with subnanochannels and specific K+ binding sites, shows an ultrahigh Li+ conductivity of 1.46 × 10-2 S cm-1 and selectivities of 9.56 and 6.43 for Li+/K+ and Na+/K+, respectively. The Li+ conductivity is around 1-2 orders of magnitude higher than reported values for the other MOF materials. It is the first time that MOFs with subnanochannels realize selective transport of Na+ (ionic diameter of 1.9 Å) over K+ (2.6 Å) based on subangstrom differences in their ionic diameter. Our work opens new avenues to develop crown ether@MOF platforms toward efficient ion transistors, fluidic logic devices, and biosensors.
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Affiliation(s)
- Liang Ma
- Institute of microelectronics, School of Electronics Engineering and Computer Science, Peking University, Beijing 100871, PR China
| | - Xiao Han
- Institute of microelectronics, School of Electronics Engineering and Computer Science, Peking University, Beijing 100871, PR China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, PR China
| | - Shengping Zhang
- Institute of microelectronics, School of Electronics Engineering and Computer Science, Peking University, Beijing 100871, PR China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, PR China
| | - Zhiyang Zeng
- Institute of microelectronics, School of Electronics Engineering and Computer Science, Peking University, Beijing 100871, PR China
| | - Ruiyang Song
- Institute of microelectronics, School of Electronics Engineering and Computer Science, Peking University, Beijing 100871, PR China
| | - Xiaobo Chen
- Institute of microelectronics, School of Electronics Engineering and Computer Science, Peking University, Beijing 100871, PR China
| | - Dandan Hou
- Institute of microelectronics, School of Electronics Engineering and Computer Science, Peking University, Beijing 100871, PR China
| | - Luda Wang
- Institute of microelectronics, School of Electronics Engineering and Computer Science, Peking University, Beijing 100871, PR China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, PR China
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5
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Linsdell P, Irving CL, Cowley EA. Functionally Additive Fixed Positive and Negative Charges in the CFTR Channel Pore Control Anion Binding and Conductance. J Biol Chem 2022; 298:101659. [PMID: 35101441 PMCID: PMC8881524 DOI: 10.1016/j.jbc.2022.101659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/14/2022] [Accepted: 01/26/2022] [Indexed: 11/17/2022] Open
Abstract
Ion channels use charged amino-acid residues to attract oppositely charged permeant ions into the channel pore. In the cystic fibrosis transmembrane conductance regulator (CFTR) Cl− channel, a number of arginine and lysine residues have been shown to be important for Cl− permeation. Among these, two in close proximity in the pore—Lys95 and Arg134—are indispensable for anion binding and high Cl− conductance, suggesting that high positive charge density is required for pore function. Here we used mutagenesis and functional characterization to show that a nearby pore-lining negatively charged residue (Glu92) plays a functionally additive role with these two positive charges. While neutralization of this negative charge had little effect on anion binding or Cl− conductance, such neutralization was able to reverse the detrimental effects of removing the positive charge at either Lys95 or Arg134, as well as the similar effects of introducing a negative charge at a neighboring residue (Ser1141). Furthermore, neutralization of Glu92 greatly increased the susceptibility of the channel to blockage by divalent S2O32− anions, mimicking the effect of introducing additional positive charge in this region; this effect was reversed by concurrent neutralization of either Lys95 or Arg134. Across a panel of mutant channels that introduced or removed fixed charges at these four positions, we found that many pore properties are dependent on the overall charge or charge density. We propose that the CFTR pore uses a combination of positively and negatively charged residues to optimize the anion binding and Cl− conductance properties of the channel.
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Affiliation(s)
- Paul Linsdell
- Department of Physiology & Biophysics, Dalhousie University, Halifax, Nova Scotia, Canada.
| | - Christina L Irving
- Department of Physiology & Biophysics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Elizabeth A Cowley
- Department of Physiology & Biophysics, Dalhousie University, Halifax, Nova Scotia, Canada
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6
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Mikhailova VB, Karpushev AV, Vavilova VD, Klimenko ES, Tulintseva T, Yudina YS, Vasichkina ES, Zhorov BS, Kostareva A. Functional Analysis of SCN5A Genetic Variants Associated with Brugada Syndrome. Cardiology 2021; 147:35-46. [PMID: 34628415 DOI: 10.1159/000519857] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 09/23/2021] [Indexed: 11/19/2022]
Abstract
BACKGROUND Brugada syndrome (BrS) is a rare inherited cardiac arrhythmia with increased risk of sudden cardiac death. Mutations in gene SCN5A, which encodes the α-subunit of cardiac voltage-gated sodium channel NaV1.5, have been identified in over 20% of patients with BrS. However, only a small fraction of NaV1.5 variants, which are associated with BrS, are characterized in electrophysiological experiments. RESULTS Here we explored variants V281A and L1582P, which were found in our patients with BrS, and variants F543L and K1419E, which are reportedly associated with BrS. Heterologous expression of the variants in CHO-K1 cells and the Western blot analysis demonstrated that each variant appeared at the cell surface. We further measured sodium current in the whole-cell voltage clamp configuration. Variant F543L produced robust sodium current with a hyperpolarizing shift in the voltage dependence of steady-state fast inactivation. Other variants did not produce detectable sodium currents, indicating a complete loss of function. In a recent cryoEM structure of the hNaV1.5 channel, residues V281, K1419, and L1582 are in close contacts with residues whose mutations are reportedly associated with BrS, indicating functional importance of respective contacts. CONCLUSIONS Our results support the notion that loss of function of NaV1.5 or decrease of the channel activity is involved in the pathogenesis of BrS.
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Affiliation(s)
| | - Alexey V Karpushev
- Almazov National Medical Research Centre, St. Petersburg, Russian Federation
| | - Viola D Vavilova
- Almazov National Medical Research Centre, St. Petersburg, Russian Federation
| | | | - Tatyana Tulintseva
- Almazov National Medical Research Centre, St. Petersburg, Russian Federation
| | - Yulia S Yudina
- Almazov National Medical Research Centre, St. Petersburg, Russian Federation
| | - Elena S Vasichkina
- Almazov National Medical Research Centre, St. Petersburg, Russian Federation
| | - Boris S Zhorov
- Almazov National Medical Research Centre, St. Petersburg, Russian Federation.,Sechenov Institute of Evolutionary Physiology and Biochemistry, RAS, St. Petersburg, Russian Federation.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Anna Kostareva
- Almazov National Medical Research Centre, St. Petersburg, Russian Federation.,Karolinska Institute, Stockholm, Sweden
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7
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Zhorov BS. Possible Mechanism of Ion Selectivity in Eukaryotic Voltage-Gated Sodium Channels. J Phys Chem B 2021; 125:2074-2088. [DOI: 10.1021/acs.jpcb.0c11181] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Boris S. Zhorov
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8K 4K1, Canada
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, St. Petersburg 194223, Russian Federation
- Almazov National Medical Research Centre, St. Petersburg 197341, Russian Federation
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8
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Abstract
Voltage gated sodium channels (VGSC) are implicated in cancer cell invasion and metastasis. However, the mechanism by which VGSC increase cell invasiveness and probability of metastasis is still unknown. In this review we outline lesser known functions of VGSC outside of action potential propagation, and the current understanding of the effects of VGSC in cancer. Finally, we discuss possible downstream effects of VGSC activation in cancer cells. After extensive review of the literature, the most likely role of VGSC in cancer is in the invadopodia, the leading edge of metastatic cancer cells. Sodium gradients are used to drive many biological processes in the body, and invadopodia may be similar. The function of the sodium hydrogen exchanger (NHE) and sodium calcium exchanger (NCX) are driven by sodium gradients. Voltage gated calcium channels, activated by membrane depolarization, are also capable of becoming activated in response to VGSC activity. Changes to hydrogen ion exchange or calcium handling have functional consequences for invadopodia and would explain the relationship between VGSC expression and invasiveness of cancer cells.
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Affiliation(s)
- Madeline Angus
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University , Burnaby , BC , Canada
| | - Peter Ruben
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University , Burnaby , BC , Canada
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9
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Denomme N, Hull JM, Mashour GA. Role of Voltage-Gated Sodium Channels in the Mechanism of Ether-Induced Unconsciousness. Pharmacol Rev 2019; 71:450-466. [PMID: 31471460 DOI: 10.1124/pr.118.016592] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Despite continuous clinical use for more than 170 years, the mechanism of general anesthetics has not been completely characterized. In this review, we focus on the role of voltage-gated sodium channels in the sedative-hypnotic actions of halogenated ethers, describing the history of anesthetic mechanisms research, the basic neurobiology and pharmacology of voltage-gated sodium channels, and the evidence for a mechanistic interaction between halogenated ethers and sodium channels in the induction of unconsciousness. We conclude with a more integrative perspective of how voltage-gated sodium channels might provide a critical link between molecular actions of the halogenated ethers and the more distributed network-level effects associated with the anesthetized state across species.
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Affiliation(s)
- Nicholas Denomme
- Departments of Pharmacology (N.D.) and Anesthesiology (G.A.M.), Center for Consciousness Science (N.D., G.A.M.), and Neuroscience Graduate Program (J.M.H., G.A.M.), University of Michigan, Ann Arbor, Michigan
| | - Jacob M Hull
- Departments of Pharmacology (N.D.) and Anesthesiology (G.A.M.), Center for Consciousness Science (N.D., G.A.M.), and Neuroscience Graduate Program (J.M.H., G.A.M.), University of Michigan, Ann Arbor, Michigan
| | - George A Mashour
- Departments of Pharmacology (N.D.) and Anesthesiology (G.A.M.), Center for Consciousness Science (N.D., G.A.M.), and Neuroscience Graduate Program (J.M.H., G.A.M.), University of Michigan, Ann Arbor, Michigan
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10
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Li R, Lu B, Xie Z, Zhai J. The Confinement Effect of Angstrom-Sized Pores in Asymmetrical Membrane Constructed by Zeolitic Imidazolate Frameworks: Partially Dehydrated Ion Transport Performance. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1904866. [PMID: 31778019 DOI: 10.1002/smll.201904866] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/29/2019] [Indexed: 06/10/2023]
Abstract
The confinement effect in asymmetrical biological ion channels makes the state of molecules and ions differs from that in the external environment, and the mass transfer confined in the biological ion channels is in a single strand form. Herein, an asymmetrical membrane with angstrom-sized pores is constructed by growth of ZIF-90 membrane on the porous anodic aluminum oxide film. Due to the confinement effect of angstrom-sized pores of ZIF-90, ions transport through the pores of ZIF-90 suffer from multiple dehydration-hydration-dehydration process in the form of a single ionic chain. Molecular dynamics simulations imply that ions inside the pores of ZIF-90 are partially dehydrated. In alkaline condition, high rectification ratios of 237, 295, and 357 can be achieved in 10 × 10-3 m KCl, NaCl, and LiCl electrolyte, respectively. Besides, the strong electrostatic interaction between ions and the confined ZIF-90 pores makes the ions transport through the asymmetrical membrane suffer from an energy barrier, and the energy barrier is different with different ion species. This work helps to understand the ions transfer mechanism through angstrom-sized pores, which can provide guidance for the design of asymmetrical membrane and boost their applications.
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Affiliation(s)
- Ruirui Li
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Chemistry, Beihang University, Beijing, 100191, P. R. China
| | - Bingxin Lu
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Chemistry, Beihang University, Beijing, 100191, P. R. China
| | - Zhiqiang Xie
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Chemistry, Beihang University, Beijing, 100191, P. R. China
| | - Jin Zhai
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Chemistry, Beihang University, Beijing, 100191, P. R. China
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11
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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: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Emelie Flood
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia
| | - Céline Boiteux
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia
| | - Bogdan Lev
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia
| | - Igor Vorobyov
- Department of Physiology & Membrane Biology/Department of Pharmacology, University of California, Davis, 95616, United States
| | - Toby W. Allen
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia
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12
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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: 0.8] [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]
Abstract
Voltage-gated sodium channels are the molecular components of electrical signaling in the body, yet the molecular origins of Na+-selective transport remain obscured by diverse protein chemistries within this family of ion channels. In particular, bacterial and mammalian sodium channels are known to exhibit similar relative ion permeabilities for Na+ over K+ ions, despite their distinct signature EEEE and DEKA sequences. Atomic-level molecular dynamics simulations using high-resolution bacterial channel structures and mammalian channel models have begun to describe how these sequences lead to analogous high field strength ion binding sites that drive Na+ conduction. Similar complexes have also been identified in unrelated acid sensing ion channels involving glutamate and aspartate side chains that control their selectivity. These studies suggest the possibility of a common origin for Na+ selective binding and transport.
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Affiliation(s)
- Céline Boiteux
- School of Science, RMIT University, Melbourne, Australia
| | - Emelie Flood
- School of Science, RMIT University, Melbourne, Australia
| | - Toby W Allen
- School of Science, RMIT University, Melbourne, Australia.
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13
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Zhang H, Hou J, Hu Y, Wang P, Ou R, Jiang L, Liu JZ, Freeman BD, Hill AJ, Wang H. Ultrafast selective transport of alkali metal ions in metal organic frameworks with subnanometer pores. SCIENCE ADVANCES 2018; 4:eaaq0066. [PMID: 29487910 PMCID: PMC5817922 DOI: 10.1126/sciadv.aaq0066] [Citation(s) in RCA: 222] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Accepted: 01/11/2018] [Indexed: 05/18/2023]
Abstract
Porous membranes with ultrafast ion permeation and high ion selectivity are highly desirable for efficient mineral separation, water purification, and energy conversion, but it is still a huge challenge to efficiently separate monatomic ions of the same valence and similar sizes using synthetic membranes. We report metal organic framework (MOF) membranes, including ZIF-8 and UiO-66 membranes with uniform subnanometer pores consisting of angstrom-sized windows and nanometer-sized cavities for ultrafast selective transport of alkali metal ions. The angstrom-sized windows acted as ion selectivity filters for selection of alkali metal ions, whereas the nanometer-sized cavities functioned as ion conductive pores for ultrafast ion transport. The ZIF-8 and UiO-66 membranes showed a LiCl/RbCl selectivity of ~4.6 and ~1.8, respectively, which are much greater than the LiCl/RbCl selectivity of 0.6 to 0.8 measured in traditional porous membranes. Molecular dynamics simulations suggested that ultrafast and selective ion transport in ZIF-8 was associated with partial dehydration effects. This study reveals ultrafast and selective transport of monovalent ions in subnanometer MOF pores and opens up a new avenue to develop unique MOF platforms for efficient ion separations in the future.
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Affiliation(s)
- Huacheng Zhang
- Department of Chemical Engineering, Monash University, Melbourne, Victoria 3800, Australia
- Corresponding author. (H.Z.); (J.Z.L.); (H.W.)
| | - Jue Hou
- Department of Chemical Engineering, Monash University, Melbourne, Victoria 3800, Australia
| | - Yaoxin Hu
- Department of Chemical Engineering, Monash University, Melbourne, Victoria 3800, Australia
| | - Peiyao Wang
- Department of Mechanical and Aerospace Engineering, Monash University, Melbourne, Victoria 3800, Australia
| | - Ranwen Ou
- Department of Chemical Engineering, Monash University, Melbourne, Victoria 3800, Australia
| | - Lei Jiang
- Department of Chemical Engineering, Monash University, Melbourne, Victoria 3800, Australia
- Key Laboratory of Bioinspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
| | - Jefferson Zhe Liu
- Department of Mechanical and Aerospace Engineering, Monash University, Melbourne, Victoria 3800, Australia
- Corresponding author. (H.Z.); (J.Z.L.); (H.W.)
| | - Benny D. Freeman
- Department of Chemical Engineering, The University of Texas at Austin, 200 E. Dean Keeton Street, Austin, TX 78712, USA
| | - Anita J. Hill
- Future Industries, Commonwealth Scientific and Industrial Research Organization, Private Bag 10, Clayton South MDC, Victoria 3169, Australia
| | - Huanting Wang
- Department of Chemical Engineering, Monash University, Melbourne, Victoria 3800, Australia
- Corresponding author. (H.Z.); (J.Z.L.); (H.W.)
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Ahmed M, Jalily Hasani H, Ganesan A, Houghton M, Barakat K. Modeling the human Na v1.5 sodium channel: structural and mechanistic insights of ion permeation and drug blockade. Drug Des Devel Ther 2017; 11:2301-2324. [PMID: 28831242 PMCID: PMC5552146 DOI: 10.2147/dddt.s133944] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Abnormalities in the human Nav1.5 (hNav1.5) voltage-gated sodium ion channel (VGSC) are associated with a wide range of cardiac problems and diseases in humans. Current structural models of hNav1.5 are still far from complete and, consequently, their ability to study atomistic interactions of this channel is very limited. Here, we report a comprehensive atomistic model of the hNav1.5 ion channel, constructed using homology modeling technique and refined through long molecular dynamics simulations (680 ns) in the lipid membrane bilayer. Our model was comprehensively validated by using reported mutagenesis data, comparisons with previous models, and binding to a panel of known hNav1.5 blockers. The relatively long classical MD simulation was sufficient to observe a natural sodium permeation event across the channel's selectivity filters to reach the channel's central cavity, together with the identification of a unique role of the lysine residue. Electrostatic potential calculations revealed the existence of two potential binding sites for the sodium ion at the outer selectivity filters. To obtain further mechanistic insight into the permeation event from the central cavity to the intracellular region of the channel, we further employed "state-of-the-art" steered molecular dynamics (SMD) simulations. Our SMD simulations revealed two different pathways through which a sodium ion can be expelled from the channel. Further, the SMD simulations identified the key residues that are likely to control these processes. Finally, we discuss the potential binding modes of a panel of known hNav1.5 blockers to our structural model of hNav1.5. We believe that the data presented here will enhance our understanding of the structure-property relationships of the hNav1.5 ion channel and the underlying molecular mechanisms in sodium ion permeation and drug interactions. The results presented here could be useful for designing safer drugs that do not block the hNav1.5 channel.
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Affiliation(s)
| | | | | | - Michael Houghton
- Li Ka Shing Institute of Virology
- Li Ka Shing Applied Virology Institute
- Department of Medical Microbiology and Immunology, Katz Centre for Health Research, University of Alberta, Edmonton, AB, Canada
| | - Khaled Barakat
- Faculty of Pharmacy and Pharmaceutical Sciences
- Li Ka Shing Institute of Virology
- Li Ka Shing Applied Virology Institute
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15
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Boullot F, Castrec J, Bidault A, Dantas N, Payton L, Perrigault M, Tran D, Amzil Z, Boudry P, Soudant P, Hégaret H, Fabioux C. Molecular Characterization of Voltage-Gated Sodium Channels and Their Relations with Paralytic Shellfish Toxin Bioaccumulation in the Pacific Oyster Crassostrea gigas. Mar Drugs 2017; 15:md15010021. [PMID: 28106838 PMCID: PMC5295241 DOI: 10.3390/md15010021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 01/04/2017] [Accepted: 01/06/2017] [Indexed: 12/28/2022] Open
Abstract
Paralytic shellfish toxins (PST) bind to voltage-gated sodium channels (Nav) and block conduction of action potential in excitable cells. This study aimed to (i) characterize Nav sequences in Crassostrea gigas and (ii) investigate a putative relation between Nav and PST-bioaccumulation in oysters. The phylogenetic analysis highlighted two types of Nav in C. gigas: a Nav1 (CgNav1) and a Nav2 (CgNav2) with sequence properties of sodium-selective and sodium/calcium-selective channels, respectively. Three alternative splice transcripts of CgNav1 named A, B and C, were characterized. The expression of CgNav1, analyzed by in situ hybridization, is specific to nervous cells and to structures corresponding to neuromuscular junctions. Real-time PCR analyses showed a strong expression of CgNav1A in the striated muscle while CgNav1B is mainly expressed in visceral ganglia. CgNav1C expression is ubiquitous. The PST binding site (domain II) of CgNav1 variants possess an amino acid Q that could potentially confer a partial saxitoxin (STX)-resistance to the channel. The CgNav1 genotype or alternative splicing would not be the key point determining PST bioaccumulation level in oysters.
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Affiliation(s)
- Floriane Boullot
- Laboratoire des Sciences de l'Environnement Marin (LEMAR), Institut Universitaire Européen de la Mer, Université de Bretagne Occidentale, UMR 6539 CNRS/UBO/IRD/Ifremer, 29280 Plouzané, France.
| | - Justine Castrec
- Laboratoire des Sciences de l'Environnement Marin (LEMAR), Institut Universitaire Européen de la Mer, Université de Bretagne Occidentale, UMR 6539 CNRS/UBO/IRD/Ifremer, 29280 Plouzané, France.
| | - Adeline Bidault
- Laboratoire des Sciences de l'Environnement Marin (LEMAR), Institut Universitaire Européen de la Mer, Université de Bretagne Occidentale, UMR 6539 CNRS/UBO/IRD/Ifremer, 29280 Plouzané, France.
| | - Natanael Dantas
- Laboratory of Immunology and Pathology of Invertebrates, Department of Molecular Biology, Exact and Natural Sciences Center, Federal University of Paraíba-Campus I, 58051-900 João Pessoa, PB, Brazil.
| | - Laura Payton
- UMR 5805 EPOC, CNRS-Équipe Écotoxicologie Aquatique, Université de Bordeaux, Station Marine d'Arcachon, 33120 Arcachon, France.
| | - Mickael Perrigault
- UMR 5805 EPOC, CNRS-Équipe Écotoxicologie Aquatique, Université de Bordeaux, Station Marine d'Arcachon, 33120 Arcachon, France.
| | - Damien Tran
- UMR 5805 EPOC, CNRS-Équipe Écotoxicologie Aquatique, Université de Bordeaux, Station Marine d'Arcachon, 33120 Arcachon, France.
| | - Zouher Amzil
- Laboratoire Phycotoxines, IFREMER, BP 21105, 44311 Nantes, France.
| | - Pierre Boudry
- Ifremer, UMR 6539 LEMAR CNRS/UBO/IRD/Ifremer, 29280 Plouzané, France.
| | - Philippe Soudant
- Laboratoire des Sciences de l'Environnement Marin (LEMAR), Institut Universitaire Européen de la Mer, Université de Bretagne Occidentale, UMR 6539 CNRS/UBO/IRD/Ifremer, 29280 Plouzané, France.
| | - Hélène Hégaret
- Laboratoire des Sciences de l'Environnement Marin (LEMAR), Institut Universitaire Européen de la Mer, Université de Bretagne Occidentale, UMR 6539 CNRS/UBO/IRD/Ifremer, 29280 Plouzané, France.
| | - Caroline Fabioux
- Laboratoire des Sciences de l'Environnement Marin (LEMAR), Institut Universitaire Européen de la Mer, Université de Bretagne Occidentale, UMR 6539 CNRS/UBO/IRD/Ifremer, 29280 Plouzané, France.
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16
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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: 217] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Eukaryotic voltage-gated sodium (Nav) channels contribute to the rising phase of action potentials and served as an early muse for biophysicists laying the foundation for our current understanding of electrical signaling. Given their central role in electrical excitability, it is not surprising that (a) inherited mutations in genes encoding for Nav channels and their accessory subunits have been linked to excitability disorders in brain, muscle, and heart; and (b) Nav channels are targeted by various drugs and naturally occurring toxins. Although the overall architecture and behavior of these channels are likely to be similar to the more well-studied voltage-gated potassium channels, eukaryotic Nav channels lack structural and functional symmetry, a notable difference that has implications for gating and selectivity. Activation of voltage-sensing modules of the first three domains in Nav channels is sufficient to open the channel pore, whereas movement of the domain IV voltage sensor is correlated with inactivation. Also, structure–function studies of eukaryotic Nav channels show that a set of amino acids in the selectivity filter, referred to as DEKA locus, is essential for Na+ selectivity. Structures of prokaryotic Nav channels have also shed new light on mechanisms of drug block. These structures exhibit lateral fenestrations that are large enough to allow drugs or lipophilic molecules to gain access into the inner vestibule, suggesting that this might be the passage for drug entry into a closed channel. In this Review, we will synthesize our current understanding of Nav channel gating mechanisms, ion selectivity and permeation, and modulation by therapeutics and toxins in light of the new structures of the prokaryotic Nav channels that, for the time being, serve as structural models of their eukaryotic counterparts.
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Affiliation(s)
- Christopher A Ahern
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA 52242
| | - Jian Payandeh
- Department of Structural Biology, Genentech, Inc., South San Francisco, CA 94080
| | - Frank Bosmans
- Department of Physiology and Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, School of Medicine, Baltimore, MD 21205 Department of Physiology and Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, School of Medicine, Baltimore, MD 21205
| | - Baron Chanda
- Department of Neuroscience and Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705 Department of Neuroscience and Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705
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17
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Li Y, Liu H, Xia M, Gong H. Lysine and the Na+/K+ Selectivity in Mammalian Voltage-Gated Sodium Channels. PLoS One 2016; 11:e0162413. [PMID: 27584582 PMCID: PMC5008630 DOI: 10.1371/journal.pone.0162413] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 08/22/2016] [Indexed: 12/28/2022] Open
Abstract
Voltage-gated sodium (Nav) channels are critical in the generation and transmission of neuronal signals in mammals. The crystal structures of several prokaryotic Nav channels determined in recent years inspire the mechanistic studies on their selection upon the permeable cations (especially between Na+ and K+ ions), a property that is proposed to be mainly determined by residues in the selectivity filter. However, the mechanism of cation selection in mammalian Nav channels lacks direct explanation at atomic level due to the difference in amino acid sequences between mammalian and prokaryotic Nav homologues, especially at the constriction site where the DEKA motif has been identified to determine the Na+/K+ selectivity in mammalian Nav channels but is completely absent in the prokaryotic counterparts. Among the DEKA residues, Lys is of the most importance since its mutation to Arg abolishes the Na+/K+ selectivity. In this work, we modeled the pore domain of mammalian Nav channels by mutating the four residues at the constriction site of a prokaryotic Nav channel (NavRh) to DEKA, and then mechanistically investigated the contribution of Lys in cation selection using molecular dynamics simulations. The DERA mutant was generated as a comparison to understand the loss of ion selectivity caused by the K-to-R mutation. Simulations and free energy calculations on the mutants indicate that Lys facilitates Na+/K+ selection by electrostatically repelling the cation to a highly Na+-selective location sandwiched by the carboxylate groups of Asp and Glu at the constriction site. In contrast, the electrostatic repulsion is substantially weakened when Lys is mutated to Arg, because of two intrinsic properties of the Arg side chain: the planar geometric design and the sparse charge distribution of the guanidine group.
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Affiliation(s)
- Yang Li
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Huihui Liu
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Mengdie Xia
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Haipeng Gong
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
- * E-mail:
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18
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Li Y, Gong H. Theoretical and simulation studies on voltage-gated sodium channels. Protein Cell 2015; 6:413-22. [PMID: 25894089 PMCID: PMC4444806 DOI: 10.1007/s13238-015-0152-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 03/05/2015] [Indexed: 12/19/2022] Open
Abstract
Voltage-gated sodium (Nav) channels are indispensable membrane elements for the generation and propagation of electric signals in excitable cells. The successes in the crystallographic studies on prokaryotic Nav channels in recent years greatly promote the mechanistic investigation of these proteins and their eukaryotic counterparts. In this paper, we mainly review the progress in computational studies, especially the simulation studies, on these proteins in the past years.
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Affiliation(s)
- Yang Li
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Haipeng Gong
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084 China
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19
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Scior T, Paiz-Candia B, Islas ÁA, Sánchez-Solano A, Millan-Perez Peña L, Mancilla-Simbro C, Salinas-Stefanon EM. Predicting a double mutant in the twilight zone of low homology modeling for the skeletal muscle voltage-gated sodium channel subunit beta-1 (Nav1.4 β1). Comput Struct Biotechnol J 2015; 13:229-40. [PMID: 25904995 PMCID: PMC4402383 DOI: 10.1016/j.csbj.2015.03.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 03/18/2015] [Accepted: 03/21/2015] [Indexed: 12/18/2022] Open
Abstract
The molecular structure modeling of the β1 subunit of the skeletal muscle voltage-gated sodium channel (Nav1.4) was carried out in the twilight zone of very low homology. Structural significance can per se be confounded with random sequence similarities. Hence, we combined (i) not automated computational modeling of weakly homologous 3D templates, some with interfaces to analogous structures to the pore-bearing Nav1.4 α subunit with (ii) site-directed mutagenesis (SDM), as well as (iii) electrophysiological experiments to study the structure and function of the β1 subunit. Despite the distant phylogenic relationships, we found a 3D-template to identify two adjacent amino acids leading to the long-awaited loss of function (inactivation) of Nav1.4 channels. This mutant type (T109A, N110A, herein called TANA) was expressed and tested on cells of hamster ovary (CHO). The present electrophysiological results showed that the double alanine substitution TANA disrupted channel inactivation as if the β1 subunit would not be in complex with the α subunit. Exhaustive and unbiased sampling of “all β proteins” (Ig-like, Ig) resulted in a plethora of 3D templates which were compared to the target secondary structure prediction. The location of TANA was made possible thanks to another “all β protein” structure in complex with an irreversible bound protein as well as a reversible protein–protein interface (our “Rosetta Stone” effect). This finding coincides with our electrophysiological data (disrupted β1-like voltage dependence) and it is safe to utter that the Nav1.4 α/β1 interface is likely to be of reversible nature.
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Affiliation(s)
- Thomas Scior
- Facultad de Ciencias Químicas, Universidad Autónoma de Puebla, Puebla, Mexico
| | - Bertin Paiz-Candia
- Facultad de Ciencias Químicas, Universidad Autónoma de Puebla, Puebla, Mexico
| | - Ángel A Islas
- Laboratorio de Biofísica, Instituto de Fisiología, Universidad Autónoma de Puebla, Puebla, Mexico
| | - Alfredo Sánchez-Solano
- Laboratorio de Biofísica, Instituto de Fisiología, Universidad Autónoma de Puebla, Puebla, Mexico
| | | | - Claudia Mancilla-Simbro
- Laboratorio de Biofísica, Instituto de Fisiología, Universidad Autónoma de Puebla, Puebla, Mexico
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20
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Amey JS, O'Reilly AO, Burton MJ, Puinean AM, Mellor IR, Duce IR, Field LM, Wallace BA, Williamson MS, Davies TGE. An evolutionarily-unique heterodimeric voltage-gated cation channel found in aphids. FEBS Lett 2015; 589:598-607. [PMID: 25637326 PMCID: PMC4332693 DOI: 10.1016/j.febslet.2015.01.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 12/31/2014] [Accepted: 01/05/2015] [Indexed: 01/05/2023]
Abstract
Aphids have a unique heterodimeric voltage-gated sodium channel. The aphid channel has an atypical ion-selectivity filter (DENS rather than DEKA). The channel’s novel selectivity filter may result in a loss of sodium selectivity. This is the only identifiable voltage-gated sodium channel in aphid genome(s). This channel has most likely arisen by gene fission or gene duplication.
We describe the identification in aphids of a unique heterodimeric voltage-gated sodium channel which has an atypical ion selectivity filter and, unusually for insect channels, is highly insensitive to tetrodotoxin. We demonstrate that this channel has most likely arisen by adaptation (gene fission or duplication) of an invertebrate ancestral mono(hetero)meric channel. This is the only identifiable voltage-gated sodium channel homologue in the aphid genome(s), and the channel’s novel selectivity filter motif (DENS instead of the usual DEKA found in other eukaryotes) may result in a loss of sodium selectivity, as indicated experimentally in mutagenised Drosophila channels.
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Affiliation(s)
- Joanna S Amey
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Andrias O O'Reilly
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom; School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, United Kingdom
| | - Mark J Burton
- School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, United Kingdom; Department of Cell Physiology and Pharmacology, College of Medicine, Biological Sciences and Psychology, University of Leicester, United Kingdom
| | - Alin M Puinean
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Ian R Mellor
- School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, United Kingdom
| | - Ian R Duce
- School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, United Kingdom
| | - Linda M Field
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
| | - Martin S Williamson
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - T G Emyr Davies
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom.
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21
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Dudev T, Lim C. Ion selectivity strategies of sodium channel selectivity filters. Acc Chem Res 2014; 47:3580-7. [PMID: 25343535 DOI: 10.1021/ar5002878] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
CONSPECTUS: Sodium ion channels selectively transport Na(+) cations across the cell membrane. These integral parts of the cell machinery are implicated in regulating the cardiac, skeletal and smooth muscle contraction, nerve impulses, salt and water homeostasis, as well as pain and taste perception. Their malfunction often results in various channelopathies of the heart, brain, skeletal muscles, and lung; thus, sodium channels are key drug targets for various disorders including cardiac arrhythmias, heart attack, stroke, migraine, epilepsy, pain, cancer, and autoimmune disorders. The ability of sodium channels to discriminate the native Na(+) among other competing ions in the surrounding fluids is crucial for proper cellular functions. The selectivity filter (SF), the narrowest part of the channel's open pore, lined with amino acid residues that specifically interact with the permeating ion, plays a major role in determining Na(+) selectivity. Different sodium channels have different SFs, which vary in the symmetry, number, charge, arrangement, and chemical type of the metal-ligating groups and pore size: epithelial/degenerin/acid-sensing ion channels have generally trimeric SFs lined with three conserved neutral serines and/or backbone carbonyls; eukaryotic sodium channels have EKEE, EEKE, DKEA, and DEKA SFs with an invariant positively charged lysine from the second or third domain; and bacterial voltage-gated sodium (Nav) channels exhibit symmetrical EEEE SFs, reminiscent of eukaryotic voltage-gated calcium channels. How do these different sodium channel SFs achieve high selectivity for Na(+) over its key rivals, K(+) and Ca(2+)? What factors govern the metal competition in these SFs and which of these factors are exploited to achieve Na(+) selectivity in the different sodium channel SFs? The free energies for replacing K(+) or Ca(2+) bound inside different model SFs with Na(+), evaluated by a combination of density functional theory and continuum dielectric calculations, have shed light on these questions. The SFs of epithelial and eukaryotic Nav channels select Na(+) by providing an optimal number and ligating strength of metal ligands as well as a rigid pore whose size fits the cognate Na(+) ideally. On the other hand, the SFs of bacterial Nav channels select Na(+), as the protein matrix attenuates ion-protein interactions relative to ion-solvent interactions by enlarging the pore and allowing water to enter, so the ion interacts indirectly with the conserved glutamates via bridging water molecules. This shows how these various SFs have adapted to the specific physicochemical properties of the native ion, using different strategies to select Na(+) among its contenders.
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Affiliation(s)
- Todor Dudev
- Faculty of Chemistry and Pharmacy, Sofia University, Sofia 1164, Bulgaria
| | - Carmay Lim
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
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22
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Kalia J, Milescu M, Salvatierra J, Wagner J, Klint JK, King GF, Olivera BM, Bosmans F. From foe to friend: using animal toxins to investigate ion channel function. J Mol Biol 2014; 427:158-175. [PMID: 25088688 DOI: 10.1016/j.jmb.2014.07.027] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 07/18/2014] [Accepted: 07/18/2014] [Indexed: 12/19/2022]
Abstract
Ion channels are vital contributors to cellular communication in a wide range of organisms, a distinct feature that renders this ubiquitous family of membrane-spanning proteins a prime target for toxins found in animal venom. For many years, the unique properties of these naturally occurring molecules have enabled researchers to probe the structural and functional features of ion channels and to define their physiological roles in normal and diseased tissues. To illustrate their considerable impact on the ion channel field, this review will highlight fundamental insights into toxin-channel interactions and recently developed toxin screening methods and practical applications of engineered toxins.
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Affiliation(s)
- Jeet Kalia
- Indian Institute of Science Education and Research Pune; Pune, Maharashtra 411 008 India
| | - Mirela Milescu
- Division of Biological Sciences; University of Missouri, Columbia, MO 65211 USA
| | - Juan Salvatierra
- Department of Physiology; Johns Hopkins University, School of Medicine, Baltimore, MD 21205 USA
| | - Jordan Wagner
- Department of Physiology; Johns Hopkins University, School of Medicine, Baltimore, MD 21205 USA
| | - Julie K Klint
- Institute for Molecular Bioscience; The University of Queensland, St. Lucia, QLD 4072 Australia
| | - Glenn F King
- Institute for Molecular Bioscience; The University of Queensland, St. Lucia, QLD 4072 Australia
| | | | - Frank Bosmans
- Department of Physiology; Johns Hopkins University, School of Medicine, Baltimore, MD 21205 USA.,Solomon H. Snyder Department of Neuroscience; Johns Hopkins University, School of Medicine, Baltimore, MD 21205 USA
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23
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Abstract
The paralytic agent (+)-saxitoxin (STX), most commonly associated with oceanic red tides and shellfish poisoning, is a potent inhibitor of electrical conduction in cells. Its nefarious effects result from inhibition of voltage-gated sodium channels (Na(V)s), the obligatory proteins responsible for the initiation and propagation of action potentials. In the annals of ion channel research, the identification and characterization of Na(V)s trace to the availability of STX and an allied guanidinium derivative, tetrodotoxin. The mystique of STX is expressed in both its function and form, as this uniquely compact dication boasts more heteroatoms than carbon centers. This Review highlights both the chemistry and chemical biology of this fascinating natural product, and offers a perspective as to how molecular design and synthesis may be used to explore Na(V) structure and function.
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Affiliation(s)
- Arun P Thottumkara
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080 (USA)
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25
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Dudev T, Lim C. Evolution of Eukaryotic Ion Channels: Principles Underlying the Conversion of Ca2+-Selective to Na+-Selective Channels. J Am Chem Soc 2014; 136:3553-9. [DOI: 10.1021/ja4121132] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Todor Dudev
- Institute
of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Carmay Lim
- Institute
of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
- Department
of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
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26
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Abstract
Voltage-gated sodium channels (VGSCs) are present in many tissue types within the human body including both cardiac and neuronal tissues. Like other channels, VGSCs activate, deactivate, and inactivate in response to changes in membrane potential. VGSCs also have a similar structure to other channels: 24 transmembrane segments arranged into four domains that surround a central pore. The structure and electrical activity of these channels allows them to create and respond to electrical signals in the body. Because of their distribution throughout the body, VGSCs are implicated in a variety of diseases including epilepsy, cardiac arrhythmias, and neuropathic pain. As such the study of these channels is essential. This brief review will introduce sodium channel structure, physiology, and pathophysiology.
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Abstract
Voltage-gated sodium (Nav) channels are essential contributors to neuronal excitability, making them the most commonly targeted ion channel family by toxins found in animal venoms. These molecules can be used to probe the functional aspects of Nav channels on a molecular level and to explore their physiological role in normal and diseased tissues. This chapter summarizes our existing knowledge of the mechanisms by which animal toxins influence Nav channels as well as their potential application in designing therapeutic drugs.
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Wu M, Ye N, Sengupta B, Zakon HH. A naturally occurring amino acid substitution in the voltage-dependent sodium channel selectivity filter affects channel gating. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2013; 199:829-42. [PMID: 23979192 DOI: 10.1007/s00359-013-0845-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 07/29/2013] [Accepted: 08/01/2013] [Indexed: 12/19/2022]
Abstract
The pore of sodium channels contains a selectivity filter made of 4 amino acids, D/E/K/A. In voltage sensitive sodium channel (Nav) channels from jellyfish to human the fourth amino acid is Ala. This Ala, when mutated to Asp, promotes slow inactivation. In some Nav channels of pufferfishes, the Ala is replaced with Gly. We studied the biophysical properties of an Ala-to-Gly substitution (A1529G) in rat Nav1.4 channel expressed in Xenopus oocytes alone or with a β1 subunit. The Ala-to-Gly substitution does not affect monovalent cation selectivity and positively shifts the voltage-dependent inactivation curve, although co-expression with a β1 subunit eliminates the difference between A1529G and WT. There is almost no difference in channel fast inactivation, but the β1 subunit accelerates WT current inactivation significantly more than it does the A1529G channels. The Ala-to-Gly substitution mainly influences the rate of recovery from slow inactivation. Again, the β1 subunit is less effective on speeding recovery of A1529G than the WT. We searched Nav channels in numerous databases and noted at least four other independent Ala-to-Gly substitutions in Nav channels in teleost fishes. Thus, the Ala-to-Gly substitution occurs more frequently than previously realized, possibly under selection for alterations of channel gating.
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Affiliation(s)
- Mingming Wu
- Section of Neurobiology, Institute for Neuroscience, University of Texas at Austin, Austin, TX, 78712, USA,
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Xia M, Liu H, Li Y, Yan N, Gong H. The mechanism of Na⁺/K⁺ selectivity in mammalian voltage-gated sodium channels based on molecular dynamics simulation. Biophys J 2013; 104:2401-9. [PMID: 23746512 PMCID: PMC3672897 DOI: 10.1016/j.bpj.2013.04.035] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 04/18/2013] [Accepted: 04/19/2013] [Indexed: 01/07/2023] Open
Abstract
Voltage-gated sodium (Nav) channels and their Na⁺/K⁺ selectivity are of great importance in the mammalian neuronal signaling. According to mutational analysis, the Na⁺/K⁺ selectivity in mammalian Nav channels is mainly determined by the Lys and Asp/Glu residues located at the constriction site within the selectivity filter. Despite successful molecular dynamics simulations conducted on the prokaryotic Nav channels, the lack of Lys at the constriction site of prokaryotic Nav channels limits how much can be learned about the Na⁺/K⁺ selectivity in mammalian Nav channels. In this work, we modeled the mammalian Nav channel by mutating the key residues at the constriction site in a prokaryotic Nav channel (NavRh) to its mammalian counterpart. By simulating the mutant structure, we found that the Na⁺ preference in mammalian Nav channels is collaboratively achieved by the deselection from Lys and the selection from Asp/Glu within the constriction site.
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Affiliation(s)
- Mengdie Xia
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Huihui Liu
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Yang Li
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Nieng Yan
- State Key Laboratory of Biomembrane and Membrane Biotechnology, School of Medicine, Tsinghua University, Beijing, China
| | - Haipeng Gong
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, School of Medicine, Tsinghua University, Beijing, China
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Senatore A, Spafford JD. A uniquely adaptable pore is consistent with NALCN being an ion sensor. Channels (Austin) 2013; 7:60-8. [PMID: 23442378 PMCID: PMC3667885 DOI: 10.4161/chan.23981] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
NALCN is an intriguing, orphan ion channel among the 4x6TM family of related voltage-gated cation channels, sharing a common architecture of four homologous domains consisting of six transmembrane helices, separated by three cytoplasmic linkers and delimited by N and C-terminal ends. NALCN is one of the shortest 4x6TM family members, lacking much of the variation that provides the diverse palate of gating features, and tissue specific adaptations of sodium and calcium channels. NALCN's most distinctive feature is that that it possesses a highly adaptable pore with a calcium-like EEEE selectivity filter in radially symmetrical animals and a more sodium-like EEKE or EKEE selectivity filter in bilaterally symmetrical animals including vertebrates. Two lineages of animals evolved alternative calcium-like EEEE and sodium-like EEKE / EKEE pores, spliced to regulate NALCN functions in differing cellular environments, such as muscle (heart and skeletal) and secretory tissue (brain and glands), respectively. A highly adaptable pore in an otherwise conserved ion channel in the 4x6TM channel family is not consistent with a role for NALCN in directly gating a significant ion conductance that can be either sodium ions or calcium ions. NALCN was proposed to be an expressible Gd ( 3+) -sensitive, NMDG (+) -impermeant, non-selective and ohmic leak conductance in HEK-293T cells, but we were unable to distinguish these reported currents from leaky patch currents (ILP) in control HEK-293T cells. We suggest that NALCN functions as a sensor for the much larger UNC80/UNC79 complex, in a manner consistent with the coupling mechanism known for other weakly or non-conducting 4x6TM channel sensor proteins such as Nax or Cav 1.1. We propose that NALCN serves as a variable sensor that responds to calcium or sodium ion flux, depending on whether the total cellular current density is generated more from calcium-selective or sodium-selective channels.
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Affiliation(s)
- Adriano Senatore
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
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31
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Senatore A, Monteil A, van Minnen J, Smit AB, Spafford JD. NALCN ion channels have alternative selectivity filters resembling calcium channels or sodium channels. PLoS One 2013; 8:e55088. [PMID: 23383067 PMCID: PMC3557258 DOI: 10.1371/journal.pone.0055088] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 12/19/2012] [Indexed: 11/17/2022] Open
Abstract
NALCN is a member of the family of ion channels with four homologous, repeat domains that include voltage-gated calcium and sodium channels. NALCN is a highly conserved gene from simple, extant multicellular organisms without nervous systems such as sponges and placozoans and mostly remains a single gene compared to the calcium and sodium channels which diversified into twenty genes in humans. The single NALCN gene has alternatively-spliced exons at exons 15 or exon 31 that splices in novel selectivity filter residues that resemble calcium channels (EEEE) or sodium channels (EKEE or EEKE). NALCN channels with alternative calcium, (EEEE) and sodium, (EKEE or EEKE) -selective pores are conserved in simple bilaterally symmetrical animals like flatworms to non-chordate deuterostomes. The single NALCN gene is limited as a sodium channel with a lysine (K)-containing pore in vertebrates, but originally NALCN was a calcium-like channel, and evolved to operate as both a calcium channel and sodium channel for different roles in many invertebrates. Expression patterns of NALCN-EKEE in pond snail, Lymnaea stagnalis suggest roles for NALCN in secretion, with an abundant expression in brain, and an up-regulation in secretory organs of sexually-mature adults such as albumen gland and prostate. NALCN-EEEE is equally abundant as NALCN-EKEE in snails, but is greater expressed in heart and other muscle tissue, and 50% less expressed in the brain than NALCN-EKEE. Transfected snail NALCN-EEEE and NALCN-EKEE channel isoforms express in HEK-293T cells. We were not able to distinguish potential NALCN currents from background, non-selective leak conductances in HEK293T cells. Native leak currents without expressing NALCN genes in HEK-293T cells are NMDG(+) impermeant and blockable with 10 µM Gd(3+) ions and are indistinguishable from the hallmark currents ascribed to mammalian NALCN currents expressed in vitro by Lu et al. in Cell. 2007 Apr 20;129(2):371-83.
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32
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Finnerty JJ, Eisenberg R, Carloni P. Localizing the Charged Side Chains of Ion Channels within the Crowded Charge Models. J Chem Theory Comput 2012; 9:766-73. [DOI: 10.1021/ct300768j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Justin J. Finnerty
- Computational Biophysics, German
Research School for Simulation Sciences, 52425 Jülich, Germany
| | - Robert Eisenberg
- Department of Molecular Biophysics
and Physiology, Rush University, Chicago, Illinois 60612, United States
| | - Paolo Carloni
- Computational Biophysics, German
Research School for Simulation Sciences, 52425 Jülich, Germany
and Institute for Advanced Simulation IAS-5, Computational Biomedicine,
Forschungszentrum Jülich, 52425 Jülich, Germany
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33
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Adaptive evolution of voltage-gated sodium channels: the first 800 million years. Proc Natl Acad Sci U S A 2012; 109 Suppl 1:10619-25. [PMID: 22723361 DOI: 10.1073/pnas.1201884109] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Voltage-gated Na(+)-permeable (Nav) channels form the basis for electrical excitability in animals. Nav channels evolved from Ca(2+) channels and were present in the common ancestor of choanoflagellates and animals, although this channel was likely permeable to both Na(+) and Ca(2+). Thus, like many other neuronal channels and receptors, Nav channels predated neurons. Invertebrates possess two Nav channels (Nav1 and Nav2), whereas vertebrate Nav channels are of the Nav1 family. Approximately 500 Mya in early chordates Nav channels evolved a motif that allowed them to cluster at axon initial segments, 50 million years later with the evolution of myelin, Nav channels "capitalized" on this property and clustered at nodes of Ranvier. The enhancement of conduction velocity along with the evolution of jaws likely made early gnathostomes fierce predators and the dominant vertebrates in the ocean. Later in vertebrate evolution, the Nav channel gene family expanded in parallel in tetrapods and teleosts (∼9 to 10 genes in amniotes, 8 in teleosts). This expansion occurred during or after the late Devonian extinction, when teleosts and tetrapods each diversified in their respective habitats, and coincided with an increase in the number of telencephalic nuclei in both groups. The expansion of Nav channels may have allowed for more sophisticated neural computation and tailoring of Nav channel kinetics with potassium channel kinetics to enhance energy savings. Nav channels show adaptive sequence evolution for increasing diversity in communication signals (electric fish), in protection against lethal Nav channel toxins (snakes, newts, pufferfish, insects), and in specialized habitats (naked mole rats).
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34
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Csányi E, Boda D, Gillespie D, Kristóf T. Current and selectivity in a model sodium channel under physiological conditions: Dynamic Monte Carlo simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:592-600. [PMID: 22080102 DOI: 10.1016/j.bbamem.2011.10.029] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2011] [Revised: 10/06/2011] [Accepted: 10/26/2011] [Indexed: 11/15/2022]
Abstract
A reduced model of a sodium channel is analyzed using Dynamic Monte Carlo simulations. These include the first simulations of ionic current under approximately physiological ionic conditions through a model sodium channel and an analysis of how mutations of the sodium channel's DEKA selectivity filter motif transform the channel from being Na(+) selective to being Ca(2+) selective. Even though the model of the pore, amino acids, and permeant ions is simplified, the model reproduces the fundamental properties of a sodium channel (e.g., 10 to 1 Na(+) over K(+) selectivity, Ca(2+) exclusion, and Ca(2+) selectivity after several point mutations). In this model pore, ions move through the pore one at a time by simple diffusion and Na(+) versus K(+) selectivity is due to both the larger K(+) not fitting well into the selectivity filter that contains amino acid terminal groups and K(+) moving more slowly (compared to Na(+)) when it is in the selectivity filter.
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Affiliation(s)
- Eva Csányi
- Department of Physical Chemistry, University of Pannonia, Veszprém, Hungary
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36
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Liebeskind BJ. Evolution of sodium channels and the new view of early nervous system evolution. Commun Integr Biol 2011; 4:679-83. [PMID: 22446526 PMCID: PMC3306330 DOI: 10.4161/cib.17069] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Advances in genomics have revealed that many genes implicated in the nervous systems of bilaterians were already present in the last common ancestor (LCA) of animals, and some even before that.(1) (-) (5) This new information coincides with a growing reinterpretation of cnidarian nervous systems which holds that they are 'fundamentally conventional' with regards to bilaterian nervous systems,(6) and do not represent ancient forms. Since in general adult forms are expected to be the most derived features of organisms, the study of non-bilaterian larval forms may be a better way to investigate potential plesiomorphies. We recently showed that voltage-gated sodium channel (Na(v)) genes, which make action potentials in nerves and muscles, were present in the LCA of animals and choanoflagellates, the closest unicellular relatives to animals.(2) This addendum will attempt to put this finding within the context of the new views of nervous system evolution.
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Evolution of sodium channels predates the origin of nervous systems in animals. Proc Natl Acad Sci U S A 2011; 108:9154-9. [PMID: 21576472 DOI: 10.1073/pnas.1106363108] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Voltage-dependent sodium channels are believed to have evolved from calcium channels at the origin of the nervous system. A search of the genome of a single-celled choanoflagellate (the sister group of animals) identified a gene that is homologous to animal sodium channels and has a putative ion selectivity filter intermediate between calcium and sodium channels. Searches of a wide variety of animal genomes, including representatives of each basal lineage, revealed that similar homologs were retained in most lineages. One of these, the Placozoa, does not possess a nervous system. We cloned and sequenced the full choanoflagellate channel and parts of two placozoan channels from mRNA, showing that they are expressed. Phylogenetic analysis clusters the genes for these channels with other known sodium channels. From this phylogeny we infer ancestral states of the ion selectivity filter and show that this state has been retained in the choanoflagellate and placozoan channels. We also identify key gene duplications and losses and show convergent amino acid replacements at important points along the animal lineage.
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38
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Gurkiewicz M, Korngreen A, Waxman SG, Lampert A. Kinetic modeling of Nav1.7 provides insight into erythromelalgia-associated F1449V mutation. J Neurophysiol 2011; 105:1546-57. [PMID: 21289137 DOI: 10.1152/jn.00703.2010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Gain-of-function mutations of the voltage-gated sodium channel (VGSC) Na(v)1.7 have been linked to human pain disorders. The mutation F1449V, located at the intracellular end of transmembrane helix S6 of domain III, induces the inherited pain syndrome erythromelalgia. A kinetic model of wild-type (WT) and F1449V Na(v)1.7 may provide a basis for predicting putative intraprotein interactions. We semiautomatically constrained a Markov model using stochastic search algorithms and whole cell patch-clamp recordings from human embryonic kidney cells transfected with Na(v)1.7 and its F1449V mutation. The best models obtained simulated known differences in action potential thresholds and firing patterns in spinal sensory neurons expressing WT and F1449V. The most suitable Markov model consisted of three closed, one open, and two inactivated states. The model predicted that the F1449V mutation shifts occupancy of the closed states closer to the open state, making it easier for the channel pore to open. It also predicted that F1449V's second inactivated state is more than four times more likely to be occupied than the equivalent state in WT at hyperpolarized potentials, although the mutation still lowered the firing threshold of action potentials. The differences between WT and F1449V were not limited to a single transition. Thus a point mutation in position F1449, while phenotypically most probably affecting the activation gate, may also modify channel functions mediated by structures in more distant areas of the channel protein.
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Affiliation(s)
- Meron Gurkiewicz
- The Leslie and Susan Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat-Gan 52900, Israel.
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39
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Zarrabi T, Cervenka R, Sandtner W, Lukacs P, Koenig X, Hilber K, Mille M, Lipkind GM, Fozzard HA, Todt H. A molecular switch between the outer and the inner vestibules of the voltage-gated Na+ channel. J Biol Chem 2010; 285:39458-70. [PMID: 20926383 PMCID: PMC2998134 DOI: 10.1074/jbc.m110.132886] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Voltage-gated ion channels are transmembrane proteins that undergo complex conformational changes during their gating transitions. Both functional and structural data from K+ channels suggest that extracellular and intracellular parts of the pore communicate with each other via a trajectory of interacting amino acids. No crystal structures are available for voltage-gated Na+ channels, but functional data suggest a similar intramolecular communication involving the inner and outer vestibules. However, the mechanism of such communication is unknown. Here, we report that amino acid Ile-1575 in the middle of transmembrane segment 6 of domain IV (DIV-S6) in the adult rat skeletal muscle isoform of the voltage-gated sodium channel (rNaV1.4) may act as molecular switch allowing for interaction between outer and inner vestibules. Cysteine scanning mutagenesis of the internal part of DIV-S6 revealed that only mutations at site 1575 rescued the channel from a unique kinetic state (“ultra-slow inactivation,” IUS) produced by the mutation K1237E in the selectivity filter. A similar effect was seen with I1575A. Previously, we reported that conformational changes of both the internal and the external vestibule are involved in the generation of IUS. The fact that mutations at site 1575 modulate IUS produced by K1237E strongly suggests an interaction between these sites. Our data confirm a previously published molecular model in which Ile-1575 of DIV-S6 is in close proximity to Lys-1237 of the selectivity filter. Furthermore, these functional data define the position of the selectivity filter relative to the adjacent DIV-S6 segment within the ionic permeation pathway.
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Affiliation(s)
- Touran Zarrabi
- Center for Physiology and Pharmacology, Institute of Pharmacology, Medical University of Vienna, Vienna 1090, Austria
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40
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Roux B. Exploring the ion selectivity properties of a large number of simplified binding site models. Biophys J 2010; 98:2877-85. [PMID: 20550900 DOI: 10.1016/j.bpj.2010.03.038] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Revised: 02/24/2010] [Accepted: 03/16/2010] [Indexed: 11/16/2022] Open
Abstract
The ability to discriminate between different cations efficiently is essential for the proper physiological functioning of many membrane transport proteins. One obvious mechanism of ion selectivity is when a binding site is structurally constrained by the protein architecture and its geometry is precisely adapted to fit an ion of a given size. This mechanism is not effective in the case of flexible protein binding sites that are able to deform structurally or to adapt to a bound ion. In this study, the concept of nontrivial ion selectivity arising in a highly flexible protein binding site conceptually represented as a microdroplet of ligands confined to a small volume is explored. The environment imposed by the spatial confinement is a critical feature of the reduced models. A large number of reduced binding site models (1077) comprising typical ion-coordinating ligands (carbonyl, hydroxyl, carboxylate, water) are constructed and characterized for Na(+)/K(+) and Ca(2+)/Ba(2+) size selectivity using free energy perturbation molecular dynamics simulations. Free energies are highly correlated with the sum of ion-ligand and ligand-ligand mean interactions, but the relative balance of those two contributions is different for K(+)-selective and Na(+)-selective binding sites. The analysis indicates that both the number and the type of ligands are important factors in ion selectivity.
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Affiliation(s)
- Benoît Roux
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA.
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41
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Dudev T, Lim C. Factors Governing the Na+ vs K+ Selectivity in Sodium Ion Channels. J Am Chem Soc 2010; 132:2321-32. [DOI: 10.1021/ja909280g] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Todor Dudev
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, and the Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Carmay Lim
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, and the Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
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