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Benndorf K, Enke U, Tewari D, Kusch J, Liu H, Sun H, Schmauder R, Sattler C. Subunit-specific conductance of single homomeric and heteromeric HCN pacemaker channels at femtosiemens resolution. Proc Natl Acad Sci U S A 2025; 122:e2422533122. [PMID: 39879240 PMCID: PMC11804576 DOI: 10.1073/pnas.2422533122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2024] [Accepted: 01/03/2025] [Indexed: 01/31/2025] Open
Abstract
In mammals, the four subunit isoforms HCN1-4 assemble to form functional homotetrameric and heterotetrameric hyperpolarization-activated cyclic nucleotide-modulated (HCN) ion channels. Despite the outstanding relevance of HCN channels for organisms, including generating electrical rhythmicity in cardiac pacemaker cells and diverse types of brain neurons, key channel properties are still elusive. In particular, the unitary conductance, γ, of HCN channels is highly controversial. We analyzed the unitary conductance at femtosiemens resolution of all four homotetrameric channels of the mouse, mHCN1-4. All conductance values are in the range of 1 pS which is exceptionally small compared to most other ion channels. Surprisingly, the conductance among the isoforms differs up to threefold (γmHCN2 = 1.54 pS > γmHCN1 = 0.84 pS > γmHCN3 = 0.54 pS ≈ γmHCN4 = 0.51 pS) though the residues in the two narrow parts of the pore, the selectivity filter and the inner gate, are conserved. Mutagenesis and all-atom molecular dynamics simulations demonstrate that the differences in the conductance are generated by different amounts of negative charges in the outer channel vestibule, which control ion accumulation. In line with these results, heterotetrameric channels exhibit intermediate unitary conductance values with respect to the homotetrameric channels. Our approach demonstrates how HCN channels can be functionally differentiated at the single-channel level, paving the way to target specific channels with selective drugs.
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Affiliation(s)
- Klaus Benndorf
- Institut für Physiologie II, Universitätsklinikum Jena, Friedrich-Schiller-Universität Jena, Jena07740, Germany
| | - Uta Enke
- Institut für Physiologie II, Universitätsklinikum Jena, Friedrich-Schiller-Universität Jena, Jena07740, Germany
| | - Debanjan Tewari
- Institut für Physiologie II, Universitätsklinikum Jena, Friedrich-Schiller-Universität Jena, Jena07740, Germany
| | - Jana Kusch
- Institut für Physiologie II, Universitätsklinikum Jena, Friedrich-Schiller-Universität Jena, Jena07740, Germany
| | - Haoran Liu
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin13125, Germany
- Institute of Chemistry, Technical University of Berlin, Berlin10623, Germany
| | - Han Sun
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin13125, Germany
- Institute of Chemistry, Technical University of Berlin, Berlin10623, Germany
| | - Ralf Schmauder
- Institut für Physiologie II, Universitätsklinikum Jena, Friedrich-Schiller-Universität Jena, Jena07740, Germany
| | - Christian Sattler
- Institut für Physiologie II, Universitätsklinikum Jena, Friedrich-Schiller-Universität Jena, Jena07740, Germany
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2
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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: 0.5] [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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3
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Bielopolski N, Heyman E, Bassan H, BenZeev B, Tzadok M, Ginsberg M, Blumkin L, Michaeli Y, Sokol R, Yosha-Orpaz N, Hady-Cohen R, Banne E, Lev D, Lerman-Sagie T, Wald-Altman S, Nissenkorn A. "Virtual patch clamp analysis" for predicting the functional significance of pathogenic variants in sodium channels. Epilepsy Res 2022; 186:107002. [PMID: 36027690 DOI: 10.1016/j.eplepsyres.2022.107002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/28/2022] [Accepted: 08/11/2022] [Indexed: 11/03/2022]
Abstract
OBJECTIVE Opening of voltage-gated sodium channels is crucial for neuronal depolarization. Proper channel opening and influx of Na+ through the ion pore, is dependent upon binding of Na+ ion to a specific amino-acid motif (DEKA) within the pore. In this study we used molecular dynamic simulations, an advanced bioinformatic tool, to research the dysfunction caused by pathogenic variants in SCN1a, SCN2a and SCN8a genes. METHOD Molecular dynamic simulations were performed in six patients: three patients with Dravet syndrome (p.Gly177Ala,p.Ser259Arg and p.Met1267Ile, SCN1a), two patients with early onset drug resistant epilepsy(p.Ala263Val, SCN2a and p.Ile251Arg, SCN8a), and a patient with autism (p.Thr155Ala, SCN2a). After predicting the 3D-structure of mutated proteins by homology modeling, time dependent molecular dynamic simulations were performed, using the Schrödinger algorithm. The opening of the sodium channel, including the detachment of the sodium ion to the DEKA motif and pore diameter were assessed. Results were compared to the existent patch clamp analysis in four patients, and consistency with clinical phenotype was noted. RESULTS The Na+ ion remained attached to DEKA filter longer when compared to wild type in the p.Gly177Ala, p.Ser259Arg,SCN1a, and p.Thr155Ala, SCN2a variants, consistent with loss-of-function. In contrast, it detached quicker from DEKA than wild type in the p.Ala263Val,SCN2a variant, consistent with gain-of-function. In the p.Met1267Ile,SCN1a variant, detachment from DEKA was quicker, but pore diameter decreased, suggesting partial loss-of-function. In the p.Leu251Arg,SCN8a variant, the pore remained opened longer when compared to wild type, consistent with a gain-of-function. The molecular dynamic simulation results were consistent with the existing patch-clamp analysis studies, as well as the clinical phenotype. SIGNIFICANCE Molecular dynamic simulation can be useful in predicting pathogenicity of variants and the disease phenotype, and selecting targeted treatment based on channel dysfunction. Further development of these bioinformatic tools may lead to "virtual patch-clamp analysis".
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Affiliation(s)
| | - E Heyman
- Pediatric Epilepsy Department, Shamir Medical Center, Asaf Ha Rofeh, Israel; Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - H Bassan
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel; Pediatric Neurology Unit, Shamir Medical Center, Asaf HaRofeh, Israel.
| | - B BenZeev
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel; Pediatric Neurology Unit, Safra Children's Hospital, Sheba Medical Center, Tel HaShomer, Israel.
| | - M Tzadok
- Pediatric Neurology Unit, Safra Children's Hospital, Sheba Medical Center, Tel HaShomer, Israel.
| | - M Ginsberg
- Rare Diseases Institute-Magen, Edith Wolfson Medical Center, Holon, Israel; Pediatric Neurology Unit, Edith Wolfson Medical Center, Holon, Israel.
| | - L Blumkin
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel; Rare Diseases Institute-Magen, Edith Wolfson Medical Center, Holon, Israel; Pediatric Neurology Unit, Edith Wolfson Medical Center, Holon, Israel.
| | - Y Michaeli
- Rare Diseases Institute-Magen, Edith Wolfson Medical Center, Holon, Israel; Pediatric Neurology Unit, Edith Wolfson Medical Center, Holon, Israel.
| | - R Sokol
- Pediatric Neurology Unit, Edith Wolfson Medical Center, Holon, Israel.
| | - N Yosha-Orpaz
- Rare Diseases Institute-Magen, Edith Wolfson Medical Center, Holon, Israel; Pediatric Neurology Unit, Edith Wolfson Medical Center, Holon, Israel.
| | - R Hady-Cohen
- Rare Diseases Institute-Magen, Edith Wolfson Medical Center, Holon, Israel.
| | - E Banne
- Pediatric Epilepsy Department, Shamir Medical Center, Asaf Ha Rofeh, Israel; Genetics Institute, Edith Wolfson Medical Center, Holon, Israel
| | - D Lev
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel; Rare Diseases Institute-Magen, Edith Wolfson Medical Center, Holon, Israel; Genetics Institute, Edith Wolfson Medical Center, Holon, Israel.
| | - T Lerman-Sagie
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel; Rare Diseases Institute-Magen, Edith Wolfson Medical Center, Holon, Israel; Pediatric Neurology Unit, Edith Wolfson Medical Center, Holon, Israel.
| | | | - A Nissenkorn
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel; Rare Diseases Institute-Magen, Edith Wolfson Medical Center, Holon, Israel; Pediatric Neurology Unit, Edith Wolfson Medical Center, Holon, Israel.
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4
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Kim S, Choi S, Lee HG, Jin D, Kim G, Kim T, Lee JS, Shim W. Neuromorphic van der Waals crystals for substantial energy generation. Nat Commun 2021; 12:47. [PMID: 33397938 PMCID: PMC7782783 DOI: 10.1038/s41467-020-20296-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 11/23/2020] [Indexed: 01/29/2023] Open
Abstract
Controlling ion transport in nanofluidics is fundamental to water purification, bio-sensing, energy storage, energy conversion, and numerous other applications. For any of these, it is essential to design nanofluidic channels that are stable in the liquid phase and enable specific ions to pass. A human neuron is one such system, where electrical signals are transmitted by cation transport for high-speed communication related to neuromorphic computing. Here, we present a concept of neuro-inspired energy harvesting that uses confined van der Waals crystal and demonstrate a method to maximise the ion diffusion flux to generate an electromotive force. The confined nanochannel is robust in liquids as in neuron cells, enabling steady-state ion diffusion for hundred of hours and exhibiting ion selectivity of 95.8%, energy conversion efficiency of 41.4%, and power density of 5.26 W/m2. This fundamental understanding and rational design strategy can enable previously unrealisable applications of passive-type large-scale power generation.
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Affiliation(s)
- Sungsoon Kim
- grid.15444.300000 0004 0470 5454Department of Materials Science and Engineering, Yonsei University, Seoul, 03722 Korea ,grid.15444.300000 0004 0470 5454Center for Multi-Dimensional Materials, Yonsei University, Seoul, 03722 Korea
| | - Sangjin Choi
- grid.15444.300000 0004 0470 5454Department of Materials Science and Engineering, Yonsei University, Seoul, 03722 Korea ,grid.15444.300000 0004 0470 5454Center for Multi-Dimensional Materials, Yonsei University, Seoul, 03722 Korea
| | - Hae Gon Lee
- grid.15444.300000 0004 0470 5454Department of Mechanical Engineering, Yonsei University, Seoul, 03722 Korea
| | - Dana Jin
- grid.15444.300000 0004 0470 5454Department of Materials Science and Engineering, Yonsei University, Seoul, 03722 Korea ,grid.15444.300000 0004 0470 5454Center for Multi-Dimensional Materials, Yonsei University, Seoul, 03722 Korea
| | - Gwangmook Kim
- grid.15444.300000 0004 0470 5454Department of Materials Science and Engineering, Yonsei University, Seoul, 03722 Korea ,grid.15444.300000 0004 0470 5454Center for Multi-Dimensional Materials, Yonsei University, Seoul, 03722 Korea
| | - Taehoon Kim
- grid.15444.300000 0004 0470 5454Department of Materials Science and Engineering, Yonsei University, Seoul, 03722 Korea ,grid.15444.300000 0004 0470 5454Center for Multi-Dimensional Materials, Yonsei University, Seoul, 03722 Korea
| | - Joon Sang Lee
- grid.15444.300000 0004 0470 5454Department of Mechanical Engineering, Yonsei University, Seoul, 03722 Korea
| | - Wooyoung Shim
- grid.15444.300000 0004 0470 5454Department of Materials Science and Engineering, Yonsei University, Seoul, 03722 Korea ,grid.15444.300000 0004 0470 5454Center for Multi-Dimensional Materials, Yonsei University, Seoul, 03722 Korea
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5
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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: 10.8] [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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Zhang J, Mao W, Ren Y, Sun RN, Yan N, Gong H. Simulating the ion permeation and ion selection for a eukaryotic voltage-gated sodium channel Na VPaS. Protein Cell 2019. [PMID: 29532417 PMCID: PMC5966359 DOI: 10.1007/s13238-018-0522-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Juanrong Zhang
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China
| | - Wenzhi Mao
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China
| | - Yanhui Ren
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China
| | - Rui-Ning Sun
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China
| | - Nieng Yan
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China.
- State Key Laboratory of Membrane Biology, 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.
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China.
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DeMarco KR, Bekker S, Vorobyov I. Challenges and advances in atomistic simulations of potassium and sodium ion channel gating and permeation. J Physiol 2018; 597:679-698. [PMID: 30471114 DOI: 10.1113/jp277088] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 10/15/2018] [Indexed: 12/19/2022] Open
Abstract
Ion channels are implicated in many essential physiological events such as electrical signal propagation and cellular communication. The advent of K+ and Na+ ion channel structure determination has facilitated numerous investigations of molecular determinants of their behaviour. At the same time, rapid development of computer hardware and molecular simulation methodologies has made computational studies of large biological molecules in all-atom representation tractable. The concurrent evolution of experimental structural biology with biomolecular computer modelling has yielded mechanistic details of fundamental processes unavailable through experiments alone, such as ion conduction and ion channel gating. This review is a short survey of the atomistic computational investigations of K+ and Na+ ion channels, focusing on KcsA and several voltage-gated channels from the KV and NaV families, which have garnered many successes and engendered several long-standing controversies regarding the nature of their structure-function relationship. We review the latest advancements and challenges facing the field of molecular modelling and simulation regarding the structural and energetic determinants of ion channel function and their agreement with experimental observations.
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Affiliation(s)
- Kevin R DeMarco
- Department of Physiology and Membrane Biology, School of Medicine, University of California, Davis, CA, USA.,Department of Pharmacology, School of Medicine, University of California, Davis, CA, USA
| | - Slava Bekker
- Department of Physiology and Membrane Biology, School of Medicine, University of California, Davis, CA, USA.,Chemistry Department, American River College, Sacramento, CA, USA
| | - Igor Vorobyov
- Department of Physiology and Membrane Biology, School of Medicine, University of California, Davis, CA, USA.,Department of Pharmacology, School of Medicine, University of California, Davis, CA, USA
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8
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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: 20] [Impact Index Per Article: 2.9] [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
Abstract
Bacterial and human voltage-gated sodium channels (Navs) exhibit similar cation selectivity, despite their distinct EEEE and DEKA selectivity filter signature sequences. Recent high-resolution structures for bacterial Navs have allowed us to learn about ion conduction mechanisms in these simpler homo-tetrameric channels, but our understanding of the function of their mammalian counterparts remains limited. To probe these conduction mechanisms, a model of the human Nav1.2 channel has been constructed by grafting residues of its selectivity filter and external vestibular region onto the bacterial NavRh channel with atomic-resolution structure. Multi-μs fully atomistic simulations capture long time-scale ion and protein movements associated with the permeation of Na+ and K+ ions, and their differences. We observe a Na+ ion knock-on conduction mechanism facilitated by low energy multi-carboxylate/multi-Na+ complexes, akin to the bacterial channels. These complexes involve both the DEKA and vestibular EEDD rings, acting to draw multiple Na+ into the selectivity filter and promote permeation. When the DEKA ring lysine is protonated, we observe that its ammonium group is actively participating in Na+ permeation, presuming the role of another ion. It participates in the formation of a stable complex involving carboxylates that collectively bind both Na+ and the Lys ammonium group in a high-field strength site, permitting pass-by translocation of Na+. In contrast, multiple K+ ion complexes with the DEKA and EEDD rings are disfavored by up to 8.3 kcal/mol, with the K+-lysine-carboxylate complex non-existent. As a result, lysine acts as an electrostatic plug that partially blocks the flow of K+ ions, which must instead wait for isomerization of lysine downward to clear the path for K+ passage. These distinct mechanisms give us insight into the nature of ion conduction and selectivity in human Nav channels, while uncovering high field strength carboxylate binding complexes that define the more general phenomenon of Na+-selective ion transport in nature.
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Affiliation(s)
- Emelie Flood
- School of Science, RMIT University, Melbourne, Vic, Australia
| | - Céline Boiteux
- School of Science, RMIT University, Melbourne, Vic, Australia
| | - Toby W. Allen
- School of Science, RMIT University, Melbourne, Vic, Australia
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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: 0.7] [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]
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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10
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Zangari A, Micheli D, Galeazzi R, Tozzi A. Node of Ranvier as an Array of Bio-Nanoantennas for Infrared Communication in Nerve Tissue. Sci Rep 2018; 8:539. [PMID: 29323217 PMCID: PMC5764955 DOI: 10.1038/s41598-017-18866-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 12/18/2017] [Indexed: 01/21/2023] Open
Abstract
Electromagnetic radiation, in the visible and infrared spectrum, is increasingly being investigated for its possible role in the most evolved brain capabilities. Beside experimental evidence of electromagnetic cellular interactions, the possibility of light propagation in the axon has been recently demonstrated using computational modelling, although an explanation of its source is still not completely understood. We studied electromagnetic radiation onset and propagation at optical frequencies in myelinated axons, under the assumption that ion channel currents in the node of Ranvier behave like an array of nanoantennas emitting in the wavelength range from 300 to 2500 nm. Our results suggest that the wavelengths below 1600 nm are most likely to propagate throughout myelinated segments. Therefore, a broad wavelength window exists where both generation and propagation could happen, which in turn raises the possibility that such a radiation may play some role in neurotransmission.
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Affiliation(s)
- Andrea Zangari
- Azienda Ospedaliera San Camillo Forlanini, Pediatric Surgery and Urology Unit, Circonvallazione Gianicolense 87-00152, Roma, Italy
| | - Davide Micheli
- TIM S.P.A., Wireless Access Engineering Department, Viale Parco de' Medici, 61 - 00148, Roma, Italy.
| | - Roberta Galeazzi
- Dipartimento di Scienze della Vita e dell'Ambiente, università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Antonio Tozzi
- UOC Fisica Sanitaria, Azienda USL Toscana Sud Est, via Senese 161, 58100, Grosseto, Italy
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11
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Durán-Riveroll LM, Cembella AD. Guanidinium Toxins and Their Interactions with Voltage-Gated Sodium Ion Channels. Mar Drugs 2017; 15:E303. [PMID: 29027912 PMCID: PMC5666411 DOI: 10.3390/md15100303] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 09/14/2017] [Accepted: 09/27/2017] [Indexed: 12/19/2022] Open
Abstract
Guanidinium toxins, such as saxitoxin (STX), tetrodotoxin (TTX) and their analogs, are naturally occurring alkaloids with divergent evolutionary origins and biogeographical distribution, but which share the common chemical feature of guanidinium moieties. These guanidinium groups confer high biological activity with high affinity and ion flux blockage capacity for voltage-gated sodium channels (NaV). Members of the STX group, known collectively as paralytic shellfish toxins (PSTs), are produced among three genera of marine dinoflagellates and about a dozen genera of primarily freshwater or brackish water cyanobacteria. In contrast, toxins of the TTX group occur mainly in macrozoa, particularly among puffer fish, several species of marine invertebrates and a few terrestrial amphibians. In the case of TTX and analogs, most evidence suggests that symbiotic bacteria are the origin of the toxins, although endogenous biosynthesis independent from bacteria has not been excluded. The evolutionary origin of the biosynthetic genes for STX and analogs in dinoflagellates and cyanobacteria remains elusive. These highly potent molecules have been the subject of intensive research since the latter half of the past century; first to study the mode of action of their toxigenicity, and later as tools to characterize the role and structure of NaV channels, and finally as therapeutics. Their pharmacological activities have provided encouragement for their use as therapeutants for ion channel-related pathologies, such as pain control. The functional role in aquatic and terrestrial ecosystems for both groups of toxins is unproven, although plausible mechanisms of ion channel regulation and chemical defense are often invoked. Molecular approaches and the development of improved detection methods will yield deeper understanding of their physiological and ecological roles. This knowledge will facilitate their further biotechnological exploitation and point the way towards development of pharmaceuticals and therapeutic applications.
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Affiliation(s)
- Lorena M Durán-Riveroll
- CONACYT-Instituto de Ciencias del Mary Limnología, Universidad Nacional Autónoma de México, Mexico 04510, Mexico.
| | - Allan D Cembella
- Alfred-Wegener-Institut, Helmholtz Zentrum für Polar-und Meeresforschung, 27570 Bremerhaven, Germany.
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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: 2.6] [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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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]
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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: 0.7] [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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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]
Abstract
Structures of several voltage-gated sodium (NaV) channels from bacteria have been determined recently, but the same feat might not be achieved for the mammalian counterparts in the near future. Thus, at present, computational studies of the mammalian NaV channels have to be performed using homology models based on the bacterial crystal structures. A successful homology model for the mammalian NaV1.4 channel was recently constructed using the extensive mutation data for binding of μ-conotoxin GIIIA to NaV1.4, which was further validated through studies of binding of other μ-conotoxins and ion permeation. Understanding the similarities and differences between the bacterial and mammalian NaV channels is an important issue, and the NaV1.4-GIIIA system provides a good opportunity for such a comparison. To this end, we study the binding of GIIIA to the bacterial channels NaVAb and NaVRh. The complex structures are obtained using docking and molecular dynamics simulations, and the dissociation of GIIIA is studied through umbrella sampling simulations. The results are compared to those obtained from the NaV1.4-GIIIA system, and the differences in the binding modes arising from the changes in the selectivity filters are highlighted.
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Affiliation(s)
- Dharmeshkumar Patel
- School of Physics, University of Sydney , Sydney, New South Wales 2006, Australia
| | - Somayeh Mahdavi
- School of Physics, University of Sydney , Sydney, New South Wales 2006, Australia
| | - Serdar Kuyucak
- School of Physics, University of Sydney , Sydney, New South Wales 2006, Australia
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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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Convergent Evolution of Tetrodotoxin-Resistant Sodium Channels in Predators and Prey. CURRENT TOPICS IN MEMBRANES 2016; 78:87-113. [DOI: 10.1016/bs.ctm.2016.07.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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