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Catterall WA, Gamal El-Din TM, Wisedchaisri G. The chemistry of electrical signaling in sodium channels from bacteria and beyond. Cell Chem Biol 2024; 31:1405-1421. [PMID: 39151407 DOI: 10.1016/j.chembiol.2024.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 06/27/2024] [Accepted: 07/22/2024] [Indexed: 08/19/2024]
Abstract
Electrical signaling is essential for all fast processes in biology, but its molecular mechanisms have been uncertain. This review article focuses on studies of bacterial sodium channels in order to home in on the essential molecular and chemical mechanisms underlying transmembrane ion conductance and voltage-dependent gating without the overlay of complex protein interactions and regulatory mechanisms in mammalian sodium channels. This minimalist approach has yielded a nearly complete picture of sodium channel function at the atomic level that are mostly conserved in mammalian sodium channels, including sodium selectivity and conductance, voltage sensing and activation, electromechanical coupling to pore opening and closing, slow inactivation, and pathogenic dysfunction in a debilitating channelopathy. Future studies of nature's simplest sodium channels may continue to yield key insights into the fundamental molecular and chemical principles of their function and further elucidate the chemical basis of electrical signaling.
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Affiliation(s)
- William A Catterall
- Department of Pharmacology, University of Washington, Seattle WA 98195-7280, USA.
| | - Tamer M Gamal El-Din
- Department of Pharmacology, University of Washington, Seattle WA 98195-7280, USA.
| | - Goragot Wisedchaisri
- Department of Pharmacology, University of Washington, Seattle WA 98195-7280, USA.
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2
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Chen AY, Brooks BR, Damjanovic A. Ion channel selectivity through ion-modulated changes of selectivity filter p Ka values. Proc Natl Acad Sci U S A 2023; 120:e2220343120. [PMID: 37339196 PMCID: PMC10293820 DOI: 10.1073/pnas.2220343120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 04/26/2023] [Indexed: 06/22/2023] Open
Abstract
In bacterial voltage-gated sodium channels, the passage of ions through the pore is controlled by a selectivity filter (SF) composed of four glutamate residues. The mechanism of selectivity has been the subject of intense research, with suggested mechanisms based on steric effects, and ion-triggered conformational change. Here, we propose an alternative mechanism based on ion-triggered shifts in pKa values of SF glutamates. We study the NavMs channel for which the open channel structure is available. Our free-energy calculations based on molecular dynamics simulations suggest that pKa values of the four glutamates are higher in solution of K+ ions than in solution of Na+ ions. Higher pKa in the presence of K+ stems primarily from the higher population of dunked conformations of the protonated Glu sidechain, which exhibit a higher pKa shift. Since pKa values are close to the physiological pH, this results in predominant population of the fully deprotonated state of glutamates in Na+ solution, while protonated states are predominantly populated in K+ solution. Through molecular dynamics simulations we calculate that the deprotonated state is the most conductive, the singly protonated state is less conductive, and the doubly protonated state has significantly reduced conductance. Thus, we propose that a significant component of selectivity is achieved through ion-triggered shifts in the protonation state, which favors more conductive states for Na+ ions and less conductive states for K+ ions. This mechanism also suggests a strong pH dependence of selectivity, which has been experimentally observed in structurally similar NaChBac channels.
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Affiliation(s)
- Ada Y. Chen
- Department of Physics & Astronomy, Johns Hopkins University, Baltimore, MD21218
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, NIH, Bethesda, MD20892
| | - Bernard R. Brooks
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, NIH, Bethesda, MD20892
| | - Ana Damjanovic
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, NIH, Bethesda, MD20892
- Department of Biophysics, Johns Hopkins University, Baltimore, MD21218
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3
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Ives CM, Thomson NJ, Zachariae U. A cooperative knock-on mechanism underpins Ca2+-selective cation permeation in TRPV channels. J Gen Physiol 2023; 155:213957. [PMID: 36943243 PMCID: PMC10038842 DOI: 10.1085/jgp.202213226] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 11/15/2022] [Accepted: 02/28/2023] [Indexed: 03/23/2023] Open
Abstract
The selective exchange of ions across cellular membranes is a vital biological process. Ca2+-mediated signaling is implicated in a broad array of physiological processes in cells, while elevated intracellular concentrations of Ca2+ are cytotoxic. Due to the significance of this cation, strict Ca2+ concentration gradients are maintained across the plasma and organelle membranes. Therefore, Ca2+ signaling relies on permeation through selective ion channels that control the flux of Ca2+ ions. A key family of Ca2+-permeable membrane channels is the polymodal signal-detecting transient receptor potential (TRP) ion channels. TRP channels are activated by a wide variety of cues including temperature, small molecules, transmembrane voltage, and mechanical stimuli. While most members of this family permeate a broad range of cations non-selectively, TRPV5 and TRPV6 are unique due to their strong Ca2+ selectivity. Here, we address the question of how some members of the TRPV subfamily show a high degree of Ca2+ selectivity while others conduct a wider spectrum of cations. We present results from all-atom molecular dynamics simulations of ion permeation through two Ca2+-selective and two non-selective TRPV channels. Using a new method to quantify permeation cooperativity based on mutual information, we show that Ca2+-selective TRPV channel permeation occurs by a three-binding site knock-on mechanism, whereas a two-binding site knock-on mechanism is observed in non-selective TRPV channels. Each of the ion binding sites involved displayed greater affinity for Ca2+ over Na+. As such, our results suggest that coupling to an extra binding site in the Ca2+-selective TRPV channels underpins their increased selectivity for Ca2+ over Na+ ions. Furthermore, analysis of all available TRPV channel structures shows that the selectivity filter entrance region is wider for the non-selective TRPV channels, slightly destabilizing ion binding at this site, which is likely to underlie mechanistic decoupling.
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Affiliation(s)
- Callum M Ives
- Computational Biology, School of Life Sciences, University of Dundee , Dundee, UK
| | - Neil J Thomson
- Computational Biology, School of Life Sciences, University of Dundee , Dundee, UK
| | - Ulrich Zachariae
- Computational Biology, School of Life Sciences, University of Dundee , Dundee, UK
- Biochemistry and Drug Discovery, School of Life Sciences, University of Dundee , Dundee, UK
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4
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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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5
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Minniberger S, Abdolvand S, Braunbeck S, Sun H, Plested AJR. Asymmetry and Ion Selectivity Properties of Bacterial Channel NaK Mutants Derived from Ionotropic Glutamate Receptors. J Mol Biol 2023; 435:167970. [PMID: 36682679 DOI: 10.1016/j.jmb.2023.167970] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/17/2022] [Accepted: 01/12/2023] [Indexed: 01/22/2023]
Abstract
Ionotropic glutamate receptors are ligand-gated cation channels that play essential roles in the excitatory synaptic transmission throughout the central nervous system. A number of open-pore structures of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic-acid (AMPA)-type glutamate receptors became available recently by cryo-electron microscopy (cryo-EM). These structures provide valuable insights into the conformation of the selectivity filter (SF), the part of the ion channel that determines the ion selectivity. Nonetheless, due to the moderate resolution of the cryo-EM structures, detailed information such as ion occupancy of monovalent and divalent cations as well as positioning of the side-chains in the SF is still missing. Here, in an attempt to obtain high-resolution information about glutamate receptor SFs, we incorporated partial SF sequences of the AMPA and kainate receptors into the bacterial tetrameric cation channel NaK, which served as a structural scaffold. We determined a series of X-ray structures of NaK-CDI, NaK-SDI and NaK-SELM mutants at 1.42-2.10 Å resolution, showing distinct ion occupation of different monovalent cations. Molecular dynamics (MD) simulations of NaK-CDI indicated the channel to be conductive to monovalent cations, which agrees well with our electrophysiology recordings. Moreover, previously unobserved structural asymmetry of the SF was revealed by the X-ray structures and MD simulations, implying its importance in ion non-selectivity of tetrameric cation channels.
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Affiliation(s)
- Sonja Minniberger
- Institute of Biology, Cellular Biophysics, Humboldt Universität zu Berlin, 10115 Berlin, Germany; NeuroCure, Charité Universitätsmedizin, 10117 Berlin, Germany; Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Saeid Abdolvand
- Institute of Biology, Cellular Biophysics, Humboldt Universität zu Berlin, 10115 Berlin, Germany; NeuroCure, Charité Universitätsmedizin, 10117 Berlin, Germany; Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Sebastian Braunbeck
- Institute of Biology, Cellular Biophysics, Humboldt Universität zu Berlin, 10115 Berlin, Germany; NeuroCure, Charité Universitätsmedizin, 10117 Berlin, Germany; Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Han Sun
- Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Institute of Chemistry, Department of Chemistry, Technische Universität Berlin, 10623 Berlin, Germany.
| | - Andrew J R Plested
- Institute of Biology, Cellular Biophysics, Humboldt Universität zu Berlin, 10115 Berlin, Germany; NeuroCure, Charité Universitätsmedizin, 10117 Berlin, Germany; Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany.
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6
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Wang G, Xu L, Chen H, Liu Y, Pan P, Hou T. Recent advances in computational studies on voltage‐gated sodium channels: Drug design and mechanism studies. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2023. [DOI: 10.1002/wcms.1641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Affiliation(s)
- Gaoang Wang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University College of Pharmaceutical Sciences, Zhejiang University Hangzhou Zhejiang China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering School of Electrical and Information Engineering, Jiangsu University of Technology Changzhou Jiangsu China
| | - Haiyi Chen
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University College of Pharmaceutical Sciences, Zhejiang University Hangzhou Zhejiang China
| | - Yifei Liu
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University College of Pharmaceutical Sciences, Zhejiang University Hangzhou Zhejiang China
| | - Peichen Pan
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University College of Pharmaceutical Sciences, Zhejiang University Hangzhou Zhejiang China
| | - Tingjun Hou
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University College of Pharmaceutical Sciences, Zhejiang University Hangzhou Zhejiang China
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7
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Wilson MA, Pohorille A. Structure and Computational Electrophysiology of Ac-LS3, a Synthetic Ion Channel. J Phys Chem B 2022; 126:8985-8999. [PMID: 36306164 DOI: 10.1021/acs.jpcb.2c05965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Computer simulations are reported on Ac-LS3, a synthetic ion channel, containing 21 residues with a Leu-Ser-Ser-Leu-Leu-Ser-Leu heptad repeat, which forms ions channels upon application of voltage. A hexameric, coiled-coil bundle initially positioned perpendicular to the membrane settled into a stable, tilted structure after 1.5 μs, most likely to improve contacts between the non-polar exterior of the channel and the hydrophobic core of the membrane. Once tilted, the bundle remained in this state during subsequent simulations of nearly 10 μs at voltages ranging from 200 to -100 mV. In contrast, attempts to identify a stable pentameric structure failed, thus supporting the hypothesis that the channel is a hexamer. Results at 100 mV were used to reconstruct the free energy profiles for K+ and Cl- in the channel. This was done by way of several methods in which results of molecular dynamics (MD) simulations were combined with the electrodiffusion model. Two of them developed recently do not require knowledge of the diffusivity. Instead, they utilize one-sided density profiles and committor probabilities. The consistency between different methods is very good, supporting the utility of the newly developed methods for reconstructing free energies of ions in channels. The flux of K+, which accounts for most of the current through the channel, calculated directly from MD matches well the total measured current. However, the current of Cl- is somewhat overestimated, possibly due to a slightly unbalanced force field involving chloride. The current-voltage dependence was also reconstructed by way of a recently developed, efficient method that requires simulations only at a single voltage, yielding good agreement with the experiment. Taken together, the results demonstrate that computational electrophysiology has become a reliable tool for studying how channels mediate ion transport through membranes.
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Affiliation(s)
- Michael A Wilson
- Exobiology Branch, MS239-4, NASA Ames Research Center, Moffett Field, California94035, United States.,SETI Institute, 189 Bernardo Avenue, Suite 200, Mountain View, California94043, United States
| | - Andrew Pohorille
- Exobiology Branch, MS239-4, NASA Ames Research Center, Moffett Field, California94033, United States.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California94132, United States
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8
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Berselli A, Alberini G, Benfenati F, Maragliano L. Computational study of ion permeation through claudin-4 paracellular channels. Ann N Y Acad Sci 2022; 1516:162-174. [PMID: 35811406 PMCID: PMC9796105 DOI: 10.1111/nyas.14856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Claudins (Cldns) form a large family of protein homologs that are essential for the assembly of paracellular tight junctions (TJs), where they form channels or barriers with tissue-specific selectivity for permeants. In contrast to several family members whose physiological role has been identified, the function of claudin 4 (Cldn4) remains elusive, despite experimental evidence suggesting that it can form anion-selective TJ channels in the renal epithelium. Computational approaches have recently been employed to elucidate the molecular basis of Cldns' function, and hence could help in clarifying the role of Cldn4. In this work, we use structural modeling and all-atom molecular dynamics simulations to transfer two previously introduced structural models of Cldn-based paracellular complexes to Cldn4 to reproduce a paracellular anion channel. Free energy calculations for ionic transport through the pores allow us to establish the thermodynamic properties driving the ion-selectivity of the structures. While one model shows a cavity permeable to chloride and repulsive to cations, the other forms barrier to the passage of all the major physiological ions. Furthermore, our results confirm the charge selectivity role of the residue Lys65 in the first extracellular loop of the protein, rationalizing Cldn4 control of paracellular permeability.
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Affiliation(s)
- Alessandro Berselli
- Center for Synaptic Neuroscience and Technology (NSYN@UniGe)Istituto Italiano di TecnologiaGenovaItaly
- Department of Experimental MedicineUniversità degli Studi di GenovaGenovaItaly
| | - Giulio Alberini
- Center for Synaptic Neuroscience and Technology (NSYN@UniGe)Istituto Italiano di TecnologiaGenovaItaly
- IRCCS Ospedale Policlinico San MartinoGenovaItaly
| | - Fabio Benfenati
- Center for Synaptic Neuroscience and Technology (NSYN@UniGe)Istituto Italiano di TecnologiaGenovaItaly
- IRCCS Ospedale Policlinico San MartinoGenovaItaly
| | - Luca Maragliano
- Center for Synaptic Neuroscience and Technology (NSYN@UniGe)Istituto Italiano di TecnologiaGenovaItaly
- Department of Life and Environmental SciencesPolytechnic University of MarcheAnconaItaly
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9
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Molecular Events behind the Selectivity and Inactivation Properties of Model NaK-Derived Ion Channels. Int J Mol Sci 2022; 23:ijms23169246. [PMID: 36012519 PMCID: PMC9409022 DOI: 10.3390/ijms23169246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/10/2022] [Accepted: 08/14/2022] [Indexed: 11/17/2022] Open
Abstract
Y55W mutants of non-selective NaK and partly K+-selective NaK2K channels have been used to explore the conformational dynamics at the pore region of these channels as they interact with either Na+ or K+. A major conclusion is that these channels exhibit a remarkable pore conformational flexibility. Homo-FRET measurements reveal a large change in W55–W55 intersubunit distances, enabling the selectivity filter (SF) to admit different species, thus, favoring poor or no selectivity. Depending on the cation, these channels exhibit wide-open conformations of the SF in Na+, or tight induced-fit conformations in K+, most favored in the four binding sites containing NaK2K channels. Such conformational flexibility seems to arise from an altered pattern of restricting interactions between the SF and the protein scaffold behind it. Additionally, binding experiments provide clues to explain such poor selectivity. Compared to the K+-selective KcsA channel, these channels lack a high affinity K+ binding component and do not collapse in Na+. Thus, they cannot properly select K+ over competing cations, nor reject Na+ by collapsing, as K+-selective channels do. Finally, these channels do not show C-type inactivation, likely because their submillimolar K+ binding affinities prevent an efficient K+ loss from their SF, thus favoring permanently open channel states.
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10
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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: 0] [Impact Index Per Article: 0] [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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11
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Zhu Z, Deng Z, Wang Q, Wang Y, Zhang D, Xu R, Guo L, Wen H. Simulation and Machine Learning Methods for Ion-Channel Structure Determination, Mechanistic Studies and Drug Design. Front Pharmacol 2022; 13:939555. [PMID: 35837274 PMCID: PMC9275593 DOI: 10.3389/fphar.2022.939555] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
Ion channels are expressed in almost all living cells, controlling the in-and-out communications, making them ideal drug targets, especially for central nervous system diseases. However, owing to their dynamic nature and the presence of a membrane environment, ion channels remain difficult targets for the past decades. Recent advancement in cryo-electron microscopy and computational methods has shed light on this issue. An explosion in high-resolution ion channel structures paved way for structure-based rational drug design and the state-of-the-art simulation and machine learning techniques dramatically improved the efficiency and effectiveness of computer-aided drug design. Here we present an overview of how simulation and machine learning-based methods fundamentally changed the ion channel-related drug design at different levels, as well as the emerging trends in the field.
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Affiliation(s)
- Zhengdan Zhu
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Beijing Institute of Big Data Research, Beijing, China
| | - Zhenfeng Deng
- DP Technology, Beijing, China
- School of Pharmaceutical Sciences, Peking University, Beijing, China
| | | | | | - Duo Zhang
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- DP Technology, Beijing, China
| | - Ruihan Xu
- DP Technology, Beijing, China
- National Engineering Research Center of Visual Technology, Peking University, Beijing, China
| | | | - Han Wen
- DP Technology, Beijing, China
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12
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Tikhonov DB, Zhorov BS. P-Loop Channels: Experimental Structures, and Physics-Based and Neural Networks-Based Models. MEMBRANES 2022; 12:membranes12020229. [PMID: 35207150 PMCID: PMC8876033 DOI: 10.3390/membranes12020229] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/09/2022] [Accepted: 02/09/2022] [Indexed: 01/27/2023]
Abstract
The superfamily of P-loop channels includes potassium, sodium, and calcium channels, as well as TRP channels and ionotropic glutamate receptors. A rapidly increasing number of crystal and cryo-EM structures have revealed conserved and variable elements of the channel structures. Intriguing differences are seen in transmembrane helices of channels, which may include π-helical bulges. The bulges reorient residues in the helices and thus strongly affect their intersegment contacts and patterns of ligand-sensing residues. Comparison of the experimental structures suggests that some π-bulges are dynamic: they may appear and disappear upon channel gating and ligand binding. The AlphaFold2 models represent a recent breakthrough in the computational prediction of protein structures. We compared some crystal and cryo-EM structures of P-loop channels with respective AlphaFold2 models. Folding of the regions, which are resolved experimentally, is generally similar to that predicted in the AlphaFold2 models. The models also reproduce some subtle but significant differences between various P-loop channels. However, patterns of π-bulges do not necessarily coincide in the experimental and AlphaFold2 structures. Given the importance of dynamic π-bulges, further studies involving experimental and theoretical approaches are necessary to understand the cause of the discrepancy.
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13
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Choudhury K, Kasimova MA, McComas S, Howard RJ, Delemotte L. An open state of a voltage-gated sodium channel involving a π-helix and conserved pore-facing asparagine. Biophys J 2022; 121:11-22. [PMID: 34890580 PMCID: PMC8758419 DOI: 10.1016/j.bpj.2021.12.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/26/2021] [Accepted: 12/06/2021] [Indexed: 01/07/2023] Open
Abstract
Voltage-gated sodium (Nav) channels play critical roles in propagating action potentials and otherwise manipulating ionic gradients in excitable cells. These channels open in response to membrane depolarization, selectively permeating sodium ions until rapidly inactivating. Structural characterization of the gating cycle in this channel family has proved challenging, particularly due to the transient nature of the open state. A structure from the bacterium Magnetococcus marinus Nav (NavMs) was initially proposed to be open, based on its pore diameter and voltage-sensor conformation. However, the functional annotation of this model, and the structural details of the open state, remain disputed. In this work, we used molecular modeling and simulations to test possible open-state models of NavMs. The full-length experimental structure, termed here the α-model, was consistently dehydrated at the activation gate, indicating an inability to conduct ions. Based on a spontaneous transition observed in extended simulations, and sequence/structure comparison to other Nav channels, we built an alternative π-model featuring a helix transition and the rotation of a conserved asparagine residue into the activation gate. Pore hydration, ion permeation, and state-dependent drug binding in this model were consistent with an open functional state. This work thus offers both a functional annotation of the full-length NavMs structure and a detailed model for a stable Nav open state, with potential conservation in diverse ion-channel families.
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Affiliation(s)
- Koushik Choudhury
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Solna, Sweden
| | - Marina A. Kasimova
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Solna, Sweden
| | - Sarah McComas
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Rebecca J. Howard
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Solna, Sweden,Corresponding author
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14
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Direct proof of soft knock-on mechanism of ion permeation in a voltage gated sodium channel. Int J Biol Macromol 2021; 188:369-374. [PMID: 34371044 DOI: 10.1016/j.ijbiomac.2021.08.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/09/2021] [Accepted: 08/02/2021] [Indexed: 11/22/2022]
Abstract
Sodium channels selectively conduct Na+ ions across cellular membrane with extraordinary efficiency, which is essential for initiating action potentials. However, how Na+ ions permeate the ionic channels remains obscure and ambiguous. With more than 40 conductance events from microsecond molecular dynamics simulation, the soft knock-on ion permeation mediated by water molecules was observed and confirmed by the free energy profile and electrostatic potential calculation in this study. During the soft knock-on process, the change of average distance between four oxygen atoms in Glu177-Glu177 plays a very important role for the permeation of Na+ ion. Exploration of the ionic conductance mechanism could provide a guideline for designing ion channel targeted drug.
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15
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Abstract
Fast excitatory synaptic transmission in the central nervous system relies on the AMPA-type glutamate receptor (AMPAR). This receptor incorporates a nonselective cation channel, which is opened by the binding of glutamate. Although the open pore structure has recently became available from cryo-electron microscopy (Cryo-EM), the molecular mechanisms governing cation permeability in AMPA receptors are not understood. Here, we combined microsecond molecular dynamic (MD) simulations on a putative open-state structure of GluA2 with electrophysiology on cloned channels to elucidate ion permeation mechanisms. Na+, K+, and Cs+ permeated at physiological rates, consistent with a structure that represents a true open state. A single major ion binding site for Na+ and K+ in the pore represents the simplest selectivity filter (SF) structure for any tetrameric cation channel of known structure. The minimal SF comprised only Q586 and Q587, and other residues on the cytoplasmic side formed a water-filled cavity with a cone shape that lacked major interactions with ions. We observed that Cl- readily enters the upper pore, explaining anion permeation in the RNA-edited (Q586R) form of GluA2. A permissive architecture of the SF accommodated different alkali metals in distinct solvation states to allow rapid, nonselective cation permeation and copermeation by water. Simulations suggested Cs+ uses two equally populated ion binding sites in the filter, and we confirmed with electrophysiology of GluA2 that Cs+ is slightly more permeant than Na+, consistent with serial binding sites preferentially driving selectivity.
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16
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17
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Chen AY, Brooks BR, Damjanovic A. Determinants of conductance of a bacterial voltage-gated sodium channel. Biophys J 2021; 120:3050-3069. [PMID: 34214541 DOI: 10.1016/j.bpj.2021.06.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/22/2021] [Accepted: 06/08/2021] [Indexed: 10/21/2022] Open
Abstract
Through molecular dynamics (MD) and free energy simulations in electric fields, we examine the factors influencing conductance of bacterial voltage-gated sodium channel NavMs. The channel utilizes four glutamic acid residues in the selectivity filter (SF). Previously, we have shown, through constant pH and free energy calculations of pKa values, that fully deprotonated, singly protonated, and doubly protonated states are all feasible at physiological pH, depending on how many ions are bound in the SF. With 173 MD simulations of 450 or 500 ns and additional free energy simulations, we determine that the conductance is highest for the deprotonated state and decreases with each additional proton bound. We also determine that the pKa value of the four glutamic residues for the transition between deprotonated and singly protonated states is close to the physiological pH and that there is a small voltage dependence. The pKa value and conductance trends are in agreement with experimental work on bacterial Nav channels, which show a decrease in maximal conductance with lowering of pH, with pKa in the physiological range. We examine binding sites for Na+ in the SF, compare with previous work, and note a dependence on starting structures. We find that narrowing of the gate backbone to values lower than the crystal structure's backbone radius reduces the conductance, whereas increasing the gate radius further does not affect the conductance. Simulations with some amount of negatively charged lipids as opposed to purely neutral lipids increases the conductance, as do simulations at higher voltages.
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Affiliation(s)
- Ada Y Chen
- Department of Physics & Astronomy, Johns Hopkins University, Baltimore, Maryland; Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Ana Damjanovic
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland; Department of Biophysics, Johns Hopkins University, Baltimore, Maryland.
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18
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van Putten MJ, Fahlke C, Kafitz KW, Hofmeijer J, Rose CR. Dysregulation of Astrocyte Ion Homeostasis and Its Relevance for Stroke-Induced Brain Damage. Int J Mol Sci 2021; 22:5679. [PMID: 34073593 PMCID: PMC8198632 DOI: 10.3390/ijms22115679] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/21/2021] [Accepted: 05/22/2021] [Indexed: 12/14/2022] Open
Abstract
Ischemic stroke is a leading cause of mortality and chronic disability. Either recovery or progression towards irreversible failure of neurons and astrocytes occurs within minutes to days, depending on remaining perfusion levels. Initial damage arises from energy depletion resulting in a failure to maintain homeostasis and ion gradients between extra- and intracellular spaces. Astrocytes play a key role in these processes and are thus central players in the dynamics towards recovery or progression of stroke-induced brain damage. Here, we present a synopsis of the pivotal functions of astrocytes at the tripartite synapse, which form the basis of physiological brain functioning. We summarize the evidence of astrocytic failure and its consequences under ischemic conditions. Special emphasis is put on the homeostasis and stroke-induced dysregulation of the major monovalent ions, namely Na+, K+, H+, and Cl-, and their involvement in maintenance of cellular volume and generation of cerebral edema.
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Affiliation(s)
- Michel J.A.M. van Putten
- Department of Clinical Neurophysiology, University of Twente, 7522 NB Enschede, The Netherlands; (M.J.A.M.v.P.); (J.H.)
| | - Christoph Fahlke
- Institut für Biologische Informationsprozesse, Molekular-und Zellphysiologie (IBI-1), Forschungszentrum Jülich, 52425 Jülich, Germany;
| | - Karl W. Kafitz
- Institute of Neurobiology, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany;
| | - Jeannette Hofmeijer
- Department of Clinical Neurophysiology, University of Twente, 7522 NB Enschede, The Netherlands; (M.J.A.M.v.P.); (J.H.)
| | - Christine R. Rose
- Institute of Neurobiology, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany;
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19
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Wilson MA, Pohorille A. Electrophysiological Properties from Computations at a Single Voltage: Testing Theory with Stochastic Simulations. ENTROPY 2021; 23:e23050571. [PMID: 34066581 PMCID: PMC8148522 DOI: 10.3390/e23050571] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 04/24/2021] [Accepted: 04/28/2021] [Indexed: 12/13/2022]
Abstract
We use stochastic simulations to investigate the performance of two recently developed methods for calculating the free energy profiles of ion channels and their electrophysiological properties, such as current–voltage dependence and reversal potential, from molecular dynamics simulations at a single applied voltage. These methods require neither knowledge of the diffusivity nor simulations at multiple voltages, which greatly reduces the computational effort required to probe the electrophysiological properties of ion channels. They can be used to determine the free energy profiles from either forward or backward one-sided properties of ions in the channel, such as ion fluxes, density profiles, committor probabilities, or from their two-sided combination. By generating large sets of stochastic trajectories, which are individually designed to mimic the molecular dynamics crossing statistics of models of channels of trichotoxin, p7 from hepatitis C and a bacterial homolog of the pentameric ligand-gated ion channel, GLIC, we find that the free energy profiles obtained from stochastic simulations corresponding to molecular dynamics simulations of even a modest length are burdened with statistical errors of only 0.3 kcal/mol. Even with many crossing events, applying two-sided formulas substantially reduces statistical errors compared to one-sided formulas. With a properly chosen reference voltage, the current–voltage curves can be reproduced with good accuracy from simulations at a single voltage in a range extending for over 200 mV. If possible, the reference voltages should be chosen not simply to drive a large current in one direction, but to observe crossing events in both directions.
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Affiliation(s)
- Michael A. Wilson
- Exobiology Branch, MS 239-4, NASA Ames Research Center, Moffett Field, CA 94035, USA;
- SETI Institute, 189 Bernardo Ave, Suite 200, Mountain View, CA 94043, USA
| | - Andrew Pohorille
- Exobiology Branch, MS 239-4, NASA Ames Research Center, Moffett Field, CA 94035, USA;
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94132, USA
- Correspondence: ; Tel.: +1-650-604-5759
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20
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Structure of the full-length human Pannexin1 channel and insights into its role in pyroptosis. Cell Discov 2021; 7:30. [PMID: 33947837 PMCID: PMC8096850 DOI: 10.1038/s41421-021-00259-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 03/10/2021] [Indexed: 12/11/2022] Open
Abstract
Pannexin1 (PANX1) is a large-pore ATP efflux channel with a broad distribution, which allows the exchange of molecules and ions smaller than 1 kDa between the cytoplasm and extracellular space. In this study, we show that in human macrophages PANX1 expression is upregulated by diverse stimuli that promote pyroptosis, which is reminiscent of the previously reported lipopolysaccharide-induced upregulation of PANX1 during inflammasome activation. To further elucidate the function of PANX1, we propose the full-length human Pannexin1 (hPANX1) model through cryo-electron microscopy (cryo-EM) and molecular dynamics (MD) simulation studies, establishing hPANX1 as a homo-heptamer and revealing that both the N-termini and C-termini protrude deeply into the channel pore funnel. MD simulations also elucidate key energetic features governing the channel that lay a foundation to understand the channel gating mechanism. Structural analyses, functional characterizations, and computational studies support the current hPANX1-MD model, suggesting the potential role of hPANX1 in pyroptosis during immune responses.
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21
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Mantegazza M, Cestèle S, Catterall WA. Sodium channelopathies of skeletal muscle and brain. Physiol Rev 2021; 101:1633-1689. [PMID: 33769100 DOI: 10.1152/physrev.00025.2020] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Voltage-gated sodium channels initiate action potentials in nerve, skeletal muscle, and other electrically excitable cells. Mutations in them cause a wide range of diseases. These channelopathy mutations affect every aspect of sodium channel function, including voltage sensing, voltage-dependent activation, ion conductance, fast and slow inactivation, and both biosynthesis and assembly. Mutations that cause different forms of periodic paralysis in skeletal muscle were discovered first and have provided a template for understanding structure, function, and pathophysiology at the molecular level. More recent work has revealed multiple sodium channelopathies in the brain. Here we review the well-characterized genetics and pathophysiology of the periodic paralyses of skeletal muscle and then use this information as a foundation for advancing our understanding of mutations in the structurally homologous α-subunits of brain sodium channels that cause epilepsy, migraine, autism, and related comorbidities. We include studies based on molecular and structural biology, cell biology and physiology, pharmacology, and mouse genetics. Our review reveals unexpected connections among these different types of sodium channelopathies.
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Affiliation(s)
- Massimo Mantegazza
- Université Cote d'Azur, Valbonne-Sophia Antipolis, France.,CNRS UMR7275, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne-Sophia Antipolis, France.,INSERM, Valbonne-Sophia Antipolis, France
| | - Sandrine Cestèle
- Université Cote d'Azur, Valbonne-Sophia Antipolis, France.,CNRS UMR7275, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne-Sophia Antipolis, France
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22
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Pohorille A, Wilson MA. Computational Electrophysiology from a Single Molecular Dynamics Simulation and the Electrodiffusion Model. J Phys Chem B 2021; 125:3132-3144. [DOI: 10.1021/acs.jpcb.0c10737] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrew Pohorille
- Exobiology Branch, MS239-4, NASA Ames Research Center, Moffett Field, California 94035, United States
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94132, United States
| | - Michael A. Wilson
- Exobiology Branch, MS239-4, NASA Ames Research Center, Moffett Field, California 94035, United States
- SETI Institute, 189 Bernardo Avenue, Suite 200, Mountain View, California 94043, United States
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23
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Gibby WAT, Fedorenko OA, Guardiani C, Barabash ML, Mumby T, Roberts SK, Luchinsky DG, McClintock PVE. Application of a Statistical and Linear Response Theory to Multi-Ion Na + Conduction in NaChBac. ENTROPY (BASEL, SWITZERLAND) 2021; 23:249. [PMID: 33670053 PMCID: PMC7926348 DOI: 10.3390/e23020249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/03/2021] [Accepted: 02/11/2021] [Indexed: 01/04/2023]
Abstract
Biological ion channels are fundamental to maintaining life. In this manuscript we apply our recently developed statistical and linear response theory to investigate Na+ conduction through the prokaryotic Na+ channel NaChBac. This work is extended theoretically by the derivation of ionic conductivity and current in an electrochemical gradient, thus enabling us to compare to a range of whole-cell data sets performed on this channel. Furthermore, we also compare the magnitudes of the currents and populations at each binding site to previously published single-channel recordings and molecular dynamics simulations respectively. In doing so, we find excellent agreement between theory and data, with predicted energy barriers at each of the four binding sites of ∼4,2.9,3.6, and 4kT.
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Affiliation(s)
- William A. T. Gibby
- Department of Physics, Lancaster University, Lancaster LA1 4YB, UK; (C.G.); (M.L.B.); (T.M.); (D.G.L.)
| | - Olena A. Fedorenko
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK;
- Division of Biomedical and Life Sciences, Lancaster University, Lancaster LA1 4YQ, UK;
| | - Carlo Guardiani
- Department of Physics, Lancaster University, Lancaster LA1 4YB, UK; (C.G.); (M.L.B.); (T.M.); (D.G.L.)
- Department of Mechanical and Aerospace Engineering, Sapienza University, 00185 Rome, Italy
| | - Miraslau L. Barabash
- Department of Physics, Lancaster University, Lancaster LA1 4YB, UK; (C.G.); (M.L.B.); (T.M.); (D.G.L.)
| | - Thomas Mumby
- Department of Physics, Lancaster University, Lancaster LA1 4YB, UK; (C.G.); (M.L.B.); (T.M.); (D.G.L.)
| | - Stephen K. Roberts
- Division of Biomedical and Life Sciences, Lancaster University, Lancaster LA1 4YQ, UK;
| | - Dmitry G. Luchinsky
- Department of Physics, Lancaster University, Lancaster LA1 4YB, UK; (C.G.); (M.L.B.); (T.M.); (D.G.L.)
- KBR Inc., Ames Research Center, Mountain View, CA 94035, USA
| | - Peter V. E. McClintock
- Department of Physics, Lancaster University, Lancaster LA1 4YB, UK; (C.G.); (M.L.B.); (T.M.); (D.G.L.)
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24
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Sula A, Hollingworth D, Ng LCT, Larmore M, DeCaen PG, Wallace BA. A tamoxifen receptor within a voltage-gated sodium channel. Mol Cell 2021; 81:1160-1169.e5. [PMID: 33503406 PMCID: PMC7980221 DOI: 10.1016/j.molcel.2020.12.048] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 08/24/2020] [Accepted: 12/14/2020] [Indexed: 12/22/2022]
Abstract
Voltage-gated sodium channels are targets for many analgesic and antiepileptic drugs whose therapeutic mechanisms and binding sites have been well characterized. We describe the identification of a previously unidentified receptor site within the NavMs voltage-gated sodium channel. Tamoxifen, an estrogen receptor modulator, and its primary and secondary metabolic products bind at the intracellular exit of the channel, which is a site that is distinct from other previously characterized sodium channel drug sites. These compounds inhibit NavMs and human sodium channels with similar potencies and prevent sodium conductance by delaying channel recovery from the inactivated state. This study therefore not only describes the structure and pharmacology of a site that could be leveraged for the development of new drugs for the treatment of sodium channelopathies but may also have important implications for off-target health effects of this widely used therapeutic drug.
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Affiliation(s)
- Altin Sula
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, UK
| | - David Hollingworth
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, UK
| | - Leo C T Ng
- Department of Pharmacology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Megan Larmore
- Department of Pharmacology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Paul G DeCaen
- Department of Pharmacology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA.
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, UK.
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25
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Pore-forming proteins: From defense factors to endogenous executors of cell death. Chem Phys Lipids 2020; 234:105026. [PMID: 33309552 DOI: 10.1016/j.chemphyslip.2020.105026] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 12/07/2020] [Accepted: 12/07/2020] [Indexed: 02/06/2023]
Abstract
Pore-forming proteins (PFPs) and small antimicrobial peptides (AMPs) represent a large family of molecules with the common ability to punch holes in cell membranes to alter their permeability. They play a fundamental role as infectious bacteria's defensive tools against host's immune system and as executors of endogenous machineries of regulated cell death in eukaryotic cells. Despite being highly divergent in primary sequence and 3D structure, specific folds of pore-forming domains have been conserved. In fact, pore formation is considered an ancient mechanism that takes place through a general multistep process involving: membrane partitioning and insertion, oligomerization and pore formation. However, different PFPs and AMPs assemble and form pores following different mechanisms that could end up either in the formation of protein-lined or protein-lipid pores. In this review, we analyze the current findings in the mechanism of action of different PFPs and AMPs that support a wide role of membrane pore formation in nature. We also provide the newest insights into the development of state-of-art techniques that have facilitated the characterization of membrane pores. To understand the physiological role of these peptides/proteins or develop clinical applications, it is essential to uncover the molecular mechanism of how they perforate membranes.
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26
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Changes in Ion Selectivity Following the Asymmetrical Addition of Charge to the Selectivity Filter of Bacterial Sodium Channels. ENTROPY 2020; 22:e22121390. [PMID: 33316962 PMCID: PMC7764494 DOI: 10.3390/e22121390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/30/2020] [Accepted: 12/07/2020] [Indexed: 12/30/2022]
Abstract
Voltage-gated sodium channels (NaVs) play fundamental roles in eukaryotes, but their exceptional size hinders their structural resolution. Bacterial NaVs are simplified homologues of their eukaryotic counterparts, but their use as models of eukaryotic Na+ channels is limited by their homotetrameric structure at odds with the asymmetric Selectivity Filter (SF) of eukaryotic NaVs. This work aims at mimicking the SF of eukaryotic NaVs by engineering radial asymmetry into the SF of bacterial channels. This goal was pursued with two approaches: the co-expression of different monomers of the NaChBac bacterial channel to induce the random assembly of heterotetramers, and the concatenation of four bacterial monomers to form a concatemer that can be targeted by site-specific mutagenesis. Patch-clamp measurements and Molecular Dynamics simulations showed that an additional gating charge in the SF leads to a significant increase in Na+ and a modest increase in the Ca2+ conductance in the NavMs concatemer in agreement with the behavior of the population of random heterotetramers with the highest proportion of channels with charge -5e. We thus showed that charge, despite being important, is not the only determinant of conduction and selectivity, and we created new tools extending the use of bacterial channels as models of eukaryotic counterparts.
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27
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Sait LG, Sula A, Ghovanloo MR, Hollingworth D, Ruben PC, Wallace BA. Cannabidiol interactions with voltage-gated sodium channels. eLife 2020; 9:58593. [PMID: 33089780 PMCID: PMC7641581 DOI: 10.7554/elife.58593] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 10/15/2020] [Indexed: 12/19/2022] Open
Abstract
Voltage-gated sodium channels are targets for a range of pharmaceutical drugs developed for the treatment of neurological diseases. Cannabidiol (CBD), the non-psychoactive compound isolated from cannabis plants, was recently approved for treatment of two types of epilepsy associated with sodium channel mutations. This study used high-resolution X-ray crystallography to demonstrate the detailed nature of the interactions between CBD and the NavMs voltage-gated sodium channel, and electrophysiology to show the functional effects of binding CBD to these channels. CBD binds at a novel site at the interface of the fenestrations and the central hydrophobic cavity of the channel. Binding at this site blocks the transmembrane-spanning sodium ion translocation pathway, providing a molecular mechanism for channel inhibition. Modelling studies suggest why the closely-related psychoactive compound tetrahydrocannabinol may not have the same effects on these channels. Finally, comparisons are made with the TRPV2 channel, also recently proposed as a target site for CBD. In summary, this study provides novel insight into a possible mechanism for CBD interactions with sodium channels.
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Affiliation(s)
- Lily Goodyer Sait
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
| | - Altin Sula
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
| | - Mohammad-Reza Ghovanloo
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, Canada
| | - David Hollingworth
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
| | - Peter C Ruben
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, Canada
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
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28
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Rems L, Kasimova MA, Testa I, Delemotte L. Pulsed Electric Fields Can Create Pores in the Voltage Sensors of Voltage-Gated Ion Channels. Biophys J 2020; 119:190-205. [PMID: 32559411 PMCID: PMC7335976 DOI: 10.1016/j.bpj.2020.05.030] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 03/31/2020] [Accepted: 05/15/2020] [Indexed: 12/21/2022] Open
Abstract
Pulsed electric fields are increasingly used in medicine to transiently increase the cell membrane permeability via electroporation to deliver therapeutic molecules into the cell. One type of event that contributes to this increase in membrane permeability is the formation of pores in the membrane lipid bilayer. However, electrophysiological measurements suggest that membrane proteins are affected as well, particularly voltage-gated ion channels (VGICs). The molecular mechanisms by which the electric field could affects these molecules remain unidentified. In this study, we used molecular dynamics simulations to unravel the molecular events that take place in different VGICs when exposing them to electric fields mimicking electroporation conditions. We show that electric fields can induce pores in the voltage-sensor domains (VSDs) of different VGICs and that these pores form more easily in some channels than in others. We demonstrate that poration is more likely in VSDs that are more hydrated and are electrostatically more favorable for the entry of ions. We further show that pores in VSDs can expand into so-called complex pores, which become stabilized by lipid headgroups. Our results suggest that such complex pores are considerably more stable than conventional lipid pores, and their formation can lead to severe unfolding of VSDs from the channel. We anticipate that such VSDs become dysfunctional and unable to respond to changes in transmembrane voltage, which is in agreement with previous electrophysiological measurements showing a decrease in the voltage-dependent transmembrane ionic currents after pulse treatment. Finally, we discuss the possibility of activation of VGICs by submicrosecond-duration pulses. Overall, our study reveals a new, to our knowledge, mechanism of electroporation through membranes containing VGICs.
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Affiliation(s)
- Lea Rems
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Solna, Sweden
| | - Marina A Kasimova
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Solna, Sweden
| | - Ilaria Testa
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Solna, Sweden
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Solna, Sweden.
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29
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Brewer KR, Kuenze G, Vanoye CG, George AL, Meiler J, Sanders CR. Structures Illuminate Cardiac Ion Channel Functions in Health and in Long QT Syndrome. Front Pharmacol 2020; 11:550. [PMID: 32431610 PMCID: PMC7212895 DOI: 10.3389/fphar.2020.00550] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/09/2020] [Indexed: 12/13/2022] Open
Abstract
The cardiac action potential is critical to the production of a synchronized heartbeat. This electrical impulse is governed by the intricate activity of cardiac ion channels, among them the cardiac voltage-gated potassium (Kv) channels KCNQ1 and hERG as well as the voltage-gated sodium (Nav) channel encoded by SCN5A. Each channel performs a highly distinct function, despite sharing a common topology and structural components. These three channels are also the primary proteins mutated in congenital long QT syndrome (LQTS), a genetic condition that predisposes to cardiac arrhythmia and sudden cardiac death due to impaired repolarization of the action potential and has a particular proclivity for reentrant ventricular arrhythmias. Recent cryo-electron microscopy structures of human KCNQ1 and hERG, along with the rat homolog of SCN5A and other mammalian sodium channels, provide atomic-level insight into the structure and function of these proteins that advance our understanding of their distinct functions in the cardiac action potential, as well as the molecular basis of LQTS. In this review, the gating, regulation, LQTS mechanisms, and pharmacological properties of KCNQ1, hERG, and SCN5A are discussed in light of these recent structural findings.
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Affiliation(s)
- Kathryn R. Brewer
- Center for Structural Biology, Vanderbilt University School of Medicine Basic Sciences, Nashville, TN, United States
- Department of Biochemistry, Vanderbilt University, Nashville, TN, United States
| | - Georg Kuenze
- Center for Structural Biology, Vanderbilt University School of Medicine Basic Sciences, Nashville, TN, United States
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States
| | - Carlos G. Vanoye
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Alfred L. George
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Jens Meiler
- Center for Structural Biology, Vanderbilt University School of Medicine Basic Sciences, Nashville, TN, United States
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States
- Department of Pharmacology, Vanderbilt University School of Medicine Basic Sciences, Nashville, TN, United States
- Institute for Drug Discovery, Leipzig University Medical School, Leipzig, Germany
| | - Charles R. Sanders
- Center for Structural Biology, Vanderbilt University School of Medicine Basic Sciences, Nashville, TN, United States
- Department of Biochemistry, Vanderbilt University, Nashville, TN, United States
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30
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The Ca 2+ permeation mechanism of the ryanodine receptor revealed by a multi-site ion model. Nat Commun 2020; 11:922. [PMID: 32066742 PMCID: PMC7026163 DOI: 10.1038/s41467-020-14573-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 01/16/2020] [Indexed: 12/22/2022] Open
Abstract
Ryanodine receptors (RyR) are ion channels responsible for the release of Ca2+ from the sarco/endoplasmic reticulum and play a crucial role in the precise control of Ca2+ concentration in the cytosol. The detailed permeation mechanism of Ca2+ through RyR is still elusive. By using molecular dynamics simulations with a specially designed Ca2+ model, we show that multiple Ca2+ ions accumulate in the upper selectivity filter of RyR1, but only one Ca2+ can occupy and translocate in the narrow pore at a time, assisted by electrostatic repulsion from the Ca2+ within the upper selectivity filter. The Ca2+ is nearly fully hydrated with the first solvation shell intact during the whole permeation process. These results suggest a remote knock-on permeation mechanism and one-at-a-time occupation pattern for the hydrated Ca2+ within the narrow pore, uncovering the basis underlying the high permeability and low selectivity of the RyR channels.
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31
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Catterall WA, Lenaeus MJ, Gamal El-Din TM. Structure and Pharmacology of Voltage-Gated Sodium and Calcium Channels. Annu Rev Pharmacol Toxicol 2020; 60:133-154. [PMID: 31537174 DOI: 10.1146/annurev-pharmtox-010818-021757] [Citation(s) in RCA: 132] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Voltage-gated sodium and calcium channels are evolutionarily related transmembrane signaling proteins that initiate action potentials, neurotransmission, excitation-contraction coupling, and other physiological processes. Genetic or acquired dysfunction of these proteins causes numerous diseases, termed channelopathies, and sodium and calcium channels are the molecular targets for several major classes of drugs. Recent advances in the structural biology of these proteins using X-ray crystallography and cryo-electron microscopy have given new insights into the molecular basis for their function and pharmacology. Here we review this recent literature and integrate findings on sodium and calcium channels to reveal the structural basis for their voltage-dependent activation, fast and slow inactivation, ion conductance and selectivity, and complex pharmacology at the atomic level. We conclude with the theme that new understanding of the diseases and therapeutics of these channels will be derived from application of the emerging structural principles from these recent structural analyses.
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Affiliation(s)
- William A Catterall
- Department of Pharmacology and Division of General Internal Medicine, Department of Medicine, University of Washington, Seattle, Washington 98195, USA;
| | - Michael J Lenaeus
- Department of Pharmacology and Division of General Internal Medicine, Department of Medicine, University of Washington, Seattle, Washington 98195, USA;
| | - Tamer M Gamal El-Din
- Department of Pharmacology and Division of General Internal Medicine, Department of Medicine, University of Washington, Seattle, Washington 98195, USA;
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32
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Damjanovic A, Chen AY, Rosenberg RL, Roe DR, Wu X, Brooks BR. Protonation state of the selectivity filter of bacterial voltage‐gated sodium channels is modulated by ions. Proteins 2019; 88:527-539. [DOI: 10.1002/prot.25831] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 09/03/2019] [Accepted: 09/17/2019] [Indexed: 01/28/2023]
Affiliation(s)
- Ana Damjanovic
- Department of BiophysicsJohns Hopkins University Baltimore Maryland
| | - Ada Y. Chen
- Department of PhysicsJohns Hopkins University Baltimore Maryland
| | | | - Daniel R. Roe
- Laboratory of Computational Biology, National Heart, Lung and Blood InstituteNational Institutes of Health Bethesda Maryland
| | - Xiongwu Wu
- Laboratory of Computational Biology, National Heart, Lung and Blood InstituteNational Institutes of Health Bethesda Maryland
| | - Bernard R. Brooks
- Laboratory of Computational Biology, National Heart, Lung and Blood InstituteNational Institutes of Health Bethesda Maryland
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33
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Wang Y, Finol-Urdaneta RK, Ngo VA, French RJ, Noskov SY. Bases of Bacterial Sodium Channel Selectivity Among Organic Cations. Sci Rep 2019; 9:15260. [PMID: 31649292 PMCID: PMC6813354 DOI: 10.1038/s41598-019-51605-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 10/03/2019] [Indexed: 12/15/2022] Open
Abstract
Hille's (1971) seminal study of organic cation selectivity of eukaryotic voltage-gated sodium channels showed a sharp size cut-off for ion permeation, such that no ion possessing a methyl group was permeant. Using the prokaryotic channel, NaChBac, we found some similarity and two peculiar differences in the selectivity profiles for small polyatomic cations. First, we identified a diverse group of minimally permeant cations for wildtype NaChBac, ranging in sizes from ammonium to guanidinium and tetramethylammonium; and second, for both ammonium and hydrazinium, the charge-conserving selectivity filter mutation (E191D) yielded substantial increases in relative permeability (PX/PNa). The relative permeabilities varied inversely with relative Kd calculated from 1D Potential of Mean Force profiles (PMFs) for the single cations traversing the channel. Several of the cations bound more strongly than Na+, and hence appear to act as blockers, as well as charge carriers. Consistent with experimental observations, the E191D mutation had little impact on Na+ binding to the selectivity filter, but disrupted the binding of ammonium and hydrazinium, consequently facilitating ion permeation across the NaChBac-like filter. We concluded that for prokaryotic sodium channels, a fine balance among filter size, binding affinity, occupancy, and flexibility seems to contribute to observed functional differences.
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Affiliation(s)
- Yibo Wang
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- Centre for Molecular Simulation and the Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Rocio K Finol-Urdaneta
- Department of Physiology and Pharmacology, and the Hotchkiss Brain Institute, University of Calgary, Calgary, Canada
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, New South Wales, Australia
| | - Van Anh Ngo
- Centre for Molecular Simulation and the Department of Biological Sciences, University of Calgary, Calgary, Canada
- Center for Nonlinear Studies, Los Alamos National Lab, Los Alamos, NM, 87544, USA
| | - Robert J French
- Department of Physiology and Pharmacology, and the Hotchkiss Brain Institute, University of Calgary, Calgary, Canada.
| | - Sergei Yu Noskov
- Centre for Molecular Simulation and the Department of Biological Sciences, University of Calgary, Calgary, Canada.
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34
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León-Pimentel CI, Martínez-Jiménez M, Saint-Martin H. Study of the Elusive Hydration of Pb2+ from the Gas Phase to the Liquid Aqueous Solution: Modeling the Hemidirected Solvation with a Polarizable MCDHO Force-Field. J Phys Chem B 2019; 123:9155-9166. [DOI: 10.1021/acs.jpcb.9b04541] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- C. I. León-Pimentel
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Apdo. Postal 48-3, Cuernavaca, Morelos 62251, Ḿexico
| | - M. Martínez-Jiménez
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Apdo. Postal 48-3, Cuernavaca, Morelos 62251, Ḿexico
| | - H. Saint-Martin
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Apdo. Postal 48-3, Cuernavaca, Morelos 62251, Ḿexico
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35
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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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36
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Xu L, Ding X, Wang T, Mou S, Sun H, Hou T. Voltage-gated sodium channels: structures, functions, and molecular modeling. Drug Discov Today 2019; 24:1389-1397. [PMID: 31129313 DOI: 10.1016/j.drudis.2019.05.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 04/02/2019] [Accepted: 05/17/2019] [Indexed: 10/26/2022]
Abstract
Voltage-gated sodium channels (VGSCs), formed by 24 transmembrane segments arranged into four domains, have a key role in the initiation and propagation of electrical signaling in excitable cells. VGSCs are involved in a variety of diseases, including epilepsy, cardiac arrhythmias, and neuropathic pain, and therefore have been regarded as appealing therapeutic targets for the development of anticonvulsant, antiarrhythmic, and local anesthetic drugs. In this review, we discuss recent advances in understanding the structures and biological functions of VGSCs. In addition, we systematically summarize eight pharmacologically distinct ligand-binding sites in VGSCs and representative isoform-selective VGSC modulators in clinical trials. Finally, we review studies on molecular modeling and computer-aided drug design (CADD) for VGSCs to help understanding of biological processes involving VGSCs.
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Affiliation(s)
- Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Xiaoqin Ding
- Beijing Institute of Pharmaceutical Chemistry, Beijing 102205, China
| | - Tianhu Wang
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Shanzhi Mou
- School of Mathematics and Physics, Jiangsu University of Technology, Changzhou 213001, China
| | - Huiyong Sun
- Department of Medicinal Chemistry, School of Pharmacy, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China.
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
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37
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Corradi V, Sejdiu BI, Mesa-Galloso H, Abdizadeh H, Noskov SY, Marrink SJ, Tieleman DP. Emerging Diversity in Lipid-Protein Interactions. Chem Rev 2019; 119:5775-5848. [PMID: 30758191 PMCID: PMC6509647 DOI: 10.1021/acs.chemrev.8b00451] [Citation(s) in RCA: 260] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Indexed: 02/07/2023]
Abstract
Membrane lipids interact with proteins in a variety of ways, ranging from providing a stable membrane environment for proteins to being embedded in to detailed roles in complicated and well-regulated protein functions. Experimental and computational advances are converging in a rapidly expanding research area of lipid-protein interactions. Experimentally, the database of high-resolution membrane protein structures is growing, as are capabilities to identify the complex lipid composition of different membranes, to probe the challenging time and length scales of lipid-protein interactions, and to link lipid-protein interactions to protein function in a variety of proteins. Computationally, more accurate membrane models and more powerful computers now enable a detailed look at lipid-protein interactions and increasing overlap with experimental observations for validation and joint interpretation of simulation and experiment. Here we review papers that use computational approaches to study detailed lipid-protein interactions, together with brief experimental and physiological contexts, aiming at comprehensive coverage of simulation papers in the last five years. Overall, a complex picture of lipid-protein interactions emerges, through a range of mechanisms including modulation of the physical properties of the lipid environment, detailed chemical interactions between lipids and proteins, and key functional roles of very specific lipids binding to well-defined binding sites on proteins. Computationally, despite important limitations, molecular dynamics simulations with current computer power and theoretical models are now in an excellent position to answer detailed questions about lipid-protein interactions.
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Affiliation(s)
- Valentina Corradi
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Besian I. Sejdiu
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Haydee Mesa-Galloso
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Haleh Abdizadeh
- Groningen
Biomolecular Sciences and Biotechnology Institute and Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Sergei Yu. Noskov
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute and Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - D. Peter Tieleman
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
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38
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Kudaibergenova M, Perissinotti LL, Noskov SY. Lipid roles in hERG function and interactions with drugs. Neurosci Lett 2019; 700:70-77. [DOI: 10.1016/j.neulet.2018.05.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 05/08/2018] [Accepted: 05/11/2018] [Indexed: 01/29/2023]
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39
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Wu M, Sun L, Zhou Q, Peng Y, Liu Z, Zhao S. Molecular Mechanism of Acetate Transport through the Acetate Channel SatP. J Chem Inf Model 2019; 59:2374-2382. [DOI: 10.1021/acs.jcim.8b00975] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Meng Wu
- iHuman Institute, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
- University of Chinese
Academy of Sciences, No. 19A, Yuquan Road, Beijing 100049, China
| | - Liping Sun
- iHuman Institute, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Qingtong Zhou
- iHuman Institute, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Yao Peng
- iHuman Institute, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Zhijie Liu
- iHuman Institute, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Suwen Zhao
- iHuman Institute, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
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40
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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: 4.5] [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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41
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Guardiani C, Fedorenko OA, Khovanov IA, Roberts SK. Different roles for aspartates and glutamates for cation permeation in bacterial sodium channels. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1861:495-503. [PMID: 30529079 DOI: 10.1016/j.bbamem.2018.11.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 11/16/2018] [Accepted: 11/30/2018] [Indexed: 12/21/2022]
Abstract
A key driving force for ion channel selectivity is represented by the negative charge of the Selectivity Filter carried by aspartate (D) and glutamate (E) residues. However, the structural effects and specific properties of D and E residues have not been extensively studied. In order to investigate this issue we studied the mutants of NaChBac channel with all possible combinations of D and E in the charged rings in position 191 and 192. Electrophysiological measurements showed significant Ca2+ currents only when position 191 was occupied by E. Equilibrium Molecular Dynamics simulations revealed the existence of two binding sites, corresponding to the charged rings and another one, more internal, at the level of L190. The simulations showed that the ion in the innermost site can interact with the residue in position 191 only when this is glutamate. Based on the MD simulations, we suggest that a D in position 191 leads to a high affinity Ca2+ block site resulting from a significant drop in the free energy of binding for an ion moving between the binding sites; in contrast, the free energy change is more gradual when an E residue occupies position 191, resulting in Ca2+ permeability. This scenario is consistent with the model of ion channel selectivity through stepwise changes in binding affinity proposed by Dang and McCleskey. Our study also highlights the importance of the structure of the selectivity filter which should contribute to the development of more detailed physical models for ion channel selectivity.
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Affiliation(s)
- Carlo Guardiani
- School of Engineering, University of Warwick, Coventry CV4 7AL, United Kingdom; Department of Physics, University of Lancaster, Lancaster LA1 4YB, United Kingdom.
| | - Olena A Fedorenko
- Division of Biomedical and Life Sciences, Lancaster University, Lancaster, United Kingdom; School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, United Kingdom
| | - Igor A Khovanov
- School of Engineering, University of Warwick, Coventry CV4 7AL, United Kingdom; Centre for Scientific Computing, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Stephen K Roberts
- Division of Biomedical and Life Sciences, Lancaster University, Lancaster, United Kingdom.
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42
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Myers JB, Haddad BG, O'Neill SE, Chorev DS, Yoshioka CC, Robinson CV, Zuckerman DM, Reichow SL. Structure of native lens connexin 46/50 intercellular channels by cryo-EM. Nature 2018; 564:372-377. [PMID: 30542154 PMCID: PMC6309215 DOI: 10.1038/s41586-018-0786-7] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 10/29/2018] [Indexed: 11/19/2022]
Abstract
Gap junctions establish direct pathways for cell-to-cell communication through the assembly of twelve connexin subunits that form intercellular channels connecting neighbouring cells. Co-assembly of different connexin isoforms produces channels with unique properties and enables communication across cell types. Here we used single-particle cryo-electron microscopy to investigate the structural basis of connexin co-assembly in native lens gap junction channels composed of connexin 46 and connexin 50 (Cx46/50). We provide the first comparative analysis to connexin 26 (Cx26), which-together with computational studies-elucidates key energetic features governing gap junction permselectivity. Cx46/50 adopts an open-state conformation that is distinct from the Cx26 crystal structure, yet it appears to be stabilized by a conserved set of hydrophobic anchoring residues. 'Hot spots' of genetic mutations linked to hereditary cataract formation map to the core structural-functional elements identified in Cx46/50, suggesting explanations for many of the disease-causing effects.
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Affiliation(s)
- Janette B Myers
- Department of Chemistry, Portland State University, Portland, OR, USA
| | - Bassam G Haddad
- Department of Chemistry, Portland State University, Portland, OR, USA
| | - Susan E O'Neill
- Department of Chemistry, Portland State University, Portland, OR, USA
| | - Dror S Chorev
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Craig C Yoshioka
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Daniel M Zuckerman
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
| | - Steve L Reichow
- Department of Chemistry, Portland State University, Portland, OR, USA.
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43
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Comparisons of voltage-gated sodium channel structures with open and closed gates and implications for state-dependent drug design. Biochem Soc Trans 2018; 46:1567-1575. [PMID: 30381338 DOI: 10.1042/bst20180295] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 09/07/2018] [Accepted: 09/10/2018] [Indexed: 01/15/2023]
Abstract
Voltage-gated sodium channels (Navs) are responsible for the initiation of the action potential in excitable cells. Several prokaryotic sodium channels, most notably NavMs from Magnetococcus marinus and NavAb from Arcobacter butzleri, have been shown to be good models for human sodium channels based on their sequence homologies and high levels of functional similarities, including ion flux, and functional consequences of critical mutations. The complete full-length crystal structures of these prokaryotic sodium channels captured in different functional states have now revealed the molecular natures of changes associated with the gating process. These include the structures of the intracellular gate, the selectivity filter, the voltage sensors, the intra-membrane fenestrations, and the transmembrane (TM) pore. Here we have identified for the first time how changes in the fenestrations in the hydrophobic TM region associated with the opening of the intracellular gate could modulate the state-dependent ingress and binding of drugs in the TM cavity, in a way that could be exploited for rational drug design.
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Callahan KM, Roux B. Molecular Dynamics of Ion Conduction through the Selectivity Filter of the Na VAb Sodium Channel. J Phys Chem B 2018; 122:10126-10142. [PMID: 30351118 DOI: 10.1021/acs.jpcb.8b09678] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The determination of the atomic structures of voltage-gated bacterial sodium channels using X-ray crystallography has provided a first view of this family of membrane proteins. Molecular dynamics simulations offer one approach to clarify the underlying mechanism of permeation and selectivity in these channels. However, it appears that the intracellular gate of the pore domain is either closed or only open partially in the available X-ray structures. The lack of structure with a fully open intracellular gate poses a special challenge to computational studies aimed at simulating ion conduction. To circumvent this problem, we simulated a model of the NaVAb channel in which the transmembrane S5 and S6 helices of the pore domain have been truncated to provide direct open access to the intracellular entryway to the pore. Molecular dynamics simulations were carried out over a range of membrane potential and ion concentration of sodium and potassium. The simulations show that the NaVAb selectivity filter is essentially a cationic pore supporting the conduction of ions at a rate comparable to aqueous diffusion with no significant selectivity for sodium. Conductance and selectivity vary as a function of ion concentration for both cations. Permeation occurs primarily via a knock-on mechanism for both sodium and potassium, although the ion ordering in single file along the pore is not strictly maintained. The character of the outward current appears quite different from the inward current, with a buildup on ions in the selectivity filter prior to escape toward the extracellular side, indicating the presence of a rectification effect that is overcome by nonphysiological applied voltages.
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Affiliation(s)
- Karen M Callahan
- Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science , The University of Chicago , Chicago , Illinois 60637 , United States
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science , The University of Chicago , Chicago , Illinois 60637 , United States
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Alberini G, Benfenati F, Maragliano L. Molecular Dynamics Simulations of Ion Selectivity in a Claudin-15 Paracellular Channel. J Phys Chem B 2018; 122:10783-10792. [DOI: 10.1021/acs.jpcb.8b06484] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Giulio Alberini
- 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
| | - 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
- IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi, 10, 16132 Genova, Italy
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Ke S, Ulmschneider MB, Wallace BA, Ulmschneider JP. Role of the Interaction Motif in Maintaining the Open Gate of an Open Sodium Channel. Biophys J 2018; 115:1920-1930. [PMID: 30366630 DOI: 10.1016/j.bpj.2018.10.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 09/27/2018] [Accepted: 10/01/2018] [Indexed: 01/09/2023] Open
Abstract
Voltage-gated sodium channels undergo transitions between open, closed, and inactivated states, enabling regulation of the translocation of sodium ions across membranes. A recently published crystal structure of the full-length prokaryotic NavMs crystal structure in the activated open conformation has revealed the presence of a novel motif consisting of an extensive network of salt bridges involving residues in the voltage sensor, S4-S5 linker, pore, and C-terminal domains. This motif has been proposed to be responsible for maintaining an open conformation that enables ion translocation through the channel. In this study, we have used long-time molecular dynamics calculations without artificial restraints to demonstrate that the interaction network of full-length NavMs indeed prevents a rapid collapse and closure of the gate, in marked difference to earlier studies of the pore-only construct in which the gate had to be restrained to remain open. Interestingly, a frequently discussed "hydrophobic gating" mechanism at nanoscopic level is also observed in our simulations, in which the discontinuous water wire close to the gate region leads to an energetic barrier for ion conduction. In addition, we demonstrate the effects of in silico mutations of several of the key residues in the motif on the open channel's stability and functioning, correlating them with existing functional studies on this channel and homologous disease-associated mutations in human sodium channels; we also examine the effects of truncating/removing the voltage sensor and C-terminal domains in maintaining an open gate.
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Affiliation(s)
- Song Ke
- Institute of Natural Sciences and School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, China
| | | | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom.
| | - Jakob P Ulmschneider
- Institute of Natural Sciences and School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, China.
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Gamal El-Din TM, Lenaeus MJ, Catterall WA. Structural and Functional Analysis of Sodium Channels Viewed from an Evolutionary Perspective. Handb Exp Pharmacol 2018; 246:53-72. [PMID: 29043505 DOI: 10.1007/164_2017_61] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Voltage-gated sodium channels initiate and propagate action potentials in excitable cells. They respond to membrane depolarization through opening, followed by fast inactivation that terminates the sodium current. This ON-OFF behavior of voltage-gated sodium channels underlays the coding of information and its transmission from one location in the nervous system to another. In this review, we explore and compare structural and functional data from prokaryotic and eukaryotic channels to infer the effects of evolution on sodium channel structure and function.
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Affiliation(s)
- Tamer M Gamal El-Din
- Department of Pharmacology, University of Washington, Seattle, WA, 98195-7280, USA.
| | - Michael J Lenaeus
- Department of Pharmacology, University of Washington, Seattle, WA, 98195-7280, USA
| | - William A Catterall
- Department of Pharmacology, University of Washington, Seattle, WA, 98195-7280, USA
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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: 3.3] [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
- * E-mail:
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Yang E, Granata D, Eckenhoff RG, Carnevale V, Covarrubias M. Propofol inhibits prokaryotic voltage-gated Na + channels by promoting activation-coupled inactivation. J Gen Physiol 2018; 150:1299-1316. [PMID: 30018038 PMCID: PMC6122921 DOI: 10.1085/jgp.201711924] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 06/12/2018] [Indexed: 12/21/2022] Open
Abstract
Propofol is widely used in the clinic for the induction and maintenance of general anesthesia. As with most general anesthetics, however, our understanding of its mechanism of action remains incomplete. Local and general anesthetics largely inhibit voltage-gated Na+ channels (Navs) by inducing an apparent stabilization of the inactivated state, associated in some instances with pore block. To determine the biophysical and molecular basis of propofol action in Navs, we investigated NaChBac and NavMs, two prokaryotic Navs with distinct voltage dependencies and gating kinetics, by whole-cell patch clamp electrophysiology in the absence and presence of propofol at clinically relevant concentrations (2-10 µM). In both Navs, propofol induced a hyperpolarizing shift of the pre-pulse inactivation curve without any significant effects on recovery from inactivation at strongly hyperpolarized voltages, demonstrating that propofol does not stabilize the inactivated state. Moreover, there was no evidence of fast or slow pore block by propofol in a non-inactivating NaChBac mutant (T220A). Propofol also induced hyperpolarizing shifts of the conductance-voltage relationships with negligible effects on the time constants of deactivation at hyperpolarized voltages, indicating that propofol does not stabilize the open state. Instead, propofol decreases the time constants of macroscopic activation and inactivation. Adopting a kinetic scheme of Nav gating that assumes preferential closed-state recovery from inactivation, a 1.7-fold acceleration of the rate constant of activation and a 1.4-fold acceleration of the rate constant of inactivation were sufficient to reproduce experimental observations with computer simulations. In addition, molecular dynamics simulations and molecular docking suggest that propofol binding involves interactions with gating machinery in the S4-S5 linker and external pore regions. Our findings show that propofol is primarily a positive gating modulator of prokaryotic Navs, which ultimately inhibits the channels by promoting activation-coupled inactivation.
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Affiliation(s)
- Elaine Yang
- Vickie and Jack Farber Institute for Neuroscience and Department of Neuroscience, Sidney Kimmel Medical College and Jefferson College of Biomedical Sciences, Thomas Jefferson University, Philadelphia, PA
| | - Daniele Granata
- Institute for Computational Molecular Science, College of Science and Technology, Temple University, Philadelphia, PA
| | - Roderic G Eckenhoff
- Department of Anesthesiology and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Vincenzo Carnevale
- Institute for Computational Molecular Science, College of Science and Technology, Temple University, Philadelphia, PA
| | - Manuel Covarrubias
- Vickie and Jack Farber Institute for Neuroscience and Department of Neuroscience, Sidney Kimmel Medical College and Jefferson College of Biomedical Sciences, Thomas Jefferson University, Philadelphia, PA
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