1
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Karoii DH, Azizi H, Skutella T. Whole transcriptome analysis to identify non-coding RNA regulators and hub genes in sperm of non-obstructive azoospermia by microarray, single-cell RNA sequencing, weighted gene co-expression network analysis, and mRNA-miRNA-lncRNA interaction analysis. BMC Genomics 2024; 25:583. [PMID: 38858625 PMCID: PMC11165898 DOI: 10.1186/s12864-024-10506-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 06/06/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND The issue of male fertility is becoming increasingly common due to genetic differences inherited over generations. Gene expression and evaluation of non-coding RNA (ncRNA), crucial for sperm development, are significant factors. This gene expression can affect sperm motility and, consequently, fertility. Understanding the intricate protein interactions that play essential roles in sperm differentiation and development is vital. This knowledge could lead to more effective treatments and interventions for male infertility. MATERIALS AND METHODS Our research aim to identify new and key genes and ncRNA involved in non-obstructive azoospermia (NOA), improving genetic diagnosis and offering more accurate estimates for successful sperm extraction based on an individual's genotype. RESULTS We analyzed the transcript of three NOA patients who tested negative for genetic sperm issues, employing comprehensive genome-wide analysis of approximately 50,000 transcript sequences using microarray technology. This compared gene expression profiles between NOA sperm and normal sperm. We found significant gene expression differences: 150 genes were up-regulated, and 78 genes were down-regulated, along with 24 ncRNAs up-regulated and 13 ncRNAs down-regulated compared to normal conditions. By cross-referencing our results with a single-cell genomics database, we identified overexpressed biological process terms in differentially expressed genes, such as "protein localization to endosomes" and "xenobiotic transport." Overrepresented molecular function terms in up-regulated genes included "voltage-gated calcium channel activity," "growth hormone-releasing hormone receptor activity," and "sialic acid transmembrane transporter activity." Analysis revealed nine hub genes associated with NOA sperm: RPL34, CYB5B, GOL6A6, LSM1, ARL4A, DHX57, STARD9, HSP90B1, and VPS36. CONCLUSIONS These genes and their interacting proteins may play a role in the pathophysiology of germ cell abnormalities and infertility.
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Affiliation(s)
- Danial Hashemi Karoii
- Department of Cell and Molecular Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran
- Faculty of Biotechnology, Amol University of Special Modern Technologies, Amol, Iran
| | - Hossein Azizi
- Faculty of Biotechnology, Amol University of Special Modern Technologies, Amol, Iran.
| | - Thomas Skutella
- Institute for Anatomy and Cell Biology, Medical Faculty, University of Heidelberg, Im Neuenheimer Feld 307, 69120, Heidelberg, Germany.
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2
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del Rivero Morfin PJ, Kochiss AL, Liedl KR, Flucher BE, Fernández-Quintero ML, Ben-Johny M. Asymmetric contribution of a selectivity filter gate in triggering inactivation of CaV1.3 channels. J Gen Physiol 2024; 156:e202313365. [PMID: 38175169 PMCID: PMC10771039 DOI: 10.1085/jgp.202313365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 10/08/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
Voltage-dependent and Ca2+-dependent inactivation (VDI and CDI, respectively) of CaV channels are two biologically consequential feedback mechanisms that fine-tune Ca2+ entry into neurons and cardiomyocytes. Although known to be initiated by distinct molecular events, how these processes obstruct conduction through the channel pore remains poorly defined. Here, focusing on ultrahighly conserved tryptophan residues in the interdomain interfaces near the selectivity filter of CaV1.3, we demonstrate a critical role for asymmetric conformational changes in mediating VDI and CDI. Specifically, mutagenesis of the domain III-IV interface, but not others, enhanced VDI. Molecular dynamics simulations demonstrate that mutations in distinct selectivity filter interfaces differentially impact conformational flexibility. Furthermore, mutations in distinct domains preferentially disrupt CDI mediated by the N- versus C-lobes of CaM, thus uncovering a scheme of structural bifurcation of CaM signaling. These findings highlight the fundamental importance of the asymmetric arrangement of the pseudotetrameric CaV pore domain for feedback inhibition.
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Affiliation(s)
| | - Audrey L. Kochiss
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Bernhard E. Flucher
- Department of Physiology and Medical Physics, Institute of Physiology, Medical University Innsbruck, Innsbruck, Austria
| | | | - Manu Ben-Johny
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
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3
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Özkan M, Yılmaz H, Ergenekon P, Erdoğan EM, Erbakan M. Microbial membrane transport proteins and their biotechnological applications. World J Microbiol Biotechnol 2024; 40:71. [PMID: 38225445 PMCID: PMC10789880 DOI: 10.1007/s11274-024-03891-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/09/2024] [Indexed: 01/17/2024]
Abstract
Because of the hydrophobic nature of the membrane lipid bilayer, the majority of the hydrophilic solutes require special transportation mechanisms for passing through the cell membrane. Integral membrane transport proteins (MTPs), which belong to the Major Intrinsic Protein Family, facilitate the transport of these solutes across cell membranes. MTPs including aquaporins and carrier proteins are transmembrane proteins spanning across the cell membrane. The easy handling of microorganisms enabled the discovery of a remarkable number of transport proteins specific to different substances. It has been realized that these transporters have very important roles in the survival of microorganisms, their pathogenesis, and antimicrobial resistance. Astonishing features related to the solute specificity of these proteins have led to the acceleration of the research on the discovery of their properties and the development of innovative products in which these unique properties are used or imitated. Studies on microbial MTPs range from the discovery and characterization of a novel transporter protein to the mining and screening of them in a large transporter library for particular functions, from simulations and modeling of specific transporters to the preparation of biomimetic synthetic materials for different purposes such as biosensors or filtration membranes. This review presents recent discoveries on microbial membrane transport proteins and focuses especially on formate nitrite transport proteins and aquaporins, and advances in their biotechnological applications.
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Affiliation(s)
- Melek Özkan
- Environmental Engineering Department, Gebze Technical University, Kocaeli, 41400, Türkiye.
| | - Hilal Yılmaz
- Environmental Engineering Department, Gebze Technical University, Kocaeli, 41400, Türkiye
| | - Pınar Ergenekon
- Environmental Engineering Department, Gebze Technical University, Kocaeli, 41400, Türkiye
| | - Esra Meşe Erdoğan
- Environmental Engineering Department, Gebze Technical University, Kocaeli, 41400, Türkiye
| | - Mustafa Erbakan
- Biosystem Engineering Department, Bozok University, Yozgat , 66900, Türkiye
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4
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Catterall WA. Voltage gated sodium and calcium channels: Discovery, structure, function, and Pharmacology. Channels (Austin) 2023; 17:2281714. [PMID: 37983307 PMCID: PMC10761118 DOI: 10.1080/19336950.2023.2281714] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 10/11/2023] [Indexed: 11/22/2023] Open
Abstract
Voltage-gated sodium channels initiate action potentials in nerve and muscle, and voltage-gated calcium channels couple depolarization of the plasma membrane to intracellular events such as secretion, contraction, synaptic transmission, and gene expression. In this Review and Perspective article, I summarize early work that led to identification, purification, functional reconstitution, and determination of the amino acid sequence of the protein subunits of sodium and calcium channels and showed that their pore-forming subunits are closely related. Decades of study by antibody mapping, site-directed mutagenesis, and electrophysiological recording led to detailed two-dimensional structure-function maps of the amino acid residues involved in voltage-dependent activation and inactivation, ion permeation and selectivity, and pharmacological modulation. Most recently, high-resolution three-dimensional structure determination by X-ray crystallography and cryogenic electron microscopy has revealed the structural basis for sodium and calcium channel function and pharmacological modulation at the atomic level. These studies now define the chemical basis for electrical signaling and provide templates for future development of new therapeutic agents for a range of neurological and cardiovascular diseases.
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5
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del Rivero Morfin PJ, Kochiss AL, Liedl KR, Flucher BE, Fernández-Quintero ML, Ben-Johny M. Asymmetric Contribution of a Selectivity Filter Gate in Triggering Inactivation of Ca V1.3 Channels. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.21.558864. [PMID: 37790368 PMCID: PMC10542529 DOI: 10.1101/2023.09.21.558864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Voltage-dependent and Ca2+-dependent inactivation (VDI and CDI, respectively) of CaV channels are two biologically consequential feedback mechanisms that fine-tune Ca2+ entry into neurons and cardiomyocytes. Although known to be initiated by distinct molecular events, how these processes obstruct conduction through the channel pore remains poorly defined. Here, focusing on ultra-highly conserved tryptophan residues in the inter-domain interfaces near the selectivity filter of CaV1.3, we demonstrate a critical role for asymmetric conformational changes in mediating VDI and CDI. Specifically, mutagenesis of the domain III-IV interface, but not others, enhanced VDI. Molecular dynamics simulations demonstrate that mutations in distinct selectivity filter interfaces differentially impact conformational flexibility. Furthermore, mutations in distinct domains preferentially disrupt CDI mediated by the N- versus C-lobes of CaM, thus uncovering a scheme of structural bifurcation of CaM signaling. These findings highlight the fundamental importance of the asymmetric arrangement of the pseudo-tetrameric CaV pore domain for feedback inhibition.
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Affiliation(s)
| | - Audrey L. Kochiss
- Department of Physiology and Cellular Biophysics, Columbia University
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Bernhard E. Flucher
- Institute of Physiology, Department of Physiology and Medical Physics, Medical University Innsbruck, Innsbruck, Austria
| | | | - Manu Ben-Johny
- Department of Physiology and Cellular Biophysics, Columbia University
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6
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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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7
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Choudhury K, Howard RJ, Delemotte L. An α-π transition in S6 shapes the conformational cycle of the bacterial sodium channel NavAb. J Gen Physiol 2022; 155:213748. [PMID: 36515966 PMCID: PMC9754703 DOI: 10.1085/jgp.202213214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/17/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022] Open
Abstract
Voltage-gated sodium channels play an important role in electrical signaling in excitable cells. In response to changes in membrane potential, they cycle between nonconducting and conducting conformations. With recent advances in structural biology, structures of sodium channels have been captured in several distinct conformations, which are thought to represent different functional states. However, it has been difficult to capture the intrinsically transient open state. We recently showed that a proposed open state of the bacterial sodium channel NavMs was not conductive and that a conformational change involving a transition to a π-helix in the pore-lining S6 helix converted this structure into a conducting state. However, the relevance of this structural feature in other sodium channels, and its implications for the broader gating cycle, remained unclear. Here, we propose a comparable open state of another class of bacterial channel from Aliarcobacter butzleri (NavAb) with characteristic pore hydration, ion permeation, and drug binding properties. Furthermore, we show that a π-helix transition can lead to pore opening and that such a conformational change blocks fenestrations in the inner helix bundle. We also discover that a region in the C-terminal domain can undergo a disordering transition proposed to be important for pore opening. These results support a role for a π-helix transition in the opening of NavAb, enabling new proposals for the structural annotation and drug modulation mechanisms in this important sodium channel model.
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Affiliation(s)
- Koushik Choudhury
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Solna, 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,Correspondence to Lucie Delemotte:
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8
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Quaternary structure independent folding of voltage-gated ion channel pore domain subunits. Nat Struct Mol Biol 2022; 29:537-548. [PMID: 35655098 PMCID: PMC9809158 DOI: 10.1038/s41594-022-00775-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 04/08/2022] [Indexed: 01/07/2023]
Abstract
Every voltage-gated ion channel (VGIC) has a pore domain (PD) made from four subunits, each comprising an antiparallel transmembrane helix pair bridged by a loop. The extent to which PD subunit structure requires quaternary interactions is unclear. Here, we present crystal structures of a set of bacterial voltage-gated sodium channel (BacNaV) 'pore only' proteins that reveal a surprising collection of non-canonical quaternary arrangements in which the PD tertiary structure is maintained. This context-independent structural robustness, supported by molecular dynamics simulations, indicates that VGIC-PD tertiary structure is independent of quaternary interactions. This fold occurs throughout the VGIC superfamily and in diverse transmembrane and soluble proteins. Strikingly, characterization of PD subunit-binding Fabs indicates that non-canonical quaternary PD conformations can occur in full-length VGICs. Together, our data demonstrate that the VGIC-PD is an autonomously folded unit. This property has implications for VGIC biogenesis, understanding functional states, de novo channel design, and VGIC structural origins.
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9
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Bacterial Homologs of Progestin and AdipoQ Receptors (PAQRs) Affect Membrane Energetics Homeostasis but Not Fluidity. J Bacteriol 2022; 204:e0058321. [PMID: 35285724 PMCID: PMC9017321 DOI: 10.1128/jb.00583-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Membrane potential homeostasis is essential for cell survival. Defects in membrane potential lead to pleiotropic phenotypes, consistent with the central role of membrane energetics in cell physiology. Homologs of the progestin and AdipoQ receptors (PAQRs) are conserved in multiple phyla of Bacteria and Eukarya. In eukaryotes, PAQRs are proposed to modulate membrane fluidity and fatty acid (FA) metabolism. The role of bacterial homologs has not been elucidated. Here, we use Escherichia coli and Bacillus subtilis to show that bacterial PAQR homologs, which we name “TrhA,” have a role in membrane energetics homeostasis. Using transcriptional fusions, we show that E. coli TrhA (encoded by yqfA) is part of the unsaturated fatty acid biosynthesis regulon. Fatty acid analyses and physiological assays show that a lack of TrhA in both E. coli and B. subtilis (encoded by yplQ) provokes subtle but consistent changes in membrane fatty acid profiles that do not translate to control of membrane fluidity. Instead, membrane proteomics in E. coli suggested a disrupted energy metabolism and dysregulated membrane energetics in the mutant, though it grew similarly to its parent. These changes translated into a disturbed membrane potential in the mutant relative to its parent under various growth conditions. Similar dysregulation of membrane energetics was observed in a different E. coli strain and in the distantly related B. subtilis. Together, our findings are consistent with a role for TrhA in membrane energetics homeostasis, through a mechanism that remains to be elucidated. IMPORTANCE Eukaryotic homologs of the progestin and AdipoQ receptor family (PAQR) have been shown to regulate membrane fluidity by affecting, through unknown mechanisms, unsaturated fatty acid (FA) metabolism. The bacterial homologs studied here mediate small and consistent changes in unsaturated FA metabolism that do not seem to impact membrane fluidity but, rather, alter membrane energetics homeostasis. Together, the findings here suggest that bacterial and eukaryotic PAQRs share functions in maintaining membrane homeostasis (fluidity in eukaryotes and energetics for bacteria with TrhA homologs).
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10
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Dickinson MS, Lu J, Gupta M, Marten I, Hedrich R, Stroud RM. Molecular basis of multistep voltage activation in plant two-pore channel 1. Proc Natl Acad Sci U S A 2022; 119:e2110936119. [PMID: 35210362 PMCID: PMC8892357 DOI: 10.1073/pnas.2110936119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 11/29/2021] [Indexed: 12/26/2022] Open
Abstract
Voltage-gated ion channels confer excitability to biological membranes, initiating and propagating electrical signals across large distances on short timescales. Membrane excitation requires channels that respond to changes in electric field and couple the transmembrane voltage to gating of a central pore. To address the mechanism of this process in a voltage-gated ion channel, we determined structures of the plant two-pore channel 1 at different stages along its activation coordinate. These high-resolution structures of activation intermediates, when compared with the resting-state structure, portray a mechanism in which the voltage-sensing domain undergoes dilation and in-membrane plane rotation about the gating charge-bearing helix, followed by charge translocation across the charge transfer seal. These structures, in concert with patch-clamp electrophysiology, show that residues in the pore mouth sense inhibitory Ca2+ and are allosterically coupled to the voltage sensor. These conformational changes provide insight into the mechanism of voltage-sensor domain activation in which activation occurs vectorially over a series of elementary steps.
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Affiliation(s)
- Miles Sasha Dickinson
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, CA 94143
| | - Jinping Lu
- Department of Molecular Plant Physiology and Biophysics, University of Würzburg, D-97082 Würzburg, Germany
| | - Meghna Gupta
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143
| | - Irene Marten
- Department of Molecular Plant Physiology and Biophysics, University of Würzburg, D-97082 Würzburg, Germany
| | - Rainer Hedrich
- Department of Molecular Plant Physiology and Biophysics, University of Würzburg, D-97082 Würzburg, Germany
| | - Robert M Stroud
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143;
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11
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Pope L, Minor DL. The Polysite Pharmacology of TREK K 2P Channels. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1349:51-65. [PMID: 35138610 DOI: 10.1007/978-981-16-4254-8_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
K2P (KCNK) potassium channels form "background" or "leak" currents that have critical roles in cell excitability control in the brain, cardiovascular system, and somatosensory neurons. Similar to many ion channel families, studies of K2Ps have been limited by poor pharmacology. Of six K2P subfamilies, the thermo- and mechanosensitive TREK subfamily comprising K2P2.1 (TREK-1), K2P4.1 (TRAAK), and K2P10.1 (TREK-2) are the first to have structures determined for each subfamily member. These structural studies have revealed key architectural features that underlie K2P function and have uncovered sites residing at every level of the channel structure with respect to the membrane where small molecules or lipids can control channel function. This polysite pharmacology within a relatively small (~70 kDa) ion channel comprises four structurally defined modulator binding sites that occur above (Keystone inhibitor site), at the level of (K2P modulator pocket), and below (Fenestration and Modulatory lipid sites) the C-type selectivity filter gate that is at the heart of K2P function. Uncovering this rich structural landscape provides the framework for understanding and developing subtype-selective modulators to probe K2P function that may provide leads for drugs for anesthesia, pain, arrhythmia, ischemia, and migraine.
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Affiliation(s)
- Lianne Pope
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, US
| | - Daniel L Minor
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, US. .,Departments of Biochemistry and Biophysics, and Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA. .,California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA, USA. .,Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, CA, USA. .,Molecular Biophysics and Integrated Bio-imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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12
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Nguyen HX, Wu T, Needs D, Zhang H, Perelli RM, DeLuca S, Yang R, Pan M, Landstrom AP, Henriquez C, Bursac N. Engineered bacterial voltage-gated sodium channel platform for cardiac gene therapy. Nat Commun 2022; 13:620. [PMID: 35110560 PMCID: PMC8810800 DOI: 10.1038/s41467-022-28251-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 01/11/2022] [Indexed: 12/19/2022] Open
Abstract
Therapies for cardiac arrhythmias could greatly benefit from approaches to enhance electrical excitability and action potential conduction in the heart by stably overexpressing mammalian voltage-gated sodium channels. However, the large size of these channels precludes their incorporation into therapeutic viral vectors. Here, we report a platform utilizing small-size, codon-optimized engineered prokaryotic sodium channels (BacNav) driven by muscle-specific promoters that significantly enhance excitability and conduction in rat and human cardiomyocytes in vitro and adult cardiac tissues from multiple species in silico. We also show that the expression of BacNav significantly reduces occurrence of conduction block and reentrant arrhythmias in fibrotic cardiac cultures. Moreover, functional BacNav channels are stably expressed in healthy mouse hearts six weeks following intravenous injection of self-complementary adeno-associated virus (scAAV) without causing any adverse effects on cardiac electrophysiology. The large diversity of prokaryotic sodium channels and experimental-computational platform reported in this study should facilitate the development and evaluation of BacNav-based gene therapies for cardiac conduction disorders.
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Affiliation(s)
- Hung X Nguyen
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Tianyu Wu
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Daniel Needs
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Hengtao Zhang
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Robin M Perelli
- Department of Pediatrics, Division of Cardiology, Duke University School of Medicine, Durham, NC, USA
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
| | - Sophia DeLuca
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
| | - Rachel Yang
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Michael Pan
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Andrew P Landstrom
- Department of Pediatrics, Division of Cardiology, Duke University School of Medicine, Durham, NC, USA
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
| | - Craig Henriquez
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Nenad Bursac
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
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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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MacKenzie TMG, Abderemane-Ali F, Garrison CE, Minor DL, Bois JD. Differential effects of modified batrachotoxins on voltage-gated sodium channel fast and slow inactivation. Cell Chem Biol 2021; 29:615-624.e5. [PMID: 34963066 PMCID: PMC9035044 DOI: 10.1016/j.chembiol.2021.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 09/14/2021] [Accepted: 11/29/2021] [Indexed: 11/19/2022]
Abstract
Voltage-gated sodium channels (NaVs) are targets for a number of acute poisons. Many of these agents act as allosteric modulators of channel activity and serve as powerful chemical tools for understanding channel function. Herein, we detail studies with batrachotoxin (BTX), a potent steroidal amine, and three ester derivatives prepared through de novo synthesis against recombinant NaV subtypes (rNaV1.4 and hNaV1.5). Two of these compounds, BTX-B and BTX-cHx, are functionally equivalent to BTX, hyperpolarizing channel activation and blocking both fast and slow inactivation. BTX-yne-a C20-n-heptynoate ester-is a conspicuous outlier, eliminating fast but not slow inactivation. This property differentiates BTX-yne among other NaV modulators as a unique reagent that separates inactivation processes. These findings are supported by functional studies with bacterial NaVs (BacNaVs) that lack a fast inactivation gate. The availability of BTX-yne should advance future efforts aimed at understanding NaV gating mechanisms and designing allosteric regulators of NaV activity.
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Affiliation(s)
- Tim M G MacKenzie
- Department of Chemistry, Stanford University, 337 Campus Drive, Stanford, CA 94305, USA
| | - Fayal Abderemane-Ali
- Cardiovascular Research Institute, University of California, San Francisco, Box 3122, 555 Mission Bay Boulevard South, Rm. 452Z, San Francisco, CA 94158-9001, USA
| | - Catherine E Garrison
- Department of Chemistry, Stanford University, 337 Campus Drive, Stanford, CA 94305, USA
| | - Daniel L Minor
- Cardiovascular Research Institute, University of California, San Francisco, Box 3122, 555 Mission Bay Boulevard South, Rm. 452Z, San Francisco, CA 94158-9001, USA; Departments of Biochemistry and Biophysics, and Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158-9001, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 94158-9001, USA; Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, CA 94158-9001, USA; Molecular Biophysics and Integrated Bio-imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - J Du Bois
- Department of Chemistry, Stanford University, 337 Campus Drive, Stanford, CA 94305, USA.
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15
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Structural Pharmacology of Voltage-Gated Sodium Channels. J Mol Biol 2021; 433:166967. [PMID: 33794261 DOI: 10.1016/j.jmb.2021.166967] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/22/2021] [Accepted: 03/22/2021] [Indexed: 12/19/2022]
Abstract
Voltage-gated sodium (NaV) channels initiate and propagate action potentials in excitable tissues to mediate key physiological processes including heart contraction and nervous system function. Accordingly, NaV channels are major targets for drugs, toxins and disease-causing mutations. Recent breakthroughs in cryo-electron microscopy have led to the visualization of human NaV1.1, NaV1.2, NaV1.4, NaV1.5 and NaV1.7 channel subtypes at high-resolution. These landmark studies have greatly advanced our structural understanding of channel architecture, ion selectivity, voltage-sensing, electromechanical coupling, fast inactivation, and the molecular basis underlying NaV channelopathies. NaV channel structures have also been increasingly determined in complex with toxin and small molecule modulators that target either the pore module or voltage sensor domains. These structural studies have provided new insights into the mechanisms of pharmacological action and opportunities for subtype-selective NaV channel drug design. This review will highlight the structural pharmacology of human NaV channels as well as the potential use of engineered and chimeric channels in future drug discovery efforts.
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16
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Földi MC, Pesti K, Zboray K, Toth AV, Hegedűs T, Málnási-Csizmadia A, Lukacs P, Mike A. The mechanism of non-blocking inhibition of sodium channels revealed by conformation-selective photolabeling. Br J Pharmacol 2021; 178:1200-1217. [PMID: 33450052 DOI: 10.1111/bph.15365] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 12/10/2020] [Accepted: 01/03/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND AND PURPOSE Sodium channel inhibitors can be used to treat hyperexcitability-related diseases, including epilepsies, pain syndromes, neuromuscular disorders and cardiac arrhythmias. The applicability of these drugs is limited by their nonspecific effect on physiological function. They act mainly by sodium channel block and in addition by modulation of channel kinetics. While channel block inhibits healthy and pathological tissue equally, modulation can preferentially inhibit pathological activity. An ideal drug designed to target the sodium channels of pathological tissue would act predominantly by modulation. Thus far, no such drug has been described. EXPERIMENTAL APPROACH Patch-clamp experiments with ultra-fast solution exchange and photolabeling-coupled electrophysiology were applied to describe the unique mechanism of riluzole on Nav1.4 sodium channels. In silico docking experiments were used to study the molecular details of binding. KEY RESULTS We present evidence that riluzole acts predominantly by non-blocking modulation. We propose that, being a relatively small molecule, riluzole is able to stay bound to the binding site, but nonetheless stay off the conduction pathway, by residing in one of the fenestrations. We demonstrate how this mechanism can be recognized. CONCLUSIONS AND IMPLICATIONS Our results identify riluzole as the prototype of this new class of sodium channel inhibitors. Drugs of this class are expected to selectively prevent hyperexcitability, while having minimal effect on cells firing at a normal rate from a normal resting potential.
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Affiliation(s)
- Mátyás C Földi
- MTA-ELTE NAP B Opto-Neuropharmacology Group, Budapest, Hungary.,Plant Protection Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - Krisztina Pesti
- MTA-ELTE NAP B Opto-Neuropharmacology Group, Budapest, Hungary.,Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary.,School of PhD Studies, Semmelweis University, Budapest, Hungary
| | - Katalin Zboray
- Plant Protection Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - Adam V Toth
- Plant Protection Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - Tamás Hegedűs
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - András Málnási-Csizmadia
- Motor Pharmacology Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Peter Lukacs
- MTA-ELTE NAP B Opto-Neuropharmacology Group, Budapest, Hungary.,Plant Protection Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - Arpad Mike
- MTA-ELTE NAP B Opto-Neuropharmacology Group, Budapest, Hungary.,Plant Protection Institute, Centre for Agricultural Research, Martonvásár, Hungary.,Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
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17
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Zhu W, Li T, Silva JR, Chen J. Conservation and divergence in NaChBac and Na V1.7 pharmacology reveals novel drug interaction mechanisms. Sci Rep 2020; 10:10730. [PMID: 32612253 PMCID: PMC7329812 DOI: 10.1038/s41598-020-67761-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 05/13/2020] [Indexed: 01/16/2023] Open
Abstract
Voltage-gated Na+ (NaV) channels regulate homeostasis in bacteria and control membrane electrical excitability in mammals. Compared to their mammalian counterparts, bacterial NaV channels possess a simpler, fourfold symmetric structure and have facilitated studies of the structural basis of channel gating. However, the pharmacology of bacterial NaV remains largely unexplored. Here we systematically screened 39 NaV modulators on a bacterial channel (NaChBac) and characterized a selection of compounds on NaChBac and a mammalian channel (human NaV1.7). We found that while many compounds interact with both channels, they exhibit distinct functional effects. For example, the local anesthetics ambroxol and lidocaine block both NaV1.7 and NaChBac but affect activation and inactivation of the two channels to different extents. The voltage-sensing domain targeting toxin BDS-I increases NaV1.7 but decreases NaChBac peak currents. The pore binding toxins aconitine and veratridine block peak currents of NaV1.7 and shift activation (aconitine) and inactivation (veratridine) respectively. In NaChBac, they block the peak current by binding to the pore residue F224. Nonetheless, aconitine has no effect on activation or inactivation, while veratridine only modulates activation of NaChBac. The conservation and divergence in the pharmacology of bacterial and mammalian NaV channels provide insights into the molecular basis of channel gating and will facilitate organism-specific drug discovery.
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Affiliation(s)
- Wandi Zhu
- Biochemical and Cellular Pharmacology, Genentech Inc., 103 DNA Way, South San Francisco, CA, USA. .,Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
| | - Tianbo Li
- Biochemical and Cellular Pharmacology, Genentech Inc., 103 DNA Way, South San Francisco, CA, USA
| | - Jonathan R Silva
- Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Jun Chen
- Biochemical and Cellular Pharmacology, Genentech Inc., 103 DNA Way, South San Francisco, CA, USA.
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18
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Fedorenko OA, Kaufman IK, Gibby WAT, Barabash ML, Luchinsky DG, Roberts SK, McClintock PVE. Ionic Coulomb blockade and the determinants of selectivity in the NaChBac bacterial sodium channel. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183301. [PMID: 32360369 DOI: 10.1016/j.bbamem.2020.183301] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 01/30/2020] [Accepted: 03/29/2020] [Indexed: 10/24/2022]
Abstract
Mutation-induced transformations of conductivity and selectivity in NaChBac bacterial channels are studied experimentally and interpreted within the framework of ionic Coulomb blockade (ICB), while also taking account of resonant quantised dehydration (QD) and site protonation. Site-directed mutagenesis and whole-cell patch-clamp experiments are used to investigate how the fixed charge Qf at the selectivity filter (SF) affects both valence selectivity and same-charge selectivity. The new ICB/QD model predicts that increasing ∣Qf∣ should lead to a shift in selectivity sequences toward larger ion sizes, in agreement with the present experiments and with earlier work. Comparison of the model with experimental data leads to the introduction of an effective charge Qf∗ at the SF, which was found to differ between Aspartate and Glutamate charged rings, and also to depend on position within the SF. It is suggested that protonation of the residues within the restricted space of the SF is important in significantly reducing the effective charge of the EEEE ring. Values of Qf∗ derived from experiments on divalent blockade agree well with expectations based on the ICB/QD model and have led to the first demonstration of ICB oscillations in Ca2+ conduction as a function of the fixed charge. Preliminary studies of the dependence of Ca2+ conduction on pH are qualitatively consistent with the predictions of the model.
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Affiliation(s)
- O A Fedorenko
- Division of Biomedical and Life Sciences, Lancaster University, Lancaster LA1 4YQ, UK; School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK.
| | - I Kh Kaufman
- Department of Physics, Lancaster University, Lancaster LA1 4YB, UK
| | - W A T Gibby
- Department of Physics, Lancaster University, Lancaster LA1 4YB, UK.
| | - M L Barabash
- Department of Physics, Lancaster University, Lancaster LA1 4YB, UK.
| | - D G Luchinsky
- Department of Physics, Lancaster University, Lancaster LA1 4YB, UK; SGT, Inc., Greenbelt, MD 20770, USA.
| | - S K Roberts
- Division of Biomedical and Life Sciences, Lancaster University, Lancaster LA1 4YQ, UK.
| | - P V E McClintock
- Department of Physics, Lancaster University, Lancaster LA1 4YB, UK.
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19
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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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20
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Stratford JP, Edwards CLA, Ghanshyam MJ, Malyshev D, Delise MA, Hayashi Y, Asally M. Electrically induced bacterial membrane-potential dynamics correspond to cellular proliferation capacity. Proc Natl Acad Sci U S A 2019; 116:9552-9557. [PMID: 31000597 PMCID: PMC6511025 DOI: 10.1073/pnas.1901788116] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Membrane-potential dynamics mediate bacterial electrical signaling at both intra- and intercellular levels. Membrane potential is also central to cellular proliferation. It is unclear whether the cellular response to external electrical stimuli is influenced by the cellular proliferative capacity. A new strategy enabling electrical stimulation of bacteria with simultaneous monitoring of single-cell membrane-potential dynamics would allow bridging this knowledge gap and further extend electrophysiological studies into the field of microbiology. Here we report that an identical electrical stimulus can cause opposite polarization dynamics depending on cellular proliferation capacity. This was demonstrated using two model organisms, namely Bacillus subtilis and Escherichia coli, and by developing an apparatus enabling exogenous electrical stimulation and single-cell time-lapse microscopy. Using this bespoke apparatus, we show that a 2.5-second electrical stimulation causes hyperpolarization in unperturbed cells. Measurements of intracellular K+ and the deletion of the K+ channel suggested that the hyperpolarization response is caused by the K+ efflux through the channel. When cells are preexposed to 400 ± 8 nm wavelength light, the same electrical stimulation depolarizes cells instead of causing hyperpolarization. A mathematical model extended from the FitzHugh-Nagumo neuron model suggested that the opposite response dynamics are due to the shift in resting membrane potential. As predicted by the model, electrical stimulation only induced depolarization when cells are treated with antibiotics, protonophore, or alcohol. Therefore, electrically induced membrane-potential dynamics offer a reliable approach for rapid detection of proliferative bacteria and determination of their sensitivity to antimicrobial agents at the single-cell level.
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Affiliation(s)
- James P Stratford
- School of Life Sciences, University of Warwick, Coventry, West Midlands, CV4 7AL, United Kingdom
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, West Midlands, CV4 7AL,United Kingdom
| | - Conor L A Edwards
- School of Life Sciences, University of Warwick, Coventry, West Midlands, CV4 7AL, United Kingdom
| | - Manjari J Ghanshyam
- School of Life Sciences, University of Warwick, Coventry, West Midlands, CV4 7AL, United Kingdom
| | - Dmitry Malyshev
- School of Life Sciences, University of Warwick, Coventry, West Midlands, CV4 7AL, United Kingdom
| | - Marco A Delise
- School of Life Sciences, University of Warwick, Coventry, West Midlands, CV4 7AL, United Kingdom
| | - Yoshikatsu Hayashi
- Department of Biomedical Engineering, School of Biological Sciences, University of Reading, Reading, Berkshire, RG6 6AH, United Kingdom
| | - Munehiro Asally
- School of Life Sciences, University of Warwick, Coventry, West Midlands, CV4 7AL, United Kingdom;
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, West Midlands, CV4 7AL,United Kingdom
- Bio-Electrical Engineering Innovation Hub, University of Warwick, Coventry, West Midlands, CV4 7AL, United Kingdom
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21
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Hedrich R. Diatom Signaling: A Novel Channel Type Identified. Curr Biol 2019; 29:R319-R321. [PMID: 31063722 DOI: 10.1016/j.cub.2019.03.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Our nerve and muscle cells communicate using voltage-dependent four-domain sodium channels. A recent study in eukaryotic phytoplankton reveals that single-domain, prokaryote-like, voltage-gated Na+- and Ca2+-permeable channels are key to environmental sensing in the oceans.
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Affiliation(s)
- Rainer Hedrich
- University of Würtzburg, Biocentre, Julius-von-Sachs-Institut for Biosciences, Department of Molecular Plant Physiology and Biophysics, Würtzburg, Germany.
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22
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A Selectivity Filter Gate Controls Voltage-Gated Calcium Channel Calcium-Dependent Inactivation. Neuron 2019; 101:1134-1149.e3. [DOI: 10.1016/j.neuron.2019.01.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 11/12/2018] [Accepted: 12/31/2018] [Indexed: 11/22/2022]
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23
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Nguyen HX, Bursac N. Ion channel engineering for modulation and de novo generation of electrical excitability. Curr Opin Biotechnol 2019; 58:100-107. [PMID: 30776744 DOI: 10.1016/j.copbio.2019.01.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 01/02/2019] [Indexed: 02/07/2023]
Abstract
Ion channels play essential roles in regulating electrical properties of excitable tissues. By leveraging various ion channel gating mechanisms, scientists have developed a versatile set of genetically encoded tools to modulate intrinsic tissue excitability under different experimental settings. In this article, we will review how ion channels activated by voltage, light, small chemicals, stretch, and temperature have been customized to enable control of tissue excitability both in vitro and in vivo. Advantages and limitations of each of these ion channel-engineering platforms will be discussed and notable applications will be highlighted. Furthermore, we will describe recent progress on de novo generation of excitable tissues via expression of appropriate sets of engineered voltage-gated ion channels and discuss potential therapeutic implications.
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Affiliation(s)
- Hung X Nguyen
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Nenad Bursac
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA.
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24
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Finol-Urdaneta RK, McArthur JR, Goldschen-Ohm MP, Gaudet R, Tikhonov DB, Zhorov BS, French RJ. Batrachotoxin acts as a stent to hold open homotetrameric prokaryotic voltage-gated sodium channels. J Gen Physiol 2018; 151:186-199. [PMID: 30587506 PMCID: PMC6363421 DOI: 10.1085/jgp.201812278] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 11/30/2018] [Indexed: 11/20/2022] Open
Abstract
Batrachotoxin (BTX), an alkaloid from skin secretions of dendrobatid frogs, causes paralysis and death by facilitating activation and inhibiting deactivation of eukaryotic voltage-gated sodium (Nav) channels, which underlie action potentials in nerve, muscle, and heart. A full understanding of the mechanism by which BTX modifies eukaryotic Nav gating awaits determination of high-resolution structures of functional toxin-channel complexes. Here, we investigate the action of BTX on the homotetrameric prokaryotic Nav channels NaChBac and NavSp1. By combining mutational analysis and whole-cell patch clamp with molecular and kinetic modeling, we show that BTX hinders deactivation and facilitates activation in a use-dependent fashion. Our molecular model shows the horseshoe-shaped BTX molecule bound within the open pore, forming hydrophobic H-bonds and cation-π contacts with the pore-lining helices, leaving space for partially dehydrated sodium ions to permeate through the hydrophilic inner surface of the horseshoe. We infer that bulky BTX, bound at the level of the gating-hinge residues, prevents the S6 rearrangements that are necessary for closure of the activation gate. Our results reveal general similarities to, and differences from, BTX actions on eukaryotic Nav channels, whose major subunit is a single polypeptide formed by four concatenated, homologous, nonidentical domains that form a pseudosymmetric pore. Our determination of the mechanism by which BTX activates homotetrameric voltage-gated channels reveals further similarities between eukaryotic and prokaryotic Nav channels and emphasizes the tractability of bacterial Nav channels as models of voltage-dependent ion channel gating. The results contribute toward a deeper, atomic-level understanding of use-dependent natural and synthetic Nav channel agonists and antagonists, despite their overlapping binding motifs on the channel proteins.
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Affiliation(s)
- Rocio K Finol-Urdaneta
- Department of Physiology & Pharmacology and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada .,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA.,Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, New South Wales, Australia
| | - Jeffrey R McArthur
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA.,Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, New South Wales, Australia
| | | | - Rachelle Gaudet
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA
| | - Denis B Tikhonov
- Sechenov Institute of Evolutionary Physiology and Biochemistry, St. Petersburg, Russia
| | - Boris S Zhorov
- Sechenov Institute of Evolutionary Physiology and Biochemistry, St. Petersburg, Russia.,Department of Biological Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Robert J French
- Department of Physiology & Pharmacology and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
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25
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Hutchings CJ, Colussi P, Clark TG. Ion channels as therapeutic antibody targets. MAbs 2018; 11:265-296. [PMID: 30526315 PMCID: PMC6380435 DOI: 10.1080/19420862.2018.1548232] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 11/01/2018] [Accepted: 11/03/2018] [Indexed: 12/12/2022] Open
Abstract
It is now well established that antibodies have numerous potential benefits when developed as therapeutics. Here, we evaluate the technical challenges of raising antibodies to membrane-spanning proteins together with enabling technologies that may facilitate the discovery of antibody therapeutics to ion channels. Additionally, we discuss the potential targeting opportunities in the anti-ion channel antibody landscape, along with a number of case studies where functional antibodies that target ion channels have been reported. Antibodies currently in development and progressing towards the clinic are highlighted.
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Affiliation(s)
| | | | - Theodore G. Clark
- TetraGenetics Inc, Arlington Massachusetts, USA
- Department of Microbiology and Immunology, Cornell University, Ithaca New York, USA
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26
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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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27
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Abstract
A new study reveals that conformational flexibility in the pore of a voltage-gated sodium channel may underlie slow inactivation.
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28
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Ogawara H. Comparison of Strategies to Overcome Drug Resistance: Learning from Various Kingdoms. Molecules 2018; 23:E1476. [PMID: 29912169 PMCID: PMC6100412 DOI: 10.3390/molecules23061476] [Citation(s) in RCA: 3] [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] [Received: 05/04/2018] [Revised: 06/13/2018] [Accepted: 06/15/2018] [Indexed: 11/16/2022] Open
Abstract
Drug resistance, especially antibiotic resistance, is a growing threat to human health. To overcome this problem, it is significant to know precisely the mechanisms of drug resistance and/or self-resistance in various kingdoms, from bacteria through plants to animals, once more. This review compares the molecular mechanisms of the resistance against phycotoxins, toxins from marine and terrestrial animals, plants and fungi, and antibiotics. The results reveal that each kingdom possesses the characteristic features. The main mechanisms in each kingdom are transporters/efflux pumps in phycotoxins, mutation and modification of targets and sequestration in marine and terrestrial animal toxins, ABC transporters and sequestration in plant toxins, transporters in fungal toxins, and various or mixed mechanisms in antibiotics. Antibiotic producers in particular make tremendous efforts for avoiding suicide, and are more flexible and adaptable to the changes of environments. With these features in mind, potential alternative strategies to overcome these resistance problems are discussed. This paper will provide clues for solving the issues of drug resistance.
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Affiliation(s)
- Hiroshi Ogawara
- HO Bio Institute, Yushima-2, Bunkyo-ku, Tokyo 113-0034, Japan.
- Department of Biochemistry, Meiji Pharmaceutical University, Noshio-2, Kiyose, Tokyo 204-8588, Japan.
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29
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Non-blocking modulation contributes to sodium channel inhibition by a covalently attached photoreactive riluzole analog. Sci Rep 2018; 8:8110. [PMID: 29802266 PMCID: PMC5970139 DOI: 10.1038/s41598-018-26444-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 05/04/2018] [Indexed: 11/08/2022] Open
Abstract
Sodium channel inhibitor drugs decrease pathological hyperactivity in various diseases including pain syndromes, myotonia, arrhythmias, nerve injuries and epilepsies. Inhibiting pathological but not physiological activity, however, is a major challenge in drug development. Sodium channel inhibitors exert their effects by a dual action: they obstruct ion flow ("block"), and they alter the energetics of channel opening and closing ("modulation"). Ideal drugs would be modulators without blocking effect, because modulation is inherently activity-dependent, therefore selective for pathological hyperactivity. Can block and modulation be separated? It has been difficult to tell, because the effect of modulation is obscured by conformation-dependent association/dissociation of the drug. To eliminate dynamic association/dissociation, we used a photoreactive riluzole analog which could be covalently bound to the channel; and found, unexpectedly, that drug-bound channels could still conduct ions, although with modulated gating. The finding that non-blocking modulation is possible, may open a novel avenue for drug development because non-blocking modulators could be more specific in treating hyperactivity-linked diseases.
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Yang E, Zhi L, Liang Q, Covarrubias M. Electrophysiological Analysis of Voltage-Gated Ion Channel Modulation by General Anesthetics. Methods Enzymol 2018; 602:339-368. [PMID: 29588038 DOI: 10.1016/bs.mie.2018.01.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Voltage-gated ion channels (VGICs) of excitable tissues are emerging as targets likely involved in both the therapeutic and toxic effects of inhaled and intravenous general anesthetics. Whereas sevoflurane and propofol inhibit voltage-gated Na+ channels (Navs), sevoflurane potentiates certain voltage-gated K+ channels (Kvs). The combination of these effects would dampen neural excitability and, therefore, might contribute to the clinical endpoints of general anesthesia. As the body of work regarding the interaction of general anesthetics with VGICs continues to grow, a multidisciplinary approach involving functional, biochemical, structural, and computational techniques, many of which are detailed in other chapters, has increasingly become necessary to solve the molecular mechanism of general anesthetic action on VGICs. Here, we focus on electrophysiological and modeling approaches and methodologies to describe how our work has elucidated the biophysical basis of the inhibition Navs by propofol and the potentiation of Kvs by sevoflurane.
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Affiliation(s)
- Elaine Yang
- Vickie and Jack Farber Institute for Neuroscience, Sidney Kimmel Medical College, Jefferson College of Biomedical Sciences, Thomas Jefferson University, Philadelphia, PA, United States.
| | - Lianteng Zhi
- Vickie and Jack Farber Institute for Neuroscience, Sidney Kimmel Medical College, Jefferson College of Biomedical Sciences, Thomas Jefferson University, Philadelphia, PA, United States
| | - Qiansheng Liang
- Vickie and Jack Farber Institute for Neuroscience, Sidney Kimmel Medical College, Jefferson College of Biomedical Sciences, Thomas Jefferson University, Philadelphia, PA, United States
| | - Manuel Covarrubias
- Vickie and Jack Farber Institute for Neuroscience, Sidney Kimmel Medical College, Jefferson College of Biomedical Sciences, Thomas Jefferson University, Philadelphia, PA, United States
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Chang A, Abderemane-Ali F, Hura GL, Rossen ND, Gate RE, Minor DL. A Calmodulin C-Lobe Ca 2+-Dependent Switch Governs Kv7 Channel Function. Neuron 2018; 97:836-852.e6. [PMID: 29429937 DOI: 10.1016/j.neuron.2018.01.035] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 12/07/2017] [Accepted: 01/12/2018] [Indexed: 12/22/2022]
Abstract
Kv7 (KCNQ) voltage-gated potassium channels control excitability in the brain, heart, and ear. Calmodulin (CaM) is crucial for Kv7 function, but how this calcium sensor affects activity has remained unclear. Here, we present X-ray crystallographic analysis of CaM:Kv7.4 and CaM:Kv7.5 AB domain complexes that reveal an Apo/CaM clamp conformation and calcium binding preferences. These structures, combined with small-angle X-ray scattering, biochemical, and functional studies, establish a regulatory mechanism for Kv7 CaM modulation based on a common architecture in which a CaM C-lobe calcium-dependent switch releases a shared Apo/CaM clamp conformation. This C-lobe switch inhibits voltage-dependent activation of Kv7.4 and Kv7.5 but facilitates Kv7.1, demonstrating that mechanism is shared by Kv7 isoforms despite the different directions of CaM modulation. Our findings provide a unified framework for understanding how CaM controls different Kv7 isoforms and highlight the role of membrane proximal domains for controlling voltage-gated channel function. VIDEO ABSTRACT.
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Affiliation(s)
- Aram Chang
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA 94158, USA
| | - Fayal Abderemane-Ali
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA 94158, USA
| | - Greg L Hura
- Molecular Biophysics and Integrated Bio-imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Nathan D Rossen
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA 94158, USA
| | - Rachel E Gate
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA 94158, USA
| | - Daniel L Minor
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA 94158, USA; Molecular Biophysics and Integrated Bio-imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Departments of Biochemistry and Biophysics, and Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California San Francisco, San Francisco, CA 94158, USA; Kavli Institute for Fundamental Neuroscience, University of California San Francisco, San Francisco, CA 94158, USA.
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32
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Global versus local mechanisms of temperature sensing in ion channels. Pflugers Arch 2018; 470:733-744. [PMID: 29340775 DOI: 10.1007/s00424-017-2102-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 12/15/2017] [Accepted: 12/19/2017] [Indexed: 02/07/2023]
Abstract
Ion channels turn diverse types of inputs, ranging from neurotransmitters to physical forces, into electrical signals. Channel responses to ligands generally rely on binding to discrete sensor domains that are coupled to the portion of the channel responsible for ion permeation. By contrast, sensing physical cues such as voltage, pressure, and temperature arises from more varied mechanisms. Voltage is commonly sensed by a local, domain-based strategy, whereas the predominant paradigm for pressure sensing employs a global response in channel structure to membrane tension changes. Temperature sensing has been the most challenging response to understand and whether discrete sensor domains exist for pressure and temperature has been the subject of much investigation and debate. Recent exciting advances have uncovered discrete sensor modules for pressure and temperature in force-sensitive and thermal-sensitive ion channels, respectively. In particular, characterization of bacterial voltage-gated sodium channel (BacNaV) thermal responses has identified a coiled-coil thermosensor that controls channel function through a temperature-dependent unfolding event. This coiled-coil thermosensor blueprint recurs in other temperature sensitive ion channels and thermosensitive proteins. Together with the identification of ion channel pressure sensing domains, these examples demonstrate that "local" domain-based solutions for sensing force and temperature exist and highlight the diversity of both global and local strategies that channels use to sense physical inputs. The modular nature of these newly discovered physical signal sensors provides opportunities to engineer novel pressure-sensitive and thermosensitive proteins and raises new questions about how such modular sensors may have evolved and empowered ion channel pores with new sensibilities.
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33
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Abstract
Every cell within living organisms actively maintains an intracellular Na+ concentration that is 10-12 times lower than the extracellular concentration. The cells then utilize this transmembrane Na+ concentration gradient as a driving force to produce electrical signals, sometimes in the form of action potentials. The protein family comprising voltage-gated sodium channels (NaVs) is essential for such signaling and enables cells to change their status in a regenerative manner and to rapidly communicate with one another. NaVs were first predicted in squid and were later identified through molecular biology in the electric eel. Since then, these proteins have been discovered in organisms ranging from bacteria to humans. Recent research has succeeded in decoding the amino acid sequences of a wide variety of NaV family members, as well as the three-dimensional structures of some. These studies and others have uncovered several of the major steps in the functional and structural transition of NaV proteins that has occurred along the course of the evolutionary history of organisms. Here we present an overview of the molecular evolutionary innovations that established present-day NaV α subunits and discuss their contribution to the evolutionary changes in animal bodies.
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Affiliation(s)
- Atsuo Nishino
- Department of Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori, Japan.
| | - Yasushi Okamura
- Integrative Physiology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
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34
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Lolicato M, Arrigoni C, Mori T, Sekioka Y, Bryant C, Clark KA, Minor DL. K 2P2.1 (TREK-1)-activator complexes reveal a cryptic selectivity filter binding site. Nature 2017; 547:364-368. [PMID: 28693035 PMCID: PMC5778891 DOI: 10.1038/nature22988] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 05/12/2017] [Indexed: 12/11/2022]
Abstract
Polymodal K2P (KCNK) thermo- and mechanosensitive TREK1 potassium channels, generate ‘leak’ currents that regulate neuronal excitability, respond to lipids, temperature, and mechanical stretch, and influence pain, temperature perception, and anesthetic responses1–3. These dimeric voltage-gated ion channel (VGIC) superfamily members have a unique topology comprising two pore forming regions per subunit4–6. Contrasting other potassium channels, K2Ps use a selectivity filter ‘C-type’ gate7–10 as the principal gating site. Despite recent advances3,11,12, K2Ps suffer from a poor pharmacologic profile limiting mechanistic and biological studies. Here, we describe a new small molecule TREK activator class that directly stimulates the C-type gate by acting as molecular wedges that restrict interdomain interface movement behind the selectivity filter. Structures of K2P2.1(TREK-1) alone with two selective K2P2.1(TREK-1) and K2P10.1(TREK-2) activators, an N-aryl-sulfonamide, ML335, and a thiophene-carboxamide, ML402, define a cryptic binding pocket unlike other ion channel small molecule binding sites and, together with functional studies, identify a cation-π interaction that controls selectivity. Together, our data unveil a previously unknown, druggable K2P site that stabilizes the C-type gate ‘leak mode’ and provide direct evidence for K2P selectivity filter gating.
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Affiliation(s)
- Marco Lolicato
- Cardiovascular Research Institute, University of California, San Francisco, California 941158-9001, USA
| | - Cristina Arrigoni
- Cardiovascular Research Institute, University of California, San Francisco, California 941158-9001, USA
| | - Takahiro Mori
- Ono Pharmaceutical Co. Ltd, Mishima-Gun, Osaka 618-8585, Japan
| | - Yoko Sekioka
- Ono Pharmaceutical Co. Ltd, Mishima-Gun, Osaka 618-8585, Japan
| | - Clifford Bryant
- Small Molecule Discovery Center, University of California, San Francisco, California 93858-2330, USA
| | - Kimberly A Clark
- Cardiovascular Research Institute, University of California, San Francisco, California 941158-9001, USA
| | - Daniel L Minor
- Cardiovascular Research Institute, University of California, San Francisco, California 941158-9001, USA.,Departments of Biochemistry and Biophysics, and Cellular and Molecular Pharmacology, University of California, San Francisco, California 941158-9001, USA.,California Institute for Quantitative Biomedical Research, University of California, San Francisco, California 941158-9001, USA.,Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, California 941158-9001, USA.,Molecular Biophysics and Integrated Bio-imaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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35
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Tetrodotoxin-Producing Bacteria: Detection, Distribution and Migration of the Toxin in Aquatic Systems. Toxins (Basel) 2017; 9:toxins9050166. [PMID: 28513564 PMCID: PMC5450714 DOI: 10.3390/toxins9050166] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 05/12/2017] [Accepted: 05/12/2017] [Indexed: 01/18/2023] Open
Abstract
This review is devoted to the marine bacterial producers of tetrodotoxin (TTX), a potent non-protein neuroparalytic toxin. In addition to the issues of the ecology and distribution of TTX-producing bacteria, this review examines issues relating to toxin migration from bacteria to TTX-bearing animals. It is shown that the mechanism of TTX extraction from toxin-producing bacteria to the environment occur through cell death, passive/active toxin excretion, or spore germination of spore-forming bacteria. Data on TTX microdistribution in toxic organs of TTX-bearing animals indicate toxin migration from the digestive system to target organs through the transport system of the organism. The role of symbiotic microflora in animal toxicity is also discussed: despite low toxin production by bacterial strains in laboratory conditions, even minimal amounts of TTX produced by intestinal microflora of an animal can contribute to its toxicity. Special attention is paid to methods of TTX detection applicable to bacteria. Due to the complexity of toxin detection in TTX-producing bacteria, it is necessary to use several methods based on different methodological approaches. Issues crucial for further progress in detecting natural sources of TTX investigation are also considered.
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36
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Pryde DC, Swain NA, Stupple PA, West CW, Marron B, Markworth CJ, Printzenhoff D, Lin Z, Cox PJ, Suzuki R, McMurray S, Waldron GJ, Payne CE, Warmus JS, Chapman ML. The discovery of a potent Na v1.3 inhibitor with good oral pharmacokinetics. MEDCHEMCOMM 2017; 8:1255-1267. [PMID: 30108836 DOI: 10.1039/c7md00131b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 04/26/2017] [Indexed: 11/21/2022]
Abstract
In this article, we describe the discovery of an aryl ether series of potent and selective Nav1.3 inhibitors. Based on structural analogy to a similar series of compounds we have previously shown bind to the domain IV voltage sensor region of Nav channels, we propose this series binds in the same location. We describe the development of this series from a published starting point, highlighting key selectivity and potency data, and several studies designed to validate Nav1.3 as a target for pain.
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Affiliation(s)
- D C Pryde
- Worldwide Medicinal Chemistry , Pfizer Neuroscience and Pain Research Unit , Portway Building, Granta Park , Cambridge , CB21 6GS , UK .
| | - N A Swain
- Worldwide Medicinal Chemistry , Pfizer Neuroscience and Pain Research Unit , Portway Building, Granta Park , Cambridge , CB21 6GS , UK .
| | - P A Stupple
- Worldwide Medicinal Chemistry , Pfizer Neuroscience and Pain Research Unit , Portway Building, Granta Park , Cambridge , CB21 6GS , UK .
| | - C W West
- Pfizer Neuroscience and Pain Research Unit , 4222 Emperor Boulevard, Suite 350 , Durham , North Carolina NC27703 , USA
| | - B Marron
- Pfizer Neuroscience and Pain Research Unit , 4222 Emperor Boulevard, Suite 350 , Durham , North Carolina NC27703 , USA
| | - C J Markworth
- Pfizer Neuroscience and Pain Research Unit , 4222 Emperor Boulevard, Suite 350 , Durham , North Carolina NC27703 , USA
| | - D Printzenhoff
- Pfizer Neuroscience and Pain Research Unit , 4222 Emperor Boulevard, Suite 350 , Durham , North Carolina NC27703 , USA
| | - Z Lin
- Pfizer Neuroscience and Pain Research Unit , 4222 Emperor Boulevard, Suite 350 , Durham , North Carolina NC27703 , USA
| | - P J Cox
- Pfizer Neuroscience and Pain Research Unit , Portway Building, Granta Park , Cambridge , CB21 6GS , UK
| | - R Suzuki
- Pfizer Neuroscience and Pain Research Unit , Portway Building, Granta Park , Cambridge , CB21 6GS , UK
| | - S McMurray
- Pfizer Neuroscience and Pain Research Unit , Portway Building, Granta Park , Cambridge , CB21 6GS , UK
| | - G J Waldron
- Pfizer Neuroscience and Pain Research Unit , Portway Building, Granta Park , Cambridge , CB21 6GS , UK
| | - C E Payne
- Pfizer Neuroscience and Pain Research Unit , Portway Building, Granta Park , Cambridge , CB21 6GS , UK
| | - J S Warmus
- Worldwide Medicinal Chemistry , Pfizer Neuroscience and Pain Research Unit , Groton , CT , USA
| | - M L Chapman
- Pfizer Neuroscience and Pain Research Unit , 4222 Emperor Boulevard, Suite 350 , Durham , North Carolina NC27703 , USA
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37
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Sand RM, Gingrich KJ, Macharadze T, Herold KF, Hemmings HC. Isoflurane modulates activation and inactivation gating of the prokaryotic Na + channel NaChBac. J Gen Physiol 2017; 149:623-638. [PMID: 28416648 PMCID: PMC5460948 DOI: 10.1085/jgp.201611600] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 09/04/2016] [Accepted: 03/15/2017] [Indexed: 02/01/2023] Open
Abstract
The pharmacological effects of inhaled anesthetics on ion channel function are poorly understood. Sand et al. analyze macroscopic gating of the prokaryotic voltage-gated sodium channel, NaChBac, using a six-state kinetic scheme and demonstrate that isoflurane modulates microscopic gating properties. Voltage-gated Na+ channels (Nav) have emerged as important presynaptic targets for volatile anesthetic (VA) effects on synaptic transmission. However, the detailed biophysical mechanisms by which VAs modulate Nav function remain unclear. VAs alter macroscopic activation and inactivation of the prokaryotic Na+ channel, NaChBac, which provides a useful structural and functional model of mammalian Nav. Here, we study the effects of the common general anesthetic isoflurane on NaChBac function by analyzing macroscopic Na+ currents (INa) in wild-type (WT) channels and mutants with impaired (G229A) or enhanced (G219A) inactivation. We use a previously described six-state Markov model to analyze empirical WT and mutant NaChBac channel gating data. The model reproduces the mean empirical gating manifest in INa time courses and optimally estimates microscopic rate constants, valences (z), and fractional electrical distances (x) of forward and backward transitions. The model also reproduces gating observed for all three channels in the absence or presence of isoflurane, providing further validation. We show using this model that isoflurane increases forward activation and inactivation rate constants at 0 mV, which are associated with estimated chemical free energy changes of approximately −0.2 and −0.7 kcal/mol, respectively. Activation is voltage dependent (z ≈ 2e0, x ≈ 0.3), inactivation shows little voltage dependence, and isoflurane has no significant effect on either. Forward inactivation rate constants are more than 20-fold greater than backward rate constants in the absence or presence of isoflurane. These results indicate that isoflurane modulates NaChBac gating primarily by increasing forward activation and inactivation rate constants. These findings support accumulating evidence for multiple sites of anesthetic interaction with the channel.
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Affiliation(s)
- Rheanna M Sand
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY 10065
| | - Kevin J Gingrich
- Department of Anesthesiology, University of Texas Southwestern Medical Center, Dallas, TX 75235
| | - Tamar Macharadze
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY 10065
| | - Karl F Herold
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY 10065
| | - Hugh C Hemmings
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY 10065 .,Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065
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38
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Structures of closed and open states of a voltage-gated sodium channel. Proc Natl Acad Sci U S A 2017; 114:E3051-E3060. [PMID: 28348242 DOI: 10.1073/pnas.1700761114] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial voltage-gated sodium channels (BacNavs) serve as models of their vertebrate counterparts. BacNavs contain conserved voltage-sensing and pore-forming domains, but they are homotetramers of four identical subunits, rather than pseudotetramers of four homologous domains. Here, we present structures of two NaVAb mutants that capture tightly closed and open states at a resolution of 2.8-3.2 Å. Introduction of two humanizing mutations in the S6 segment (NaVAb/FY: T206F and V213Y) generates a persistently closed form of the activation gate in which the intracellular ends of the four S6 segments are drawn tightly together to block ion permeation completely. This construct also revealed the complete structure of the four-helix bundle that forms the C-terminal domain. In contrast, truncation of the C-terminal 40 residues in NavAb/1-226 captures the activation gate in an open conformation, revealing the open state of a BacNav with intact voltage sensors. Comparing these structures illustrates the full range of motion of the activation gate, from closed with its orifice fully occluded to open with an orifice of ∼10 Å. Molecular dynamics and free-energy simulations confirm designation of NaVAb/1-226 as an open state that allows permeation of hydrated Na+, and these results also support a hydrophobic gating mechanism for control of ion permeation. These two structures allow completion of a closed-open-inactivated conformational cycle in a single voltage-gated sodium channel and give insight into the structural basis for state-dependent binding of sodium channel-blocking drugs.
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Barhoumi L, Baraket A, Nooredeen NM, Ali MB, Abbas MN, Bausells J, Errachid A. Silicon Nitride Capacitive Chemical Sensor for Phosphate Ion Detection Based on Copper Phthalocyanine - Acrylate-polymer. ELECTROANAL 2017. [DOI: 10.1002/elan.201700005] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Lassaad Barhoumi
- University of Sousse, Higher Institute of Applied Sciences and Technology of Sousse, GREENS-ISSAT; Cité Ettafala 4003 Ibn Khaldoun Sousse Tunisia
- NANOMESENE Lab, LR16CRMN01; Centre for Research on Microelectronics and Nanotechnology of Sousse; Technopole of Sousse B. P. 334, Sahloul 4034 Sousse Tunisia
| | - Abdoullatif Baraket
- Université de Lyon; Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1, ENS Lyon - 5, rue de la Doua; F-69100 Villeurbanne France
| | | | - Mounir Ben Ali
- University of Sousse, Higher Institute of Applied Sciences and Technology of Sousse, GREENS-ISSAT; Cité Ettafala 4003 Ibn Khaldoun Sousse Tunisia
- NANOMESENE Lab, LR16CRMN01; Centre for Research on Microelectronics and Nanotechnology of Sousse; Technopole of Sousse B. P. 334, Sahloul 4034 Sousse Tunisia
| | | | - Joan Bausells
- Centro Nacional de Microelectrónica (CSIC), Campus UAB; 08193 Bellaterra Spain
| | - Abdelhamid Errachid
- Université de Lyon; Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1, ENS Lyon - 5, rue de la Doua; F-69100 Villeurbanne France
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40
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Sun RN, Gong H. Simulating the Activation of Voltage Sensing Domain for a Voltage-Gated Sodium Channel Using Polarizable Force Field. J Phys Chem Lett 2017; 8:901-908. [PMID: 28171721 DOI: 10.1021/acs.jpclett.7b00023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Voltage-gated sodium (NaV) channels play vital roles in the signal transduction of excitable cells. Upon activation of a NaV channel, the change of transmembrane voltage triggers conformational change of the voltage sensing domain, which then elicits opening of the pore domain and thus allows an influx of Na+ ions. Description of this process with atomistic details is in urgent demand. In this work, we simulated the partial activation process of the voltage sensing domain of a prokaryotic NaV channel using a polarizable force field. We not only observed the conformational change of the voltage sensing domain from resting to preactive state, but also rigorously estimated the free energy profile along the identified reaction pathway. Comparison with the control simulation using an additive force field indicates that voltage-gating thermodynamics of NaV channels may be inaccurately described without considering the electrostatic polarization effect.
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Affiliation(s)
- Rui-Ning Sun
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Haipeng Gong
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University , Beijing 100084, China
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41
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Ezquerra-Romano I, Ezquerra A. Highway to thermosensation: a traced review, from the proteins to the brain. Rev Neurosci 2017; 28:45-57. [PMID: 27754972 DOI: 10.1515/revneuro-2016-0039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 08/07/2016] [Indexed: 01/09/2023]
Abstract
Temperature maintenance and detection are essential for the survival and perpetuation of any species. This review is focused on thermosensation; thus a detailed and traced explanation of the anatomical and physiological characteristics of each component of this sensation is given. First, the proteins that react to temperature changes are identified; next, the nature of the neurons involved in thermosensation is described; and then, the pathways from the skin through the spinal cord to the brain are outlined. Finally, the areas of the brain and their interconnections where thermoperception arises are explained. Transduction of the external and internal temperature information is essentially mediated by the transient receptor potential ion channels (TRPs). These proteins are embedded in the neurons' membrane and they hyper- or de-polarize neurons in function of the intrinsic voltage and the temperature changes. There are distinct TRP sensors for different temperature ranges. Interestingly, the primary afferent neurons have either cold or hot receptors, so they are dedicated separately to cold or hot sensation. The information is transmitted by different pathways from the skin to the brain, where it either remains separated or is integrated to generate a response. It seems that both the determination of how thermoperception is produced and how we interact with the world are dependent on the particular arrangement and nature of the components, the way of transduction of information and the communication between these elements.
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42
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Voltage-gated sodium channels viewed through a structural biology lens. Curr Opin Struct Biol 2016; 45:74-84. [PMID: 27988421 DOI: 10.1016/j.sbi.2016.11.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 11/28/2016] [Indexed: 02/07/2023]
Abstract
Voltage-gated sodium (Nav) channels initiate and propagate action potentials in excitable cells, and are frequently dysregulated or mutated in human disease. Despite decades of intense physiological and biophysical research, eukaryotic Nav channels have so far eluded high-resolution structure determination because of their biochemical complexity. Recently, simpler bacterial voltage-gated sodium (BacNav) channels have provided templates to understand the structural basis of voltage-dependent activation, inactivation, ion selectivity, and drug block in eukaryotic Nav and related voltage-gated calcium (Cav) channels. Further breakthroughs employing BacNav channels have also enabled visualization of bound small molecule modulators that can guide the rational design of next generation therapeutics. This review will highlight the emerging structural biology of BacNav channels and its contribution to our understanding of the gating, ion selectivity, and pharmacological regulation of eukaryotic Nav (and Cav) channels.
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43
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Toma T, Logan MM, Menard F, Devlin AS, Du Bois J. Inhibition of Sodium Ion Channel Function with Truncated Forms of Batrachotoxin. ACS Chem Neurosci 2016; 7:1463-1468. [PMID: 27501251 DOI: 10.1021/acschemneuro.6b00212] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
A novel family of small molecule inhibitors of voltage-gated sodium channels (NaVs) based on the structure of batrachotoxin (BTX), a well-known channel agonist, is described. Protein mutagenesis and electrophysiology experiments reveal the binding site as the inner pore region of the channel, analogous to BTX, alkaloid toxins, and local anesthetics. Homology modeling of the eukaryotic channel based on recent crystallographic analyses of bacterial NaVs suggests a mechanism of action for ion conduction block.
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Affiliation(s)
- Tatsuya Toma
- Department
of Chemistry, Stanford University, Stanford, California 94305-5080, United States
| | - Matthew M. Logan
- Department
of Chemistry, Stanford University, Stanford, California 94305-5080, United States
| | - Frederic Menard
- Department
of Chemistry, Stanford University, Stanford, California 94305-5080, United States
| | - A. Sloan Devlin
- Department
of Chemistry, Stanford University, Stanford, California 94305-5080, United States
| | - J. Du Bois
- Department
of Chemistry, Stanford University, Stanford, California 94305-5080, United States
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Nguyen HX, Kirkton RD, Bursac N. Engineering prokaryotic channels for control of mammalian tissue excitability. Nat Commun 2016; 7:13132. [PMID: 27752065 PMCID: PMC5071848 DOI: 10.1038/ncomms13132] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 09/06/2016] [Indexed: 12/19/2022] Open
Abstract
The ability to directly enhance electrical excitability of human cells is hampered by the lack of methods to efficiently overexpress large mammalian voltage-gated sodium channels (VGSC). Here we describe the use of small prokaryotic sodium channels (BacNav) to create de novo excitable human tissues and augment impaired action potential conduction in vitro. Lentiviral co-expression of specific BacNav orthologues, an inward-rectifying potassium channel, and connexin-43 in primary human fibroblasts from the heart, skin or brain yields actively conducting cells with customizable electrophysiological phenotypes. Engineered fibroblasts ('E-Fibs') retain stable functional properties following extensive subculture or differentiation into myofibroblasts and rescue conduction slowing in an in vitro model of cardiac interstitial fibrosis. Co-expression of engineered BacNav with endogenous mammalian VGSCs enhances action potential conduction and prevents conduction failure during depolarization by elevated extracellular K+, decoupling or ischaemia. These studies establish the utility of engineered BacNav channels for induction, control and recovery of mammalian tissue excitability.
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Affiliation(s)
- Hung X Nguyen
- Department of Biomedical Engineering, Duke University, 101 Science Drive, Room 1427, Fitzpatrick CIEMAS, Durham, North Carolina 27708, USA
| | - Robert D Kirkton
- Department of Biomedical Engineering, Duke University, 101 Science Drive, Room 1427, Fitzpatrick CIEMAS, Durham, North Carolina 27708, USA
| | - Nenad Bursac
- Department of Biomedical Engineering, Duke University, 101 Science Drive, Room 1427, Fitzpatrick CIEMAS, Durham, North Carolina 27708, USA
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45
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Ahern CA, Payandeh J, Bosmans F, Chanda B. The hitchhiker's guide to the voltage-gated sodium channel galaxy. ACTA ACUST UNITED AC 2016; 147:1-24. [PMID: 26712848 PMCID: PMC4692491 DOI: 10.1085/jgp.201511492] [Citation(s) in RCA: 234] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Eukaryotic voltage-gated sodium (Nav) channels contribute to the rising phase of action potentials and served as an early muse for biophysicists laying the foundation for our current understanding of electrical signaling. Given their central role in electrical excitability, it is not surprising that (a) inherited mutations in genes encoding for Nav channels and their accessory subunits have been linked to excitability disorders in brain, muscle, and heart; and (b) Nav channels are targeted by various drugs and naturally occurring toxins. Although the overall architecture and behavior of these channels are likely to be similar to the more well-studied voltage-gated potassium channels, eukaryotic Nav channels lack structural and functional symmetry, a notable difference that has implications for gating and selectivity. Activation of voltage-sensing modules of the first three domains in Nav channels is sufficient to open the channel pore, whereas movement of the domain IV voltage sensor is correlated with inactivation. Also, structure–function studies of eukaryotic Nav channels show that a set of amino acids in the selectivity filter, referred to as DEKA locus, is essential for Na+ selectivity. Structures of prokaryotic Nav channels have also shed new light on mechanisms of drug block. These structures exhibit lateral fenestrations that are large enough to allow drugs or lipophilic molecules to gain access into the inner vestibule, suggesting that this might be the passage for drug entry into a closed channel. In this Review, we will synthesize our current understanding of Nav channel gating mechanisms, ion selectivity and permeation, and modulation by therapeutics and toxins in light of the new structures of the prokaryotic Nav channels that, for the time being, serve as structural models of their eukaryotic counterparts.
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Affiliation(s)
- Christopher A Ahern
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA 52242
| | - Jian Payandeh
- Department of Structural Biology, Genentech, Inc., South San Francisco, CA 94080
| | - Frank Bosmans
- Department of Physiology and Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, School of Medicine, Baltimore, MD 21205 Department of Physiology and Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, School of Medicine, Baltimore, MD 21205
| | - Baron Chanda
- Department of Neuroscience and Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705 Department of Neuroscience and Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705
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46
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Vien TN, DeCaen PG. Biophysical Adaptations of Prokaryotic Voltage-Gated Sodium Channels. CURRENT TOPICS IN MEMBRANES 2016; 78:39-64. [PMID: 27586280 DOI: 10.1016/bs.ctm.2015.12.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
This chapter describes the adaptive features found in voltage-gated sodium channels (NaVs) of prokaryotes and eukaryotes. These two families are distinct, having diverged early in evolutionary history but maintain a surprising degree of convergence in function. While prokaryotic NaVs are required for growth and motility, eukaryotic NaVs selectively conduct fast electrical currents for short- and long-range signaling across cell membranes in mammalian organs. Current interest in prokaryotic NaVs is stoked by their resolved high-resolution structures and functional features which are reminiscent of eukaryotic NaVs. In this chapter, comparisons between eukaryotic and prokaryotic NaVs are made to highlight the shared and unique aspects of ion selectivity, voltage sensitivity, and pharmacology. Examples of prokaryotic and eukaryotic NaV convergent evolution will be discussed within the context of their structural features.
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Affiliation(s)
- T N Vien
- Tufts University, Boston, MA, United States
| | - P G DeCaen
- Children's Hospital Boston, Boston, MA, United States; Harvard Medical School, Boston, MA, United States; Northwestern University, Chicago, IL, United States
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47
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Boiteux C, Allen TW. Understanding Sodium Channel Function and Modulation Using Atomistic Simulations of Bacterial Channel Structures. CURRENT TOPICS IN MEMBRANES 2016; 78:145-82. [PMID: 27586284 DOI: 10.1016/bs.ctm.2016.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Sodium channels are chief proteins involved in electrical signaling in the nervous system, enabling critical functions like heartbeat and brain activity. New high-resolution X-ray structures for bacterial sodium channels have created an opportunity to see how these proteins operate at the molecular level. An important challenge to overcome is establishing relationships between the structures and functions of mammalian and bacterial channels. Bacterial sodium channels are known to exhibit the main structural features of their mammalian counterparts, as well as several key functional characteristics, including selective ion conduction, voltage-dependent gating, pore-based inactivation and modulation by local anesthetic, antiarrhythmic and antiepileptic drugs. Simulations have begun to shed light on each of these features in the past few years. Despite deviations in selectivity signatures for bacterial and mammalian channels, simulations have uncovered the nature of the multiion conduction mechanism associated with Na(+) binding to a high-field strength site established by charged glutamate side chains. Simulations demonstrated a surprising level of flexibility of the protein, showing that these side chains are active participants in the permeation process. They have also uncovered changes in protein structure, leading to asymmetrical collapses of the activation gate that have been proposed to correspond to inactivated structures. These observations offer the potential to examine the mechanisms of state-dependent drug activity, focusing on pore-blocking and pore-based slow inactivation in bacterial channels, without the complexities of inactivation on multiple timescales seen in eukaryotic channels. Simulations have provided molecular views of the interactions of drugs, consistent with sites predicted in mammalian channels, as well as a wealth of other sites as potential new drug targets. In this chapter, we survey the new insights into sodium channel function that have emerged from studies of simpler bacterial channels, which provide an excellent learning platform, and promising avenues for mechanistic discovery and pharmacological development.
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Affiliation(s)
- C Boiteux
- RMIT University, Melbourne, VIC, Australia
| | - T W Allen
- RMIT University, Melbourne, VIC, Australia; University of California Davis, Davis, CA, United States
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48
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Arrigoni C, Rohaim A, Shaya D, Findeisen F, Stein RA, Nurva SR, Mishra S, Mchaourab HS, Minor DL. Unfolding of a Temperature-Sensitive Domain Controls Voltage-Gated Channel Activation. Cell 2016; 164:922-36. [PMID: 26919429 DOI: 10.1016/j.cell.2016.02.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 12/22/2015] [Accepted: 01/28/2016] [Indexed: 02/07/2023]
Abstract
Voltage-gated ion channels (VGICs) are outfitted with diverse cytoplasmic domains that impact function. To examine how such elements may affect VGIC behavior, we addressed how the bacterial voltage-gated sodium channel (BacNa(V)) C-terminal cytoplasmic domain (CTD) affects function. Our studies show that the BacNa(V) CTD exerts a profound influence on gating through a temperature-dependent unfolding transition in a discrete cytoplasmic domain, the neck domain, proximal to the pore. Structural and functional studies establish that the BacNa(V) CTD comprises a bi-partite four-helix bundle that bears an unusual hydrophilic core whose integrity is central to the unfolding mechanism and that couples directly to the channel activation gate. Together, our findings define a general principle for how the widespread four-helix bundle cytoplasmic domain architecture can control VGIC responses, uncover a mechanism underlying the diverse BacNa(V) voltage dependencies, and demonstrate that a discrete domain can encode the temperature-dependent response of a channel.
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Affiliation(s)
- Cristina Arrigoni
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ahmed Rohaim
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Biophysics, Faculty of Science, Cairo University, Giza, Egypt
| | - David Shaya
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Felix Findeisen
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Richard A Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Shailika Reddy Nurva
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Smriti Mishra
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Daniel L Minor
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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49
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Liebeskind BJ. What makes a sodium channel? J Gen Physiol 2016; 148:89-90. [PMID: 27432997 PMCID: PMC4969801 DOI: 10.1085/jgp.201611652] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 06/24/2016] [Indexed: 12/03/2022] Open
Affiliation(s)
- Benjamin J Liebeskind
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712
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50
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Shimomura T, Irie K, Fujiyoshi Y. Molecular determinants of prokaryotic voltage-gated sodium channels for recognition of local anesthetics. FEBS J 2016; 283:2881-95. [DOI: 10.1111/febs.13776] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Revised: 05/22/2016] [Accepted: 06/06/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Takushi Shimomura
- Cellular and Structural Physiology Institute (CeSPI); Nagoya University; Japan
| | - Katsumasa Irie
- Cellular and Structural Physiology Institute (CeSPI); Nagoya University; Japan
- Graduate School of Pharmaceutical Science; Nagoya University; Japan
| | - Yoshinori Fujiyoshi
- Cellular and Structural Physiology Institute (CeSPI); Nagoya University; Japan
- Graduate School of Pharmaceutical Science; Nagoya University; Japan
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