1
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Heigl T, Netzer MA, Zanetti L, Ganglberger M, Fernández-Quintero ML, Koschak A. Characterization of two pathological gating-charge substitutions in Cav1.4 L-type calcium channels. Channels (Austin) 2023; 17:2192360. [PMID: 36943941 PMCID: PMC10038055 DOI: 10.1080/19336950.2023.2192360] [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: 11/07/2022] [Accepted: 03/14/2023] [Indexed: 03/23/2023] Open
Abstract
Cav1.4 L-type calcium channels are predominantly expressed at the photoreceptor terminals and in bipolar cells, mediating neurotransmitter release. Mutations in its gene, CACNA1F, can cause congenital stationary night-blindness type 2 (CSNB2). Due to phenotypic variability in CSNB2, characterization of pathological variants is necessary to better determine pathological mechanism at the site of action. A set of known mutations affects conserved gating charges in the S4 voltage sensor, two of which have been found in male CSNB2 patients. Here, we describe two disease-causing Cav1.4 mutations with gating charge neutralization, exchanging an arginine 964 with glycine (RG) or arginine 1288 with leucine (RL). In both, charge neutralization was associated with a reduction channel expression also reflected in smaller ON gating currents. In RL channels, the strong decrease in whole-cell current densities might additionally be explained by a reduction of single-channel currents. We further identified alterations in their biophysical properties, such as a hyperpolarizing shift of the activation threshold and an increase in slope factor of activation and inactivation. Molecular dynamic simulations in RL substituted channels indicated water wires in both, resting and active, channel states, suggesting the development of omega (ω)currents as a new pathological mechanism in CSNB2. This sum of the respective channel property alterations might add to the differential symptoms in patients beside other factors, such as genomic and environmental deviations.
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Affiliation(s)
- Thomas Heigl
- University of Innsbruck, Institute of Pharmacy, Pharmacology and Toxicology, Innsbruck, Austria
| | - Michael A. Netzer
- University of Innsbruck, Institute of Pharmacy, Pharmacology and Toxicology, Innsbruck, Austria
| | - Lucia Zanetti
- University of Innsbruck, Institute of Pharmacy, Pharmacology and Toxicology, Innsbruck, Austria
| | - Matthias Ganglberger
- University of Innsbruck, Institute of Pharmacy, Pharmacology and Toxicology, Innsbruck, Austria
| | - Monica L. Fernández-Quintero
- Institute of General, Inorganic and Theoretical Chemistry, Center for Chemistry and Biomedicine, University of Innsbruck, Innsbruck, Austria
- Division of Pharmacology and Toxicology, Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Alexandra Koschak
- University of Innsbruck, Institute of Pharmacy, Pharmacology and Toxicology, Innsbruck, Austria
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2
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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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3
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Priest MF, Lee EE, Bezanilla F. Tracking the movement of discrete gating charges in a voltage-gated potassium channel. eLife 2021; 10:58148. [PMID: 34779404 PMCID: PMC8635975 DOI: 10.7554/elife.58148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 11/08/2021] [Indexed: 01/18/2023] Open
Abstract
Positively charged amino acids respond to membrane potential changes to drive voltage sensor movement in voltage-gated ion channels, but determining the displacements of voltage sensor gating charges has proven difficult. We optically tracked the movement of the two most extracellular charged residues (R1 and R2) in the Shaker potassium channel voltage sensor using a fluorescent positively charged bimane derivative (qBBr) that is strongly quenched by tryptophan. By individually mutating residues to tryptophan within the putative pathway of gating charges, we observed that the charge motion during activation is a rotation and a tilted translation that differs between R1 and R2. Tryptophan-induced quenching of qBBr also indicates that a crucial residue of the hydrophobic plug is linked to the Cole-Moore shift through its interaction with R1. Finally, we show that this approach extends to additional voltage-sensing membrane proteins using the Ciona intestinalis voltage-sensitive phosphatase (CiVSP).
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Affiliation(s)
- Michael F Priest
- Committee on Neurobiology and Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States
| | - Elizabeth El Lee
- Committee on Neurobiology and Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States
| | - Francisco Bezanilla
- Committee on Neurobiology and Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States.,Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, United States
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4
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Zhu Q, Du Y, Nomura Y, Gao R, Cang Z, Wei GW, Gordon D, Gurevitz M, Groome J, Dong K. Charge substitutions at the voltage-sensing module of domain III enhance actions of site-3 and site-4 toxins on an insect sodium channel. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2021; 137:103625. [PMID: 34358664 PMCID: PMC9376739 DOI: 10.1016/j.ibmb.2021.103625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/29/2021] [Accepted: 07/29/2021] [Indexed: 06/13/2023]
Abstract
Scorpion α-toxins bind at the pharmacologically-defined site-3 on the sodium channel and inhibit channel inactivation by preventing the outward movement of the voltage sensor in domain IV (IVS4), whereas scorpion β-toxins bind at site-4 on the sodium channel and enhance channel activation by trapping the voltage sensor of domain II (IIS4) in its outward position. However, limited information is available on the role of the voltage-sensing modules (VSM, comprising S1-S4) of domains I and III in toxin actions. We have previously shown that charge reversing substitutions of the innermost positively-charged residues in IIIS4 (R4E, R5E) increase the activity of an insect-selective site-4 scorpion toxin, Lqh-dprIT3-c, on BgNav1-1a, a cockroach sodium channel. Here we show that substitutions R4E and R5E in IIIS4 also increase the activity of two site-3 toxins, LqhαIT from Leiurusquinquestriatus hebraeus and insect-selective Av3 from Anemonia viridis. Furthermore, charge reversal of either of two conserved negatively-charged residues, D1K and E2K, in IIIS2 also increase the action of the site-3 and site-4 toxins. Homology modeling suggests that S2-D1 and S2-E2 interact with S4-R4 and S4-R5 in the VSM of domain III (III-VSM), respectively, in the activated state of the channel. However, charge swapping between S2-D1 and S4-R4 had no compensatory effects on gating or toxin actions, suggesting that charged residue interactions are complex. Collectively, our results highlight the involvement of III-VSM in the actions of both site 3 and site 4 toxins, suggesting that charge reversing substitutions in III-VSM allosterically facilitate IIS4 or IVS4 voltage sensor trapping by these toxins.
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Affiliation(s)
- Qing Zhu
- Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Ministry of Agriculture, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China; Department of Entomology, Michigan State University, East Lansing, MI, USA
| | - Yuzhe Du
- Department of Entomology, Michigan State University, East Lansing, MI, USA
| | - Yoshiko Nomura
- Department of Entomology, Michigan State University, East Lansing, MI, USA
| | - Rong Gao
- Department of Hygienic Analysis and Detection, School of Public Health, Nanjing Medical University, 818 Tianyuan East Road, Nanjing, Jiangsu, China
| | - Zixuan Cang
- Department of Mathematics, Michigan State University, East Lansing, MI, USA
| | - Guo-Wei Wei
- Department of Mathematics, Michigan State University, East Lansing, MI, USA
| | - Dalia Gordon
- Department of Plant Molecular Biology & Ecology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv, Israel
| | - Michael Gurevitz
- Department of Plant Molecular Biology & Ecology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv, Israel.
| | - James Groome
- Department of Biological Sciences, Idaho State University, Pocatello, ID, USA
| | - Ke Dong
- Department of Entomology, Michigan State University, East Lansing, MI, USA; Department of Biology, Duke University, Durham, NC, USA.
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5
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Boonamnaj P, Pandey RB, Sompornpisut P. Interaction fingerprint of transmembrane segments in voltage sensor domains. Biophys Chem 2021; 277:106649. [PMID: 34147849 DOI: 10.1016/j.bpc.2021.106649] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 06/06/2021] [Accepted: 06/09/2021] [Indexed: 11/30/2022]
Abstract
Voltage sensor domain (VSD) in channel and non-channel membrane proteins shares a common function in the detection of changes in the transmembrane electric potential. The VSD is made of four helical transmembrane segments (S1-S4) that form a structurally conserved scaffold through inter-transmembrane residue-residue interactions. Details about these interactions are yet to be fully understood in the context of the unique structural and physical characteristics of the voltage sensor unit. In this study, molecular dynamics simulations were carried out to investigate transmembrane helix-helix interactions via residue-based nonbonding energies using the activated and resting state conformations of VSD from Hv1, CiVSP, KvAP and NavAb. Inter-transmembrane interaction energies within the VSD were determined. Analysis of electrostatic and van der Waals components revealed the strengths and weaknesses of the interactions between each pair of transmembrane segments. In all cases the S4 helix had the highest electrostatic contribution to favor the key role as the voltage sensitive segment. Electrostatic interactions for the S1-S2 pair as well as the S1-S3 pair were relatively weak. Van der Waal interaction energies between adjacent segments were on average greater than that between diagonally opposite segments. Salt bridge interactions between S4-arginines and the negatively charged residues in other segments appear to contribute more to stabilizing the energy than the van der Waals interactions between nonpolar residues. The overall behavior of residue-residue contacts is similar among the transmembrane domains, reflecting the common inter- transmembrane interaction pattern in the VSD. In addition, analysis of the residue positions suggested that subtle differences in the orientation of the salt-bridges can be attributed to the difference in the inter-transmembrane interaction strengths inside the VSDs.
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Affiliation(s)
- Panisak Boonamnaj
- The Center of Excellence in Computational Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - R B Pandey
- School of Mathematics and Natural Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Pornthep Sompornpisut
- The Center of Excellence in Computational Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
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6
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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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7
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Groome JR, Bayless-Edwards L. Roles for Countercharge in the Voltage Sensor Domain of Ion Channels. Front Pharmacol 2020; 11:160. [PMID: 32180723 PMCID: PMC7059764 DOI: 10.3389/fphar.2020.00160] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 02/07/2020] [Indexed: 12/19/2022] Open
Abstract
Voltage-gated ion channels share a common structure typified by peripheral, voltage sensor domains. Their S4 segments respond to alteration in membrane potential with translocation coupled to ion permeation through a central pore domain. The mechanisms of gating in these channels have been intensely studied using pioneering methods such as measurement of charge displacement across a membrane, sequencing of genes coding for voltage-gated ion channels, and the development of all-atom molecular dynamics simulations using structural information from prokaryotic and eukaryotic channel proteins. One aspect of this work has been the description of the role of conserved negative countercharges in S1, S2, and S3 transmembrane segments to promote sequential salt-bridge formation with positively charged residues in S4 segments. These interactions facilitate S4 translocation through the lipid bilayer. In this review, we describe functional and computational work investigating the role of these countercharges in S4 translocation, voltage sensor domain hydration, and in diseases resulting from countercharge mutations.
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Affiliation(s)
- James R. Groome
- Department of Biological Sciences, Idaho State University, Pocatello, ID, United States
| | - Landon Bayless-Edwards
- Department of Biological Sciences, Idaho State University, Pocatello, ID, United States
- Oregon Health and Sciences University School of Medicine, Portland, OR, United States
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8
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Boonamnaj P, Sompornpisut P. Effect of Ionization State on Voltage-Sensor Structure in Resting State of the Hv1 Channel. J Phys Chem B 2019; 123:2864-2873. [DOI: 10.1021/acs.jpcb.9b00634] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Panisak Boonamnaj
- Center of Excellence in Computational Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pornthep Sompornpisut
- Center of Excellence in Computational Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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9
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Basak S, Chatterjee S, Chakrapani S. Site Directed Spin Labeling and EPR Spectroscopic Studies of Pentameric Ligand-Gated Ion Channels. J Vis Exp 2016. [PMID: 27403967 DOI: 10.3791/54127] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Ion channel gating is a stimulus-driven orchestration of protein motions that leads to transitions between closed, open, and desensitized states. Fundamental to these transitions is the intrinsic flexibility of the protein, which is critically modulated by membrane lipid-composition. To better understand the structural basis of channel function, it is necessary to study protein dynamics in a physiological membrane environment. Electron Paramagnetic Resonance (EPR) spectroscopy is an important tool to characterize conformational transitions between functional states. In comparison to NMR and X-ray crystallography, the information obtained from EPR is intrinsically of lower resolution. However, unlike in other techniques, in EPR there is no upper-limit to the molecular weight of the protein, the sample requirements are significantly lower, and more importantly the protein is not constrained by the crystal lattice forces. Therefore, EPR is uniquely suited for studying large protein complexes and proteins in reconstituted systems. In this article, we will discuss general protocols for site-directed spin labeling and membrane reconstitution using a prokaryotic proton-gated pentameric Ligand-Gated Ion Channel (pLGIC) from Gloeobacter violaceus (GLIC) as an example. A combination of steady-state Continuous Wave (CW) and Pulsed (Double Electron Electron Resonance-DEER) EPR approaches will be described that will enable a complete quantitative characterization of channel dynamics.
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Affiliation(s)
- Sandip Basak
- Department of Physiology and Biophysics, Case Western Reserve University
| | - Soumili Chatterjee
- Department of Physiology and Biophysics, Case Western Reserve University
| | - Sudha Chakrapani
- Department of Physiology and Biophysics, Case Western Reserve University; School of Medicine, Case Western Reserve University;
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10
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Zhu W, Varga Z, Silva JR. Molecular motions that shape the cardiac action potential: Insights from voltage clamp fluorometry. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 120:3-17. [PMID: 26724572 DOI: 10.1016/j.pbiomolbio.2015.12.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 11/11/2015] [Accepted: 12/16/2015] [Indexed: 01/04/2023]
Abstract
Very recently, voltage-clamp fluorometry (VCF) protocols have been developed to observe the membrane proteins responsible for carrying the ventricular ionic currents that form the action potential (AP), including those carried by the cardiac Na(+) channel, NaV1.5, the L-type Ca(2+) channel, CaV1.2, the Na(+)/K(+) ATPase, and the rapid and slow components of the delayed rectifier, KV11.1 and KV7.1. This development is significant, because VCF enables simultaneous observation of ionic current kinetics with conformational changes occurring within specific channel domains. The ability gained from VCF, to connect nanoscale molecular movement to ion channel function has revealed how the voltage-sensing domains (VSDs) control ion flux through channel pores, mechanisms of post-translational regulation and the molecular pathology of inherited mutations. In the future, we expect that this data will be of great use for the creation of multi-scale computational AP models that explicitly represent ion channel conformations, connecting molecular, cell and tissue electrophysiology. Here, we review the VCF protocol, recent results, and discuss potential future developments, including potential use of these experimental findings to create novel computational models.
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Affiliation(s)
- Wandi Zhu
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Zoltan Varga
- MTA-DE-NAP B Ion Channel Structure-Function Research Group, RCMM, University of Debrecen, Debrecen, Hungary
| | - Jonathan R Silva
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
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11
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Li Q, Shen R, Treger JS, Wanderling SS, Milewski W, Siwowska K, Bezanilla F, Perozo E. Resting state of the human proton channel dimer in a lipid bilayer. Proc Natl Acad Sci U S A 2015; 112:E5926-35. [PMID: 26443860 PMCID: PMC4640771 DOI: 10.1073/pnas.1515043112] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The voltage-gated proton channel Hv1 plays a critical role in the fast proton translocation that underlies a wide range of physiological functions, including the phagocytic respiratory burst, sperm motility, apoptosis, and metastatic cancer. Both voltage activation and proton conduction are carried out by a voltage-sensing domain (VSD) with strong similarity to canonical VSDs in voltage-dependent cation channels and enzymes. We set out to determine the structural properties of membrane-reconstituted human proton channel (hHv1) in its resting conformation using electron paramagnetic resonance spectroscopy together with biochemical and computational methods. We evaluated existing structural templates and generated a spectroscopically constrained model of the hHv1 dimer based on the Ci-VSD structure at resting state. Mapped accessibility data revealed deep water penetration through hHv1, suggesting a highly focused electric field, comprising two turns of helix along the fourth transmembrane segment. This region likely contains the H(+) selectivity filter and the conduction pore. Our 3D model offers plausible explanations for existing electrophysiological and biochemical data, offering an explicit mechanism for voltage activation based on a one-click sliding helix conformational rearrangement.
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Affiliation(s)
- Qufei Li
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637
| | - Rong Shen
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637
| | - Jeremy S Treger
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637
| | - Sherry S Wanderling
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637
| | - Wieslawa Milewski
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637
| | - Klaudia Siwowska
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637
| | - Francisco Bezanilla
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637
| | - Eduardo Perozo
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637
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12
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Fischer AW, Alexander NS, Woetzel N, Karakas M, Weiner BE, Meiler J. BCL::MP-fold: Membrane protein structure prediction guided by EPR restraints. Proteins 2015; 83:1947-62. [PMID: 25820805 PMCID: PMC5064833 DOI: 10.1002/prot.24801] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 03/11/2015] [Accepted: 03/20/2015] [Indexed: 11/05/2022]
Abstract
For many membrane proteins, the determination of their topology remains a challenge for methods like X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy. Electron paramagnetic resonance (EPR) spectroscopy has evolved as an alternative technique to study structure and dynamics of membrane proteins. The present study demonstrates the feasibility of membrane protein topology determination using limited EPR distance and accessibility measurements. The BCL::MP-Fold (BioChemical Library membrane protein fold) algorithm assembles secondary structure elements (SSEs) in the membrane using a Monte Carlo Metropolis (MCM) approach. Sampled models are evaluated using knowledge-based potential functions and agreement with the EPR data and a knowledge-based energy function. Twenty-nine membrane proteins of up to 696 residues are used to test the algorithm. The RMSD100 value of the most accurate model is better than 8 Å for 27, better than 6 Å for 22, and better than 4 Å for 15 of the 29 proteins, demonstrating the algorithms' ability to sample the native topology. The average enrichment could be improved from 1.3 to 2.5, showing the improved discrimination power by using EPR data.
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Affiliation(s)
- Axel W Fischer
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, 37232
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, 37232
| | - Nathan S Alexander
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, 37232
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, 37232
| | - Nils Woetzel
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, 37232
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, 37232
| | - Mert Karakas
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, 37232
| | - Brian E Weiner
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, 37232
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, 37232
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, 37232
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, 37232
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13
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Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments. PLoS Comput Biol 2015; 11:e1004368. [PMID: 26505197 PMCID: PMC4624691 DOI: 10.1371/journal.pcbi.1004368] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 06/01/2015] [Indexed: 11/25/2022] Open
Abstract
The knowledge of multiple conformational states is a prerequisite to understand the function of membrane transport proteins. Unfortunately, the determination of detailed atomic structures for all these functionally important conformational states with conventional high-resolution approaches is often difficult and unsuccessful. In some cases, biophysical and biochemical approaches can provide important complementary structural information that can be exploited with the help of advanced computational methods to derive structural models of specific conformational states. In particular, functional and spectroscopic measurements in combination with site-directed mutations constitute one important source of information to obtain these mixed-resolution structural models. A very common problem with this strategy, however, is the difficulty to simultaneously integrate all the information from multiple independent experiments involving different mutations or chemical labels to derive a unique structural model consistent with the data. To resolve this issue, a novel restrained molecular dynamics structural refinement method is developed to simultaneously incorporate multiple experimentally determined constraints (e.g., engineered metal bridges or spin-labels), each treated as an individual molecular fragment with all atomic details. The internal structure of each of the molecular fragments is treated realistically, while there is no interaction between different molecular fragments to avoid unphysical steric clashes. The information from all the molecular fragments is exploited simultaneously to constrain the backbone to refine a three-dimensional model of the conformational state of the protein. The method is illustrated by refining the structure of the voltage-sensing domain (VSD) of the Kv1.2 potassium channel in the resting state and by exploring the distance histograms between spin-labels attached to T4 lysozyme. The resulting VSD structures are in good agreement with the consensus model of the resting state VSD and the spin-spin distance histograms from ESR/DEER experiments on T4 lysozyme are accurately reproduced. Knowledge of multiple conformational states of membrane transport proteins is a prerequisite to understand their function. However, the determination of atomic structures for all these states with conventional high-resolution approaches can be very challenging due to inherent difficulties in high yield purification of functional membrane transport proteins. Various complementary structural information of proteins in their native states can be obtained by a variety of biophysical and biochemical methods with site-directed mutations. Here, a novel restrained molecular dynamics structural refinement method is developed to help derive a structural model that is consistent with experimental data by incorporating all the experimental constraints simultaneously through the use of non-interacting all-atom molecular fragments. The method can be easily and effectively extended to incorporate many kinds of structural constraints from a variety of biophysical and biochemical experiments, and should be very useful in generating and refining models of proteins in specific functional states.
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14
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Gamal El-Din TM, Scheuer T, Catterall WA. Tracking S4 movement by gating pore currents in the bacterial sodium channel NaChBac. ACTA ACUST UNITED AC 2015; 144:147-57. [PMID: 25070432 PMCID: PMC4113903 DOI: 10.1085/jgp.201411210] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Comparison of the kinetics and voltage dependence of gating pore current conducted by S4 gating charge mutants supports the sliding-helix model of voltage sensor function and elucidates the pathogenic mechanisms underlying periodic paralysis syndromes. Voltage-gated sodium channels mediate the initiation and propagation of action potentials in excitable cells. Transmembrane segment S4 of voltage-gated sodium channels resides in a gating pore where it senses the membrane potential and controls channel gating. Substitution of individual S4 arginine gating charges (R1–R3) with smaller amino acids allows ionic currents to flow through the mutant gating pore, and these gating pore currents are pathogenic in some skeletal muscle periodic paralysis syndromes. The voltage dependence of gating pore currents provides information about the transmembrane position of the gating charges as S4 moves in response to membrane potential. Here we studied gating pore current in mutants of the homotetrameric bacterial sodium channel NaChBac in which individual arginine gating charges were replaced by cysteine. Gating pore current was observed for each mutant channel, but with different voltage-dependent properties. Mutating the first (R1C) or second (R2C) arginine to cysteine resulted in gating pore current at hyperpolarized membrane potentials, where the channels are in resting states, but not at depolarized potentials, where the channels are activated. Conversely, the R3C gating pore is closed at hyperpolarized membrane potentials and opens with channel activation. Negative conditioning pulses revealed time-dependent deactivation of the R3C gating pore at the most hyperpolarized potentials. Our results show sequential voltage dependence of activation of gating pore current from R1 to R3 and support stepwise outward movement of the substituted cysteines through the narrow portion of the gating pore that is sealed by the arginine side chains in the wild-type channel. This pattern of voltage dependence of gating pore current is consistent with a sliding movement of the S4 helix through the gating pore. Through comparison with high-resolution models of the voltage sensor of bacterial sodium channels, these results shed light on the structural basis for pathogenic gating pore currents in periodic paralysis syndromes.
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Affiliation(s)
| | - Todd Scheuer
- Department of Pharmacology, University of Washington, Seattle, WA 98195
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15
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Abstract
Ion channels open and close in response to diverse stimuli, and the molecular events underlying these processes are extensively modulated by ligands of both endogenous and exogenous origin. In the past decade, high-resolution structures of several channel types have been solved, providing unprecedented details of the molecular architecture of these membrane proteins. Intrinsic conformational flexibility of ion channels critically governs their functions. However, the dynamics underlying gating mechanisms and modulations are obscured in the information from crystal structures. While nuclear magnetic resonance spectroscopic methods allow direct measurements of protein dynamics, they are limited by the large size of these membrane protein assemblies in detergent micelles or lipid membranes. Electron paramagnetic resonance (EPR) spectroscopy has emerged as a key biophysical tool to characterize structural dynamics of ion channels and to determine stimulus-driven conformational transition between functional states in a physiological environment. This review will provide an overview of the recent advances in the field of voltage- and ligand-gated channels and highlight some of the challenges and controversies surrounding the structural information available. It will discuss general methods used in site-directed spin labeling and EPR spectroscopy and illustrate how findings from these studies have narrowed the gap between high-resolution structures and gating mechanisms in membranes, and have thereby helped reconcile seemingly disparate models of ion channel function.
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16
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Slingsby JG, Vyas S, Maupin CM. A charge-modified general amber force field for phospholipids: improved structural properties in the tensionless ensemble. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.985675] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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17
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Payandeh J, Minor DL. Bacterial voltage-gated sodium channels (BacNa(V)s) from the soil, sea, and salt lakes enlighten molecular mechanisms of electrical signaling and pharmacology in the brain and heart. J Mol Biol 2014; 427:3-30. [PMID: 25158094 DOI: 10.1016/j.jmb.2014.08.010] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 08/11/2014] [Accepted: 08/18/2014] [Indexed: 12/19/2022]
Abstract
Voltage-gated sodium channels (Na(V)s) provide the initial electrical signal that drives action potential generation in many excitable cells of the brain, heart, and nervous system. For more than 60years, functional studies of Na(V)s have occupied a central place in physiological and biophysical investigation of the molecular basis of excitability. Recently, structural studies of members of a large family of bacterial voltage-gated sodium channels (BacNa(V)s) prevalent in soil, marine, and salt lake environments that bear many of the core features of eukaryotic Na(V)s have reframed ideas for voltage-gated channel function, ion selectivity, and pharmacology. Here, we analyze the recent advances, unanswered questions, and potential of BacNa(V)s as templates for drug development efforts.
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Affiliation(s)
- Jian Payandeh
- Department of Structural Biology, Genentech, Inc., South San Francisco, CA 94080, USA.
| | - Daniel L Minor
- Cardiovascular Research Institute, Departments of Biochemistry and Biophysics and Cellular and Molecular Pharmacology, California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 93858-2330, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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18
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Li Q, Wanderling S, Sompornpisut P, Perozo E. Structural basis of lipid-driven conformational transitions in the KvAP voltage-sensing domain. Nat Struct Mol Biol 2014; 21:160-6. [PMID: 24413055 PMCID: PMC3946318 DOI: 10.1038/nsmb.2747] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 11/14/2013] [Indexed: 11/30/2022]
Abstract
Voltage-gated ion channels respond to transmembrane electric fields through reorientations of the positively charged S4 helix within the voltage-sensing domain (VSD). Despite a wealth of structural and functional data, the details of this conformational change remain controversial. Recent electrophysiological evidence showed that equilibrium between the resting ('down') and activated ('up') conformations of the KvAP VSD from Aeropyrum pernix can be biased through reconstitution in lipids with or without phosphate groups. We investigated the structural transition between these functional states, using site-directed spin-labeling and EPR spectroscopic methods. Solvent accessibility and interhelical distance determinations suggest that KvAP gates through S4 movements involving an ∼3-Å upward tilt and simultaneous ∼2-Å axial shift. This motion leads to large accessibly changes in the intracellular water-filled crevice and supports a new model of gating that combines structural rearrangements and electric-field remodeling.
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Affiliation(s)
- Qufei Li
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA
| | - Sherry Wanderling
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA
| | - Pornthep Sompornpisut
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Eduardo Perozo
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA
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19
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Adasme-Carreño F, Muñoz-Gutierrez C, Caballero J, Alzate-Morales JH. Performance of the MM/GBSA scoring using a binding site hydrogen bond network-based frame selection: the protein kinase case. Phys Chem Chem Phys 2014; 16:14047-58. [DOI: 10.1039/c4cp01378f] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Conformational clustering using hydrogen bond network analysis improved the MM/GBSA scoring for some protein-kinase–ligand systems used as case studies.
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Affiliation(s)
- Francisco Adasme-Carreño
- Centro de Bioinformática y Simulación Molecular (CBSM)
- Escuela de Ingeniería en Bioinformática
- Facultad de Ingeniería
- Universidad de Talca
- Talca, Chile
| | - Camila Muñoz-Gutierrez
- Centro de Bioinformática y Simulación Molecular (CBSM)
- Escuela de Ingeniería en Bioinformática
- Facultad de Ingeniería
- Universidad de Talca
- Talca, Chile
| | - Julio Caballero
- Centro de Bioinformática y Simulación Molecular (CBSM)
- Escuela de Ingeniería en Bioinformática
- Facultad de Ingeniería
- Universidad de Talca
- Talca, Chile
| | - Jans H. Alzate-Morales
- Centro de Bioinformática y Simulación Molecular (CBSM)
- Escuela de Ingeniería en Bioinformática
- Facultad de Ingeniería
- Universidad de Talca
- Talca, Chile
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20
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Abstract
The mechanism by which voltage-gated ion channels respond to changes in membrane polarization during action potential signaling in excitable cells has been the subject of research attention since the original description of voltage-dependent sodium and potassium flux in the squid giant axon. The cloning of ion channel genes and the identification of point mutations associated with channelopathy diseases in muscle and brain has facilitated an electrophysiological approach to the study of ion channels. Experimental approaches to the study of voltage gating have incorporated the use of thiosulfonate reagents to test accessibility, fluorescent probes, and toxins to define domain-specific roles of voltage-sensing S4 segments. Crystallography, structural and homology modeling, and molecular dynamics simulations have added computational approaches to study the relationship of channel structure to function. These approaches have tested models of voltage sensor translocation in response to membrane depolarization and incorporate the role of negative countercharges in the S1 to S3 segments to define our present understanding of the mechanism by which the voltage sensor module dictates gating particle permissiveness in excitable cells.
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Affiliation(s)
- James R Groome
- Department of Biological Sciences, Idaho State University, Pocatello, ID, 83209, USA,
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21
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Isacoff EY, Jan LY, Minor DL. Conduits of life's spark: a perspective on ion channel research since the birth of neuron. Neuron 2013; 80:658-74. [PMID: 24183018 DOI: 10.1016/j.neuron.2013.10.040] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Heartbeats, muscle twitches, and lightning-fast thoughts are all manifestations of bioelectricity and rely on the activity of a class of membrane proteins known as ion channels. The basic function of an ion channel can be distilled into, "The hole opens. Ions go through. The hole closes." Studies of the fundamental mechanisms by which this process happens and the consequences of such activity in the setting of excitable cells remains the central focus of much of the field. One might wonder after so many years of detailed poking at such a seemingly simple process, is there anything left to learn?
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Affiliation(s)
- Ehud Y Isacoff
- Helen Wills Neuroscience Institute, University of California, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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22
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Tomašić T, Hartzoulakis B, Zidar N, Chan F, Kirby RW, Madge DJ, Peigneur S, Tytgat J, Kikelj D. Ligand- and Structure-Based Virtual Screening for Clathrodin-Derived Human Voltage-Gated Sodium Channel Modulators. J Chem Inf Model 2013; 53:3223-32. [DOI: 10.1021/ci400505e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Tihomir Tomašić
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Basil Hartzoulakis
- Xention Limited, Iconix Park, London
Road, Pampisford, Cambridge CB22 3EG, United Kingdom
| | - Nace Zidar
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Fiona Chan
- Xention Limited, Iconix Park, London
Road, Pampisford, Cambridge CB22 3EG, United Kingdom
| | - Robert W. Kirby
- Xention Limited, Iconix Park, London
Road, Pampisford, Cambridge CB22 3EG, United Kingdom
| | - David J. Madge
- Xention Limited, Iconix Park, London
Road, Pampisford, Cambridge CB22 3EG, United Kingdom
| | - Steve Peigneur
- University of Leuven (K. U. Leuven), Toxicology and Pharmacology, Campus Gasthuisberg O&N2, Herestraat 49, P.O. Box 922, 3000 Leuven, Belgium
| | - Jan Tytgat
- University of Leuven (K. U. Leuven), Toxicology and Pharmacology, Campus Gasthuisberg O&N2, Herestraat 49, P.O. Box 922, 3000 Leuven, Belgium
| | - Danijel Kikelj
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000 Ljubljana, Slovenia
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23
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Villalba-Galea CA, Frezza L, Sandtner W, Bezanilla F. Sensing charges of the Ciona intestinalis voltage-sensing phosphatase. ACTA ACUST UNITED AC 2013; 142:543-55. [PMID: 24127524 PMCID: PMC3813379 DOI: 10.1085/jgp.201310993] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Voltage control over enzymatic activity in voltage-sensitive phosphatases (VSPs) is conferred by a voltage-sensing domain (VSD) located in the N terminus. These VSDs are constituted by four putative transmembrane segments (S1 to S4) resembling those found in voltage-gated ion channels. The putative fourth segment (S4) of the VSD contains positive residues that likely function as voltage-sensing elements. To study in detail how these residues sense the plasma membrane potential, we have focused on five arginines in the S4 segment of the Ciona intestinalis VSP (Ci-VSP). After implementing a histidine scan, here we show that four arginine-to-histidine mutants, namely R223H to R232H, mediate voltage-dependent proton translocation across the membrane, indicating that these residues transit through the hydrophobic core of Ci-VSP as a function of the membrane potential. These observations indicate that the charges carried by these residues are sensing charges. Furthermore, our results also show that the electrical field in VSPs is focused in a narrow hydrophobic region that separates the extracellular and intracellular space and constitutes the energy barrier for charge crossing.
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Affiliation(s)
- Carlos A Villalba-Galea
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298
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24
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Malhotra K, Sathappa M, Landin JS, Johnson AE, Alder NN. Structural changes in the mitochondrial Tim23 channel are coupled to the proton-motive force. Nat Struct Mol Biol 2013; 20:965-72. [DOI: 10.1038/nsmb.2613] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 05/14/2013] [Indexed: 01/11/2023]
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25
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Groome JR, Winston V. S1-S3 counter charges in the voltage sensor module of a mammalian sodium channel regulate fast inactivation. ACTA ACUST UNITED AC 2013; 141:601-18. [PMID: 23589580 PMCID: PMC3639575 DOI: 10.1085/jgp.201210935] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The movement of positively charged S4 segments through the electric field drives the voltage-dependent gating of ion channels. Studies of prokaryotic sodium channels provide a mechanistic view of activation facilitated by electrostatic interactions of negatively charged residues in S1 and S2 segments, with positive counterparts in the S4 segment. In mammalian sodium channels, S4 segments promote domain-specific functions that include activation and several forms of inactivation. We tested the idea that S1-S3 countercharges regulate eukaryotic sodium channel functions, including fast inactivation. Using structural data provided by bacterial channels, we constructed homology models of the S1-S4 voltage sensor module (VSM) for each domain of the mammalian skeletal muscle sodium channel hNaV1.4. These show that side chains of putative countercharges in hNaV1.4 are oriented toward the positive charge complement of S4. We used mutagenesis to define the roles of conserved residues in the extracellular negative charge cluster (ENC), hydrophobic charge region (HCR), and intracellular negative charge cluster (INC). Activation was inhibited with charge-reversing VSM mutations in domains I-III. Charge reversal of ENC residues in domains III (E1051R, D1069K) and IV (E1373K, N1389K) destabilized fast inactivation by decreasing its probability, slowing entry, and accelerating recovery. Several INC mutations increased inactivation from closed states and slowed recovery. Our results extend the functional characterization of VSM countercharges to fast inactivation, and support the premise that these residues play a critical role in domain-specific gating transitions for a mammalian sodium channel.
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Affiliation(s)
- James R Groome
- Department of Biological Sciences, Idaho State University, Pocatello, ID 83209, USA.
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26
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Energetic role of the paddle motif in voltage gating of Shaker K(+) channels. Nat Struct Mol Biol 2013; 20:574-81. [PMID: 23542156 PMCID: PMC3777420 DOI: 10.1038/nsmb.2535] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 02/08/2013] [Indexed: 11/23/2022]
Abstract
Voltage-gated ion channels underlie rapid electric signaling in excitable cells. Electrophysiological studies have established that the N-terminal half of the fourth transmembrane segment (NTS4) of these channels functions as the primary voltage sensor, whereas crystallographic studies have shown that NTS4 is not located within a proteinaceous pore. Rather, NTS4 and the C-terminal half of S3 (CTS3 or S3b) form a helix-turn-helix motif, termed the voltage-sensor paddle. This unexpected structural finding raises two fundamental questions: does the paddle motif also exist in voltage-gated channels in a biological membrane and, if so, what is its function in voltage gating. Here, we provide evidence that the paddle motif exists in the open state of Drosophila Shaker voltage-gated K+ channels expressed in Xenopus oocytes and that CTS3 acts as an extracellular hydrophobic "stabilizer" for NTS4, biasing the gating chemical equilibrium towards the open state.
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27
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Abstract
The number of membrane protein structures in the Protein Data Bank is becoming significant and growing. Here, the transmembrane domain structures of the helical membrane proteins are evaluated to assess the influences of the membrane mimetic environments. Toward this goal, many of the biophysical properties of membranes are discussed and contrasted with those of the membrane mimetics commonly used for structure determination. Although the mimetic environments can perturb the protein structures to an extent that potentially gives rise to misinterpretation of functional mechanisms, there are also many structures that have a native-like appearance. From this assessment, an initial set of guidelines is proposed for distinguishing native-like from nonnative-like membrane protein structures. With experimental techniques for validation and computational methods for refinement and quality assessment and enhancement, there are good prospects for achieving native-like structures for these very important proteins.
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Affiliation(s)
- Huan-Xiang Zhou
- Institute of Molecular Biophysic, Florida State University, Tallahassee, USA
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28
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Stock L, Souza C, Treptow W. Structural Basis for Activation of Voltage-Gated Cation Channels. Biochemistry 2013; 52:1501-13. [DOI: 10.1021/bi3013017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Letícia Stock
- Laboratório
de Biofísica Teórica
e Computacional, Departamento de Biologia Celular, Universidade de Brasília, DF, Brasília, Brazil
| | - Caio Souza
- Laboratório
de Biofísica Teórica
e Computacional, Departamento de Biologia Celular, Universidade de Brasília, DF, Brasília, Brazil
| | - Werner Treptow
- Laboratório
de Biofísica Teórica
e Computacional, Departamento de Biologia Celular, Universidade de Brasília, DF, Brasília, Brazil
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29
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Robertson JWF, Kasianowicz JJ, Banerjee S. Analytical Approaches for Studying Transporters, Channels and Porins. Chem Rev 2012; 112:6227-49. [DOI: 10.1021/cr300317z] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Joseph W. F. Robertson
- Physical Measurement Laboratory,
National Institute of Standards and Technology, Gaithersburg, Maryland
20899, United States
| | - John J. Kasianowicz
- Physical Measurement Laboratory,
National Institute of Standards and Technology, Gaithersburg, Maryland
20899, United States
| | - Soojay Banerjee
- National
Institute of Neurological
Disorders and Stroke, Bethesda, Maryland 20824, United States
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30
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Exploring conformational states of the bacterial voltage-gated sodium channel NavAb via molecular dynamics simulations. Proc Natl Acad Sci U S A 2012; 109:21336-41. [PMID: 23150565 DOI: 10.1073/pnas.1218087109] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The X-ray structure of the bacterial voltage-gated sodium channel NavAb has been reported in a conformation with a closed conduction pore. Comparison between this structure and the activated-open and resting-closed structures of the voltage-gated Kv1.2 potassium channel suggests that the voltage-sensor domains (VSDs) of the reported structure are not fully activated. Using the aforementioned structures of Kv1.2 as templates, molecular dynamics simulations are used to identify analogous functional conformations of NavAb. Specifically, starting from the NavAb crystal structure, conformations of the membrane-bound channel are sampled along likely pathways for activation of the VSD and opening of the pore domain. Gating charge computations suggest that a structural rearrangement comparable to that occurring between activated-open and resting-closed states is required to explain experimental values of the gating charge, thereby confirming that the reported VSD structure is likely an intermediate along the channel activation pathway. Our observation that the X-ray structure exhibits a low pore domain-opening propensity further supports this notion. The present molecular dynamics study also identifies conformations of NavAb that are seemingly related to the resting-closed and activated-open states. Our findings are consistent with recent structural and functional studies of the orthologous channels NavRh, NaChBac, and NavMs and offer possible structures for the functionally relevant conformations of NavAb.
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31
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Li Q, Jogini V, Wanderling S, Cortes DM, Perozo E. Expression, purification, and reconstitution of the voltage-sensing domain from Ci-VSP. Biochemistry 2012; 51:8132-42. [PMID: 22989304 DOI: 10.1021/bi300980q] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The voltage-sensing domain (VSD) is the common scaffold responsible for the functional behavior of voltage-gated ion channels, voltage sensitive enzymes, and proton channels. Because of the position of the voltage dependence of the available VSD structures, at present, they all represent the activated state of the sensor. Yet in the absence of a consensus resting state structure, the mechanistic details of voltage sensing remain controversial. The voltage dependence of the VSD from Ci-VSP (Ci-VSD) is dramatically right shifted, so that at 0 mV it presumably populates the putative resting state. Appropriate biochemical methods are an essential prerequisite for generating sufficient amounts of Ci-VSD protein for high-resolution structural studies. Here, we present a simple and robust protocol for the expression of eukaryotic Ci-VSD in Escherichia coli at milligram levels. The protein is pure, homogeneous, monodisperse, and well-folded after solubilization in Anzergent 3-14 at the analyzed concentration (~0.3 mg/mL). Ci-VSD can be reconstituted into liposomes of various compositions, and initial site-directed spin labeling and electron paramagnetic resonance (EPR) spectroscopic measurements indicate its first transmembrane segment folds into an α-helix, in agreement with the homologous region of other VSDs. On the basis of our results and enhanced relaxation EPR spectroscopy measurement, Ci-VSD reconstitutes essentially randomly in proteoliposomes, precluding straightforward application of transmembrane voltages in combination with spectroscopic methods. Nevertheless, these results represent an initial step that makes the resting state of a VSD accessible to a variety of biophysical and structural approaches, including X-ray crystallography, spectroscopic methods, and electrophysiology in lipid bilayers.
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Affiliation(s)
- Qufei Li
- Department of Biochemistry and Molecular Biology, Center for Integrative Science, University of Chicago, Chicago, IL 60637, USA
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32
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Blunck R, Batulan Z. Mechanism of electromechanical coupling in voltage-gated potassium channels. Front Pharmacol 2012; 3:166. [PMID: 22988442 PMCID: PMC3439648 DOI: 10.3389/fphar.2012.00166] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 08/24/2012] [Indexed: 01/10/2023] Open
Abstract
Voltage-gated ion channels play a central role in the generation of action potentials in the nervous system. They are selective for one type of ion - sodium, calcium, or potassium. Voltage-gated ion channels are composed of a central pore that allows ions to pass through the membrane and four peripheral voltage sensing domains that respond to changes in the membrane potential. Upon depolarization, voltage sensors in voltage-gated potassium channels (Kv) undergo conformational changes driven by positive charges in the S4 segment and aided by pairwise electrostatic interactions with the surrounding voltage sensor. Structure-function relations of Kv channels have been investigated in detail, and the resulting models on the movement of the voltage sensors now converge to a consensus; the S4 segment undergoes a combined movement of rotation, tilt, and vertical displacement in order to bring 3-4e(+) each through the electric field focused in this region. Nevertheless, the mechanism by which the voltage sensor movement leads to pore opening, the electromechanical coupling, is still not fully understood. Thus, recently, electromechanical coupling in different Kv channels has been investigated with a multitude of techniques including electrophysiology, 3D crystal structures, fluorescence spectroscopy, and molecular dynamics simulations. Evidently, the S4-S5 linker, the covalent link between the voltage sensor and pore, plays a crucial role. The linker transfers the energy from the voltage sensor movement to the pore domain via an interaction with the S6 C-termini, which are pulled open during gating. In addition, other contact regions have been proposed. This review aims to provide (i) an in-depth comparison of the molecular mechanisms of electromechanical coupling in different Kv channels; (ii) insight as to how the voltage sensor and pore domain influence one another; and (iii) theoretical predictions on the movement of the cytosolic face of the Kv channels during gating.
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Affiliation(s)
- Rikard Blunck
- Groupe d’étude des protéines membranairesMontreal, QC, Canada
- Department of Physiology, Université de MontréalMontreal, QC, Canada
- Department of Physics, Université de MontréalMontreal, QC, Canada
| | - Zarah Batulan
- Groupe d’étude des protéines membranairesMontreal, QC, Canada
- Department of Physiology, Université de MontréalMontreal, QC, Canada
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33
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Conformational state of the MscS mechanosensitive channel in solution revealed by pulsed electron-electron double resonance (PELDOR) spectroscopy. Proc Natl Acad Sci U S A 2012; 109:E2675-82. [PMID: 23012406 DOI: 10.1073/pnas.1202286109] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The heptameric mechanosensitive channel of small conductance (MscS) provides a critical function in Escherichia coli where it opens in response to increased bilayer tension. Three approaches have defined different closed and open structures of the channel, resulting in mutually incompatible models of gating. We have attached spin labels to cysteine mutants on key secondary structural elements specifically chosen to discriminate between the competing models. The resulting pulsed electron-electron double resonance (PELDOR) spectra matched predicted distance distributions for the open crystal structure of MscS. The fit for the predictions by structural models of MscS derived by other techniques was not convincing. The assignment of MscS as open in detergent by PELDOR was unexpected but is supported by two crystal structures of spin-labeled MscS. PELDOR is therefore shown to be a powerful experimental tool to interrogate the conformation of transmembrane regions of integral membrane proteins.
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34
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Roy S, Brownell WE, Spector AA. Modeling electrically active viscoelastic membranes. PLoS One 2012; 7:e37667. [PMID: 22701528 PMCID: PMC3365126 DOI: 10.1371/journal.pone.0037667] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Accepted: 04/27/2012] [Indexed: 11/18/2022] Open
Abstract
The membrane protein prestin is native to the cochlear outer hair cell that is crucial to the ear's amplification and frequency selectivity throughout the whole acoustic frequency range. The outer hair cell exhibits interrelated dimensional changes, force generation, and electric charge transfer. Cells transfected with prestin acquire unique active properties similar to those in the native cell that have also been useful in understanding the process. Here we propose a model describing the major electromechanical features of such active membranes. The model derived from thermodynamic principles is in the form of integral relationships between the history of voltage and membrane resultants as independent variables and the charge density and strains as dependent variables. The proposed model is applied to the analysis of an active force produced by the outer hair cell in response to a harmonic electric field. Our analysis reveals the mechanism of the outer hair cell active (isometric) force having an almost constant amplitude and phase up to 80 kHz. We found that the frequency-invariance of the force is a result of interplay between the electrical filtering associated with prestin and power law viscoelasticity of the surrounding membrane. Paradoxically, the membrane viscoelasticity boosts the force balancing the electrical filtering effect. We also consider various modes of electromechanical coupling in membrane with prestin associated with mechanical perturbations in the cell. We consider pressure or strains applied step-wise or at a constant rate and compute the time course of the resulting electric charge. The results obtained here are important for the analysis of electromechanical properties of membranes, cells, and biological materials as well as for a better understanding of the mechanism of hearing and the role of the protein prestin in this mechanism.
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Affiliation(s)
- Sitikantha Roy
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - William E. Brownell
- Bobby R. Alford Department of Otolaryngology, Head & Neck Surgery, Baylor College of Medicine, Houston, Texas, United States of America
| | - Alexander A. Spector
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
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Hinge-bending motions in the pore domain of a bacterial voltage-gated sodium channel. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:2120-5. [PMID: 22579978 DOI: 10.1016/j.bbamem.2012.05.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Revised: 04/11/2012] [Accepted: 05/02/2012] [Indexed: 12/20/2022]
Abstract
Computational methods and experimental data are used to provide structural models for NaChBac, the homo-tetrameric voltage-gated sodium channel from the bacterium Bacillus halodurans, with a closed and partially open pore domain. Molecular dynamic (MD) simulations on membrane-bound homo-tetrameric NaChBac structures, each comprising six helical transmembrane segments (labeled S1 through S6), reveal that the shape of the lumen, which is defined by the bundle of four alpha-helical S6 segments, is modulated by hinge bending motions around the S6 glycine residues. Mutation of these glycine residues into proline and alanine affects, respectively, the structure and conformational flexibility of the S6 bundle. In the closed channel conformation, a cluster of stacked phenylalanine residues from the four S6 helices hinders diffusion of water molecules and Na(+) ions. Activation of the voltage sensor domains causes destabilization of the aforementioned cluster of phenylalanines, leading to a more open structure. The conformational change involving the phenylalanine cluster promotes a kink in S6, suggesting that channel gating likely results from the combined action of hinge-bending motions of the S6 bundle and concerted reorientation of the aromatic phenylalanine side-chains.
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Abstract
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In excitable cells, the main mediators of sodium conductance
across
membranes are voltage-gated sodium channels (NaVs). Eukaryotic
NaVs are essential elements in neuronal signaling and muscular
contraction and in humans have been causally related to a variety
of neurological and cardiovascular channelopathies. They are complex
heavily glycosylated intrinsic membrane proteins present in only trace
quantities that have proven to be challenging objects of study. However,
in recent years, a number of simpler prokaryotic sodium channels have
been identified, with NaChBac from Bacillus halodurans being the most well-characterized to date. The availability of a
bacterial NaV that is amenable to heterologous expression
and functional characterization in both bacterial and mammalian systems
has provided new opportunities for structure–function studies.
This review describes features of NaChBac as an exemplar of this class
of bacterial channels, compares prokaryotic and eukaryotic NaVs with respect to their structural organization, pharmacological
profiling, and functional kinetics, and discusses how voltage-gated
ion channels may have evolved to deal with the complex functional
demands of higher organisms.
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Affiliation(s)
- Kalypso Charalambous
- Department of Crystallography, Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, UK
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37
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Contributions of counter-charge in a potassium channel voltage-sensor domain. Nat Chem Biol 2011; 7:617-23. [PMID: 21785425 PMCID: PMC4933587 DOI: 10.1038/nchembio.622] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 05/11/2011] [Indexed: 12/24/2022]
Abstract
Voltage-sensor domains couple membrane potential to conformational changes in voltage-gated ion channels and phosphatases. Highly co-evolved acidic and aromatic side-chains assist the transfer of cationic side-chains across the transmembrane electric field during voltage-sensing. We investigated the functional contribution of negative electrostatic potentials from these residues to channel gating and voltage-sensing with unnatural amino acid mutagenesis, electrophysiology, voltage-clamp fluorometry and ab initio calculations. The data show that neutralization of two conserved acidic side-chains in transmembrane segments S2 and S3, Glu293 and Asp316 in Shaker potassium channels, have little functional effect on conductance-voltage relationships, although Glu293 appears to catalyze S4 movement. Our results suggest that neither Glu293 nor Asp316 engages in electrostatic state-dependent charge-charge interactions with S4, likely because they occupy, and possibly help create, a water-filled vestibule.
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Mokrab Y, Sansom MSP. Interaction of diverse voltage sensor homologs with lipid bilayers revealed by self-assembly simulations. Biophys J 2011; 100:875-84. [PMID: 21320431 DOI: 10.1016/j.bpj.2010.11.049] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 11/17/2010] [Accepted: 11/18/2010] [Indexed: 12/31/2022] Open
Abstract
Voltage sensors (VS) domains couple the activation of ion channels/enzymes to changes in membrane voltage. We used molecular dynamics simulations to examine interactions with lipids of several VS homologs. VSs in intact channels in the activated state are exposed to phospholipids, leading to a characteristic local distortion of the lipid bilayer which decreases its thickness by ∼10 Å. This effect is mediated by a conserved hydrophilic stretch in the S4-S5 segment linking the VS and the pore domains, and may favor gating charges crossing the membrane. In cationic lipid bilayers lacking phosphate groups, VSs form fewer contacts with lipid headgroups. The S3-S4 paddle motifs show persistent interactions of individual lipid molecules, influenced by the hairpin loop. In conclusion, our results suggest common interactions with phospholipids for various VS homologs, providing insights into the molecular basis of their stabilization in the membrane and how they are altered by lipid modification.
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Affiliation(s)
- Younes Mokrab
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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39
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McCusker EC, D'Avanzo N, Nichols CG, Wallace BA. Simplified bacterial "pore" channel provides insight into the assembly, stability, and structure of sodium channels. J Biol Chem 2011; 286:16386-91. [PMID: 21454659 PMCID: PMC3091244 DOI: 10.1074/jbc.c111.228122] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Eukaryotic sodium channels are important membrane proteins involved in ion
permeation, homeostasis, and electrical signaling. They are long, multidomain
proteins that do not express well in heterologous systems, and hence,
structure/function and biochemical studies on purified sodium channel proteins
have been limited. Bacteria produce smaller, homologous tetrameric single domain
channels specific for the conductance of sodium ions. They consist of N-terminal
voltage sensor and C-terminal pore subdomains. We designed a functional
pore-only channel consisting of the final two transmembrane helices, the
intervening P-region, and the C-terminal extramembranous region of the sodium
channel from the marine bacterium Silicibacter pomeroyi. This
sodium “pore” channel forms a tetrameric, folded structure that is
capable of supporting sodium flux in phospholipid vesicles. The pore-only
channel is more thermally stable than its full-length counterpart, suggesting
that the voltage sensor subdomain may destabilize the full-length channel. The
pore subdomains can assemble, fold, and function independently from the voltage
sensor and exhibit similar ligand-blocking characteristics as the intact
channel. The availability of this simple pore-only construct should enable
high-level expression for the testing of potential new ligands and enhance our
understanding of the structural features that govern sodium selectivity and
permeability.
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Affiliation(s)
- Emily C McCusker
- Department of Crystallography, Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
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40
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Shimomura T, Irie K, Nagura H, Imai T, Fujiyoshi Y. Arrangement and mobility of the voltage sensor domain in prokaryotic voltage-gated sodium channels. J Biol Chem 2010; 286:7409-17. [PMID: 21177850 DOI: 10.1074/jbc.m110.186510] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Prokaryotic voltage-gated sodium channels (Na(V)s) form homotetramers with each subunit contributing six transmembrane α-helices (S1-S6). Helices S5 and S6 form the ion-conducting pore, and helices S1-S4 function as the voltage sensor with helix S4 thought to be the essential element for voltage-dependent activation. Although the crystal structures have provided insight into voltage-gated K channels (K(V)s), revealing a characteristic domain arrangement in which the voltage sensor domain of one subunit is close to the pore domain of an adjacent subunit in the tetramer, the structural and functional information on Na(V)s remains limited. Here, we show that the domain arrangement in NaChBac, a firstly cloned prokaryotic Na(V), is similar to that in K(V)s. Cysteine substitutions of three residues in helix S4, Q107C, T110C, and R113C, effectively induced intersubunit disulfide bond formation with a cysteine introduced in helix S5, M164C, of the adjacent subunit. In addition, substituting two acidic residues with lysine, E43K and D60K, shifted the activation of the channel to more positive membrane potentials and consistently shifted the preferentially formed disulfide bond from T110C/M164C to Q107C/M164C. Because Gln-107 is located closer to the extracellular side of helix S4 than Thr-110, this finding suggests that the functional shift in the voltage dependence of activation is related to a restriction of the position of helix S4 in the lipid bilayer. The domain arrangement and vertical mobility of helix S4 in NaChBac indicate that the structure and the mechanism of voltage-dependent activation in prokaryotic Na(V)s are similar to those in canonical K(V)s.
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Affiliation(s)
- Takushi Shimomura
- Department of Biophysics, Graduate School of Science, Kyoto University, Oiwake, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
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41
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Subbotina J, Yarov-Yarovoy V, Lees-Miller J, Durdagi S, Guo J, Duff HJ, Noskov SY. Structural refinement of the hERG1 pore and voltage-sensing domains with ROSETTA-membrane and molecular dynamics simulations. Proteins 2010; 78:2922-34. [PMID: 20740484 PMCID: PMC2939218 DOI: 10.1002/prot.22815] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The hERG1 gene (Kv11.1) encodes a voltage-gated potassium channel. Mutations in this gene lead to one form of the Long QT Syndrome (LQTS) in humans. Promiscuous binding of drugs to hERG1 is known to alter the structure/function of the channel leading to an acquired form of the LQTS. Expectably, creation and validation of reliable 3D model of the channel have been a key target in molecular cardiology and pharmacology for the last decade. Although many models were built, they all were limited to pore domain. In this work, a full model of the hERG1 channel is developed which includes all transmembrane segments. We tested a template-driven de-novo design with ROSETTA-membrane modeling using side-chain placements optimized by subsequent molecular dynamics (MD) simulations. Although backbone templates for the homology modeled parts of the pore and voltage sensors were based on the available structures of KvAP, Kv1.2 and Kv1.2-Kv2.1 chimera channels, the missing parts are modeled de-novo. The impact of several alignments on the structure of the S4 helix in the voltage-sensing domain was also tested. Herein, final models are evaluated for consistency to the reported structural elements discovered mainly on the basis of mutagenesis and electrophysiology. These structural elements include salt bridges and close contacts in the voltage-sensor domain; and the topology of the extracellular S5-pore linker compared with that established by toxin foot-printing and nuclear magnetic resonance studies. Implications of the refined hERG1 model to binding of blockers and channels activators (potent new ligands for channel activations) are discussed.
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Affiliation(s)
- Julia Subbotina
- Institute for Biocomplexity and Informatics, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | | | - James Lees-Miller
- Libin Cardiovascular Institute of Alberta, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Serdar Durdagi
- Institute for Biocomplexity and Informatics, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Jiqing Guo
- Libin Cardiovascular Institute of Alberta, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Henry J. Duff
- Libin Cardiovascular Institute of Alberta, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Sergei Yu. Noskov
- Institute for Biocomplexity and Informatics, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
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42
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Eisenberg B. Multiple Scales in the Simulation of Ion Channels and Proteins. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2010; 114:20719-20733. [PMID: 21135913 PMCID: PMC2996618 DOI: 10.1021/jp106760t] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Computation of living processes creates great promise for the everyday life of mankind and great challenges for physical scientists. Simulations molecular dynamics have great appeal to biologists as a natural extension of structural biology. Once a biologist sees a structure, she/he wants to see it move. Molecular biology has shown that a small number of atoms, sometimes even one messenger ion, like Ca(2+), can control biological function on the scale of cells, organs, tissues, and organisms. Enormously concentrated ions-at number densities of ~20 M-in protein channels and enzymes are responsible for many of the characteristics of living systems, just as highly concentrated ions near electrodes are responsible for many of the characteristics of electrochemical systems. Here we confront the reality of the scale differences of ions. We show that the scale differences needed to simulate all the atoms of biological cells are 10(7) in linear dimension, 10(21) in three dimensions, 10(9) in resolution, 10(11) in time, and 10(13) in particle number (to deal with concentrations of Ca(2+)). These scales must be dealt with simultaneously if the simulation is to deal with most biological functions. Biological function extends across all of them, all at once in most cases. We suggest a computational approach using explicit multiscale analysis instead of implicit simulation of all scales. The approach is based on an energy variational principle EnVarA introduced by Chun Liu to deal with complex fluids. Variational methods deal automatically with multiple interacting components and scales. When an additional component is added to the system, the resulting Euler Lagrange field equations change form automatically-by algebra alone-without additional unknown parameters. Multifaceted interactions are solutions of the resulting equations. We suggest that ionic solutions should be viewed as complex fluids with simple components. Highly concentrated solutions-dominated by interactions of components-are easily computed by EnVarA. Successful computation of ions concentrated in special places may be a significant step to understanding the defining characteristics of biological and electrochemical systems. Indeed, computing ions near proteins and nucleic acids may prove as important to molecular biology and chemical technology as computing holes and electrons has been to our semiconductor and digital technology.
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Affiliation(s)
- Bob Eisenberg
- Department of Molecular Biophysics and Physiology, Rush University, Chicago IL 60612
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43
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Catterall WA. Ion channel voltage sensors: structure, function, and pathophysiology. Neuron 2010; 67:915-28. [PMID: 20869590 DOI: 10.1016/j.neuron.2010.08.021] [Citation(s) in RCA: 363] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2010] [Indexed: 10/19/2022]
Abstract
Voltage-gated ion channels generate electrical signals in species from bacteria to man. Their voltage-sensing modules are responsible for initiation of action potentials and graded membrane potential changes in response to synaptic input and other physiological stimuli. Extensive structure-function studies, structure determination, and molecular modeling are now converging on a sliding-helix mechanism for electromechanical coupling in which outward movement of gating charges in the S4 transmembrane segments catalyzed by sequential formation of ion pairs pulls the S4-S5 linker, bends the S6 segment, and opens the pore. Impairment of voltage-sensor function by mutations in Na+ channels contributes to several ion channelopathies, and gating pore current conducted by mutant voltage sensors in Na(V)1.4 channels is the primary pathophysiological mechanism in hypokalemic periodic paralysis. The emerging structural model for voltage sensor function opens the way to development of a new generation of ion-channel drugs that act on voltage sensors rather than blocking the pore.
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Affiliation(s)
- William A Catterall
- Department of Pharmacology, University of Washington, Seattle, WA 98195-7280, USA.
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