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Zhang Y, Xue Y, Ma Y, Du X, Lu B, Wang Y, Yan Z. Improved classification and pathogenicity assessment by comprehensive functional studies in a large data set of KCNQ2 variants. Life Sci 2024; 339:122378. [PMID: 38142737 DOI: 10.1016/j.lfs.2023.122378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 12/11/2023] [Accepted: 12/19/2023] [Indexed: 12/26/2023]
Abstract
AIMS The paucity of functional annotations on hundreds of KCNQ2 variants impedes the diagnosis and treatment of KCNQ2-related disorders. The aims of this work were to determine the functional properties of 331 clinical KCNQ2 variants, interpreted the pathogenicity of 331 variants using functional data,and explored the association between homomeric channel functions and phenotypes. MAIN METHODS We collected 145 KCNQ2 variants from 232 epilepsy patients and 186 KCNQ2 missense variants from the ClinVar database. Whole-cell patch-clamp recording was used to classify the function of 331 variants. Subsequently, we proposed 24 criteria for the pathogenicity interpretation of KCNQ2 variants and used them to assess pathogenicity of 331 variants. Finally, we analyzed the clinical phenotypes of patients carrying these variants, and explored the correlations between functional mechanisms and phenotypes. KEY FINDINGS In the homozygous state, 287 were classified as loss-of-function and 14 as gain-of-function. In the more clinically relative heterozygous state, 200 variants exhibited functional impairment, 121 of which showed dominant-negative effects on wild-type KCNQ2 subunits. After introducing functional data as strong-level evidence to interpret pathogenicity, over half of variants (169/331) were reclassified and 254 were classified as pathogenic/likely pathogenic. Moreover, dominant-negative effect and haploinsufficiency were identified as primary mechanisms in DEE/ID and SeLNE, respectively. The degree of impairment of channel function correlated with the phenotype severity. SIGNIFICANCE Our study reveals the possible cause of KCNQ2-related disorders at the molecular level, provides compelling evidence for clinical classification of KCNQ2 variants, and expands the knowledge of correlations between functional mechanisms and phenotypes.
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Affiliation(s)
- Yuwei Zhang
- Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai 200438, China; State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai 200438, China; Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen 518132, China.
| | - Yuqing Xue
- Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai 200438, China; State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai 200438, China; Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen 518132, China.
| | - Yu Ma
- Department of Neurology, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Xiaonan Du
- Department of Neurology, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Boxun Lu
- Neurology Department at Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, School of Life Sciences, Fudan University, Shanghai, China.
| | - Yi Wang
- Department of Neurology, Children's Hospital of Fudan University, Shanghai 201102, China.
| | - Zhiqiang Yan
- Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai 200438, China; State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai 200438, China; Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen 518132, China.
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2
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García-Morales A, Balleza D. Exploring Flexibility and Folding Patterns Throughout Time in Voltage Sensors. J Mol Evol 2023; 91:819-836. [PMID: 37955698 DOI: 10.1007/s00239-023-10140-1] [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: 08/01/2023] [Accepted: 10/27/2023] [Indexed: 11/14/2023]
Abstract
The voltage-sensing domain (VSD) is a module capable of responding to changes in the membrane potential through conformational changes and facilitating electromechanical coupling to open a pore gate, activate proton permeation pathways, or promote enzymatic activity in some membrane-anchored phosphatases. To carry out these functions, this module acts cooperatively through conformational changes. The VSD is formed by four transmembrane segments (S1-S4) but the S4 segment is critical since it carries positively charged residues, mainly Arg or Lys, which require an aqueous environment for its proper function. The discovery of this module in voltage-gated ion channels (VGICs), proton channels (Hv1), and voltage sensor-containing phosphatases (VSPs) has expanded our understanding of the principle of modularity in the voltage-sensing mechanism of these proteins. Here, by sequence comparison and the evaluation of the relationship between sequence composition, intrinsic flexibility, and structural analysis in 14 selected representatives of these three major protein groups, we report five interesting differences in the folding patterns of the VSD both in prokaryotes and eukaryotes. Our main findings indicate that this module is highly conserved throughout the evolutionary scale, however: (1) segments S1 to S3 in eukaryotes are significantly more hydrophobic than those present in prokaryotes; (2) the S4 segment has retained its hydrophilic character; (3) in eukaryotes the extramembranous linkers are significantly larger and more flexible in comparison with those present in prokaryotes; (4) the sensors present in the kHv1 proton channel and the ciVSP phosphatase, both of eukaryotic origin, exhibit relationships of flexibility and folding patterns very close to the typical ones found in prokaryotic voltage sensors; and (5) archaeal channels KvAP and MVP have flexibility profiles which are clearly contrasting in the S3-S4 region, which could explain their divergent activation mechanisms. Finally, to elucidate the obscure origins of this module, we show further evidence for a possible connection between voltage sensors and TolQ proteins.
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Affiliation(s)
- Abigail García-Morales
- Tecnológico Nacional de México, Instituto Tecnológico de Veracruz, Unidad de Investigación y Desarrollo en Alimentos, Calz. Miguel Angel de Quevedo 2779, Col. Formando Hogar, CP. 91897, Veracruz, Ver, Mexico
| | - Daniel Balleza
- Tecnológico Nacional de México, Instituto Tecnológico de Veracruz, Unidad de Investigación y Desarrollo en Alimentos, Calz. Miguel Angel de Quevedo 2779, Col. Formando Hogar, CP. 91897, Veracruz, Ver, Mexico.
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3
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Catacuzzeno L, Conti F, Franciolini F. Fifty years of gating currents and channel gating. J Gen Physiol 2023; 155:e202313380. [PMID: 37410612 PMCID: PMC10324510 DOI: 10.1085/jgp.202313380] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/12/2023] [Accepted: 06/02/2023] [Indexed: 07/08/2023] Open
Abstract
We celebrate this year the 50th anniversary of the first electrophysiological recordings of the gating currents from voltage-dependent ion channels done in 1973. This retrospective tries to illustrate the context knowledge on channel gating and the impact gating-current recording had then, and how it continued to clarify concepts, elaborate new ideas, and steer the scientific debate in these 50 years. The notion of gating particles and gating currents was first put forward by Hodgkin and Huxley in 1952 as a necessary assumption for interpreting the voltage dependence of the Na and K conductances of the action potential. 20 years later, gating currents were actually recorded, and over the following decades have represented the most direct means of tracing the movement of the gating charges and gaining insights into the mechanisms of channel gating. Most work in the early years was focused on the gating currents from the Na and K channels as found in the squid giant axon. With channel cloning and expression on heterologous systems, other channels as well as voltage-dependent enzymes were investigated. Other approaches were also introduced (cysteine mutagenesis and labeling, site-directed fluorometry, cryo-EM crystallography, and molecular dynamics [MD] modeling) to provide an integrated and coherent view of voltage-dependent gating in biological macromolecules. The layout of this retrospective reflects the past 50 years of investigations on gating currents, first addressing studies done on Na and K channels and then on other voltage-gated channels and non-channel structures. The review closes with a brief overview of how the gating-charge/voltage-sensor movements are translated into pore opening and the pathologies associated with mutations targeting the structures involved with the gating currents.
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Affiliation(s)
- Luigi Catacuzzeno
- Department of Chemistry Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Franco Conti
- Department of Physics, University of Genova, Genova, Italy
| | - Fabio Franciolini
- Department of Chemistry Biology and Biotechnology, University of Perugia, Perugia, Italy
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4
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Okamura Y, Yoshioka D. What voltage-sensing phosphatases can reveal about the mechanisms of ion channel regulation by phosphoinositides. Biochem Soc Trans 2023; 51:827-839. [PMID: 37052219 DOI: 10.1042/bst20221065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/20/2023] [Accepted: 03/30/2023] [Indexed: 04/14/2023]
Abstract
Many membrane proteins including ion channels and ion transporters are regulated by membrane phospholipids such as phosphoinositides in cell membranes and organelles. Voltage-sensing phosphatase, VSP, is a voltage-sensitive phosphoinositide phosphatase which dephosphorylates PI(4,5)P2 into PI(4)P. VSP rapidly reduces the level of PI(4,5)P2 upon membrane depolarization, thus serving as a useful tool to quantitatively study phosphoinositide-regulation of ion channels and ion transporters using a cellular electrophysiology system. In this review, we focus on the application of VSPs to Kv7 family potassium channels, which have been important research targets in biophysics, pharmacology and medicine.
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Affiliation(s)
- Yasushi Okamura
- Laboratory of Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Yamada Oka 2-2, Suita, Osaka 565-0871, Japan
| | - Daisuke Yoshioka
- Laboratory of Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Yamada Oka 2-2, Suita, Osaka 565-0871, Japan
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5
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How to study a highly toxic protein to bacteria: A case of voltage sensor domain of mouse sperm-specific sodium/proton exchanger. Protein Expr Purif 2023; 201:106172. [DOI: 10.1016/j.pep.2022.106172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/30/2022] [Accepted: 09/09/2022] [Indexed: 11/21/2022]
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García-Fernández MD, Chatelain FC, Nury H, Moroni A, Moreau CJ. Distinct classes of potassium channels fused to GPCRs as electrical signaling biosensors. CELL REPORTS METHODS 2021; 1:None. [PMID: 34977850 PMCID: PMC8688152 DOI: 10.1016/j.crmeth.2021.100119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 08/05/2021] [Accepted: 10/26/2021] [Indexed: 11/23/2022]
Abstract
Ligand-gated ion channels (LGICs) are natural biosensors generating electrical signals in response to the binding of specific ligands. Creating de novo LGICs for biosensing applications is technically challenging. We have previously designed modified LGICs by linking G protein-coupled receptors (GPCRs) to the Kir6.2 channel. In this article, we extrapolate these design concepts to other channels with different structures and oligomeric states, namely a tetrameric viral Kcv channel and the dimeric mouse TREK-1 channel. After precise engineering of the linker regions, the two ion channels were successfully regulated by a GPCR fused to their N-terminal domain. Two-electrode voltage-clamp recordings showed that Kcv and mTREK-1 fusions were inhibited and activated by GPCR agonists, respectively, and antagonists abolished both effects. Thus, dissimilar ion channels can be allosterically regulated through their N-terminal domains, suggesting that this is a generalizable approach for ion channel engineering.
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Affiliation(s)
| | - Franck C. Chatelain
- Université Côte d’Azur, IPMC CNRS UMR7275, Laboratory of Excellence ICST, 660 route des Lucioles, 06650 Valbonne, France
| | - Hugues Nury
- Université Grenoble Alpes, CNRS, CEA, IBS, 71, av. Martyrs, CS10090, 38044 Grenoble Cedex9, France
| | - Anna Moroni
- University of Milan, Department of Biosciences, Via Celoria 26, 20133 Milano, Italy
| | - Christophe J. Moreau
- Université Grenoble Alpes, CNRS, CEA, IBS, 71, av. Martyrs, CS10090, 38044 Grenoble Cedex9, France
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7
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CNG channel structure, function, and gating: a tale of conformational flexibility. Pflugers Arch 2021; 473:1423-1435. [PMID: 34357442 DOI: 10.1007/s00424-021-02610-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 10/20/2022]
Abstract
Cyclic nucleotide-gated (CNG) channels are key to the signal transduction machinery of certain sensory modalities both in vertebrate and invertebrate organisms. They translate a chemical change in cyclic nucleotide concentration into an electrical signal that can spread through sensory cells. Despite CNG and voltage-gated potassium channels sharing a remarkable amino acid sequence homology and basic architectural plan, their functional properties are dramatically different. While voltage-gated potassium channels are highly selective and require membrane depolarization to open, CNG channels have low ion selectivity and are not very sensitive to voltage. In the last few years, many high-resolution structures of intact CNG channels have been released. This wealth of new structural information has provided enormous progress toward the understanding of the molecular mechanisms and driving forces underpinning CNG channel activation. In this review, we report on the current understanding and controversies surrounding the gating mechanism in CNG channels, as well as the deep intertwining existing between gating, the ion permeation process, and its modulation by membrane voltage. While the existence of this powerful coupling was recognized many decades ago, its direct structural demonstration, and ties to the CNG channel inherent pore flexibility, is a recent achievement.
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8
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Cowgill J, Chanda B. Mapping Electromechanical Coupling Pathways in Voltage-Gated Ion Channels: Challenges and the Way Forward. J Mol Biol 2021; 433:167104. [PMID: 34139217 PMCID: PMC8579740 DOI: 10.1016/j.jmb.2021.167104] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/07/2021] [Accepted: 06/10/2021] [Indexed: 01/06/2023]
Abstract
Inter- and intra-molecular allosteric interactions underpin regulation of activity in a variety of biological macromolecules. In the voltage-gated ion channel superfamily, the conformational state of the voltage-sensing domain regulates the activity of the pore domain via such long-range allosteric interactions. Although the overall structure of these channels is conserved, allosteric interactions between voltage-sensor and pore varies quite dramatically between the members of this superfamily. Despite the progress in identifying key residues and structural interfaces involved in mediating electromechanical coupling, our understanding of the biophysical mechanisms remains limited. Emerging new structures of voltage-gated ion channels in various conformational states will provide a better three-dimensional view of the process but to conclusively establish a mechanism, we will also need to quantitate the energetic contribution of various structural elements to this process. Using rigorous unbiased metrics, we want to compare the efficiency of electromechanical coupling between various sub-families in order to gain a comprehensive understanding. Furthermore, quantitative understanding of the process will enable us to correctly parameterize computational approaches which will ultimately enable us to predict allosteric activation mechanisms from structures. In this review, we will outline the challenges and limitations of various experimental approaches to measure electromechanical coupling and highlight the best practices in the field.
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Affiliation(s)
- John Cowgill
- Department of Anesthesiology, Washington University, St. Louis, MO 63110, United States; Center for Investigations of Membrane Excitability Disorders (CIMED), Washington University, St. Louis, MO 63110, United States
| | - Baron Chanda
- Department of Anesthesiology, Washington University, St. Louis, MO 63110, United States; Center for Investigations of Membrane Excitability Disorders (CIMED), Washington University, St. Louis, MO 63110, United States.
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9
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Tsutsui H, Mizutani N, Okamura Y. Engineering voltage sensing phosphatase (VSP). Methods Enzymol 2021; 654:85-114. [PMID: 34120726 DOI: 10.1016/bs.mie.2021.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Voltage sensing phosphatase (VSP), consists of a voltage sensor domain (VSD) like that found in voltage-gated ion channels and a phosphoinositide (PIP) phosphatase region exhibiting remarkable structural similarity to a tumor suppressor enzyme, PTEN. Membrane depolarization activates the enzyme activity through tight coupling between the VSD and enzyme region. The VSD of VSP has a unique nature; it is a self-contained module that can be transferred to other proteins, conferring voltage sensitivity. Thanks to this nature, numerous versions of gene-encoded voltage indicators (GEVIs) have been developed through combination of a fluorescent protein with the VSD of VSP. In addition, VSP itself can also serve as a tool to alter PIP levels in cells. Cellular levels of PIPs, PI(4,5)P2 in particular, can be acutely and transiently reduced using a simple voltage protocol after heterologous expression of VSP. Recent progress in our understanding of the molecular structure and mechanisms underlying VSP facilitates optimization of its molecular properties for its use as a molecular tool.
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Affiliation(s)
- Hidekazu Tsutsui
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), Nomi, Ishikawa, Japan.
| | - Natsuki Mizutani
- Graduate School of Medicine, Japan Advanced Institute of Science and Technology (JAIST), Osaka University, Suita, Osaka, Japan
| | - Yasushi Okamura
- Graduate School of Medicine, Japan Advanced Institute of Science and Technology (JAIST), Osaka University, Suita, Osaka, Japan.
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10
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Van Etten JL, Agarkova IV, Dunigan DD. Chloroviruses. Viruses 2019; 12:E20. [PMID: 31878033 PMCID: PMC7019647 DOI: 10.3390/v12010020] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/13/2019] [Accepted: 12/15/2019] [Indexed: 12/20/2022] Open
Abstract
Chloroviruses are large dsDNA, plaque-forming viruses that infect certain chlorella-like green algae; the algae are normally mutualistic endosymbionts of protists and metazoans and are often referred to as zoochlorellae. The viruses are ubiquitous in inland aqueous environments throughout the world and occasionally single types reach titers of thousands of plaque-forming units per ml of native water. The viruses are icosahedral in shape with a spike structure located at one of the vertices. They contain an internal membrane that is required for infectivity. The viral genomes are 290 to 370 kb in size, which encode up to 16 tRNAs and 330 to ~415 proteins, including many not previously seen in viruses. Examples include genes encoding DNA restriction and modification enzymes, hyaluronan and chitin biosynthetic enzymes, polyamine biosynthetic enzymes, ion channel and transport proteins, and enzymes involved in the glycan synthesis of the virus major capsid glycoproteins. The proteins encoded by many of these viruses are often the smallest or among the smallest proteins of their class. Consequently, some of the viral proteins are the subject of intensive biochemical and structural investigation.
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Affiliation(s)
- James L. Van Etten
- Department of Plant Pathology, Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583-0900, USA; (I.V.A.); (D.D.D.)
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11
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Romero-Romero S, Martínez-Delgado G, Balleza D. Voltage vs. Ligand II: Structural insights of the intrinsic flexibility in cyclic nucleotide-gated channels. Channels (Austin) 2019; 13:382-399. [PMID: 31552786 PMCID: PMC6768053 DOI: 10.1080/19336950.2019.1666456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 08/30/2019] [Accepted: 09/03/2019] [Indexed: 12/23/2022] Open
Abstract
In the preceding article, we present a flexibility analysis of the voltage-gated ion channel (VGIC) superfamily. In this study, we describe in detail the flexibility profile of the voltage-sensor domain (VSD) and the pore domain (PD) concerning the evolution of 6TM ion channels. In particular, we highlight the role of flexibility in the emergence of CNG channels and describe a significant level of sequence similarity between the archetypical VSD and the TolQ proteins. A highly flexible S4-like segment exhibiting Lys instead Arg for these membrane proteins is reported. Sequence analysis indicates that, in addition to this S4-like segment, TolQ proteins also show similarity with specific motifs in S2 and S3 from typical V-sensors. Notably, S3 flexibility profiles from typical VSDs and S3-like in TolQ proteins are also similar. Interestingly, TolQ from early divergent prokaryotes are comparatively more flexible than those in modern counterparts or true V-sensors. Regarding the PD, we also found that 2TM K+-channels in early prokaryotes are considerably more flexible than the ones in modern microbes, and such flexibility is comparable to the one present in CNG channels. Voltage dependence is mainly exhibited in prokaryotic CNG channels whose VSD is rigid whereas the eukaryotic CNG channels are considerably more flexible and poorly V-dependent. The implication of the flexibility present in CNG channels, their sensitivity to cyclic nucleotides and the cation selectivity are discussed. Finally, we generated a structural model of the putative cyclic nucleotide-modulated ion channel, which we coined here as AqK, from the thermophilic bacteria Aquifex aeolicus, one of the earliest diverging prokaryotes known. Overall, our analysis suggests that V-sensors in CNG-like channels were essentially rigid in early prokaryotes but raises the possibility that this module was probably part of a very flexible stator protein of the bacterial flagellum motor complex.
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Affiliation(s)
- Sergio Romero-Romero
- Facultad de Medicina, Departamento de Bioquímica, Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico. Current address: Department of Biochemistry, University of Bayreuth, Bayreuth, Germany
| | - Gustavo Martínez-Delgado
- Laboratorio de Genómica de Enfermedades Cardiovasculares, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Daniel Balleza
- Departamento de Química ICET, Universidad Autónoma de Guadalajara, Zapopan, Jalisco, Mexico
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12
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Schönrock M, Thiel G, Laube B. Coupling of a viral K +-channel with a glutamate-binding-domain highlights the modular design of ionotropic glutamate-receptors. Commun Biol 2019; 2:75. [PMID: 30820470 PMCID: PMC6385376 DOI: 10.1038/s42003-019-0320-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 01/22/2019] [Indexed: 01/12/2023] Open
Abstract
Ionotropic glutamate receptors (iGluRs) mediate excitatory neuronal signaling in the mammalian CNS. These receptors are critically involved in diverse physiological processes; including learning and memory formation, as well as neuronal damage associated with neurological diseases. Based on partial sequence and structural similarities, these complex cation-permeable iGluRs are thought to descend from simple bacterial proteins emerging from a fusion of a substrate binding protein (SBP) and an inverted potassium (K+)-channel. Here, we fuse the pore module of the viral K+-channel KcvATCV-1 to the isolated glutamate-binding domain of the mammalian iGluR subunit GluA1 which is structural homolog to SBPs. The resulting chimera (GluATCV*) is functional and displays the ligand recognition characteristics of GluA1 and the K+-selectivity of KcvATCV-1. These results are consistent with a conserved activation mechanism between a glutamate-binding domain and the pore-module of a K+-channel and support the expected phylogenetic link between the two protein families. Michael Schönrock et al. created a functional chimeric channel composed of the pore domain of the potassium channel, KcvATCV-1, and the glutamate binding domain of the mammalian ionotropic glutamate receptor, GluA1. This chimera recognized glutamate as a ligand while displaying the potassium selectivity of KcvATCV-1; highlighting the modular design of ionotropic glutamate receptors.
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Affiliation(s)
- Michael Schönrock
- Department of Biology, Neurophysiology and Neurosensory Systems, Technische Universität Darmstadt, 64289, Darmstadt, Germany
| | - Gerhard Thiel
- Department of Biology, Plant Membrane Biophysics, Technische Universität Darmstadt, 64289, Darmstadt, Germany
| | - Bodo Laube
- Department of Biology, Neurophysiology and Neurosensory Systems, Technische Universität Darmstadt, 64289, Darmstadt, Germany.
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Barros F, Pardo LA, Domínguez P, Sierra LM, de la Peña P. New Structures and Gating of Voltage-Dependent Potassium (Kv) Channels and Their Relatives: A Multi-Domain and Dynamic Question. Int J Mol Sci 2019; 20:ijms20020248. [PMID: 30634573 PMCID: PMC6359393 DOI: 10.3390/ijms20020248] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 12/30/2018] [Accepted: 01/07/2019] [Indexed: 12/15/2022] Open
Abstract
Voltage-dependent potassium channels (Kv channels) are crucial regulators of cell excitability that participate in a range of physiological and pathophysiological processes. These channels are molecular machines that display a mechanism (known as gating) for opening and closing a gate located in a pore domain (PD). In Kv channels, this mechanism is triggered and controlled by changes in the magnitude of the transmembrane voltage sensed by a voltage-sensing domain (VSD). In this review, we consider several aspects of the VSD–PD coupling in Kv channels, and in some relatives, that share a common general structure characterized by a single square-shaped ion conduction pore in the center, surrounded by four VSDs located at the periphery. We compile some recent advances in the knowledge of their architecture, based in cryo-electron microscopy (cryo-EM) data for high-resolution determination of their structure, plus some new functional data obtained with channel variants in which the covalent continuity between the VSD and PD modules has been interrupted. These advances and new data bring about some reconsiderations about the use of exclusively a classical electromechanical lever model of VSD–PD coupling by some Kv channels, and open a view of the Kv-type channels as allosteric machines in which gating may be dynamically influenced by some long-range interactional/allosteric mechanisms.
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Affiliation(s)
- Francisco Barros
- Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, Edificio Santiago Gascón, Campus de El Cristo, 33006 Oviedo, Asturias, Spain.
| | - Luis A Pardo
- Oncophysiology Group, Max Planck Institute of Experimental Medicine, Hermann-Rein-Strasse 3, 37075 Göttingen, Germany.
| | - Pedro Domínguez
- Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, Edificio Santiago Gascón, Campus de El Cristo, 33006 Oviedo, Asturias, Spain.
| | - Luisa Maria Sierra
- Departamento de Biología Funcional (Area de Genética), Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33006 Oviedo, Asturias, Spain.
| | - Pilar de la Peña
- Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, Edificio Santiago Gascón, Campus de El Cristo, 33006 Oviedo, Asturias, Spain.
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14
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Okamura Y, Kawanabe A, Kawai T. Voltage-Sensing Phosphatases: Biophysics, Physiology, and Molecular Engineering. Physiol Rev 2019; 98:2097-2131. [PMID: 30067160 DOI: 10.1152/physrev.00056.2017] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Voltage-sensing phosphatase (VSP) contains a voltage sensor domain (VSD) similar to that in voltage-gated ion channels, and a phosphoinositide phosphatase region similar to phosphatase and tensin homolog deleted on chromosome 10 (PTEN). The VSP gene is conserved from unicellular organisms to higher vertebrates. Membrane depolarization induces electrical driven conformational rearrangement in the VSD, which is translated into catalytic enzyme activity. Biophysical and structural characterization has revealed details of the mechanisms underlying the molecular functions of VSP. Coupling between the VSD and the enzyme is tight, such that enzyme activity is tuned in a graded fashion to the membrane voltage. Upon VSP activation, multiple species of phosphoinositides are simultaneously altered, and the profile of enzyme activity depends on the history of the membrane potential. VSPs have been the obvious candidate link between membrane potential and phosphoinositide regulation. However, patterns of voltage change regulating VSP in native cells remain largely unknown. This review addresses the current understanding of the biophysical biochemical properties of VSP and provides new insight into the proposed functions of VSP.
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Affiliation(s)
- Yasushi Okamura
- Department of Physiology, Laboratory of Integrative Physiology, Graduate School of Medicine, Osaka University , Osaka , Japan ; and Graduate School of Frontier Biosciences, Osaka University , Osaka , Japan
| | - Akira Kawanabe
- Department of Physiology, Laboratory of Integrative Physiology, Graduate School of Medicine, Osaka University , Osaka , Japan ; and Graduate School of Frontier Biosciences, Osaka University , Osaka , Japan
| | - Takafumi Kawai
- Department of Physiology, Laboratory of Integrative Physiology, Graduate School of Medicine, Osaka University , Osaka , Japan ; and Graduate School of Frontier Biosciences, Osaka University , Osaka , Japan
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15
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OKAMURA Y, OKOCHI Y. Molecular mechanisms of coupling to voltage sensors in voltage-evoked cellular signals. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2019; 95:111-135. [PMID: 30853698 PMCID: PMC6541726 DOI: 10.2183/pjab.95.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 01/07/2019] [Indexed: 06/09/2023]
Abstract
The voltage sensor domain (VSD) has long been studied as a unique domain intrinsic to voltage-gated ion channels (VGICs). Within VGICs, the VSD is tightly coupled to the pore-gate domain (PGD) in diverse ways suitable for its specific function in each physiological context, including action potential generation, muscle contraction and relaxation, hormone and neurotransmitter secretion, and cardiac pacemaking. However, some VSD-containing proteins lack a PGD. Voltage-sensing phosphatase contains a cytoplasmic phosphoinositide phosphatase with similarity to phosphatase and tensin homolog (PTEN). Hv1, a voltage-gated proton channel, also lacks a PGD. Within Hv1, the VSD operates as a voltage sensor, gate, and pore for both proton sensing and permeation. Hv1 has a C-terminal coiled coil that mediates dimerization for cooperative gating. Recent progress in the structural biology of VGICs and VSD proteins provides insights into the principles of VSD coupling conserved among these proteins as well as the hierarchy of protein organization for voltage-evoked cell signaling.
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Affiliation(s)
- Yasushi OKAMURA
- Department of Physiology, Graduate School of Medicine, Osaka University, Suita, Japan
- Graduate School of Frontier Bioscience, Osaka University, Suita, Japan
| | - Yoshifumi OKOCHI
- Department of Physiology, Graduate School of Medicine, Osaka University, Suita, Japan
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16
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Abstract
Hyperpolarization-activated, cyclic nucleotide-gated (HCN) channels show an inverted voltage response compared with virtually all other voltage-gated channels, opening on hyperpolarization rather than depolarization. Although the structure of the HCN1 channel was recently solved, the structural element(s) responsible for the inverted gating polarity of HCN is not known. Here, we use a hierarchical approach, by first characterizing the functional contribution of each structural element to channel gating, and then identifying the critical interactions between these elements. Our studies reveal that the HCN voltage sensor can gate the same pore open on both depolarization and hyperpolarization, thereby acting as a bipolar switch. Elements in the pore domain shut off the depolarization-activation pathway in wild-type channels. Despite sharing a common architecture with archetypal voltage-gated ion channels (VGICs), hyperpolarization- and cAMP-activated ion (HCN) channels open upon hyperpolarization rather than depolarization. The basic motions of the voltage sensor and pore gates are conserved, implying that these domains are inversely coupled in HCN channels. Using structure-guided protein engineering, we systematically assembled an array of mosaic channels that display the full complement of voltage-activation phenotypes observed in the VGIC superfamily. Our studies reveal that the voltage sensor of the HCN channel has an intrinsic ability to drive pore opening in either direction and that the extra length of the HCN S4 is not the primary determinant for hyperpolarization activation. Tight interactions at the HCN voltage sensor–pore interface drive the channel into an hERG-like inactivated state, thereby obscuring its opening upon depolarization. This structural element in synergy with the HCN cyclic nucleotide-binding domain and specific interactions near the pore gate biases the channel toward hyperpolarization-dependent opening. Our findings reveal an unexpected common principle underpinning voltage gating in the VGIC superfamily and identify the essential determinants of gating polarity.
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17
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Sakata S, Okamura Y. Dynamic structural rearrangements and functional regulation of voltage-sensing phosphatase. J Physiol 2018; 597:29-40. [PMID: 30311949 DOI: 10.1113/jp274113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/02/2018] [Indexed: 11/08/2022] Open
Abstract
The voltage-sensing phosphatase (VSP) consists of a voltage sensor domain (VSD) and a cytoplasmic catalytic region. The latter contains a phosphatase domain and a C2 domain, showing remarkable similarity to the tumour suppressor enzyme PTEN. In VSP, membrane depolarization induces a conformational change in the VSD, which activates the phosphoinositide phosphatase. The final outcome in VSP is enzymatic activity in the cytoplasmic region, unlike in voltage-gated ion channels where conformational change of the transmembrane pore is induced by the VSD. Therefore, it is crucial to detect structural change in the cytoplasmic catalytic region to gain insights into the operating mechanisms of VSP. This review summarizes a recent study in which a method of genetic incorporation of a non-canonical amino acid, Anap, was used to detect dynamic membrane voltage-controlled rearrangements of the structure of the catalytic region of sea squirt VSP (Ci-VSP). Upon membrane depolarization, both the phosphatase domain and the C2 domain move in a similar time frame, suggesting that the two regions are coupled to each other. Measurement of Förster resonance energy transfer (FRET) between Anap introduced into the C2 domain of Ci-VSP and dipicrylamine in the cell membrane suggested no large movement of the enzyme towards the membrane. Fluorescence changes in Anap induced by different membrane potentials indicate the presence of multiple conformations of the active enzyme.
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Affiliation(s)
- Souhei Sakata
- Department of Physiology, Division of Life Sciences, Faculty of Medicine, Osaka Medical College, Takatsuki, Osaka, Japan
| | - Yasushi Okamura
- Laboratory of Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
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Mackie TD, Brodsky JL. Investigating Potassium Channels in Budding Yeast: A Genetic Sandbox. Genetics 2018; 209:637-650. [PMID: 29967058 PMCID: PMC6028241 DOI: 10.1534/genetics.118.301026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 05/15/2018] [Indexed: 12/26/2022] Open
Abstract
Like all species, the model eukaryote Saccharomyces cerevisiae, or Bakers' yeast, concentrates potassium in the cytosol as an electrogenic osmolyte and enzyme cofactor. Yeast are capable of robust growth on a wide variety of potassium concentrations, ranging from 10 µM to 2.5 M, due to the presence of a high-affinity potassium uptake system and a battery of cation exchange transporters. Genetic perturbation of either of these systems retards yeast growth on low or high potassium, respectively. However, these potassium-sensitized yeast are a powerful genetic tool, which has been leveraged for diverse studies. Notably, the potassium-sensitive cells can be transformed with plasmids encoding potassium channels from bacteria, plants, or mammals, and subsequent changes in growth rate have been found to correlate with the activity of the introduced potassium channel. Discoveries arising from the use of this assay over the past three decades have increased our understanding of the structure-function relationships of various potassium channels, the mechanisms underlying the regulation of potassium channel function and trafficking, and the chemical basis of potassium channel modulation. In this article, we provide an overview of the major genetic tools used to study potassium channels in S. cerevisiae, a survey of seminal studies utilizing these tools, and a prospective for the future use of this elegant genetic approach.
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Affiliation(s)
- Timothy D Mackie
- Department of Biological Sciences, University of Pittsburgh, Pennsylvania 15260
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pennsylvania 15260
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19
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Gating interaction maps reveal a noncanonical electromechanical coupling mode in the Shaker K + channel. Nat Struct Mol Biol 2018; 25:320-326. [PMID: 29581567 PMCID: PMC6170002 DOI: 10.1038/s41594-018-0047-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 02/05/2018] [Indexed: 11/08/2022]
Abstract
Membrane potential regulates the activity of voltage-dependent ion channels via specialized voltage-sensing modules but the mechanisms involved in coupling voltage-sensor movement to pore opening remain unclear due to lack of resting state structures and robust methods to identify allosteric pathways. Here, using a newly developed interaction energy analysis, we probe the interfaces of the voltage-sensing and pore modules in the drosophila Shaker K+ channel. Our measurements reveal unexpectedly strong equilibrium gating interactions between contacts at the S4 and S5 helices in addition to those between S6 and S4–S5 linker. Network analysis of MD trajectories shows that the voltage-sensor and pore motions are linked by two distinct pathways- canonical one through the S4–S5 linker and a hitherto unknown pathway akin to rack and pinion coupling involving S4 and S5 helices. Our findings highlight the central role of the S5 helix in electromechanical transduction in the VGIC superfamily.
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de la Peña P, Domínguez P, Barros F. Functional characterization of Kv11.1 (hERG) potassium channels split in the voltage-sensing domain. Pflugers Arch 2018; 470:1069-1085. [PMID: 29572566 PMCID: PMC6013512 DOI: 10.1007/s00424-018-2135-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 02/26/2018] [Accepted: 02/28/2018] [Indexed: 12/20/2022]
Abstract
Voltage-dependent KCNH family potassium channel functionality can be reconstructed using non-covalently linked voltage-sensing domain (VSD) and pore modules (split channels). However, the necessity of a covalent continuity for channel function has not been evaluated at other points within the two functionally independent channel modules. We find here that by cutting Kv11.1 (hERG, KCNH2) channels at the different loops linking the transmembrane spans of the channel core, not only channels split at the S4–S5 linker level, but also those split at the intracellular S2–S3 and the extracellular S3–S4 loops, yield fully functional channel proteins. Our data indicate that albeit less markedly, channels split after residue 482 in the S2–S3 linker resemble the uncoupled gating phenotype of those split at the C-terminal end of the VSD S4 transmembrane segment. Channels split after residues 514 and 518 in the S3–S4 linker show gating characteristics similar to those of the continuous wild-type channel. However, breaking the covalent link at this level strongly accelerates the voltage-dependent accessibility of a membrane impermeable methanethiosulfonate reagent to an engineered cysteine at the N-terminal region of the S4 transmembrane helix. Thus, besides that of the S4–S5 linker, structural integrity of the intracellular S2–S3 linker seems to constitute an important factor for proper transduction of VSD rearrangements to opening and closing the cytoplasmic gate. Furthermore, our data suggest that the short and probably rigid characteristics of the extracellular S3–S4 linker are not an essential component of the Kv11.1 voltage sensing machinery.
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Affiliation(s)
- Pilar de la Peña
- Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, Edificio Santiago Gascón, Campus de El Cristo, 33006, Oviedo, Asturias, Spain.
| | - Pedro Domínguez
- Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, Edificio Santiago Gascón, Campus de El Cristo, 33006, Oviedo, Asturias, Spain
| | - Francisco Barros
- Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, Edificio Santiago Gascón, Campus de El Cristo, 33006, Oviedo, Asturias, Spain.
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Andersson AEV, Kasimova MA, Delemotte L. Exploring the Viral Channel Kcv PBCV-1 Function via Computation. J Membr Biol 2018; 251:419-430. [PMID: 29476260 PMCID: PMC6028866 DOI: 10.1007/s00232-018-0022-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 02/15/2018] [Indexed: 11/30/2022]
Abstract
Viral potassium channels (Kcv) are homologous to the pore module of complex \documentclass[12pt]{minimal}
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\begin{document}$$\hbox {K}^+$$\end{document}K+-selective ion channels of cellular organisms. Due to their relative simplicity, they have attracted interest towards understanding the principles of \documentclass[12pt]{minimal}
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\begin{document}$$\hbox {K}^+$$\end{document}K+ conduction and channel gating. In this work, we construct a homology model of the \documentclass[12pt]{minimal}
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\begin{document}$${\hbox {Kcv}}_{\text{PBCV-1}}$$\end{document}KcvPBCV-1 open state, which we validate by studying the binding of known blockers and by monitoring ion conduction through the channel. Molecular dynamics simulations of this model reveal that the re-orientation of selectivity filter carbonyl groups coincides with the transport of potassium ions, suggesting a possible mechanism for fast gating. In addition, we show that the voltage sensitivity of this mechanism can originate from the relocation of potassium ions inside the selectivity filter. We also explore the interaction of \documentclass[12pt]{minimal}
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\begin{document}$${\hbox {Kcv}}_{\text{PBCV-1}}$$\end{document}KcvPBCV-1 with the surrounding bilayer and observe the binding of lipids in the area between two adjacent subunits. The model is available to the scientific community to further explore the structure/function relationship of Kcv channels.
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Affiliation(s)
- Alma E V Andersson
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Box 1031, SE-171 21, Solna, Sweden
| | - Marina A Kasimova
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Box 1031, SE-171 21, Solna, Sweden
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Box 1031, SE-171 21, Solna, Sweden.
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Cosentino C, Alberio L, Thiel G, Moroni A. Yeast-Based Screening System for the Selection of Functional Light-Driven K + Channels. Methods Mol Biol 2018; 1596:271-285. [PMID: 28293893 DOI: 10.1007/978-1-4939-6940-1_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
Ion channels control the electrical properties of cells by opening and closing (gating) in response to a wide palette of environmental and physiological stimuli. Endowing ion channels with the possibility to be gated by remotely applied stimuli, such as light, provides a tool for in vivo control of cellular functions in behaving animals. We have engineered a synthetic light-gated potassium (K+) channel by connecting an exogenous plant photoreceptor LOV2 domain to the K+ channel pore Kcv. Here, we describe the experimental strategy that we have used to evolve the properties of the channel toward full control of light on pore gating. Our method combines rational and random mutagenesis of the channel followed by a yeast-based screening system for light-activated K+ conductance.
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Affiliation(s)
- Cristian Cosentino
- Department of Biosciences, University of Milan and Biophysics Institute, National Research Council (CNR), Via Celoria 26, 201333, Milan, Italy
| | - Laura Alberio
- Department of Biosciences, University of Milan and Biophysics Institute, National Research Council (CNR), Via Celoria 26, 201333, Milan, Italy
| | - Gerhard Thiel
- Plant Membrane Biophysics, Technical University Darmstadt, Darmstadt, Germany
| | - Anna Moroni
- Department of Biosciences, University of Milan and Biophysics Institute, National Research Council (CNR), Via Celoria 26, 201333, Milan, Italy.
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23
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Myshkin MY, Paramonov AS, Kulbatskii DS, Lyukmanova EN, Kirpichnikov MP, Shenkarev ZO. “Divide and conquer” approach to the structural studies of multidomain ion channels by the example of isolated voltage sensing domains of human Kv2.1 and Nav1.4 channels. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2018. [DOI: 10.1134/s1068162017060103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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24
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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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25
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Sakata S, Matsuda M, Kawanabe A, Okamura Y. Domain-to-domain coupling in voltage-sensing phosphatase. Biophys Physicobiol 2017; 14:85-97. [PMID: 28744425 PMCID: PMC5515349 DOI: 10.2142/biophysico.14.0_85] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 05/10/2017] [Indexed: 01/12/2023] Open
Abstract
Voltage-sensing phosphatase (VSP) consists of a transmembrane voltage sensor and a cytoplasmic enzyme region. The enzyme region contains the phosphatase and C2 domains, is structurally similar to the tumor suppressor phosphatase PTEN, and catalyzes the dephosphorylation of phosphoinositides. The transmembrane voltage sensor is connected to the phosphatase through a short linker region, and phosphatase activity is induced upon membrane depolarization. Although the detailed molecular characteristics of the voltage sensor domain and the enzyme region have been revealed, little is known how these two regions are coupled. In addition, it is important to know whether mechanism for coupling between the voltage sensor domain and downstream effector function is shared among other voltage sensor domain-containing proteins. Recent studies in which specific amino acid sites were genetically labeled using a fluorescent unnatural amino acid have enabled detection of the local structural changes in the cytoplasmic region of Ciona intestinalis VSP that occur with a change in membrane potential. The results of those studies provide novel insight into how the enzyme activity of the cytoplasmic region of VSP is regulated by the voltage sensor domain.
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Affiliation(s)
- Souhei Sakata
- Department of Physiology, Division of Life Sciences, Faculty of Medicine, Osaka Medical College, Takatsuki, Osaka 569-8686, Japan
| | - Makoto Matsuda
- Laboratory of Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Akira Kawanabe
- Laboratory of Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yasushi Okamura
- Laboratory of Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan.,Graduate School of Frontier Bioscience, Osaka University
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26
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Paramonov AS, Lyukmanova EN, Myshkin MY, Shulepko MA, Kulbatskii DS, Petrosian NS, Chugunov AO, Dolgikh DA, Kirpichnikov MP, Arseniev AS, Shenkarev ZO. NMR investigation of the isolated second voltage-sensing domain of human Nav1.4 channel. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:493-506. [PMID: 28065835 DOI: 10.1016/j.bbamem.2017.01.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 12/06/2016] [Accepted: 01/04/2017] [Indexed: 10/20/2022]
Abstract
Voltage-gated Na+ channels are essential for the functioning of cardiovascular, muscular, and nervous systems. The α-subunit of eukaryotic Na+ channel consists of ~2000 amino acid residues and encloses 24 transmembrane (TM) helices, which form five membrane domains: four voltage-sensing (VSD) and one pore domain. The structural complexity significantly impedes recombinant production and structural studies of full-sized Na+ channels. Modular organization of voltage-gated channels gives an idea for studying of the isolated second VSD of human skeletal muscle Nav1.4 channel (VSD-II). Several variants of VSD-II (~150a.a., four TM helices) with different N- and C-termini were produced by cell-free expression. Screening of membrane mimetics revealed low stability of VSD-II samples in media containing phospholipids (bicelles, nanodiscs) associated with the aggregation of electrically neutral domain molecules. The almost complete resonance assignment of 13C,15N-labeled VSD-II was obtained in LPPG micelles. The secondary structure of VSD-II showed similarity with the structures of bacterial Na+ channels. The fragment of S4 TM helix between the first and second conserved Arg residues probably adopts 310-helical conformation. Water accessibility of S3 helix, observed by the Mn2+ titration, pointed to the formation of water-filled crevices in the micelle embedded VSD-II. 15N relaxation data revealed characteristic pattern of μs-ms time scale motions in the VSD-II regions sharing expected interhelical contacts. VSD-II demonstrated enhanced mobility at ps-ns time scale as compared to isolated VSDs of K+ channels. These results validate structural studies of isolated VSDs of Na+ channels and show possible pitfalls in application of this 'divide and conquer' approach.
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Affiliation(s)
- A S Paramonov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, Moscow 117997, Russia; Lomonosov Moscow State University, Moscow 119991, Russia
| | - E N Lyukmanova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, Moscow 117997, Russia; Lomonosov Moscow State University, Moscow 119991, Russia
| | - M Yu Myshkin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, Moscow 117997, Russia; Moscow Institute of Physics and Technology (State University), Institutskiy Pereulok 9, Dolgoprudny, Moscow Region 141700, Russia
| | - M A Shulepko
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, Moscow 117997, Russia; Lomonosov Moscow State University, Moscow 119991, Russia
| | - D S Kulbatskii
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, Moscow 117997, Russia; Lomonosov Moscow State University, Moscow 119991, Russia
| | - N S Petrosian
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, Moscow 117997, Russia; Moscow Institute of Physics and Technology (State University), Institutskiy Pereulok 9, Dolgoprudny, Moscow Region 141700, Russia
| | - A O Chugunov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, Moscow 117997, Russia
| | - D A Dolgikh
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, Moscow 117997, Russia; Lomonosov Moscow State University, Moscow 119991, Russia
| | - M P Kirpichnikov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, Moscow 117997, Russia; Lomonosov Moscow State University, Moscow 119991, Russia
| | - A S Arseniev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, Moscow 117997, Russia; Moscow Institute of Physics and Technology (State University), Institutskiy Pereulok 9, Dolgoprudny, Moscow Region 141700, Russia
| | - Z O Shenkarev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, Moscow 117997, Russia; Moscow Institute of Physics and Technology (State University), Institutskiy Pereulok 9, Dolgoprudny, Moscow Region 141700, Russia.
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27
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Taylor KC, Sanders CR. Regulation of KCNQ/Kv7 family voltage-gated K + channels by lipids. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1859:586-597. [PMID: 27818172 DOI: 10.1016/j.bbamem.2016.10.023] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 10/24/2016] [Accepted: 10/31/2016] [Indexed: 12/19/2022]
Abstract
Many years of studies have established that lipids can impact membrane protein structure and function through bulk membrane effects, by direct but transient annular interactions with the bilayer-exposed surface of protein transmembrane domains, and by specific binding to protein sites. Here, we focus on how phosphatidylinositol 4,5-bisphosphate (PIP2) and polyunsaturated fatty acids (PUFAs) impact ion channel function and how the structural details of the interactions of these lipids with ion channels are beginning to emerge. We focus on the Kv7 (KCNQ) subfamily of voltage-gated K+ channels, which are regulated by both PIP2 and PUFAs and play a variety of important roles in human health and disease. This article is part of a Special Issue entitled: Lipid order/lipid defects and lipid-control of protein activity edited by Dirk Schneider.
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Affiliation(s)
- Keenan C Taylor
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Charles R Sanders
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
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28
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Zhao J, Blunck R. The isolated voltage sensing domain of the Shaker potassium channel forms a voltage-gated cation channel. eLife 2016; 5. [PMID: 27710769 PMCID: PMC5092046 DOI: 10.7554/elife.18130] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 09/30/2016] [Indexed: 01/28/2023] Open
Abstract
Domains in macromolecular complexes are often considered structurally and functionally conserved while energetically coupled to each other. In the modular voltage-gated ion channels the central ion-conducting pore is surrounded by four voltage sensing domains (VSDs). Here, the energetic coupling is mediated by interactions between the S4-S5 linker, covalently linking the domains, and the proximal C-terminus. In order to characterize the intrinsic gating of the voltage sensing domain in the absence of the pore domain, the Shaker Kv channel was truncated after the fourth transmembrane helix S4 (Shaker-iVSD). Shaker-iVSD showed significantly altered gating kinetics and formed a cation-selective ion channel with a strong preference for protons. Ion conduction in Shaker-iVSD developed despite identical primary sequence, indicating an allosteric influence of the pore domain. Shaker-iVSD also displays pronounced 'relaxation'. Closing of the pore correlates with entry into relaxation suggesting that the two processes are energetically related.
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Affiliation(s)
- Juan Zhao
- Department of Physics, Université de Montréal, Montréal, Canada.,Department of Pharmacology and Physiology, Université de Montréal, Montréal, Canada
| | - Rikard Blunck
- Department of Physics, Université de Montréal, Montréal, Canada.,Department of Pharmacology and Physiology, Université de Montréal, Montréal, Canada
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29
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Rosasco MG, Gordon SE, Bajjalieh SM. Characterization of the Functional Domains of a Mammalian Voltage-Sensitive Phosphatase. Biophys J 2016; 109:2480-2491. [PMID: 26682807 DOI: 10.1016/j.bpj.2015.11.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 10/27/2015] [Accepted: 11/03/2015] [Indexed: 12/12/2022] Open
Abstract
Voltage-sensitive phosphatases (VSPs) are proteins that directly couple changes in membrane electrical potential to inositol lipid phosphatase activity. VSPs thus couple two signaling pathways that are critical for cellular functioning. Although a number of nonmammalian VSPs have been characterized biophysically, mammalian VSPs are less well understood at both the physiological and biophysical levels. In this study, we aimed to address this gap in knowledge by determining whether the VSP from mouse, Mm-VSP, is expressed in the brain and contains a functional voltage-sensing domain (VSD) and a phosphatase domain. We report that Mm-VSP is expressed in neurons and is developmentally regulated. To address whether the functions of the VSD and phosphatase domain are retained in Mm-VSP, we took advantage of the modular nature of these domains and expressed each independently as a chimeric protein in a heterologous expression system. We found that the Mm-VSP VSD, fused to a viral potassium channel, was able to drive voltage-dependent gating of the channel pore. The Mm-VSP phosphatase domain, fused to the VSD of a nonmammalian VSP, was also functional: activation resulted in PI(4,5)P2 depletion that was sufficient to inhibit the PI(4,5)P2-regulated KCNQ2/3 channels. While testing the functionality of the VSD and phosphatase domain, we observed slight differences between the activities of Mm-VSP-based chimeras and those of nonmammalian VSPs. Although the properties of VSP chimeras may not completely reflect the properties of native VSPs, the differences we observed in voltage-sensing and phosphatase activity provide a starting point for future experiments to investigate the function of Mm-VSP and other mammalian VSPs. In conclusion, our data reveal that both the VSD and the lipid phosphatase domain of Mm-VSP are functional, indicating that Mm-VSP likely plays an important role in mouse neurophysiology.
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Affiliation(s)
- Mario G Rosasco
- Department of Pharmacology, University of Washington, Seattle, Washington; Department of Physiology and Biophysics, University of Washington, Seattle, Washington
| | - Sharona E Gordon
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington
| | - Sandra M Bajjalieh
- Department of Pharmacology, University of Washington, Seattle, Washington.
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30
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Grafting voltage and pharmacological sensitivity in potassium channels. Cell Res 2016; 26:935-45. [PMID: 27174053 DOI: 10.1038/cr.2016.57] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 03/04/2016] [Accepted: 03/29/2016] [Indexed: 11/08/2022] Open
Abstract
A classical voltage-gated ion channel consists of four voltage-sensing domains (VSDs). However, the roles of each VSD in the channels remain elusive. We developed a GVTDT (Graft VSD To Dimeric TASK3 channels that lack endogenous VSDs) strategy to produce voltage-gated channels with a reduced number of VSDs. TASK3 channels exhibit a high host tolerance to VSDs of various voltage-gated ion channels without interfering with the intrinsic properties of the TASK3 selectivity filter. The constructed channels, exemplified by the channels grafted with one or two VSDs from Kv7.1 channels, exhibit classical voltage sensitivity, including voltage-dependent opening and closing. Furthermore, the grafted Kv7.1 VSD transfers the potentiation activity of benzbromarone, an activator that acts on the VSDs of the donor channels, to the constructed channels. Our study indicates that one VSD is sufficient to voltage-dependently gate the pore and provides new insight into the roles of VSDs.
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31
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Goodchild SJ, Macdonald LC, Fedida D. Sequence of gating charge movement and pore gating in HERG activation and deactivation pathways. Biophys J 2016; 108:1435-1447. [PMID: 25809256 DOI: 10.1016/j.bpj.2015.02.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 02/08/2015] [Accepted: 02/18/2015] [Indexed: 12/26/2022] Open
Abstract
KV11.1 voltage-gated K(+) channels are noted for unusually slow activation, fast inactivation, and slow deactivation kinetics, which tune channel activity to provide vital repolarizing current during later stages of the cardiac action potential. The bulk of charge movement in human ether-a-go-go-related gene (hERG) is slow, as is return of charge upon repolarization, suggesting that the rates of hERG channel opening and, critically, that of deactivation might be determined by slow voltage sensor movement, and also by a mode-shift after activation. To test these ideas, we compared the kinetics and voltage dependence of ionic activation and deactivation with gating charge movement. At 0 mV, gating charge moved ∼threefold faster than ionic current, which suggests the presence of additional slow transitions downstream of charge movement in the physiological activation pathway. A significant voltage sensor mode-shift was apparent by 24 ms at +60 mV in gating currents, and return of charge closely tracked pore closure after pulses of 100 and 300 ms duration. A deletion of the N-terminus PAS domain, mutation R4AR5A or the LQT2-causing mutation R56Q gave faster-deactivating channels that displayed an attenuated mode-shift of charge. This indicates that charge movement is perturbed by N- and C-terminus interactions, and that these domain interactions stabilize the open state and limit the rate of charge return. We conclude that slow on-gating charge movement can only partly account for slow hERG ionic activation, and that the rate of pore closure has a limiting role in the slow return of gating charges.
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Affiliation(s)
- Samuel J Goodchild
- Department of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Logan C Macdonald
- Department of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada
| | - David Fedida
- Department of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada.
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32
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Hoffgaard F, Kast S, Moroni A, Thiel G, Hamacher K. Tectonics of a K+ channel: The importance of the N-terminus for channel gating. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:3197-204. [DOI: 10.1016/j.bbamem.2015.09.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 09/09/2015] [Accepted: 09/18/2015] [Indexed: 11/16/2022]
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33
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Cosentino C, Alberio L, Gazzarrini S, Aquila M, Romano E, Cermenati S, Zuccolini P, Petersen J, Beltrame M, Van Etten JL, Christie JM, Thiel G, Moroni A. Optogenetics. Engineering of a light-gated potassium channel. Science 2015; 348:707-10. [PMID: 25954011 DOI: 10.1126/science.aaa2787] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 04/07/2015] [Indexed: 12/18/2022]
Abstract
The present palette of opsin-based optogenetic tools lacks a light-gated potassium (K(+)) channel desirable for silencing of excitable cells. Here, we describe the construction of a blue-light-induced K(+) channel 1 (BLINK1) engineered by fusing the plant LOV2-Jα photosensory module to the small viral K(+) channel Kcv. BLINK1 exhibits biophysical features of Kcv, including K(+) selectivity and high single-channel conductance but reversibly photoactivates in blue light. Opening of BLINK1 channels hyperpolarizes the cell to the K(+) equilibrium potential. Ectopic expression of BLINK1 reversibly inhibits the escape response in light-exposed zebrafish larvae. BLINK1 therefore provides a single-component optogenetic tool that can establish prolonged, physiological hyperpolarization of cells at low light intensities.
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Affiliation(s)
| | - Laura Alberio
- Department of Biosciences, University of Milano, Italy
| | | | - Marco Aquila
- Department of Biosciences, University of Milano, Italy
| | | | | | | | - Jan Petersen
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, UK
| | | | - James L Van Etten
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583-0900, USA
| | - John M Christie
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, UK
| | - Gerhard Thiel
- Membrane Biophysics, Technical University of Darmstadt, Darmstadt, Germany
| | - Anna Moroni
- Department of Biosciences, University of Milano, Italy.
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34
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Engineering a Ca⁺⁺⁺-sensitive (bio)sensor from the pore-module of a potassium channel. SENSORS 2015; 15:4913-24. [PMID: 25734643 PMCID: PMC4435187 DOI: 10.3390/s150304913] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 12/19/2014] [Accepted: 02/02/2015] [Indexed: 11/30/2022]
Abstract
Signals recorded at the cell membrane are meaningful indicators of the physiological vs. pathological state of a cell and will become useful diagnostic elements in nanomedicine. In this project we present a coherent strategy for the design and fabrication of a bio-nano-sensor that monitors changes in intracellular cell calcium concentration and allows an easy read out by converting the calcium signal into an electrical current in the range of microampere that can be easily measured by conventional cell electrophysiology apparatus.
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35
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Pless SA, Elstone FD, Niciforovic AP, Galpin JD, Yang R, Kurata HT, Ahern CA. Asymmetric functional contributions of acidic and aromatic side chains in sodium channel voltage-sensor domains. ACTA ACUST UNITED AC 2014; 143:645-56. [PMID: 24778431 PMCID: PMC4003186 DOI: 10.1085/jgp.201311036] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Conserved acidic and aromatic residues in the four sodium channel voltage-sensor domains make domain-specific functional contributions. Voltage-gated sodium (NaV) channels mediate electrical excitability in animals. Despite strong sequence conservation among the voltage-sensor domains (VSDs) of closely related voltage-gated potassium (KV) and NaV channels, the functional contributions of individual side chains in Nav VSDs remain largely enigmatic. To this end, natural and unnatural side chain substitutions were made in the S2 hydrophobic core (HC), the extracellular negative charge cluster (ENC), and the intracellular negative charge cluster (INC) of the four VSDs of the skeletal muscle sodium channel isoform (NaV1.4). The results show that the highly conserved aromatic side chain constituting the S2 HC makes distinct functional contributions in each of the four NaV domains. No obvious cation–pi interaction exists with nearby S4 charges in any domain, and natural and unnatural mutations at these aromatic sites produce functional phenotypes that are different from those observed previously in Kv VSDs. In contrast, and similar to results obtained with Kv channels, individually neutralizing acidic side chains with synthetic derivatives and with natural amino acid substitutions in the INC had little or no effect on the voltage dependence of activation in any of the four domains. Interestingly, countercharge was found to play an important functional role in the ENC of DI and DII, but not DIII and DIV. These results suggest that electrostatic interactions with S4 gating charges are unlikely in the INC and only relevant in the ENC of DI and DII. Collectively, our data highlight domain-specific functional contributions of highly conserved side chains in NaV VSDs.
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Affiliation(s)
- Stephan A Pless
- Department of Anesthesiology, Pharmacology and Therapeutics, and 2 Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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36
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Siotto F, Martin C, Rauh O, Van Etten JL, Schroeder I, Moroni A, Thiel G. Viruses infecting marine picoplancton encode functional potassium ion channels. Virology 2014; 466-467:103-11. [PMID: 25441713 DOI: 10.1016/j.virol.2014.05.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 04/29/2014] [Accepted: 05/03/2014] [Indexed: 01/19/2023]
Abstract
Phycodnaviruses are dsDNA viruses, which infect algae. Their large genomes encode many gene products, like small K(+) channels, with homologs in prokaryotes and eukaryotes. Screening for K(+) channels revealed their abundance in viruses from fresh-water habitats. Recent sequencing of viruses from marine algae or from salt water in Antarctica revealed sequences with the predicted characteristics of K(+) channels but with some unexpected features. Two genes encode either 78 or 79 amino acid proteins, which are the smallest known K(+) channels. Also of interest is an unusual sequence in the canonical α-helixes in K(+) channels. Structural prediction algorithms indicate that the new channels have the conserved α-helix folds but the algorithms failed to identify the expected transmembrane domains flanking the K(+) channel pores. In spite of these unexpected properties electophysiological studies confirmed that the new proteins are functional K(+) channels.
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Affiliation(s)
- Fenja Siotto
- Membrane Biophysics Group, Dept. of Biology, Technical University Darmstadt, Germany
| | - Corinna Martin
- Membrane Biophysics Group, Dept. of Biology, Technical University Darmstadt, Germany
| | - Oliver Rauh
- Membrane Biophysics Group, Dept. of Biology, Technical University Darmstadt, Germany
| | - James L Van Etten
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska, Lincoln, NE 68583-0900, USA
| | - Indra Schroeder
- Membrane Biophysics Group, Dept. of Biology, Technical University Darmstadt, Germany
| | - Anna Moroni
- Dipartimento di Biologia Università degli Studi di Milano e Istituto di Biofisica, CNR, Milano, Italy
| | - Gerhard Thiel
- Membrane Biophysics Group, Dept. of Biology, Technical University Darmstadt, Germany.
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37
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Palovcak E, Delemotte L, Klein ML, Carnevale V. Evolutionary imprint of activation: the design principles of VSDs. ACTA ACUST UNITED AC 2014; 143:145-56. [PMID: 24470486 PMCID: PMC4001776 DOI: 10.1085/jgp.201311103] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Voltage-sensor domains (VSDs) are modular biomolecular machines that transduce electrical signals in cells through a highly conserved activation mechanism. Here, we investigate sequence-function relationships in VSDs with approaches from information theory and probabilistic modeling. Specifically, we collect over 6,600 unique VSD sequences from diverse, long-diverged phylogenetic lineages and relate the statistical properties of this ensemble to functional constraints imposed by evolution. The VSD is a helical bundle with helices labeled S1-S4. Surrounding conserved VSD residues such as the countercharges and the S2 phenylalanine, we discover sparse networks of coevolving residues. Additional networks are found lining the VSD lumen, tuning the local hydrophilicity. Notably, state-dependent contacts and the absence of coevolution between S4 and the rest of the bundle are imprints of the activation mechanism on the VSD sequence ensemble. These design principles rationalize existing experimental results and generate testable hypotheses.
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Affiliation(s)
- Eugene Palovcak
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA 19122
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38
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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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39
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Zaydman MA, Cui J. PIP2 regulation of KCNQ channels: biophysical and molecular mechanisms for lipid modulation of voltage-dependent gating. Front Physiol 2014; 5:195. [PMID: 24904429 PMCID: PMC4034418 DOI: 10.3389/fphys.2014.00195] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Accepted: 05/08/2014] [Indexed: 12/28/2022] Open
Abstract
Voltage-gated potassium (Kv) channels contain voltage-sensing (VSD) and pore-gate (PGD) structural domains. During voltage-dependent gating, conformational changes in the two domains are coupled giving rise to voltage-dependent opening of the channel. In addition to membrane voltage, KCNQ (Kv7) channel opening requires the membrane lipid phosphatidylinositol 4,5-bisphosphate (PIP2). Recent studies suggest that PIP2 serves as a cofactor to mediate VSD-PGD coupling in KCNQ1 channels. In this review, we put these findings in the context of the current understanding of voltage-dependent gating, lipid modulation of Kv channel activation, and PIP2-regulation of KCNQ channels. We suggest that lipid-mediated coupling of functional domains is a common mechanism among KCNQ channels that may be applicable to other Kv channels and membrane proteins.
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Affiliation(s)
- Mark A Zaydman
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Diseases, Cardiac Bioelectricity and Arrhythmia Center, Washington University in St. Louis St. Louis, MO, USA
| | - Jianmin Cui
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Diseases, Cardiac Bioelectricity and Arrhythmia Center, Washington University in St. Louis St. Louis, MO, USA
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40
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Li Q, Wanderling S, Paduch M, Medovoy D, Singharoy A, McGreevy R, Villalba-Galea C, Hulse RE, Roux B, Schulten K, Kossiakoff A, Perozo E. Structural mechanism of voltage-dependent gating in an isolated voltage-sensing domain. Nat Struct Mol Biol 2014; 21:244-52. [PMID: 24487958 PMCID: PMC4116111 DOI: 10.1038/nsmb.2768] [Citation(s) in RCA: 188] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 01/10/2014] [Indexed: 01/26/2023]
Abstract
The transduction of transmembrane electric fields into protein motion has an essential role in the generation and propagation of cellular signals. Voltage-sensing domains (VSDs) carry out these functions through reorientations of positive charges in the S4 helix. Here, we determined crystal structures of the Ciona intestinalis VSD (Ci-VSD) in putatively active and resting conformations. S4 undergoes an ~5-Å displacement along its main axis, accompanied by an ~60° rotation. This movement is stabilized by an exchange in countercharge partners in helices S1 and S3 that generates an estimated net charge transfer of ~1 eo. Gating charges move relative to a ''hydrophobic gasket' that electrically divides intra- and extracellular compartments. EPR spectroscopy confirms the limited nature of S4 movement in a membrane environment. These results provide an explicit mechanism for voltage sensing and set the basis for electromechanical coupling in voltage-dependent enzymes and ion channels.
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Affiliation(s)
- Qufei Li
- Department of Biochemistry and Molecular Biology, The University
of Chicago, Chicago, IL 60637, USA
| | - Sherry Wanderling
- Department of Biochemistry and Molecular Biology, The University
of Chicago, Chicago, IL 60637, USA
| | - Marcin Paduch
- Department of Biochemistry and Molecular Biology, The University
of Chicago, Chicago, IL 60637, USA
| | - David Medovoy
- Department of Biochemistry and Molecular Biology, The University
of Chicago, Chicago, IL 60637, USA
| | - Abhishek Singharoy
- Department of Physics and Beckman Institute, University of
Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ryan McGreevy
- Department of Physics and Beckman Institute, University of
Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Carlos Villalba-Galea
- Department of Physiology and Biophysics, Virginia Commonwealth
University School of Medicine, Richmond, VA 23298, USA
| | - Raymond E. Hulse
- Department of Biochemistry and Molecular Biology, The University
of Chicago, Chicago, IL 60637, USA
| | - Benoit Roux
- Department of Biochemistry and Molecular Biology, The University
of Chicago, Chicago, IL 60637, USA
| | - Klaus Schulten
- Department of Physics and Beckman Institute, University of
Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Anthony Kossiakoff
- Department of Biochemistry and Molecular Biology, The University
of Chicago, Chicago, IL 60637, USA
| | - Eduardo Perozo
- Department of Biochemistry and Molecular Biology, The University
of Chicago, Chicago, IL 60637, USA
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41
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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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42
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Tian C, Zhu R, Zhu L, Qiu T, Cao Z, Kang T. Potassium Channels: Structures, Diseases, and Modulators. Chem Biol Drug Des 2013; 83:1-26. [DOI: 10.1111/cbdd.12237] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Chuan Tian
- School of Life Sciences and Technology; Tongji University; Shanghai 200092 China
- School of Pharmacy; Liaoning University of Traditional Chinese Medicine; Dalian Liaoning 116600 China
| | - Ruixin Zhu
- School of Life Sciences and Technology; Tongji University; Shanghai 200092 China
| | - Lixin Zhu
- Department of Pediatrics; Digestive Diseases and Nutrition Center; The State University of New York at Buffalo; Buffalo NY 14226 USA
| | - Tianyi Qiu
- School of Life Sciences and Technology; Tongji University; Shanghai 200092 China
| | - Zhiwei Cao
- School of Life Sciences and Technology; Tongji University; Shanghai 200092 China
| | - Tingguo Kang
- School of Pharmacy; Liaoning University of Traditional Chinese Medicine; Dalian Liaoning 116600 China
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43
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Shaya D, Findeisen F, Abderemane-Ali F, Arrigoni C, Wong S, Nurva SR, Loussouarn G, Minor DL. Structure of a prokaryotic sodium channel pore reveals essential gating elements and an outer ion binding site common to eukaryotic channels. J Mol Biol 2013; 426:467-83. [PMID: 24120938 DOI: 10.1016/j.jmb.2013.10.010] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 09/20/2013] [Accepted: 10/05/2013] [Indexed: 12/18/2022]
Abstract
Voltage-gated sodium channels (NaVs) are central elements of cellular excitation. Notwithstanding advances from recent bacterial NaV (BacNaV) structures, key questions about gating and ion selectivity remain. Here, we present a closed conformation of NaVAe1p, a pore-only BacNaV derived from NaVAe1, a BacNaV from the arsenite oxidizer Alkalilimnicola ehrlichei found in Mono Lake, California, that provides insight into both fundamental properties. The structure reveals a pore domain in which the pore-lining S6 helix connects to a helical cytoplasmic tail. Electrophysiological studies of full-length BacNaVs show that two elements defined by the NaVAe1p structure, an S6 activation gate position and the cytoplasmic tail "neck", are central to BacNaV gating. The structure also reveals the selectivity filter ion entry site, termed the "outer ion" site. Comparison with mammalian voltage-gated calcium channel (CaV) selectivity filters, together with functional studies, shows that this site forms a previously unknown determinant of CaV high-affinity calcium binding. Our findings underscore commonalities between BacNaVs and eukaryotic voltage-gated channels and provide a framework for understanding gating and ion permeation in this superfamily.
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Affiliation(s)
- David Shaya
- Cardiovascular Research Institute, University of California, San Francisco, CA 94158-9001, USA
| | - Felix Findeisen
- Cardiovascular Research Institute, University of California, San Francisco, CA 94158-9001, USA
| | - Fayal Abderemane-Ali
- Institut National de la Santé et de la Recherche Médicale, UMR 1087, F-44000 Nantes, France; Centre National de la Recherche Scientifique, UMR 6291, F-44000 Nantes, France; L'institut du thorax, L'UNAM, Université de Nantes, F-44000 Nantes, France
| | - Cristina Arrigoni
- Cardiovascular Research Institute, University of California, San Francisco, CA 94158-9001, USA
| | - Stephanie Wong
- Cardiovascular Research Institute, University of California, San Francisco, CA 94158-9001, USA
| | - Shailika Reddy Nurva
- Cardiovascular Research Institute, University of California, San Francisco, CA 94158-9001, USA
| | - Gildas Loussouarn
- Institut National de la Santé et de la Recherche Médicale, UMR 1087, F-44000 Nantes, France; Centre National de la Recherche Scientifique, UMR 6291, F-44000 Nantes, France; L'institut du thorax, L'UNAM, Université de Nantes, F-44000 Nantes, France
| | - Daniel L Minor
- Cardiovascular Research Institute, University of California, 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; Physical Biosciences Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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Thiel G, Moroni A, Blanc G, Van Etten JL. Potassium ion channels: could they have evolved from viruses? PLANT PHYSIOLOGY 2013; 162:1215-24. [PMID: 23719891 PMCID: PMC3707557 DOI: 10.1104/pp.113.219360] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Accepted: 05/23/2013] [Indexed: 06/01/2023]
Abstract
Phylogenetic analyses of small viral K+ channels suggests that they did not originate from their hosts, but instead could be the source of the postulated pore precursor in the evolution of K+ channels.
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Affiliation(s)
- Gerhard Thiel
- Department of Biology, Technische Universität-Darmstadt, Schnittspahnstrasse 3, 64287 Darmstadt, Germany.
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Schroeder I, Gazzarrini S, Ferrara G, Thiel G, Hansen UP, Moroni A. Creation of a reactive oxygen species-insensitive Kcv channel. Biochemistry 2013; 52:3130-7. [PMID: 23578303 DOI: 10.1021/bi3016197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The current of the minimal viral K(+) channel Kcv(PCBV-1) heterologously expressed in Xenopus oocytes is strongly inhibited by reactive oxygen species (ROS) like H(2)O(2). Possible targets for the ROS effect are two cysteines (C53 and C79) and four methionines (M1, M15, M23, and M26). The C53A/C79A and M23L/M26L double mutations maintained the same ROS sensitivity as the wild type. However, M15L as a single mutant or in combination with C53A/C79A and/or M23L/M26L caused a complete loss of sensitivity to H(2)O(2). These results indicate a prominent role of M15 at the cytosolic end of the outer transmembrane helix for gating of Kcv(PCBV-1). Furthermore, even though the channel lacks a canonical voltage sensor, it exhibits a weak voltage sensitivity, resulting in a slight activation in the millisecond range after a voltage step to negative potentials. The M15L mutation inverts this kinetics into an inactivation, underlining the critical role of this residue for gating. The negative slope of the I-V curves of M15L is the same as in the wild type, indicating that the selectivity filter is not involved.
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Affiliation(s)
- Indra Schroeder
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milano, Italy.
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Adler EM. Looking to the past and to the future. J Gen Physiol 2013; 141:401-2. [PMID: 23530134 PMCID: PMC3607829 DOI: 10.1085/jgp.201310983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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