1
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Hu Z, Yang J. Structural basis of properties, mechanisms, and channelopathy of cyclic nucleotide-gated channels. Channels (Austin) 2023; 17:2273165. [PMID: 37905307 PMCID: PMC10761061 DOI: 10.1080/19336950.2023.2273165] [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: 09/07/2023] [Accepted: 10/07/2023] [Indexed: 11/02/2023] Open
Abstract
Recent years have seen an outpouring of atomic or near atomic resolution structures of cyclic nucleotide-gated (CNG) channels, captured in closed, transition, pre-open, partially open, and fully open states. These structures provide unprecedented molecular insights into the activation, assembly, architecture, regulation, and channelopathy of CNG channels, as well as mechanistic explanations for CNG channel biophysical and pharmacological properties. This article summarizes recent advances in CNG channel structural biology, describes key structural features and elements, and illuminates a detailed conformational landscape of activation by cyclic nucleotides. The review also correlates structures with findings and properties delineated in functional studies, including nonselective monovalent cation selectivity, Ca2+ permeation and block, block by L-cis-diltiazem, location of the activation gate, lack of voltage-dependent gating, and modulation by lipids and calmodulin. A perspective on future research is also offered.
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Affiliation(s)
- Zhengshan Hu
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Jian Yang
- Department of Biological Sciences, Columbia University, New York, NY, USA
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2
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Chen YS, Gehring K. New insights into the structure and function of CNNM proteins. FEBS J 2023; 290:5475-5495. [PMID: 37222397 DOI: 10.1111/febs.16872] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/17/2023] [Accepted: 05/23/2023] [Indexed: 05/25/2023]
Abstract
Magnesium (Mg2+ ) is the most abundant divalent cation in cells and plays key roles in almost all biological processes. CBS-pair domain divalent metal cation transport mediators (CNNMs) are a newly characterized class of Mg2+ transporters present throughout biology. Originally discovered in bacteria, there are four CNNM proteins in humans, which are involved in divalent cation transport, genetic diseases, and cancer. Eukaryotic CNNMs are composed of four domains: an extracellular domain, a transmembrane domain, a cystathionine-β-synthase (CBS)-pair domain, and a cyclic nucleotide-binding homology domain. The transmembrane and CBS-pair core are the defining features of CNNM proteins with over 20 000 protein sequences known from over 8000 species. Here, we review the structural and functional studies of eukaryotic and prokaryotic CNNMs that underlie our understanding of their regulation and mechanism of ion transport. Recent structures of prokaryotic CNNMs confirm the transmembrane domain mediates ion transport with the CBS-pair domain likely playing a regulatory role through binding divalent cations. Studies of mammalian CNNMs have identified new binding partners. These advances are driving progress in understanding this deeply conserved and widespread family of ion transporters.
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Affiliation(s)
- Yu Seby Chen
- Department of Biochemistry & Molecular Biology, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Kalle Gehring
- Department of Biochemistry & Centre de Recherche en Biologie Structurale, McGill University, Montreal, QC, Canada
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3
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Sidoli M, Chen LC, Lu AJ, Wandless TJ, Talbot WS. A cAMP Sensor Based on Ligand-Dependent Protein Stabilization. ACS Chem Biol 2022; 17:2024-2030. [PMID: 35839076 PMCID: PMC9396618 DOI: 10.1021/acschembio.2c00333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 07/12/2022] [Indexed: 11/28/2022]
Abstract
cAMP is a ubiquitous second messenger with many functions in diverse organisms. Current cAMP sensors, including Föster resonance energy transfer (FRET)-based and single-wavelength-based sensors, allow for real time visualization of this small molecule in cultured cells and in some cases in vivo. Nonetheless the observation of cAMP in living animals is still difficult, typically requiring specialized microscopes and ex vivo tissue processing. Here we used ligand-dependent protein stabilization to create a new cAMP sensor. This sensor allows specific and sensitive detection of cAMP in living zebrafish embryos, which may enable new understanding of the functions of cAMP in living vertebrates.
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Affiliation(s)
- Mariapaola Sidoli
- Department
of Developmental Biology, School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Ling-chun Chen
- Department
of Chemical and Systems Biology, School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Alexander J. Lu
- Department
of Chemical and Systems Biology, School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Thomas J. Wandless
- Department
of Chemical and Systems Biology, School of Medicine, Stanford University, Stanford, California 94305, United States
| | - William S. Talbot
- Department
of Developmental Biology, School of Medicine, Stanford University, Stanford, California 94305, United States
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4
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Barret DCA, Schertler GFX, Kaupp UB, Marino J. The structure of the native CNGA1/CNGB1 CNG channel from bovine retinal rods. Nat Struct Mol Biol 2022; 29:32-39. [PMID: 34969975 DOI: 10.1038/s41594-021-00700-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 11/09/2021] [Indexed: 11/09/2022]
Abstract
In rod photoreceptors of the retina, the cyclic nucleotide-gated (CNG) channel is composed of three CNGA and one CNGB subunits, and it closes in response to light activation to generate an electrical signal that is conveyed to the brain. Here we report the cryo-EM structure of the closed state of the native rod CNG channel isolated from bovine retina. The structure reveals differences between CNGA1 and CNGB1 subunits. Three CNGA1 subunits are tethered at their C terminus by a coiled-coil region. The C-helix in the cyclic nucleotide-binding domain of CNGB1 features a different orientation from that in the three CNGA1 subunits. The arginine residue R994 of CNGB1 reaches into the ionic pathway and blocks the pore, thus introducing an additional gate, which is different from the central hydrophobic gate known from homomeric CNGA channels. These results address the long-standing question of how CNGB1 subunits contribute to the function of CNG channels in visual and olfactory neurons.
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Affiliation(s)
- Diane C A Barret
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen, Switzerland
| | - Gebhard F X Schertler
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen, Switzerland.,Department of Biology, ETH-Zurich, Zurich, Switzerland
| | - U Benjamin Kaupp
- Center for Advanced European Studies and Research (CAESAR), Bonn, Germany.,Life and Medical Sciences Institute LIMES, University of Bonn, Bonn, Germany
| | - Jacopo Marino
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen, Switzerland.
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5
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Hett T, Zbik T, Mukherjee S, Matsuoka H, Bönigk W, Klose D, Rouillon C, Brenner N, Peuker S, Klement R, Steinhoff HJ, Grubmüller H, Seifert R, Schiemann O, Kaupp UB. Spatiotemporal Resolution of Conformational Changes in Biomolecules by Combining Pulsed Electron-Electron Double Resonance Spectroscopy with Microsecond Freeze-Hyperquenching. J Am Chem Soc 2021; 143:6981-6989. [PMID: 33905249 DOI: 10.1021/jacs.1c01081] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The function of proteins is linked to their conformations that can be resolved with several high-resolution methods. However, only a few methods can provide the temporal order of intermediates and conformational changes, with each having its limitations. Here, we combine pulsed electron-electron double resonance spectroscopy with a microsecond freeze-hyperquenching setup to achieve spatiotemporal resolution in the angstrom range and lower microsecond time scale. We show that the conformational change of the Cα-helix in the cyclic nucleotide-binding domain of the Mesorhizobium loti potassium channel occurs within about 150 μs and can be resolved with angstrom precision. Thus, this approach holds great promise for obtaining 4D landscapes of conformational changes in biomolecules.
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Affiliation(s)
- Tobias Hett
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstraße 12, 53115 Bonn, Germany
| | - Tobias Zbik
- Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Shatanik Mukherjee
- Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Hideto Matsuoka
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstraße 12, 53115 Bonn, Germany
| | - Wolfgang Bönigk
- Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Daniel Klose
- Fachbereich Physik, Universität Osnabrück, Barbarastraße 7, 49076 Osnabrück, Germany
| | - Christophe Rouillon
- Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Norbert Brenner
- Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Sebastian Peuker
- Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Reinhard Klement
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | | | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Reinhard Seifert
- Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstraße 12, 53115 Bonn, Germany
| | - U Benjamin Kaupp
- Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany.,Life & Medical Sciences Institute (LIMES), University of Bonn, Carl-Troll-Straße 31, 53115 Bonn, Germany
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6
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Structural mechanisms of gating and selectivity of human rod CNGA1 channel. Neuron 2021; 109:1302-1313.e4. [PMID: 33651975 DOI: 10.1016/j.neuron.2021.02.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/22/2021] [Accepted: 02/03/2021] [Indexed: 11/22/2022]
Abstract
Mammalian cyclic nucleotide-gated (CNG) channels play an essential role in the signal transduction of the visual and olfactory sensory systems. Here we reveal the structural mechanism of ligand gating in human rod CNGA1 channel by determining its cryo-EM structures in both the apo closed and cGMP-bound open states. Distinct from most other members of voltage-gated tetrameric cation channels, CNGA1 forms a central channel gate in the middle of the membrane, occluding the central cavity. Structural analyses of ion binding profiles in the selectivity filters of the wild-type channel and the E365Q filter mutant allow us to unambiguously define the two Ca2+ binding sites inside the selectivity filter, providing structural insights into Ca2+ blockage and permeation in CNG channels. The structure of the E365Q mutant also reveals two alternative side-chain conformations at Q365, providing a plausible explanation for the voltage-dependent gating of CNG channel acquired upon E365 mutation.
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7
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Byun JA, Van K, Huang J, Henning P, Franz E, Akimoto M, Herberg FW, Kim C, Melacini G. Mechanism of allosteric inhibition in the Plasmodium falciparum cGMP-dependent protein kinase. J Biol Chem 2020; 295:8480-8491. [PMID: 32317283 DOI: 10.1074/jbc.ra120.013070] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/16/2020] [Indexed: 11/06/2022] Open
Abstract
Most malaria deaths are caused by the protozoan parasite Plasmodium falciparum Its life cycle is regulated by a cGMP-dependent protein kinase (PfPKG), whose inhibition is a promising antimalaria strategy. Allosteric kinase inhibitors, such as cGMP analogs, offer enhanced selectivity relative to competitive kinase inhibitors. However, the mechanisms underlying allosteric PfPKG inhibition are incompletely understood. Here, we show that 8-NBD-cGMP is an effective PfPKG antagonist. Using comparative NMR analyses of a key regulatory domain, PfD, in its apo, cGMP-bound, and cGMP analog-bound states, we elucidated its inhibition mechanism of action. Using NMR chemical shift analyses, molecular dynamics simulations, and site-directed mutagenesis, we show that 8-NBD-cGMP inhibits PfPKG not simply by reverting a two-state active versus inactive equilibrium, but by sampling also a distinct inactive "mixed" intermediate. Surface plasmon resonance indicates that the ability to stabilize a mixed intermediate provides a means to effectively inhibit PfPKG, without losing affinity for the cGMP analog. Our proposed model may facilitate the rational design of PfPKG-selective inhibitors for improved management of malaria.
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Affiliation(s)
- Jung Ah Byun
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4L8, Canada
| | - Katherine Van
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4L8, Canada
| | - Jinfeng Huang
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4L8, Canada
| | - Philipp Henning
- Department of Biochemistry, University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - Eugen Franz
- Biaffin GmbH & Co. KG, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - Madoka Akimoto
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4L8, Canada
| | - Friedrich W Herberg
- Department of Biochemistry, University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - Choel Kim
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030.,Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Giuseppe Melacini
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4L8, Canada .,Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4L8, Canada
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8
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Mg2+-ATP Sensing in CNNM, a Putative Magnesium Transporter. Structure 2020; 28:324-335.e4. [DOI: 10.1016/j.str.2019.11.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/06/2019] [Accepted: 11/27/2019] [Indexed: 01/10/2023]
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9
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Cadby IT, Basford SM, Nottingham R, Meek R, Lowry R, Lambert C, Tridgett M, Till R, Ahmad R, Fung R, Hobley L, Hughes WS, Moynihan PJ, Sockett RE, Lovering AL. Nucleotide signaling pathway convergence in a cAMP-sensing bacterial c-di-GMP phosphodiesterase. EMBO J 2019; 38:e100772. [PMID: 31355487 PMCID: PMC6717892 DOI: 10.15252/embj.2018100772] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 06/11/2019] [Accepted: 06/13/2019] [Indexed: 01/06/2023] Open
Abstract
Bacterial usage of the cyclic dinucleotide c‐di‐GMP is widespread, governing the transition between motile/sessile and unicellular/multicellular behaviors. There is limited information on c‐di‐GMP metabolism, particularly on regulatory mechanisms governing control of EAL c‐di‐GMP phosphodiesterases. Herein, we provide high‐resolution structures for an EAL enzyme Bd1971, from the predatory bacterium Bdellovibrio bacteriovorus, which is controlled by a second signaling nucleotide, cAMP. The full‐length cAMP‐bound form reveals the sensory N‐terminus to be a domain‐swapped variant of the cNMP/CRP family, which in the cAMP‐activated state holds the C‐terminal EAL enzyme in a phosphodiesterase‐active conformation. Using a truncation mutant, we trap both a half‐occupied and inactive apo‐form of the protein, demonstrating a series of conformational changes that alter juxtaposition of the sensory domains. We show that Bd1971 interacts with several GGDEF proteins (c‐di‐GMP producers), but mutants of Bd1971 do not share the discrete phenotypes of GGDEF mutants, instead having an elevated level of c‐di‐GMP, suggesting that the role of Bd1971 is to moderate these levels, allowing “action potentials” to be generated by each GGDEF protein to effect their specific functions.
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Affiliation(s)
- Ian T Cadby
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK
| | - Sarah M Basford
- Centre for Genetics and Genomics, School of Biology, Medical School, Queen's Medical Centre, Nottingham University, Nottingham, UK
| | - Ruth Nottingham
- Centre for Genetics and Genomics, School of Biology, Medical School, Queen's Medical Centre, Nottingham University, Nottingham, UK
| | - Richard Meek
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK
| | - Rebecca Lowry
- Centre for Genetics and Genomics, School of Biology, Medical School, Queen's Medical Centre, Nottingham University, Nottingham, UK
| | - Carey Lambert
- Centre for Genetics and Genomics, School of Biology, Medical School, Queen's Medical Centre, Nottingham University, Nottingham, UK
| | - Matthew Tridgett
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK
| | - Rob Till
- Centre for Genetics and Genomics, School of Biology, Medical School, Queen's Medical Centre, Nottingham University, Nottingham, UK
| | - Rashidah Ahmad
- Centre for Genetics and Genomics, School of Biology, Medical School, Queen's Medical Centre, Nottingham University, Nottingham, UK
| | - Rowena Fung
- Centre for Genetics and Genomics, School of Biology, Medical School, Queen's Medical Centre, Nottingham University, Nottingham, UK
| | - Laura Hobley
- Centre for Genetics and Genomics, School of Biology, Medical School, Queen's Medical Centre, Nottingham University, Nottingham, UK
| | - William S Hughes
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK
| | - Patrick J Moynihan
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK
| | - R Elizabeth Sockett
- Centre for Genetics and Genomics, School of Biology, Medical School, Queen's Medical Centre, Nottingham University, Nottingham, UK
| | - Andrew L Lovering
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK
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10
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Wang ZJ, Tiwari PB, Üren A, Brelidze TI. Identification of undecylenic acid as EAG channel inhibitor using surface plasmon resonance-based screen of KCNH channels. BMC Pharmacol Toxicol 2019; 20:42. [PMID: 31315662 PMCID: PMC6637479 DOI: 10.1186/s40360-019-0324-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 07/11/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND KCNH family of potassium channels is responsible for diverse physiological functions ranging from the regulation of neuronal excitability and cardiac contraction to the regulation of cancer progression. KCNH channels contain a Per-Arn-Sim (PAS) domain in their N-terminal and cyclic nucleotide-binding homology (CNBH) domain in their C-terminal regions. These intracellular domains shape the function of KCNH channels and are important targets for drug development. METHODS Here we describe a surface plasmon resonance (SPR)-based screening method aimed in identifying small molecule binders of PAS and CNBH domains for three KCNH channel subfamilies: ether-à-go-go (EAG), EAG-related gene (ERG), and EAG-like K+ (ELK). The method involves purification of the PAS and CNBH domains, immobilization of the purified domains on the SPR senor chip and screening small molecules in a chemical library for binding to the immobilized domains using changes in the SPR response as a reporter of the binding. The advantages of this method include low quantity of purified PAS and CNBH domains necessary for the implementation of the screen, direct assessment of the small molecule binding to the PAS and CNBH domains and easiness of assessing KCNH subfamily specificity of the small molecule binders. RESULTS Using the SPR-based method we screened the Spectrum Collection Library of 2560 compounds against the PAS and CNBH domains of the three KCNH channel subfamilies and identified a pool of small molecules that bind to the PAS or CNBH domains. To further evaluate the effectiveness of the screen we tested the functional effect of one of the identified mEAG PAS domain specific small molecule binders on currents recorded from EAG channels. Undecylenic acid inhibited currents recorded from EAG channels in a concentration-dependent manner with IC50 of ~ 1 μM. CONCLUSION Our results show that the SPR-based method is well suited for identifying small molecule binders of KCNH channels and can facilitate drug discovery for other ion channels as well.
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Affiliation(s)
- Ze-Jun Wang
- Department of Pharmacology and Physiology, Georgetown University Medical Center, Washington, DC USA
| | | | - Aykut Üren
- Department of Oncology, Georgetown University Medical Center, Washington, DC USA
| | - Tinatin I. Brelidze
- Department of Pharmacology and Physiology, Georgetown University Medical Center, Washington, DC USA
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11
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Chen YS, Kozlov G, Fakih R, Funato Y, Miki H, Gehring K. The cyclic nucleotide-binding homology domain of the integral membrane protein CNNM mediates dimerization and is required for Mg 2+ efflux activity. J Biol Chem 2018; 293:19998-20007. [PMID: 30341174 PMCID: PMC6311497 DOI: 10.1074/jbc.ra118.005672] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 10/16/2018] [Indexed: 01/07/2023] Open
Abstract
Proteins of the cyclin M family (CNNMs; also called ancient conserved domain proteins, or ACDPs) are represented by four integral membrane proteins that have been proposed to function as Mg2+ transporters. CNNMs are associated with a number of genetic diseases affecting ion movement and cancer via their association with highly oncogenic phosphatases of regenerating liver (PRLs). Structurally, CNNMs contain an N-terminal extracellular domain, a transmembrane domain (DUF21), and a large cytosolic region containing a cystathionine-β-synthase (CBS) domain and a putative cyclic nucleotide-binding homology (CNBH) domain. Although the CBS domain has been extensively characterized, little is known about the CNBH domain. Here, we determined the first crystal structures of the CNBH domains of CNNM2 and CNNM3 at 2.6 and 1.9 Å resolutions. Contrary to expectation, these domains did not bind cyclic nucleotides, but mediated dimerization both in crystals and in solution. Analytical ultracentrifugation experiments revealed an inverse correlation between the propensity of the CNBH domains to dimerize and the ability of CNNMs to mediate Mg2+ efflux. CNBH domains from active family members were observed as both dimers and monomers, whereas the inactive member, CNNM3, was observed only as a dimer. Mutational analysis revealed that the CNBH domain was required for Mg2+ efflux activity of CNNM4. This work provides a structural basis for understanding the function of CNNM proteins in Mg2+ transport and associated diseases.
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Affiliation(s)
- Yu Seby Chen
- From the Department of Biochemistry and Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada and
| | - Guennadi Kozlov
- From the Department of Biochemistry and Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada and
| | - Rayan Fakih
- From the Department of Biochemistry and Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada and
| | - Yosuke Funato
- the Department of Cellular Regulation, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hiroaki Miki
- the Department of Cellular Regulation, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kalle Gehring
- From the Department of Biochemistry and Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada and , To whom correspondence should be addressed:
Dept. of Biochemistry, McGill University, 3649 Promenade Sir-William-Osler, Rm. 469, Montreal, Quebec H3G 0B1, Canada. Tel.:
514-398-7287; E-mail:
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12
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Rheinberger J, Gao X, Schmidpeter PA, Nimigean CM. Ligand discrimination and gating in cyclic nucleotide-gated ion channels from apo and partial agonist-bound cryo-EM structures. eLife 2018; 7:39775. [PMID: 30028291 PMCID: PMC6093708 DOI: 10.7554/elife.39775] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 07/19/2018] [Indexed: 12/11/2022] Open
Abstract
Cyclic nucleotide-modulated channels have important roles in visual signal transduction and pacemaking. Binding of cyclic nucleotides (cAMP/cGMP) elicits diverse functional responses in different channels within the family despite their high sequence and structure homology. The molecular mechanisms responsible for ligand discrimination and gating are unknown due to lack of correspondence between structural information and functional states. Using single particle cryo-electron microscopy and single-channel recording, we assigned functional states to high-resolution structures of SthK, a prokaryotic cyclic nucleotide-gated channel. The structures for apo, cAMP-bound, and cGMP-bound SthK in lipid nanodiscs, correspond to no, moderate, and low single-channel activity, respectively, consistent with the observation that all structures are in resting, closed states. The similarity between apo and ligand-bound structures indicates that ligand-binding domains are strongly coupled to pore and SthK gates in an allosteric, concerted fashion. The different orientations of cAMP and cGMP in the ‘resting’ and ‘activated’ structures suggest a mechanism for ligand discrimination. Ion channels are essential for transmitting signals in the nervous system and brain. One large group of ion channels includes members that are activated by cyclic nucleotides, small molecules used to transmit signals within cells. These cyclic nucleotide-gated channels play an important role in regulating our ability to see and smell. The activity of these ion channels has been studied for years, but scientists have only recently been able to look into their structure. Since structural biology methods require purified, well-behaved proteins, the members of this ion channel family selected for structural studies do not necessarily match those whose activity has been well established. There is a need for a good model that would allow both the structure and activity of a cyclic nucleotide-gated ion channel to be characterized. The cyclic nucleotide-gated ion channel, SthK, from bacteria called Spirochaeta thermophila, was identified as such model because both its activity and its structure are accessible. Rheinberger et al. have used cryo electron microscopy to solve several high-resolution structures of SthK channels. In two of the structures, SthK was bound to either one of two types of activating cyclic nucleotides – cAMP or cGMP – and in another structure, no cyclic nucleotides were bound. Separately recording the activity of individual channels allowed the activity states likely to be represented by these structures to be identified. Combining the results of the experiments revealed no activity from channels in an unbound state, low levels of activity for channels bound to cGMP, and moderate activity for channels bound to cAMP. Rheinberger et al. show that the channel, under the conditions experienced in cryo electron microscopy, is closed in all of the states studied. Unexpectedly, the binding of cyclic nucleotides produced no structural change even in the cyclic nucleotide-binding pocket of the channel, a region that was previously observed to undergo such changes when this region alone was crystallized. Rheinberger et al. deduce from this that the four subunits that make up the channel likely undergo the conformational change towards an open state all at once, rather than one by one. The structures and the basic functional characterization of SthK channels provide a strong starting point for future research into determining the entire opening and closing cycle for a cyclic nucleotide-gated channel. Human equivalents of the channel are likely to work in similar ways. The results presented by Rheinberger et al. could therefore be built upon to help address diseases that result from deficiencies in cyclic nucleotide-gated channels, such as loss of vision due to retinal degradation (retinitis pigmentosa or progressive cone dystrophy) and achromatopsia.
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Affiliation(s)
- Jan Rheinberger
- Departments of Anesthesiology, Weill Cornell Medical College, New York, United States
| | - Xiaolong Gao
- Departments of Anesthesiology, Weill Cornell Medical College, New York, United States
| | | | - Crina M Nimigean
- Departments of Anesthesiology, Weill Cornell Medical College, New York, United States.,Department of Physiology and Biophysics, Weill Cornell Medical College, New York, United States.,Department of Biochemistry, Weill Cornell Medical College, New York, United States
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13
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Alvarez-Baron CP, Klenchin VA, Chanda B. Minimal molecular determinants of isoform-specific differences in efficacy in the HCN channel family. J Gen Physiol 2018; 150:1203-1213. [PMID: 29980633 PMCID: PMC6080897 DOI: 10.1085/jgp.201812031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 05/29/2018] [Indexed: 01/08/2023] Open
Abstract
Hyperpolarization-activated, cyclic nucleotide-gated (HCN) channels generate rhythmic activity in the heart and brain. Isoform-specific functional differences reflect the specializations required for the various roles that they play. Despite a high sequence and structural similarity, HCN isoforms differ greatly in their response to cyclic nucleotides. Cyclic AMP (cAMP) enhances the activity of HCN2 and HCN4 isoforms by shifting the voltage dependence of activation to more depolarized potentials, whereas HCN1 and HCN3 isoforms are practically insensitive to this ligand. Here, to determine the molecular basis for increased cAMP efficacy in HCN2 channels, we progressively mutate residues in the C-linker and cyclic nucleotide-binding domain (CNBD) of the mouse HCN2 to their equivalents in HCN1. We identify two clusters of mutations that determine the differences in voltage-dependent activation between these two isoforms. One maps to the C-linker region, whereas the other is in proximity to the cAMP-binding site in the CNBD. A mutant channel containing just five mutations (M485I, G497D, S514T, V562A, and S563G) switches cAMP sensitivity of full-length HCN2 to that of HCN1 channels. These findings, combined with a detailed analysis of various allosteric models for voltage- and ligand-dependent gating, indicate that these residues alter the ability of the C-linker to transduce signals from the CNBD to the pore gates of the HCN channel.
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Affiliation(s)
| | - Vadim A Klenchin
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI
| | - Baron Chanda
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI .,Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI
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14
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Schmidpeter PAM, Gao X, Uphadyay V, Rheinberger J, Nimigean CM. Ligand binding and activation properties of the purified bacterial cyclic nucleotide-gated channel SthK. J Gen Physiol 2018; 150:821-834. [PMID: 29752414 PMCID: PMC5987880 DOI: 10.1085/jgp.201812023] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/09/2018] [Indexed: 11/20/2022] Open
Abstract
SthK is a bacterial cyclic nucleotide–gated ion channel from Spirochaeta thermophila. By optimizing the expression and purification of SthK, Schmidpeter et al. show that cAMP and cGMP bind to the channel with similar affinity but activate it with different efficacy. Cyclic nucleotide–modulated ion channels play several essential physiological roles. They are involved in signal transduction in photoreceptors and olfactory sensory neurons as well as pacemaking activity in the heart and brain. Investigations of the molecular mechanism of their actions, including structural and electrophysiological characterization, are restricted by the availability of stable, purified protein obtained from accessible systems. Here, we establish that SthK, a cyclic nucleotide–gated (CNG) channel from Spirochaeta thermophila, is an excellent model for investigating the gating of eukaryotic CNG channels at the molecular level. The channel has high sequence similarity with its eukaryotic counterparts and was previously reported to be activated by cyclic nucleotides in patch-clamp experiments with Xenopus laevis oocytes. We optimized protein expression and purification to obtain large quantities of pure, homogeneous, and active recombinant SthK protein from Escherichia coli. A negative-stain electron microscopy (EM) single-particle analysis indicated that this channel is a promising candidate for structural studies with cryo-EM. Using radioactivity and fluorescence flux assays, as well as single-channel recordings in lipid bilayers, we show that the protein is partially activated by micromolar concentrations of cyclic adenosine monophosphate (cAMP) and that channel activity is increased by depolarization. Unlike previous studies, we find that cyclic guanosine monophosphate (cGMP) is also able to activate SthK, but with much lower efficiency than cAMP. The distinct sensitivities to different ligands resemble eukaryotic CNG and hyperpolarization-activated and cyclic nucleotide–modulated channels. Using a fluorescence binding assay, we show that cGMP and cAMP bind to SthK with similar apparent affinities, suggesting that the large difference in channel activation by cAMP or cGMP is caused by the efficacy with which each ligand promotes the conformational changes toward the open state. We conclude that the functional characteristics of SthK reported here will permit future studies to analyze ligand gating and discrimination in CNG channels.
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Affiliation(s)
| | - Xiaolong Gao
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY
| | - Vikrant Uphadyay
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY
| | - Jan Rheinberger
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY .,Department of Biochemistry, Weill Cornell Medicine, New York, NY.,Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY
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15
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Uchihashi T, Scheuring S. Applications of high-speed atomic force microscopy to real-time visualization of dynamic biomolecular processes. Biochim Biophys Acta Gen Subj 2018; 1862:229-240. [DOI: 10.1016/j.bbagen.2017.07.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/13/2017] [Indexed: 12/12/2022]
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16
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Sharma S, Visweswariah SS. Illuminating Cyclic Nucleotides: Sensors for cAMP and cGMP and Their Application in Live Cell Imaging. J Indian Inst Sci 2017. [DOI: 10.1007/s41745-016-0014-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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17
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Zhao Y, Goldschen-Ohm MP, Morais-Cabral JH, Chanda B, Robertson GA. The intrinsically liganded cyclic nucleotide-binding homology domain promotes KCNH channel activation. J Gen Physiol 2017; 149:249-260. [PMID: 28122815 PMCID: PMC5299623 DOI: 10.1085/jgp.201611701] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 11/29/2016] [Accepted: 12/21/2016] [Indexed: 12/17/2022] Open
Abstract
hEAG1 is a member of the KCNH family of ion channels, which are characterized by C-terminal regions with homology to cyclic nucleotide–binding domains (CNBhDs). Zhao et al. show that an “intrinsic ligand” occupying the CNBhD binding pocket promotes the activated and open state of the channel. Channels in the ether-à-go-go or KCNH family of potassium channels are characterized by a conserved, C-terminal domain with homology to cyclic nucleotide–binding homology domains (CNBhDs). Instead of cyclic nucleotides, two amino acid residues, Y699 and L701, occupy the binding pocket, forming an “intrinsic ligand.” The role of the CNBhD in KCNH channel gating is still unclear, however, and a detailed characterization of the intrinsic ligand is lacking. In this study, we show that mutating both Y699 and L701 to alanine, serine, aspartate, or glycine impairs human EAG1 channel function. These mutants slow channel activation and shift the conductance–voltage (G–V) relation to more depolarized potentials. The mutations affect activation and the G-V relation progressively, indicating that the gating machinery is sensitive to multiple conformations of the CNBhD. Substitution with glycine at both sites (GG), which eliminates the side chains that interact with the binding pocket, also reduces the ability of voltage prepulses to populate more preactivated states along the activation pathway (i.e., the Cole–Moore effect), as if stabilizing the voltage sensor in deep resting states. Notably, deletion of the entire CNBhD (577–708, ΔCNBhD) phenocopies the GG mutant, suggesting that GG is a loss-of-function mutation and the CNBhD requires an intrinsic ligand to exert its functional effects. We developed a kinetic model for both wild-type and ΔCNBhD mutant channels that describes all our observations on activation kinetics, the Cole–Moore shift, and G-V relations. These findings support a model in which the CNBhD both promotes voltage sensor activation and stabilizes the open pore. The intrinsic ligand is critical for these functional effects.
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Affiliation(s)
- Yaxian Zhao
- Department of Neuroscience, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705.,Cardiovascular Research Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705
| | - Marcel P Goldschen-Ohm
- Department of Neuroscience, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705.,Cardiovascular Research Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705
| | - João H Morais-Cabral
- Instituto de Biologia Molecular e Celular, Universidade do Porto, 4150 Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4150 Porto, Portugal
| | - Baron Chanda
- Department of Neuroscience, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705.,Cardiovascular Research Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705
| | - Gail A Robertson
- Department of Neuroscience, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705 .,Cardiovascular Research Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705
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18
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Robertson GA. It's not funny: How changes in If limit maximum heart rate with aging. J Gen Physiol 2017; 149:177-179. [PMID: 28057841 PMCID: PMC5299625 DOI: 10.1085/jgp.201611746] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Robertson highlights recent work showing how aging limits pacemaking by the funny current, If, in the sinoatrial node.
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Affiliation(s)
- Gail A Robertson
- Department of Neuroscience, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705 .,Cardiovascular Research Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705
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19
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Voß B, Seifert R, Kaupp UB, Grubmüller H. A Quantitative Model for cAMP Binding to the Binding Domain of MloK1. Biophys J 2016; 111:1668-1678. [PMID: 27760354 PMCID: PMC5073059 DOI: 10.1016/j.bpj.2016.09.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 09/03/2016] [Accepted: 09/12/2016] [Indexed: 01/03/2023] Open
Abstract
Ligand-protein binding processes are essential in biological systems. A well-studied system is the binding of cyclic adenosine monophosphate to the cyclic nucleotide binding domain of the bacterial potassium channel MloK1. Strikingly, the measured on-rate for cyclic adenosine monophosphate binding is two orders of magnitude slower than a simple Smoluchowski diffusion model would suggest. To resolve this discrepancy and to characterize the ligand-binding path in structural and energetic terms, we calculated 1100 ligand-binding molecular dynamics trajectories and tested two scenarios: In the first scenario, the ligand transiently binds to the protein surface and then diffuses along the surface into the binding site. In the second scenario, only ligands that reach the protein surface in the vicinity of the binding site proceed into the binding site. Here, a binding funnel, which increasingly confines the translational as well as the rotational degrees of freedom, determines the binding pathways and limits the on-rate. From the simulations, we identified five surface binding states and calculated the rates between these surface binding states, the binding site, and the bulk. We find that the transient binding of the ligands to the surface binding states does not affect the on-rate, such that this effect alone cannot explain the observed low on-rate. Rather, by quantifying the translational and rotational degrees of freedom and by calculating the binding committor, our simulations confirmed the existence of a binding funnel as the main bottleneck. Direct binding via the binding funnel dominates the binding kinetics, and only ∼10% of all ligands proceed via the surface into the binding site. The simulations further predict an on-rate between 15 and 40μs-1(mol/l)-1, which agrees with the measured on-rate.
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Affiliation(s)
- Béla Voß
- Department for Theoretical and Computational Biophysics, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | | | - U Benjamin Kaupp
- Department of Sensory Systems, Forschungszentrum Caesar, Bonn, Germany
| | - Helmut Grubmüller
- Department for Theoretical and Computational Biophysics, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany.
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20
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Rangl M, Miyagi A, Kowal J, Stahlberg H, Nimigean CM, Scheuring S. Real-time visualization of conformational changes within single MloK1 cyclic nucleotide-modulated channels. Nat Commun 2016; 7:12789. [PMID: 27647260 PMCID: PMC5034309 DOI: 10.1038/ncomms12789] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 08/01/2016] [Indexed: 01/11/2023] Open
Abstract
Eukaryotic cyclic nucleotide-modulated (CNM) ion channels perform various physiological roles by opening in response to cyclic nucleotides binding to a specialized cyclic nucleotide-binding domain. Despite progress in structure-function analysis, the conformational rearrangements underlying the gating of these channels are still unknown. Here, we image ligand-induced conformational changes in single CNM channels from Mesorhizobium loti (MloK1) in real-time, using high-speed atomic force microscopy. In the presence of cAMP, most channels are in a stable conformation, but a few molecules dynamically switch back and forth (blink) between at least two conformations with different heights. Upon cAMP depletion, more channels start blinking, with blinking heights increasing over time, suggestive of slow, progressive loss of ligands from the tetramer. We propose that during gating, MloK1 transitions from a set of mobile conformations in the absence to a stable conformation in the presence of ligand and that these conformations are central for gating the pore.
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Affiliation(s)
- Martina Rangl
- INSERM U1006, Aix-Marseille Université, Parc Scientifique et Technologique de Luminy, 163 Avenue de Luminy, Marseille 13009, France
| | - Atsushi Miyagi
- INSERM U1006, Aix-Marseille Université, Parc Scientifique et Technologique de Luminy, 163 Avenue de Luminy, Marseille 13009, France
| | - Julia Kowal
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, Basel CH-4058, Switzerland
| | - Henning Stahlberg
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, Basel CH-4058, Switzerland
| | - Crina M Nimigean
- INSERM U1006, Aix-Marseille Université, Parc Scientifique et Technologique de Luminy, 163 Avenue de Luminy, Marseille 13009, France.,Departments of Anesthesiology, Physiology and Biophysics, and Biochemistry, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065, USA
| | - Simon Scheuring
- INSERM U1006, Aix-Marseille Université, Parc Scientifique et Technologique de Luminy, 163 Avenue de Luminy, Marseille 13009, France
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21
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Mukherjee S, Jansen V, Jikeli JF, Hamzeh H, Alvarez L, Dombrowski M, Balbach M, Strünker T, Seifert R, Kaupp UB, Wachten D. A novel biosensor to study cAMP dynamics in cilia and flagella. eLife 2016; 5. [PMID: 27003291 PMCID: PMC4811770 DOI: 10.7554/elife.14052] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 03/05/2016] [Indexed: 01/09/2023] Open
Abstract
The cellular messenger cAMP regulates multiple cellular functions, including signaling in cilia and flagella. The cAMP dynamics in these subcellular compartments are ill-defined. We introduce a novel FRET-based cAMP biosensor with nanomolar sensitivity that is out of reach for other sensors. To measure cAMP dynamics in the sperm flagellum, we generated transgenic mice and reveal that the hitherto methods determining total cAMP levels do not reflect changes in free cAMP levels. Moreover, cAMP dynamics in the midpiece and principal piece of the flagellum are distinctively different. The sole cAMP source in the flagellum is the soluble adenylate cyclase (SACY). Although bicarbonate-dependent SACY activity requires Ca2+, basal SACY activity is suppressed by Ca2+. Finally, we also applied the sensor to primary cilia. Our new cAMP biosensor features unique characteristics that allow gaining new insights into cAMP signaling and unravel the molecular mechanisms underlying ciliary function in vitro and in vivo. DOI:http://dx.doi.org/10.7554/eLife.14052.001 Cells can change the way they grow, move or develop in response to information from their environment. This information is first detected at the surface of the cell and then the information is relayed around the interior of the cell by signaling molecules known as “second messengers”. A molecule called cAMP is a well-known second messenger that is involved in many different signaling pathways. Therefore, the levels of cAMP in specific areas of the cell need to be precisely regulated to enable different signaling pathways to be activated at specific times and locations. Some cells have hair-like structures called cilia or flagella on their surface. Cilia and flagella are able to move the fluid that surrounds the cells or even move the cells themselves. The second messenger cAMP plays an essential role in making cilia move, but it is challenging to analyze the dynamics of cAMP – that this, how the levels of this molecule change over time – in these structures. The levels of cAMP in live cells can only be measured using fluorescent biosensors. Introducing these biosensors into specific cell structures is difficult and they are not sensitive enough to respond to low levels of cAMP. Furthermore, it is difficult to measure cAMP activity inside such tiny structures using these biosensors. Mukherjee, Jansen, Jikeli et al. now address some of these challenges by creating a new cAMP biosensor that has several unique features. Most importantly, it can respond to very low levels of cAMP, making it more sensitive than previous biosensors. Mukherjee et al. test this new biosensor in the flagella of sperm cells from mice, which reveals how the production of cAMP is regulated in the flagellum. The new biosensor also shows that different parts of the flagellum can have different cAMP dynamics. In the future, this new biosensor could be used to study cAMP in other structures and compartments within cells. DOI:http://dx.doi.org/10.7554/eLife.14052.002
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Affiliation(s)
- Shatanik Mukherjee
- Department of Molecular Sensory Systems, Center of Advanced European Studies and Research, Bonn, Germany
| | - Vera Jansen
- Minerva Max Planck Research Group, Molecular Physiology, Center of Advanced European Studies and Research, Bonn, Germany
| | - Jan F Jikeli
- Minerva Max Planck Research Group, Molecular Physiology, Center of Advanced European Studies and Research, Bonn, Germany
| | - Hussein Hamzeh
- Minerva Max Planck Research Group, Molecular Physiology, Center of Advanced European Studies and Research, Bonn, Germany
| | - Luis Alvarez
- Department of Molecular Sensory Systems, Center of Advanced European Studies and Research, Bonn, Germany
| | - Marco Dombrowski
- Minerva Max Planck Research Group, Molecular Physiology, Center of Advanced European Studies and Research, Bonn, Germany
| | - Melanie Balbach
- Department of Molecular Sensory Systems, Center of Advanced European Studies and Research, Bonn, Germany
| | - Timo Strünker
- Department of Molecular Sensory Systems, Center of Advanced European Studies and Research, Bonn, Germany.,Centrum für Reproduktionsmedizin und Andrologie, Universitätsklinikum Münster, Münster, Germany
| | - Reinhard Seifert
- Department of Molecular Sensory Systems, Center of Advanced European Studies and Research, Bonn, Germany
| | - U Benjamin Kaupp
- Department of Molecular Sensory Systems, Center of Advanced European Studies and Research, Bonn, Germany
| | - Dagmar Wachten
- Minerva Max Planck Research Group, Molecular Physiology, Center of Advanced European Studies and Research, Bonn, Germany
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22
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Goldschen-Ohm MP, Klenchin VA, White DS, Cowgill JB, Cui Q, Goldsmith RH, Chanda B. Structure and dynamics underlying elementary ligand binding events in human pacemaking channels. eLife 2016; 5:e20797. [PMID: 27858593 PMCID: PMC5115869 DOI: 10.7554/elife.20797] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 11/01/2016] [Indexed: 01/07/2023] Open
Abstract
Although molecular recognition is crucial for cellular signaling, mechanistic studies have relied primarily on ensemble measures that average over and thereby obscure underlying steps. Single-molecule observations that resolve these steps are lacking due to diffraction-limited resolution of single fluorophores at relevant concentrations. Here, we combined zero-mode waveguides with fluorescence resonance energy transfer (FRET) to directly observe binding at individual cyclic nucleotide-binding domains (CNBDs) from human pacemaker ion channels critical for heart and brain function. Our observations resolve the dynamics of multiple distinct steps underlying cyclic nucleotide regulation: a slow initial binding step that must select a 'receptive' conformation followed by a ligand-induced isomerization of the CNBD. X-ray structure of the apo CNBD and atomistic simulations reveal that the isomerization involves both local and global transitions. Our approach reveals fundamental mechanisms underpinning ligand regulation of pacemaker channels, and is generally applicable to weak-binding interactions governing a broad spectrum of signaling processes.
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Affiliation(s)
| | - Vadim A Klenchin
- Department of Neuroscience, University of Wisconsin-Madison, Madison, United States
| | - David S White
- Department of Neuroscience, University of Wisconsin-Madison, Madison, United States,Department of Chemistry, University of Wisconsin-Madison, Madison, United States
| | - John B Cowgill
- Department of Neuroscience, University of Wisconsin-Madison, Madison, United States
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, United States
| | - Randall H Goldsmith
- Department of Chemistry, University of Wisconsin-Madison, Madison, United States
| | - Baron Chanda
- Department of Neuroscience, University of Wisconsin-Madison, Madison, United States,Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, United States,
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23
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Fechner S, Alvarez L, Bönigk W, Müller A, Berger TK, Pascal R, Trötschel C, Poetsch A, Stölting G, Siegfried KR, Kremmer E, Seifert R, Kaupp UB. A K(+)-selective CNG channel orchestrates Ca(2+) signalling in zebrafish sperm. eLife 2015; 4:e07624. [PMID: 26650356 PMCID: PMC4749565 DOI: 10.7554/elife.07624] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 12/09/2015] [Indexed: 01/03/2023] Open
Abstract
Calcium in the flagellum controls sperm navigation. In sperm of marine invertebrates and mammals, Ca(2+) signalling has been intensely studied, whereas for fish little is known. In sea urchin sperm, a cyclic nucleotide-gated K(+) channel (CNGK) mediates a cGMP-induced hyperpolarization that evokes Ca(2+) influx. Here, we identify in sperm of the freshwater fish Danio rerio a novel CNGK family member featuring non-canonical properties. It is located in the sperm head rather than the flagellum and is controlled by intracellular pH, but not cyclic nucleotides. Alkalization hyperpolarizes sperm and produces Ca(2+) entry. Ca(2+) induces spinning-like swimming, different from swimming of sperm from other species. The "spinning" mode probably guides sperm into the micropyle, a narrow entrance on the surface of fish eggs. A picture is emerging of sperm channel orthologues that employ different activation mechanisms and serve different functions. The channel inventories probably reflect adaptations to species-specific challenges during fertilization.
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Affiliation(s)
- Sylvia Fechner
- Abteilung Molekulare Neurosensorik, Center of Advanced European Studies and Research, Bonn, Germany
| | - Luis Alvarez
- Abteilung Molekulare Neurosensorik, Center of Advanced European Studies and Research, Bonn, Germany
| | - Wolfgang Bönigk
- Abteilung Molekulare Neurosensorik, Center of Advanced European Studies and Research, Bonn, Germany
| | - Astrid Müller
- Abteilung Molekulare Neurosensorik, Center of Advanced European Studies and Research, Bonn, Germany
| | - Thomas K Berger
- Abteilung Molekulare Neurosensorik, Center of Advanced European Studies and Research, Bonn, Germany
| | - Rene Pascal
- Abteilung Molekulare Neurosensorik, Center of Advanced European Studies and Research, Bonn, Germany
| | | | - Ansgar Poetsch
- Lehrstuhl Biochemie der Pflanzen, Ruhr-Universität Bochum, Bochum, Germany
| | - Gabriel Stölting
- Institute of Complex Systems 4, Forschungszentrum Jülich, Jülich, Germany
| | - Kellee R Siegfried
- Biology Department, University of Massachusetts Boston, Boston, United States
| | - Elisabeth Kremmer
- Institut für Molekulare Immunologie, Helmholtz-Zentrum München, München, Germany
| | - Reinhard Seifert
- Abteilung Molekulare Neurosensorik, Center of Advanced European Studies and Research, Bonn, Germany
| | - U Benjamin Kaupp
- Abteilung Molekulare Neurosensorik, Center of Advanced European Studies and Research, Bonn, Germany
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24
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Kowal J, Chami M, Baumgartner P, Arheit M, Chiu PL, Rangl M, Scheuring S, Schröder GF, Nimigean CM, Stahlberg H. Ligand-induced structural changes in the cyclic nucleotide-modulated potassium channel MloK1. Nat Commun 2015; 5:3106. [PMID: 24469021 PMCID: PMC4086158 DOI: 10.1038/ncomms4106] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 12/13/2013] [Indexed: 12/25/2022] Open
Abstract
Cyclic nucleotide-modulated ion channels are important for signal transduction and pacemaking in eukaryotes. The molecular determinants of ligand gating in these channels are still unknown, mainly because of a lack of direct structural information. Here we report ligand-induced conformational changes in full-length MloK1, a cyclic nucleotide-modulated potassium channel from the bacterium Mesorhizobium loti, analysed by electron crystallography and atomic force microscopy. Upon cAMP binding, the cyclic nucleotide-binding domains move vertically towards the membrane, and directly contact the S1–S4 voltage sensor domains. This is accompanied by a significant shift and tilt of the voltage sensor domain helices. In both states, the inner pore-lining helices are in an ‘open’ conformation. We propose a mechanism in which ligand binding can favour pore opening via a direct interaction between the cyclic nucleotide-binding domains and voltage sensors. This offers a simple mechanistic hypothesis for the coupling between ligand gating and voltage sensing in eukaryotic HCN channels. The molecular determinants underlying ligand gating of cyclic nucleotide-modulated ion channels remain unclear. Kowal et al. determine the conformational changes underlying cAMP binding to the bacterial channel MloK1, and propose a mechanism for coupling of ligand gating and voltage sensing in eukaryotic HCN channels.
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Affiliation(s)
- Julia Kowal
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Mohamed Chami
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Paul Baumgartner
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Marcel Arheit
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | | | - Martina Rangl
- U1006 INSERM, Aix-Marseille Université, Parc Scientifique et Technologique de Luminy, 163 Avenue de Luminy, 13009 Marseille, France
| | - Simon Scheuring
- U1006 INSERM, Aix-Marseille Université, Parc Scientifique et Technologique de Luminy, 163 Avenue de Luminy, 13009 Marseille, France
| | - Gunnar F Schröder
- 1] Forschungszentrum Jülich, Institute of Complex Systems, ICS-6: Structural Biochemistry, 52425 Jülich, Germany [2] Department of Physics, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Crina M Nimigean
- Departments of Anesthesiology, Physiology and Biophysics, and Biochemistry, Weill Cornell Medical College, 1300 York Ave, New York, New York 10065, USA
| | - Henning Stahlberg
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
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25
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Pessoa J, Fonseca F, Furini S, Morais-Cabral JH. Determinants of ligand selectivity in a cyclic nucleotide-regulated potassium channel. ACTA ACUST UNITED AC 2015; 144:41-54. [PMID: 24981229 PMCID: PMC4076524 DOI: 10.1085/jgp.201311145] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Preference for cGMP binding to a cyclic nucleotide–binding domain can achieved by compensating for ligand dehydration or through retention of solvation waters in the bound state. Cyclic nucleotide–binding (CNB) domains regulate the activity of channels, kinases, exchange factors, and transcription factors. These proteins are highly variable in their ligand selectivity; some are highly selective for either cAMP or cGMP, whereas others are not. Several molecular determinants of ligand selectivity in CNB domains have been defined, but these do not provide a complete view of the selectivity mechanism. We performed a thorough analysis of the ligand-binding properties of mutants of the CNB domain from the MlotiK1 potassium channel. In particular, we defined which residues specifically favor cGMP or cAMP. Inversion of ligand selectivity, from favoring cAMP to favoring cGMP, was only achieved through a combination of three mutations in the ligand-binding pocket. We determined the x-ray structure of the triple mutant bound to cGMP and performed molecular dynamics simulations and a biochemical analysis of the effect of the mutations. We concluded that the increase in cGMP affinity and selectivity does not result simply from direct interactions between the nucleotide base and the amino acids introduced in the ligand-binding pocket residues. Rather, tighter cGMP binding over cAMP results from the polar chemical character of the mutations, from greater accessibility of water molecules to the ligand in the bound state, and from an increase in the structural flexibility of the mutated binding pocket.
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Affiliation(s)
- João Pessoa
- Instituto de Biologia Molecular e Celular and Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4150-180 Porto, PortugalInstituto de Biologia Molecular e Celular and Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4150-180 Porto, Portugal
| | - Fátima Fonseca
- Instituto de Biologia Molecular e Celular and Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4150-180 Porto, Portugal
| | - Simone Furini
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - João H Morais-Cabral
- Instituto de Biologia Molecular e Celular and Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4150-180 Porto, Portugal
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Börger C, Schünke S, Lecher J, Stoldt M, Winkhaus F, Kaupp UB, Willbold D. Resonance assignment of the ligand-free cyclic nucleotide-binding domain from the murine ion channel HCN2. BIOMOLECULAR NMR ASSIGNMENTS 2015; 9:243-246. [PMID: 25324217 DOI: 10.1007/s12104-014-9583-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 09/26/2014] [Indexed: 06/04/2023]
Abstract
Hyperpolarization activated and cyclic nucleotide-gated (HCN) ion channels as well as cyclic nucleotide-gated (CNG) ion channels are essential for the regulation of cardiac cells, neuronal excitability, and signaling in sensory cells. Both classes are composed of four subunits. Each subunit comprises a transmembrane region, intracellular N- and C-termini, and a C-terminal cyclic nucleotide-binding domain (CNBD). Binding of cyclic nucleotides to the CNBD promotes opening of both CNG and HCN channels. In case of CNG channels, binding of cyclic nucleotides to the CNBD is sufficient to open the channel. In contrast, HCN channels open upon membrane hyperpolarization and their activity is modulated by binding of cyclic nucleotides shifting the activation potential to more positive values. Although several high-resolution structures of CNBDs from HCN and CNG channels are available, the gating mechanism for murine HCN2 channel, which leads to the opening of the channel pore, is still poorly understood. As part of a structural investigation, here, we report the complete backbone and side chain resonance assignments of the murine HCN2 CNBD with part of the C-linker.
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Affiliation(s)
- Claudia Börger
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität, 40225, Düsseldorf, Germany
| | - Sven Schünke
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Justin Lecher
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität, 40225, Düsseldorf, Germany
| | - Matthias Stoldt
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität, 40225, Düsseldorf, Germany
| | - Friederike Winkhaus
- Department of Molecular Sensory Systems, Center of Advanced European Studies and Research, 53175, Bonn, Germany
- Pharma Technical Development Penzberg, Roche Diagnostics GmbH, Nonnenwald 2, 82377, Penzberg, Germany
| | - U Benjamin Kaupp
- Department of Molecular Sensory Systems, Center of Advanced European Studies and Research, 53175, Bonn, Germany
| | - Dieter Willbold
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany.
- Institut für Physikalische Biologie, Heinrich-Heine-Universität, 40225, Düsseldorf, Germany.
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Moran Y, Barzilai MG, Liebeskind BJ, Zakon HH. Evolution of voltage-gated ion channels at the emergence of Metazoa. J Exp Biol 2015; 218:515-25. [DOI: 10.1242/jeb.110270] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Voltage-gated ion channels are large transmembrane proteins that enable the passage of ions through their pore across the cell membrane. These channels belong to one superfamily and carry pivotal roles such as the propagation of neuronal and muscular action potentials and the promotion of neurotransmitter secretion in synapses. In this review, we describe in detail the current state of knowledge regarding the evolution of these channels with a special emphasis on the metazoan lineage. We highlight the contribution of the genomic revolution to the understanding of ion channel evolution and for revealing that these channels appeared long before the appearance of the first animal. We also explain how the elucidation of channel selectivity properties and function in non-bilaterian animals such as cnidarians (sea anemones, corals, jellyfish and hydroids) can contribute to the study of channel evolution. Finally, we point to open questions and future directions in this field of research.
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Affiliation(s)
- Yehu Moran
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Maya Gur Barzilai
- Department of Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Benjamin J. Liebeskind
- Department of Integrative Biology and Center for Computational Biology and Bioinformatics, University of Texas, Austin, TX 78712, USA
| | - Harold H. Zakon
- Department of Integrative Biology and Center for Computational Biology and Bioinformatics, University of Texas, Austin, TX 78712, USA
- Department of Neuroscience, University of Texas at Austin, TX 78712, USA
- Josephine Bay Paul Center for Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA
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Gofman Y, Schärfe C, Marks DS, Haliloglu T, Ben-Tal N. Structure, dynamics and implied gating mechanism of a human cyclic nucleotide-gated channel. PLoS Comput Biol 2014; 10:e1003976. [PMID: 25474149 PMCID: PMC4256070 DOI: 10.1371/journal.pcbi.1003976] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 10/09/2014] [Indexed: 11/18/2022] Open
Abstract
Cyclic nucleotide-gated (CNG) ion channels are nonselective cation channels, essential for visual and olfactory sensory transduction. Although the channels include voltage-sensor domains (VSDs), their conductance is thought to be independent of the membrane potential, and their gating regulated by cytosolic cyclic nucleotide-binding domains. Mutations in these channels result in severe, degenerative retinal diseases, which remain untreatable. The lack of structural information on CNG channels has prevented mechanistic understanding of disease-causing mutations, precluded structure-based drug design, and hampered in silico investigation of the gating mechanism. To address this, we built a 3D model of the cone tetrameric CNG channel, based on homology to two distinct templates with known structures: the transmembrane (TM) domain of a bacterial channel, and the cyclic nucleotide-binding domain of the mouse HCN2 channel. Since the TM-domain template had low sequence-similarity to the TM domains of the CNG channels, and to reconcile conflicts between the two templates, we developed a novel, hybrid approach, combining homology modeling with evolutionary coupling constraints. Next, we used elastic network analysis of the model structure to investigate global motions of the channel and to elucidate its gating mechanism. We found the following: (i) In the main mode of motion, the TM and cytosolic domains counter-rotated around the membrane normal. We related this motion to gating, a proposition that is supported by previous experimental data, and by comparison to the known gating mechanism of the bacterial KirBac channel. (ii) The VSDs could facilitate gating (supplementing the pore gate), explaining their presence in such 'voltage-insensitive' channels. (iii) Our elastic network model analysis of the CNGA3 channel supports a modular model of allosteric gating, according to which protein domains are quasi-independent: they can move independently, but are coupled to each other allosterically.
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Affiliation(s)
- Yana Gofman
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv, Israel
| | - Charlotta Schärfe
- Center for Bioinformatics, Quantitative Biology Center, and Department of Computer Science, Tübingen University, Tübingen, Germany
- Department of Systems Biology, Harvard University, Boston, Massachusetts, United States of America
| | - Debora S. Marks
- Department of Systems Biology, Harvard University, Boston, Massachusetts, United States of America
| | - Turkan Haliloglu
- Polymer Research Centre and Chemical Engineering Department, Bogazici University, Bebek-Istanbul, Turkey
| | - Nir Ben-Tal
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv, Israel
- * E-mail:
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Double electron-electron resonance reveals cAMP-induced conformational change in HCN channels. Proc Natl Acad Sci U S A 2014; 111:9816-21. [PMID: 24958877 DOI: 10.1073/pnas.1405371111] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Binding of 3',5'-cyclic adenosine monophosphate (cAMP) to hyperpolarization-activated cyclic nucleotide-gated (HCN) ion channels regulates their gating. cAMP binds to a conserved intracellular cyclic nucleotide-binding domain (CNBD) in the channel, increasing the rate and extent of activation of the channel and shifting activation to less hyperpolarized voltages. The structural mechanism underlying this regulation, however, is unknown. We used double electron-electron resonance (DEER) spectroscopy to directly map the conformational ensembles of the CNBD in the absence and presence of cAMP. Site-directed, double-cysteine mutants in a soluble CNBD fragment were spin-labeled, and interspin label distance distributions were determined using DEER. We found motions of up to 10 Å induced by the binding of cAMP. In addition, the distributions were narrower in the presence of cAMP. Continuous-wave electron paramagnetic resonance studies revealed changes in mobility associated with cAMP binding, indicating less conformational heterogeneity in the cAMP-bound state. From the measured DEER distributions, we constructed a coarse-grained elastic-network structural model of the cAMP-induced conformational transition. We find that binding of cAMP triggers a reorientation of several helices within the CNBD, including the C-helix closest to the cAMP-binding site. These results provide a basis for understanding how the binding of cAMP is coupled to channel opening in HCN and related channels.
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30
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Seok SH, Im H, Won HS, Seo MD, Lee YS, Yoon HJ, Cha MJ, Park JY, Lee BJ. Structures of inactive CRP species reveal the atomic details of the allosteric transition that discriminates cyclic nucleotide second messengers. ACTA ACUST UNITED AC 2014; 70:1726-42. [PMID: 24914983 DOI: 10.1107/s139900471400724x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 04/01/2014] [Indexed: 11/10/2022]
Abstract
The prokaryotic global transcription factor CRP has been considered to be an ideal model for in-depth study of both the allostery of the protein and the differential utilization of the homologous cyclic nucleotide second messengers cAMP and cGMP. Here, atomic details from the crystal structures of two inactive CRP species, an apo form and a cGMP-bound form, in comparison with a known active conformation, the cAMP-CRP complex, provide macroscopic and microscopic insights into CRP allostery, which is coupled to specific discrimination between the two effectors. The cAMP-induced conformational transition, including dynamic fluctuations, can be driven by the fundamental folding forces that cause water-soluble globular proteins to construct an optimized hydrophobic core, including secondary-structure formation. The observed conformational asymmetries underlie a negative cooperativity in the sequential binding of cyclic nucleotides and a stepwise manner of binding with discrimination between the effector molecules. Additionally, the finding that cGMP, which is specifically recognized in a syn conformation, induces an inhibitory conformational change, rather than a null effect, on CRP supports the intriguing possibility that cGMP signalling could be widely utilized in prokaryotes, including in aggressive inhibition of CRP-like proteins.
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Affiliation(s)
- Seung-Hyeon Seok
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Hookang Im
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Hyung-Sik Won
- Department of Biotechnology, RIBHS and RIID, College of Biomedical and Health Science, Konkuk University, Chungju, Chungbuk 380-701, Republic of Korea
| | - Min-Duk Seo
- College of Pharmacy, Ajou University, Suwon, Kyeonggi 443-749, Republic of Korea
| | - Yoo-Sup Lee
- Department of Biotechnology, RIBHS and RIID, College of Biomedical and Health Science, Konkuk University, Chungju, Chungbuk 380-701, Republic of Korea
| | - Hye-Jin Yoon
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea
| | - Min-Jeong Cha
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Jin-Young Park
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Bong-Jin Lee
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
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31
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Family of prokaryote cyclic nucleotide-modulated ion channels. Proc Natl Acad Sci U S A 2014; 111:7855-60. [PMID: 24821777 DOI: 10.1073/pnas.1401917111] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Cyclic nucleotide-modulated ion channels are molecular pores that mediate the passage of ions across the cell membrane in response to cAMP or GMP. Structural insight into this class of ion channels currently comes from a related homolog, MloK1, that contains six transmembrane domains and a cytoplasmic cyclic nucleotide binding domain. However, unlike eukaryote hyperpolarization-activated cyclic nucleotide-modulated (HCN) and cyclic nucleotide-gated (CNG) channels, MloK1 lacks a C-linker region, which critically contributes to the molecular coupling between ligand binding and channel opening. In this study, we report the identification and characterization of five previously unidentified prokaryote homologs with high sequence similarity (24-32%) to eukaryote HCN and CNG channels and that contain a C-linker region. Biochemical characterization shows that two homologs, termed AmaK and SthK, can be expressed and purified as detergent-solubilized protein from Escherichia coli membranes. Expression of SthK channels in Xenopus laevis oocytes and functional characterization using the patch-clamp technique revealed that the channels are gated by cAMP, but not cGMP, are highly selective for K(+) ions over Na(+) ions, generate a large unitary conductance, and are only weakly voltage dependent. These properties resemble essential properties of various eukaryote HCN or CNG channels. Our results contribute to an understanding of the evolutionary origin of cyclic nucleotide-modulated ion channels and pave the way for future structural and functional studies.
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32
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Cyclic dinucleotides bind the C-linker of HCN4 to control channel cAMP responsiveness. Nat Chem Biol 2014; 10:457-62. [PMID: 24776929 DOI: 10.1038/nchembio.1521] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 03/27/2014] [Indexed: 02/03/2023]
Abstract
cAMP mediates autonomic regulation of heart rate by means of hyperpolarization-activated cyclic nucleotide-gated (HCN) channels, which underlie the pacemaker current If. cAMP binding to the C-terminal cyclic nucleotide binding domain enhances HCN open probability through a conformational change that reaches the pore via the C-linker. Using structural and functional analysis, we identified a binding pocket in the C-linker of HCN4. Cyclic dinucleotides, an emerging class of second messengers in mammals, bind the C-linker pocket (CLP) and antagonize cAMP regulation of the channel. Accordingly, cyclic dinucleotides prevent cAMP regulation of If in sinoatrial node myocytes, reducing heart rate by 30%. Occupancy of the CLP hence constitutes an efficient mechanism to hinder β-adrenergic stimulation on If. Our results highlight the regulative role of the C-linker and identify a potential drug target in HCN4. Furthermore, these data extend the signaling scope of cyclic dinucleotides in mammals beyond their first reported role in innate immune system.
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33
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McCoy JG, Rusinova R, Kim DM, Kowal J, Banerjee S, Jaramillo Cartagena A, Thompson AN, Kolmakova-Partensky L, Stahlberg H, Andersen OS, Nimigean CM. A KcsA/MloK1 chimeric ion channel has lipid-dependent ligand-binding energetics. J Biol Chem 2014; 289:9535-46. [PMID: 24515111 DOI: 10.1074/jbc.m113.543389] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Cyclic nucleotide-modulated ion channels play crucial roles in signal transduction in eukaryotes. The molecular mechanism by which ligand binding leads to channel opening remains poorly understood, due in part to the lack of a robust method for preparing sufficient amounts of purified, stable protein required for structural and biochemical characterization. To overcome this limitation, we designed a stable, highly expressed chimeric ion channel consisting of the transmembrane domains of the well characterized potassium channel KcsA and the cyclic nucleotide-binding domains of the prokaryotic cyclic nucleotide-modulated channel MloK1. This chimera demonstrates KcsA-like pH-sensitive activity which is modulated by cAMP, reminiscent of the dual modulation in hyperpolarization-activated and cyclic nucleotide-gated channels that display voltage-dependent activity that is also modulated by cAMP. Using this chimeric construct, we were able to measure for the first time the binding thermodynamics of cAMP to an intact cyclic nucleotide-modulated ion channel using isothermal titration calorimetry. The energetics of ligand binding to channels reconstituted in lipid bilayers are substantially different from those observed in detergent micelles, suggesting that the conformation of the chimera's transmembrane domain is sensitive to its (lipid or lipid-mimetic) environment and that ligand binding induces conformational changes in the transmembrane domain. Nevertheless, because cAMP on its own does not activate these chimeric channels, cAMP binding likely has a smaller energetic contribution to gating than proton binding suggesting that there is only a small difference in cAMP binding energy between the open and closed states of the channel.
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CRIS-a novel cAMP-binding protein controlling spermiogenesis and the development of flagellar bending. PLoS Genet 2013; 9:e1003960. [PMID: 24339785 PMCID: PMC3854790 DOI: 10.1371/journal.pgen.1003960] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 09/30/2013] [Indexed: 12/17/2022] Open
Abstract
The second messengers cAMP and cGMP activate their target proteins by binding to a conserved cyclic nucleotide-binding domain (CNBD). Here, we identify and characterize an entirely novel CNBD-containing protein called CRIS (cyclic nucleotide receptor involved in sperm function) that is unrelated to any of the other members of this protein family. CRIS is exclusively expressed in sperm precursor cells. Cris-deficient male mice are either infertile due to a lack of sperm resulting from spermatogenic arrest, or subfertile due to impaired sperm motility. The motility defect is caused by altered Ca(2+) regulation of flagellar beat asymmetry, leading to a beating pattern that is reminiscent of sperm hyperactivation. Our results suggest that CRIS interacts during spermiogenesis with Ca(2+)-regulated proteins that--in mature sperm--are involved in flagellar bending.
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35
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Cukkemane A, Baldus M. Characterization of a cyclic nucleotide-activated K(+) channel and its lipid environment by using solid-state NMR spectroscopy. Chembiochem 2013; 14:1789-98. [PMID: 23956185 DOI: 10.1002/cbic.201300182] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Indexed: 01/31/2023]
Abstract
Voltage-gated ion channels are large tetrameric multidomain membrane proteins that play crucial roles in various cellular transduction pathways. Because of their large size and domain-related mobility, structural characterization has proved challenging. We analyzed high-resolution solid-state NMR data on different isotope-labeled protein constructs of a bacterial cyclic nucleotide-activated K(+) channel (MlCNG) in lipid bilayers. We could identify the different subdomains of the 4×355 residue protein, such as the voltage-sensing domain and the cyclic nucleotide binding domain. Comparison to ssNMR data obtained on isotope-labeled cell membranes suggests a tight association of negatively charged lipids to the channel. We detected spectroscopic polymorphism that extends beyond the ligand binding site, and the corresponding protein segments have been associated with mutant channel types in eukaryotic systems. These findings illustrate the potential of ssNMR for structural investigations on large membrane-embedded proteins, even in the presence of local disorder.
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Affiliation(s)
- Abhishek Cukkemane
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 Utrecht (The Netherlands)
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36
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Unstructured to structured transition of an intrinsically disordered protein peptide in coupling Ca²⁺-sensing and SK channel activation. Proc Natl Acad Sci U S A 2013; 110:4828-33. [PMID: 23487779 DOI: 10.1073/pnas.1220253110] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Most proteins, such as ion channels, form well-organized 3D structures to carry out their specific functions. A typical voltage-gated potassium channel subunit has six transmembrane segments (S1-S6) to form the voltage-sensing domain and the pore domain. Conformational changes of these domains result in opening of the channel pore. Intrinsically disordered (ID) proteins/peptides are considered equally important for the protein functions. However, it is difficult to explore the structural features underlying the functions of ID proteins/peptides by conventional methods, such as X-ray crystallography, because of the flexibility of their secondary structures. Unlike voltage-gated potassium channels, families of small- and intermediate-conductance Ca(2+)-activated potassium (SK/IK) channels with important roles in regulating membrane excitability are activated exclusively by Ca(2+)-bound calmodulin (CaM). Upon binding of Ca(2+) to CaM, a 2 × 2 structure forms between CaM and the CaM-binding domain. A channel fragment that connects S6 and the CaM-binding domain is not visible in the protein crystal structure, suggesting that this fragment is an ID fragment. Here we show that the conformation of the ID fragment in SK channels becomes readily identifiable in the presence of NS309, the most potent compound that potentiates the channel activities. This well-defined conformation of the ID fragment, stabilized by NS309, increases the channel open probability at a given Ca(2+) concentration. Our results demonstrate that the ID fragment, itself a target for drugs modulating SK channel activities, plays a unique role in coupling Ca(2+) sensing by CaM and mechanical opening of SK channels.
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37
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Eberhardt RY, Bartholdson SJ, Punta M, Bateman A. The SHOCT domain: a widespread domain under-represented in model organisms. PLoS One 2013; 8:e57848. [PMID: 23451277 PMCID: PMC3581485 DOI: 10.1371/journal.pone.0057848] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 01/29/2013] [Indexed: 11/18/2022] Open
Abstract
We have identified a new protein domain, which we have named the SHOCT domain (Short C-terminal domain). This domain is widespread in bacteria with over a thousand examples. But we found it is missing from the most commonly studied model organisms, despite being present in closely related species. It's predominantly C-terminal location, co-occurrence with numerous other domains and short size is reminiscent of the Gram-positive anchor motif, however it is present in a much wider range of species. We suggest several hypotheses about the function of SHOCT, including oligomerisation and nucleic acid binding. Our initial experiments do not support its role as an oligomerisation domain.
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Affiliation(s)
- Ruth Y Eberhardt
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom.
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38
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Peuker S, Cukkemane A, Held M, Noé F, Kaupp UB, Seifert R. Kinetics of ligand-receptor interaction reveals an induced-fit mode of binding in a cyclic nucleotide-activated protein. Biophys J 2013; 104:63-74. [PMID: 23332059 DOI: 10.1016/j.bpj.2012.11.3816] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Revised: 11/14/2012] [Accepted: 11/27/2012] [Indexed: 12/17/2022] Open
Abstract
Many receptors and ion channels are activated by ligands. One key question concerns the binding mechanism. Does the ligand induce conformational changes in the protein via the induced-fit mechanism? Or does the protein preexist as an ensemble of conformers and the ligand selects the most complementary one, via the conformational selection mechanism? Here, we study ligand binding of a tetrameric cyclic nucleotide-gated channel from Mesorhizobium loti and of its monomeric binding domain (CNBD) using rapid mixing, mutagenesis, and structure-based computational biology. Association rate constants of ∼10(7) M(-1) s(-1) are compatible with diffusion-limited binding. Ligand binding to the full-length CNG channel and the isolated CNBD differ, revealing allosteric control of the CNBD by the effector domain. Finally, mutagenesis of allosteric residues affects only the dissociation rate constant, suggesting that binding follows the induced-fit mechanism. This study illustrates the strength of combining mutational, kinetic, and computational approaches to unravel important mechanistic features of ligand binding.
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Affiliation(s)
- Sebastian Peuker
- Department of Molecular Sensory Systems, Center of Advanced European Studies and Research, Bonn, Germany
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39
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Chen T, Zhu L, Zhou Y, Pi B, Liu X, Deng G, Zhang R, Wang Y, Wu Z, Han M, Luo X, Ning Q. KCTD9 contributes to liver injury through NK cell activation during hepatitis B virus-induced acute-on-chronic liver failure. Clin Immunol 2013; 146:207-16. [PMID: 23376586 DOI: 10.1016/j.clim.2012.12.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 12/18/2012] [Accepted: 12/19/2012] [Indexed: 12/11/2022]
Abstract
We explored the expression of a newly identified potassium channel tetramerisation domain containing 9 (KCTD9) protein in 113 blood and 81 liver samples, from patients with mild chronic hepatitis B (CHB) or HBV-induced acute-on-chronic liver failure (HBV-ACLF). KCTD9 was highly expressed in peripheral and hepatic NK cells from HBV-ACLF patients compared with mild CHB patients, and this correlated positively with the severity of liver injury. The role of KCTD9 was further investigated in NK92 cells in vitro. KCTD9 overexpressed NK92 cells exhibited a marked increase in CD69 expression, cytotoxicity, IFN-γ secretion and a significant decrease in NKG2A receptor expression. Inhibition of KCTD9 by shRNA resulted in reduced cytotoxic function. These results suggest the involvement of KCTD9 in NK cell activation and provide additional insight into a potential therapeutic target for molecular manipulation for HBV-ACLF patients.
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Affiliation(s)
- Tao Chen
- Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
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Robertson JWF, Kasianowicz JJ, Banerjee S. Analytical Approaches for Studying Transporters, Channels and Porins. Chem Rev 2012; 112:6227-49. [DOI: 10.1021/cr300317z] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Joseph W. F. Robertson
- Physical Measurement Laboratory,
National Institute of Standards and Technology, Gaithersburg, Maryland
20899, United States
| | - John J. Kasianowicz
- Physical Measurement Laboratory,
National Institute of Standards and Technology, Gaithersburg, Maryland
20899, United States
| | - Soojay Banerjee
- National
Institute of Neurological
Disorders and Stroke, Bethesda, Maryland 20824, United States
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41
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Cukkemane A, Nand D, Gradmann S, Weingarth M, Kaupp UB, Baldus M. Solid-state NMR [13C,15N] resonance assignments of the nucleotide-binding domain of a bacterial cyclic nucleotide-gated channel. BIOMOLECULAR NMR ASSIGNMENTS 2012; 6:225-9. [PMID: 22302441 PMCID: PMC3438399 DOI: 10.1007/s12104-012-9363-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 01/17/2012] [Indexed: 05/21/2023]
Abstract
Channels regulated by cyclic nucleotides are key signalling proteins in several biological pathways. The regulatory aspect is conferred by a C-terminal cyclic nucleotide-binding domain (CNBD). We report resonance assignments of the CNBD of a bacterial mlCNG channel obtained using 2D and 3D solid-state NMR under Magic-angle Spinning conditions. A secondary chemical shift analysis of the 141 residue protein suggests a three-dimensional fold seen in earlier X-ray and solution-state NMR work and points to spectroscopic polymorphism for a selected set of resonances.
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Affiliation(s)
- Abhishek Cukkemane
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Deepak Nand
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Sabine Gradmann
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Markus Weingarth
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - U. Benjamin Kaupp
- Center of Advanced European Studies and Research (Caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Marc Baldus
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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42
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Nache V, Zimmer T, Wongsamitkul N, Schmauder R, Kusch J, Reinhardt L, Bönigk W, Seifert R, Biskup C, Schwede F, Benndorf K. Differential regulation by cyclic nucleotides of the CNGA4 and CNGB1b subunits in olfactory cyclic nucleotide-gated channels. Sci Signal 2012; 5:ra48. [PMID: 22786723 DOI: 10.1126/scisignal.2003110] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Olfactory cyclic nucleotide-gated (CNG) ion channels are essential contributors to signal transduction of olfactory sensory neurons. The activity of the channels is controlled by the cyclic nucleotides guanosine 3',5'-monophosphate (cGMP) and adenosine 3',5'-monophosphate (cAMP). The olfactory CNG channels are composed of two CNGA2 subunits, one CNGA4 and one CNGB1b subunit, each containing a cyclic nucleotide-binding domain. Using patch-clamp fluorometry, we measured ligand binding and channel activation simultaneously and showed that cGMP activated olfactory CNG channels not only by binding to the two CNGA2 subunits but also by binding to the CNGA4 subunit. In a channel in which the CNGA2 subunits were compromised for ligand binding, cGMP binding to CNGA4 was sufficient to partly activate the channel. In contrast, in heterotetrameric channels, the CNGB1b subunit did not bind cGMP, but channels with this subunit showed activation by cAMP. Thus, the modulatory subunits participate actively in translating ligand binding to activation of heterotetrameric olfactory CNG channels and enable the channels to differentiate between cyclic nucleotides.
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Affiliation(s)
- Vasilica Nache
- Institute of Physiology II, University Hospital Jena, Friedrich-Schiller-University Jena, D-07740 Jena, Germany
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43
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Structural, biochemical, and functional characterization of the cyclic nucleotide binding homology domain from the mouse EAG1 potassium channel. J Mol Biol 2012; 423:34-46. [PMID: 22732247 DOI: 10.1016/j.jmb.2012.06.025] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Revised: 06/14/2012] [Accepted: 06/16/2012] [Indexed: 11/21/2022]
Abstract
KCNH channels are voltage-gated potassium channels with important physiological functions. In these channels, a C-terminal cytoplasmic region, known as the cyclic nucleotide binding homology (CNB-homology) domain displays strong sequence similarity to cyclic nucleotide binding (CNB) domains. However, the isolated domain does not bind cyclic nucleotides. Here, we report the X-ray structure of the CNB-homology domain from the mouse EAG1 channel. Through comparison with the recently determined structure of the CNB-homology domain from the zebrafish ELK (eag-like K(+)) channel and the CNB domains from the MlotiK1 and HCN (hyperpolarization-activated cyclic nucleotide-gated) potassium channels, we establish the structural features of CNB-homology domains that explain the low affinity for cyclic nucleotides. Our structure establishes that the "self-liganded" conformation, where two residues of the C-terminus of the domain are bound in an equivalent position to cyclic nucleotides in CNB domains, is a conserved feature of CNB-homology domains. Importantly, we provide biochemical evidence that suggests that there is also an unliganded conformation where the C-terminus of the domain peels away from its bound position. A functional characterization of this unliganded conformation reveals a role of the CNB-homology domain in channel gating.
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44
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Gushchin IY, Gordeliy VI, Grudinin S. A novel dimerization interface of cyclic nucleotide binding domain, which is disrupted in presence of cAMP: implications for CNG channels gating. J Mol Model 2012; 18:4053-60. [PMID: 22476580 DOI: 10.1007/s00894-012-1404-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2011] [Accepted: 03/07/2012] [Indexed: 11/30/2022]
Abstract
Cyclic nucleotide binding domain (CNBD) is a ubiquitous domain of effector proteins involved in signalling cascades of prokaryota and eukaryota. CNBD activation by cyclic nucleotide monophosphate (cNMP) is studied well in the case of several proteins. However, this knowledge is hardly applicable to cNMP-modulated cation channels. Despite the availability of CNBD crystal structures of bacterial cyclic nucleotide-gated (CNG) and mammalian hyperpolarization-activated cyclic nucleotide-modulated (HCN) channels in presence and absence of the cNMP, the full understanding of CNBD conformational changes during activation is lacking. Here, we describe a novel CNBD dimerization interface found in crystal structures of bacterial CNG channel MlotiK1 and mammalian cAMP-activated guanine nucleotide-exchange factor Epac2. Molecular dynamics simulations show that the found interface is stable on the studied timescale of 100 ns, in contrast to the dimerization interface, reported previously. Comparisons with cN-bound structures of CNBD show that the dimerization is incompatible with cAMP binding. Thus, the cAMP-dependent monomerization of CNBD may be an alternative mechanism of the cAMP sensing. Based on these findings, we propose a model of the bacterial CNG channel modulation by cAMP.
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Affiliation(s)
- Ivan Y Gushchin
- Institut de Biologie Structurale Jean-Pierre Ebel, Université Joseph Fourier - Grenoble 1, Grenoble, France
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45
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Marques-Carvalho MJ, Morais-Cabral JH. Crystallization and preliminary X-ray crystallographic characterization of a cyclic nucleotide-binding homology domain from the mouse EAG potassium channel. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:337-9. [PMID: 22442238 PMCID: PMC3310546 DOI: 10.1107/s1744309112004216] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Accepted: 02/01/2012] [Indexed: 11/10/2022]
Abstract
The members of the family of voltage-gated KCNH potassium channels play important roles in cardiac and neuronal repolarization, tumour proliferation and hormone secretion. These channels have a C-terminal cytoplasmic domain which is homologous to cyclic nucleotide-binding domains (CNB-homology domains), but it has been demonstrated that channel function is not affected by cyclic nucleotides and that the domain does not bind nucleotides in vitro. Here, the crystallization and preliminary crystallographic analysis of a CNB-homology domain from a member of the KCNH family, the mouse EAG channel, is reported. X-ray diffraction data were collected to 2.2 Å resolution and the crystal belonged to the hexagonal space group P3(1)21.
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Affiliation(s)
- Maria João Marques-Carvalho
- IBMC – Instituto de Biologia Molecular e Celular, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
- ICBAS – Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Largo Professor Abel Salazar 2, 4099-003 Porto, Portugal
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46
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Evolutionary genomics reveals the premetazoan origin of opposite gating polarity in animal-type voltage-gated ion channels. Genomics 2012; 99:241-5. [PMID: 22326743 DOI: 10.1016/j.ygeno.2012.01.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Revised: 01/21/2012] [Accepted: 01/26/2012] [Indexed: 11/22/2022]
Abstract
Electrical signaling in animals ensures the rapid and accurate transmission of information, often carried by voltage-gated Na(+), Ca(2+) and K(+) channels that are activated by membrane depolarization. In heart and neurons, a distinct type of ion channel called the hyperpolarization-activated, cyclic nucleotide-regulated (HCN) channel is activated by membrane hyperpolarization. Recent genomic studies have revealed that animal-type voltage-gated Na(+) channels (Liebeskind BJ, et al. 2011. Proc Natl Acad Sci U S A. 108:9154) had evolved in choanoflagellates, one of the unicellular relatives of animals. To date, HCN channels have been considered to be animal-specific. Here, we demonstrate the presence of an HCN channel homolog (SroHCN) in the choanoflagellate protist Salpingoeca rosetta. SroHCN contains highly conserved functional domains and sequence motifs that are correlated with the unique biophysical activities of HCN channels. These findings provide novel genomic insights into the evolution of complex electrical signaling before the emergence of multicellular animals.
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47
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Structure of the carboxy-terminal region of a KCNH channel. Nature 2012; 481:530-3. [PMID: 22230959 PMCID: PMC3267858 DOI: 10.1038/nature10735] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2011] [Accepted: 11/23/2011] [Indexed: 11/15/2022]
Abstract
The KCNH family of ion channels, comprising ether-à-go-go (EAG), EAG-related gene (ERG), and EAG-like (ELK) K+ channel subfamilies, is crucial for repolarization of the cardiac action potential1, regulation of neuronal excitability2, and proliferation of tumor cells3. The C-terminal region of KCNH channels contains a cyclic nucleotide-binding homology domain (CNBHD) and C-linker that couples the CNBHD to the pore4. The C-linker/CNBHD is essential for proper function and trafficking of ion channels in the KCNH family5–9. However, despite the importance of the C-linker/CNBHD for the function of KCNH channels, the structural basis of ion channel regulation by the C-linker/CNBHD is unknown. Here we report the crystal structure of the C-linker/CNBHD of zebrafish ELK channels at 2.2 Å resolution. While the overall structure of the C-linker/CNBHD of zELK channels is similar to the cyclic nucleotide-binding domain (CNBD) structure of the related HCN channels10, there are dramatic differences. Unlike the CNBD of HCN, the CNBHD of zELK displays a negatively charged electrostatic profile that explains the lack of binding and regulation of KCNH channels by cyclic nucleotides4,11. Instead of cyclic nucleotide, the binding pocket is occupied by a short β-strand. Mutations of the β-strand shift the voltage dependence of activation to more depolarized voltages, implicating the β-strand as an intrinsic ligand for the CNBHD of zELK channels. In both zELK and HCN channels the C-linker is the site of virtually all of the intersubunit interactions in the C-terminal region. However, in the zELK structure there is a reorientation in the C-linker so the subunits form dimers instead of tetramers as observed in HCN channels. These results provide a structural framework for understanding the regulation of ion channels in the KCNH family by the C-linker/CNBHD and may guide the design of specific drugs.
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48
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Malcolm HR, Elmore DE, Maurer JA. Mechanosensitive behavior of bacterial cyclic nucleotide gated (bCNG) ion channels: Insights into the mechanism of channel gating in the mechanosensitive channel of small conductance superfamily. Biochem Biophys Res Commun 2011; 417:972-6. [PMID: 22206667 DOI: 10.1016/j.bbrc.2011.12.049] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 12/13/2011] [Indexed: 10/14/2022]
Abstract
We have recently identified and characterized the bacterial cyclic nucleotide gated (bCNG) subfamily of the larger mechanosensitive channel of small conductance (MscS) superfamily of ion channels. The channel domain of bCNG channels exhibits significant sequence homology to the mechanosensitive subfamily of MscS in the regions that have previously been used as a hallmark for channels that gate in response to mechanical stress. However, we have previously demonstrated that three of these channels are unable to rescue Escherichiacoli from osmotic downshock. Here, we examine an additional nine bCNG homologues and further demonstrate that the full-length bCNG channels are unable to rescue E. coli from hypoosmotic stress. However, limited mechanosensation is restored upon removal of the cyclic nucleotide binding domain. This indicates that the C-terminal domain of the MscS superfamily can drive channel gating and further highlight the ability of a superfamily of ion channels to be gated by multiple stimuli.
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Affiliation(s)
- Hannah R Malcolm
- Department of Chemistry, Washington University in St. Louis, MO 63130, United States
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49
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Gating of the MlotiK1 potassium channel involves large rearrangements of the cyclic nucleotide-binding domains. Proc Natl Acad Sci U S A 2011; 108:20802-7. [PMID: 22135457 DOI: 10.1073/pnas.1111149108] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cyclic nucleotide-regulated ion channels are present in bacteria, plants, vertebrates, and humans. In higher organisms, they are closely involved in signaling networks of vision and olfaction. Binding of cAMP or cGMP favors the activation of these ion channels. Despite a wealth of structural and studies, there is a lack of structural data describing the gating process in a full-length cyclic nucleotide-regulated channel. We used high-resolution atomic force microscopy (AFM) to directly observe the conformational change of the membrane embedded bacterial cyclic nucleotide-regulated channel MlotiK1. In the nucleotide-bound conformation, the cytoplasmic cyclic nucleotide-binding (CNB) domains of MlotiK1 are disposed in a fourfold symmetric arrangement forming a pore-like vestibule. Upon nucleotide-unbinding, the four CNB domains undergo a large rearrangement, stand up by ∼1.7 nm, and adopt a structurally variable grouped conformation that closes the cytoplasmic vestibule. This fully reversible conformational change provides insight into how CNB domains rearrange when regulating the potassium channel.
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50
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Wong WF, Chan KSC, Michaleski MS, Haesler A, Young EC. Ligand-binding domain subregions contributing to bimodal agonism in cyclic nucleotide-gated channels. ACTA ACUST UNITED AC 2011; 137:591-603. [PMID: 21624949 PMCID: PMC3105518 DOI: 10.1085/jgp.201010560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Cyclic nucleotide–gated (CNG) channels bind cGMP or cAMP in a cytoplasmic ligand–binding domain (BD), and this binding typically increases channel open probability (Po) without inducing desensitization. However, the catfish CNGA2 (fCNGA2) subtype exhibits bimodal agonism, whereby steady-state Po increases with initial cGMP-binding events (“pro” action) up to a maximum of 0.4, but decreases with subsequent cGMP-binding events (“con” action) occurring at concentrations >3 mM. We sought to clarify if low pro-action efficacy was either necessary or sufficient for con action to operate. To find BD residues responsible for con action or low pro-action efficacy or both, we constructed chimeric CNG channels: subregions of the fCNGA2 BD were substituted with corresponding sequence from the rat CNGA4 BD, which does not support con action. Constructs were expressed in frog oocytes and tested by patch clamp of cell-free membranes. For nearly all BD elements, we found at least one construct where replacing that element preserved robust con action, with a ratio of steady-state conductances, g(10 mM cGMP)/g(3 mM cGMP) < 0.75. When all of the BD sequence C terminal of strand β6 was replaced, g(10 mM cGMP)/g(3 mM cGMP) was increased to 0.95 ± 0.05 (n = 7). However, this apparent attenuation of con action could be explained by an increase in the efficacy of pro action for all agonists, controlled by a conserved “phosphate-binding cassette” motif that contacts ligand; this produces high Po values that are less sensitive to shifts in gating equilibrium. In contrast, substituting a single valine in the N-terminal helix αA abolished con action (g(30 mM cGMP)/g(3 mM cGMP) increased to 1.26 ± 0.24; n = 7) without large increases in pro-action efficacy. Our work dissociates the two functional features of low pro-action efficacy and con action, and moreover identifies a separate structural determinant for each.
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Affiliation(s)
- Wai-Fung Wong
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
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