1
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Tiwari PB, Kamgar-Dayhoff P, Tiwari P, McKillop MI, Brelidze TI. Use of Surface Plasmon Resonance Technique for Studies of Inter-domain Interactions in Ion Channels. Methods Mol Biol 2024; 2796:105-118. [PMID: 38856898 PMCID: PMC11225882 DOI: 10.1007/978-1-0716-3818-7_7] [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] [Indexed: 06/11/2024]
Abstract
Ion channels are transmembrane proteins essential for cellular functions and are important drug targets. Surface plasmon resonance (SPR) is a powerful technique for investigating protein-protein and protein-small molecule ligand interactions. SPR has been underutilized for studies of ion channels, even though it could provide a wealth of information on the mechanisms of ion channel regulation and aid in ion channel drug discovery. Here we provide a detailed description of the use of SPR technology for investigating inter-domain interactions in KCNH potassium-selective and voltage-gated ion channels.
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Affiliation(s)
- Purushottam B Tiwari
- Department of Oncology, Georgetown University Medical Center, Washington, DC, USA
| | - Pareesa Kamgar-Dayhoff
- Department of Pharmacology and Physiology, Georgetown University Medical Center, Washington, DC, USA
| | - Prakriti Tiwari
- Department of Oncology, Georgetown University Medical Center, Washington, DC, USA
- Department of Biology, College of Arts & Sciences, Georgetown University, Washington, DC, USA
| | - Maria I McKillop
- Department of Pharmacology and Physiology, 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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2
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Yüksel S, Bonus M, Schwabe T, Pfleger C, Zimmer T, Enke U, Saß I, Gohlke H, Benndorf K, Kusch J. Uncoupling of Voltage- and Ligand-Induced Activation in HCN2 Channels by Glycine Inserts. Front Physiol 2022; 13:895324. [PMID: 36091400 PMCID: PMC9452628 DOI: 10.3389/fphys.2022.895324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 06/20/2022] [Indexed: 11/24/2022] Open
Abstract
Hyperpolarization-activated cyclic nucleotide-modulated (HCN) channels are tetramers that generate electrical rhythmicity in special brain neurons and cardiomyocytes. The channels are activated by membrane hyperpolarization. The binding of cAMP to the four available cyclic nucleotide-binding domains (CNBD) enhances channel activation. We analyzed in the present study the mechanism of how the effect of cAMP binding is transmitted to the pore domain. Our strategy was to uncouple the C-linker (CL) from the channel core by inserting one to five glycine residues between the S6 gate and the A′-helix (constructs 1G to 5G). We quantified in full-length HCN2 channels the resulting functional effects of the inserted glycines by current activation as well as the structural dynamics and statics using molecular dynamics simulations and Constraint Network Analysis. We show functionally that already in 1G the cAMP effect on activation is lost and that with the exception of 3G and 5G the concentration-activation relationships are shifted to depolarized voltages with respect to HCN2. The strongest effect was found for 4G. Accordingly, the activation kinetics were accelerated by all constructs, again with the strongest effect in 4G. The simulations reveal that the average residue mobility of the CL and CNBD domains is increased in all constructs and that the junction between the S6 and A′-helix is turned into a flexible hinge, resulting in a destabilized gate in all constructs. Moreover, for 3G and 4G, there is a stronger downward displacement of the CL-CNBD than in HCN2 and the other constructs, resulting in an increased kink angle between S6 and A′-helix, which in turn loosens contacts between the S4-helix and the CL. This is suggested to promote a downward movement of the S4-helix, similar to the effect of hyperpolarization. In addition, exclusively in 4G, the selectivity filter in the upper pore region and parts of the S4-helix are destabilized. The results provide new insights into the intricate activation of HCN2 channels.
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Affiliation(s)
- Sezin Yüksel
- Universitätsklinikum Jena, Institut für Physiologie II, Jena, Germany
| | - Michele Bonus
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Tina Schwabe
- Universitätsklinikum Jena, Institut für Physiologie II, Jena, Germany
| | - Christopher Pfleger
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Thomas Zimmer
- Universitätsklinikum Jena, Institut für Physiologie II, Jena, Germany
| | - Uta Enke
- Universitätsklinikum Jena, Institut für Physiologie II, Jena, Germany
| | - Inga Saß
- Universitätsklinikum Jena, Institut für Physiologie II, Jena, Germany
| | - Holger Gohlke
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, Jülich, Germany
- *Correspondence: Holger Gohlke, ; Klaus Benndorf, ; Jana Kusch,
| | - Klaus Benndorf
- Universitätsklinikum Jena, Institut für Physiologie II, Jena, Germany
- *Correspondence: Holger Gohlke, ; Klaus Benndorf, ; Jana Kusch,
| | - Jana Kusch
- Universitätsklinikum Jena, Institut für Physiologie II, Jena, Germany
- *Correspondence: Holger Gohlke, ; Klaus Benndorf, ; Jana Kusch,
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3
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Kondapuram M, Frieg B, Yüksel S, Schwabe T, Sattler C, Lelle M, Schweinitz A, Schmauder R, Benndorf K, Gohlke H, Kusch J. Functional and structural characterization of interactions between opposite subunits in HCN pacemaker channels. Commun Biol 2022; 5:430. [PMID: 35534535 PMCID: PMC9085832 DOI: 10.1038/s42003-022-03360-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 04/13/2022] [Indexed: 11/13/2022] Open
Abstract
Hyperpolarization-activated and cyclic nucleotide (HCN) modulated channels are tetrameric cation channels. In each of the four subunits, the intracellular cyclic nucleotide-binding domain (CNBD) is coupled to the transmembrane domain via a helical structure, the C-linker. High-resolution channel structures suggest that the C-linker enables functionally relevant interactions with the opposite subunit, which might be critical for coupling the conformational changes in the CNBD to the channel pore. We combined mutagenesis, patch-clamp technique, confocal patch-clamp fluorometry, and molecular dynamics (MD) simulations to show that residue K464 of the C-linker is relevant for stabilizing the closed state of the mHCN2 channel by forming interactions with the opposite subunit. MD simulations revealed that in the K464E channel, a rotation of the intracellular domain relative to the channel pore is induced, which is similar to the cAMP-induced rotation, weakening the autoinhibitory effect of the unoccupied CL-CNBD region. We suggest that this CL-CNBD rotation is considerably involved in activation-induced affinity increase but only indirectly involved in gate modulation. The adopted poses shown herein are in excellent agreement with previous structural results. Interactions between opposite subunits of HCN channels are relevant for stabilizing the auto-inhibited state of the channel. Like cAMP-binding, K464E-mutation breaks these interactions to favor a channel’s pre-activated state.
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Affiliation(s)
- Mahesh Kondapuram
- Universitätsklinikum Jena, Institut für Physiologie II, Jena, Germany
| | - Benedikt Frieg
- John von Neumann-Institut für Computing (NIC), Jülich Supercomputing Centre (JSC), and Institut für Biologische Informationsprozesse (IBI-7: Strukturbiochemie), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Sezin Yüksel
- Universitätsklinikum Jena, Institut für Physiologie II, Jena, Germany
| | - Tina Schwabe
- Universitätsklinikum Jena, Institut für Physiologie II, Jena, Germany
| | - Christian Sattler
- Universitätsklinikum Jena, Institut für Physiologie II, Jena, Germany
| | - Marco Lelle
- Universitätsklinikum Jena, Institut für Physiologie II, Jena, Germany
| | - Andrea Schweinitz
- Universitätsklinikum Jena, Institut für Physiologie II, Jena, Germany
| | - Ralf Schmauder
- Universitätsklinikum Jena, Institut für Physiologie II, Jena, Germany
| | - Klaus Benndorf
- Universitätsklinikum Jena, Institut für Physiologie II, Jena, Germany
| | - Holger Gohlke
- John von Neumann-Institut für Computing (NIC), Jülich Supercomputing Centre (JSC), and Institut für Biologische Informationsprozesse (IBI-7: Strukturbiochemie), Forschungszentrum Jülich GmbH, Jülich, Germany. .,Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany. .,Institut für Bio- und Geowissenschaften (IBG-4: Bioinformatik), Forschungszentrum Jülich GmbH, Jülich, Germany.
| | - Jana Kusch
- Universitätsklinikum Jena, Institut für Physiologie II, Jena, Germany.
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4
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Structural and functional approaches to studying cAMP regulation of HCN channels. Biochem Soc Trans 2021; 49:2573-2579. [PMID: 34812892 DOI: 10.1042/bst20210290] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/19/2021] [Accepted: 10/25/2021] [Indexed: 11/17/2022]
Abstract
Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels are primarily activated by voltage and further modulated by cAMP. While cAMP binding alone does not open the channel, its presence facilitates the action of voltage, increasing channel open probability. Functional results indicate that the membrane-based voltage sensor domain (VSD) communicates with the cytosolic cyclic nucleotide-binding domain (CNBD), and vice-versa. Yet, a mechanistic explanation on how this could occur in structural terms is still lacking. In this review, we will discuss the recent advancement in understanding the molecular mechanisms connecting the VSD with the CNBD in the tetrameric organization of HCN channels unveiled by the 3D structures of HCN1 and HCN4. Data show that the HCN domain transmits cAMP signal to the VSD by bridging the cytosolic to the membrane domains. Furthermore, a metal ion coordination site connects the C-linker to the S4-S5 linker in HCN4, further facilitating cAMP signal transmission to the VSD in this isoform.
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5
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Saponaro A, Bauer D, Giese MH, Swuec P, Porro A, Gasparri F, Sharifzadeh AS, Chaves-Sanjuan A, Alberio L, Parisi G, Cerutti G, Clarke OB, Hamacher K, Colecraft HM, Mancia F, Hendrickson WA, Siegelbaum SA, DiFrancesco D, Bolognesi M, Thiel G, Santoro B, Moroni A. Gating movements and ion permeation in HCN4 pacemaker channels. Mol Cell 2021; 81:2929-2943.e6. [PMID: 34166608 PMCID: PMC8294335 DOI: 10.1016/j.molcel.2021.05.033] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/12/2021] [Accepted: 05/27/2021] [Indexed: 10/31/2022]
Abstract
The HCN1-4 channel family is responsible for the hyperpolarization-activated cation current If/Ih that controls automaticity in cardiac and neuronal pacemaker cells. We present cryoelectron microscopy (cryo-EM) structures of HCN4 in the presence or absence of bound cAMP, displaying the pore domain in closed and open conformations. Analysis of cAMP-bound and -unbound structures sheds light on how ligand-induced transitions in the channel cytosolic portion mediate the effect of cAMP on channel gating and highlights the regulatory role of a Mg2+ coordination site formed between the C-linker and the S4-S5 linker. Comparison of open/closed pore states shows that the cytosolic gate opens through concerted movements of the S5 and S6 transmembrane helices. Furthermore, in combination with molecular dynamics analyses, the open pore structures provide insights into the mechanisms of K+/Na+ permeation. Our results contribute mechanistic understanding on HCN channel gating, cyclic nucleotide-dependent modulation, and ion permeation.
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Affiliation(s)
- Andrea Saponaro
- Department of Biosciences, University of Milan, Milan, Italy
| | - Daniel Bauer
- Department of Biology, TU-Darmstadt, Darmstadt, Germany
| | - M Hunter Giese
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
| | - Paolo Swuec
- Department of Biosciences, University of Milan, Milan, Italy; Pediatric Research Center "Romeo ed Enrica Invernizzi," University of Milan, Milan, Italy
| | | | | | | | - Antonio Chaves-Sanjuan
- Department of Biosciences, University of Milan, Milan, Italy; Pediatric Research Center "Romeo ed Enrica Invernizzi," University of Milan, Milan, Italy
| | - Laura Alberio
- Department of Biosciences, University of Milan, Milan, Italy; Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Giacomo Parisi
- Center for Life Nano Science, Istituto Italiano di Tecnologia, Rome, Italy
| | - Gabriele Cerutti
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Oliver B Clarke
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA; Department of Anesthesiology, Columbia University, New York, NY, USA
| | - Kay Hamacher
- Department of Biology, TU-Darmstadt, Darmstadt, Germany
| | - Henry M Colecraft
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
| | - Wayne A Hendrickson
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Steven A Siegelbaum
- Department of Neuroscience, Zuckerman Institute, Columbia University, New York, NY, USA
| | - Dario DiFrancesco
- Department of Biosciences, University of Milan, Milan, Italy; Institute of Biophysics-Milano, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Martino Bolognesi
- Department of Biosciences, University of Milan, Milan, Italy; Pediatric Research Center "Romeo ed Enrica Invernizzi," University of Milan, Milan, Italy
| | - Gerhard Thiel
- Department of Biology, TU-Darmstadt, Darmstadt, Germany
| | - Bina Santoro
- Department of Neuroscience, Zuckerman Institute, Columbia University, New York, NY, USA.
| | - Anna Moroni
- Department of Biosciences, University of Milan, Milan, Italy; Institute of Biophysics-Milano, Consiglio Nazionale delle Ricerche, Rome, Italy.
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6
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Electromechanical coupling mechanism for activation and inactivation of an HCN channel. Nat Commun 2021; 12:2802. [PMID: 33990563 PMCID: PMC8121817 DOI: 10.1038/s41467-021-23062-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 04/01/2021] [Indexed: 11/08/2022] Open
Abstract
Pacemaker hyperpolarization-activated cyclic nucleotide-gated (HCN) ion channels exhibit a reversed voltage-dependent gating, activating by membrane hyperpolarization instead of depolarization. Sea urchin HCN (spHCN) channels also undergo inactivation with hyperpolarization which occurs only in the absence of cyclic nucleotide. Here we applied transition metal ion FRET, patch-clamp fluorometry and Rosetta modeling to measure differences in the structural rearrangements between activation and inactivation of spHCN channels. We found that removing cAMP produced a largely rigid-body rotation of the C-linker relative to the transmembrane domain, bringing the A’ helix of the C-linker in close proximity to the voltage-sensing S4 helix. In addition, rotation of the C-linker was elicited by hyperpolarization in the absence but not the presence of cAMP. These results suggest that — in contrast to electromechanical coupling for channel activation — the A’ helix serves to couple the S4-helix movement for channel inactivation, which is likely a conserved mechanism for CNBD-family channels. Sea urchin hyperpolarization-activated cyclic nucleotide-gated (spHCN) ion channels channels are activated by membrane hyperpolarization instead of depolarization and undergo inactivation with hyperpolarization. Here authors apply transition metal ion FRET, patch-clamp fluorometry and Rosetta modeling to measure differences in the structural rearrangements between activation and inactivation of spHCN channels.
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7
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Pfleger C, Kusch J, Kondapuram M, Schwabe T, Sattler C, Benndorf K, Gohlke H. Allosteric signaling in C-linker and cyclic nucleotide-binding domain of HCN2 channels. Biophys J 2021; 120:950-963. [PMID: 33515603 DOI: 10.1016/j.bpj.2021.01.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 01/04/2021] [Accepted: 01/19/2021] [Indexed: 12/22/2022] Open
Abstract
Opening of hyperpolarization-activated cyclic nucleotide-modulated (HCN) channels is controlled by membrane hyperpolarization and binding of cyclic nucleotides to the tetrameric cyclic nucleotide-binding domain (CNBD), attached to the C-linker (CL) disk. Confocal patch-clamp fluorometry revealed pronounced cooperativity of ligand binding among protomers. However, by which pathways allosteric signal transmission occurs remained elusive. Here, we investigate how changes in the structural dynamics of the CL-CNBD of mouse HCN2 upon cAMP binding relate to inter- and intrasubunit signal transmission. Applying a rigidity-theory-based approach, we identify two intersubunit and one intrasubunit pathways that differ in allosteric coupling strength between cAMP-binding sites or toward the CL. These predictions agree with results from electrophysiological and patch-clamp fluorometry experiments. Our results map out distinct routes within the CL-CNBD that modulate different cAMP-binding responses in HCN2 channels. They signify that functionally relevant submodules may exist within and across structurally discernable subunits in HCN channels.
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Affiliation(s)
- Christopher Pfleger
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Jana Kusch
- Institute of Physiology II, Jena University Hospital, Jena, Germany
| | | | - Tina Schwabe
- Institute of Physiology II, Jena University Hospital, Jena, Germany
| | | | - Klaus Benndorf
- Institute of Physiology II, Jena University Hospital, Jena, Germany
| | - Holger Gohlke
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany; John von Neumann Institute for Computing, Jülich Supercomputing Centre, and Institute of Biological Information Processing (IBI-7, Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany.
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8
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Porro A, Thiel G, Moroni A, Saponaro A. cyclic AMP Regulation and Its Command in the Pacemaker Channel HCN4. Front Physiol 2020; 11:771. [PMID: 32733276 PMCID: PMC7358946 DOI: 10.3389/fphys.2020.00771] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/11/2020] [Indexed: 11/13/2022] Open
Abstract
Direct regulation of the pacemaker “funny” current (If) by cyclic AMP (cAMP) underlies heart rate modulation by the autonomic nervous system. At the molecular level, cAMP activates hyperpolarization-activated cyclic nucleotide-gated (HCN) channels that drive If in sinoatrial node (SAN) myocytes. Even though HCN channel genes were identified more than 20 years ago, the understanding of how cAMP regulates their gating is still fragmented. Here we summarize present understanding on how the cAMP signal is transmitted from the cytosolic to the transmembrane (TM) domain in HCN4. We further discuss how detailed structural knowledge prompted the development of pharmacological/genetic tools for the control of cAMP regulation in these channels.
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Affiliation(s)
| | - Gerhard Thiel
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Anna Moroni
- Department of Biosciences, University of Milan, Milan, Italy
| | - Andrea Saponaro
- Department of Biosciences, University of Milan, Milan, Italy
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9
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Zheng X, Fu Z, Su D, Zhang Y, Li M, Pan Y, Li H, Li S, Grassucci RA, Ren Z, Hu Z, Li X, Zhou M, Li G, Frank J, Yang J. Mechanism of ligand activation of a eukaryotic cyclic nucleotide-gated channel. Nat Struct Mol Biol 2020; 27:625-634. [PMID: 32483338 PMCID: PMC7354226 DOI: 10.1038/s41594-020-0433-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 04/10/2020] [Indexed: 01/21/2023]
Abstract
Cyclic nucleotide-gated (CNG) channels convert cyclic nucleotide (CN) binding and unbinding into electrical signals in sensory receptors and neurons. The molecular conformational changes underpinning ligand activation are largely undefined. We report both closed- and open-state atomic cryo-EM structures of a full-length Caenorhabditis elegans cyclic GMP-activated channel TAX-4, reconstituted in lipid nanodiscs. These structures, together with computational and functional analyses and a mutant channel structure, reveal a double-barrier hydrophobic gate formed by two S6 amino acids in the central cavity. cGMP binding produces global conformational changes that open the cavity gate located ~52 Å away but do not alter the structure of the selectivity filter-the commonly presumed activation gate. Our work provides mechanistic insights into the allosteric gating and regulation of CN-gated and nucleotide-modulated channels and CNG channel-related channelopathies.
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Affiliation(s)
- Xiangdong Zheng
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA,These authors contributed equally to this work
| | - Ziao Fu
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA,These authors contributed equally to this work
| | - Deyuan Su
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Chinese Academy of Sciences, Kunming 650223, China,These authors contributed equally to this work
| | - Yuebin Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Minghui Li
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA,Current address: HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Yaping Pan
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Huan Li
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Shufang Li
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Robert A. Grassucci
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Zhenning Ren
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhengshan Hu
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Xueming Li
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ming Zhou
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Guohui Li
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Joachim Frank
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Jian Yang
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA,Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Chinese Academy of Sciences, Kunming 650223, China
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10
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Evans EGB, Morgan JLW, DiMaio F, Zagotta WN, Stoll S. Allosteric conformational change of a cyclic nucleotide-gated ion channel revealed by DEER spectroscopy. Proc Natl Acad Sci U S A 2020; 117:10839-10847. [PMID: 32358188 PMCID: PMC7245078 DOI: 10.1073/pnas.1916375117] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Cyclic nucleotide-gated (CNG) ion channels are essential components of mammalian visual and olfactory signal transduction. CNG channels open upon direct binding of cyclic nucleotides (cAMP and/or cGMP), but the allosteric mechanism by which this occurs is incompletely understood. Here, we employed double electron-electron resonance (DEER) spectroscopy to measure intersubunit distance distributions in SthK, a bacterial CNG channel from Spirochaeta thermophila Spin labels were introduced into the SthK C-linker, a domain that is essential for coupling cyclic nucleotide binding to channel opening. DEER revealed an agonist-dependent conformational change in which residues of the B'-helix displayed outward movement with respect to the symmetry axis of the channel in the presence of the full agonist cAMP, but not with the partial agonist cGMP. This conformational rearrangement was observed both in detergent-solubilized SthK and in channels reconstituted into lipid nanodiscs. In addition to outward movement of the B'-helix, DEER-constrained Rosetta structural models suggest that channel activation involves upward translation of the cytoplasmic domain and formation of state-dependent interactions between the C-linker and the transmembrane domain. Our results demonstrate a previously unrecognized structural transition in a CNG channel and suggest key interactions that may be responsible for allosteric gating in these channels.
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Affiliation(s)
- Eric G B Evans
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195
- Department of Chemistry, University of Washington, Seattle, WA 98195
| | - Jacob L W Morgan
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA 98195
| | - William N Zagotta
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195;
| | - Stefan Stoll
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195;
- Department of Chemistry, University of Washington, Seattle, WA 98195
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11
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Wang ZJ, Blanco I, Hayoz S, Brelidze TI. The HCN domain is required for HCN channel cell-surface expression and couples voltage- and cAMP-dependent gating mechanisms. J Biol Chem 2020; 295:8164-8173. [PMID: 32341127 DOI: 10.1074/jbc.ra120.013281] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/23/2020] [Indexed: 11/06/2022] Open
Abstract
Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels are major regulators of synaptic plasticity and rhythmic activity in the heart and brain. Opening of HCN channels requires membrane hyperpolarization and is further facilitated by intracellular cyclic nucleotides (cNMPs). In HCN channels, membrane hyperpolarization is sensed by the membrane-spanning voltage sensor domain (VSD), and the cNMP-dependent gating is mediated by the intracellular cyclic nucleotide-binding domain (CNBD) connected to the pore-forming S6 transmembrane segment via the C-linker. Previous functional analysis of HCN channels has suggested a direct or allosteric coupling between the voltage- and cNMP-dependent activation mechanisms. However, the specifics of this coupling remain unclear. The first cryo-EM structure of an HCN1 channel revealed that a novel structural element, dubbed the HCN domain (HCND), forms a direct structural link between the VSD and C-linker-CNBD. In this study, we investigated the functional significance of the HCND. Deletion of the HCND prevented surface expression of HCN2 channels. Based on the HCN1 structure analysis, we identified Arg237 and Gly239 residues on the S2 of the VSD that form direct interactions with Ile135 on the HCND. Disrupting these interactions abolished HCN2 currents. We also identified three residues on the C-linker-CNBD (Glu478, Gln482, and His559) that form direct interactions with residues Arg154 and Ser158 on the HCND. Disrupting these interactions affected both voltage- and cAMP-dependent gating of HCN2 channels. These findings indicate that the HCND is necessary for the cell-surface expression of HCN channels and provides a functional link between voltage- and cAMP-dependent mechanisms of HCN channel gating.
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Affiliation(s)
- Ze-Jun Wang
- Department of Pharmacology and Physiology, Georgetown University Medical Center, Washington, D. C., USA
| | - Ismary Blanco
- Interdisciplinary Program in Neuroscience, Georgetown University Medical Center, Washington, D. C., USA
| | - Sebastien Hayoz
- Department of Pharmacology and Physiology, Georgetown University Medical Center, Washington, D. C., USA
| | - Tinatin I Brelidze
- Department of Pharmacology and Physiology, Georgetown University Medical Center, Washington, D. C., USA .,Interdisciplinary Program in Neuroscience, Georgetown University Medical Center, Washington, D. C., USA
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12
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Barros F, de la Peña P, Domínguez P, Sierra LM, Pardo LA. The EAG Voltage-Dependent K + Channel Subfamily: Similarities and Differences in Structural Organization and Gating. Front Pharmacol 2020; 11:411. [PMID: 32351384 PMCID: PMC7174612 DOI: 10.3389/fphar.2020.00411] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 03/18/2020] [Indexed: 12/17/2022] Open
Abstract
EAG (ether-à-go-go or KCNH) are a subfamily of the voltage-gated potassium (Kv) channels. Like for all potassium channels, opening of EAG channels drives the membrane potential toward its equilibrium value for potassium, thus setting the resting potential and repolarizing action potentials. As voltage-dependent channels, they switch between open and closed conformations (gating) when changes in membrane potential are sensed by a voltage sensing domain (VSD) which is functionally coupled to a pore domain (PD) containing the permeation pathway, the potassium selectivity filter, and the channel gate. All Kv channels are tetrameric, with four VSDs formed by the S1-S4 transmembrane segments of each subunit, surrounding a central PD with the four S5-S6 sections arranged in a square-shaped structure. Structural information, mutagenesis, and functional experiments, indicated that in "classical/Shaker-type" Kv channels voltage-triggered VSD reorganizations are transmitted to PD gating via the α-helical S4-S5 sequence that links both modules. Importantly, these Shaker-type channels share a domain-swapped VSD/PD organization, with each VSD contacting the PD of the adjacent subunit. In this case, the S4-S5 linker, acting as a rigid mechanical lever (electromechanical lever coupling), would lead to channel gate opening at the cytoplasmic S6 helices bundle. However, new functional data with EAG channels split between the VSD and PD modules indicate that, in some Kv channels, alternative VSD/PD coupling mechanisms do exist. Noticeably, recent elucidation of the architecture of some EAG channels, and other relatives, showed that their VSDs are non-domain swapped. Despite similarities in primary sequence and predicted structural organization for all EAG channels, they show marked kinetic differences whose molecular basis is not completely understood. Thus, while a common general architecture may establish the gating system used by the EAG channels and the physicochemical coupling of voltage sensing to gating, subtle changes in that common structure, and/or allosteric influences of protein domains relatively distant from the central gating machinery, can crucially influence the gating process. We consider here the latest advances on these issues provided by the elucidation of eag1 and erg1 three-dimensional structures, and by both classical and more recent functional studies with different members of the EAG subfamily.
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Affiliation(s)
- Francisco Barros
- Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, Edificio Santiago Gascón, Oviedo, Spain
| | - Pilar de la Peña
- Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, Edificio Santiago Gascón, Oviedo, Spain
| | - Pedro Domínguez
- Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, Edificio Santiago Gascón, Oviedo, Spain
| | - Luisa Maria Sierra
- Departamento de Biología Funcional (Area de Genética), Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Universidad de Oviedo, Oviedo, Spain
| | - Luis A. Pardo
- Oncophysiology Group, Max Planck Institute of Experimental Medicine, Göttingen, Germany
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13
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Page DA, Magee KEA, Li J, Jung M, Young EC. Cytoplasmic Autoinhibition in HCN Channels is Regulated by the Transmembrane Region. J Membr Biol 2020; 253:153-166. [PMID: 32146488 PMCID: PMC7150657 DOI: 10.1007/s00232-020-00111-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 02/16/2020] [Indexed: 12/25/2022]
Abstract
Hyperpolarization-activated cation-nonselective (HCN) channels regulate electrical activity in the brain and heart in a cAMP-dependent manner. The voltage-gating of these channels is mediated by a transmembrane (TM) region but is additionally regulated by direct binding of cAMP to a cyclic nucleotide-binding (CNB) fold in the cytoplasmic C-terminal region. Cyclic AMP potentiation has been explained by an autoinhibition model which views the unliganded CNB fold as an inhibitory module whose influence is disrupted by cAMP binding. However, the HCN2 subtype uses two other CNB fold-mediated mechanisms called open-state trapping and Quick-Activation to respectively slow the deactivation kinetics and speed the activation kinetics, against predictions of an autoinhibition model. To test how these multiple mechanisms are influenced by the TM region, we replaced the TM region of HCN2 with that of HCN4. This HCN4 TM-replacement preserved cAMP potentiation but augmented the magnitude of autoinhibition by the unliganded CNB fold; it moreover disrupted open-state trapping and Quick-Activation so that autoinhibition became the dominant mechanism contributed by the C-terminal region to determine kinetics. Truncation within the CNB fold partially relieved this augmented autoinhibition. This argues against the C-terminal region acting like a portable module with consistent effects on TM regions of different subtypes. Our findings provide evidence that functional interactions between the HCN2 TM region and C-terminal region govern multiple CNB fold-mediated mechanisms, implying that the molecular mechanisms of autoinhibition, open-state trapping, and Quick-Activation include participation of TM region structures.
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Affiliation(s)
- Dana A Page
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Kaylee E A Magee
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada.,Department of Biology, Kwantlen Polytechnic University, 12666 72 Avenue, Surrey, BC, V3W 2M8, Canada
| | - Jessica Li
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Matthew Jung
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Edgar C Young
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada.
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14
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Porro A, Saponaro A, Gasparri F, Bauer D, Gross C, Pisoni M, Abbandonato G, Hamacher K, Santoro B, Thiel G, Moroni A. The HCN domain couples voltage gating and cAMP response in hyperpolarization-activated cyclic nucleotide-gated channels. eLife 2019; 8:e49672. [PMID: 31769408 PMCID: PMC6894927 DOI: 10.7554/elife.49672] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 11/22/2019] [Indexed: 12/17/2022] Open
Abstract
Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels control spontaneous electrical activity in heart and brain. Binding of cAMP to the cyclic nucleotide-binding domain (CNBD) facilitates channel opening by relieving a tonic inhibition exerted by the CNBD. Despite high resolution structures of the HCN1 channel in the cAMP bound and unbound states, the structural mechanism coupling ligand binding to channel gating is unknown. Here we show that the recently identified helical HCN-domain (HCND) mechanically couples the CNBD and channel voltage sensing domain (VSD), possibly acting as a sliding crank that converts the planar rotational movement of the CNBD into a rotational upward displacement of the VSD. This mode of operation and its impact on channel gating are confirmed by computational and experimental data showing that disruption of critical contacts between the three domains affects cAMP- and voltage-dependent gating in three HCN isoforms.
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Affiliation(s)
| | | | | | - Daniel Bauer
- Department of BiologyTU-DarmstadtDarmstadtGermany
| | | | - Matteo Pisoni
- Department of BiosciencesUniversity of MilanMilanItaly
| | | | - Kay Hamacher
- Department of BiologyTU-DarmstadtDarmstadtGermany
| | - Bina Santoro
- Department of NeuroscienceColumbia UniversityNew YorkUnited States
| | | | - Anna Moroni
- Department of BiosciencesUniversity of MilanMilanItaly
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15
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The C-terminal HCN4 variant P883R alters channel properties and acts as genetic modifier of atrial fibrillation and structural heart disease. Biochem Biophys Res Commun 2019; 519:141-147. [DOI: 10.1016/j.bbrc.2019.08.150] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 08/26/2019] [Indexed: 12/18/2022]
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16
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Ng LCT, Zhuang M, Van Petegem F, Li YX, Accili EA. Binding and structural asymmetry governs ligand sensitivity in a cyclic nucleotide-gated ion channel. J Gen Physiol 2019; 151:1190-1212. [PMID: 31481514 PMCID: PMC6785730 DOI: 10.1085/jgp.201812162] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 04/26/2019] [Accepted: 07/31/2019] [Indexed: 12/17/2022] Open
Abstract
HCN channel opening is facilitated by cyclic nucleotides, but what determines the sensitivity of these channels to cAMP or cGMP is unclear. Ng et al. propose that ligand sensitivity depends on negative cooperativity and the asymmetric effects of ligand binding on channel structure and pore opening. Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels open more easily when cAMP or cGMP bind to a domain in the intracellular C-terminus in each of four identical subunits. How sensitivity of the channels to these ligands is determined is not well understood. Here, we apply a mathematical model, which incorporates negative cooperativity, to gating and mutagenesis data available in the literature and combine the results with binding data collected using isothermal titration calorimetry. This model recapitulates the concentration–response data for the effects of cAMP and cGMP on wild-type HCN2 channel opening and, remarkably, predicts the concentration–response data for a subset of mutants with single-point amino acid substitutions in the binding site. Our results suggest that ligand sensitivity is determined by negative cooperativity and asymmetric effects on structure and channel opening, which are tuned by ligand-specific interactions and residues within the binding site.
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Affiliation(s)
- Leo C T Ng
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Meiying Zhuang
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Yue Xian Li
- Department of Mathematics, University of British Columbia, Vancouver, BC, Canada
| | - Eric A Accili
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, Canada
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17
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Mbaye MN, Hou Q, Basu S, Teheux F, Pucci F, Rooman M. A comprehensive computational study of amino acid interactions in membrane proteins. Sci Rep 2019; 9:12043. [PMID: 31427701 PMCID: PMC6700154 DOI: 10.1038/s41598-019-48541-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 08/07/2019] [Indexed: 01/26/2023] Open
Abstract
Transmembrane proteins play a fundamental role in a wide series of biological processes but, despite their importance, they are less studied than globular proteins, essentially because their embedding in lipid membranes hampers their experimental characterization. In this paper, we improved our understanding of their structural stability through the development of new knowledge-based energy functions describing amino acid pair interactions that prevail in the transmembrane and extramembrane regions of membrane proteins. The comparison of these potentials and those derived from globular proteins yields an objective view of the relative strength of amino acid interactions in the different protein environments, and their role in protein stabilization. Separate potentials were also derived from α-helical and β-barrel transmembrane regions to investigate possible dissimilarities. We found that, in extramembrane regions, hydrophobic residues are less frequent but interactions between aromatic and aliphatic amino acids as well as aromatic-sulfur interactions contribute more to stability. In transmembrane regions, polar residues are less abundant but interactions between residues of equal or opposite charges or non-charged polar residues as well as anion-π interactions appear stronger. This shows indirectly the preference of the water and lipid molecules to interact with polar and hydrophobic residues, respectively. We applied these new energy functions to predict whether a residue is located in the trans- or extramembrane region, and obtained an AUC score of 83% in cross validation, which demonstrates their accuracy. As their application is, moreover, extremely fast, they are optimal instruments for membrane protein design and large-scale investigations of membrane protein stability.
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Affiliation(s)
- Mame Ndew Mbaye
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium.,Department of Mathematics and Informatics, Cheikh Anta Diop University, Dakar-Fann, Senegal
| | - Qingzhen Hou
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium
| | - Sankar Basu
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium
| | - Fabian Teheux
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium
| | - Fabrizio Pucci
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium.,John von Neumann Institute for Computing, Jülich Supercomputer Centre, Forschungszentrum Jülich, Jülich, Germany
| | - Marianne Rooman
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium.
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18
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Morgan JLW, Evans EGB, Zagotta WN. Functional characterization and optimization of a bacterial cyclic nucleotide-gated channel. J Biol Chem 2019; 294:7503-7515. [PMID: 30885945 DOI: 10.1074/jbc.ra119.007699] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/15/2019] [Indexed: 02/01/2023] Open
Abstract
Cyclic nucleotide-gated (CNG) channels produce the initial electrical signal in mammalian vision and olfaction. They open in response to direct binding of cyclic nucleotide (cAMP or cGMP) to a cytoplasmic region of the channel. However, the conformational rearrangements occurring upon binding to produce pore opening (i.e. gating) are not well understood. SthK is a bacterial CNG channel that has the potential to serve as an ideal model for structure-function studies of gating but is currently limited by its toxicity, native cysteines, and low open probability (P o). Here, we expressed SthK in giant Escherichia coli spheroplasts and performed patch-clamp recordings to characterize SthK gating in a bacterial membrane. We demonstrated that the P o in cAMP is higher than has been previously published and that cGMP acts as a weak partial SthK agonist. Additionally, we determined that SthK expression is toxic to E. coli because of gating by cytoplasmic cAMP. We overcame this toxicity by developing an adenylate cyclase-knockout E. coli cell line. Finally, we generated a cysteine-free SthK construct and introduced mutations that further increase the P o in cAMP. We propose that this SthK model will help elucidate the gating mechanism of CNG channels.
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Affiliation(s)
- Jacob L W Morgan
- From the Department of Physiology and Biophysics, University of Washington, Seattle, Washington 98195
| | - Eric G B Evans
- From the Department of Physiology and Biophysics, University of Washington, Seattle, Washington 98195
| | - William N Zagotta
- From the Department of Physiology and Biophysics, University of Washington, Seattle, Washington 98195
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19
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Baruscotti M, Bucchi A, Milanesi R, Paina M, Barbuti A, Gnecchi-Ruscone T, Bianco E, Vitali-Serdoz L, Cappato R, DiFrancesco D. A gain-of-function mutation in the cardiac pacemaker HCN4 channel increasing cAMP sensitivity is associated with familial Inappropriate Sinus Tachycardia. Eur Heart J 2019; 38:280-288. [PMID: 28182231 DOI: 10.1093/eurheartj/ehv582] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 10/01/2015] [Accepted: 10/07/2015] [Indexed: 01/09/2023] Open
Affiliation(s)
- Mirko Baruscotti
- Department of Biosciences, The PaceLab and 'Centro Interuniversitario di Medicina Molecolare e Biofisica Applicata', Università degli Studi di Milano, via Celoria 26, 20133 Milano, Italy
| | - Annalisa Bucchi
- Department of Biosciences, The PaceLab and 'Centro Interuniversitario di Medicina Molecolare e Biofisica Applicata', Università degli Studi di Milano, via Celoria 26, 20133 Milano, Italy
| | - Raffaella Milanesi
- Department of Biosciences, The PaceLab and 'Centro Interuniversitario di Medicina Molecolare e Biofisica Applicata', Università degli Studi di Milano, via Celoria 26, 20133 Milano, Italy
| | - Manuel Paina
- Department of Biosciences, The PaceLab and 'Centro Interuniversitario di Medicina Molecolare e Biofisica Applicata', Università degli Studi di Milano, via Celoria 26, 20133 Milano, Italy
| | - Andrea Barbuti
- Department of Biosciences, The PaceLab and 'Centro Interuniversitario di Medicina Molecolare e Biofisica Applicata', Università degli Studi di Milano, via Celoria 26, 20133 Milano, Italy
| | | | - Elisabetta Bianco
- Cardiovascular Department, 'Ospedali Riuniti di Trieste', University Hospital, Trieste, Italy
| | | | | | - Dario DiFrancesco
- Department of Biosciences, The PaceLab and 'Centro Interuniversitario di Medicina Molecolare e Biofisica Applicata', Università degli Studi di Milano, via Celoria 26, 20133 Milano, Italy
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20
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Joyce RL, Beyer NP, Vasilopoulos G, Woll KA, Hall AC, Eckenhoff RG, Barman DN, Warren JD, Tibbs GR, Goldstein PA. Alkylphenol inverse agonists of HCN1 gating: H-bond propensity, ring saturation and adduct geometry differentially determine efficacy and potency. Biochem Pharmacol 2019; 163:493-508. [PMID: 30768926 DOI: 10.1016/j.bcp.2019.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/11/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND AND PURPOSE In models of neuropathic pain, inhibition of HCN1 is anti-hyperalgesic. 2,6-di-iso-propyl phenol (propofol) and its non-anesthetic congener, 2,6-di-tert-butyl phenol, inhibit HCN1 channels by stabilizing closed state(s). EXPERIMENTAL APPROACH Using in vitro electrophysiology and kinetic modeling, we systematically explore the contribution of ligand architecture to alkylphenol-channel coupling. KEY RESULTS When corrected for changes in hydrophobicity (and propensity for intra-membrane partitioning), the decrease in potency upon 1-position substitution (NCO∼OH >> SH >>> F) mirrors the ligands' H-bond acceptor (NCO > OH > SH >>> F) but not donor profile (OH > SH >>> NCO∼F). H-bond elimination (OH to F) corresponds to a ΔΔG of ∼4.5 kCal mol-1 loss of potency with little or no disruption of efficacy. Substitution of compact alkyl groups (iso-propyl, tert-butyl) with shorter (ethyl, methyl) or more extended (sec-butyl) adducts disrupts both potency and efficacy. Ring saturation (with the obligate loss of both planarity and π electrons) primarily disrupts efficacy. CONCLUSIONS AND IMPLICATIONS A hydrophobicity-independent decrement in potency at higher volumes suggests the alkylbenzene site has a volume of ≥800 Å3. Within this, a relatively static (with respect to ligand) H-bond donor contributes to initial binding with little involvement in generation of coupling energy. The influence of π electrons/ring planarity and alkyl adducts on efficacy reveals these aspects of the ligand present towards a face of the channel that undergoes structural changes during opening. The site's characteristics suggest it is "druggable"; introduction of other adducts on the ring may generate higher potency inverse agonists.
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Affiliation(s)
| | | | | | - Kellie A Woll
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
| | - Adam C Hall
- Smith College, Northampton, MA, United States
| | - Roderic G Eckenhoff
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
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21
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Kume S, Shimomura T, Tateyama M, Kubo Y. Two mutations at different positions in the CNBH domain of the hERG channel accelerate deactivation and impair the interaction with the EAG domain. J Physiol 2018; 596:4629-4650. [PMID: 30086184 DOI: 10.1113/jp276208] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 08/06/2018] [Indexed: 12/24/2022] Open
Abstract
KEY POINTS In the human ether-a-go-go related gene (hERG) channel, both the ether-a-go-go (EAG) domain in the N-terminal and the cyclic nucleotide (CN) binding homology (CNBH) domain in the C-terminal cytoplasmic region are known to contribute to the characteristic slow deactivation. Mutations of Phe860 in the CNBH domain, reported to fill the CN binding pocket, accelerate the deactivation and decrease the fluorescence resonance energy transfer (FRET) efficiencies between the EAG and CNBH domains. An electrostatic interaction between Arg696 and Asp727 in the C-linker domain, critical for HCN and CNG channels, is not formed in the hERG channel. Mutations of newly identified electrostatically interacting pair, Asp727 in the C-linker and Arg752 in the CNBH domains, accelerate the deactivation and decrease FRET efficiency. Voltage-dependent changes in FRET efficiency were not detected. These results suggest that the acceleration of the deactivation by mutations of C-terminal domains is a result of the lack of interaction between the EAG and CNBH domains. ABSTRACT The human ether-a-go-go related gene (hERG) channel shows characteristic slow deactivation, and the contribution of both of the N-terminal cytoplasmic ether-a-go-go (EAG) domain and the C-terminal cytoplasmic cyclic nucleotide (CN) binding homology (CNBH) domain is well known. The interaction between these domains is known to be critical for slow deactivation. We analysed the effects of mutations in the CNBH domain and its upstream C-linker domain on slow deactivation and the interaction between the EAG and CNBH domains by electrophysiological and fluorescence resonance energy transfer (FRET) analyses using Xenopus oocyte and HEK293T cell expression systems. We first observed that mutations of Phe860 in the CNBH domain, which is reported to fill the CN binding pocket as an intrinsic ligand, accelerate deactivation and eliminate the inter-domain interaction. Next, we observed that the salt bridge between Arg696 and Asp727 in the C-linker domain, which is reported to be critical for the function of CN-regulated channels, is not formed. We newly identified an electrostatically interacting pair critical for slow deactivation: Asp727 and Arg752 in the CNBH domain. Their mutations also impaired the inter-domain interaction. Taking these results together, both mutations of the intrinsic ligand (Phe860) and a newly identified salt bridge pair (Asp727 and Arg752) in the hERG channel accelerated deactivation and also decreased the interaction between the EAG and CNBH domains. Voltage-dependent changes in FRET efficiency between the two domains were not detected. The results suggest that the CNBH domain contributes to slow deactivation of the hERG channel by a mechanism involving the EAG domain.
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Affiliation(s)
- Shinichiro Kume
- Division of Biophysics and Neurobiology, Department of Molecular and Cellular Physiology, National Institute for Physiological Sciences, Okazaki, Japan.,Department of Physiological Sciences, School of Life Science, SOKENDAI, Hayama, Japan.,Present address: Department of Pathophysiology, Oita University School of Medicine, Yufu, Oita, Japan
| | - Takushi Shimomura
- Division of Biophysics and Neurobiology, Department of Molecular and Cellular Physiology, National Institute for Physiological Sciences, Okazaki, Japan.,Department of Physiological Sciences, School of Life Science, SOKENDAI, Hayama, Japan
| | - Michihiro Tateyama
- Division of Biophysics and Neurobiology, Department of Molecular and Cellular Physiology, National Institute for Physiological Sciences, Okazaki, Japan.,Department of Physiological Sciences, School of Life Science, SOKENDAI, Hayama, Japan
| | - Yoshihiro Kubo
- Division of Biophysics and Neurobiology, Department of Molecular and Cellular Physiology, National Institute for Physiological Sciences, Okazaki, Japan.,Department of Physiological Sciences, School of Life Science, SOKENDAI, Hayama, Japan
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22
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Campostrini G, DiFrancesco JC, Castellotti B, Milanesi R, Gnecchi-Ruscone T, Bonzanni M, Bucchi A, Baruscotti M, Ferrarese C, Franceschetti S, Canafoglia L, Ragona F, Freri E, Labate A, Gambardella A, Costa C, Gellera C, Granata T, Barbuti A, DiFrancesco D. A Loss-of-Function HCN4 Mutation Associated With Familial Benign Myoclonic Epilepsy in Infancy Causes Increased Neuronal Excitability. Front Mol Neurosci 2018; 11:269. [PMID: 30127718 PMCID: PMC6089338 DOI: 10.3389/fnmol.2018.00269] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 07/16/2018] [Indexed: 01/03/2023] Open
Abstract
HCN channels are highly expressed and functionally relevant in neurons and increasing evidence demonstrates their involvement in the etiology of human epilepsies. Among HCN isoforms, HCN4 is important in cardiac tissue, where it underlies pacemaker activity. Despite being expressed also in deep structures of the brain, mutations of this channel functionally shown to be associated with epilepsy have not been reported yet. Using Next Generation Sequencing for the screening of patients with idiopathic epilepsy, we identified the p.Arg550Cys (c.1648C>T) heterozygous mutation on HCN4 in two brothers affected by benign myoclonic epilepsy of infancy. Functional characterization in heterologous expression system and in neurons showed that the mutation determines a loss of function of HCN4 contribution to activity and an increase of neuronal discharge, potentially predisposing to epilepsy. Expressed in cardiomyocytes, mutant channels activate at slightly more negative voltages than wild-type (WT), in accordance with borderline bradycardia. While HCN4 variants have been frequently associated with cardiac arrhythmias, these data represent the first experimental evidence that functional alteration of HCN4 can also be involved in human epilepsy through a loss-of-function effect and associated increased neuronal excitability. Since HCN4 appears to be highly expressed in deep brain structures only early during development, our data provide a potential explanation for a link between dysfunctional HCN4 and infantile epilepsy. These findings suggest that it may be useful to include HCN4 screening to extend the knowledge of the genetic causes of infantile epilepsies, potentially paving the way for the identification of innovative therapeutic strategies.
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Affiliation(s)
- Giulia Campostrini
- Molecular Physiology and Neurobiology, The PaceLab, Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Jacopo C DiFrancesco
- Clinical Neurophysiology and Epilepsy Center, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy.,Laboratory of Neurobiology, Department of Neurology, Milan Center for Neuroscience, San Gerardo Hospital, University of Milano-Bicocca, Monza, Italy
| | - Barbara Castellotti
- Unit of Genetics of Neurodegenerative and Metabolic Diseases, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Raffaella Milanesi
- Molecular Physiology and Neurobiology, The PaceLab, Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | | | - Mattia Bonzanni
- Molecular Physiology and Neurobiology, The PaceLab, Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Annalisa Bucchi
- Molecular Physiology and Neurobiology, The PaceLab, Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Mirko Baruscotti
- Molecular Physiology and Neurobiology, The PaceLab, Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Carlo Ferrarese
- Laboratory of Neurobiology, Department of Neurology, Milan Center for Neuroscience, San Gerardo Hospital, University of Milano-Bicocca, Monza, Italy
| | - Silvana Franceschetti
- Clinical Neurophysiology and Epilepsy Center, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Laura Canafoglia
- Clinical Neurophysiology and Epilepsy Center, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Francesca Ragona
- Department of Pediatric Neuroscience, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Elena Freri
- Department of Pediatric Neuroscience, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Angelo Labate
- Institute of Neurology, Università degli Studi Magna Græcia di Catanzaro, Catanzaro, Italy
| | - Antonio Gambardella
- Institute of Neurology, Università degli Studi Magna Græcia di Catanzaro, Catanzaro, Italy
| | - Cinzia Costa
- Neurology Unit, Ospedale S. Maria della Misericordia, Department of Medicine, University of Perugia, Perugia, Italy
| | - Cinzia Gellera
- Unit of Genetics of Neurodegenerative and Metabolic Diseases, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Tiziana Granata
- Department of Pediatric Neuroscience, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Andrea Barbuti
- Molecular Physiology and Neurobiology, The PaceLab, Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Dario DiFrancesco
- Molecular Physiology and Neurobiology, The PaceLab, Department of Biosciences, Università degli Studi di Milano, Milan, Italy
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23
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Insights into the molecular mechanism for hyperpolarization-dependent activation of HCN channels. Proc Natl Acad Sci U S A 2018; 115:E8086-E8095. [PMID: 30076228 DOI: 10.1073/pnas.1805596115] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hyperpolarization-activated, cyclic nucleotide-gated (HCN) ion channels are both voltage- and ligand-activated membrane proteins that contribute to electrical excitability and pace-making activity in cardiac and neuronal cells. These channels are members of the voltage-gated Kv channel superfamily and cyclic nucleotide-binding domain subfamily of ion channels. HCN channels have a unique feature that distinguishes them from other voltage-gated channels: the HCN channel pore opens in response to hyperpolarizing voltages instead of depolarizing voltages. In the canonical model of electromechanical coupling, based on Kv channels, a change in membrane voltage activates the voltage-sensing domains (VSD) and the activation energy passes to the pore domain (PD) through a covalent linker that connects the VSD to the PD. In this investigation, the covalent linkage between the VSD and PD, the S4-S5 linker, and nearby regions of spHCN channels were mutated to determine the functional role each plays in hyperpolarization-dependent activation. The results show that: (i) the S4-S5 linker is not required for hyperpolarization-dependent activation or ligand-dependent gating; (ii) the S4 C-terminal region (S4C-term) is not necessary for ligand-dependent gating but is required for hyperpolarization-dependent activation and acts like an autoinhibitory domain on the PD; (iii) the S5N-term region is involved in VSD-PD coupling and holding the pore closed; and (iv) spHCN channels have two voltage-dependent processes, a hyperpolarization-dependent activation and a depolarization-dependent recovery from inactivation. These results are inconsistent with the canonical model of VSD-PD coupling in Kv channels and elucidate the mechanism for hyperpolarization-dependent activation of HCN channels.
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24
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Gross C, Saponaro A, Santoro B, Moroni A, Thiel G, Hamacher K. Mechanical transduction of cytoplasmic-to-transmembrane-domain movements in a hyperpolarization-activated cyclic nucleotide-gated cation channel. J Biol Chem 2018; 293:12908-12918. [PMID: 29936413 PMCID: PMC6102142 DOI: 10.1074/jbc.ra118.002139] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 06/05/2018] [Indexed: 01/26/2023] Open
Abstract
Hyperpolarization-activated cyclic nucleotide–gated cation (HCN) channels play a critical role in the control of pacemaking in the heart and repetitive firing in neurons. In HCN channels, the intracellular cyclic nucleotide–binding domain (CNBD) is connected to the transmembrane portion of the channel (TMPC) through a helical domain, the C-linker. Although this domain is critical for mechanical signal transduction, the conformational dynamics in the C-linker that transmit the nucleotide-binding signal to the HCN channel pore are unknown. Here, we use linear response theory to analyze conformational changes in the C-linker of the human HCN1 protein, which couple cAMP binding in the CNBD with gating in the TMPC. By applying a force to the tip of the so-called “elbow” of the C-linker, the coarse-grained calculations recapitulate the same conformational changes triggered by cAMP binding in experimental studies. Furthermore, in our simulations, a displacement of the C-linker parallel to the membrane plane (i.e. horizontally) induced a rotational movement resulting in a distinct tilting of the transmembrane helices. This movement, in turn, increased the distance between the voltage-sensing S4 domain and the surrounding transmembrane domains and led to a widening of the intracellular channel gate. In conclusion, our computational approach, combined with experimental data, thus provides a more detailed understanding of how cAMP binding is mechanically coupled over long distances to promote voltage-dependent opening of HCN channels.
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Affiliation(s)
- Christine Gross
- Computational Biology and Simulation Group, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Andrea Saponaro
- Department of Biosciences, University of Milan, 20133 Milan, Italy
| | - Bina Santoro
- Department of Neuroscience, Columbia University, New York, New York 10032
| | - Anna Moroni
- Department of Biosciences, University of Milan, 20133 Milan, Italy
| | - Gerhard Thiel
- Membrane Biophysics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany.
| | - Kay Hamacher
- Computational Biology and Simulation Group, Technische Universität Darmstadt, 64287 Darmstadt, Germany
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25
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Saponaro A, Cantini F, Porro A, Bucchi A, DiFrancesco D, Maione V, Donadoni C, Introini B, Mesirca P, Mangoni ME, Thiel G, Banci L, Santoro B, Moroni A. A synthetic peptide that prevents cAMP regulation in mammalian hyperpolarization-activated cyclic nucleotide-gated (HCN) channels. eLife 2018; 7:35753. [PMID: 29923826 PMCID: PMC6023613 DOI: 10.7554/elife.35753] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 06/14/2018] [Indexed: 12/13/2022] Open
Abstract
Binding of TRIP8b to the cyclic nucleotide binding domain (CNBD) of mammalian hyperpolarization-activated cyclic nucleotide-gated (HCN) channels prevents their regulation by cAMP. Since TRIP8b is expressed exclusively in the brain, we envisage that it can be used for orthogonal control of HCN channels beyond the central nervous system. To this end, we have identified by rational design a 40-aa long peptide (TRIP8bnano) that recapitulates affinity and gating effects of TRIP8b in HCN isoforms (hHCN1, mHCN2, rbHCN4) and in the cardiac current If in rabbit and mouse sinoatrial node cardiomyocytes. Guided by an NMR-derived structural model that identifies the key molecular interactions between TRIP8bnano and the HCN CNBD, we further designed a cell-penetrating peptide (TAT-TRIP8bnano) which successfully prevented β-adrenergic activation of mouse If leaving the stimulation of the L-type calcium current (ICaL) unaffected. TRIP8bnano represents a novel approach to selectively control HCN activation, which yields the promise of a more targeted pharmacology compared to pore blockers.
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Affiliation(s)
- Andrea Saponaro
- Department of Biosciences, University of Milan, Milan, Italy
| | - Francesca Cantini
- Department of Chemistry, University of Florence, Florence, Italy.,Magnetic Resonance Center, University of Florence, Florence, Italy
| | | | - Annalisa Bucchi
- Department of Biosciences, University of Milan, Milan, Italy
| | | | - Vincenzo Maione
- Interuniversity Consortium for Magnetic Resonance of Metalloproteins, Sesto Fiorentino, Italy
| | - Chiara Donadoni
- Department of Biosciences, University of Milan, Milan, Italy
| | - Bianca Introini
- Department of Biosciences, University of Milan, Milan, Italy
| | - Pietro Mesirca
- Institut de Génomique Fonctionnelle, CNRS, INSERM F-34094, Université de Montpellier, Montpellier, France.,Laboratory of Excellence Ion Channels Science and Therapeutics, Valbonne, France
| | - Matteo E Mangoni
- Institut de Génomique Fonctionnelle, CNRS, INSERM F-34094, Université de Montpellier, Montpellier, France.,Laboratory of Excellence Ion Channels Science and Therapeutics, Valbonne, France
| | - Gerhard Thiel
- Department of Biology, TU-Darmstadt, Darmstadt, Germany
| | - Lucia Banci
- Department of Chemistry, University of Florence, Florence, Italy.,Magnetic Resonance Center, University of Florence, Florence, Italy.,Interuniversity Consortium for Magnetic Resonance of Metalloproteins, Sesto Fiorentino, Italy.,Institute of Neurosciences, Consiglio Nazionale delle Ricerche, Florence, Italy
| | - Bina Santoro
- Department of Neuroscience, Columbia University, New York, United States
| | - Anna Moroni
- Department of Biosciences, University of Milan, Milan, Italy.,Institute of Biophysics, Consiglio Nazionale delle Ricerche, Milan, Italy
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26
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VanSchouwen B, Melacini G. Role of Dimers in the cAMP-Dependent Activation of Hyperpolarization-Activated Cyclic-Nucleotide-Modulated (HCN) Ion Channels. J Phys Chem B 2018; 122:2177-2190. [PMID: 29461059 DOI: 10.1021/acs.jpcb.7b10125] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Hyperpolarization-activated cyclic-nucleotide-modulated (HCN) ion channels control rhythmicity in neurons and cardiomyocytes. Cyclic AMP (cAMP) modulates HCN activity through the cAMP-induced formation of a tetrameric gating ring spanning the intracellular region (IR) of HCN. Although evidence from confocal patch-clamp fluorometry indicates that the cAMP-dependent gating of HCN occurs through a dimer of dimers, the structural and dynamical basis of cAMP allostery in HCN dimers has so far remained elusive. Thus, here we examine how dimers influence IR structural dynamics, and the role that such structural dynamics play in HCN allostery. To this end, we performed molecular dynamics (MD) simulations of HCN4 IR dimers in their fully apo, fully holo, and partially cAMP-bound states, resulting in a total simulated time of 1.2 μs. Comparative analyses of these MD trajectories, as well as previous monomer and tetramer simulations utilized as benchmarks for comparison, reveal that dimers markedly sensitize the HCN IR to cAMP-modulated allostery. Our results indicate that dimerization fine-tunes the IR dynamics to enhance, relative to both monomers and tetramers, the allosteric intra- and interprotomer coupling between the cAMP-binding domain and tetramerization domain components of the IR. The resulting allosteric model provides a viable rationalization of electrophysiological data on the role of IR dimers in HCN activation.
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Affiliation(s)
- Bryan VanSchouwen
- Department of Chemistry and Chemical Biology and ‡Department of Biochemistry and Biomedical Sciences, McMaster University , 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
| | - Giuseppe Melacini
- Department of Chemistry and Chemical Biology and ‡Department of Biochemistry and Biomedical Sciences, McMaster University , 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
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27
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James ZM, Zagotta WN. Structural insights into the mechanisms of CNBD channel function. J Gen Physiol 2017; 150:225-244. [PMID: 29233886 PMCID: PMC5806680 DOI: 10.1085/jgp.201711898] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 11/28/2017] [Indexed: 12/28/2022] Open
Abstract
James and Zagotta discuss how recent cryoEM structures inform our understanding of cyclic nucleotide–binding domain channels. Cyclic nucleotide-binding domain (CNBD) channels are a family of ion channels in the voltage-gated K+ channel superfamily that play crucial roles in many physiological processes. CNBD channels are structurally similar but functionally very diverse. This family includes three subfamilies: (1) the cyclic nucleotide-gated (CNG) channels, which are cation-nonselective, voltage-independent, and cyclic nucleotide-gated; (2) the hyperpolarization-activated cyclic nucleotide-gated (HCN) channels, which are weakly K+ selective, hyperpolarization-activated, and cyclic nucleotide-gated; and (3) the ether-à-go-go-type (KCNH) channels, which are strongly K+ selective, depolarization-activated, and cyclic nucleotide-independent. Recently, several high-resolution structures have been reported for intact CNBD channels, providing a structural framework to better understand their diverse function. In this review, we compare and contrast the recent structures and discuss how they inform our understanding of ion selectivity, voltage-dependent gating, and cyclic nucleotide–dependent gating within this channel family.
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Affiliation(s)
- Zachary M James
- Department of Physiology and Biophysics, University of Washington, Seattle, WA
| | - William N Zagotta
- Department of Physiology and Biophysics, University of Washington, Seattle, WA
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28
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VanSchouwen B, Melacini G. Regulation of HCN Ion Channels by Non-canonical Cyclic Nucleotides. Handb Exp Pharmacol 2017; 238:123-133. [PMID: 28181007 DOI: 10.1007/164_2016_5006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The hyperpolarization-activated cyclic-nucleotide-modulated (HCN) proteins are cAMP-regulated ion channels that play a key role in nerve impulse transmission and heart rate modulation in neuronal and cardiac cells, respectively. Although they are regulated primarily by cAMP, other cyclic nucleotides such as cGMP, cCMP, and cUMP serve as partial agonists for the HCN2 and HCN4 isoforms. By competing with cAMP for binding, these non-canonical ligands alter ion channel gating, and in turn, modulate the cAMP-dependent activation profiles. The partial activation of non-canonical cyclic nucleotides can be rationalized by either a partial reversal of a two-state inactive/active conformational equilibrium, or by sampling of a third conformational state with partial activity. Furthermore, different mechanisms and degrees of activation have been observed upon binding of non-canonical cyclic nucleotides to HCN2 versus HCN4, suggesting that these ligands control HCN ion channels in an isoform-specific manner. While more work remains to be done to achieve a complete understanding of ion channel modulation by non-canonical cyclic nucleotides, it is already clear that such knowledge will ultimately prove invaluable in achieving a more complete understanding of ion channel signaling in vivo, as well as in the development of therapeutics designed to selectively modulate ion channel gating.
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Affiliation(s)
- Bryan VanSchouwen
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, Canada, L8S 4M1
| | - Giuseppe Melacini
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, Canada, L8S 4M1. .,Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, Canada, L8S 4M1.
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29
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Abstract
Cyclic nucleotide-gated (CNG) and hyperpolarization-activated cyclic nucleotide-regulated (HCN) ion channels play crucial physiological roles in phototransduction, olfaction, and cardiac pace making. These channels are characterized by the presence of a carboxyl-terminal cyclic nucleotide-binding domain (CNBD) that connects to the channel pore via a C-linker domain. Although cyclic nucleotide binding has been shown to promote CNG and HCN channel opening, the precise mechanism underlying gating remains poorly understood. Here we used cryoEM to determine the structure of the intact LliK CNG channel isolated from Leptospira licerasiae-which shares sequence similarity to eukaryotic CNG and HCN channels-in the presence of a saturating concentration of cAMP. A short S4-S5 linker connects nearby voltage-sensing and pore domains to produce a non-domain-swapped transmembrane architecture, which appears to be a hallmark of this channel family. We also observe major conformational changes of the LliK C-linkers and CNBDs relative to the crystal structures of isolated C-linker/CNBD fragments and the cryoEM structures of related CNG, HCN, and KCNH channels. The conformation of our LliK structure may represent a functional state of this channel family not captured in previous studies.
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30
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VanSchouwen B, Melacini G. Structural Basis of Tonic Inhibition by Dimers of Dimers in Hyperpolarization-Activated Cyclic-Nucleotide-Modulated (HCN) Ion Channels. J Phys Chem B 2016; 120:10936-10950. [DOI: 10.1021/acs.jpcb.6b07735] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bryan VanSchouwen
- Department
of Chemistry and Chemical Biology, McMaster University, 1280 Main
Street West, Hamilton, Ontario L8S 4M1, Canada
| | - Giuseppe Melacini
- Department
of Chemistry and Chemical Biology, McMaster University, 1280 Main
Street West, Hamilton, Ontario L8S 4M1, Canada
- Department
of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4M1, Canada
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31
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Cyclic Purine and Pyrimidine Nucleotides Bind to the HCN2 Ion Channel and Variably Promote C-Terminal Domain Interactions and Opening. Structure 2016; 24:1629-1642. [PMID: 27568927 DOI: 10.1016/j.str.2016.06.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 06/22/2016] [Accepted: 06/23/2016] [Indexed: 11/21/2022]
Abstract
Cyclic AMP is thought to facilitate the opening of the HCN2 channel by binding to a C-terminal domain and promoting or inhibiting interactions between subunits. Here, we correlated the ability of cyclic nucleotides to promote interactions of isolated HCN2 C-terminal domains in solution with their ability to facilitate channel opening. Cyclic IMP, a cyclic purine nucleotide, and cCMP, a cyclic pyrimidine nucleotide, bind to a C-terminal domain containing the cyclic nucleotide-binding domain but, in contrast to other cyclic nucleotides examined, fail to promote its oligomerization, and produce only modest facilitation of opening of the full-length channel. Comparisons between ligand bound structures identify a region between the sixth and seventh β strands and the distal C helix as important for facilitation and tight binding. We propose that promotion of interactions between the C-terminal domains by a given ligand contribute to its ability to facilitate opening of the full-length channel.
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32
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Syeda R, Qiu Z, Dubin AE, Murthy SE, Florendo MN, Mason DE, Mathur J, Cahalan SM, Peters EC, Montal M, Patapoutian A. LRRC8 Proteins Form Volume-Regulated Anion Channels that Sense Ionic Strength. Cell 2016; 164:499-511. [PMID: 26824658 DOI: 10.1016/j.cell.2015.12.031] [Citation(s) in RCA: 178] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 11/16/2015] [Accepted: 12/04/2015] [Indexed: 01/03/2023]
Abstract
The volume-regulated anion channel (VRAC) is activated when a cell swells, and it plays a central role in maintaining cell volume in response to osmotic challenges. SWELL1 (LRRC8A) was recently identified as an essential component of VRAC. However, the identity of the pore-forming subunits of VRAC and how the channel is gated by cell swelling are unknown. Here, we show that SWELL1 and up to four other LRRC8 subunits assemble into heterogeneous complexes of ∼800 kDa. When reconstituted into bilayers, LRRC8 complexes are sufficient to form anion channels activated by osmolality gradients. In bilayers, as well as in cells, the single-channel conductance of the complexes depends on the LRRC8 composition. Finally, low ionic strength (Γ) in the absence of an osmotic gradient activates the complexes in bilayers. These data demonstrate that LRRC8 proteins together constitute the VRAC pore and that hypotonic stress can activate VRAC through a decrease in cytoplasmic Γ.
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Affiliation(s)
- Ruhma Syeda
- Department of Molecular and Cellular Neuroscience, Howard Hughes Medical Institute, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Zhaozhu Qiu
- Department of Molecular and Cellular Neuroscience, Howard Hughes Medical Institute, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Genomics Institute of the Novartis Research Foundation (GNF), San Diego, CA 92121, USA
| | - Adrienne E Dubin
- Department of Molecular and Cellular Neuroscience, Howard Hughes Medical Institute, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Swetha E Murthy
- Department of Molecular and Cellular Neuroscience, Howard Hughes Medical Institute, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Maria N Florendo
- Department of Molecular and Cellular Neuroscience, Howard Hughes Medical Institute, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel E Mason
- Genomics Institute of the Novartis Research Foundation (GNF), San Diego, CA 92121, USA
| | - Jayanti Mathur
- Genomics Institute of the Novartis Research Foundation (GNF), San Diego, CA 92121, USA
| | - Stuart M Cahalan
- Department of Molecular and Cellular Neuroscience, Howard Hughes Medical Institute, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Eric C Peters
- Genomics Institute of the Novartis Research Foundation (GNF), San Diego, CA 92121, USA
| | - Mauricio Montal
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ardem Patapoutian
- Department of Molecular and Cellular Neuroscience, Howard Hughes Medical Institute, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA.
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33
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Bai D. Structural analysis of key gap junction domains--Lessons from genome data and disease-linked mutants. Semin Cell Dev Biol 2015; 50:74-82. [PMID: 26658099 DOI: 10.1016/j.semcdb.2015.11.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 11/26/2015] [Indexed: 12/27/2022]
Abstract
A gap junction (GJ) channel is formed by docking of two GJ hemichannels and each of these hemichannels is a hexamer of connexins. All connexin genes have been identified in human, mouse, and rat genomes and their homologous genes in many other vertebrates are available in public databases. The protein sequences of these connexins align well with high sequence identity in the same connexin across different species. Domains in closely related connexins and several residues in all known connexins are also well-conserved. These conserved residues form signatures (also known as sequence logos) in these domains and are likely to play important biological functions. In this review, the sequence logos of individual connexins, groups of connexins with common ancestors, and all connexins are analyzed to visualize natural evolutionary variations and the hot spots for human disease-linked mutations. Several gap junction domains are homologous, likely forming similar structures essential for their function. The availability of a high resolution Cx26 GJ structure and the subsequently-derived homology structure models for other connexin GJ channels elevated our understanding of sequence logos at the three-dimensional GJ structure level, thus facilitating the understanding of how disease-linked connexin mutants might impair GJ structure and function. This knowledge will enable the design of complementary variants to rescue disease-linked mutants.
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Affiliation(s)
- Donglin Bai
- Department of Physiology and Pharmacology, The University of Western Ontario, London, ON, Canada N6A 5C1.
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34
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DeBerg HA, Brzovic PS, Flynn GE, Zagotta WN, Stoll S. Structure and Energetics of Allosteric Regulation of HCN2 Ion Channels by Cyclic Nucleotides. J Biol Chem 2015; 291:371-81. [PMID: 26559974 PMCID: PMC4697172 DOI: 10.1074/jbc.m115.696450] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Indexed: 12/20/2022] Open
Abstract
Hyperpolarization-activated cyclic nucleotide-gated (HCN) ion channels play an important role in regulating electrical activity in the heart and brain. They are gated by the binding of cyclic nucleotides to a conserved, intracellular cyclic nucleotide-binding domain (CNBD), which is connected to the channel pore by a C-linker region. Binding of cyclic nucleotides increases the rate and extent of channel activation and shifts it to less hyperpolarized voltages. We probed the allosteric mechanism of different cyclic nucleotides on the CNBD and on channel gating. Electrophysiology experiments showed that cAMP, cGMP, and cCMP were effective agonists of the channel and produced similar increases in the extent of channel activation. In contrast, electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) on the isolated CNBD indicated that the induced conformational changes and the degrees of stabilization of the active conformation differed for the three cyclic nucleotides. We explain these results with a model where different allosteric mechanisms in the CNBD all converge to have the same effect on the C-linker and render all three cyclic nucleotides similarly potent activators of the channel.
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Affiliation(s)
- Hannah A DeBerg
- From the Departments of Chemistry, Physiology and Biophysics, and
| | - Peter S Brzovic
- Biochemistry, University of Washington, Seattle, Washington 98195
| | | | | | - Stefan Stoll
- From the Departments of Chemistry, Physiology and Biophysics, and
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35
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Magee KEA, Madden Z, Young EC. HCN Channel C-Terminal Region Speeds Activation Rates Independently of Autoinhibition. J Membr Biol 2015; 248:1043-60. [PMID: 26123597 DOI: 10.1007/s00232-015-9816-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 06/08/2015] [Indexed: 01/13/2023]
Abstract
Hyperpolarization- and cyclic nucleotide-activated (HCN) channels contribute to rhythmic oscillations in excitable cells. They possess an intrinsic autoinhibition with a hyperpolarized V 1/2, which can be relieved by cAMP binding to the cyclic nucleotide binding (CNB) fold in the C-terminal region or by deletion of the CNB fold. We questioned whether V 1/2 shifts caused by altering the autoinhibitory CNB fold would be accompanied by parallel changes in activation rates. We used two-electrode voltage clamp on Xenopus oocytes to compare wildtype (WT) HCN2, a constitutively autoinhibited point mutant incapable of cAMP binding (HCN2 R591E), and derivatives with various C-terminal truncations. Activation V 1/2 and deactivation t 1/2 measurements confirmed that a truncated channel lacking the helix αC of the CNB fold (ΔαC) had autoinhibition comparable to HCN2 R591E; however, ΔαC activated approximately two-fold slower than HCN2 R591E over a 60-mV range of hyperpolarizations. A channel with a more drastic truncation deleting the entire CNB fold (ΔCNB) had similar V 1/2 values to HCN2 WT with endogenous cAMP bound, confirming autoinhibition relief, yet it surprisingly activated slower than the autoinhibited HCN2 R591E. Whereas CNB fold truncation slowed down voltage-dependent reaction steps, the voltage-independent closed-open equilibrium subject to autoinhibition in HCN2 was not rate-limiting. Chemically inhibiting formation of the endogenous lipid PIP2 hyperpolarized the V 1/2 of HCN2 WT but did not slow down activation to match ΔCNB rates. Our findings suggest a "quickening conformation" mechanism, requiring a full-length CNB that ensures fast rates for voltage-dependent steps during activation regardless of potentiation by cAMP or PIP2.
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Affiliation(s)
- Kaylee E A Magee
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Zarina Madden
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Edgar C Young
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada.
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36
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VanSchouwen B, Akimoto M, Sayadi M, Fogolari F, Melacini G. Role of Dynamics in the Autoinhibition and Activation of the Hyperpolarization-activated Cyclic Nucleotide-modulated (HCN) Ion Channels. J Biol Chem 2015; 290:17642-17654. [PMID: 25944904 DOI: 10.1074/jbc.m115.651877] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Indexed: 01/01/2023] Open
Abstract
The hyperpolarization-activated cyclic nucleotide-modulated (HCN) ion channels control rhythmicity in neurons and cardiomyocytes. Cyclic AMP allosterically modulates HCN through the cAMP-dependent formation of a tetrameric gating ring spanning the intracellular region (IR) of HCN, to which cAMP binds. Although the apo versus holo conformational changes of the cAMP-binding domain (CBD) have been previously mapped, only limited information is currently available on the HCN IR dynamics, which have been hypothesized to play a critical role in the cAMP-dependent gating of HCN. Here, using molecular dynamics simulations validated and complemented by experimental NMR and CD data, we comparatively analyze HCN IR dynamics in the four states of the thermodynamic cycle arising from the coupling between cAMP binding and tetramerization equilibria. This extensive set of molecular dynamics trajectories captures the active-to-inactive transition that had remained elusive for other CBDs, and it provides unprecedented insight on the role of IR dynamics in HCN autoinhibition and its release by cAMP. Specifically, the IR tetramerization domain becomes more flexible in the monomeric states, removing steric clashes that the apo-CDB structure would otherwise impose. Furthermore, the simulations reveal that the active/inactive structural transition for the apo-monomeric CBD occurs through a manifold of pathways that are more divergent than previously anticipated. Upon cAMP binding, these pathways become disallowed, pre-confining the CBD conformational ensemble to a tetramer-compatible state. This conformational confinement primes the IR for tetramerization and thus provides a model of how cAMP controls HCN channel gating.
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Affiliation(s)
- Bryan VanSchouwen
- Departments of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Madoka Akimoto
- Departments of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Maryam Sayadi
- Departments of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Federico Fogolari
- Department of Biomedical Science and Technology, University of Udine, Piazzale Kolbe 4, 33100 Udine, Italy
| | - Giuseppe Melacini
- Departments of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada; Departments of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4M1, Canada.
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37
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Kesters D, Brams M, Nys M, Wijckmans E, Spurny R, Voets T, Tytgat J, Kusch J, Ulens C. Structure of the SthK carboxy-terminal region reveals a gating mechanism for cyclic nucleotide-modulated ion channels. PLoS One 2015; 10:e0116369. [PMID: 25625648 PMCID: PMC4308110 DOI: 10.1371/journal.pone.0116369] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Accepted: 12/09/2014] [Indexed: 11/19/2022] Open
Abstract
Cyclic nucleotide-sensitive ion channels are molecular pores that open in response to cAMP or cGMP, which are universal second messengers. Binding of a cyclic nucleotide to the carboxyterminal cyclic nucleotide binding domain (CNBD) of these channels is thought to cause a conformational change that promotes channel opening. The C-linker domain, which connects the channel pore to this CNBD, plays an important role in coupling ligand binding to channel opening. Current structural insight into this mechanism mainly derives from X-ray crystal structures of the C-linker/CNBD from hyperpolarization-activated cyclic nucleotide-modulated (HCN) channels. However, these structures reveal little to no conformational changes upon comparison of the ligand-bound and unbound form. In this study, we take advantage of a recently identified prokaryote ion channel, SthK, which has functional properties that strongly resemble cyclic nucleotide-gated (CNG) channels and is activated by cAMP, but not by cGMP. We determined X-ray crystal structures of the C-linker/CNBD of SthK in the presence of cAMP or cGMP. We observe that the structure in complex with cGMP, which is an antagonist, is similar to previously determined HCN channel structures. In contrast, the structure in complex with cAMP, which is an agonist, is in a more open conformation. We observe that the CNBD makes an outward swinging movement, which is accompanied by an opening of the C-linker. This conformation mirrors the open gate structures of the Kv1.2 channel or MthK channel, which suggests that the cAMP-bound C-linker/CNBD from SthK represents an activated conformation. These results provide a structural framework for better understanding cyclic nucleotide modulation of ion channels, including HCN and CNG channels.
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Affiliation(s)
- Divya Kesters
- Laboratory of Structural Neurobiology, KU Leuven, Herestraat 49, PB601, Leuven, B-3000, Belgium
| | - Marijke Brams
- Laboratory of Structural Neurobiology, KU Leuven, Herestraat 49, PB601, Leuven, B-3000, Belgium
| | - Mieke Nys
- Laboratory of Structural Neurobiology, KU Leuven, Herestraat 49, PB601, Leuven, B-3000, Belgium
| | - Eveline Wijckmans
- Laboratory of Structural Neurobiology, KU Leuven, Herestraat 49, PB601, Leuven, B-3000, Belgium
| | - Radovan Spurny
- Laboratory of Structural Neurobiology, KU Leuven, Herestraat 49, PB601, Leuven, B-3000, Belgium
| | - Thomas Voets
- Laboratory of Ion Channel Research, KU Leuven, Herestraat 49, PB802, Leuven, B-3000, Belgium
| | - Jan Tytgat
- Laboratory of Toxicology and Pharmacology, KU Leuven, Herestraat 49, PB922, Leuven, B-3000, Belgium
| | - Jana Kusch
- University Hospital Jena, Institute of Physiologie II, Kollegiengasse 9, 07743, Jena, Germany
| | - Chris Ulens
- Laboratory of Structural Neurobiology, KU Leuven, Herestraat 49, PB601, Leuven, B-3000, Belgium
- * E-mail:
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38
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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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39
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Dynamic measurements for funny channels. Proc Natl Acad Sci U S A 2014; 111:14320-1. [PMID: 25249634 DOI: 10.1073/pnas.1416137111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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40
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Structural basis for the mutual antagonism of cAMP and TRIP8b in regulating HCN channel function. Proc Natl Acad Sci U S A 2014; 111:14577-82. [PMID: 25197093 DOI: 10.1073/pnas.1410389111] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
cAMP signaling in the brain mediates several higher order neural processes. Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels directly bind cAMP through their cytoplasmic cyclic nucleotide binding domain (CNBD), thus playing a unique role in brain function. Neuronal HCN channels are also regulated by tetratricopeptide repeat-containing Rab8b interacting protein (TRIP8b), an auxiliary subunit that antagonizes the effects of cAMP by interacting with the channel CNBD. To unravel the molecular mechanisms underlying the dual regulation of HCN channel activity by cAMP/TRIP8b, we determined the NMR solution structure of the HCN2 channel CNBD in the cAMP-free form and mapped on it the TRIP8b interaction site. We reconstruct here the full conformational changes induced by cAMP binding to the HCN channel CNBD. Our results show that TRIP8b does not compete with cAMP for the same binding region; rather, it exerts its inhibitory action through an allosteric mechanism, preventing the cAMP-induced conformational changes in the HCN channel CNBD.
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41
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Morais-Cabral JH, Robertson GA. The enigmatic cytoplasmic regions of KCNH channels. J Mol Biol 2014; 427:67-76. [PMID: 25158096 DOI: 10.1016/j.jmb.2014.08.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 08/14/2014] [Accepted: 08/15/2014] [Indexed: 01/09/2023]
Abstract
KCNH channels are expressed across a vast phylogenetic and evolutionary spectrum. In humans, they function in a wide range of tissues and serve as biomarkers and targets for diseases such as cancer and cardiac arrhythmias. These channels share a general architecture with other voltage-gated ion channels but are distinguished by the presence of an N-terminal PAS (Per-Arnt-Sim) domain and a C-terminal domain with homology to cyclic nucleotide binding domains (referred to as the CNBh domain). Cytosolic regions outside these domains show little conservation between KCNH families but are strongly conserved across species within a family, likely reflecting variability that confers specificity to individual channel types. PAS and CNBh domains participate in channel gating, but at least twice in evolutionary history, the PAS domain has been lost and it is omitted by alternate transcription to create a distinct channel subunit in one family. In this focused review, we present current knowledge of the structure and function of these cytosolic regions, discuss their evolution as modular domains and provide our perspective on the important questions moving forward.
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Affiliation(s)
- João H Morais-Cabral
- Instituto de Biologia Molecular e Celular, Universidade do Porto, 4150-180 Porto, Portugal.
| | - Gail A Robertson
- Department of Neuroscience, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
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42
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Hu L, Santoro B, Saponaro A, Liu H, Moroni A, Siegelbaum S. Binding of the auxiliary subunit TRIP8b to HCN channels shifts the mode of action of cAMP. ACTA ACUST UNITED AC 2014; 142:599-612. [PMID: 24277603 PMCID: PMC3840918 DOI: 10.1085/jgp.201311013] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Hyperpolarization-activated cyclic nucleotide–regulated cation (HCN) channels generate the hyperpolarization-activated cation current Ih present in many neurons. These channels are directly regulated by the binding of cAMP, which both shifts the voltage dependence of HCN channel opening to more positive potentials and increases maximal Ih at extreme negative voltages where voltage gating is complete. Here we report that the HCN channel brain-specific auxiliary subunit TRIP8b produces opposing actions on these two effects of cAMP. In the first action, TRIP8b inhibits the effect of cAMP to shift voltage gating, decreasing both the sensitivity of the channel to cAMP (K1/2) and the efficacy of cAMP (maximal voltage shift); conversely, cAMP binding inhibits these actions of TRIP8b. These mutually antagonistic actions are well described by a cyclic allosteric mechanism in which TRIP8b binding reduces the affinity of the channel for cAMP, with the affinity of the open state for cAMP being reduced to a greater extent than the cAMP affinity of the closed state. In a second apparently independent action, TRIP8b enhances the action of cAMP to increase maximal Ih. This latter effect cannot be explained by the cyclic allosteric model but results from a previously uncharacterized action of TRIP8b to reduce maximal current through the channel in the absence of cAMP. Because the binding of cAMP also antagonizes this second effect of TRIP8b, application of cAMP produces a larger increase in maximal Ih in the presence of TRIP8b than in its absence. These findings may provide a mechanistic explanation for the wide variability in the effects of modulatory transmitters on the voltage gating and maximal amplitude of Ih reported for different neurons in the brain.
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Affiliation(s)
- Lei Hu
- Department of Neuroscience, 2 Department of Pharmacology, and 3 Howard Hughes Medical Institute, Columbia University, New York, NY 10032
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43
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Lyashchenko AK, Redd KJ, Goldstein PA, Tibbs GR. cAMP control of HCN2 channel Mg2+ block reveals loose coupling between the cyclic nucleotide-gating ring and the pore. PLoS One 2014; 9:e101236. [PMID: 24983358 PMCID: PMC4077740 DOI: 10.1371/journal.pone.0101236] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 06/04/2014] [Indexed: 12/24/2022] Open
Abstract
Hyperpolarization-activated cyclic nucleotide-regulated HCN channels underlie the Na+-K+ permeable IH pacemaker current. As with other voltage-gated members of the 6-transmembrane KV channel superfamily, opening of HCN channels involves dilation of a helical bundle formed by the intracellular ends of S6 albeit this is promoted by inward, not outward, displacement of S4. Direct agonist binding to a ring of cyclic nucleotide-binding sites, one of which lies immediately distal to each S6 helix, imparts cAMP sensitivity to HCN channel opening. At depolarized potentials, HCN channels are further modulated by intracellular Mg2+ which blocks the open channel pore and blunts the inhibitory effect of outward K+ flux. Here, we show that cAMP binding to the gating ring enhances not only channel opening but also the kinetics of Mg2+ block. A combination of experimental and simulation studies demonstrates that agonist acceleration of block is mediated via acceleration of the blocking reaction itself rather than as a secondary consequence of the cAMP enhancement of channel opening. These results suggest that the activation status of the gating ring and the open state of the pore are not coupled in an obligate manner (as required by the often invoked Monod-Wyman-Changeux allosteric model) but couple more loosely (as envisioned in a modular model of protein activation). Importantly, the emergence of second messenger sensitivity of open channel rectification suggests that loose coupling may have an unexpected consequence: it may endow these erstwhile “slow” channels with an ability to exert voltage and ligand-modulated control over cellular excitability on the fastest of physiologically relevant time scales.
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Affiliation(s)
- Alex K. Lyashchenko
- Department of Anesthesiology, Columbia University, New York, New York, United States of America
| | - Kacy J. Redd
- Department of Neuroscience, Columbia University, New York, New York, United States of America
| | - Peter A. Goldstein
- Department of Anesthesiology, Weill Cornell Medical College, New York, New York, United States of America
| | - Gareth R. Tibbs
- Department of Anesthesiology, Columbia University, New York, New York, United States of America
- Department of Anesthesiology, Weill Cornell Medical College, New York, New York, United States of America
- * E-mail:
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44
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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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45
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Extracellular domains play different roles in gap junction formation and docking compatibility. Biochem J 2014; 458:1-10. [PMID: 24438327 DOI: 10.1042/bj20131162] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
GJ (gap junction) channels mediate direct intercellular communication and play an important role in many physiological processes. Six connexins oligomerize to form a hemichannel and two hemichannels dock together end-to-end to form a GJ channel. Connexin extracellular domains (E1 and E2) have been shown to be important for the docking, but the molecular mechanisms behind the docking and formation of GJ channels are not clear. Recent developments in atomic GJ structure and functional studies on a series of connexin mutants revealed that E1 and E2 are likely to play different roles in the docking. Non-covalent interactions at the docking interface, including hydrogen bonds, are predicted to form between interdocked extracellular domains. Protein sequence alignment analysis on the docking compatible/incompatible connexins indicate that the E1 domain is important for the formation of the GJ channel and the E2 domain is important in the docking compatibility in heterotypic channels. Interestingly, the hydrogen-bond forming or equivalent residues in both E1 and E2 domains are mutational hot spots for connexin-linked human diseases. Understanding the molecular mechanisms of GJ docking can assist us to develop novel strategies in rescuing the disease-linked connexin mutants.
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46
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Lopez W, Gonzalez J, Liu Y, Harris AL, Contreras JE. Insights on the mechanisms of Ca(2+) regulation of connexin26 hemichannels revealed by human pathogenic mutations (D50N/Y). ACTA ACUST UNITED AC 2014; 142:23-35. [PMID: 23797420 PMCID: PMC3691447 DOI: 10.1085/jgp.201210893] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Because of the large size and modest selectivity of the connexin hemichannel aqueous pore, hemichannel opening must be highly regulated to maintain cell viability. At normal resting potentials, this regulation is achieved predominantly by the physiological extracellular Ca2+ concentration, which drastically reduces hemichannel activity. Here, we characterize the Ca2+ regulation of channels formed by wild-type human connexin26 (hCx26) and its human mutations, D50N/Y, that cause aberrant hemichannel opening and result in deafness and skin disorders. We found that in hCx26 wild-type channels, deactivation kinetics are accelerated as a function of Ca2+ concentration, indicating that Ca2+ facilitates transition to, and stabilizes, the closed state of the hemichannels. The D50N/Y mutant hemichannels show lower apparent affinities for Ca2+-induced closing than wild-type channels and have more rapid deactivation kinetics, which are Ca2+ insensitive. These results suggest that D50 plays a role in (a) stabilizing the open state in the absence of Ca2+, and (b) facilitating closing and stabilization of the closed state in the presence of Ca2+. To explore the role of a negatively charged residue at position 50 in regulation by Ca2+, this position was substituted with a cysteine residue, which was then modified with a negatively charged methanethiosulfonate reagent, sodium (2-sulfanoethyl) methanethiosulfonate (MTSES)−. D50C mutant hemichannels display properties similar to those of D50N/Y mutants. Recovery of the negative charge with chemical modification by MTSES− restores the wild-type Ca2+ regulation of the channels. These results confirm the essential role of a negative charge at position 50 for Ca2+ regulation. Additionally, charge-swapping mutagenesis studies suggest involvement of a salt bridge interaction between D50 and K61 in the adjacent connexin subunit in stabilizing the open state in low extracellular Ca2+. Mutant cycle analysis supports a Ca2+-sensitive interaction between these two residues in the open state of the channel. We propose that disruption of this interaction by extracellular Ca2+ destabilizes the open state and facilitates hemichannel closing. Our data provide a mechanistic understanding of how mutations at position 50 that cause human diseases are linked to dysfunction of hemichannel gating by external Ca2+.
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Affiliation(s)
- William Lopez
- Department of Pharmacology and Physiology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, NJ 07103, USA
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47
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Young E. Will the Real Single HCN Channel Please Stand Up? Biophys J 2013; 105:1549-50. [DOI: 10.1016/j.bpj.2013.08.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 08/06/2013] [Indexed: 11/25/2022] Open
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48
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Gianulis EC, Liu Q, Trudeau MC. Direct interaction of eag domains and cyclic nucleotide-binding homology domains regulate deactivation gating in hERG channels. ACTA ACUST UNITED AC 2013; 142:351-66. [PMID: 24043860 PMCID: PMC3787778 DOI: 10.1085/jgp.201310995] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Human ether-á-go-go (eag)-related gene (hERG) potassium channels play a critical role in cardiac repolarization and are characterized by unusually slow closing (deactivation) kinetics. The N-terminal “eag” domain and a C-terminal C-linker/cyclic nucleotide–binding homology domain (CNBHD) are required for regulation of slow deactivation. The region between the S4 and S5 transmembrane domains (S4–S5 linker) is also implicated in this process, but the mechanism for regulation of slow deactivation is unclear. Here, using an eag domain–deleted channel (hERG Δeag) fused to Citrine fluorescent protein, we found that most channels bearing individual alanine mutations in the S4–S5 linker were directly regulated by recombinant eag domains fused to a cyan fluorescent protein (N-eag-CFP) and had robust Förster resonance energy transfer (FRET). Additionally, a channel bearing a group of eight alanine residues in the S4–S5 linker was not measurably regulated by N-eag-CFP domains, but robust FRET was measured. These findings demonstrate that the eag domain associated with all of the S4–S5 linker mutant channels. In contrast, channels that also lacked the CNBHD (hERG Δeag ΔCNBHD-Citrine) were not measurably regulated by N-eag-CFP nor was FRET detected, suggesting that the C-linker/CNBHD was required for eag domains to directly associate with the channel. In a FRET hybridization assay, N-eag-CFP had robust FRET with a C-linker/CNBHD-Citrine, suggesting a direct and specific interaction between the eag domain and the C-linker/CNBHD. Lastly, coexpression of a hERG subunit lacking the CNBHD and the distal C-terminal region (hERG ΔpCT-Citrine) with hERG Δeag-CFP subunits had FRET and partial restoration of slow deactivation. Collectively, these findings reveal that the C-linker/CNBHD, but not the S4–S5 linker, was necessary for the eag domain to associate with the channel, that the eag domain and the C-linker/CNBHD were sufficient for a direct interaction, and that an intersubunit interaction between the eag domain and the C-linker/CNBHD regulated slow deactivation in hERG channels at the plasma membrane.
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Affiliation(s)
- Elena C Gianulis
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD 21201
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49
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Dai G, Peng C, Liu C, Varnum MD. Two structural components in CNGA3 support regulation of cone CNG channels by phosphoinositides. ACTA ACUST UNITED AC 2013; 141:413-30. [PMID: 23530136 PMCID: PMC3607822 DOI: 10.1085/jgp.201210944] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Cyclic nucleotide-gated (CNG) channels in retinal photoreceptors play a crucial role in vertebrate phototransduction. The ligand sensitivity of photoreceptor CNG channels is adjusted during adaptation and in response to paracrine signals, but the mechanisms involved in channel regulation are only partly understood. Heteromeric cone CNGA3 (A3) + CNGB3 (B3) channels are inhibited by membrane phosphoinositides (PIP(n)), including phosphatidylinositol 3,4,5-triphosphate (PIP(3)) and phosphatidylinositol 4,5-bisphosphate (PIP(2)), demonstrating a decrease in apparent affinity for cyclic guanosine monophosphate (cGMP). Unlike homomeric A1 or A2 channels, A3-only channels paradoxically did not show a decrease in apparent affinity for cGMP after PIP(n) application. However, PIP(n) induced an ∼2.5-fold increase in cAMP efficacy for A3 channels. The PIP(n)-dependent change in cAMP efficacy was abolished by mutations in the C-terminal region (R643Q/R646Q) or by truncation distal to the cyclic nucleotide-binding domain (613X). In addition, A3-613X unmasked a threefold decrease in apparent cGMP affinity with PIP(n) application to homomeric channels, and this effect was dependent on conserved arginines within the N-terminal region of A3. Together, these results indicate that regulation of A3 subunits by phosphoinositides exhibits two separable components, which depend on structural elements within the N- and C-terminal regions, respectively. Furthermore, both N and C regulatory modules in A3 supported PIP(n) regulation of heteromeric A3+B3 channels. B3 subunits were not sufficient to confer PIP(n) sensitivity to heteromeric channels formed with PIP(n)-insensitive A subunits. Finally, channels formed by mixtures of PIP(n)-insensitive A3 subunits, having complementary mutations in N- and/or C-terminal regions, restored PIP(n) regulation, implying that intersubunit N-C interactions help control the phosphoinositide sensitivity of cone CNG channels.
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Affiliation(s)
- Gucan Dai
- Department of Integrative Physiology and Neuroscience, Washington State University, Pullman, WA 99164, USA
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50
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Abdel-Hamid H, Chin K, Moeder W, Shahinas D, Gupta D, Yoshioka K. A suppressor screen of the chimeric AtCNGC11/12 reveals residues important for intersubunit interactions of cyclic nucleotide-gated ion channels. PLANT PHYSIOLOGY 2013; 162:1681-93. [PMID: 23735507 PMCID: PMC3707543 DOI: 10.1104/pp.113.217539] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 06/01/2013] [Indexed: 05/23/2023]
Abstract
To investigate the structure-function relationship of plant cyclic nucleotide-gated ion channels (CNGCs), we identified a total of 29 mutant alleles of the chimeric AtCNGC11/12 gene that induces multiple defense responses in the Arabidopsis (Arabidopsis thaliana) mutant, constitutive expresser of PR genes22 (cpr22). Based on computational modeling, two new alleles, S100 (AtCNGC11/12:G459R) and S137 (AtCNGC11/12:R381H), were identified as counterparts of human CNGA3 (a human CNGC) mutants. Both mutants lost all cpr22-mediated phenotypes. Transient expression in Nicotiana benthamiana as well as functional complementation in yeast (Saccharomyces cerevisiae) showed that both AtCNGC11/12:G459R and AtCNGC11/12:R381H have alterations in their channel function. Site-directed mutagenesis coupled with fast-protein liquid chromatography using recombinantly expressed C-terminal peptides indicated that both mutations significantly influence subunit stoichiometry to form multimeric channels. This observation was confirmed by bimolecular fluorescence complementation in planta. Taken together, we have identified two residues that are likely important for subunit interaction for plant CNGCs and likely for animal CNGCs as well.
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