1
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Alhalhooly L, Sine SM. Ion transport in muscle acetylcholine receptor maintained by conserved salt bridges between the pore and lipid membrane. Proc Natl Acad Sci U S A 2024; 121:e2320416121. [PMID: 38588428 PMCID: PMC11032472 DOI: 10.1073/pnas.2320416121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/07/2024] [Indexed: 04/10/2024] Open
Abstract
Pores through ion channels rapidly transport small inorganic ions along their electrochemical gradients. Here, applying single-channel electrophysiology and mutagenesis to the archetypal muscle nicotinic acetylcholine receptor (AChR) channel, we show that a conserved pore-peripheral salt bridge partners with those in the other subunits to regulate ion transport. Disrupting the salt bridges in all five receptor subunits greatly decreases the amplitude of the unitary current and increases its fluctuations. However, disrupting individual salt bridges has unequal effects that depend on the structural status of the other salt bridges. The AChR ε- and δ-subunits are structurally unique in harboring a putative palmitoylation site near each salt bridge and bordering the lipid membrane. The effects of disrupting the palmitoylation sites mirror those of disrupting the salt bridges, but the effect of disrupting either of these structures depends on the structural status of the other. Thus, rapid ion transport through the AChR channel is maintained by functionally interdependent salt bridges linking the pore to the lipid membrane.
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Affiliation(s)
- Lina Alhalhooly
- Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine and Science, Rochester, MN55905
| | - Steven M. Sine
- Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine and Science, Rochester, MN55905
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN55905
- Department of Neurology, Mayo Clinic College of Medicine and Science, Rochester, MN55905
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2
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Strikwerda JR, Natarajan K, Sine SM. Impact on AChR open channel noise by pore-peripheral salt bridge depends on voltage and divalent cations. Biophys J 2023; 122:2430-2444. [PMID: 37113056 PMCID: PMC10322898 DOI: 10.1016/j.bpj.2023.04.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 02/16/2023] [Accepted: 04/24/2023] [Indexed: 04/29/2023] Open
Abstract
Mechanisms behind the fluctuations in the ionic current through single acetylcholine receptor (AChR) channels have remained elusive. In a recent study of muscle AChR we showed that mutation of a conserved intramembrane salt bridge in the β- and δ-subunits markedly increased fluctuations in the open channel current that extended from low to high frequency. Here, we show that extracellular divalent cations reduce the high-frequency fluctuations and increase the low-frequency fluctuations. The low-frequency fluctuations are shown to arise from steps between two current levels, with the ratio of the time at each level changing e-fold for a 70 mV increase in membrane potential, indicating modulation by a charged element within the membrane field. Increasing the charge on the ion selectivity filter biases the ratio of current levels equivalent to a 50 mV increase in membrane potential but does not alter the voltage dependence of the ratio. The magnitudes of the voltage dependence and voltage bias allow estimates of the distance between the ion selectivity filter and the voltage-sensing element. Studies with either calcium or magnesium show that the two divalent cations synergize to increase the low-frequency fluctuations, whereas they act independently to decrease the high-frequency fluctuations, indicating multiple divalent cation binding sites. Molecular dynamics simulations applied to the structure of the Torpedo AChR reveal that mutation of the salt bridge alters the equilibrium positions and dynamics of residues local to the site of the mutation and within the adjacent ion selectivity filter in a calcium-dependent manner. Thus, disruption of a conserved intramembrane salt bridge in the muscle AChR induces fluctuations in open channel current that are sensitive to divalent cation binding at multiple sites and modulated by a charged element within the membrane field.
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Affiliation(s)
- John R Strikwerda
- Receptor Biology Laboratory, Department of Physiology and Biomedical Engineering, Rochester, Minnesota
| | - Kathiresan Natarajan
- Receptor Biology Laboratory, Department of Physiology and Biomedical Engineering, Rochester, Minnesota
| | - Steven M Sine
- Receptor Biology Laboratory, Department of Physiology and Biomedical Engineering, Rochester, Minnesota; Department of Molecular Pharmacology and Experimental Therapeutics, Rochester, Minnesota; Department of Neurology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota.
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3
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Petroff JT, Dietzen NM, Santiago-McRae E, Deng B, Washington MS, Chen LJ, Trent Moreland K, Deng Z, Rau M, Fitzpatrick JAJ, Yuan P, Joseph TT, Hénin J, Brannigan G, Cheng WWL. Open-channel structure of a pentameric ligand-gated ion channel reveals a mechanism of leaflet-specific phospholipid modulation. Nat Commun 2022; 13:7017. [PMID: 36385237 PMCID: PMC9668969 DOI: 10.1038/s41467-022-34813-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 11/08/2022] [Indexed: 11/18/2022] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs) mediate synaptic transmission and are sensitive to their lipid environment. The mechanism of phospholipid modulation of any pLGIC is not well understood. We demonstrate that the model pLGIC, ELIC (Erwinia ligand-gated ion channel), is positively modulated by the anionic phospholipid, phosphatidylglycerol, from the outer leaflet of the membrane. To explore the mechanism of phosphatidylglycerol modulation, we determine a structure of ELIC in an open-channel conformation. The structure shows a bound phospholipid in an outer leaflet site, and structural changes in the phospholipid binding site unique to the open-channel. In combination with streamlined alchemical free energy perturbation calculations and functional measurements in asymmetric liposomes, the data support a mechanism by which an anionic phospholipid stabilizes the activated, open-channel state of a pLGIC by specific, state-dependent binding to this site.
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Affiliation(s)
- John T Petroff
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Noah M Dietzen
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Ezry Santiago-McRae
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, USA
| | - Brett Deng
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Maya S Washington
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Lawrence J Chen
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - K Trent Moreland
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Zengqin Deng
- Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO, USA
- Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, Saint Louis, MO, USA
| | - Michael Rau
- Center for Cellular Imaging, Washington University School of Medicine, Saint Louis, MO, USA
| | - James A J Fitzpatrick
- Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO, USA
- Center for Cellular Imaging, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Neuroscience, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Biomedical Engineering, Washington University School of Medicine, Saint Louis, MO, USA
| | - Peng Yuan
- Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO, USA
- Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, Saint Louis, MO, USA
| | - Thomas T Joseph
- Department of Anesthesiology and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jérôme Hénin
- Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Université Paris Cité, CNRS UPR 9080, Paris, France
| | - Grace Brannigan
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, USA
- Department of Physics, Rutgers University, Camden, NJ, USA
| | - Wayland W L Cheng
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA.
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4
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Strikwerda JR, Sine SM. Unmasking coupling between channel gating and ion permeation in the muscle nicotinic receptor. eLife 2021; 10:66225. [PMID: 33821794 PMCID: PMC8024024 DOI: 10.7554/elife.66225] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 03/19/2021] [Indexed: 11/24/2022] Open
Abstract
Whether ion channel gating is independent of ion permeation has been an enduring, unresolved question. Here, applying single channel recording to the archetypal muscle nicotinic receptor, we unmask coupling between channel gating and ion permeation by structural perturbation of a conserved intramembrane salt bridge. A charge-neutralizing mutation suppresses channel gating, reduces unitary current amplitude, and increases fluctuations of the open channel current. Power spectra of the current fluctuations exhibit low- and high-frequency Lorentzian components, which increase in charge-neutralized mutant receptors. After aligning channel openings and closings at the time of transition, the average unitary current exhibits asymmetric relaxations just after channel opening and before channel closing. A theory in which structural motions contribute jointly to channel gating and ion conduction describes both the power spectrum and the current relaxations. Coupling manifests as a transient increase in the open channel current upon channel opening and a decrease upon channel closing.
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Affiliation(s)
- John R Strikwerda
- Receptor Biology Laboratory, Department of Physiology and Biomedical Engineering, Rochester, United States
| | - Steven M Sine
- Receptor Biology Laboratory, Department of Physiology and Biomedical Engineering, Rochester, United States.,Department of Molecular Pharmacology and Experimental Therapeutics, Rochester, United States.,Department of Neurology, Mayo Clinic College of Medicine, Rochester, United States
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5
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Cottone G, Chiodo L, Maragliano L. Thermodynamics and Kinetics of Ion Permeation in Wild-Type and Mutated Open Active Conformation of the Human α7 Nicotinic Receptor. J Chem Inf Model 2020; 60:5045-5056. [PMID: 32803965 PMCID: PMC8011927 DOI: 10.1021/acs.jcim.0c00549] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Molecular
studies of human pentameric ligand-gated ion channels
(LGICs) expressed in neurons and at neuromuscular junctions are of
utmost importance in the development of therapeutic strategies for
neurological disorders. We focus here on the nicotinic acetylcholine
receptor nAChR-α7, a homopentameric channel widely expressed
in the human brain, with a proven role in a wide spectrum of disorders
including schizophrenia and Alzheimer’s disease. By exploiting
an all-atom structural model of the full (transmembrane and extracellular)
protein in the open, agonist-bound conformation we recently developed,
we evaluate the free energy and the mean first passage time of single-ion
permeation using molecular dynamics simulations and the milestoning
method with Voronoi tessellation. The results for the wild-type channel
provide the first available mapping of the potential of mean force
in the full-length α7 nAChR, reveal its expected cationic nature,
and are in good agreement with simulation data for other channels
of the LGIC family and with experimental data on nAChRs. We then investigate
the role of a specific mutation directly related to ion selectivity
in LGICs, the E-1′ → A-1′ substitution at the
cytoplasmatic selectivity filter. We find that the mutation strongly
affects sodium and chloride permeation in opposite directions, leading
to a complete inversion of selectivity, at variance with the limited
experimental results available that classify this mutant as cationic.
We thus provide structural determinants for the observed cationic-to-anionic
inversion, revealing a key role of the protonation state of residue
rings far from the mutation, in the proximity of the hydrophobic channel
gate.
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Affiliation(s)
- Grazia Cottone
- Department of Physics and Chemistry-Emilio Segrè, University of Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
| | - Letizia Chiodo
- Department of Engineering, Campus Bio-Medico University of Rome, Via Á. del Portillo 21, 00128 Rome, Italy
| | - Luca Maragliano
- Center for Synaptic Neuroscience and Technology (NSYN@UniGe), Istituto Italiano di Tecnologia, Largo Rosanna Benzi, 10, 16132 Genova, Italy.,IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi, 10, 16132 Genova, Italy
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6
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Progress in nicotinic receptor structural biology. Neuropharmacology 2020; 171:108086. [PMID: 32272141 DOI: 10.1016/j.neuropharm.2020.108086] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 03/31/2020] [Indexed: 02/07/2023]
Abstract
Here we begin by briefly reviewing landmark structural studies on the nicotinic acetylcholine receptor. We highlight challenges that had to be overcome to push through resolution barriers, then focus on what has been gleaned in the past few years from crystallographic and single particle cryo-EM studies of different nicotinic receptor subunit assemblies and ligand complexes. We discuss insights into ligand recognition, ion permeation, and allosteric gating. We then highlight some foundational aspects of nicotinic receptor structural biology that remain unresolved and are areas ripe for future exploration. This article is part of the special issue on 'Contemporary Advances in Nicotine Neuropharmacology'.
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7
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Calvelo M, Granja JR, Garcia-Fandino R. Competitive double-switched self-assembled cyclic peptide nanotubes: a dual internal and external control. Phys Chem Chem Phys 2019; 21:20750-20756. [PMID: 31513191 DOI: 10.1039/c9cp02327e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
"Intelligent" materials based on synthetic small molecules that become functional only under specific conditions provide new opportunities for developing regulated systems aimed at a large number of applications. For instance, biologically active supramolecular entities that are sensitive to environmental conditions, such as the presence of bacterial membranes, are extremely interesting in biomedicine. In this work, we have designed and investigated, using molecular dynamics simulations, a doubly modulable nanotube formed by the self-assembly of cyclic peptides sensitive to both the presence of a lipid membrane and the pH of the aqueous media. The cyclic peptides were designed to self-assemble into peptide nanotubes in the presence of a lipid bilayer and at low pH values. Under these conditions, the residual side chains point outside the cyclic peptides, being exposed to the lipid bilayer, and the inner groups (carboxylic acids) are protonated, thus allowing the permeation of water and preventing that of ions. Higher pH values are expected to create carboxylate groups at the lumen of the peptides, leading to the disassembly of the nanotube, the attraction and translocation of ions towards the hydrophobic core of the bilayer, and eventually killing the target malignant cells. Our results suggest that by introducing a second switch in a membrane sensitive system, it is possible to modulate its interaction with the lipid bilayer. This opens the door to new strategies for the preparation of antimicrobial peptides that interact at the membrane level.
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Affiliation(s)
- Martín Calvelo
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
| | - Juan R Granja
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
| | - Rebeca Garcia-Fandino
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
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8
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Harpole TJ, Grosman C. A Crucial Role for Side-Chain Conformation in the Versatile Charge Selectivity of Cys-Loop Receptors. Biophys J 2019; 116:1667-1681. [PMID: 31005237 PMCID: PMC6506641 DOI: 10.1016/j.bpj.2019.03.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 03/18/2019] [Accepted: 03/25/2019] [Indexed: 10/27/2022] Open
Abstract
Whether synaptic transmission is excitatory or inhibitory depends, to a large extent, on whether the ion channels that open upon binding the released neurotransmitter conduct cations or anions. The mechanistic basis of the opposite charge selectivities of Cys-loop receptors has only recently begun to emerge. It is now clear that ionized side chains-whether pore-facing or buried-in the first α-helical turn of the second transmembrane segments underlie this phenomenon and that the electrostatics of backbone atoms are not critically involved. Moreover, on the basis of electrophysiological observations, it has recently been suggested that not only the sign of charged side chains but also their conformation are crucial determinants of cation-anion selectivity. To challenge these ideas with the chemical and structural rigor that electrophysiological observations naturally lack, we performed molecular dynamics, Brownian dynamics, and electrostatics calculations of ion permeation. To this end, we used structural models of the open-channel conformation of the α1 glutamate-gated Cl- channel and the α1 glycine receptor. Our results provided full support to the notion that the conformation of charged sides chains matters for charge selectivity. Indeed, whereas some rotamers of the buried arginines at position 0' conferred high selectivity for anions, others supported the permeation of cations and anions at similar rates or even allowed the faster permeation of cations. Furthermore, we found that modeling glutamates at position -1' of the anion-selective α1 glycine receptor open-state structure-instead of the five native alanines-switches charge selectivity also in a conformation-dependent manner, with some glutamate rotamers being much more effective at conferring selectivity for cations than others. Regarding pore size, we found that the mere expansion of the pore has only a minimal impact on cation-anion selectivity. Overall, these results bring to light the previously unappreciated impact of side-chain conformation on charge selectivity in Cys-loop receptors.
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Affiliation(s)
- Tyler J Harpole
- Center for Biophysics and Quantitative Biology, Urbana, Illinois
| | - Claudio Grosman
- Center for Biophysics and Quantitative Biology, Urbana, Illinois; Department of Molecular and Integrative Physiology, Urbana, Illinois; Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois.
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9
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Polovinkin L, Hassaine G, Perot J, Neumann E, Jensen AA, Lefebvre SN, Corringer PJ, Neyton J, Chipot C, Dehez F, Schoehn G, Nury H. Conformational transitions of the serotonin 5-HT 3 receptor. Nature 2018; 563:275-279. [PMID: 30401839 DOI: 10.1038/s41586-018-0672-3] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 09/07/2018] [Indexed: 01/03/2023]
Abstract
The serotonin 5-HT3 receptor is a pentameric ligand-gated ion channel (pLGIC). It belongs to a large family of receptors that function as allosteric signal transducers across the plasma membrane1,2; upon binding of neurotransmitter molecules to extracellular sites, the receptors undergo complex conformational transitions that result in transient opening of a pore permeable to ions. 5-HT3 receptors are therapeutic targets for emesis and nausea, irritable bowel syndrome and depression3. In spite of several reported pLGIC structures4-8, no clear unifying view has emerged on the conformational transitions involved in channel gating. Here we report four cryo-electron microscopy structures of the full-length mouse 5-HT3 receptor in complex with the anti-emetic drug tropisetron, with serotonin, and with serotonin and a positive allosteric modulator, at resolutions ranging from 3.2 Å to 4.5 Å. The tropisetron-bound structure resembles those obtained with an inhibitory nanobody5 or without ligand9. The other structures include an 'open' state and two ligand-bound states. We present computational insights into the dynamics of the structures, their pore hydration and free-energy profiles, and characterize movements at the gate level and cation accessibility in the pore. Together, these data deepen our understanding of the gating mechanism of pLGICs and capture ligand binding in unprecedented detail.
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Affiliation(s)
| | | | - Jonathan Perot
- CNRS, Université Grenoble Alpes, CEA, IBS, Grenoble, France
| | | | - Anders A Jensen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Solène N Lefebvre
- Channel Receptors Unit, CNRS UMR 3571, Institut Pasteur, Paris, France
| | | | - Jacques Neyton
- CNRS, Université Grenoble Alpes, CEA, IBS, Grenoble, France.
| | - Christophe Chipot
- Université de Lorraine, CNRS, LPCT, Nancy, France.,Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, Vandoeuvre-les-Nancy, France.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Francois Dehez
- Université de Lorraine, CNRS, LPCT, Nancy, France.,Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, Vandoeuvre-les-Nancy, France
| | - Guy Schoehn
- CNRS, Université Grenoble Alpes, CEA, IBS, Grenoble, France
| | - Hugues Nury
- CNRS, Université Grenoble Alpes, CEA, IBS, Grenoble, France.
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10
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Bouzat C, Mukhtasimova N. The nicotinic acetylcholine receptor as a molecular machine for neuromuscular transmission. CURRENT OPINION IN PHYSIOLOGY 2018. [DOI: 10.1016/j.cophys.2018.04.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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11
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Gonzalez-Gutierrez G, Wang Y, Cymes GD, Tajkhorshid E, Grosman C. Chasing the open-state structure of pentameric ligand-gated ion channels. J Gen Physiol 2017; 149:1119-1138. [PMID: 29089419 PMCID: PMC5715906 DOI: 10.1085/jgp.201711803] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 09/14/2017] [Accepted: 10/05/2017] [Indexed: 11/25/2022] Open
Abstract
Members of the pentameric ligand-gated ion channel family have been crystallized in different conformations, including one in which the transmembrane pore is surprisingly wide. Gonzalez-Gutierrez et al. show that the open-channel conformation of animal members is more similar to the models with narrow pores. Remarkable advances have been made toward the structural characterization of ion channels in the last two decades. However, the unambiguous assignment of well-defined functional states to the obtained structural models has proved challenging. In the case of the superfamily of nicotinic-receptor channels (also referred to as pentameric ligand-gated ion channels [pLGICs]), for example, two different types of model of the open-channel conformation have been proposed on the basis of structures solved to resolutions better than 4.0 Å. At the level of the transmembrane pore, the open-state models of the proton-gated pLGIC from Gloeobacter violaceus (GLIC) and the invertebrate glutamate-gated Cl– channel (GluCl) are very similar to each other, but that of the glycine receptor (GlyR) is considerably wider. Indeed, the mean distances between the axis of ion permeation and the Cα atoms at the narrowest constriction of the pore (position −2′) differ by ∼2 Å in these two classes of model, a large difference when it comes to understanding the physicochemical bases of ion conduction and charge selectivity. Here, we take advantage of the extreme open-channel stabilizing effect of mutations at pore-facing position 9′. We find that the I9′A mutation slows down entry into desensitization of GLIC to the extent that macroscopic currents decay only slightly by the end of pH 4.5 solution applications to the extracellular side for several minutes. We crystallize (at pH 4.5) two variants of GLIC carrying this mutation and solve their structures to resolutions of 3.12 Å and 3.36 Å. Furthermore, we perform all-atom molecular dynamics simulations of ion permeation and picrotoxinin block, using the different open-channel structural models. On the basis of these results, we favor the notion that the open-channel structure of pLGICs from animals is much closer to that of the narrow models (of GLIC and GluCl) than it is to that of the GlyR.
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Affiliation(s)
| | - Yuhang Wang
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Gisela D Cymes
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Emad Tajkhorshid
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL.,Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Claudio Grosman
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL .,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL.,Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL
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12
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Nemecz Á, Prevost MS, Menny A, Corringer PJ. Emerging Molecular Mechanisms of Signal Transduction in Pentameric Ligand-Gated Ion Channels. Neuron 2017; 90:452-70. [PMID: 27151638 DOI: 10.1016/j.neuron.2016.03.032] [Citation(s) in RCA: 154] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 01/07/2016] [Accepted: 03/24/2016] [Indexed: 10/21/2022]
Abstract
Nicotinic acetylcholine, serotonin type 3, γ-amminobutyric acid type A, and glycine receptors are major players of human neuronal communication. They belong to the family of pentameric ligand-gated ion channels, sharing a highly conserved modular 3D structure. Recently, high-resolution structures of both open- and closed-pore conformations have been solved for a bacterial, an invertebrate, and a vertebrate receptor in this family. These data suggest that a common gating mechanism occurs, coupling neurotransmitter binding to pore opening, but they also pinpoint significant differences among subtypes. In this Review, we summarize the structural and functional data in light of these gating models and speculate about their mechanistic consequences on ion permeation, pathological mutations, as well as functional regulation by orthosteric and allosteric effectors.
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Affiliation(s)
- Ákos Nemecz
- Channel-Receptors Unit, Institut Pasteur, 75015 Paris, France; CNRS UMR 3571, 75015 Paris, France
| | - Marie S Prevost
- Institute of Structural and Molecular Biology, University College London and Birkbeck, Malet Street, London WC1E 7HX, UK
| | - Anaïs Menny
- Channel-Receptors Unit, Institut Pasteur, 75015 Paris, France; CNRS UMR 3571, 75015 Paris, France; Université Pierre et Marie Curie (UPMC), Cellule Pasteur, 75005 Paris, France
| | - Pierre-Jean Corringer
- Channel-Receptors Unit, Institut Pasteur, 75015 Paris, France; CNRS UMR 3571, 75015 Paris, France.
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13
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Arcario MJ, Mayne CG, Tajkhorshid E. A membrane-embedded pathway delivers general anesthetics to two interacting binding sites in the Gloeobacter violaceus ion channel. J Biol Chem 2017; 292:9480-9492. [PMID: 28420728 PMCID: PMC5465477 DOI: 10.1074/jbc.m117.780197] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 04/10/2017] [Indexed: 12/30/2022] Open
Abstract
General anesthetics exert their effects on the central nervous system by acting on ion channels, most notably pentameric ligand-gated ion channels. Although numerous studies have focused on pentameric ligand-gated ion channels, the details of anesthetic binding and channel modulation are still debated. A better understanding of the anesthetic mechanism of action is necessary for the development of safer and more efficacious drugs. Herein, we present a computational study identifying two anesthetic binding sites in the transmembrane domain of the Gloeobacter violaceus ligand-gated ion channel (GLIC) channel, characterize the putative binding pathway, and observe structural changes associated with channel function. Molecular simulations of desflurane reveal a binding pathway to GLIC via a membrane-embedded tunnel using an intrasubunit protein lumen as the conduit, an observation that explains the Meyer-Overton hypothesis, or why the lipophilicity of an anesthetic and its potency are generally proportional. Moreover, employing high concentrations of ligand led to the identification of a second transmembrane site (TM2) that inhibits dissociation of anesthetic from the TM1 site and is consistent with the high concentrations of anesthetics required to achieve clinical effects. Finally, asymmetric binding patterns of anesthetic to the channel were found to promote an iris-like conformational change that constricts and dehydrates the ion pore, creating a 13.5 kcal/mol barrier to ion translocation. Together with previous studies, the simulations presented herein demonstrate a novel anesthetic binding site in GLIC that is accessed through a membrane-embedded tunnel and interacts with a previously known site, resulting in conformational changes that produce a non-conductive state of the channel.
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Affiliation(s)
- Mark J Arcario
- From the Center for Biophysics and Quantitative Biology.,Department of Biochemistry, College of Medicine, and.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Christopher G Mayne
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Emad Tajkhorshid
- From the Center for Biophysics and Quantitative Biology, .,Department of Biochemistry, College of Medicine, and.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
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14
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Gupta S, Chakraborty S, Vij R, Auerbach A. A mechanism for acetylcholine receptor gating based on structure, coupling, phi, and flip. J Gen Physiol 2016; 149:85-103. [PMID: 27932572 PMCID: PMC5217088 DOI: 10.1085/jgp.201611673] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 09/20/2016] [Accepted: 11/10/2016] [Indexed: 01/29/2023] Open
Abstract
Gupta et al. use single-channel electrophysiology to investigate the gating mechanism of acetylcholine receptor ion channels. They propose that channel opening starts at the M2–M3 linker and ligand-binding sites and proceeds through four brief intermediate conformations before ending with the collapse of a gate bubble. Nicotinic acetylcholine receptors are allosteric proteins that generate membrane currents by isomerizing (“gating”) between resting and active conformations under the influence of neurotransmitters. Here, to explore the mechanisms that link the transmitter-binding sites (TBSs) with the distant gate, we use mutant cycle analyses to measure coupling between residue pairs, phi value analyses to sequence domain rearrangements, and current simulations to reproduce a microsecond shut component (“flip”) apparent in single-channel recordings. Significant interactions between amino acids separated by >15 Å are rare; an exception is between the αM2–M3 linkers and the TBSs that are ∼30 Å apart. Linker residues also make significant, local interactions within and between subunits. Phi value analyses indicate that without agonists, the linker is the first region in the protein to reach the gating transition state. Together, the phi pattern and flip component suggest that a complete, resting↔active allosteric transition involves passage through four brief intermediate states, with brief shut events arising from sojourns in all or a subset. We derive energy landscapes for gating with and without agonists, and propose a structure-based model in which resting→active starts with spontaneous rearrangements of the M2–M3 linkers and TBSs. These conformational changes stabilize a twisted extracellular domain to promote transmembrane helix tilting, gate dilation, and the formation of a “bubble” that collapses to initiate ion conduction. The energy landscapes suggest that twisting is the most energetically unfavorable step in the resting→active conformational change and that the rate-limiting step in the reverse process is bubble formation.
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Affiliation(s)
- Shaweta Gupta
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY 14214
| | - Srirupa Chakraborty
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY 14214
| | - Ridhima Vij
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY 14214
| | - Anthony Auerbach
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY 14214
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15
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Abstract
Specific ion binding by carboxylates (-COO-) is a broadly important topic because -COO- is one of the most common functional groups coordinated to metal ions in metalloproteins and synthetic polymers. We apply quantum chemical methods and the quasi-chemical free-energy theory to investigate how variations in the number of -COO- ligands in a binding site determine ion-binding preferences. We study a series of monovalent (Li+, Na+, K+, Cs+) and divalent (Zn2+, Ca2+) ions relevant to experimental work on ion channels and ionomers. Of two competing hypotheses, our results support the ligand field strength hypothesis and follow the reverse Hofmeister series for ion solvation and ion transfer from aqueous solution to binding sites with the preferred number of ligands. New insight arises from the finding that ion-binding sequences can be manipulated and even reversed just by constraining the number of carboxylate ligands in the binding sites. Our results help clarify the discrepancy in ion association between molecular ligands in aqueous solutions and ionomers, and their chemical analogues in ion-channel binding sites.
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Affiliation(s)
- Mark J Stevens
- Center for Integrated Nanotechnologies and ‡Biological and Engineering Sciences, Sandia National Laboratories , Albuquerque, New Mexico 87185, United States
| | - Susan L B Rempe
- Center for Integrated Nanotechnologies and ‡Biological and Engineering Sciences, Sandia National Laboratories , Albuquerque, New Mexico 87185, United States
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16
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Cymes GD, Grosman C. Identifying the elusive link between amino acid sequence and charge selectivity in pentameric ligand-gated ion channels. Proc Natl Acad Sci U S A 2016; 113:E7106-E7115. [PMID: 27791102 PMCID: PMC5111664 DOI: 10.1073/pnas.1608519113] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Among neurotransmitter-gated ion channels, the superfamily of pentameric ligand-gated ion channels (pLGICs) is unique in that its members display opposite permeant-ion charge selectivities despite sharing the same structural fold. Although much effort has been devoted to the identification of the mechanism underlying the cation-versus-anion selectivity of these channels, a careful analysis of past work reveals that discrepancies exist, that different explanations for the same phenomenon have often been put forth, and that no consensus view has yet been reached. To elucidate the molecular basis of charge selectivity for the superfamily as a whole, we performed extensive mutagenesis and electrophysiological recordings on six different cation-selective and anion-selective homologs from vertebrate, invertebrate, and bacterial origin. We present compelling evidence for the critical involvement of ionized side chains-whether pore-facing or buried-rather than backbone atoms and propose a mechanism whereby not only their charge sign but also their conformation determines charge selectivity. Insertions, deletions, and residue-to-residue mutations involving nonionizable residues in the intracellular end of the pore seem to affect charge selectivity by changing the rotamer preferences of the ionized side chains in the first turn of the M2 α-helices. We also found that, upon neutralization of the charged residues in the first turn of M2, the control of charge selectivity is handed over to the many other ionized side chains that decorate the pore. This explains the long-standing puzzle as to why the neutralization of the intracellular-mouth glutamates affects charge selectivity to markedly different extents in different cation-selective pLGICs.
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Affiliation(s)
- Gisela D Cymes
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Claudio Grosman
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801;
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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17
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Bupropion and its photoreactive analog (±)-SADU-3-72 interact with luminal and non-luminal sites at human α4β2 nicotinic acetylcholine receptors. Neurochem Int 2016; 100:67-77. [DOI: 10.1016/j.neuint.2016.08.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 08/05/2016] [Accepted: 08/31/2016] [Indexed: 11/20/2022]
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18
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Morales-Perez CL, Noviello CM, Hibbs RE. X-ray structure of the human α4β2 nicotinic receptor. Nature 2016; 538:411-415. [PMID: 27698419 PMCID: PMC5161573 DOI: 10.1038/nature19785] [Citation(s) in RCA: 305] [Impact Index Per Article: 38.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 08/22/2016] [Indexed: 02/07/2023]
Abstract
Nicotinic acetylcholine receptors are ligand-gated ion channels that mediate fast chemical neurotransmission at the neuromuscular junction and have diverse signalling roles in the central nervous system. The nicotinic receptor has been a model system for cell-surface receptors, and specifically for ligand-gated ion channels, for well over a century. In addition to the receptors' prominent roles in the development of the fields of pharmacology and neurobiology, nicotinic receptors are important therapeutic targets for neuromuscular disease, addiction, epilepsy and for neuromuscular blocking agents used during surgery. The overall architecture of the receptor was described in landmark studies of the nicotinic receptor isolated from the electric organ of Torpedo marmorata. Structures of a soluble ligand-binding domain have provided atomic-scale insights into receptor-ligand interactions, while high-resolution structures of other members of the pentameric receptor superfamily provide touchstones for an emerging allosteric gating mechanism. All available high-resolution structures are of homopentameric receptors. However, the vast majority of pentameric receptors (called Cys-loop receptors in eukaryotes) present physiologically are heteromeric. Here we present the X-ray crystallographic structure of the human α4β2 nicotinic receptor, the most abundant nicotinic subtype in the brain. This structure provides insights into the architectural principles governing ligand recognition, heteromer assembly, ion permeation and desensitization in this prototypical receptor class.
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Affiliation(s)
- Claudio L. Morales-Perez
- Departments of Neuroscience and Biophysics, University of Texas
Southwestern Medical Center, Dallas, TX 75390, USA
| | - Colleen M. Noviello
- Departments of Neuroscience and Biophysics, University of Texas
Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ryan E. Hibbs
- Departments of Neuroscience and Biophysics, University of Texas
Southwestern Medical Center, Dallas, TX 75390, USA
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19
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Cymes GD, Grosman C. Engineered Ionizable Side Chains. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 869:5-23. [PMID: 26381938 DOI: 10.1007/978-1-4939-2845-3_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
One of the great challenges of mechanistic ion-channel biology is to obtain structural information from well-defined functional states. In the case of neurotransmitter-gated ion channels, the open-channel conformation is particularly elusive owing to its transient nature and brief mean lifetime. In this Chapter, we show how the analysis of single-channel currents recorded from mutants engineered to contain single ionizable side chains in the transmembrane region can provide specific information about the open-channel conformation without any interference from the closed or desensitized conformations. The method takes advantage of the fact that the alternate binding and unbinding of protons to and from an ionizable side chain causes the charge of the protein to fluctuate by 1 unit. We show that, in mutant muscle acetylcholine nicotinic receptors (AChRs), this fluctuating charge affects the rate of ion conduction in such a way that individual proton-transfer events can be identified in a most straightforward manner. From the extent to which the single-channel current amplitude is reduced every time a proton binds, we can learn about the proximity of the engineered side chain to the lumen of the pore. And from the kinetics of proton binding and unbinding, we can calculate the side-chain's affinity for protons (pK a), and hence, we can learn about the electrostatic properties of the microenvironment around the introduced ionizable group. The application of this method to systematically mutated AChRs allowed us to identify unambiguously the stripes of the M1, M2 and M3 transmembrane α-helices that face the pore's lumen in the open-channel conformation in the context of a native membrane.
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Affiliation(s)
- Gisela D Cymes
- Department of Molecular and Integrative Physiology, Center for Biophysics and Computational Biology, Program in Neuroscience, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Claudio Grosman
- Department of Molecular and Integrative Physiology, Center for Biophysics and Computational Biology, Program in Neuroscience, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,, 524 Burrill Hall, 407 S. Goodwin Ave, 61801, Urbana, IL, USA.
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20
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Kinde MN, Chen Q, Lawless MJ, Mowrey DD, Xu J, Saxena S, Xu Y, Tang P. Conformational Changes Underlying Desensitization of the Pentameric Ligand-Gated Ion Channel ELIC. Structure 2015; 23:995-1004. [PMID: 25960405 DOI: 10.1016/j.str.2015.03.017] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 03/24/2015] [Accepted: 03/30/2015] [Indexed: 11/18/2022]
Abstract
Structural rearrangements underlying functional transitions of pentameric ligand-gated ion channels (pLGICs) are not fully understood. Using (19)F nuclear magnetic resonance and electron spin resonance spectroscopy, we found that ELIC, a pLGIC from Erwinia chrysanthemi, expanded the extracellular end and contracted the intracellular end of its pore during transition from the resting to an apparent desensitized state. Importantly, the contraction at the intracellular end of the pore likely forms a gate to restrict ion transport in the desensitized state. This gate differs from the hydrophobic gate present in the resting state. Conformational changes of the TM2-TM3 loop were limited to the N-terminal end. The TM4 helices and the TM3-TM4 loop appeared relatively insensitive to agonist-mediated structural rearrangement. These results indicate that conformational changes accompanying functional transitions are not uniform among different ELIC regions. This work also revealed the co-existence of multiple conformations for a given state and suggested asymmetric conformational arrangements in a homomeric pLGIC.
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Affiliation(s)
- Monica N Kinde
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Qiang Chen
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Matthew J Lawless
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - David D Mowrey
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA; Department of Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Jiawei Xu
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Yan Xu
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA; Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA; Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Pei Tang
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA; Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA; Department of Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA.
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21
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Musumeci G, Imbesi R, Trovato FM, Szychlinska MA, Aiello FC, Buffa P, Castrogiovanni P. Importance of serotonin (5-HT) and its precursor l-tryptophan for homeostasis and function of skeletal muscle in rats. A morphological and endocrinological study. Acta Histochem 2015; 117:267-74. [PMID: 25805417 DOI: 10.1016/j.acthis.2015.03.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 03/02/2015] [Accepted: 03/03/2015] [Indexed: 01/08/2023]
Abstract
Serotonin (5-HT) is a neurotransmitter, synthesized in serotonergic neurons of the central nervous system and in enterochromaffin cells of the gastrointestinal tract, which is involved in the regulation of several body functions, including muscle tissue development and growth and its contractile response. l-Tryptophan (l-Trp) is an essential amino acid and precursor of 5-HT. The aim of the present study was to better understand the mechanisms that govern neuroendocrine homeostasis of muscle tissue and emphasize the importance of a diet, complete in all its elements, referring specifically to the essential amino acids such as l-Trp, crucial in several neuroendocrine functions.We analyzed the possible consequences of l-Trp-free diet on 5-HT production and on skeletal muscle morphology and function in young female rats. We also evaluated the eventual alterations of hormone production such as growth hormone (GH), thyroid stimulating hormone (TSH) and thyroid hormones (T3 and T4) that control and regulate growth, metabolism and efficiency of the skeletal muscle. Our results showed a strong decrease of 5-HT, GH, TSH, T3 and T4 levels associated to a clear difference in body weight between experimental and control rats. Moreover, the muscle samples of experimental rats showed histological and ultrastructural alterations. These findings thus supported a strong link between l-Trp, serotonergic system, hormone secretion and morphology of skeletal muscle tissue and thus, the importance of a balanced daily diet.
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Affiliation(s)
- Giuseppe Musumeci
- Department of Biomedical and Biotechnological Sciences, Human Anatomy and Histology Section, School of Medicine, University of Catania, Via S. Sofia 87, 95123 Catania, Italy.
| | - Rosa Imbesi
- Department of Biomedical and Biotechnological Sciences, Human Anatomy and Histology Section, School of Medicine, University of Catania, Via S. Sofia 87, 95123 Catania, Italy
| | - Francesca Maria Trovato
- Department of Clinical and Experimental Medicine, Internal Medicine Division, University of Catania, Via S. Sofia 78, 95123 Catania, Italy
| | - Marta Anna Szychlinska
- Department of Biomedical and Biotechnological Sciences, Human Anatomy and Histology Section, School of Medicine, University of Catania, Via S. Sofia 87, 95123 Catania, Italy
| | - Flavia Concetta Aiello
- Department of Biomedical and Biotechnological Sciences, Human Anatomy and Histology Section, School of Medicine, University of Catania, Via S. Sofia 87, 95123 Catania, Italy
| | - Pietro Buffa
- Randall Division of Cell and Molecular Biophysics, King's College London, London, UK
| | - Paola Castrogiovanni
- Department of Biomedical and Biotechnological Sciences, Human Anatomy and Histology Section, School of Medicine, University of Catania, Via S. Sofia 87, 95123 Catania, Italy
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22
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Baronas VA, Kurata HT. Inward rectifiers and their regulation by endogenous polyamines. Front Physiol 2014; 5:325. [PMID: 25221519 PMCID: PMC4145359 DOI: 10.3389/fphys.2014.00325] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Accepted: 08/06/2014] [Indexed: 12/02/2022] Open
Abstract
Inwardly-rectifying potassium (Kir) channels contribute to maintenance of the resting membrane potential and regulation of electrical excitation in many cell types. Strongly rectifying Kir channels exhibit a very steep voltage dependence resulting in silencing of their activity at depolarized membrane voltages. The mechanism underlying this steep voltage dependence is blockade by endogenous polyamines. These small multifunctional, polyvalent metabolites enter the long Kir channel pore from the intracellular side, displacing multiple occupant ions as they migrate to a stable binding site in the transmembrane region of the channel. Numerous structure-function studies have revealed structural elements of Kir channels that determine their susceptibility to polyamine block, and enable the steep voltage dependence of this process. In addition, various channelopathies have been described that result from alteration of the polyamine sensitivity or activity of strongly rectifying channels. The primary focus of this article is to summarize current knowledge of the molecular mechanisms of polyamine block, and provide some perspective on lingering uncertainties related to this physiologically important mechanism of ion channel blockade. We also briefly review some of the important and well understood physiological roles of polyamine sensitive, strongly rectifying Kir channels, primarily of the Kir2 family.
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Affiliation(s)
- Victoria A Baronas
- Department of Anesthesiology, Pharmacology, and Therapeutics, University of British Columbia Vancouver, BC, Canada
| | - Harley T Kurata
- Department of Anesthesiology, Pharmacology, and Therapeutics, University of British Columbia Vancouver, BC, Canada
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23
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X-ray structure of the mouse serotonin 5-HT3 receptor. Nature 2014; 512:276-81. [PMID: 25119048 DOI: 10.1038/nature13552] [Citation(s) in RCA: 301] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Accepted: 06/02/2014] [Indexed: 01/03/2023]
Abstract
Neurotransmitter-gated ion channels of the Cys-loop receptor family mediate fast neurotransmission throughout the nervous system. The molecular processes of neurotransmitter binding, subsequent opening of the ion channel and ion permeation remain poorly understood. Here we present the X-ray structure of a mammalian Cys-loop receptor, the mouse serotonin 5-HT3 receptor, at 3.5 Å resolution. The structure of the proteolysed receptor, made up of two fragments and comprising part of the intracellular domain, was determined in complex with stabilizing nanobodies. The extracellular domain reveals the detailed anatomy of the neurotransmitter binding site capped by a nanobody. The membrane domain delimits an aqueous pore with a 4.6 Å constriction. In the intracellular domain, a bundle of five intracellular helices creates a closed vestibule where lateral portals are obstructed by loops. This 5-HT3 receptor structure, revealing part of the intracellular domain, expands the structural basis for understanding the operating mechanism of mammalian Cys-loop receptors.
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24
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Side-chain conformation at the selectivity filter shapes the permeation free-energy landscape of an ion channel. Proc Natl Acad Sci U S A 2014; 111:E3196-205. [PMID: 25049389 DOI: 10.1073/pnas.1408950111] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
On the basis of single-channel currents recorded from the muscle nicotinic acetylcholine receptor (AChR), we have recently hypothesized that the conformation adopted by the glutamate side chains at the first turn of the pore-lining α-helices is a key determinant of the rate of ion permeation. In this paper, we set out to test these ideas within a framework of atomic detail and stereochemical rigor by conducting all-atom molecular dynamics and Brownian dynamics simulations on an extensively validated model of the open-channel muscle AChR. Our simulations provided ample support to the notion that the different rotamers of these glutamates partition into two classes that differ markedly in their ability to catalyze ion conduction, and that the conformations of the four wild-type glutamates are such that two of them "fall" in each rotamer class. Moreover, the simulations allowed us to identify the mm (χ(1) ≅ -60°; χ(2) ≅ -60°) and tp (χ(1) ≅ 180°; χ(2) ≅ +60°) rotamers as the likely conduction-catalyzing conformations of the AChR's selectivity-filter glutamates. More generally, our work shows an example of how experimental benchmarks can guide molecular simulations into providing a type of structural and mechanistic insight that seems otherwise unattainable.
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25
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Morgan D, Musset B, Kulleperuma K, Smith SME, Rajan S, Cherny VV, Pomès R, DeCoursey TE. Peregrination of the selectivity filter delineates the pore of the human voltage-gated proton channel hHV1. ACTA ACUST UNITED AC 2013; 142:625-40. [PMID: 24218398 PMCID: PMC3840923 DOI: 10.1085/jgp.201311045] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Extraordinary selectivity is crucial to all proton-conducting molecules, including the human voltage-gated proton channel (hHV1), because the proton concentration is >106 times lower than that of other cations. Here we use “selectivity filter scanning” to elucidate the molecular requirements for proton-specific conduction in hHV1. Asp112, in the middle of the S1 transmembrane helix, is an essential part of the selectivity filter in wild-type (WT) channels. After neutralizing Asp112 by mutating it to Ala (D112A), we introduced Asp at each position along S1 from 108 to 118, searching for “second site suppressor” activity. Surprisingly, most mutants lacked even the anion conduction exhibited by D112A. Proton-specific conduction was restored only with Asp or Glu at position 116. The D112V/V116D channel strikingly resembled WT in selectivity, kinetics, and ΔpH-dependent gating. The S4 segment of this mutant has similar accessibility to WT in open channels, because R211H/D112V/V116D was inhibited by internally applied Zn2+. Asp at position 109 allowed anion permeation in combination with D112A but did not rescue function in the nonconducting D112V mutant, indicating that selectivity is established externally to the constriction at F150. The three positions that permitted conduction all line the pore in our homology model, clearly delineating the conduction pathway. Evidently, a carboxyl group must face the pore directly to enable conduction. Molecular dynamics simulations indicate reorganization of hydrogen bond networks in the external vestibule in D112V/V116D. At both positions where it produces proton selectivity, Asp frequently engages in salt linkage with one or more Arg residues from S4. Surprisingly, mean hydration profiles were similar in proton-selective, anion-permeable, and nonconducting constructs. That the selectivity filter functions in a new location helps to define local environmental features required to produce proton-selective conduction.
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Affiliation(s)
- Deri Morgan
- Department of Molecular Biophysics and Physiology, Rush University, Chicago, IL 60612
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26
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Gating of the proton-gated ion channel from Gloeobacter violaceus at pH 4 as revealed by X-ray crystallography. Proc Natl Acad Sci U S A 2013; 110:18716-21. [PMID: 24167270 DOI: 10.1073/pnas.1313156110] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cryoelectron microscopy and X-ray crystallography have recently been used to generate structural models that likely represent the unliganded closed-channel conformation and the fully liganded open-channel conformation of different members of the nicotinic-receptor superfamily. To characterize the structure of the closed-channel conformation in its liganded state, we identified a number of positions in the loop between transmembrane segments 2 (M2) and 3 (M3) of a proton-gated ortholog from the bacterium Gloeobacter violaceus (GLIC) where mutations to alanine reduce the liganded-gating equilibrium constant, and solved the crystal structures of two such mutants (T25'A and Y27'A) at pH ~4.0. At the level of backbone atoms, the liganded closed-channel model presented here differs from the liganded open-channel structure of GLIC in the pre-M1 linker, the M3-M4 loop, and much more prominently, in the extracellular half of the pore lining, where the more pronounced tilt of the closed-channel M2 α-helices toward the pore's long axis narrows the permeation pathway. On the other hand, no differences between the liganded closed-channel and open-channel models could be detected at the level of the extracellular domain, where conformational changes are expected to underlie the low-to-high proton-affinity switch that drives gating of proton-bound channels. Thus, the liganded closed-channel model is nearly indistinguishable from the recently described "locally closed" structure. However, because cross-linking strategies (which could have stabilized unstable conformations) and mutations involving ionizable side chains (which could have affected proton-gated channel activation) were purposely avoided, we favor the notion that this structure represents one of the end states of liganded gating rather than an unstable intermediate.
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27
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Structural basis for ion permeation mechanism in pentameric ligand-gated ion channels. EMBO J 2013; 32:728-41. [PMID: 23403925 PMCID: PMC3590989 DOI: 10.1038/emboj.2013.17] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 01/07/2013] [Indexed: 12/14/2022] Open
Abstract
To understand the molecular mechanism of ion permeation in pentameric ligand-gated ion channels (pLGIC), we solved the structure of an open form of GLIC, a prokaryotic pLGIC, at 2.4 Å. Anomalous diffraction data were used to place bound anions and cations. This reveals ordered water molecules at the level of two rings of hydroxylated residues (named Ser6' and Thr2') that contribute to the ion selectivity filter. Two water pentagons are observed, a self-stabilized ice-like water pentagon and a second wider water pentagon, with one sodium ion between them. Single-channel electrophysiology shows that the side-chain hydroxyl of Ser6' is crucial for ion translocation. Simulations and electrostatics calculations complemented the description of hydration in the pore and suggest that the water pentagons observed in the crystal are important for the ion to cross hydrophobic constriction barriers. Simulations that pull a cation through the pore reveal that residue Ser6' actively contributes to ion translocation by reorienting its side chain when the ion is going through the pore. Generalization of these findings to the pLGIC family is proposed.
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Akabas MH. Channels: Rotamers affect ion conductance. Nat Chem Biol 2012. [PMID: 23183578 DOI: 10.1038/nchembio.1115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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