DOCSLIB.ORG

Elucidating the Gating Mechanism of Cys-Loop Receptors

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Elucidating the Gating Mechanism of Cys-Loop Receptors Elucidating the Gating Mechanism of Cys-Loop Receptors ÖZGE YOLUK Doctoral Thesis Stockholm, Sweden 2016 TRITA FYS 2016-26 ISSN 0280-316X KTH School of Engineering Sciences ISRN KTH/FYS/–16:26–SE SE-100 44 Stockholm ISBN 978-91-7729-009-4 SWEDEN Akademisk avhandling som med tillstånd av Kungl Tekniska högskolan framlägges till offentlig granskning för avläggande av teknologie doktorsexamen i biologisk fysik måndagen den 13 juni 2016 klockan 14.00 i F3, Lindstedtsvägen 26, KTH Campus, Kungl Tekniska högskolan, Stockholm. © Özge Yoluk, June 2016 Tryck: Universitetsservice US-AB iii Abstract Cys-loop receptors are membrane proteins that are key players for the fast synaptic neurotransmission. Their ion transport initiates new nerve signals after activation by small agonist molecules, but this function is also highly sensitive to allosteric modulation by a number of compounds such as anes- thetics, alcohol or anti-parasitic agents. For a long time, these modulators were believed to act primarily on the membrane, but the availability of high- resolution structures has made it possible to identify several binding sites in the transmembrane domains of the ion channels. It is known that lig- and binding in the extracellular domain causes a conformational earthquake that interacts with the transmembrane domain (and the allosteric modula- tor sites), which leads to channel opening. The investigations carried out in this thesis aim at understanding the connection between ligand binding and channel opening with molecular modeling and computer simulations. I present new models of the mammalian GABAA receptor based on the eukaryotic structure GluCl co-crystallized with an anti-parasitic agent, and show how these models can be used to study receptor-modulator interactions. I also show how removal of the bound modulator leads to gradual closing of the channel in molecular dynamics simulations. In contrast, simulations of the receptor with both the agonist and the modulator remain stable in an open-like conformation. This makes it possible to extract several key interac- tions, and I propose mechanisms for how the extracellular domain motion is initiated. The rapid increase in the number of cys-loop receptor structures the last few years has further made it possible to use principal component analysis (PCA) to create low-dimensional descriptions of the conformational land- scape. By performing PCA on the crystal structure ensemble, I have been able to divide the structures into functional clusters. Sampling of these clus- ters with molecular dynamics simulations reveals transitions that occupy the intermediate positions in the principal component space. The studies presented in this thesis contribute to our understanding of the gating mechanism and the functional clustering of the cys-loop recep- tor structures, which both are important to design new allosteric modulator drugs that influence the channel function, in particular to treat neurological disorders. Keywords: cys-loop receptor, ion channel, neuroscience, molecular dy- namics, activation, modulation, modeling, gating, GABAA iv Sammanfattning Cys-loop-receptorer är membranproteiner som spelar en nyckelroll för snabb synaptisk neurotransmission. Deras jontransport initierar nya nerv- signaler efter aktivering av små agonistmolekyler, men denna funktion är också mycket känslig för allosterisk modulering av ett antal föreningar såsom bedövningsmedel, alkohol eller antiparasitmedel. Under en lång tid troddes dessa modulatorer främst verka på membranet, men tillgången till högupp- lösta strukturer har gjort det möjligt att identifiera flera bindningsställen i transmembrandomänerna hos jonkanalerna. Det är känt att ligandbindning i den extracellulära domänen orsakar en jordbävningsliknande stor konfor- mationsförändring som interagerar med transmembrandomänen och regioner specifika för de allosteriska modulatorerna, vilket leder till att kanalen öpp- nas. De studier som presenteras i denna avhandling syftar till att förstå sam- bandet mellan ligandbindning och kanalöppning med molekylmodellering och datorsimuleringar. Jag presenterar nya modeller för GABAA-receptor för däggdjur som är baserade på en eukaryot struktur av GluCl vars struktur bestämts bunden till ett antiparasitmedel, och visar hur dessa modeller kan användas för att studera interaktioner mellan receptor och modulator. Jag visar också hur kanalen gradvis stänger i molekyldynamiksimuleringar om den bundna mo- dulatorn tas bort. I simuleringar med både agonist och modulator bundna förblir kanalen i en relativt öppen konformation. Detta gör det möjligt att identifera flera viktiga interaktioner, och jag föreslår mekanismer för hur den extracellulära domänens rörelse initieras. Den snabba ökningen av antalet cys-loop-receptorstrukturer de senas- te åren har vidare gjort det möjligt att använda principalkomponentanalys (PCA) för att skapa lågdimensionella beskrivningar av hela det tillgängli- ga rummet av strukturer. Genom att utföra PCA på en stor grupp av kri- stallstrukturer har jag kunnat dela in strukturerna i funktionella grupper. Molekyldynamiksimuleringar av dessa grupper gör det möjligt att identifiera övergångar som motsvarar mellantillstånd i rummet av principalkomponenter. De studier som presenteras i denna avhandling bidrar till vår förståelse av kanalöppningsmekanismen och den funktionella grupperingen av cys-loop receptorstrukturer. Denna kunskap är viktig för att kunna utforma nya läke- medel som genom allosterisk modulering påverkar funktionen hos proteinet, i synnerhet för att behandla neurologiska störningar. Nyckelord: cys-loop-receptor, jonkanal, neurovetenskap, molekyldynamik, aktivering, modulering, modellering, grind, GABAA “Feet, what do I need you for when I have wings to fly?” Frida Kahlo v List of Publications This thesis is based on following publications, which are referred to in the text by their roman numerals: Paper I Edward J Bertaccini, Özge Yoluk, Erik R Lindahl, and James R Trudell. Assessment of Homology Templates and an Anesthetic Binding Site within the γ-Aminobutyric Acid Receptor. Anesthesiology, 2013 vol. 119 (5) pp. 1087–1095. Paper II Özge Yoluk, Torben Broemstrup, Edward J Bertaccini, James R Trudell, and Erik Lindahl. Stabilization of the GluCl Ligand-Gated Ion Channel in the Presence and Absence of Ivermectin. Biophys. J., 2013 vol. 105 (3) pp. 640–647. Paper III Özge Yoluk, Erik Lindahl, and Magnus Andersson. Conformational Gating Dynamics in the GluCl Anion-Selective Chloride Channel. ACS Chem Neurosci. 2015 vol. 6 (8) pp. 1459–1467. Paper IV Stephanie A. Heusser, Özge Yoluk, Göran Klement, Erika A. Riederer, Erik Lindahl, Rebecca J. Howard. Functional Characterization of Neuro- transmitter Activation and Modulation in a Nematode Model Ligand-gated Ion Channel. J. Neurochem., in press. doi: 10.1111/jnc.13644 Paper V Laura Orellana, Özge Yoluk, Oliver Carrillo, Modesto Orozco and Erik Lindahl. Prediction and Validation of Protein Intermediate States from Struc- turally Rich Ensembles and Coarse-Grained Simulations. Revision submitted to Nat. Commun. Additional publications: Mieke Nys, Ana Farinha, Özge Yoluk, Magnus Andersson, Eveline Wijck- mans, Marijke Brams, Radovan Spurny, Erik Lindahl, Chris Ulens. A Novel Al- losteric Binding Site in a Cys-Loop Receptor Ligand-Binding Domain Unveiled in the Crystal Structure of ELIC in Complex with Chlorpromazine. Revision submit- ted to Proc. Natl. Acad. Sci. U.S.A. vii viii Author Contributions to the Papers For paper I E.B. came up with the idea, did most of the calculations, and most of the manuscript writing together with J.R.T and E.L.. Ö.Y. created and analyzed the Rosetta model. For paper II, E.L. developed the idea. Ö.Y. did all the calculations and the analysis. T.B. parametrised the ivermectin molecule. Ö.Y. and E.L. did most of the manuscript writing in collaboration with the other co-authors. Paper III was initiated by M.A. All the calculations and the analysis were performed by Ö.Y. in discussion with M.A. and E.L. Manuscript writing was done by all co-authors. The mutational analysis in Paper IV was designed by Ö.Y. based on the re- sults in paper III. Ö.Y. generated the mutated constructs. S.A.H. did the functional studies in oocytes, and the data analysis in collaboration with G.K. and R.J.H., ex- cept for the modulation data which was obtained by E.A.R and R.J.H. Manuscript writing was done mostly by S.A.H. and R.J.H. in collaboration with the author co-authors. The code for eBDIMS in Paper V was written by L.O. and O.C. L.O. came up with the idea, did most of the calculations and the manuscript writing. Ö.Y. helped with the ensemble preparations and analysis, ran some of the transition methods, and helped with figure preparations. All authors contributed to the manuscript writing and discussions. Contents Contents ix Abbreviations xi 1 Introduction 1 2 Molecular Neurobiology 5 2.1 Neurons . 5 2.1.1 Sensory Neurons . 7 2.1.2 Interneurons . 7 2.1.3 Motor Neurons . 7 2.2 Neuronal Activity . 8 2.2.1 Electrical synapses . 9 2.2.2 Chemical synapses . 10 2.3 The Ion Channel Superfamily . 11 3 Cys-Loop Receptors 13 3.1 The Discovery of Cys-Loop Receptors . 13 3.2 Channelopathies . 14 3.2.1 Hyperekplexia . 14 3.2.2 Epilepsy . 15 3.3 Anesthesia and Substance Abuse . 15 3.4 The First Structure . 16 3.5 Origins of Cys-Loop Receptors . 17 3.5.1 ELIC . 18 ix x CONTENTS 3.5.2 GLIC . 18 3.5.3 Are Prokaryotic Models Relevant? . 19 4 Modeling and Channel Dynamics in GluCl 21 4.1 Glutamate-Gated Chloride Channel . 21 4.1.1 Topology . 22 4.1.2 GluCl-based Models Capture Modulator Properties . 24 4.2 Channel Dynamics of GluCl . 26 4.2.1 Simulations of GluCl can Capture Closing Dynamics . 27 4.2.2 From Agonist Binding to Channel Opening . 30 4.3 From in silico to in vitro ......................... 33 5 A Gating Mechanism 35 5.1 Principal Component Analysis . 35 5.2 Gating Intermediates in the GLIC ensemble . 36 5.3 Functional Clusters of Eukaryotic Structures . 37 5.4 Cys-loop Receptor Dynamics Derived From Long-Scale Simulations . 39 6 Methods 45 6.1 Homology Modeling .
Load more

Recommended publications
  • Ion Channels
    UC Davis UC Davis Previously Published Works Title THE CONCISE GUIDE TO PHARMACOLOGY 2019/20: Ion channels. Permalink https://escholarship.org/uc/item/1442g5hg Journal British journal of pharmacology, 176 Suppl 1(S1) ISSN 0007-1188 Authors Alexander, Stephen PH Mathie, Alistair Peters, John A et al. Publication Date 2019-12-01 DOI 10.1111/bph.14749 License https://creativecommons.org/licenses/by/4.0/ 4.0 Peer reviewed eScholarship.org Powered by the California Digital Library University of California S.P.H. Alexander et al. The Concise Guide to PHARMACOLOGY 2019/20: Ion channels. British Journal of Pharmacology (2019) 176, S142–S228 THE CONCISE GUIDE TO PHARMACOLOGY 2019/20: Ion channels Stephen PH Alexander1 , Alistair Mathie2 ,JohnAPeters3 , Emma L Veale2 , Jörg Striessnig4 , Eamonn Kelly5, Jane F Armstrong6 , Elena Faccenda6 ,SimonDHarding6 ,AdamJPawson6 , Joanna L Sharman6 , Christopher Southan6 , Jamie A Davies6 and CGTP Collaborators 1School of Life Sciences, University of Nottingham Medical School, Nottingham, NG7 2UH, UK 2Medway School of Pharmacy, The Universities of Greenwich and Kent at Medway, Anson Building, Central Avenue, Chatham Maritime, Chatham, Kent, ME4 4TB, UK 3Neuroscience Division, Medical Education Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, UK 4Pharmacology and Toxicology, Institute of Pharmacy, University of Innsbruck, A-6020 Innsbruck, Austria 5School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, BS8 1TD, UK 6Centre for Discovery Brain Science, University of Edinburgh, Edinburgh, EH8 9XD, UK Abstract The Concise Guide to PHARMACOLOGY 2019/20 is the fourth in this series of biennial publications. The Concise Guide provides concise overviews of the key properties of nearly 1800 human drug targets with an emphasis on selective pharmacology (where available), plus links to the open access knowledgebase source of drug targets and their ligands (www.guidetopharmacology.org), which provides more detailed views of target and ligand properties.
    [Show full text]
  • Lipid Sensitivity of a Prokaryotic Plgic 1 Structural Sensitivity of a Prokaryotic Pentameric Ligand-Gated Ion Channel To
    JBC Papers in Press. Published on March 5, 2013 as Manuscript M113.458133 The latest version is at http://www.jbc.org/cgi/doi/10.1074/jbc.M113.458133 Lipid sensitivity of a prokaryotic pLGIC Structural sensitivity of a prokaryotic pentameric ligand-gated ion channel to its membrane environment* Jonathan M. Labriola1, Akash Pandhare2, Michaela Jansen3, Michael P. Blanton2, Pierre-Jean Corringer4, and John E. Baenziger1 1From the Department of Biochemistry, Microbiology, and Immunology University of Ottawa, Ottawa ON, K1H 8M5, Canada 2Department of Pharmacology and Neuroscience and the Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430 3Department of Cell Physiology and Molecular Biophysics and the Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX. 79430. Downloaded from 4G5 Group of Channel-Receptors, CNRS URA 2182 Pasteur Institute, F75015, Paris, France *Running title: Lipid sensitivity of a prokaryotic pLGIC www.jbc.org 1To whom correspondence should be addressed: John E. Baenziger, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, 451 Smyth Rd. Ottawa, ON, K1H 8M5, Canada, Tel.: (613) 562-5800 x8222; Fax.: (613) 562-5440; E-mail: [email protected]. at TTU-HEALTH SCIENCES CTR, on March 5, 2013 Keywords: prokaryotic pentameric ligand-gated ion channels, membrane sensitivity, structure, function _____________________________________________________________________________________ Background: The lipid sensitivity of the expression, and amenability to prokaryotic pentameric ligand-gated ion channel crystallographic analysis. We show here that (pLGIC), GLIC, is poorly characterized. membrane-reconstituted GLIC exhibits structural and biophysical properties similar Results: GLIC is more thermally stable and to those of the membrane-reconstituted does not exhibit the same propensity to adopt an nAChR, although GLIC is substantially more uncoupled conformation as the Torpedo nAChR.
    [Show full text]
  • Ligand-Gated Ion Channels
    S.P.H. Alexander et al. The Concise Guide to PHARMACOLOGY 2015/16: Ligand-gated ion channels. British Journal of Pharmacology (2015) 172, 5870–5903 THE CONCISE GUIDE TO PHARMACOLOGY 2015/16: Ligand-gated ion channels Stephen PH Alexander1, John A Peters2, Eamonn Kelly3, Neil Marrion3, Helen E Benson4, Elena Faccenda4, Adam J Pawson4, Joanna L Sharman4, Christopher Southan4, Jamie A Davies4 and CGTP Collaborators L 1 School of Biomedical Sciences, University of Nottingham Medical School, Nottingham, NG7 2UH, UK, N 2Neuroscience Division, Medical Education Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, UK, 3School of Physiology and Pharmacology, University of Bristol, Bristol, BS8 1TD, UK, 4Centre for Integrative Physiology, University of Edinburgh, Edinburgh, EH8 9XD, UK Abstract The Concise Guide to PHARMACOLOGY 2015/16 provides concise overviews of the key properties of over 1750 human drug targets with their pharmacology, plus links to an open access knowledgebase of drug targets and their ligands (www.guidetopharmacology.org), which provides more detailed views of target and ligand properties. The full contents can be found at http://onlinelibrary.wiley.com/ doi/10.1111/bph.13350/full. Ligand-gated ion channels are one of the eight major pharmacological targets into which the Guide is divided, with the others being: ligand-gated ion channels, voltage- gated ion channels, other ion channels, nuclear hormone receptors, catalytic receptors, enzymes and transporters. These are presented with nomenclature guidance and summary information on the best available pharmacological tools, alongside key references and suggestions for further reading. The Concise Guide is published in landscape format in order to facilitate comparison of related targets.
    [Show full text]
  • Hydrocarbon Molar Water Solubility Predicts NMDA Vs. GABAA Receptor Modulation Robert J Brosnan* and Trung L Pham
    Brosnan and Pham BMC Pharmacology and Toxicology 2014, 15:62 http://www.biomedcentral.com/2050-6511/15/62 RESEARCH ARTICLE Open Access Hydrocarbon molar water solubility predicts NMDA vs. GABAA receptor modulation Robert J Brosnan* and Trung L Pham Abstract Background: Many anesthetics modulate 3-transmembrane (such as NMDA) and 4-transmembrane (such as GABAA) receptors. Clinical and experimental anesthetics exhibiting receptor family specificity often have low water solubility. We hypothesized that the molar water solubility of a hydrocarbon could be used to predict receptor modulation in vitro. Methods: GABAA (α1β2γ2s) or NMDA (NR1/NR2A) receptors were expressed in oocytes and studied using standard two-electrode voltage clamp techniques. Hydrocarbons from 14 different organic functional groups were studied at saturated concentrations, and compounds within each group differed only by the carbon number at the ω-position or within a saturated ring. An effect on GABAA or NMDA receptors was defined as a 10% or greater reversible current change from baseline that was statistically different from zero. Results: Hydrocarbon moieties potentiated GABAA and inhibited NMDA receptor currents with at least some members from each functional group modulating both receptor types. A water solubility cut-off for NMDA receptors occurred at 1.1 mM with a 95% CI = 0.45 to 2.8 mM. NMDA receptor cut-off effects were not well correlated with hydrocarbon chain length or molecular volume. No cut-off was observed for GABAA receptors within the solubility range of hydrocarbons studied. Conclusions: Hydrocarbon modulation of NMDA receptor function exhibits a molar water solubility cut-off. Differences between unrelated receptor cut-off values suggest that the number, affinity, or efficacy of protein- hydrocarbon interactions at these sites likely differ.
    [Show full text]
  • Are Nicotinic Acetylcholine Receptors Coupled to G Proteins?
    Insights & Perspectives Hypotheses Are nicotinic acetylcholine receptors coupled to G proteins? Nadine Kabbani1)*, Jacob C. Nordman1), Brian A. Corgiat1), Daniel P. Veltri2), Amarda Shehu2), Victoria A. Seymour3) and David J. Adams3) It was, until recently, accepted that the two classes of acetylcholine (ACh) synaptic plasticity [2, 3]. Mutations receptors are distinct in an important sense: muscarinic ACh receptors within nAChR genes are implicated signal via heterotrimeric GTP binding proteins (G proteins), whereas in a number of human disorders þ 2þ þ including drug addiction and schizo- nicotinic ACh receptors (nAChRs) open to allow flux of Na ,Ca ,andK phrenia [4]. ions into the cell after activation. Here we present evidence of direct coupling Nicotinic receptors belong to an between G proteins and nAChRs in neurons. Based on proteomic, evolutionarily conserved class of cys- biophysical, and functional evidence, we hypothesize that binding to G loop containing receptor channels that proteins modulates the activity and signaling of nAChRs in cells. It is includes GABAA,glycine,and5HT3 important to note that while this hypothesis is new for the nAChR, it is receptorsaswellastwonewlydiscovered channels: a zinc-activated channel and consistent with known interactions between G proteins and structurally an invertebrate GABA-gated cation chan- related ligand-gated ion channels. Therefore, it underscores an evolution- nel [5]. In mammals, genes encoding arily conserved metabotropic mechanism of G protein signaling via nAChR neuronal nAChR subunits have been channels. identified and labeled a (a1–a10) and b (b1–b4). Functional nAChRs are derived Keywords: from an arrangement of five subunits into .acetylcholine; G protein coupling; intracellular loop; ligand-gated ion channel; heteromeric or homomeric receptors [6] loop modeling; protein interaction; signal transduction (Fig.
    [Show full text]
  • Direct Visualization of Ion-Channel Gating in a Native Environment COMMENTARY Yvonne Gicherua and Sudha Chakrapania,1
    COMMENTARY Direct visualization of ion-channel gating in a native environment COMMENTARY Yvonne Gicherua and Sudha Chakrapania,1 Pentameric ligand-gated ion channels (pLGICs), also Impact of Membrane Environment on Channel known as Cys-loop receptors, are localized primarily in Gating and Dynamics the postsynaptic membranes, and mediate fast chem- Interestingly, high-resolution pLGIC structures solved ical transmission in the central and peripheral nervous thus far are in nonnative (detergent) environments, systems. Binding of neurotransmitter activates these leading to speculations on the possible alteration of receptors, causing changes in postsynaptic membrane channel structures in the absence of membranes. Mem- potential and consequently modulation of neuronal or brane composition has been shown to be critical for muscle activity. pLGIC functions are altered by a vari- channel gating of the nAChR (5) and possibly other ety of drugs, making them significant pharmaceutical eukaryotic channels. GLIC has served as an archetypal targets. Indeed, the rise in pLGIC crystal and cryoelec- pLGIC because of the overall conservation of its archi- tron microscopy structures underscores the magnitude tecture and pharmacological properties (6). GLIC crystal of research efforts that have gone into unraveling the structuresintheopenandresting conformations were molecular details of channel function. Current structure the first high-resolution pLGIC structures available (7–9). determination methods of pLGICs capture stationary Importantly, the global concerted movements resulting images and, most often, in nonnative environments. in opening of the channel pore in GLIC are comparable As a result, gaps remain in our understanding of the to the gating mechanism emerging from recent eukary- dynamic properties, intermediate conformational otic pLGIC structures.
    [Show full text]
  • Anesthetic Binding in a Pentameric Ligand-Gated Ion Channel: GLIC
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Biophysical Journal Volume 99 September 2010 1801–1809 1801 Anesthetic Binding in a Pentameric Ligand-Gated Ion Channel: GLIC Qiang Chen,†6 Mary Hongying Cheng,‡6 Yan Xu,†§{ and Pei Tang†§k* † ‡ § { k Departments of Anesthesiology, Chemistry, Pharmacology and Chemical Biology, Structural Biology, and Computational Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania ABSTRACT Cys-loop receptors are molecular targets of general anesthetics, but the knowledge of anesthetic binding to these proteins remains limited. Here we investigate anesthetic binding to the bacterial Gloeobacter violaceus pentameric ligand-gated ion channel (GLIC), a structural homolog of cys-loop receptors, using an experimental and computational hybrid approach. Tryp- tophan fluorescence quenching experiments showed halothane and thiopental binding at three tryptophan-associated sites in the extracellular (EC) domain, transmembrane (TM) domain, and EC-TM interface of GLIC. An additional binding site at the EC-TM interface was predicted by docking analysis and validated by quenching experiments on the N200W GLIC mutant. The binding affinities (KD) of 2.3 5 0.1 mM and 0.10 5 0.01 mM were derived from the fluorescence quenching data of halo- thane and thiopental, respectively. Docking these anesthetics to the original GLIC crystal structure and the structures relaxed by molecular dynamics simulations revealed intrasubunit sites for most halothane binding and intersubunit sites for thiopental binding. Tryptophans were within reach of both intra- and intersubunit binding sites. Multiple molecular dynamics simulations on GLIC in the presence of halothane at different sites suggested that anesthetic binding at the EC-TM interface disrupted the critical interactions for channel gating, altered motion of the TM23 linker, and destabilized the open-channel conformation that can lead to inhibition of GLIC channel current.
    [Show full text]
  • Dynamic Closed States of a Ligand-Gated Ion Channel Captured by Cryo-EM and Simulations
    Published Online: 1 July, 2021 | Supp Info: http://doi.org/10.26508/lsa.202101011 Downloaded from life-science-alliance.org on 27 September, 2021 Research Article Dynamic closed states of a ligand-gated ion channel captured by cryo-EM and simulations Urskaˇ Rovsnikˇ 1, Yuxuan Zhuang1,Bjorn¨ O Forsberg1,2, Marta Carroni1, Linnea Yvonnesdotter1, Rebecca J Howard1 , Erik Lindahl1,3 Ligand-gated ion channels are critical mediators of electro- between principal and complementary subunits. The transmem- chemical signal transduction across evolution. Biophysical and brane domain (TMD) contains α-helices M1–M4, with M2 lining the pharmacological characterization of these receptor proteins relies channel pore, and an intracellular domain of varying length (2–80 on high-quality structures in multiple, subtly distinct functional residues) inserted between M3 and M4. Extracellular agonist states. However, structural data in this family remain limited, binding is thought to favor subtle structural transitions from resting particularly for resting and intermediate states on the activation to intermediate or “flip” states (2), opening of a transmembrane pathway. Here, we report cryo-electron microscopy (cryo-EM) pore (5), and in most cases, a refractory desensitized phase (6). structures of the proton-activated Gloeobacter violaceus ligand- Accordingly, a detailed understanding of pentameric channel gated ion channel (GLIC) under three pH conditions. Decreased pH biophysics and pharmacology depends on high-quality structural was associated with improved resolution and side chain rear- templates in multiple functional states. However, high-resolution rangements at the subunit/domain interface, particularly involving structures can be biased by stabilizing measures such as ligands, functionally important residues in the β1–β2andM2–M3 loops.
    [Show full text]
  • Mechanisms of Nmda Receptor Inhibition by Memantine and Ketamine
    MECHANISMS OF NMDA RECEPTOR INHIBITION BY MEMANTINE AND KETAMINE by Nathan G. Glasgow Bachelor of Science, University of Toledo, 2010 Submitted to the Graduate Faculty of the Kenneth P. Dietrich School of Arts and Sciences in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Pittsburgh 2016 UNIVERSITY OF PITTSBURGH DIETRICH SCHOOL OF ARTS AND SCIENCES This dissertation was presented by Nathan G. Glasgow It was defended on April 21, 2016 and approved by Dr. Stephen D. Meriney, Professor, Department of Neuroscience Dr. Anne-Marie Oswald, Assistant Professor, Department of Neuroscience Dr. Elias Aizenman, Professor, Department of Neurobiology Dr. Michael S. Gold, Professor, Department of Anesthesiology Dr. Stephen F. Traynelis, Professor, Department of Pharmacology, Emory University Dissertation Advisor: Dr. Jon W. Johnson, Professor, Department of Neuroscience ii Copyright © by Nathan G. Glasgow 2016 iii MECHANISMS OF NMDA RECEPTOR INHIBITION BY MEMANTINE AND KETAMINE Nathan G. Glasgow, PhD University of Pittsburgh, 2016 NMDA receptors (NMDARs), a subfamily of ionotropic glutamate receptors, have unique biophysical properties including high permeability to Ca2+. Activation of NMDARs increases the concentration of intracellular Ca2+ that can activate a vast array of signaling pathways. NMDARs are necessary for many processes including synaptic plasticity, dendritic integration, and cell survival. Aberrant NMDAR activation is implicated in many central nervous system disorders including neurodegenerative disorders, neuronal loss following ischemia, and neuropsychiatric disorders. Hope that NMDARs may serve as useful therapeutic targets is bolstered by the clinical success of two NMDAR antagonists, memantine and ketamine. Memantine and ketamine act as open channel blockers of the NMDAR-associated ion channel, and exhibit similar IC50 values and kinetics.
    [Show full text]
  • Multiple Binding Sites for the General Anesthetic Isoflurane Identified in the Nicotinic Acetylcholine Receptor Transmembrane Domain
    Multiple binding sites for the general anesthetic isoflurane identified in the nicotinic acetylcholine receptor transmembrane domain Grace Brannigana,1, David N. LeBarda, Jérôme Héninb, Roderic G. Eckenhoffc, and Michael L. Kleina,1 aInstitute for Computational and Molecular Science, Temple University, Philadelphia, PA 19122; bLaboratoire d’Ingénierie des Systèmes Macromoléculaires, Centre National de la Recherche Scientifique—Aix-Marseille Université, 13402 Marseille, France; and cDepartment of Anesthesiology and Critical Care, University of Pennsylvania School of Medicine, Philadelphia, PA 19104 Contributed by Michael L. Klein, June 24, 2010 (sent for review May 12, 2010) An extensive search for isoflurane binding sites in the nicotinic An intriguing difference between the nAChR structure acetylcholine receptor (nAChR) and the proton gated ion channel reported in 2BG9 and the prokaryotic structures are the large from Gloebacter violaceus (GLIC) has been carried out based on mo- gaps in protein density in the extracellular half of the nAChR lecular dynamics (MD) simulations in fully hydrated lipid membrane transmembrane domain (TMD). The high-resolution prokaryotic environments. Isoflurane introduced into the aqueous phase readily structures do not display such gaps (Fig. S1). Recently (14), we partitions into the lipid membrane and the membrane-bound pro- proposed that such gaps are occupied by cholesterol, which is tein. Specifically, isoflurane binds persistently to three classes of essential for nAChR function (15). Because cholesterol is not sites in the nAChR transmembrane domain: (i) An isoflurane dimer found in prokaryotic membranes, this hypothesis provides an occludes the pore, contacting residues identified by previous muta- alternate explanation to the source of differences between the genesis studies; analogous behavior is observed in GLIC.
    [Show full text]
  • Polish Neuroscience Society (PTBUN)
    ORGANIZATION Organizer: Polish Neuroscience Society (PTBUN) Co-organizers: Department for Experimental Medicine, Medical University of Silesia in Katowice Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw Mossakowski Medical Research Centre, Polish Academy of Sciences, Warsaw Institute of Pharmacology, Polish Academy of Sciences, Kraków International Institute of Molecular and Cell Biology, Warsaw SCIENTIFIC PROGRAM COMMITTEE Chairmen: Members: Jan Celichowski Agata Adamczyk Grzegorz Hess Vice-Chairmen: Ewa Kublik Jarosław J. Barski Monika Liguz-Lęcznar Jacek Jaworski Jan Rodriguez Parkitna Małgorzata Skup LOCAL ORGANIZING COMMITTEE Chairmen: Members: Jarosław J. Barski Dominika Chojnacka Aniela Grajoszek Vice-Chairmen: Daniela Kasprowska-Liśkiewicz Marta Nowacka-Chmielewska Arkadiusz Liśkiewicz Marta Przybyła Anna Sługocka Acta Neurobiol Exp 2019_79_supp_inner_v4.indd 1 17/08/2019 22:16 II 14th International Congress of the Polish Neuroscience Society Acta Neurobiol Exp 2019, 79: I–XCIX HONORARY PATRONATE The Mayor of Katowice Rector of Medical Katowice City City University of Silesia SPONSORS AND FINANCIAL SUPPORT Ministry of Science and Higher Education Polish Academy of Sciences Katowice City Vivari s.c. Noldus Information Technology European Brain and Behavior Society CED MMM Muenchener Medizin Mechanik Polska Sp. z o.o. OMIXYS Sp. z o.o. Science Products GmbH SHIM-POL A.M. Borzymowski Femtonics Acta Neurobiol Exp 2019_79_supp_inner_v4.indd 2 17/08/2019 22:16 Acta Neurobiol Exp 2019, 79: I–XCIX Programme III PROGRAMME 27.08.2019, TUESDAY 12:00–14:00 Workshop on Ultrasonic Vocalization (USV) ‑ theory 14:00–15:00 Lunch 15:00–18:00 Workshop on Ultrasonic Vocalization (USV) ‑ practice 28.08.2019, WEDNESDAY 12:00–14:30 General Assembly of PTBUN 14:30–15:00 Opening Ceremony 15:00–16:00 Plenary lecture 1 (PL 1) Speaker: Magdalena Götz, Helmholtz Center Munich, German Research Center for Environmental Health, Munich, Germany Title: “Novel mechanisms of neurogenesis and neural repair” Introduced by: Jarosław J.
    [Show full text]
  • Probing Solution Structure of the Pentameric Ligand-Gated Ion Channel GLIC by Small-Angle Neutron Scattering
    bioRxiv preprint doi: https://doi.org/10.1101/2021.04.10.439285; this version posted April 11, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Probing solution structure of the pentameric ligand-gated ion channel GLIC by small-angle neutron scattering Marie Lycksell1, Urˇska Rovˇsnik1,CathrineBergh2, Nicolai T Johansen3, Anne Martel4,LionelPorcar4, Lise Arleth3, Rebecca J Howard1,ErikLindahl1,2* 1Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden. 2Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden. 3Structural Biophysics, X-ray and Neutron Science, The Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark. 4Institut Laue-Langevin, Grenoble, France. *email: [email protected]. Abstract Pentameric ligand-gated ion channels undergo subtle conformational cycling to control electrochemical signal transduction in many kingdoms of life. Several crystal structures have now been reported in this family, but the functional relevance of such models remains unclear. Here, we used small-angle neutron scattering (SANS) to probe ambient solution-phase properties of the pH-gated bacterial ion channel GLIC under resting and activating conditions. Data collection was optimized by inline paused-flow size-exclusion chromatography, and exchanging into deuterated detergent to hide the micelle contribution. Resting-state GLIC was the best-fit crystal structure to SANS curves, with no evidence for divergent mechanisms. Moreover, enhanced-sampling molecular dynamics simulations enabled di↵erential modeling in resting versus activating conditions, with the latter corresponding to an intermediate ensemble of both the extracellular and transmembrane domains.
    [Show full text]