1
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Identification of N-acyl amino acids that are positive allosteric modulators of glycine receptors. Biochem Pharmacol 2020; 180:114117. [PMID: 32579961 DOI: 10.1016/j.bcp.2020.114117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/16/2020] [Accepted: 06/18/2020] [Indexed: 01/31/2023]
Abstract
Glycine receptors (GlyRs) mediate inhibitory neurotransmission within the spinal cord and play a crucial role in nociceptive signalling. This makes them primary targets for the development of novel chronic pain therapies. Endogenous lipids have previously been shown to modulate glycine receptors and produce analgesia in pain models, however little is known about what chemical features mediate these effects. In this study, we characterised lipid modulation of GlyRs by screening a library of N-acyl amino acids across all receptor subtypes and determined chemical features crucial for their activity. Acyl-glycine's with a C18 carbon tail were found to produce the greatest potentiation, and require a cis double bond within the central region of the carbon tail (ω6 - ω9) to be active. At 1 µM, C18 ω6,9 glycine potentiated glycine induced currents in α3 and α3β receptors by over 50%, and α1, α2, α1β and α2β receptors by over 100%. C18 ω9 glycine (N-oleoyl glycine) significantly enhance glycine induced peak currents and cause a dose-dependent shift in the glycine concentration response. In the presence of 3 µM C18 ω9 glycine, the EC5o of glycine at the α1 receptor was reduced from 17 µM to 10 µM. This study has identified several acyl-amino acids which are positive allosteric modulators of GlyRs and make promising lead compounds for the development of novel chronic pain therapies.
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2
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Guros NB, Balijepalli A, Klauda JB. Microsecond-timescale simulations suggest 5-HT-mediated preactivation of the 5-HT 3A serotonin receptor. Proc Natl Acad Sci U S A 2020; 117:405-414. [PMID: 31871207 PMCID: PMC6955379 DOI: 10.1073/pnas.1908848117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Aided by efforts to improve their speed and efficiency, molecular dynamics (MD) simulations provide an increasingly powerful tool to study the structure-function relationship of pentameric ligand-gated ion channels (pLGICs). However, accurate reporting of the channel state and observation of allosteric regulation by agonist binding with MD remains difficult due to the timescales necessary to equilibrate pLGICs from their artificial and crystalized conformation to a more native, membrane-bound conformation in silico. Here, we perform multiple all-atom MD simulations of the homomeric 5-hydroxytryptamine 3A (5-HT3A) serotonin receptor for 15 to 20 μs to demonstrate that such timescales are critical to observe the equilibration of a pLGIC from its crystalized conformation to a membrane-bound conformation. These timescales, which are an order of magnitude longer than any previous simulation of 5-HT3A, allow us to observe the dynamic binding and unbinding of 5-hydroxytryptamine (5-HT) (i.e., serotonin) to the binding pocket located on the extracellular domain (ECD) and allosteric regulation of the transmembrane domain (TMD) from synergistic 5-HT binding. While these timescales are not long enough to observe complete activation of 5-HT3A, the allosteric regulation of ion gating elements by 5-HT binding is indicative of a preactive state, which provides insight into molecular mechanisms that regulate channel activation from a resting state. This mechanistic insight, enabled by microsecond-timescale MD simulations, will allow a careful examination of the regulation of pLGICs at a molecular level, expanding our understanding of their function and elucidating key structural motifs that can be targeted for therapeutic regulation.
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Affiliation(s)
- Nicholas B Guros
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742
- Biophysics Group, Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899
| | - Arvind Balijepalli
- Biophysics Group, Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742;
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3
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Duncan AL, Song W, Sansom MSP. Lipid-Dependent Regulation of Ion Channels and G Protein-Coupled Receptors: Insights from Structures and Simulations. Annu Rev Pharmacol Toxicol 2019; 60:31-50. [PMID: 31506010 DOI: 10.1146/annurev-pharmtox-010919-023411] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Ion channels and G protein-coupled receptors (GPCRs) are regulated by lipids in their membrane environment. Structural studies combined with biophysical and molecular simulation investigations reveal interaction sites for specific lipids on membrane protein structures. For K channels, PIP2 plays a key role in regulating Kv and Kir channels. Likewise, several recent cryo-EM structures of TRP channels have revealed bound lipids, including PIP2 and cholesterol. Among the pentameric ligand-gated ion channel family, structural and biophysical studies suggest the M4 TM helix may act as a lipid sensor, e.g., forming part of the binding sites for neurosteroids on the GABAA receptor. Structures of GPCRs have revealed multiple cholesterol sites, which may modulate both receptor dynamics and receptor oligomerization. PIP2 also interacts with GPCRs and may modulate their interactions with G proteins. Overall, it is evident that multiple lipid binding sites exist on channels and receptors that modulate their function allosterically and are potential druggable sites.
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Affiliation(s)
- Anna L Duncan
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom;
| | - Wanling Song
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom;
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom;
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4
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Corradi V, Sejdiu BI, Mesa-Galloso H, Abdizadeh H, Noskov SY, Marrink SJ, Tieleman DP. Emerging Diversity in Lipid-Protein Interactions. Chem Rev 2019; 119:5775-5848. [PMID: 30758191 PMCID: PMC6509647 DOI: 10.1021/acs.chemrev.8b00451] [Citation(s) in RCA: 245] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Membrane
lipids interact with proteins in a variety of ways, ranging
from providing a stable membrane environment for proteins to being
embedded in to detailed roles in complicated and well-regulated protein
functions. Experimental and computational advances are converging
in a rapidly expanding research area of lipid–protein interactions.
Experimentally, the database of high-resolution membrane protein structures
is growing, as are capabilities to identify the complex lipid composition
of different membranes, to probe the challenging time and length scales
of lipid–protein interactions, and to link lipid–protein
interactions to protein function in a variety of proteins. Computationally,
more accurate membrane models and more powerful computers now enable
a detailed look at lipid–protein interactions and increasing
overlap with experimental observations for validation and joint interpretation
of simulation and experiment. Here we review papers that use computational
approaches to study detailed lipid–protein interactions, together
with brief experimental and physiological contexts, aiming at comprehensive
coverage of simulation papers in the last five years. Overall, a complex
picture of lipid–protein interactions emerges, through a range
of mechanisms including modulation of the physical properties of the
lipid environment, detailed chemical interactions between lipids and
proteins, and key functional roles of very specific lipids binding
to well-defined binding sites on proteins. Computationally, despite
important limitations, molecular dynamics simulations with current
computer power and theoretical models are now in an excellent position
to answer detailed questions about lipid–protein interactions.
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Affiliation(s)
- Valentina Corradi
- Centre for Molecular Simulation and Department of Biological Sciences , University of Calgary , 2500 University Drive NW , Calgary , Alberta T2N 1N4 , Canada
| | - Besian I Sejdiu
- Centre for Molecular Simulation and Department of Biological Sciences , University of Calgary , 2500 University Drive NW , Calgary , Alberta T2N 1N4 , Canada
| | - Haydee Mesa-Galloso
- Centre for Molecular Simulation and Department of Biological Sciences , University of Calgary , 2500 University Drive NW , Calgary , Alberta T2N 1N4 , Canada
| | - Haleh Abdizadeh
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Nijenborgh 7 , 9747 AG Groningen , The Netherlands
| | - Sergei Yu Noskov
- Centre for Molecular Simulation and Department of Biological Sciences , University of Calgary , 2500 University Drive NW , Calgary , Alberta T2N 1N4 , Canada
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Nijenborgh 7 , 9747 AG Groningen , The Netherlands
| | - D Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences , University of Calgary , 2500 University Drive NW , Calgary , Alberta T2N 1N4 , Canada
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5
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Chiodo L, Malliavin TE, Giuffrida S, Maragliano L, Cottone G. Closed-Locked and Apo-Resting State Structures of the Human α7 Nicotinic Receptor: A Computational Study. J Chem Inf Model 2018; 58:2278-2293. [PMID: 30359518 DOI: 10.1021/acs.jcim.8b00412] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nicotinic acetylcholine receptors, belonging to the Cys-loop superfamily of ligand-gated ion channels (LGICs), are membrane proteins present in neurons and at neuromuscular junctions. They are responsible for signal transmission, and their function is regulated by neurotransmitters, agonists, and antagonists drugs. A detailed knowledge of their conformational transition in response to ligand binding is critical to understanding the basis of ligand-receptor interaction, in view of new pharmacological approaches to control receptor activity. However, the scarcity of experimentally derived structures of human channels makes this perspective extremely challenging. To contribute overcoming this issue, we have recently reported structural models for the open and the desensitized states of the human α7 nicotinic receptor. Here, we provide all-atom structural models of the same receptor in two different nonconductive states. The first structure, built via homology modeling and relaxed with extensive Molecular Dynamics simulations, represents the receptor bound to the natural antagonist α-conotoxin ImI. After comparison with available experimental data and computational models of other eukaryotic LGICs, we deem it consistent with the "closed-locked" state. The second model, obtained with simulations from the spontaneous relaxation of the open, agonist-bound α7 structure after ligand removal, recapitulates the characteristics of the apo-resting state of the receptor. These results add to our previous work on the active and desensitized state conformations, contributing to the structural characterization of the conformational landscape of the human α7 receptor and suggesting benchmarks to discriminate among conformations found in experiments or in simulations of LGICs. In particular key interactions at the interface between the extracellular domain and the transmembrane domain are identified, that could be critical to the α7 receptor function.
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Affiliation(s)
- Letizia Chiodo
- Department of Engineering , Campus Bio-Medico University of Rome , Via Á. del Portillo 21 , 00128 Rome , Italy
| | - Thérèse E Malliavin
- Institut Pasteur and CNRS UMR 3528, Unité de Bioinformatique Structurale , 25-28 rue du Dr Roux , 75015 Paris , France.,Centre de Bioinformatique, Biostatistique et Biologie Intégrative , Institut Pasteur and CNRS USR 3756 , 25-28 rue du Dr Roux , 75015 Paris , France
| | - Sergio Giuffrida
- Department of Physics and Chemistry , University of Palermo , Viale delle Scienze Ed. 17 , 90128 Palermo , Italy
| | - Luca Maragliano
- Center for Synaptic Neuroscience and Technology (NSYN@UniGe) , Istituto Italiano di Tecnologia , Largo Rosanna Benzi, 10 , 16132 Genoa , Italy.,IRCCS Ospedale Policlinico San Martino , Largo Rosanna Benzi 10 , 16132 Genoa , Italy
| | - Grazia Cottone
- Department of Physics and Chemistry , University of Palermo , Viale delle Scienze Ed. 17 , 90128 Palermo , Italy
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6
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Oakes V, Domene C. Capturing the Molecular Mechanism of Anesthetic Action by Simulation Methods. Chem Rev 2018; 119:5998-6014. [DOI: 10.1021/acs.chemrev.8b00366] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Victoria Oakes
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
| | - Carmen Domene
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
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7
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Ayan M, Essiz S. The neural γ 2α 1β 2α 1β 2 gamma amino butyric acid ion channel receptor: structural analysis of the effects of the ivermectin molecule and disulfide bridges. J Mol Model 2018; 24:206. [PMID: 30008086 DOI: 10.1007/s00894-018-3739-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 06/27/2018] [Indexed: 12/21/2022]
Abstract
While ~30% of the human genome encodes membrane proteins, only a handful of structures of membrane proteins have been resolved to high resolution. Here, we studied the structure of a member of the Cys-loop ligand gated ion channel protein superfamily of receptors, human type A γ2α1β2α1β2 gamma amino butyric acid receptor complex in a lipid bilayer environment. Studying the correlation between the structure and function of the gamma amino butyric acid receptor may enhance our understanding of the molecular basis of ion channel dysfunctions linked with epilepsy, ataxia, migraine, schizophrenia and other neurodegenerative diseases. The structure of human γ2α1β2α1β2 has been modeled based on the X-ray structure of the Caenorhabditis elegans glutamate-gated chloride channel via homology modeling. The template provided the first inhibitory channel structure for the Cys-loop superfamily of ligand-gated ion channels. The only available template structure before this glutamate-gated chloride channel was a cation selective channel which had very low sequence identity with gamma aminobutyric acid receptor. Here, our aim was to study the effect of structural corrections originating from modeling on a more reliable template structure. The homology model was analyzed for structural properties via a 100 ns molecular dynamics (MD) study. Due to the structural shifts and the removal of an open channel potentiator molecule, ivermectin, from the template structure, helical packing changes were observed in the transmembrane segment. Namely removal of ivermectin molecule caused a closure around the Leu 9 position along the ion channel. In terms of the structural shifts, there are three potential disulfide bridges between the M1 and M3 helices of the γ2 and 2 α1 subunits in the model. The effect of these disulfide bridges was investigated via monitoring the differences in root mean square fluctuations (RMSF) of individual amino acids and principal component analysis of the MD trajectory of the two homology models-one with the disulfide bridge and one with protonated Cys residues. In all subunit types, RMSF of the transmembrane domain helices are reduced in the presence of disulfide bridges. Additionally, loop A, loop F and loop C fluctuations were affected in the extracellular domain. In cross-correlation analysis of the trajectory, the two model structures displayed different coupling in between the M2-M3 linker region, protruding from the membrane, and the β1-β2/D loop and cys-loop regions in the extracellular domain. Correlations of the C loop, which collapses directly over the bound ligand molecule, were also affected by differences in the packing of transmembrane helices. Finally, more localized correlations were observed in the transmembrane helices when disulfide bridges were present in the model. The differences observed in this study suggest that dynamic coupling at the interface of extracellular and ion channel domains differs from the coupling introduced by disulfide bridges in the transmembrane region. We hope that this hypothesis will be tested experimentally in the near future.
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Affiliation(s)
- Meral Ayan
- Bioinformatics and Genetics Department, Faculty of Engineering and Natural Sciences, Kadir Has University, 34083, Fatih, Istanbul, Turkey
| | - Sebnem Essiz
- Bioinformatics and Genetics Department, Faculty of Engineering and Natural Sciences, Kadir Has University, 34083, Fatih, Istanbul, Turkey.
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8
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Pflanz NC, Daszkowski AW, Cornelison GL, Trudell JR, Mihic SJ. An intersubunit electrostatic interaction in the GABA A receptor facilitates its responses to benzodiazepines. J Biol Chem 2018; 293:8264-8274. [PMID: 29622679 DOI: 10.1074/jbc.ra118.002128] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 04/04/2018] [Indexed: 02/01/2023] Open
Abstract
Benzodiazepines are positive allosteric modulators of the GABAA receptor (GABAAR), acting at the α-γ subunit interface to enhance GABAAR function. GABA or benzodiazepine binding induces distinct conformational changes in the GABAAR. The molecular rearrangements in the GABAAR following benzodiazepine binding remain to be fully elucidated. Using two molecular models of the GABAAR, we identified electrostatic interactions between specific amino acids at the α-γ subunit interface that were broken by, or formed after, benzodiazepine binding. Using two-electrode voltage clamp electrophysiology in Xenopus laevis oocytes, we investigated these interactions by substituting one or both amino acids of each potential pair. We found that Lys104 in the α1 subunit forms an electrostatic bond with Asp75 of the γ2 subunit after benzodiazepine binding and that this bond stabilizes the positively modified state of the receptor. Substitution of these two residues to cysteine and subsequent covalent linkage between them increased the receptor's sensitivity to low GABA concentrations and decreased its response to benzodiazepines, producing a GABAAR that resembles a benzodiazepine-bound WT GABAAR. Breaking this bond restored sensitivity to GABA to WT levels and increased the receptor's response to benzodiazepines. The α1 Lys104 and γ2 Asp75 interaction did not play a role in ethanol or neurosteroid modulation of GABAAR, suggesting that different modulators induce different conformational changes in the receptor. These findings may help explain the additive or synergistic effects of modulators acting at the GABAAR.
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Affiliation(s)
- Natasha C Pflanz
- Department of Neuroscience, Division of Pharmacology and Toxicology, Waggoner Center for Alcohol and Addiction Research, Institutes for Neuroscience and Cell and Molecular Biology, University of Texas, Austin, Texas 78712
| | - Anna W Daszkowski
- Department of Neuroscience, Division of Pharmacology and Toxicology, Waggoner Center for Alcohol and Addiction Research, Institutes for Neuroscience and Cell and Molecular Biology, University of Texas, Austin, Texas 78712
| | - Garrett L Cornelison
- Department of Neuroscience, Division of Pharmacology and Toxicology, Waggoner Center for Alcohol and Addiction Research, Institutes for Neuroscience and Cell and Molecular Biology, University of Texas, Austin, Texas 78712
| | - James R Trudell
- Department of Anesthesia, Stanford University School of Medicine, Stanford, California 94305
| | - S John Mihic
- Department of Neuroscience, Division of Pharmacology and Toxicology, Waggoner Center for Alcohol and Addiction Research, Institutes for Neuroscience and Cell and Molecular Biology, University of Texas, Austin, Texas 78712.
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9
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Un-gating and allosteric modulation of a pentameric ligand-gated ion channel captured by molecular dynamics. PLoS Comput Biol 2017; 13:e1005784. [PMID: 29069080 PMCID: PMC5673239 DOI: 10.1371/journal.pcbi.1005784] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 11/06/2017] [Accepted: 09/14/2017] [Indexed: 11/19/2022] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs) mediate intercellular communication at synapses through the opening of an ion pore in response to the binding of a neurotransmitter. Despite the increasing availability of high-resolution structures of pLGICs, a detailed understanding of the functional isomerization from closed to open (gating) and back is currently missing. Here, we provide the first atomistic description of the transition from open to closed (un-gating) in the glutamate-gated chloride channel (GluCl) from Caenorhabditis Elegans. Starting with the active-state structure solved in complex with the neurotransmitter L-glutamate and the positive allosteric modulator (PAM) ivermectin, we analyze the spontaneous relaxation of the channel upon removal of ivermectin by explicit solvent/membrane Molecular Dynamics (MD) simulations. The μs-long trajectories support the conclusion that ion-channel deactivation is mediated by two distinct quaternary transitions, i.e. a global receptor twisting followed by the radial expansion (or blooming) of the extracellular domain. At variance with previous models, we show that pore closing is exclusively regulated by the global twisting, which controls the position of the β1-β2 loop relative to the M2-M3 loop at the EC/TM domain interface. Additional simulations with L-glutamate restrained to the crystallographic binding mode and ivermectin removed indicate that the same twisting isomerization is regulated by agonist binding at the orthosteric site. These results provide a structural model for gating in pLGICs and suggest a plausible mechanism for the pharmacological action of PAMs in this neurotransmitter receptor family. The simulated un-gating converges to the X-ray structure of GluCl resting state both globally and locally, demonstrating the predictive character of state-of-art MD simulations.
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10
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A possible desensitized state conformation of the human α 7 nicotinic receptor: A molecular dynamics study. Biophys Chem 2017; 229:99-109. [DOI: 10.1016/j.bpc.2017.06.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 06/22/2017] [Accepted: 06/22/2017] [Indexed: 11/18/2022]
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11
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From hopanoids to cholesterol: Molecular clocks of pentameric ligand-gated ion channels. Prog Lipid Res 2016; 63:1-13. [DOI: 10.1016/j.plipres.2016.03.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 03/22/2016] [Accepted: 03/24/2016] [Indexed: 11/21/2022]
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12
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McCracken ML, Gorini G, McCracken LM, Mayfield RD, Harris RA, Trudell JR. Inter- and Intra-Subunit Butanol/Isoflurane Sites of Action in the Human Glycine Receptor. Front Mol Neurosci 2016; 9:45. [PMID: 27378846 PMCID: PMC4906044 DOI: 10.3389/fnmol.2016.00045] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 05/26/2016] [Indexed: 11/24/2022] Open
Abstract
Glycine receptors (GlyRs) mediate inhibitory neurotransmission and are targets for alcohols and anesthetics in brain. GlyR transmembrane (TM) domains contain critical residues for alcohol/anesthetic action: amino acid A288 in TM3 forms crosslinks with TM1 (I229) in the adjacent subunit as well as TM2 (S267) and TM4 (Y406, W407, I409, Y410) in the same subunit. We hypothesized that these residues may participate in intra-subunit and inter-subunit sites of alcohol/anesthetic action. The following double and triple mutants of GLRA1 cDNA (encoding human glycine receptor alpha 1 subunit) were injected into Xenopus laevis oocytes: I229C/A288C, I229C/A288C/C290S, A288C/Y406C, A288C/W407C, A288C/I409C, and A288C/Y410C along with the corresponding single mutants and wild-type GLRA1. Butanol (22 mM) or isoflurane (0.6 mM) potentiation of GlyR-mediated currents before and after application of the cysteine crosslinking agent HgCl2 (10 μM) was measured using two-electrode voltage clamp electrophysiology. Crosslinking nearly abolished butanol and isoflurane potentiation in the I229C/A288C and I229C/A288C/C290S mutants but had no effect in single mutants or wild-type. Crosslinking also inhibited butanol and isoflurane potentiation in the TM3-4 mutants (A288C/Y406C, A288C/W407C, A288C/I409C, A288C/Y410C) with no effect in single mutants or wild-type. We extracted proteins from oocytes expressing I229C/288C, A288C/Y410C, or wild-type GlyRs, used mass spectrometry to verify their expression and possible inter-subunit dimerization, plus immunoblotting to investigate the biochemical features of proposed crosslinks. Wild-type GlyR subunits measured about 50 kDa; after crosslinking, the dimeric/monomeric 100:50 kDa band ratio was significantly increased in I229C/288C but not A288C/Y410C mutants or wild-type, providing support for TM1-3 inter-subunit and TM3-4 intra-subunit crosslinking. A GlyR homology model based on the GluCl template provides further evidence for a multi-site model for alcohol/anesthetic interaction with human GLRA1.
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Affiliation(s)
- Mandy L McCracken
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at AustinAustin, TX, USA; Integrative Neuroscience Research Branch, Neurobiology of Addiction Section, National Institute on Drug Abuse, National Institutes of HealthBaltimore, MD, USA
| | - Giorgio Gorini
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin Austin, TX, USA
| | - Lindsay M McCracken
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin Austin, TX, USA
| | - R Dayne Mayfield
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin Austin, TX, USA
| | - R Adron Harris
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin Austin, TX, USA
| | - James R Trudell
- Department of Anesthesia and Beckman Program for Molecular and Genetic Medicine, Stanford School of Medicine Stanford, CA, USA
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13
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Heusser SA, Yoluk Ö, Klement G, Riederer EA, Lindahl E, Howard RJ. Functional characterization of neurotransmitter activation and modulation in a nematode model ligand-gated ion channel. J Neurochem 2016; 138:243-53. [PMID: 27102368 DOI: 10.1111/jnc.13644] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 03/21/2016] [Accepted: 04/07/2016] [Indexed: 11/29/2022]
Abstract
The superfamily of pentameric ligand-gated ion channels includes neurotransmitter receptors that mediate fast synaptic transmission in vertebrates, and are targets for drugs including alcohols, anesthetics, benzodiazepines, and anticonvulsants. However, the mechanisms of ion channel opening, gating, and modulation in these receptors leave many open questions, despite their pharmacological importance. Subtle conformational changes in both the extracellular and transmembrane domains are likely to influence channel opening, but have been difficult to characterize given the limited structural data available for human membrane proteins. Recent crystal structures of a modified Caenorhabditis elegans glutamate-gated chloride channel (GluCl) in multiple states offer an appealing model system for structure-function studies. However, the pharmacology of the crystallographic GluCl construct is not well established. To establish the functional relevance of this system, we used two-electrode voltage-clamp electrophysiology in Xenopus oocytes to characterize activation of crystallographic and native-like GluCl constructs by L-glutamate and ivermectin. We also tested modulation by ethanol and other anesthetic agents, and used site-directed mutagenesis to explore the role of a region of Loop F which was implicated in ligand gating by molecular dynamics simulations. Our findings indicate that the crystallographic construct functionally models concentration-dependent agonism and allosteric modulation of pharmacologically relevant receptors. Specific substitutions at residue Leu174 in loop F altered direct L-glutamate activation, consistent with computational evidence for this region's role in ligand binding. These insights demonstrate conservation of activation and modulation properties in this receptor family, and establish a framework for GluCl as a model system, including new possibilities for drug discovery. In this study, we elucidate the validity of a modified glutamate-gated chloride channel (GluClcryst ) as a structurally accessible model for GABAA receptors. In contrast to native-like controls, GluClcryst exhibits classical activation by its neurotransmitter ligand L-glutamate. The modified channel is also sensitive to allosteric modulators associated with human GABAA receptors, and to site-directed mutations predicted to alter channel opening.
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Affiliation(s)
- Stephanie A Heusser
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Özge Yoluk
- Swedish e-Science Research Center, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Göran Klement
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Erika A Riederer
- Department of Chemistry, Skidmore College, Saratoga Springs, NY, USA
| | - Erik Lindahl
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden.,Swedish e-Science Research Center, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Rebecca J Howard
- Department of Chemistry, Skidmore College, Saratoga Springs, NY, USA
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14
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Borghese CM, Ruiz CI, Lee US, Cullins MA, Bertaccini EJ, Trudell JR, Harris RA. Identification of an Inhibitory Alcohol Binding Site in GABAA ρ1 Receptors. ACS Chem Neurosci 2016; 7:100-8. [PMID: 26571107 DOI: 10.1021/acschemneuro.5b00246] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Alcohols inhibit γ-aminobutyric acid type A ρ1 receptor function. After introducing mutations in several positions of the second transmembrane helix in ρ1, we studied the effects of ethanol and hexanol on GABA responses using two-electrode voltage clamp electrophysiology in Xenopus laevis oocytes. The 6' mutations produced the following effects on ethanol and hexanol responses: small increase or no change (T6'M), increased inhibition (T6'V), and small potentiation (T6'Y and T6'F). The 5' mutations produced mainly increases in hexanol inhibition. Other mutations produced small (3' and 9') or no changes (2' and L277 in the first transmembrane domain) in alcohol effects. These results suggest an inhibitory alcohol binding site near the 6' position. Homology models of ρ1 receptors based on the X-ray structure of GluCl showed that the 2', 5', 6', and 9' residues were easily accessible from the ion pore, with 5' and 6' residues from neighboring subunits facing each other; L3' and L277 also faced the neighboring subunit. We tested ethanol through octanol on single and double mutated ρ1 receptors [ρ1(I15'S), ρ1(T6'Y), and ρ1(T6'Y,I15'S)] to further characterize the inhibitory alcohol pocket in the wild-type ρ1 receptor. The pocket can only bind relatively short-chain alcohols and is eliminated by introducing Y in the 6' position. Replacing the bulky 15' residue with a smaller side chain introduced a potentiating binding site, more sensitive to long-chain than to short-chain alcohols. In conclusion, the net alcohol effect on the ρ1 receptor is determined by the sum of its actions on inhibitory and potentiating sites.
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Affiliation(s)
- Cecilia M. Borghese
- Waggoner
Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Carlos I. Ruiz
- Waggoner
Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Ui S. Lee
- Waggoner
Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Madeline A. Cullins
- Waggoner
Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Edward J. Bertaccini
- Department of Anesthesia & Beckman Program for Molecular and Genetic Medicine, Stanford University, Palo Alto, California 94305, United States
| | - James R. Trudell
- Department of Anesthesia & Beckman Program for Molecular and Genetic Medicine, Stanford University, Palo Alto, California 94305, United States
| | - R. Adron Harris
- Waggoner
Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, Texas 78712, United States
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15
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Subunit stoichiometry and arrangement in a heteromeric glutamate-gated chloride channel. Proc Natl Acad Sci U S A 2016; 113:E644-53. [PMID: 26792524 DOI: 10.1073/pnas.1423753113] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The invertebrate glutamate-gated chloride-selective receptors (GluClRs) are ion channels serving as targets for ivermectin (IVM), a broad-spectrum anthelmintic drug used to treat human parasitic diseases like river blindness and lymphatic filariasis. The native GluClR is a heteropentamer consisting of α and β subunit types, with yet unknown subunit stoichiometry and arrangement. Based on the recent crystal structure of a homomeric GluClαR, we introduced mutations at the intersubunit interfaces where Glu (the neurotransmitter) binds. By electrophysiological characterization of these mutants, we found heteromeric assemblies with two equivalent Glu-binding sites at β/α intersubunit interfaces, where the GluClβ and GluClα subunits, respectively, contribute the "principal" and "complementary" components of the putative Glu-binding pockets. We identified a mutation in the IVM-binding site (far away from the Glu-binding sites), which significantly increased the sensitivity of the heteromeric mutant receptor to both Glu and IVM, and improved the receptor subunits' cooperativity. We further characterized this heteromeric GluClR mutant as a receptor having a third Glu-binding site at an α/α intersubunit interface. Altogether, our data unveil heteromeric GluClR assemblies having three α and two β subunits arranged in a counterclockwise β-α-β-α-α fashion, as viewed from the extracellular side, with either two or three Glu-binding site interfaces.
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16
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Wennberg CL, Murtola T, Páll S, Abraham MJ, Hess B, Lindahl E. Direct-Space Corrections Enable Fast and Accurate Lorentz-Berthelot Combination Rule Lennard-Jones Lattice Summation. J Chem Theory Comput 2015; 11:5737-46. [PMID: 26587968 DOI: 10.1021/acs.jctc.5b00726] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Long-range lattice summation techniques such as the particle-mesh Ewald (PME) algorithm for electrostatics have been revolutionary to the precision and accuracy of molecular simulations in general. Despite the performance penalty associated with lattice summation electrostatics, few biomolecular simulations today are performed without it. There are increasingly strong arguments for moving in the same direction for Lennard-Jones (LJ) interactions, and by using geometric approximations of the combination rules in reciprocal space, we have been able to make a very high-performance implementation available in GROMACS. Here, we present a new way to correct for these approximations to achieve exact treatment of Lorentz-Berthelot combination rules within the cutoff, and only a very small approximation error remains outside the cutoff (a part that would be completely ignored without LJ-PME). This not only improves accuracy by almost an order of magnitude but also achieves absolute biomolecular simulation performance that is an order of magnitude faster than any other available lattice summation technique for LJ interactions. The implementation includes both CPU and GPU acceleration, and its combination with improved scaling LJ-PME simulations now provides performance close to the truncated potential methods in GROMACS but with much higher accuracy.
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Affiliation(s)
- Christian L Wennberg
- Swedish e-Science Research Center, Department of Theoretical Physics, KTH Royal Institute of Technology , Box 1031, 171 21 Solna, Sweden.,Center for Biomembrane Research, Department of Biophysics & Biochemistry, Stockholm University , 106 91 Stockholm, Sweden
| | - Teemu Murtola
- Swedish e-Science Research Center, Department of Theoretical Physics, KTH Royal Institute of Technology , Box 1031, 171 21 Solna, Sweden.,Center for Biomembrane Research, Department of Biophysics & Biochemistry, Stockholm University , 106 91 Stockholm, Sweden
| | - Szilárd Páll
- Swedish e-Science Research Center, Department of Theoretical Physics, KTH Royal Institute of Technology , Box 1031, 171 21 Solna, Sweden.,Center for Biomembrane Research, Department of Biophysics & Biochemistry, Stockholm University , 106 91 Stockholm, Sweden
| | - Mark J Abraham
- Swedish e-Science Research Center, Department of Theoretical Physics, KTH Royal Institute of Technology , Box 1031, 171 21 Solna, Sweden.,Center for Biomembrane Research, Department of Biophysics & Biochemistry, Stockholm University , 106 91 Stockholm, Sweden
| | - Berk Hess
- Swedish e-Science Research Center, Department of Theoretical Physics, KTH Royal Institute of Technology , Box 1031, 171 21 Solna, Sweden.,Center for Biomembrane Research, Department of Biophysics & Biochemistry, Stockholm University , 106 91 Stockholm, Sweden
| | - Erik Lindahl
- Swedish e-Science Research Center, Department of Theoretical Physics, KTH Royal Institute of Technology , Box 1031, 171 21 Solna, Sweden.,Center for Biomembrane Research, Department of Biophysics & Biochemistry, Stockholm University , 106 91 Stockholm, Sweden
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17
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Interactions of L-3,5,3'-Triiodothyronine [corrected], Allopregnanolone, and Ivermectin with the GABAA Receptor: Evidence for Overlapping Intersubunit Binding Modes. PLoS One 2015; 10:e0139072. [PMID: 26421724 PMCID: PMC4589331 DOI: 10.1371/journal.pone.0139072] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 09/09/2015] [Indexed: 11/28/2022] Open
Abstract
Structural mechanisms of modulation of γ-aminobutyric acid (GABA) type A receptors by neurosteroids and hormones remain unclear. The thyroid hormone L-3,5,3’-triiodothyronine (T3) inhibits GABAA receptors at micromolar concentrations and has common features with neurosteroids such as allopregnanolone (ALLOP). Here we use functional experiments on α2β1γ2 GABAA receptors expressed in Xenopus oocytes to detect competitive interactions between T3 and an agonist (ivermectin, IVM) with a crystallographically determined binding site at subunit interfaces in the transmembrane domain of a homologous receptor (glutamate-gated chloride channel, GluCl). T3 and ALLOP also show competitive effects, supporting the presence of both a T3 and ALLOP binding site at one or more subunit interfaces. Molecular dynamics (MD) simulations over 200 ns are used to investigate the dynamics and energetics of T3 in the identified intersubunit sites. In these simulations, T3 molecules occupying all intersubunit sites (with the exception of the α-β interface) display numerous energetically favorable conformations with multiple hydrogen bonding partners, including previously implicated polar/acidic sidechains and a structurally conserved deformation in the M1 backbone.
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18
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Estrada-Mondragon A, Lynch JW. Functional characterization of ivermectin binding sites in α1β2γ2L GABA(A) receptors. Front Mol Neurosci 2015; 8:55. [PMID: 26441518 PMCID: PMC4585179 DOI: 10.3389/fnmol.2015.00055] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Accepted: 09/07/2015] [Indexed: 11/28/2022] Open
Abstract
GABAA receptors (GABAARs) are the major inhibitory neurotransmitter receptors in the brain and are therapeutic targets for many indications including sedation, anesthesia and anxiolysis. There is, however, considerable scope for the development of new therapeutics with improved beneficial effects and reduced side-effect profiles. The anthelminthic drug, ivermectin, activates the GABAAR although its binding site is not known. The molecular site of action of ivermectin has, however, been defined by crystallography in the homologous glutamate-gated chloride channel. Resolving the molecular mechanisms of ivermectin binding to α1β2γ2L GABAARs may provide insights into the design of improved therapeutics. Given that ivermectin binds to subunit interfaces, we sought to define (1) which subunit interface sites it binds to, (2) whether these sites are equivalent in terms of ivermectin sensitivity or efficacy, and (3) how many must be occupied for maximal efficacy. Our approach involved precluding ivermectin from binding to particular interfaces by introducing bulky M3 domain 36′F sidechains to the “+” side of those interfaces. We thereby demonstrated that ivermectin produces irreversible channel activation only when it binds to the single γ2L-β2 interface site. When it binds to α1-β2 sites it elicits potentiation of GABA-gated currents but has no irreversible activating effect. Ivermectin cannot bind to the β2-α1 interface site due to its endogenous bulky 36′ methionine. Replacing this with an alanine creates a functional site at this interface, but surprisingly it is inhibitory. Molecular docking simulations reveal that the γ2L-β2 interface forms more contacts with ivermectin than the other interfaces, possibly explaining why ivermectin appears to bind irreversibly at this interface. This study demonstrates unexpectedly stark pharmacological differences among GABAAR ivermectin binding sites.
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Affiliation(s)
| | - Joseph W Lynch
- Queensland Brain Institute, The University of Queensland Brisbane, QLD, Australia ; School of Biomedical Sciences, The University of Queensland Brisbane, QLD, Australia
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19
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Yoluk Ö, Lindahl E, Andersson M. Conformational gating dynamics in the GluCl anion-selective chloride channel. ACS Chem Neurosci 2015; 6:1459-67. [PMID: 25992588 DOI: 10.1021/acschemneuro.5b00111] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Cys-loop receptors are central to propagation of signals in the nervous system. The gating of the membrane-spanning pore is triggered by structural rearrangements in the agonist-binding site, located some 50 Å away from the pore. A sequential conformational change, propagating from the ligand-binding site to the pore, has been proposed to govern gating in all Cys-loop receptors. Here, we identify structural and dynamic components of the conformational gating in the eukaryotic glutamate-gated chloride channel (GluCl) by means of molecular dynamics (MD) simulations with and without the l-glutamate agonist bound. A significant increase in pore opening and accompanying hydration is observed in the presence of glutamate. Potential of mean force calculations reveal that the barrier for ion passage drops from 15 kcal/mol to 5-10 kcal/mol with the agonist bound. This appears to be explained by agonist binding that leads to significant changes in the intersubunit hydrogen-bonding pattern, which induce a slight tilt of the extracellular domain relative to the transmembrane domain in the simulations. This rearrangement is subtle, but correspond to the direction of the quaternary twist observed as a key difference between open and closed X-ray structures. While the full reversible gating is still a much slower process, the observed structural dynamics sheds new light on the early stages of how the agonist influences the extracellular domain, how the extracellular domain interacts with the transmembrane domain, and how changes in the transmembrane domain alter the free energy of ion passage.
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Affiliation(s)
- Özge Yoluk
- Science for Life Laboratory, Stockholm and Uppsala, 171 21 Stockholm, Sweden
- Theoretical and Computational Biophysics, Department of Theoretical Physics, KTH Royal Institute of Technology, 106 91 Stockholm, Sweden
| | - Erik Lindahl
- Science for Life Laboratory, Stockholm and Uppsala, 171 21 Stockholm, Sweden
- Theoretical and Computational Biophysics, Department of Theoretical Physics, KTH Royal Institute of Technology, 106 91 Stockholm, Sweden
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, 114 18 Stockholm, Sweden
| | - Magnus Andersson
- Science for Life Laboratory, Stockholm and Uppsala, 171 21 Stockholm, Sweden
- Theoretical and Computational Biophysics, Department of Theoretical Physics, KTH Royal Institute of Technology, 106 91 Stockholm, Sweden
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20
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Chiodo L, Malliavin TE, Maragliano L, Cottone G, Ciccotti G. A Structural Model of the Human α7 Nicotinic Receptor in an Open Conformation. PLoS One 2015; 10:e0133011. [PMID: 26208301 PMCID: PMC4514475 DOI: 10.1371/journal.pone.0133011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 06/22/2015] [Indexed: 11/20/2022] Open
Abstract
Nicotinic acetylcholine receptors (nAchRs) are ligand-gated ion channels that regulate chemical transmission at the neuromuscular junction. Structural information is available at low resolution from open and closed forms of an eukaryotic receptor, and at high resolution from other members of the same structural family, two prokaryotic orthologs and an eukaryotic GluCl channel. Structures of human channels however are still lacking. Homology modeling and Molecular Dynamics simulations are valuable tools to predict structures of unknown proteins, however, for the case of human nAchRs, they have been unsuccessful in providing a stable open structure so far. This is due to different problems with the template structures: on one side the homology with prokaryotic species is too low, while on the other the open eukaryotic GluCl proved itself unstable in several MD studies and collapsed to a dehydrated, non-conductive conformation, even when bound to an agonist. Aim of this work is to obtain, by a mixing of state-of-the-art homology and simulation techniques, a plausible prediction of the structure (still unknown) of the open state of human α7 nAChR complexed with epibatidine, from which it is possible to start structural and functional test studies. To prevent channel closure we employ a restraint that keeps the transmembrane pore open, and obtain in this way a stable, hydrated conformation. To further validate this conformation, we run four long, unbiased simulations starting from configurations chosen at random along the restrained trajectory. The channel remains stable and hydrated over the whole runs. This allows to assess the stability of the putative open conformation over a cumulative time of 1 μs, 800 ns of which are of unbiased simulation. Mostly based on the analysis of pore hydration and size, we suggest that the obtained structure has reasonable chances to be (at least one of the possible) structures of the channel in the open conformation.
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Affiliation(s)
- Letizia Chiodo
- Center for Life Nano Science @Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Thérèse E. Malliavin
- Institut Pasteur and CNRS UMR 3528, Unité de Bioinformatique Structurale, Paris, France
| | - Luca Maragliano
- Center for Synaptic Neuroscience, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Grazia Cottone
- Department of Physics and Chemistry, University of Palermo, Palermo, Italy
- School of Physics, University College Dublin, Dublin, Ireland
| | - Giovanni Ciccotti
- School of Physics, University College Dublin, Dublin, Ireland
- Department of Physics, University of Roma “La Sapienza”, Rome, Italy
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21
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Gonzalez-Gutierrez G, Grosman C. The atypical cation-conduction and gating properties of ELIC underscore the marked functional versatility of the pentameric ligand-gated ion-channel fold. J Gen Physiol 2015; 146:15-36. [PMID: 26078054 PMCID: PMC4485021 DOI: 10.1085/jgp.201411333] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 05/14/2015] [Indexed: 01/07/2023] Open
Abstract
The superfamily of pentameric ligand-gated ion channels (pLGICs) is unique among ionotropic receptors in that the same overall structure has evolved to generate multiple members with different combinations of agonist specificities and permeant-ion charge selectivities. However, aside from these differences, pLGICs have been typically regarded as having several invariant functional properties. These include pore blockade by extracellular quaternary-ammonium cations in the micromolar-to-millimolar concentration range (in the case of the cation-selective members), and a gain-of-function phenotype, which manifests as a slower deactivation time course, as a result of mutations that reduce the hydrophobicity of the transmembrane pore lining. Here, we tested this notion on three distantly related cation-selective members of the pLGIC superfamily: the mouse muscle nicotinic acetylcholine receptor (nAChR), and the bacterial GLIC and ELIC channels. Remarkably, we found that, whereas low millimolar concentrations of TMA(+) and TEA(+) block the nAChR and GLIC, neither of these two quaternary-ammonium cations blocks ELIC at such concentrations; instead, both carry measurable inward currents when present as the only cations on the extracellular side. Also, we found that, whereas lidocaine binding speeds up the current-decay time courses of the nAChR and GLIC in the presence of saturating concentrations of agonists, the binding of lidocaine to ELIC slows this time course down. Furthermore, whereas mutations that reduce the hydrophobicity of the side chains at position 9' of the M2 α-helices greatly slowed the deactivation time course of the nAChR and GLIC, these mutations had little effect--or even sped up deactivation--when engineered in ELIC. Our data indicate that caution should be exercised when generalizing results obtained with ELIC to the rest of the pLGICs, but more intriguingly, they hint at the possibility that ELIC is a representative of a novel branch of the superfamily with markedly divergent pore properties despite a well-conserved three-dimensional architecture.
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Affiliation(s)
- Giovanni Gonzalez-Gutierrez
- Department of Molecular and Integrative Physiology, Center for Biophysics and Computational Biology, and Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Claudio Grosman
- Department of Molecular and Integrative Physiology, Center for Biophysics and Computational Biology, and Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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22
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Hénin J, Salari R, Murlidaran S, Brannigan G. A predicted binding site for cholesterol on the GABAA receptor. Biophys J 2014; 106:1938-49. [PMID: 24806926 DOI: 10.1016/j.bpj.2014.03.024] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 03/03/2014] [Accepted: 03/14/2014] [Indexed: 12/29/2022] Open
Abstract
Modulation of the GABA type A receptor (GABAAR) function by cholesterol and other steroids is documented at the functional level, yet its structural basis is largely unknown. Current data on structurally related modulators suggest that cholesterol binds to subunit interfaces between transmembrane domains of the GABAAR. We construct homology models of a human GABAAR based on the structure of the glutamate-gated chloride channel GluCl of Caenorhabditis elegans. The models show the possibility of previously unreported disulfide bridges linking the M1 and M3 transmembrane helices in the α and γ subunits. We discuss the biological relevance of such disulfide bridges. Using our models, we investigate cholesterol binding to intersubunit cavities of the GABAAR transmembrane domain. We find that very similar binding modes are predicted independently by three approaches: analogy with ivermectin in the GluCl crystal structure, automated docking by AutoDock, and spontaneous rebinding events in unbiased molecular dynamics simulations. Taken together, the models and atomistic simulations suggest a somewhat flexible binding mode, with several possible orientations. Finally, we explore the possibility that cholesterol promotes pore opening through a wedge mechanism.
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Affiliation(s)
- Jérôme Hénin
- Laboratoire de Biochimie Théorique, CNRS, IBPC, and Université Paris Diderot, Paris, France
| | - Reza Salari
- Department of Physics, Rutgers University-Camden, Camden, New Jersey; Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, New Jersey
| | - Sruthi Murlidaran
- Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, New Jersey
| | - Grace Brannigan
- Department of Physics, Rutgers University-Camden, Camden, New Jersey; Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, New Jersey.
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23
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X-ray structures of GluCl in apo states reveal a gating mechanism of Cys-loop receptors. Nature 2014; 512:333-7. [PMID: 25143115 DOI: 10.1038/nature13669] [Citation(s) in RCA: 201] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 07/10/2014] [Indexed: 01/01/2023]
Abstract
Cys-loop receptors are neurotransmitter-gated ion channels that are essential mediators of fast chemical neurotransmission and are associated with a large number of neurological diseases and disorders, as well as parasitic infections. Members of this ion channel superfamily mediate excitatory or inhibitory neurotransmission depending on their ligand and ion selectivity. Structural information for Cys-loop receptors comes from several sources including electron microscopic studies of the nicotinic acetylcholine receptor, high-resolution X-ray structures of extracellular domains and X-ray structures of bacterial orthologues. In 2011 our group published structures of the Caenorhabditis elegans glutamate-gated chloride channel (GluCl) in complex with the allosteric partial agonist ivermectin, which provided insights into the structure of a possibly open state of a eukaryotic Cys-loop receptor, the basis for anion selectivity and channel block, and the mechanism by which ivermectin and related molecules stabilize the open state and potentiate neurotransmitter binding. However, there remain unanswered questions about the mechanism of channel opening and closing, the location and nature of the shut ion channel gate, the transitions between the closed/resting, open/activated and closed/desensitized states, and the mechanism by which conformational changes are coupled between the extracellular, orthosteric agonist binding domain and the transmembrane, ion channel domain. Here we present two conformationally distinct structures of C. elegans GluCl in the absence of ivermectin. Structural comparisons reveal a quaternary activation mechanism arising from rigid-body movements between the extracellular and transmembrane domains and a mechanism for modulation of the receptor by phospholipids.
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24
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Yu R, Hurdiss E, Greiner T, Lape R, Sivilotti L, Biggin PC. Agonist and antagonist binding in human glycine receptors. Biochemistry 2014; 53:6041-51. [PMID: 25184435 DOI: 10.1021/bi500815f] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The human glycine receptor (hGlyR) is an anion-permeable ligand-gated channel that is part of a larger superfamily of receptors called the Cys-loop family. hGlyRs are particularly amenable to single-channel recordings, thus making them a model experimental system for understanding the Cys-loop receptor family in general. Understanding the relationship between agonist binding and efficacy in Cys-loop receptors should improve our future prospects for making specific agonists or antagonists. However, at present, there is no high-resolution structure for the complete hGlyR, and thus, modeling is needed to provide a physical framework on which to interpret single-channel data. The structure of the glutamate-gated chloride channel from Caenorhabditis elegans shows a much higher level of sequence identity to human hGlyR than previous templates such as AChBP or the bacterial channels, GLIC and ELIC. Thus, we constructed a model of the hGlyR and validated it against previously reported mutagenesis data. We used molecular dynamics to refine the model and to explore binding of both an agonist (glycine) and an antagonist (strychnine). The model shows excellent agreement with previous data but also suggests some unique features: (i) a water molecule that forms part of the binding site and allows us to account for some previous results that were difficult to reconcile, (ii) an interaction of the glycine agonist with S129, and (iii) an effect from E211, both of which we confirmed with new site-directed mutagenesis and patch clamp recordings. Finally, examination of the simulations suggests that strychnine binding induces movement to a conformational state distinct from the glycine-bound or apo state, not only within the ligand-binding domain but also in the transmembrane domain.
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Affiliation(s)
- Rilei Yu
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, United Kingdom
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25
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Salari R, Murlidaran S, Brannigan G. Pentameric Ligand-gated Ion Channels : Insights from Computation. MOLECULAR SIMULATION 2014; 40:821-829. [PMID: 25931676 PMCID: PMC4412168 DOI: 10.1080/08927022.2014.896462] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Pentameric ligand-gated ion channels (pLGICs) conduct upon the binding of an agonist and are fundamental to neurotransmission. New insights into the complex mechanisms underlying pLGIC gating, ion selectivity, and modulation have recently been gained via a series of crystal structures in prokaryotes and C .elegans, as well as computational studies relying on these structures. Here we review contributions from a variety of computational approaches, including normal mode analysis, automated docking, and fully atomistic molecular dynamics simulation. Examples from our own research, particularly concerning interactions with general anesthetics and lipids, are used to illustrate predictive results complementary to crystallographic studies.
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Affiliation(s)
- Reza Salari
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ
- Department of Physics, Rutgers University, Camden, NJ
| | - Sruthi Murlidaran
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ
| | - Grace Brannigan
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ
- Department of Physics, Rutgers University, Camden, NJ
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