1
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High-pressure crystallography shows noble gas intervention into protein-lipid interaction and suggests a model for anaesthetic action. Commun Biol 2022; 5:360. [PMID: 35422073 PMCID: PMC9010423 DOI: 10.1038/s42003-022-03233-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 02/22/2022] [Indexed: 11/09/2022] Open
Abstract
In this work we examine how small hydrophobic molecules such as inert gases interact with membrane proteins (MPs) at a molecular level. High pressure atmospheres of argon and krypton were used to produce noble gas derivatives of crystals of three well studied MPs (two different proton pumps and a sodium light-driven ion pump). The structures obtained using X-ray crystallography showed that the vast majority of argon and krypton binding sites were located on the outer hydrophobic surface of the MPs – a surface usually accommodating hydrophobic chains of annular lipids (which are known structural and functional determinants for MPs). In conformity with these results, supplementary in silico molecular dynamics (MD) analysis predicted even greater numbers of argon and krypton binding positions on MP surface within the bilayer. These results indicate a potential importance of such interactions, particularly as related to the phenomenon of noble gas-induced anaesthesia. Noble gases are known to interact with proteins and can be good anaesthetics in hyperbaric conditions. This study identifies argon and krypton binding sites on membrane proteins and proposes as a hypothesis that noble gases, by altering protein/lipid contacts, may affect protein function.
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2
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At least three xenon binding sites in the glycine binding domain of the N-methyl D-aspartate receptor. Arch Biochem Biophys 2022; 724:109265. [DOI: 10.1016/j.abb.2022.109265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/19/2022] [Accepted: 04/22/2022] [Indexed: 11/21/2022]
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3
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Hammami I, Farjot G, Naveau M, Rousseaud A, Prangé T, Katz I, Colloc'h N. Method for the Identification of Potentially Bioactive Argon Binding Sites in Protein Families. J Chem Inf Model 2022; 62:1318-1327. [PMID: 35179902 DOI: 10.1021/acs.jcim.2c00071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Argon belongs to the group of chemically inert noble gases, which display a remarkable spectrum of clinically useful biological properties. In an attempt to better understand noble gases, notably argon's mechanism of action, we mined a massive noble gas modeling database which lists all possible noble gas binding sites in the proteins from the Protein Data Bank. We developed a method of analysis to identify among all predicted noble gas binding sites the potentially relevant ones within protein families which are likely to be modulated by Ar. Our method consists in determining within structurally aligned proteins the conserved binding sites whose shape, localization, hydrophobicity, and binding energies are to be further examined. This method was applied to the analysis of two protein families where crystallographic noble gas binding sites have been experimentally determined. Our findings indicate that among the most conserved binding sites, either the most hydrophobic one and/or the site which has the best binding energy corresponds to the crystallographic noble gas binding sites with the best occupancies, therefore the best affinity for the gas. This method will allow us to predict relevant noble gas binding sites that have potential pharmacological interest and thus potential Ar targets that will be prioritized for further studies including in vitro validation.
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Affiliation(s)
- Islem Hammami
- ISTCT UMR 6030 CNRS Univ. Caen Normandie, GIP Cyceron, 14074 Caen, France.,Air Liquide Santé International, Innovation Campus Paris, 78354 Les Loges-en-Josas, France
| | - Géraldine Farjot
- Air Liquide Santé International, Innovation Campus Paris, 78354 Les Loges-en-Josas, France
| | - Mikaël Naveau
- UAR 3408 US 50 CNRS INSERM Université de Caen-Normandie, GIP Cyceron, 14074 Caen, France
| | - Audrey Rousseaud
- Air Liquide Santé International, Innovation Campus Paris, 78354 Les Loges-en-Josas, France
| | - Thierry Prangé
- CiTCoM UMR 8038 CNRS Université de Paris, Faculté de Pharmacie, 75006 Paris, France
| | - Ira Katz
- Air Liquide Santé International, Innovation Campus Paris, 78354 Les Loges-en-Josas, France
| | - Nathalie Colloc'h
- ISTCT UMR 6030 CNRS Univ. Caen Normandie, GIP Cyceron, 14074 Caen, France
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4
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Rovšnik U, Zhuang Y, Forsberg BO, Carroni M, Yvonnesdotter L, Howard RJ, Lindahl E. Dynamic closed states of a ligand-gated ion channel captured by cryo-EM and simulations. Life Sci Alliance 2021; 4:e202101011. [PMID: 34210687 PMCID: PMC8326787 DOI: 10.26508/lsa.202101011] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 11/25/2022] Open
Abstract
Ligand-gated ion channels are critical mediators of electrochemical signal transduction across evolution. Biophysical and pharmacological characterization of these receptor proteins relies on high-quality structures in multiple, subtly distinct functional states. However, structural data in this family remain limited, particularly for resting and intermediate states on the activation pathway. Here, we report cryo-electron microscopy (cryo-EM) structures of the proton-activated Gloeobacter violaceus ligand-gated ion channel (GLIC) under three pH conditions. Decreased pH was associated with improved resolution and side chain rearrangements at the subunit/domain interface, particularly involving functionally important residues in the β1-β2 and M2-M3 loops. Molecular dynamics simulations substantiated flexibility in the closed-channel extracellular domains relative to the transmembrane ones and supported electrostatic remodeling around E35 and E243 in proton-induced gating. Exploration of secondary cryo-EM classes further indicated a low-pH population with an expanded pore. These results allow us to define distinct protonation and activation steps in pH-stimulated conformational cycling in GLIC, including interfacial rearrangements largely conserved in the pentameric channel family.
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Affiliation(s)
- Urška Rovšnik
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Yuxuan Zhuang
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Björn O Forsberg
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Marta Carroni
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Linnea Yvonnesdotter
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Rebecca J Howard
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Erik Lindahl
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden
- Department of Applied Physics, Science for Life Laboratory, Kungliga Tekniska Högskolan Royal Institute of Technology, Solna, Sweden
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5
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Abstract
Here, we investigate the role of a dilute hydrophobic gas on the phase behavior of water confined in hydrophobic nanopores. Molecular dynamics showed that gas atoms are hydrophobically attracted within the pores, where even a single particle is able to induce spontaneous drying of the whole pore. The drying process is rationalized in terms of its free-energy landscape, revealing that the penetration of a gas atom is able to suppress the drying free-energy barriers of hydrophobic pores. Results provide insights into the role of gases on the wettability of nanopores and evidence of a possibile physical mechanism for the action of volatile anesthetics on some kinds of ion channels. Results also indicate a novel, bioinspired strategy for controlling bubble formation in nanopores for sensing and energy applications.
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Affiliation(s)
- Gaia Camisasca
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Via Eudossiana 18, 00184 Rome, Italy
| | - Antonio Tinti
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Via Eudossiana 18, 00184 Rome, Italy
| | - Alberto Giacomello
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Via Eudossiana 18, 00184 Rome, Italy
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6
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Fourati Z, Sauguet L, Delarue M. Structural evidence for the binding of monocarboxylates and dicarboxylates at pharmacologically relevant extracellular sites of a pentameric ligand-gated ion channel. Acta Crystallogr D Struct Biol 2020; 76:668-675. [PMID: 32627739 PMCID: PMC7336382 DOI: 10.1107/s205979832000772x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 06/05/2020] [Indexed: 11/21/2022] Open
Abstract
GLIC is a bacterial homologue of the pentameric ligand-gated ion channels (pLGICs) that mediate the fast chemical neurotransmission of nerve signalling in eukaryotes. Because the activation and allosteric modulation features are conserved among prokaryotic and eukaryotic pLGICs, GLIC is commonly used as a model to study the allosteric transition and structural pharmacology of pLGICs. It has previously been shown that GLIC is inhibited by some carboxylic acid derivatives. Here, experimental evidence for carboxylate binding to GLIC is provided by solving its X-ray structures with a series of monocarboxylate and dicarboxylate derivatives, and two carboxylate-binding sites are described: (i) the `intersubunit' site that partially overlaps the canonical pLGIC orthosteric site and (ii) the `intrasubunit' vestibular site, which is only occupied by a subset of the described derivatives. While the intersubunit site is widely conserved in all pLGICs, the intrasubunit site is only conserved in cationic eukaryotic pLGICs. This study sheds light on the importance of these two extracellular modulation sites as potential drug targets in pLGICs.
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Affiliation(s)
- Zaineb Fourati
- Unité Dynamique Structurale des Macromolécules, Institut Pasteur, 25 Rue du Docteur Roux, F-75015 Paris, France
- Centre National de la Recherche Scientifique, CNRS UMR3528, Biologie Structurale des Processus Cellulaires et Maladies Infectieuses, 25 Rue du Docteur Roux, F-75015 Paris, France
| | - Ludovic Sauguet
- Unité Dynamique Structurale des Macromolécules, Institut Pasteur, 25 Rue du Docteur Roux, F-75015 Paris, France
- Centre National de la Recherche Scientifique, CNRS UMR3528, Biologie Structurale des Processus Cellulaires et Maladies Infectieuses, 25 Rue du Docteur Roux, F-75015 Paris, France
| | - Marc Delarue
- Unité Dynamique Structurale des Macromolécules, Institut Pasteur, 25 Rue du Docteur Roux, F-75015 Paris, France
- Centre National de la Recherche Scientifique, CNRS UMR3528, Biologie Structurale des Processus Cellulaires et Maladies Infectieuses, 25 Rue du Docteur Roux, F-75015 Paris, France
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7
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Le Nogue D, Lavaur J, Milet A, Ramirez-Gil JF, Katz I, Lemaire M, Farjot G, Hirsch EC, Michel PP. Neuroprotection of dopamine neurons by xenon against low-level excitotoxic insults is not reproduced by other noble gases. J Neural Transm (Vienna) 2020; 127:27-34. [PMID: 31807953 PMCID: PMC6942589 DOI: 10.1007/s00702-019-02112-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 11/27/2019] [Indexed: 12/19/2022]
Abstract
Using midbrain cultures, we previously demonstrated that the noble gas xenon is robustly protective for dopamine (DA) neurons exposed to L-trans-pyrrolidine-2,4-dicarboxylate (PDC), an inhibitor of glutamate uptake used to generate sustained, low-level excitotoxic insults. DA cell rescue was observed in conditions where the control atmosphere for cell culture was substituted with a gas mix, comprising the same amount of oxygen (20%) and carbon dioxide (5%) but 75% of xenon instead of nitrogen. In the present study, we first aimed to determine whether DA cell rescue against PDC remains detectable when concentrations of xenon are progressively reduced in the cell culture atmosphere. Besides, we also sought to compare the effect of xenon to that of other noble gases, including helium, neon and krypton. Our results show that the protective effect of xenon for DA neurons was concentration-dependent with an IC50 estimated at about 44%. We also established that none of the other noble gases tested in this study protected DA neurons from PDC-mediated insults. Xenon's effectiveness was most probably due to its unique capacity to block NMDA glutamate receptors. Besides, mathematical modeling of gas diffusion in the culture medium revealed that the concentration reached by xenon at the cell layer level is the highest of all noble gases when neurodegeneration is underway. Altogether, our data suggest that xenon may be of potential therapeutic value in Parkinson disease, a chronic neurodegenerative condition where DA neurons appear vulnerable to slow excitotoxicity.
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Affiliation(s)
- Déborah Le Nogue
- Sorbonne Université, Institut du Cerveau et de la Moelle Epinière (ICM), Inserm U 1127, CNRS, UMR 7225, Paris, France
| | - Jérémie Lavaur
- Sorbonne Université, Institut du Cerveau et de la Moelle Epinière (ICM), Inserm U 1127, CNRS, UMR 7225, Paris, France
| | - Aude Milet
- Air Liquide Santé International, Campus Innovation Paris, Jouy-en-Josas, France
| | | | - Ira Katz
- Air Liquide Santé International, Campus Innovation Paris, Jouy-en-Josas, France
| | - Marc Lemaire
- Air Liquide Santé International, Campus Innovation Paris, Jouy-en-Josas, France
| | - Géraldine Farjot
- Air Liquide Santé International, Campus Innovation Paris, Jouy-en-Josas, France
| | - Etienne C Hirsch
- Sorbonne Université, Institut du Cerveau et de la Moelle Epinière (ICM), Inserm U 1127, CNRS, UMR 7225, Paris, France
| | - Patrick Pierre Michel
- Sorbonne Université, Institut du Cerveau et de la Moelle Epinière (ICM), Inserm U 1127, CNRS, UMR 7225, Paris, France.
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8
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Winkler DA, Warden AC, Prangé T, Colloc'h N, Thornton AW, Ramirez-Gil JF, Farjot G, Katz I. Massive in Silico Study of Noble Gas Binding to the Structural Proteome. J Chem Inf Model 2019; 59:4844-4854. [PMID: 31613613 DOI: 10.1021/acs.jcim.9b00640] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Noble gases are chemically inert, and it was therefore thought they would have little effect on biology. Paradoxically, it was found that they do exhibit a wide range of biological effects, many of which are target-specific and potentially useful and some of which have been demonstrated in vivo. The underlying mechanisms by which useful pharmacology, such as tissue and neuroprotection, anti-addiction effects, and analgesia, is elicited are relatively unexplored. Experiments to probe the interactions of noble gases with specific proteins are more difficult with gases than those with other chemicals. It is clearly impractical to conduct the large number of gas-protein experiments required to gain a complete picture of noble gas biology. Given the simplicity of atoms as ligands, in silico methods provide an opportunity to gain insight into which noble gas-protein interactions are worthy of further experimental or advanced computational investigation. Our previous validation studies showed that in silico methods can accurately predict experimentally determined noble gas binding sites in X-ray structures of proteins. Here, we summarize the largest reported in silico reverse docking study involving 127 854 protein structures and the five nonradioactive noble gases. We describe how these computational screening methods are implemented, summarize the main types of interactions that occur between noble gases and target proteins, describe how the massive data set that this study generated can be analyzed (freely available at group18.csiro.au), and provide the NDMA receptor as an example of how these data can be used to understand the molecular pharmacology underlying the biology of the noble gases. We encourage chemical biologists to access the data and use them to expand the knowledge base of noble gas pharmacology, and to use this information, together with more efficient delivery systems, to develop "atomic drugs" that can fully exploit their considerable and relatively unexplored potential in medicine.
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Affiliation(s)
- D A Winkler
- CSIRO Future Industries , Bayview Avenue , Clayton , Victoria 3168 , Australia.,Monash Institute of Pharmaceutical Sciences , Monash University , 392 Royal Parade , Parkville 3052 , Australia.,La Trobe Institute for Molecular Science , La Trobe University , Kingsbury Drive , Bundoora 3086 , Australia.,School of Pharmacy , University of Nottingham , Nottingham NG7 2QL , U.K
| | - A C Warden
- CSIRO Land and Water , Clunies Ross Street , Acton , New South Wales 2601 , Australia
| | - T Prangé
- CiTeCoM UMR 8038 CNRS University Paris Descartes , Paris 75006 , France
| | - N Colloc'h
- ISTCT UMR 6030 CNRS Université de Caen-Normandie CEA, CERVOxy Team, Centre Cyceron , Caen 14032 , France
| | - A W Thornton
- CSIRO Future Industries , Bayview Avenue , Clayton , Victoria 3168 , Australia
| | - J-F Ramirez-Gil
- Medical R&D, Healthcare World Business Line, Air Liquide Santé International , Paris Innovation Campus , Jouy-en-Josas 78354 , France
| | - G Farjot
- Medical R&D, Healthcare World Business Line, Air Liquide Santé International , Paris Innovation Campus , Jouy-en-Josas 78354 , France
| | - I Katz
- Medical R&D, Healthcare World Business Line, Air Liquide Santé International , Paris Innovation Campus , Jouy-en-Josas 78354 , France
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9
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Fourati Z, Howard RJ, Heusser SA, Hu H, Ruza RR, Sauguet L, Lindahl E, Delarue M. Structural Basis for a Bimodal Allosteric Mechanism of General Anesthetic Modulation in Pentameric Ligand-Gated Ion Channels. Cell Rep 2019; 23:993-1004. [PMID: 29694907 DOI: 10.1016/j.celrep.2018.03.108] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 02/02/2018] [Accepted: 03/23/2018] [Indexed: 10/17/2022] Open
Abstract
Ion channel modulation by general anesthetics is a vital pharmacological process with implications for receptor biophysics and drug development. Functional studies have implicated conserved sites of both potentiation and inhibition in pentameric ligand-gated ion channels, but a detailed structural mechanism for these bimodal effects is lacking. The prokaryotic model protein GLIC recapitulates anesthetic modulation of human ion channels, and it is accessible to structure determination in both apparent open and closed states. Here, we report ten X-ray structures and electrophysiological characterization of GLIC variants in the presence and absence of general anesthetics, including the surgical agent propofol. We show that general anesthetics can allosterically favor closed channels by binding in the pore or favor open channels via various subsites in the transmembrane domain. Our results support an integrated, multi-site mechanism for allosteric modulation, and they provide atomic details of both potentiation and inhibition by one of the most common general anesthetics.
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Affiliation(s)
- Zaineb Fourati
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur and UMR 3528 du CNRS, 75015 Paris, France
| | - Rebecca J Howard
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, 17165 Solna, Sweden
| | - Stephanie A Heusser
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, 17165 Solna, Sweden
| | - Haidai Hu
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur and UMR 3528 du CNRS, 75015 Paris, France; Sorbonne Universités, UPMC University Paris 6, 75005 Paris, France
| | - Reinis R Ruza
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur and UMR 3528 du CNRS, 75015 Paris, France
| | - Ludovic Sauguet
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur and UMR 3528 du CNRS, 75015 Paris, France
| | - Erik Lindahl
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, 17165 Solna, Sweden; Swedish e-Science Research Center, KTH Royal Institute of Technology, 11428 Stockholm, Sweden
| | - Marc Delarue
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur and UMR 3528 du CNRS, 75015 Paris, France.
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10
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Hemmings HC, Riegelhaupt PM, Kelz MB, Solt K, Eckenhoff RG, Orser BA, Goldstein PA. Towards a Comprehensive Understanding of Anesthetic Mechanisms of Action: A Decade of Discovery. Trends Pharmacol Sci 2019; 40:464-481. [PMID: 31147199 DOI: 10.1016/j.tips.2019.05.001] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 04/11/2019] [Accepted: 05/03/2019] [Indexed: 12/30/2022]
Abstract
Significant progress has been made in the 21st century towards a comprehensive understanding of the mechanisms of action of general anesthetics, coincident with progress in structural biology and molecular, cellular, and systems neuroscience. This review summarizes important new findings that include target identification through structural determination of anesthetic binding sites, details of receptors and ion channels involved in neurotransmission, and the critical roles of neuronal networks in anesthetic effects on memory and consciousness. These recent developments provide a comprehensive basis for conceptualizing pharmacological control of amnesia, unconsciousness, and immobility.
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Affiliation(s)
- Hugh C Hemmings
- Departments of Anesthesiology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA; Departments of Pharmacology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Paul M Riegelhaupt
- Departments of Anesthesiology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Max B Kelz
- Department of Anesthesiology and Critical Care, University of Pennsylvania Perelman School of Medicine, 3620 Hamilton Walk, 305 John Morgan, Philadelphia, PA 19104, USA
| | - Ken Solt
- Department of Anaesthesia, Harvard Medical School, GRB 444, 55 Fruit St., Boston, MA 02114, USA; Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA
| | - Roderic G Eckenhoff
- Department of Anesthesiology and Critical Care, University of Pennsylvania Perelman School of Medicine, 3620 Hamilton Walk, 305 John Morgan, Philadelphia, PA 19104, USA
| | - Beverley A Orser
- Departments of Anesthesia and Physiology, Room 3318 Medical Sciences Building, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Peter A Goldstein
- Departments of Anesthesiology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA; Departments of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA.
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11
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Abstract
The pentameric γ-aminobutyric acid type A receptors are ion channels activated by ligands, which intervene in the rapid inhibitory transmission in the mammalian CNS. Due to their rich pharmacology and therapeutic potential, it is essential to understand their structure and function thoroughly. This deep characterization was hampered by the lack of experimental structural information for many years. Thus, computational techniques have been extensively combined with experimental data, in order to undertake the study of γ-aminobutyric acid type A receptors and their interaction with drugs. Here, we review the exciting journey made to assess the structures of these receptors and outline major outcomes. Finally, we discuss the brand new structure of the α1β2γ2 subtype and the amazing advances it brings to the field.
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12
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Petrov E, Menon G, Rohde PR, Battle AR, Martinac B, Solioz M. Xenon-inhibition of the MscL mechano-sensitive channel and the CopB copper ATPase under different conditions suggests direct effects on these proteins. PLoS One 2018; 13:e0198110. [PMID: 29864148 PMCID: PMC5986136 DOI: 10.1371/journal.pone.0198110] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 05/14/2018] [Indexed: 11/18/2022] Open
Abstract
Xenon is frequently used as a general anesthetic in humans, but the mechanism remains an issue of debate. While for some membrane proteins, a direct interaction of xenon with the protein has been shown to be the inhibitory mechanism, other membrane protein functions could be affected by changes of membrane properties due to partitioning of the gas into the lipid bilayer. Here, the effect of xenon on a mechanosensitive ion channel and a copper ion-translocating ATPase was compared under different conditions. Xenon inhibited spontaneous gating of the Escherichia coli mechano-sensitive mutant channel MscL-G22E, as shown by patch-clamp recording techniques. Under high hydrostatic pressure, MscL-inhibition was reversed. Similarly, the activity of the Enterococcus hirae CopB copper ATPase, reconstituted into proteoliposomes, was inhibited by xenon. However, the CopB ATPase activity was also inhibited by xenon when CopB was in a solubilized state. These findings suggest that xenon acts by directly interacting with these proteins, rather than via indirect effects by altering membrane properties. Also, inhibition of copper transport may be a novel effect of xenon that contributes to anesthesia.
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Affiliation(s)
- Evgeny Petrov
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia
| | - Gopalakrishnan Menon
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia
| | - Paul R Rohde
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia
| | - Andrew R Battle
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia.,School of Biomedical Sciences, Queensland University of Technology (QUT), Brisbane, Australia
| | - Boris Martinac
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia.,St Vincent's Clinical School, University of New South Wales, Darlinghurst, Australia
| | - Marc Solioz
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia.,Department Clinical Research, University of Bern, Bern, Switzerland
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13
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Crystal structures of a pentameric ion channel gated by alkaline pH show a widely open pore and identify a cavity for modulation. Proc Natl Acad Sci U S A 2018; 115:E3959-E3968. [PMID: 29632192 DOI: 10.1073/pnas.1717700115] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs) constitute a widespread class of ion channels, present in archaea, bacteria, and eukaryotes. Upon binding of their agonists in the extracellular domain, the transmembrane pore opens, allowing ions to go through, via a gating mechanism that can be modulated by a number of drugs. Even though high-resolution structural information on pLGICs has increased in a spectacular way in recent years, both in bacterial and in eukaryotic systems, the structure of the open channel conformation of some intensively studied receptors whose structures are known in a nonactive (closed) form, such as Erwinia chrysanthemi pLGIC (ELIC), is still lacking. Here we describe a gammaproteobacterial pLGIC from an endo-symbiont of Tevnia jerichonana (sTeLIC), whose sequence is closely related to the pLGIC from ELIC with 28% identity. We provide an X-ray crystallographic structure at 2.3 Å in an active conformation, where the pore is found to be more open than any current conformation found for pLGICs. In addition, two charged restriction rings are present in the vestibule. Functional characterization shows sTeLIC to be a cationic channel activated at alkaline pH. It is inhibited by divalent cations, but not by quaternary ammonium ions, such as tetramethylammonium. Additionally, we found that sTeLIC is allosterically potentiated by aromatic amino acids Phe and Trp, as well as their derivatives, such as 4-bromo-cinnamate, whose cocrystal structure reveals a vestibular binding site equivalent to, but more deeply buried than, the one already described for benzodiazepines in ELIC.
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14
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Chen Q, Xu Y, Tang P. X-Ray Crystallographic Studies for Revealing Binding Sites of General Anesthetics in Pentameric Ligand-Gated Ion Channels. Methods Enzymol 2018; 603:21-47. [PMID: 29673527 DOI: 10.1016/bs.mie.2018.01.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
X-ray crystallography is a powerful tool in structural biology and can offer insight into structured-based understanding of general anesthetic action on various relevant molecular targets, including pentameric ligand-gated ion channels (pLGICs). In this chapter, we outline the procedures for expression and purification of pLGICs. Optimization of crystallization conditions, especially to achieve high-resolution structures of pLGICs bound with general anesthetics, is also presented. Case studies of pLGICs bound with the volatile general anesthetic isoflurane, 2-bromoethanol, and the intravenous general anesthetic ketamine are revisited.
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Affiliation(s)
- Qiang Chen
- University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Yan Xu
- University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Pei Tang
- University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.
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15
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Banerjee D, Simon CM, Elsaidi SK, Haranczyk M, Thallapally PK. Xenon Gas Separation and Storage Using Metal-Organic Frameworks. Chem 2018. [DOI: 10.1016/j.chempr.2017.12.025] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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16
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Delbart F, Brams M, Gruss F, Noppen S, Peigneur S, Boland S, Chaltin P, Brandao-Neto J, von Delft F, Touw WG, Joosten RP, Liekens S, Tytgat J, Ulens C. An allosteric binding site of the α7 nicotinic acetylcholine receptor revealed in a humanized acetylcholine-binding protein. J Biol Chem 2017; 293:2534-2545. [PMID: 29237730 PMCID: PMC5818190 DOI: 10.1074/jbc.m117.815316] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 10/24/2017] [Indexed: 11/06/2022] Open
Abstract
Nicotinic acetylcholine receptors (nAChRs) belong to the family of pentameric ligand-gated ion channels and mediate fast excitatory transmission in the central and peripheral nervous systems. Among the different existing receptor subtypes, the homomeric α7 nAChR has attracted considerable attention because of its possible implication in several neurological and psychiatric disorders, including cognitive decline associated with Alzheimer's disease or schizophrenia. Allosteric modulators of ligand-gated ion channels are of particular interest as therapeutic agents, as they modulate receptor activity without affecting normal fluctuations of synaptic neurotransmitter release. Here, we used X-ray crystallography and surface plasmon resonance spectroscopy of α7-acetylcholine-binding protein (AChBP), a humanized chimera of a snail AChBP, which has 71% sequence similarity with the extracellular ligand-binding domain of the human α7 nAChR, to investigate the structural determinants of allosteric modulation. We extended previous observations that an allosteric site located in the vestibule of the receptor offers an attractive target for receptor modulation. We introduced seven additional humanizing mutations in the vestibule-located binding site of AChBP to improve its suitability as a model for studying allosteric binding. Using a fragment-based screening approach, we uncovered an allosteric binding site located near the β8-β9 loop, which critically contributes to coupling ligand binding to channel opening in human α7 nAChR. This work expands our understanding of the topology of allosteric binding sites in AChBP and, by extrapolation, in the human α7 nAChR as determined by electrophysiology measurements. Our insights pave the way for drug design strategies targeting nAChRs involved in ion channel-mediated disorders.
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Affiliation(s)
- Florian Delbart
- From the Department of Cellular and Molecular Medicine, Laboratory of Structural Neurobiology, Faculty of Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Marijke Brams
- From the Department of Cellular and Molecular Medicine, Laboratory of Structural Neurobiology, Faculty of Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Fabian Gruss
- From the Department of Cellular and Molecular Medicine, Laboratory of Structural Neurobiology, Faculty of Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Sam Noppen
- the Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
| | - Steve Peigneur
- the Laboratory of Toxicology and Pharmacology, Faculty of Pharmaceutical Sciences, KU Leuven, 3000 Leuven, Belgium
| | - Sandro Boland
- the Center for Innovation and Stimulation of Drug Discovery Leuven, Cistim Leuven vzw, 3001 Heverlee, Belgium
| | - Patrick Chaltin
- the Center for Innovation and Stimulation of Drug Discovery Leuven, Cistim Leuven vzw, 3001 Heverlee, Belgium.,the Center for Innovation and Stimulation of Drug Discovery Leuven and Center for Drug Design and Discovery, KU Leuven, 3001 Heverlee, Belgium
| | - Jose Brandao-Neto
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0QX, United Kingdom, and
| | - Frank von Delft
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0QX, United Kingdom, and
| | - Wouter G Touw
- the Division of Biochemistry, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Robbie P Joosten
- the Division of Biochemistry, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Sandra Liekens
- the Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
| | - Jan Tytgat
- the Laboratory of Toxicology and Pharmacology, Faculty of Pharmaceutical Sciences, KU Leuven, 3000 Leuven, Belgium
| | - Chris Ulens
- From the Department of Cellular and Molecular Medicine, Laboratory of Structural Neurobiology, Faculty of Medicine, KU Leuven, 3000 Leuven, Belgium,
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17
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Xenon for tunnelling analysis of the efflux pump component OprN. PLoS One 2017; 12:e0184045. [PMID: 28886086 PMCID: PMC5590881 DOI: 10.1371/journal.pone.0184045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 08/17/2017] [Indexed: 12/02/2022] Open
Abstract
Tripartite efflux pumps are among the main actors responsible for antibiotics resistance in Gram-negative bacteria. In the last two decades, structural studies gave crucial information about the assembly interfaces and the mechanistic motions. Thus rigidifying the assembly seems to be an interesting way to hamper the drug efflux. In this context, xenon is a suitable probe for checking whether small ligands could act as conformational lockers by targeting hydrophobic cavities. Here we focus on OprN, the outer membrane channel of the MexEF efflux pump from Pseudomonas aeruginosa. After exposing OprN crystals to xenon gas pressure, 14 binding sites were observed using X-ray crystallography. These binding sites were unambiguously characterized in hydrophobic cavities of OprN. The major site is observed in the sensitive iris-like region gating the channel at the periplasmic side, built by the three key-residues Leu 405, Asp 109, and Arg 412. This arrangement defines along the tunnel axis a strong hydrophobic/polar gradient able to enhance the passive efflux mechanism of OprN. The other xenon atoms reveal strategic hydrophobic regions of the channel scaffold to target, with the aim to freeze the dynamic movements responsible of the open/close conformational equilibrium in OprN.
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18
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Lavaur J, Le Nogue D, Lemaire M, Pype J, Farjot G, Hirsch EC, Michel PP. The noble gas xenon provides protection and trophic stimulation to midbrain dopamine neurons. J Neurochem 2017; 142:14-28. [PMID: 28398653 PMCID: PMC5518208 DOI: 10.1111/jnc.14041] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 04/04/2017] [Accepted: 04/05/2017] [Indexed: 01/24/2023]
Abstract
Despite its low chemical reactivity, the noble gas xenon possesses a remarkable spectrum of biological effects. In particular, xenon is a strong neuroprotectant in preclinical models of hypoxic‐ischemic brain injury. In this study, we wished to determine whether xenon retained its neuroprotective potential in experimental settings that model the progressive loss of midbrain dopamine (DA) neurons in Parkinson's disease. Using rat midbrain cultures, we established that xenon was partially protective for DA neurons through either direct or indirect effects on these neurons. So, when DA neurons were exposed to l‐trans‐pyrrolidine‐2,4‐dicarboxylic acid so as to increase ambient glutamate levels and generate slow and sustained excitotoxicity, the effect of xenon on DA neurons was direct. The vitamin E analog Trolox also partially rescued DA neurons in this setting and enhanced neuroprotection by xenon. However, in the situation where DA cell death was spontaneous, the protection of DA neurons by xenon appeared indirect as it occurred through the repression of a mechanism mediated by proliferating glial cells, presumably astrocytes and their precursor cells. Xenon also exerted trophic effects for DA neurons in this paradigm. The effects of xenon were mimicked and improved by the N‐methyl‐d‐aspartate glutamate receptor antagonist memantine and xenon itself appeared to work by antagonizing N‐methyl‐d‐aspartate receptors. Note that another noble gas argon could not reproduce xenon effects. Overall, present data indicate that xenon can provide protection and trophic support to DA neurons that are vulnerable in Parkinson's disease. This suggests that xenon might have some therapeutic value for this disorder. ![]()
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Affiliation(s)
- Jérémie Lavaur
- Sorbonne Universités, UPMC Univ Paris 06, Inserm, CNRS, Institut du Cerveau et de la Moelle épinière (ICM), Hôpital Pitié-Salpêtrière, Paris, France
| | - Déborah Le Nogue
- Sorbonne Universités, UPMC Univ Paris 06, Inserm, CNRS, Institut du Cerveau et de la Moelle épinière (ICM), Hôpital Pitié-Salpêtrière, Paris, France
| | - Marc Lemaire
- Air Liquide Santé International, Medical R&D Paris, Saclay Research Center, Jouy-en Josas, France
| | - Jan Pype
- Air Liquide Santé International, Medical R&D Paris, Saclay Research Center, Jouy-en Josas, France
| | - Géraldine Farjot
- Air Liquide Santé International, Medical R&D Paris, Saclay Research Center, Jouy-en Josas, France
| | - Etienne C Hirsch
- Sorbonne Universités, UPMC Univ Paris 06, Inserm, CNRS, Institut du Cerveau et de la Moelle épinière (ICM), Hôpital Pitié-Salpêtrière, Paris, France
| | - Patrick P Michel
- Sorbonne Universités, UPMC Univ Paris 06, Inserm, CNRS, Institut du Cerveau et de la Moelle épinière (ICM), Hôpital Pitié-Salpêtrière, Paris, France
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19
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Colledge M, Wallace BA. AnglerFish: a webserver for defining the geometry of α-helices in membrane proteins. Bioinformatics 2017; 33:1233-1234. [PMID: 28035031 PMCID: PMC5860525 DOI: 10.1093/bioinformatics/btw781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 12/06/2016] [Indexed: 11/14/2022] Open
Abstract
Summary Integral membrane proteins that form helical pores and bundles constitute major drug targets, and many of their structures have been defined by crystallography and cryo-electron microscopy. The gating of channels and ligand binding of transporters generally involve changes in orientation of one or more the constituent helices in the structures. At present there is no standard easily accessible means for defining the orientation of a helix in a membrane protein structure. AnglerFish is a web-based tool for parameterising the angles of transmembrane helices based on PDB coordinates, with the helical orientations defined by the angles ‘tilt’ and ‘swing’. AnglerFish is particularly useful for defining changes in structure between different states, including both symmetric and asymmetric transitions, and can be used to quantitate differences between related structures or different subunits within the same structure. Availability and Implementation AnglerFish is freely available at http://anglerfish.cryst.bbk.ac.uk. The website is implemented in Perl-cgi and Apache and operation in all major browsers is supported. The source code is available at GitHub. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Matthew Colledge
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK
- To whom correspondence should be addressed.
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20
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Saidijam M, Azizpour S, Patching SG. Comprehensive analysis of the numbers, lengths and amino acid compositions of transmembrane helices in prokaryotic, eukaryotic and viral integral membrane proteins of high-resolution structure. J Biomol Struct Dyn 2017; 36:443-464. [PMID: 28150531 DOI: 10.1080/07391102.2017.1285725] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We report a comprehensive analysis of the numbers, lengths and amino acid compositions of transmembrane helices in 235 high-resolution structures of integral membrane proteins. The properties of 1551 transmembrane helices in the structures were compared with those obtained by analysis of the same amino acid sequences using topology prediction tools. Explanations for the 81 (5.2%) missing or additional transmembrane helices in the prediction results were identified. Main reasons for missing transmembrane helices were mis-identification of N-terminal signal peptides, breaks in α-helix conformation or charged residues in the middle of transmembrane helices and transmembrane helices with unusual amino acid composition. The main reason for additional transmembrane helices was mis-identification of amphipathic helices, extramembrane helices or hairpin re-entrant loops. Transmembrane helix length had an overall median of 24 residues and an average of 24.9 ± 7.0 residues and the most common length was 23 residues. The overall content of residues in transmembrane helices as a percentage of the full proteins had a median of 56.8% and an average of 55.7 ± 16.0%. Amino acid composition was analysed for the full proteins, transmembrane helices and extramembrane regions. Individual proteins or types of proteins with transmembrane helices containing extremes in contents of individual amino acids or combinations of amino acids with similar physicochemical properties were identified and linked to structure and/or function. In addition to overall median and average values, all results were analysed for proteins originating from different types of organism (prokaryotic, eukaryotic, viral) and for subgroups of receptors, channels, transporters and others.
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Affiliation(s)
- Massoud Saidijam
- a Department of Molecular Medicine and Genetics, Research Centre for Molecular Medicine, School of Medicine , Hamadan University of Medical Sciences , Hamadan , Iran
| | - Sonia Azizpour
- a Department of Molecular Medicine and Genetics, Research Centre for Molecular Medicine, School of Medicine , Hamadan University of Medical Sciences , Hamadan , Iran
| | - Simon G Patching
- b School of BioMedical Sciences and the Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds , UK
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21
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Abstract
Membrane proteins are involved in a large variety of functions. Most of these protein functions are regulated by ligand binding with diverse modes of action: agonists, partial agonists, antagonists, and allosteric modulators, potentiators and inhibitors. From the pharmacological point of view, membrane proteins are one if not the major target for drug development. However, experimental structure determination of membrane proteins in complex or in free form still represents a great challenge. Molecular dynamics (MD) simulations commonly reach the microsecond scale on membrane systems. This numerical tool is mature enough to predict and add molecular details on the different ligand-binding modes. In the present chapter, I will present the different steps to design, simulate, and analyze a MD simulation system containing a protein embedded in a membrane and surrounded by water and ligand. As an illustration, the simulation of the ligand-gated ion channel γ-aminobutyric acid type A receptor (GABAAR) surrounded by one of its allosteric potentiators, bromoform, will be presented and discussed.
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Affiliation(s)
- Samuel Murail
- Laboratoire de Biochimie Théorique, CNRS, UPR9080, University Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, F-75005, Paris, France.
- Air Liquide, Centre de Recherches Paris-Saclay, Boite Postale 126, Les Loges-en-Josas, Jouy-en-Josas, 78354, France.
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22
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Fourati Z, Ruza RR, Laverty D, Drège E, Delarue-Cochin S, Joseph D, Koehl P, Smart T, Delarue M. Barbiturates Bind in the GLIC Ion Channel Pore and Cause Inhibition by Stabilizing a Closed State. J Biol Chem 2016; 292:1550-1558. [PMID: 27986812 DOI: 10.1074/jbc.m116.766964] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 12/06/2016] [Indexed: 12/12/2022] Open
Abstract
Barbiturates induce anesthesia by modulating the activity of anionic and cationic pentameric ligand-gated ion channels (pLGICs). Despite more than a century of use in clinical practice, the prototypic binding site for this class of drugs within pLGICs is yet to be described. In this study, we present the first X-ray structures of barbiturates bound to GLIC, a cationic prokaryotic pLGIC with excellent structural homology to other relevant channels sensitive to general anesthetics and, as shown here, to barbiturates, at clinically relevant concentrations. Several derivatives of barbiturates containing anomalous scatterers were synthesized, and these derivatives helped us unambiguously identify a unique barbiturate binding site within the central ion channel pore in a closed conformation. In addition, docking calculations around the observed binding site for all three states of the receptor, including a model of the desensitized state, showed that barbiturates preferentially stabilize the closed state. The identification of this pore binding site sheds light on the mechanism of barbiturate inhibition of cationic pLGICs and allows the rationalization of several structural and functional features previously observed for barbiturates.
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Affiliation(s)
- Zaineb Fourati
- From the Unité de Dynamique Structurale des Macromolécules, UMR 3528 du CNRS, Institut Pasteur, 75015 Paris, France
| | - Reinis Reinholds Ruza
- From the Unité de Dynamique Structurale des Macromolécules, UMR 3528 du CNRS, Institut Pasteur, 75015 Paris, France
| | - Duncan Laverty
- the Department of Neuroscience, Physiology and Pharmacology, University College London, London WC1E 6BT, United Kingdom
| | - Emmanuelle Drège
- the UMR 8076 du CNRS, BioCIS, Faculté de Pharmacie, Université Paris Sud, 92296 Chatenay-Malabry, France
| | - Sandrine Delarue-Cochin
- the UMR 8076 du CNRS, BioCIS, Faculté de Pharmacie, Université Paris Sud, 92296 Chatenay-Malabry, France
| | - Delphine Joseph
- the UMR 8076 du CNRS, BioCIS, Faculté de Pharmacie, Université Paris Sud, 92296 Chatenay-Malabry, France
| | - Patrice Koehl
- the Department of Computer Science, University of California, Davis, California 95616
| | - Trevor Smart
- the Department of Neuroscience, Physiology and Pharmacology, University College London, London WC1E 6BT, United Kingdom.
| | - Marc Delarue
- From the Unité de Dynamique Structurale des Macromolécules, UMR 3528 du CNRS, Institut Pasteur, 75015 Paris, France.
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23
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Gupta S, Chakraborty S, Vij R, Auerbach A. A mechanism for acetylcholine receptor gating based on structure, coupling, phi, and flip. J Gen Physiol 2016; 149:85-103. [PMID: 27932572 PMCID: PMC5217088 DOI: 10.1085/jgp.201611673] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 09/20/2016] [Accepted: 11/10/2016] [Indexed: 01/29/2023] Open
Abstract
Gupta et al. use single-channel electrophysiology to investigate the gating mechanism of acetylcholine receptor ion channels. They propose that channel opening starts at the M2–M3 linker and ligand-binding sites and proceeds through four brief intermediate conformations before ending with the collapse of a gate bubble. Nicotinic acetylcholine receptors are allosteric proteins that generate membrane currents by isomerizing (“gating”) between resting and active conformations under the influence of neurotransmitters. Here, to explore the mechanisms that link the transmitter-binding sites (TBSs) with the distant gate, we use mutant cycle analyses to measure coupling between residue pairs, phi value analyses to sequence domain rearrangements, and current simulations to reproduce a microsecond shut component (“flip”) apparent in single-channel recordings. Significant interactions between amino acids separated by >15 Å are rare; an exception is between the αM2–M3 linkers and the TBSs that are ∼30 Å apart. Linker residues also make significant, local interactions within and between subunits. Phi value analyses indicate that without agonists, the linker is the first region in the protein to reach the gating transition state. Together, the phi pattern and flip component suggest that a complete, resting↔active allosteric transition involves passage through four brief intermediate states, with brief shut events arising from sojourns in all or a subset. We derive energy landscapes for gating with and without agonists, and propose a structure-based model in which resting→active starts with spontaneous rearrangements of the M2–M3 linkers and TBSs. These conformational changes stabilize a twisted extracellular domain to promote transmembrane helix tilting, gate dilation, and the formation of a “bubble” that collapses to initiate ion conduction. The energy landscapes suggest that twisting is the most energetically unfavorable step in the resting→active conformational change and that the rate-limiting step in the reverse process is bubble formation.
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Affiliation(s)
- Shaweta Gupta
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY 14214
| | - Srirupa Chakraborty
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY 14214
| | - Ridhima Vij
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY 14214
| | - Anthony Auerbach
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY 14214
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24
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Allosteric binding site in a Cys-loop receptor ligand-binding domain unveiled in the crystal structure of ELIC in complex with chlorpromazine. Proc Natl Acad Sci U S A 2016; 113:E6696-E6703. [PMID: 27791038 DOI: 10.1073/pnas.1603101113] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pentameric ligand-gated ion channels or Cys-loop receptors are responsible for fast inhibitory or excitatory synaptic transmission. The antipsychotic compound chlorpromazine is a widely used tool to probe the ion channel pore of the nicotinic acetylcholine receptor, which is a prototypical Cys-loop receptor. In this study, we determine the molecular determinants of chlorpromazine binding in the Erwinia ligand-gated ion channel (ELIC). We report the X-ray crystal structures of ELIC in complex with chlorpromazine or its brominated derivative bromopromazine. Unexpectedly, we do not find a chlorpromazine molecule in the channel pore of ELIC, but behind the β8-β9 loop in the extracellular ligand-binding domain. The β8-β9 loop is localized downstream from the neurotransmitter binding site and plays an important role in coupling of ligand binding to channel opening. In combination with electrophysiological recordings from ELIC cysteine mutants and a thiol-reactive derivative of chlorpromazine, we demonstrate that chlorpromazine binding at the β8-β9 loop is responsible for receptor inhibition. We further use molecular-dynamics simulations to support the X-ray data and mutagenesis experiments. Together, these data unveil an allosteric binding site in the extracellular ligand-binding domain of ELIC. Our results extend on previous observations and further substantiate our understanding of a multisite model for allosteric modulation of Cys-loop receptors.
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25
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Burgos CF, Yévenes GE, Aguayo LG. Structure and Pharmacologic Modulation of Inhibitory Glycine Receptors. Mol Pharmacol 2016; 90:318-25. [PMID: 27401877 DOI: 10.1124/mol.116.105726] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 07/08/2016] [Indexed: 01/08/2023] Open
Abstract
Glycine receptors (GlyR) are inhibitory Cys-loop ion channels that contribute to the control of excitability along the central nervous system (CNS). GlyR are found in the spinal cord and brain stem, and more recently they were reported in higher regions of the CNS such as the hippocampus and nucleus accumbens. GlyR are involved in motor coordination, respiratory rhythms, pain transmission, and sensory processing, and they are targets for relevant physiologic and pharmacologic modulators. Several studies with protein crystallography and cryoelectron microscopy have shed light on the residues and mechanisms associated with the activation, blockade, and regulation of pentameric Cys-loop ion channels at the atomic level. Initial studies conducted on the extracellular domain of acetylcholine receptors, ion channels from prokaryote homologs-Erwinia chrysanthemi ligand-gated ion channel (ELIC), Gloeobacter violaceus ligand-gated ion channel (GLIC)-and crystallized eukaryotic receptors made it possible to define the overall structure and topology of the Cys-loop receptors. For example, the determination of pentameric GlyR structures bound to glycine and strychnine have contributed to visualizing the structural changes implicated in the transition between the open and closed states of the Cys-loop receptors. In this review, we summarize how the new information obtained in functional, mutagenesis, and structural studies have contributed to a better understanding of the function and regulation of GlyR.
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Affiliation(s)
- Carlos F Burgos
- Laboratory of Neurophysiology (C.F.B., L.G.A.), and Laboratory of Neuropharmacology (G.E.Y.), Department of Physiology, University of Concepción, Concepción, Chile
| | - Gonzalo E Yévenes
- Laboratory of Neurophysiology (C.F.B., L.G.A.), and Laboratory of Neuropharmacology (G.E.Y.), Department of Physiology, University of Concepción, Concepción, Chile
| | - Luis G Aguayo
- Laboratory of Neurophysiology (C.F.B., L.G.A.), and Laboratory of Neuropharmacology (G.E.Y.), Department of Physiology, University of Concepción, Concepción, Chile
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26
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Puthenkalam R, Hieckel M, Simeone X, Suwattanasophon C, Feldbauer RV, Ecker GF, Ernst M. Structural Studies of GABAA Receptor Binding Sites: Which Experimental Structure Tells us What? Front Mol Neurosci 2016; 9:44. [PMID: 27378845 PMCID: PMC4910578 DOI: 10.3389/fnmol.2016.00044] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 05/25/2016] [Indexed: 01/23/2023] Open
Abstract
Atomic resolution structures of cys-loop receptors, including one of a γ-aminobutyric acid type A receptor (GABAA receptor) subtype, allow amazing insights into the structural features and conformational changes that these pentameric ligand-gated ion channels (pLGICs) display. Here we present a comprehensive analysis of more than 30 cys-loop receptor structures of homologous proteins that revealed several allosteric binding sites not previously described in GABAA receptors. These novel binding sites were examined in GABAA receptor homology models and assessed as putative candidate sites for allosteric ligands. Four so far undescribed putative ligand binding sites were proposed for follow up studies based on their presence in the GABAA receptor homology models. A comprehensive analysis of conserved structural features in GABAA and glycine receptors (GlyRs), the glutamate gated ion channel, the bacterial homologs Erwinia chrysanthemi (ELIC) and Gloeobacter violaceus GLIC, and the serotonin type 3 (5-HT3) receptor was performed. The conserved features were integrated into a master alignment that led to improved homology models. The large fragment of the intracellular domain that is present in the structure of the 5-HT3 receptor was utilized to generate GABAA receptor models with a corresponding intracellular domain fragment. Results of mutational and photoaffinity ligand studies in GABAA receptors were analyzed in the light of the model structures. This led to an assignment of candidate ligands to two proposed novel pockets, candidate binding sites for furosemide and neurosteroids in the trans-membrane domain were identified. The homology models can serve as hypotheses generators, and some previously controversial structural interpretations of biochemical data can be resolved in the light of the presented multi-template approach to comparative modeling. Crystal and cryo-EM microscopic structures of the closest homologs that were solved in different conformational states provided important insights into structural rearrangements of binding sites during conformational transitions. The impact of structural variation and conformational motion on the shape of the investigated binding sites was analyzed. Rules for best template and alignment choice were obtained and can generally be applied to modeling of cys-loop receptors. Overall, we provide an updated structure based view of ligand binding sites present in GABAA receptors.
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Affiliation(s)
- Roshan Puthenkalam
- Department of Molecular Neurosciences, Medical University of ViennaVienna, Austria
| | - Marcel Hieckel
- Department of Molecular Neurosciences, Medical University of ViennaVienna, Austria
| | - Xenia Simeone
- Department of Molecular Neurosciences, Medical University of ViennaVienna, Austria
| | | | - Roman V. Feldbauer
- Austrian Research Institute for Artificial Intelligence (OFAI)Vienna, Austria
| | - Gerhard F. Ecker
- Department of Pharmaceutical Chemistry, University of ViennaVienna, Austria
| | - Margot Ernst
- Department of Molecular Neurosciences, Medical University of ViennaVienna, Austria
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27
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Laurent B, Murail S, Shahsavar A, Sauguet L, Delarue M, Baaden M. Sites of Anesthetic Inhibitory Action on a Cationic Ligand-Gated Ion Channel. Structure 2016; 24:595-605. [DOI: 10.1016/j.str.2016.02.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 02/12/2016] [Accepted: 02/22/2016] [Indexed: 01/09/2023]
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28
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Abraini J, David H, Vallée N, Risso JJ. Theoretical considerations on the ultimate depth that could be reached by saturation human divers. Med Gas Res 2016; 6:119-121. [PMID: 27867478 PMCID: PMC5110125 DOI: 10.4103/2045-9912.184722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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