1
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Jalalypour F, Howard RJ, Lindahl E. Allosteric Cholesterol Site in Glycine Receptors Characterized through Molecular Simulations. J Phys Chem B 2024; 128:4996-5007. [PMID: 38747451 PMCID: PMC11129184 DOI: 10.1021/acs.jpcb.4c01703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/29/2024] [Accepted: 05/06/2024] [Indexed: 05/24/2024]
Abstract
Glycine receptors are pentameric ligand-gated ion channels that conduct chloride ions across postsynaptic membranes to facilitate fast inhibitory neurotransmission. In addition to gating by the glycine agonist, interactions with lipids and other compounds in the surrounding membrane environment modulate their function, but molecular details of these interactions remain unclear, in particular, for cholesterol. Here, we report coarse-grained simulations in a model neuronal membrane for three zebrafish glycine receptor structures representing apparent resting, open, and desensitized states. We then converted the systems to all-atom models to examine detailed lipid interactions. Cholesterol bound to the receptor at an outer-leaflet intersubunit site, with a preference for the open and desensitized versus resting states, indicating that it can bias receptor function. Finally, we used short atomistic simulations and iterative amino acid perturbations to identify residues that may mediate allosteric gating transitions. Frequent cholesterol contacts in atomistic simulations clustered with residues identified by perturbation analysis and overlapped with mutations influencing channel function and pathology. Cholesterol binding at this site was also observed in a recently reported pig heteromeric glycine receptor. These results indicate state-dependent lipid interactions relevant to allosteric transitions of glycine receptors, including specific amino acid contacts applicable to biophysical modeling and pharmaceutical design.
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Affiliation(s)
- Farzaneh Jalalypour
- Science
for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, 17121 Solna, Sweden
| | - Rebecca J. Howard
- Science
for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, 17121 Solna, Sweden
- Science
for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17121 Solna, Sweden
| | - Erik Lindahl
- Science
for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, 17121 Solna, Sweden
- Science
for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17121 Solna, Sweden
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2
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Thompson JRE, Beaudoin CA, Lummis SCR. Modelling and Molecular Dynamics Predict the Structure and Interactions of the Glycine Receptor Intracellular Domain. Biomolecules 2023; 13:1757. [PMID: 38136628 PMCID: PMC10741472 DOI: 10.3390/biom13121757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/28/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
Glycine receptors (GlyRs) are glycine-gated inhibitory pentameric ligand-gated ion channels composed of α or α + β subunits. A number of structures of these proteins have been reported, but to date, these have only revealed details of the extracellular and transmembrane domains, with the intracellular domain (ICD) remaining uncharacterised due to its high flexibility. The ICD is a region that can modulate function in addition to being critical for receptor localisation and clustering via proteins such as gephyrin. Here, we use modelling and molecular dynamics (MD) to reveal details of the ICDs of both homomeric and heteromeric GlyR. At their N and C ends, both the α and β subunit ICDs have short helices, which are major sites of stabilising interactions; there is a large flexible loop between them capable of forming transient secondary structures. The α subunit can affect the β subunit ICD structure, which is more flexible in a 4α2:1β than in a 4α1:1β GlyR. We also explore the effects of gephyrin binding by creating GlyR models bound to the gephyrin E domain; MD simulations suggest these are more stable than the unbound forms, and again there are α subunit-dependent differences, despite the fact the gephyrin binds to the β subunit. The bound models also suggest that gephyrin causes compaction of the ICD. Overall, the data expand our knowledge of this important receptor protein and in particular clarify features of the underexplored ICD.
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Affiliation(s)
| | | | - Sarah C. R. Lummis
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
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3
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Liu H, Zhang X, Shi P, Yuan J, Jia Q, Pi C, Chen T, Xiong L, Chen J, Tang J, Yue R, Liu Z, Shen H, Zuo Y, Wei Y, Zhao L. α7 Nicotinic acetylcholine receptor: a key receptor in the cholinergic anti-inflammatory pathway exerting an antidepressant effect. J Neuroinflammation 2023; 20:84. [PMID: 36973813 PMCID: PMC10041767 DOI: 10.1186/s12974-023-02768-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 03/17/2023] [Indexed: 03/28/2023] Open
Abstract
Depression is a common mental illness, which is related to monoamine neurotransmitters and the dysfunction of the cholinergic, immune, glutamatergic, and neuroendocrine systems. The hypothesis of monoamine neurotransmitters is one of the commonly recognized pathogenic mechanisms of depression; however, the drugs designed based on this hypothesis have not achieved good clinical results. A recent study demonstrated that depression and inflammation were strongly correlated, and the activation of alpha7 nicotinic acetylcholine receptor (α7 nAChR)-mediated cholinergic anti-inflammatory pathway (CAP) in the cholinergic system exhibited good therapeutic effects against depression. Therefore, anti-inflammation might be a potential direction for the treatment of depression. Moreover, it is also necessary to further reveal the key role of inflammation and α7 nAChR in the pathogenesis of depression. This review focused on the correlations between inflammation and depression as well-discussed the crucial role of α7 nAChR in the CAP.
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Affiliation(s)
- Huiyang Liu
- grid.410578.f0000 0001 1114 4286Key Laboratory of Medical Electrophysiology, Ministry of Education, School of Pharmacy of Southwest Medical University, Luzhou, 646000 People’s Republic of China
- grid.488387.8Key Laboratory of Medical Electrophysiology, Ministry of Education, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, No. 182, Chunhui Road, Longmatan District, Luzhou, 646000 Sichuan People’s Republic of China
- grid.410578.f0000 0001 1114 4286Central Nervous System Drug Key Laboratory of Sichuan Province, School of Pharmacy of Southwest Medical University, Luzhou, 646000 Sichuan People’s Republic of China
- grid.488387.8Luzhou Key Laboratory of Traditional Chinese Medicine for Chronic Diseases Jointly Built by Sichuan and Chongqing, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, 646000 Sichuan People’s Republic of China
| | - Xiaomei Zhang
- grid.469520.c0000 0004 1757 8917Luzhou Key Laboratory of Traditional Chinese Medicine for Chronic Diseases Jointly Built by Sichuan and Chongqing, Institute of Medicinal Chemistry of Chinese Medicine, Chongqing Academy of Chinese Materia Medica, Chongqing, 400065 People’s Republic of China
| | - Peng Shi
- grid.410578.f0000 0001 1114 4286Key Laboratory of Medical Electrophysiology, Ministry of Education, School of Pharmacy of Southwest Medical University, Luzhou, 646000 People’s Republic of China
- grid.488387.8Key Laboratory of Medical Electrophysiology, Ministry of Education, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, No. 182, Chunhui Road, Longmatan District, Luzhou, 646000 Sichuan People’s Republic of China
- grid.410578.f0000 0001 1114 4286Central Nervous System Drug Key Laboratory of Sichuan Province, School of Pharmacy of Southwest Medical University, Luzhou, 646000 Sichuan People’s Republic of China
- grid.488387.8Luzhou Key Laboratory of Traditional Chinese Medicine for Chronic Diseases Jointly Built by Sichuan and Chongqing, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, 646000 Sichuan People’s Republic of China
| | - Jiyuan Yuan
- grid.488387.8Clinical Trial Center, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, 646000 Sichuan People’s Republic of China
| | - Qiang Jia
- grid.488387.8Ethics Committee Office, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, 646000 Sichuan China
| | - Chao Pi
- grid.410578.f0000 0001 1114 4286Key Laboratory of Medical Electrophysiology, Ministry of Education, School of Pharmacy of Southwest Medical University, Luzhou, 646000 People’s Republic of China
| | - Tao Chen
- grid.410578.f0000 0001 1114 4286Key Laboratory of Medical Electrophysiology, Ministry of Education, School of Pharmacy of Southwest Medical University, Luzhou, 646000 People’s Republic of China
- grid.488387.8Key Laboratory of Medical Electrophysiology, Ministry of Education, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, No. 182, Chunhui Road, Longmatan District, Luzhou, 646000 Sichuan People’s Republic of China
- grid.410578.f0000 0001 1114 4286Central Nervous System Drug Key Laboratory of Sichuan Province, School of Pharmacy of Southwest Medical University, Luzhou, 646000 Sichuan People’s Republic of China
- grid.488387.8Luzhou Key Laboratory of Traditional Chinese Medicine for Chronic Diseases Jointly Built by Sichuan and Chongqing, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, 646000 Sichuan People’s Republic of China
| | - Linjin Xiong
- grid.410578.f0000 0001 1114 4286Key Laboratory of Medical Electrophysiology, Ministry of Education, School of Pharmacy of Southwest Medical University, Luzhou, 646000 People’s Republic of China
- grid.488387.8Key Laboratory of Medical Electrophysiology, Ministry of Education, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, No. 182, Chunhui Road, Longmatan District, Luzhou, 646000 Sichuan People’s Republic of China
- grid.410578.f0000 0001 1114 4286Central Nervous System Drug Key Laboratory of Sichuan Province, School of Pharmacy of Southwest Medical University, Luzhou, 646000 Sichuan People’s Republic of China
- grid.488387.8Luzhou Key Laboratory of Traditional Chinese Medicine for Chronic Diseases Jointly Built by Sichuan and Chongqing, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, 646000 Sichuan People’s Republic of China
| | - Jinglin Chen
- grid.410578.f0000 0001 1114 4286Key Laboratory of Medical Electrophysiology, Ministry of Education, School of Pharmacy of Southwest Medical University, Luzhou, 646000 People’s Republic of China
- grid.488387.8Key Laboratory of Medical Electrophysiology, Ministry of Education, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, No. 182, Chunhui Road, Longmatan District, Luzhou, 646000 Sichuan People’s Republic of China
- grid.410578.f0000 0001 1114 4286Central Nervous System Drug Key Laboratory of Sichuan Province, School of Pharmacy of Southwest Medical University, Luzhou, 646000 Sichuan People’s Republic of China
- grid.488387.8Luzhou Key Laboratory of Traditional Chinese Medicine for Chronic Diseases Jointly Built by Sichuan and Chongqing, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, 646000 Sichuan People’s Republic of China
| | - Jia Tang
- grid.410578.f0000 0001 1114 4286Key Laboratory of Medical Electrophysiology, Ministry of Education, School of Pharmacy of Southwest Medical University, Luzhou, 646000 People’s Republic of China
- grid.488387.8Key Laboratory of Medical Electrophysiology, Ministry of Education, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, No. 182, Chunhui Road, Longmatan District, Luzhou, 646000 Sichuan People’s Republic of China
- grid.410578.f0000 0001 1114 4286Central Nervous System Drug Key Laboratory of Sichuan Province, School of Pharmacy of Southwest Medical University, Luzhou, 646000 Sichuan People’s Republic of China
- grid.488387.8Luzhou Key Laboratory of Traditional Chinese Medicine for Chronic Diseases Jointly Built by Sichuan and Chongqing, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, 646000 Sichuan People’s Republic of China
| | - Ruxu Yue
- grid.410578.f0000 0001 1114 4286Key Laboratory of Medical Electrophysiology, Ministry of Education, School of Pharmacy of Southwest Medical University, Luzhou, 646000 People’s Republic of China
- grid.488387.8Key Laboratory of Medical Electrophysiology, Ministry of Education, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, No. 182, Chunhui Road, Longmatan District, Luzhou, 646000 Sichuan People’s Republic of China
- grid.410578.f0000 0001 1114 4286Central Nervous System Drug Key Laboratory of Sichuan Province, School of Pharmacy of Southwest Medical University, Luzhou, 646000 Sichuan People’s Republic of China
- grid.488387.8Luzhou Key Laboratory of Traditional Chinese Medicine for Chronic Diseases Jointly Built by Sichuan and Chongqing, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, 646000 Sichuan People’s Republic of China
| | - Zerong Liu
- Central Nervous System Drug Key Laboratory of Sichuan Province, Sichuan Credit Pharmaceutical CO., Ltd., Luzhou, 646000 Sichuan China
- grid.190737.b0000 0001 0154 0904Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400030 China
| | - Hongping Shen
- grid.488387.8Clinical Trial Center, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, 646000 Sichuan People’s Republic of China
| | - Ying Zuo
- grid.488387.8Department of Comprehensive Medicine, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, No. 182, Chunhui Road, Longmatan District, Luzhou, 646000 Sichuan China
| | - Yumeng Wei
- grid.410578.f0000 0001 1114 4286Central Nervous System Drug Key Laboratory of Sichuan Province, School of Pharmacy of Southwest Medical University, Luzhou, 646000 Sichuan People’s Republic of China
| | - Ling Zhao
- grid.488387.8Key Laboratory of Medical Electrophysiology, Ministry of Education, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, No. 182, Chunhui Road, Longmatan District, Luzhou, 646000 Sichuan People’s Republic of China
- grid.410578.f0000 0001 1114 4286Central Nervous System Drug Key Laboratory of Sichuan Province, School of Pharmacy of Southwest Medical University, Luzhou, 646000 Sichuan People’s Republic of China
- grid.488387.8Luzhou Key Laboratory of Traditional Chinese Medicine for Chronic Diseases Jointly Built by Sichuan and Chongqing, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, 646000 Sichuan People’s Republic of China
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4
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Gibbs E, Klemm E, Seiferth D, Kumar A, Ilca SL, Biggin PC, Chakrapani S. Conformational transitions and allosteric modulation in a heteromeric glycine receptor. Nat Commun 2023; 14:1363. [PMID: 36914669 PMCID: PMC10011588 DOI: 10.1038/s41467-023-37106-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 03/02/2023] [Indexed: 03/16/2023] Open
Abstract
Glycine Receptors (GlyRs) provide inhibitory neuronal input in the spinal cord and brainstem, which is critical for muscle coordination and sensory perception. Synaptic GlyRs are a heteromeric assembly of α and β subunits. Here we present cryo-EM structures of full-length zebrafish α1βBGlyR in the presence of an antagonist (strychnine), agonist (glycine), or agonist with a positive allosteric modulator (glycine/ivermectin). Each structure shows a distinct pore conformation with varying degrees of asymmetry. Molecular dynamic simulations found the structures were in a closed (strychnine) and desensitized states (glycine and glycine/ivermectin). Ivermectin binds at all five interfaces, but in a distinct binding pose at the β-α interface. Subunit-specific features were sufficient to solve structures without a fiduciary marker and to confirm the 4α:1β stoichiometry recently observed. We also report features of the extracellular and intracellular domains. Together, our results show distinct compositional and conformational properties of α1βGlyR and provide a framework for further study of this physiologically important channel.
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Affiliation(s)
- Eric Gibbs
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, 44106-4970, USA
| | - Emily Klemm
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, 44106-4970, USA
| | - David Seiferth
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Arvind Kumar
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, 44106-4970, USA
| | - Serban L Ilca
- New York Structural Biology Center, New York, NY, 10027, USA
- Simons Electron Microscopy Center, New York, NY, 10027, USA
| | - Philip C Biggin
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Sudha Chakrapani
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, 44106-4970, USA.
- Department of Neuroscience, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106-4970, USA.
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5
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Slobodyanyuk M, Banda-Vázquez JA, Thompson MJ, Dean RA, Baenziger JE, Chica RA, daCosta CJB. Origin of acetylcholine antagonism in ELIC, a bacterial pentameric ligand-gated ion channel. Commun Biol 2022; 5:1264. [PMID: 36400839 PMCID: PMC9674596 DOI: 10.1038/s42003-022-04227-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 11/04/2022] [Indexed: 11/20/2022] Open
Abstract
ELIC is a prokaryotic homopentameric ligand-gated ion channel that is homologous to vertebrate nicotinic acetylcholine receptors. Acetylcholine binds to ELIC but fails to activate it, despite bringing about conformational changes indicative of activation. Instead, acetylcholine competitively inhibits agonist-activated ELIC currents. What makes acetylcholine an agonist in an acetylcholine receptor context, and an antagonist in an ELIC context, is not known. Here we use available structures and statistical coupling analysis to identify residues in the ELIC agonist-binding site that contribute to agonism. Substitution of these ELIC residues for their acetylcholine receptor counterparts does not convert acetylcholine into an ELIC agonist, but in some cases reduces the sensitivity of ELIC to acetylcholine antagonism. Acetylcholine antagonism can be abolished by combining two substitutions that together appear to knock out acetylcholine binding. Thus, making the ELIC agonist-binding site more acetylcholine receptor-like, paradoxically reduces the apparent affinity for acetylcholine, demonstrating that residues important for agonist binding in one context can be deleterious in another. These findings reinforce the notion that although agonism originates from local interactions within the agonist-binding site, it is a global property with cryptic contributions from distant residues. Finally, our results highlight an underappreciated mechanism of antagonism, where agonists with appreciable affinity, but negligible efficacy, present as competitive antagonists. A structural and functional study of the prokaryotic ligand-gated ion channel, ELIC, provides insight into the origin of agonism and antagonism at nicotinic acetylcholine receptors.
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6
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Cerdan AH, Peverini L, Changeux JP, Corringer PJ, Cecchini M. Lateral fenestrations in the extracellular domain of the glycine receptor contribute to the main chloride permeation pathway. SCIENCE ADVANCES 2022; 8:eadc9340. [PMID: 36240268 PMCID: PMC9565810 DOI: 10.1126/sciadv.adc9340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
Glycine receptors (GlyRs) are ligand-gated ion channels mediating signal transduction at chemical synapses. Since the early patch-clamp electrophysiology studies, the details of the ion permeation mechanism have remained elusive. Here, we combine molecular dynamics simulations of a zebrafish GlyR-α1 model devoid of the intracellular domain with mutagenesis and single-channel electrophysiology of the full-length human GlyR-α1. We show that lateral fenestrations between subunits in the extracellular domain provide the main translocation pathway for chloride ions to enter/exit a central water-filled vestibule at the entrance of the transmembrane channel. In addition, we provide evidence that these fenestrations are at the origin of current rectification in known anomalous mutants and design de novo two inward-rectifying channels by introducing mutations within them. These results demonstrate the central role of lateral fenestrations on synaptic neurotransmission.
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Affiliation(s)
- Adrien H. Cerdan
- Institut de Chimie de Strasbourg, UMR7177, CNRS, Université de Strasbourg, F-67083 Strasbourg Cedex, France
- Institut Pasteur, Université Paris Cité, CNRS UMR 3571, Channel-Receptors Unit, Paris, France
| | - Laurie Peverini
- Institut Pasteur, Université Paris Cité, CNRS UMR 3571, Channel-Receptors Unit, Paris, France
| | - Jean-Pierre Changeux
- Institut Pasteur, Université Paris Cité, CNRS UMR 3571, Channel-Receptors Unit, Paris, France
- Kavli Institute for Brain and Mind, University of California, San Diego, La Jolla, CA, USA
- Collège de France, Paris, France
| | - Pierre-Jean Corringer
- Institut Pasteur, Université Paris Cité, CNRS UMR 3571, Channel-Receptors Unit, Paris, France
| | - Marco Cecchini
- Institut de Chimie de Strasbourg, UMR7177, CNRS, Université de Strasbourg, F-67083 Strasbourg Cedex, France
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7
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Ivica J, Zhu H, Lape R, Gouaux E, Sivilotti LG. Aminomethanesulfonic acid illuminates the boundary between full and partial agonists of the pentameric glycine receptor. eLife 2022; 11:79148. [PMID: 35975975 PMCID: PMC9462852 DOI: 10.7554/elife.79148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/16/2022] [Indexed: 11/26/2022] Open
Abstract
To clarify the determinants of agonist efficacy in pentameric ligand-gated ion channels, we examined a new compound, aminomethanesulfonic acid (AMS), a molecule intermediate in structure between glycine and taurine. Despite wide availability, to date there are no reports of AMS action on glycine receptors, perhaps because AMS is unstable at physiological pH. Here, we show that at pH 5, AMS is an efficacious agonist, eliciting in zebrafish α1 glycine receptors a maximum single-channel open probability of 0.85, much greater than that of β-alanine (0.54) or taurine (0.12), and second only to that of glycine itself (0.96). Thermodynamic cycle analysis of the efficacy of these closely related agonists shows supra-additive interaction between changes in the length of the agonist molecule and the size of the anionic moiety. Single particle cryo-electron microscopy structures of AMS-bound glycine receptors show that the AMS-bound agonist pocket is as compact as with glycine, and three-dimensional classification demonstrates that the channel populates the open and the desensitized states, like glycine, but not the closed intermediate state associated with the weaker partial agonists, β-alanine and taurine. Because AMS is on the cusp between full and partial agonists, it provides a new tool to help us understand agonist action in the pentameric superfamily of ligand-gated ion channels.
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Affiliation(s)
- Josip Ivica
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, United Kingdom
| | - Hongtao Zhu
- Vollum Institute, Oregon Health and Science University Hospital, Portland, United States
| | - Remigijus Lape
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, United Kingdom
| | - Eric Gouaux
- Vollum Institute, Oregon Health and Science University Hospital, Portland, United States
| | - Lucia G Sivilotti
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, United Kingdom
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8
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Bondarenko V, Wells MM, Chen Q, Tillman TS, Singewald K, Lawless MJ, Caporoso J, Brandon N, Coleman JA, Saxena S, Lindahl E, Xu Y, Tang P. Structures of highly flexible intracellular domain of human α7 nicotinic acetylcholine receptor. Nat Commun 2022; 13:793. [PMID: 35145092 PMCID: PMC8831596 DOI: 10.1038/s41467-022-28400-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 01/10/2022] [Indexed: 11/24/2022] Open
Abstract
The intracellular domain (ICD) of Cys-loop receptors mediates diverse functions. To date, no structure of a full-length ICD is available due to challenges stemming from its dynamic nature. Here, combining nuclear magnetic resonance (NMR) and electron spin resonance experiments with Rosetta computations, we determine full-length ICD structures of the human α7 nicotinic acetylcholine receptor in a resting state. We show that ~57% of the ICD residues are in highly flexible regions, primarily in a large loop (loop L) with the most mobile segment spanning ~50 Å from the central channel axis. Loop L is anchored onto the MA helix and virtually forms two smaller loops, thereby increasing its stability. Previously known motifs for cytoplasmic binding, regulation, and signaling are found in both the helices and disordered flexible regions, supporting the essential role of the ICD conformational plasticity in orchestrating a broad range of biological processes. The intracellular domain (ICD) of Cys-loop receptors mediates many of their functions, but no complete structure of a Cys-loop receptor ICD is available to date. Here, the authors combine NMR and ESR spectroscopy to determine the full-length ICD structures of the human α7 nicotinic acetylcholine receptor (α7nAChR).
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Affiliation(s)
- Vasyl Bondarenko
- Depatment of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Marta M Wells
- Depatment of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Qiang Chen
- Depatment of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Tommy S Tillman
- Depatment of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Kevin Singewald
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Matthew J Lawless
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Joel Caporoso
- Depatment of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Nicole Brandon
- Depatment of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Jonathan A Coleman
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Erik Lindahl
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden.,Department of Applied Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology, Solna, Sweden
| | - Yan Xu
- Depatment of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, PA, 15260, USA.,Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA, 15260, USA.,Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15260, USA.,Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Pei Tang
- Depatment of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, PA, 15260, USA. .,Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15260, USA. .,Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
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9
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Ivica J, Lape R, Sivilotti LG. Acidic pH reduces agonist efficacy and responses to synaptic-like glycine applications in zebrafish α1 and rat α1β recombinant glycine receptors. J Physiol 2022; 600:333-347. [PMID: 34802146 PMCID: PMC8836455 DOI: 10.1113/jp282171] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 11/16/2021] [Indexed: 11/12/2022] Open
Abstract
Many pentameric ligand-gated ion channels are modulated by extracellular pH. Glycine receptors (GlyRs) share this property, but it is not well understood how they are affected by pH changes. Whole cell experiments on HEK293 cells expressing zebrafish homomeric α1 GlyR confirmed previous reports that acidic pH (6.4) reduces GlyR sensitivity to glycine, whereas alkaline pH (8.4) has small or negligible effects. In addition to that, at pH 6.4 we observed a reduction in the maximum responses to the partial agonists β-alanine and taurine relative to the full agonist glycine. In cell-attached single-channel recording, low pH reduced agonist efficacy, as the maximum open probability decreased from 0.97, 0.91 and 0.66 to 0.93, 0.57 and 0.34 for glycine, β-alanine and taurine, respectively, reflecting a threefold decrease in efficacy equilibrium constants for all three agonists. We also tested the effect of pH 6.4 in conditions that replicate those at the native synapse, recording outside-out currents elicited by fast application of millisecond pulses of agonists on α1 and α1β GlyR, at a range of intracellular chloride concentrations. Acidic pH reduced the area under the curve of the currents, by reducing peak amplitude, slowing activation and speeding deactivation. Our results show that acidification of the extracellular pH by one unit, as may occur in pathological conditions such as ischaemia, impairs GlyR gating and is likely to reduce the effectiveness of glycinergic synaptic inhibition. KEY POINTS: Extracellular pH in the central nervous system (CNS) is known to shift towards acidic values during pathophysiological conditions such as ischaemia and seizures. Acidic extracellular pH is known to affect GABAergic inhibitory synapses, but its effect on signals mediated by glycine receptors (GlyR) is not well characterised. Moderate acidic conditions (pH 6.4) reduce the maximum single channel open probability of recombinant homomeric GlyRs produced by the neurotransmitter glycine or other agonists, such as β-alanine and taurine. When glycine was applied with a piezoelectric stepper to outside out patches, to simulate its fast rise and short duration at the synapse, responses became shorter and smaller at pH 6.4. The effect was also observed with physiologically low intracellular chloride and in mammalian heteromeric GlyRs. This suggests that acidic pH is likely to reduce the strength of inhibitory signalling at glycinergic synapses.
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Affiliation(s)
- Josip Ivica
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK
| | - Remigijus Lape
- Neurobiology Department, MRC Laboratory of Molecular Biology Cambridge Biomedical Campus Francis Crick Avenue, Cambridge, UK
| | - Lucia G Sivilotti
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK
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10
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Muñoz B, Mariqueo T, Murath P, Peters C, Yevenes GE, Moraga-Cid G, Peoples RW, Aguayo LG. Modulatory Actions of the Glycine Receptor β Subunit on the Positive Allosteric Modulation of Ethanol in α2 Containing Receptors. Front Mol Neurosci 2021; 14:763868. [PMID: 34867189 PMCID: PMC8637530 DOI: 10.3389/fnmol.2021.763868] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/18/2021] [Indexed: 01/23/2023] Open
Abstract
Alpha1-containing glycine receptors (GlyRs) are major mediators of synaptic inhibition in the spinal cord and brain stem. Recent studies reported the presence of α2-containing GlyRs in other brain regions, such as nucleus accumbens and cerebral cortex. GlyR activation decreases neuronal excitability associated with sensorial information, motor control, and respiratory functions; all of which are significantly altered during ethanol intoxication. We evaluated the role of β GlyR subunits and of two basic amino acid residues, K389 and R390, located in the large intracellular loop (IL) of the α2 GlyR subunit, which are important for binding and functional modulation by Gβγ, the dimer of the trimeric G protein conformation, using HEK-293 transfected cells combined with patch clamp electrophysiology. We demonstrate a new modulatory role of the β subunit on ethanol sensitivity of α2 subunits. Specifically, we found a differential allosteric modulation in homomeric α2 GlyRs compared with the α2β heteromeric conformation. Indeed, while α2 was insensitive, α2β GlyRs were substantially potentiated by ethanol, GTP-γ-S, propofol, Zn2+ and trichloroethanol. Furthermore, a Gβγ scavenger (ct-GRK2) selectively attenuated the effects of ethanol on recombinant α2β GlyRs. Mutations in an α2 GlyR co-expressed with the β subunit (α2AAβ) specifically blocked ethanol sensitivity, but not propofol potentiation. These results show a selective mechanism for low ethanol concentration effects on homomeric and heteromeric conformations of α2 GlyRs and provide a new mechanism for ethanol pharmacology, which is relevant to upper brain regions where α2 GlyRs are abundantly expressed.
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Affiliation(s)
- Braulio Muñoz
- Laboratory of Neurophysiology, Department of Physiology, Universidad de Concepción, Concepción, Chile
| | - Trinidad Mariqueo
- Laboratory of Neurophysiology, Department of Physiology, Universidad de Concepción, Concepción, Chile
| | - Pablo Murath
- Laboratory of Neurophysiology, Department of Physiology, Universidad de Concepción, Concepción, Chile
| | - Christian Peters
- Laboratory of Neurophysiology, Department of Physiology, Universidad de Concepción, Concepción, Chile
| | - Gonzalo E Yevenes
- Laboratory of Neuropharmacology, Department of Physiology, Universidad de Concepción, Concepción, Chile
| | | | - Robert W Peoples
- Department of Biomedical Sciences, Marquette University, Milwaukee, WI, United States
| | - Luis G Aguayo
- Laboratory of Neurophysiology, Department of Physiology, Universidad de Concepción, Concepción, Chile
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11
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Bergh C, Heusser SA, Howard R, Lindahl E. Markov state models of proton- and pore-dependent activation in a pentameric ligand-gated ion channel. eLife 2021; 10:68369. [PMID: 34652272 PMCID: PMC8635979 DOI: 10.7554/elife.68369] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 10/14/2021] [Indexed: 01/03/2023] Open
Abstract
Ligand-gated ion channels conduct currents in response to chemical stimuli, mediating electrochemical signaling in neurons and other excitable cells. For many channels, the details of gating remain unclear, partly due to limited structural data and simulation timescales. Here, we used enhanced sampling to simulate the pH-gated channel GLIC, and construct Markov state models (MSMs) of gating. Consistent with new functional recordings, we report in oocytes, our analysis revealed differential effects of protonation and mutation on free-energy wells. Clustering of closed- versus open-like states enabled estimation of open probabilities and transition rates, while higher-order clustering affirmed conformational trends in gating. Furthermore, our models uncovered state- and protonation-dependent symmetrization. This demonstrates the applicability of MSMs to map energetic and conformational transitions between ion-channel functional states, and how they reproduce shifts upon activation or mutation, with implications for modeling neuronal function and developing state-selective drugs.
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Affiliation(s)
- Cathrine Bergh
- Science for Life Laboratory and Swedish e-Science Research Center, Department of Applied Physics, KTH Royal Institute of Technology, Solna, Sweden
| | - Stephanie A Heusser
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Rebecca Howard
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Erik Lindahl
- Science for Life Laboratory and Swedish e-Science Research Center, Department of Applied Physics, KTH Royal Institute of Technology, Solna, Sweden.,Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
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12
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Cecchini M, Changeux JP. Nicotinic receptors: From protein allostery to computational neuropharmacology. Mol Aspects Med 2021; 84:101044. [PMID: 34656371 DOI: 10.1016/j.mam.2021.101044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/28/2021] [Accepted: 09/30/2021] [Indexed: 11/15/2022]
Abstract
We propose an extension and further development of the Monod-Wyman-Changeux model for allosteric transitions of regulatory proteins to brain communications and specifically to neurotransmitters receptors, with the nicotinic acetylcholine receptor (nAChR) as a model of ligand-gated ion channels. The present development offers an expression of the change of the gating isomerization constant caused by pharmacological ligand binding in terms of its value in the absence of ligands and several "modulation factors", which vary with orthosteric ligand binding (agonists/antagonists), allosteric ligand binding (positive allosteric modulators/negative allosteric modulators) and receptor desensitization. The new - explicit - formulation of such "modulation factors", provides expressions for the pharmacological attributes of potency, efficacy, and selectivity for the modulatory ligands (including endogenous neurotransmitters) in terms of their binding affinity for the active, resting, and desensitized states of the receptor. The current formulation provides ways to design neuroactive compounds with a controlled pharmacological profile, opening the field of computational neuro-pharmacology.
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Affiliation(s)
- Marco Cecchini
- Institut de Chimie de Strasbourg, UMR7177, CNRS, Université de Strasbourg, F-67083, Strasbourg Cedex, France.
| | - Jean-Pierre Changeux
- Kavli Institute for Brain & Mind University of California, San Diego La Jolla, CA, 92093, USA; Institut Pasteur, URA 2182, CNRS, F-75015, France; Collège de France, F-75005 Paris, France.
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13
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Elephants in the Dark: Insights and Incongruities in Pentameric Ligand-gated Ion Channel Models. J Mol Biol 2021; 433:167128. [PMID: 34224751 DOI: 10.1016/j.jmb.2021.167128] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 06/25/2021] [Accepted: 06/25/2021] [Indexed: 02/06/2023]
Abstract
The superfamily of pentameric ligand-gated ion channels (pLGICs) comprises key players in electrochemical signal transduction across evolution, including historic model systems for receptor allostery and targets for drug development. Accordingly, structural studies of these channels have steadily increased, and now approach 250 depositions in the protein data bank. This review contextualizes currently available structures in the pLGIC family, focusing on morphology, ligand binding, and gating in three model subfamilies: the prokaryotic channel GLIC, the cation-selective nicotinic acetylcholine receptor, and the anion-selective glycine receptor. Common themes include the challenging process of capturing and annotating channels in distinct functional states; partially conserved gating mechanisms, including remodeling at the extracellular/transmembrane-domain interface; and diversity beyond the protein level, arising from posttranslational modifications, ligands, lipids, and signaling partners. Interpreting pLGIC structures can be compared to describing an elephant in the dark, relying on touch alone to comprehend the many parts of a monumental beast: each structure represents a snapshot in time under specific experimental conditions, which must be integrated with further structure, function, and simulations data to build a comprehensive model, and understand how one channel may fundamentally differ from another.
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14
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Sheipouri D, Gallagher CI, Shimmon S, Rawling T, Vandenberg RJ. A System for Assessing Dual Action Modulators of Glycine Transporters and Glycine Receptors. Biomolecules 2020; 10:biom10121618. [PMID: 33266066 PMCID: PMC7760315 DOI: 10.3390/biom10121618] [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: 10/23/2020] [Revised: 11/23/2020] [Accepted: 11/25/2020] [Indexed: 12/13/2022] Open
Abstract
Reduced inhibitory glycinergic neurotransmission is implicated in a number of neurological conditions such as neuropathic pain, schizophrenia, epilepsy and hyperekplexia. Restoring glycinergic signalling may be an effective method of treating these pathologies. Glycine transporters (GlyTs) control synaptic and extra-synaptic glycine concentrations and slowing the reuptake of glycine using specific GlyT inhibitors will increase glycine extracellular concentrations and increase glycine receptor (GlyR) activation. Glycinergic neurotransmission can also be improved through positive allosteric modulation (PAM) of GlyRs. Despite efforts to manipulate this synapse, no therapeutics currently target it. We propose that dual action modulators of both GlyTs and GlyRs may show greater therapeutic potential than those targeting individual proteins. To show this, we have characterized a co-expression system in Xenopus laevis oocytes consisting of GlyT1 or GlyT2 co-expressed with GlyRα1. We use two electrode voltage clamp recording techniques to measure the impact of GlyTs on GlyRs and the effects of modulators of these proteins. We show that increases in GlyT density in close proximity to GlyRs diminish receptor currents. Reductions in GlyR mediated currents are not observed when non-transportable GlyR agonists are applied or when Na+ is not available. GlyTs reduce glycine concentrations across different concentration ranges, corresponding with their ion-coupling stoichiometry, and full receptor currents can be restored when GlyTs are blocked with selective inhibitors. We show that partial inhibition of GlyT2 and modest GlyRα1 potentiation using a dual action compound, is as useful in restoring GlyR currents as a full and potent single target GlyT2 inhibitor or single target GlyRα1 PAM. The co-expression system developed in this study will provide a robust means for assessing the likely impact of GlyR PAMs and GlyT inhibitors on glycine neurotransmission.
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Affiliation(s)
- Diba Sheipouri
- School of Medical Sciences, University of Sydney, Sydney, NSW 2006, Australia; (D.S.); (C.I.G.)
| | - Casey I. Gallagher
- School of Medical Sciences, University of Sydney, Sydney, NSW 2006, Australia; (D.S.); (C.I.G.)
| | - Susan Shimmon
- School of Mathematical and Physical Sciences, University of Technology Sydney, Sydney, NSW 2007, Australia; (S.S.); (T.R.)
| | - Tristan Rawling
- School of Mathematical and Physical Sciences, University of Technology Sydney, Sydney, NSW 2007, Australia; (S.S.); (T.R.)
| | - Robert J. Vandenberg
- School of Medical Sciences, University of Sydney, Sydney, NSW 2006, Australia; (D.S.); (C.I.G.)
- Correspondence:
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15
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Bernhard M, Laube B. Thermophoretic analysis of ligand-specific conformational states of the inhibitory glycine receptor embedded in copolymer nanodiscs. Sci Rep 2020; 10:16569. [PMID: 33024136 PMCID: PMC7538598 DOI: 10.1038/s41598-020-73157-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/10/2020] [Indexed: 11/28/2022] Open
Abstract
The glycine receptor (GlyR), a member of the pentameric ligand-gated ion channel family (pLGIC), displays remarkable variations in the affinity and efficacy of the full agonist glycine and the partial agonist taurine depending on the cell system used. Despite detailed insights in the GlyR three-dimensional structure and activation mechanism, little is known about conformational rearrangements induced by these agonists. Here, we characterized the conformational states of the α1 GlyR upon binding of glycine and taurine by microscale thermophoresis expressed in HEK293 cells and Xenopus oocytes after solubilization in amphipathic styrene-maleic acid copolymer nanodiscs. Our results show that glycine and taurine induce different conformational transitions of the GlyR upon ligand binding. In contrast, the variability of agonist affinity is not mediated by an altered conformational change. Thus, our data shed light on specific agonist induced conformational features and mechanisms of pLGIC upon ligand binding determining receptor activation in native environments.
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Affiliation(s)
- Max Bernhard
- Department of Biology, Neurophysiology and Neurosensory Systems, Technical University of Darmstadt, Schnittspahnstrasse 3, 64287, Darmstadt, Germany
| | - Bodo Laube
- Department of Biology, Neurophysiology and Neurosensory Systems, Technical University of Darmstadt, Schnittspahnstrasse 3, 64287, Darmstadt, Germany.
- Centre for Synthetic Biology, Technical University of Darmstadt, 64283, Darmstadt, Germany.
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16
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Mechanisms of activation and desensitization of full-length glycine receptor in lipid nanodiscs. Nat Commun 2020; 11:3752. [PMID: 32719334 PMCID: PMC7385131 DOI: 10.1038/s41467-020-17364-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 06/25/2020] [Indexed: 12/31/2022] Open
Abstract
Glycinergic synapses play a central role in motor control and pain processing in the central nervous system. Glycine receptors (GlyRs) are key players in mediating fast inhibitory neurotransmission at these synapses. While previous high-resolution structures have provided insights into the molecular architecture of GlyR, several mechanistic questions pertaining to channel function are still unanswered. Here, we present Cryo-EM structures of the full-length GlyR protein complex reconstituted into lipid nanodiscs that are captured in the unliganded (closed), glycine-bound (open and desensitized), and allosteric modulator-bound conformations. A comparison of these states reveals global conformational changes underlying GlyR channel gating and modulation. The functional state assignments were validated by molecular dynamics simulations, and the observed permeation events are in agreement with the anion selectivity and conductance of GlyR. These studies provide the structural basis for gating, ion selectivity, and single-channel conductance properties of GlyR in a lipid environment. Glycinergic synapses play a central role in motor control and pain processing in the central nervous system. Here, authors present cryo-EM structures of the full-length glycine receptors (GlyRs) reconstituted into lipid nanodiscs in the unliganded, glycine-bound and allosteric modulator-bound conformations and reveal global conformational changes underlying GlyR channel gating and modulation.
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