1
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Greger IH. Regulating calcium flux through AMPA glutamate receptors. Cell Calcium 2024; 123:102934. [PMID: 39096546 DOI: 10.1016/j.ceca.2024.102934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2024] [Accepted: 07/29/2024] [Indexed: 08/05/2024]
Affiliation(s)
- Ingo H Greger
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK.
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2
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Ives CM, Şahin AT, Thomson NJ, Zachariae U. A hydrophobic funnel governs monovalent cation selectivity in the ion channel TRPM5. Biophys J 2024:S0006-3495(24)00494-6. [PMID: 39086136 DOI: 10.1016/j.bpj.2024.07.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 06/18/2024] [Accepted: 07/25/2024] [Indexed: 08/02/2024] Open
Abstract
A key capability of ion channels is the facilitation of selective permeation of certain ionic species across cellular membranes at high rates. Due to their physiological significance, ion channels are of great pharmaceutical interest as drug targets. The polymodal signal-detecting transient receptor potential (TRP) superfamily of ion channels forms a particularly promising group of drug targets. While most members of this family permeate a broad range of cations including Ca2+, TRPM4 and TRPM5 are unique due to their strong monovalent selectivity and impermeability for divalent cations. Here, we investigated the mechanistic basis for their unique monovalent selectivity by in silico electrophysiology simulations of TRPM5. Our simulations reveal an unusual mechanism of cation selectivity, which is underpinned by the function of the central channel cavity alongside the selectivity filter. Our results suggest that a subtle hydrophobic barrier at the cavity entrance ("hydrophobic funnel") enables monovalent but not divalent cations to pass and occupy the cavity at physiologically relevant membrane voltages. Monovalent cations then permeate efficiently by a cooperative, distant knock-on mechanism between two binding regions in the extracellular pore vestibule and the central cavity. By contrast, divalent cations do not enter or interact favorably with the channel cavity due to its raised hydrophobicity. Hydrophilic mutations in the transition zone between the selectivity filter and the central channel cavity abolish the barrier for divalent cations, enabling both monovalent and divalent cations to traverse TRPM5.
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Affiliation(s)
- Callum M Ives
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Alp Tegin Şahin
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, United Kingdom; School of Medicine, University of St Andrews, St Andrews, United Kingdom
| | - Neil J Thomson
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Ulrich Zachariae
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, United Kingdom; Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom.
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3
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Gangwar SP, Yelshanskaya MV, Nadezhdin KD, Yen LY, Newton TP, Aktolun M, Kurnikova MG, Sobolevsky AI. Kainate receptor channel opening and gating mechanism. Nature 2024; 630:762-768. [PMID: 38778115 PMCID: PMC11186766 DOI: 10.1038/s41586-024-07475-0] [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: 02/05/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024]
Abstract
Kainate receptors, a subclass of ionotropic glutamate receptors, are tetrameric ligand-gated ion channels that mediate excitatory neurotransmission1-4. Kainate receptors modulate neuronal circuits and synaptic plasticity during the development and function of the central nervous system and are implicated in various neurological and psychiatric diseases, including epilepsy, depression, schizophrenia, anxiety and autism5-11. Although structures of kainate receptor domains and subunit assemblies are available12-18, the mechanism of kainate receptor gating remains poorly understood. Here we present cryo-electron microscopy structures of the kainate receptor GluK2 in the presence of the agonist glutamate and the positive allosteric modulators lectin concanavalin A and BPAM344. Concanavalin A and BPAM344 inhibit kainate receptor desensitization and prolong activation by acting as a spacer between the amino-terminal and ligand-binding domains and a stabilizer of the ligand-binding domain dimer interface, respectively. Channel opening involves the kinking of all four pore-forming M3 helices. Our structures reveal the molecular basis of kainate receptor gating, which could guide the development of drugs for treatment of neurological disorders.
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Affiliation(s)
- Shanti Pal Gangwar
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Maria V Yelshanskaya
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Kirill D Nadezhdin
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Laura Y Yen
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Cellular and Molecular Physiology and Biophysics Graduate Program, Columbia University Irving Medical Center, New York, NY, USA
| | - Thomas P Newton
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Integrated Program in Cellular, Molecular and Biomedical Studies, Columbia University Irving Medical Center, New York, NY, USA
| | - Muhammed Aktolun
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Maria G Kurnikova
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Alexander I Sobolevsky
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
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4
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Türkaydin B, Schewe M, Riel EB, Schulz F, Biedermann J, Baukrowitz T, Sun H. Atomistic mechanism of coupling between cytosolic sensor domain and selectivity filter in TREK K2P channels. Nat Commun 2024; 15:4628. [PMID: 38821927 PMCID: PMC11143257 DOI: 10.1038/s41467-024-48823-y] [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: 10/13/2023] [Accepted: 05/15/2024] [Indexed: 06/02/2024] Open
Abstract
The two-pore domain potassium (K2P) channels TREK-1 and TREK-2 link neuronal excitability to a variety of stimuli including mechanical force, lipids, temperature and phosphorylation. This regulation involves the C-terminus as a polymodal stimulus sensor and the selectivity filter (SF) as channel gate. Using crystallographic up- and down-state structures of TREK-2 as a template for full atomistic molecular dynamics (MD) simulations, we reveal that the SF in down-state undergoes inactivation via conformational changes, while the up-state structure maintains a stable and conductive SF. This suggests an atomistic mechanism for the low channel activity previously assigned to the down state, but not evident from the crystal structure. Furthermore, experimentally by using (de-)phosphorylation mimics and chemically attaching lipid tethers to the proximal C-terminus (pCt), we confirm the hypothesis that moving the pCt towards the membrane induces the up-state. Based on MD simulations, we propose two gating pathways by which movement of the pCt controls the stability (i.e., conductivity) of the filter gate. Together, these findings provide atomistic insights into the SF gating mechanism and the physiological regulation of TREK channels by phosphorylation.
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Affiliation(s)
- Berke Türkaydin
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
- Insitute of Chemistry, Technical University of Berlin, Berlin, Germany
| | - Marcus Schewe
- Institute of Physiology, Kiel University, Kiel, Germany.
| | - Elena Barbara Riel
- Institute of Physiology, Kiel University, Kiel, Germany
- Department of Anesthesiology, Weill Cornell Medical College, New York, USA
| | | | - Johann Biedermann
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | | | - Han Sun
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany.
- Insitute of Chemistry, Technical University of Berlin, Berlin, Germany.
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5
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Nakagawa T, Wang XT, Miguez-Cabello FJ, Bowie D. The open gate of the AMPA receptor forms a Ca 2+ binding site critical in regulating ion transport. Nat Struct Mol Biol 2024; 31:688-700. [PMID: 38409505 DOI: 10.1038/s41594-024-01228-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 01/18/2024] [Indexed: 02/28/2024]
Abstract
Alpha-amino-3-hydroxyl-5-methyl-4-isoxazole-propionic acid receptors (AMPARs) are cation-selective ion channels that mediate most fast excitatory neurotransmission in the brain. Although their gating mechanism has been studied extensively, understanding how cations traverse the pore has remained elusive. Here we investigated putative ion and water densities in the open pore of Ca2+-permeable AMPARs (rat GRIA2 flip-Q isoform) at 2.3-2.6 Å resolution. We show that the ion permeation pathway attains an extracellular Ca2+ binding site (site-G) when the channel gate moves into the open configuration. Site-G is highly selective for Ca2+ over Na+, favoring the movement of Ca2+ into the selectivity filter of the pore. Seizure-related N619K mutation, adjacent to site-G, promotes channel opening but attenuates Ca2+ binding and thus diminishes Ca2+ permeability. Our work identifies the importance of site-G, which coordinates with the Q/R site of the selectivity filter to ensure the preferential transport of Ca2+ through the channel pore.
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Affiliation(s)
- Terunaga Nakagawa
- Department of Molecular Physiology and Biophysics, Vanderbilt University, School of Medicine, Nashville, TN, USA.
- Center for Structural Biology, Vanderbilt University, School of Medicine, Nashville, TN, USA.
- Vanderbilt Brain Institute, Vanderbilt University, School of Medicine, Nashville, TN, USA.
| | - Xin-Tong Wang
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
- Integrated Program in Neuroscience, McGill University, Montreal, Quebec, Canada
| | | | - Derek Bowie
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
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6
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Asgharpour S, Chi LA, Spehr M, Carloni P, Alfonso-Prieto M. Fluoride Transport and Inhibition Across CLC Transporters. Handb Exp Pharmacol 2024; 283:81-100. [PMID: 36042142 DOI: 10.1007/164_2022_593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The Chloride Channel (CLC) family includes proton-coupled chloride and fluoride transporters. Despite their similar protein architecture, the former exchange two chloride ions for each proton and are inhibited by fluoride, whereas the latter efficiently transport one fluoride in exchange for one proton. The combination of structural, mutagenesis, and functional experiments with molecular simulations has pinpointed several amino acid changes in the permeation pathway that capitalize on the different chemical properties of chloride and fluoride to fine-tune protein function. Here we summarize recent findings on fluoride inhibition and transport in the two prototypical members of the CLC family, the chloride/proton transporter from Escherichia coli (CLC-ec1) and the fluoride/proton transporter from Enterococcus casseliflavus (CLCF-eca).
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Affiliation(s)
- Somayeh Asgharpour
- Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Computational Biomedicine, Forschungszentrum Jülich, Jülich, Germany
- Research Training Group 2416 MultiSenses-MultiScales, Institute for Biology II, RWTH Aachen University, Aachen, Germany
| | - L América Chi
- Laboratory for the Design and Development of New Drugs and Biotechnological Innovation, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, Ciudad de México, Mexico
| | - Marc Spehr
- Research Training Group 2416 MultiSenses-MultiScales, Institute for Biology II, RWTH Aachen University, Aachen, Germany
- Department of Chemosensation, Institute for Biology II, RWTH Aachen University, Aachen, Germany
| | - Paolo Carloni
- Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Computational Biomedicine, Forschungszentrum Jülich, Jülich, Germany.
- Research Training Group 2416 MultiSenses-MultiScales, Institute for Biology II, RWTH Aachen University, Aachen, Germany.
- Department of Physics, RWTH Aachen University, Aachen, Germany.
- JARA Institute Molecular Neuroscience and Neuroimaging (INM-11), Forschungszentrum Jülich, Jülich, Germany.
- JARA-HPC, Forschungszentrum Jülich, Jülich, Germany.
| | - Mercedes Alfonso-Prieto
- Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Computational Biomedicine, Forschungszentrum Jülich, Jülich, Germany.
- Medical Faculty, Cécile and Oskar Vogt Institute for Brain Research, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
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7
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Fricke S, Harnau M, Hetsch F, Liu H, Leonhard J, Eylmann A, Knauff P, Sun H, Semtner M, Meier JC. Cesium activates the neurotransmitter receptor for glycine. Front Mol Neurosci 2023; 16:1018530. [PMID: 37284465 PMCID: PMC10239821 DOI: 10.3389/fnmol.2023.1018530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 05/02/2023] [Indexed: 06/08/2023] Open
Abstract
The monovalent cations sodium and potassium are crucial for the proper functioning of excitable cells, but, in addition, other monovalent alkali metal ions such as cesium and lithium can also affect neuronal physiology. For instance, there have been recent reports of adverse effects resulting from self-administered high concentrations of cesium in disease conditions, prompting the Food and Drug Administration (FDA) to issue an alert concerning cesium chloride. As we recently found that the monovalent cation NH4+ activates glycine receptors (GlyRs), we investigated the effects of alkali metal ions on the function of the GlyR, which belongs to one of the most widely distributed neurotransmitter receptors in the peripheral and central nervous systems. Whole-cell voltage clamp electrophysiology was performed with HEK293T cells transiently expressing different splice and RNA-edited variants of GlyR α2 and α3 homopentameric channels. By examining the influence of various milli- and sub-millimolar concentrations of lithium, sodium, potassium, and cesium on these GlyRs in comparison to its natural ligand glycine (0.1 mM), we could show that cesium activates GlyRs in a concentration- and post-transcriptional-dependent way. Additionally, we conducted atomistic molecular dynamic simulations on GlyR α3 embedded in a membrane bilayer with potassium and cesium, respectively. The simulations revealed slightly different GlyR-ion binding profiles for potassium and cesium, identifying interactions near the glycine binding pocket (potassium and cesium) and close to the RNA-edited site (cesium) in the extracellular GlyR domain. Together, these findings show that cesium acts as an agonist of GlyRs.
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Affiliation(s)
- Steffen Fricke
- Division Cell Physiology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
| | - Magnus Harnau
- Division Cell Physiology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
| | - Florian Hetsch
- Institute of Pathophysiology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Haoran Liu
- Structural Chemistry and Computational Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
- Institute of Chemistry, Technical University of Berlin, Berlin, Germany
| | - Julia Leonhard
- Division Cell Physiology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
| | - Anna Eylmann
- Division Cell Physiology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
| | - Pina Knauff
- Division Cell Physiology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
| | - Han Sun
- Structural Chemistry and Computational Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
- Institute of Chemistry, Technical University of Berlin, Berlin, Germany
| | - Marcus Semtner
- Psychoneuroimmunology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Jochen C. Meier
- Division Cell Physiology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
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8
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Nadezhdin KD, Correia L, Narangoda C, Patel DS, Neuberger A, Gudermann T, Kurnikova MG, Chubanov V, Sobolevsky AI. Structural mechanisms of TRPM7 activation and inhibition. Nat Commun 2023; 14:2639. [PMID: 37156763 PMCID: PMC10167348 DOI: 10.1038/s41467-023-38362-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/27/2023] [Indexed: 05/10/2023] Open
Abstract
The transient receptor potential channel TRPM7 is a master regulator of the organismal balance of divalent cations that plays an essential role in embryonic development, immune responses, cell mobility, proliferation, and differentiation. TRPM7 is implicated in neuronal and cardiovascular disorders, tumor progression and has emerged as a new drug target. Here we use cryo-EM, functional analysis, and molecular dynamics simulations to uncover two distinct structural mechanisms of TRPM7 activation by a gain-of-function mutation and by the agonist naltriben, which show different conformational dynamics and domain involvement. We identify a binding site for highly potent and selective inhibitors and show that they act by stabilizing the TRPM7 closed state. The discovered structural mechanisms provide foundations for understanding the molecular basis of TRPM7 channelopathies and drug development.
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Affiliation(s)
- Kirill D Nadezhdin
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Leonor Correia
- Walther-Straub Institute of Pharmacology and Toxicology, LMU Munich, Munich, Germany
| | - Chamali Narangoda
- Chemistry Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Dhilon S Patel
- Chemistry Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Arthur Neuberger
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Thomas Gudermann
- Walther-Straub Institute of Pharmacology and Toxicology, LMU Munich, Munich, Germany
- Comprehensive Pneumology Center, German Center for Lung Research (DZL), Munich, Germany
| | - Maria G Kurnikova
- Chemistry Department, Carnegie Mellon University, Pittsburgh, PA, USA.
| | - Vladimir Chubanov
- Walther-Straub Institute of Pharmacology and Toxicology, LMU Munich, Munich, Germany.
| | - Alexander I Sobolevsky
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
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9
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Minniberger S, Abdolvand S, Braunbeck S, Sun H, Plested AJR. Asymmetry and Ion Selectivity Properties of Bacterial Channel NaK Mutants Derived from Ionotropic Glutamate Receptors. J Mol Biol 2023; 435:167970. [PMID: 36682679 DOI: 10.1016/j.jmb.2023.167970] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/17/2022] [Accepted: 01/12/2023] [Indexed: 01/22/2023]
Abstract
Ionotropic glutamate receptors are ligand-gated cation channels that play essential roles in the excitatory synaptic transmission throughout the central nervous system. A number of open-pore structures of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic-acid (AMPA)-type glutamate receptors became available recently by cryo-electron microscopy (cryo-EM). These structures provide valuable insights into the conformation of the selectivity filter (SF), the part of the ion channel that determines the ion selectivity. Nonetheless, due to the moderate resolution of the cryo-EM structures, detailed information such as ion occupancy of monovalent and divalent cations as well as positioning of the side-chains in the SF is still missing. Here, in an attempt to obtain high-resolution information about glutamate receptor SFs, we incorporated partial SF sequences of the AMPA and kainate receptors into the bacterial tetrameric cation channel NaK, which served as a structural scaffold. We determined a series of X-ray structures of NaK-CDI, NaK-SDI and NaK-SELM mutants at 1.42-2.10 Å resolution, showing distinct ion occupation of different monovalent cations. Molecular dynamics (MD) simulations of NaK-CDI indicated the channel to be conductive to monovalent cations, which agrees well with our electrophysiology recordings. Moreover, previously unobserved structural asymmetry of the SF was revealed by the X-ray structures and MD simulations, implying its importance in ion non-selectivity of tetrameric cation channels.
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Affiliation(s)
- Sonja Minniberger
- Institute of Biology, Cellular Biophysics, Humboldt Universität zu Berlin, 10115 Berlin, Germany; NeuroCure, Charité Universitätsmedizin, 10117 Berlin, Germany; Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Saeid Abdolvand
- Institute of Biology, Cellular Biophysics, Humboldt Universität zu Berlin, 10115 Berlin, Germany; NeuroCure, Charité Universitätsmedizin, 10117 Berlin, Germany; Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Sebastian Braunbeck
- Institute of Biology, Cellular Biophysics, Humboldt Universität zu Berlin, 10115 Berlin, Germany; NeuroCure, Charité Universitätsmedizin, 10117 Berlin, Germany; Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Han Sun
- Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Institute of Chemistry, Department of Chemistry, Technische Universität Berlin, 10623 Berlin, Germany.
| | - Andrew J R Plested
- Institute of Biology, Cellular Biophysics, Humboldt Universität zu Berlin, 10115 Berlin, Germany; NeuroCure, Charité Universitätsmedizin, 10117 Berlin, Germany; Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany.
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10
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Schackert F, Biedermann J, Abdolvand S, Minniberger S, Song C, Plested AJR, Carloni P, Sun H. Mechanism of Calcium Permeation in a Glutamate Receptor Ion Channel. J Chem Inf Model 2023; 63:1293-1300. [PMID: 36758214 PMCID: PMC9976283 DOI: 10.1021/acs.jcim.2c01494] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs) are neurotransmitter-activated cation channels ubiquitously expressed in vertebrate brains. The regulation of calcium flux through the channel pore by RNA-editing is linked to synaptic plasticity while excessive calcium influx poses a risk for neurodegeneration. Unfortunately, the molecular mechanisms underlying this key process are mostly unknown. Here, we investigated calcium conduction in calcium-permeable AMPAR using Molecular Dynamics (MD) simulations with recently introduced multisite force-field parameters for Ca2+. Our calculations are consistent with experiment and explain the distinct calcium permeability in different RNA-edited forms of GluA2. For one of the identified metal binding sites, multiscale Quantum Mechanics/Molecular Mechanics (QM/MM) simulations further validated the results from MD and revealed small but reproducible charge transfer between the metal ion and its first solvation shell. In addition, the ion occupancy derived from MD simulations independently reproduced the Ca2+ binding profile in an X-ray structure of an NaK channel mimicking the AMPAR selectivity filter. This integrated study comprising X-ray crystallography, multisite MD, and multiscale QM/MM simulations provides unprecedented insights into Ca2+ permeation mechanisms in AMPARs, and paves the way for studying other biological processes in which Ca2+ plays a pivotal role.
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Affiliation(s)
- Florian
Karl Schackert
- Computational
Biomedicine (IAS-5/INM-9), Forschungszentrum
Jülich GmbH, 52428 Jülich, Germany,Department
of Physics, RWTH Aachen University, 52062 Aachen, Germany
| | - Johann Biedermann
- Institute
of Biology, Cellular Biophysics, Humboldt
Universität zu Berlin, 10115 Berlin, Germany,Leibniz
Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Saeid Abdolvand
- Institute
of Biology, Cellular Biophysics, Humboldt
Universität zu Berlin, 10115 Berlin, Germany,Leibniz
Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Sonja Minniberger
- Institute
of Biology, Cellular Biophysics, Humboldt
Universität zu Berlin, 10115 Berlin, Germany,Leibniz
Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Chen Song
- Center
for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China,Peking-Tsinghua
Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Andrew J. R. Plested
- Institute
of Biology, Cellular Biophysics, Humboldt
Universität zu Berlin, 10115 Berlin, Germany,Leibniz
Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Paolo Carloni
- Computational
Biomedicine (IAS-5/INM-9), Forschungszentrum
Jülich GmbH, 52428 Jülich, Germany,Department
of Physics, RWTH Aachen University, 52062 Aachen, Germany,
| | - Han Sun
- Leibniz
Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany,Institute
of Chemistry, TU Berlin, Straße des 17 Juni 135, 10623 Berlin, Germany,
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11
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Linders LE, Supiot LF, Du W, D’Angelo R, Adan RAH, Riga D, Meye FJ. Studying Synaptic Connectivity and Strength with Optogenetics and Patch-Clamp Electrophysiology. Int J Mol Sci 2022; 23:ijms231911612. [PMID: 36232917 PMCID: PMC9570045 DOI: 10.3390/ijms231911612] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 02/07/2023] Open
Abstract
Over the last two decades the combination of brain slice patch clamp electrophysiology with optogenetic stimulation has proven to be a powerful approach to analyze the architecture of neural circuits and (experience-dependent) synaptic plasticity in such networks. Using this combination of methods, originally termed channelrhodopsin-assisted circuit mapping (CRACM), a multitude of measures of synaptic functioning can be taken. The current review discusses their rationale, current applications in the field, and their associated caveats. Specifically, the review addresses: (1) How to assess the presence of synaptic connections, both in terms of ionotropic versus metabotropic receptor signaling, and in terms of mono- versus polysynaptic connectivity. (2) How to acquire and interpret measures for synaptic strength and function, like AMPAR/NMDAR, AMPAR rectification, paired-pulse ratio (PPR), coefficient of variance and input-specific quantal sizes. We also address how synaptic modulation by G protein-coupled receptors can be studied with pharmacological approaches and advanced technology. (3) Finally, we elaborate on advances on the use of dual color optogenetics in concurrent investigation of multiple synaptic pathways. Overall, with this review we seek to provide practical insights into the methods used to study neural circuits and synapses, by combining optogenetics and patch-clamp electrophysiology.
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12
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Yelshanskaya MV, Patel DS, Kottke CM, Kurnikova MG, Sobolevsky AI. Opening of glutamate receptor channel to subconductance levels. Nature 2022; 605:172-178. [PMID: 35444281 PMCID: PMC9068512 DOI: 10.1038/s41586-022-04637-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 03/14/2022] [Indexed: 12/15/2022]
Abstract
Ionotropic glutamate receptors (iGluRs) are tetrameric ligand-gated ion channels that open their pores in response to binding of the agonist glutamate1-3. An ionic current through a single iGluR channel shows up to four discrete conductance levels (O1-O4)4-6. Higher conductance levels have been associated with an increased number of agonist molecules bound to four individual ligand-binding domains (LBDs)6-10. Here we determine structures of a synaptic complex of AMPA-subtype iGluR and the auxiliary subunit γ2 in non-desensitizing conditions with various occupancy of the LBDs by glutamate. We show that glutamate binds to LBDs of subunits B and D only after it is already bound to at least the same number of LBDs that belong to subunits A and C. Our structures combined with single-channel recordings, molecular dynamics simulations and machine-learning analysis suggest that channel opening requires agonist binding to at least two LBDs. Conversely, agonist binding to all four LBDs does not guarantee maximal channel conductance and favours subconductance states O1 and O2, with O3 and O4 being rare and not captured structurally. The lack of subunit independence and low efficiency coupling of glutamate binding to channel opening underlie the gating of synaptic complexes to submaximal conductance levels, which provide a potential for upregulation of synaptic activity.
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Affiliation(s)
- Maria V Yelshanskaya
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Dhilon S Patel
- Chemistry Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | | | - Maria G Kurnikova
- Chemistry Department, Carnegie Mellon University, Pittsburgh, PA, USA.
| | - Alexander I Sobolevsky
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
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13
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Herguedas B, Kohegyi BK, Dohrke JN, Watson JF, Zhang D, Ho H, Shaikh SA, Lape R, Krieger JM, Greger IH. Mechanisms underlying TARP modulation of the GluA1/2-γ8 AMPA receptor. Nat Commun 2022; 13:734. [PMID: 35136046 PMCID: PMC8826358 DOI: 10.1038/s41467-022-28404-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 01/13/2022] [Indexed: 01/01/2023] Open
Abstract
AMPA-type glutamate receptors (AMPARs) mediate rapid signal transmission at excitatory synapses in the brain. Glutamate binding to the receptor’s ligand-binding domains (LBDs) leads to ion channel activation and desensitization. Gating kinetics shape synaptic transmission and are strongly modulated by transmembrane AMPAR regulatory proteins (TARPs) through currently incompletely resolved mechanisms. Here, electron cryo-microscopy structures of the GluA1/2 TARP-γ8 complex, in both open and desensitized states (at 3.5 Å), reveal state-selective engagement of the LBDs by the large TARP-γ8 loop (‘β1’), elucidating how this TARP stabilizes specific gating states. We further show how TARPs alter channel rectification, by interacting with the pore helix of the selectivity filter. Lastly, we reveal that the Q/R-editing site couples the channel constriction at the filter entrance to the gate, and forms the major cation binding site in the conduction path. Our results provide a mechanistic framework of how TARPs modulate AMPAR gating and conductance. AMPA glutamate receptors, mediate the majority of excitatory signaling in the brain. Here the authors show how the auxiliary subunit TARP-γ8 shapes gating kinetics, ion conductance and rectification properties of the heteromeric GluA1/2 AMPA receptor.
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Affiliation(s)
- Beatriz Herguedas
- Neurobiology Division MRC Laboratory of Molecular Biology, Cambridge, UK.,Institute for Biocomputation and Physics of Complex Systems (BIFI) and Laboratorio de Microscopías Avanzadas (LMA), University of Zaragoza, 50018, Zaragoza, Spain
| | - Bianka K Kohegyi
- Neurobiology Division MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Jan-Niklas Dohrke
- Neurobiology Division MRC Laboratory of Molecular Biology, Cambridge, UK.,Universitätsmedizin Göttingen, Georg-August-Universität, 37075, Göttingen, Germany
| | - Jake F Watson
- Neurobiology Division MRC Laboratory of Molecular Biology, Cambridge, UK.,Institute of Science and Technology (IST) Austria, Am Campus 1, 3400, Klosterneuburg, Austria
| | - Danyang Zhang
- Neurobiology Division MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Hinze Ho
- Neurobiology Division MRC Laboratory of Molecular Biology, Cambridge, UK.,Department of Physiology, Development and Neuroscience, University of Cambridge, Physiological Laboratory, Cambridge, UK
| | - Saher A Shaikh
- Neurobiology Division MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Remigijus Lape
- Neurobiology Division MRC Laboratory of Molecular Biology, Cambridge, UK
| | - James M Krieger
- Neurobiology Division MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Ingo H Greger
- Neurobiology Division MRC Laboratory of Molecular Biology, Cambridge, UK.
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14
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Kumar S, Kumar SS. A Model for Predicting Cation Selectivity and Permeability in AMPA and NMDA Receptors Based on Receptor Subunit Composition. Front Synaptic Neurosci 2021; 13:779759. [PMID: 34912205 PMCID: PMC8667807 DOI: 10.3389/fnsyn.2021.779759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 11/04/2021] [Indexed: 11/13/2022] Open
Abstract
Glutamatergic AMPA (α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) and NMDA (N-methyl-D-aspartate) receptors are implicated in diverse functions ranging from synaptic plasticity to cell death. They are heterotetrameric proteins whose subunits are derived from multiple distinct gene families. The subunit composition of these receptors determines their permeability to monovalent and/or divalent cations, but it is not entirely clear how this selectivity arises in native and recombinantly-expressed receptor populations. By analyzing the sequence of amino acids lining the selectivity filters within the pore forming membrane helices (M2) of these subunits and by correlating subunit stoichiometry of these receptors with their ability to permeate Na+ and/or Ca2+, we propose here a mathematical model for predicting cation selectivity and permeability in these receptors. The model proposed is based on principles of charge attractivity and charge neutralization within the pore forming region of these receptors; it accurately predicts and reconciles experimental data across various platforms including Ca2+ permeability of GluA2-lacking AMPARs and ion selectivity within GluN3-containing di- and tri-heteromeric NMDARs. Additionally, the model provides insights into biophysical mechanisms regulating cation selectivity and permeability of these receptors and the role of various subunits in these processes.
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Affiliation(s)
- Sampath Kumar
- College of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, United States
| | - Sanjay S Kumar
- Department of Biomedical Sciences, College of Medicine and Program in Neuroscience, Florida State University, Tallahassee, FL, United States
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15
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Hellas JA, Andrew RD. Neuronal Swelling: A Non-osmotic Consequence of Spreading Depolarization. Neurocrit Care 2021; 35:112-134. [PMID: 34498208 PMCID: PMC8536653 DOI: 10.1007/s12028-021-01326-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 08/04/2021] [Indexed: 01/22/2023]
Abstract
An acute reduction in plasma osmolality causes rapid uptake of water by astrocytes but not by neurons, whereas both cell types swell as a consequence of lost blood flow (ischemia). Either hypoosmolality or ischemia can displace the brain downwards, potentially causing death. However, these disorders are fundamentally different at the cellular level. Astrocytes osmotically swell or shrink because they express functional water channels (aquaporins), whereas neurons lack functional aquaporins and thus maintain their volume. Yet both neurons and astrocytes immediately swell when blood flow to the brain is compromised (cytotoxic edema) as following stroke onset, sudden cardiac arrest, or traumatic brain injury. In each situation, neuronal swelling is the direct result of spreading depolarization (SD) generated when the ATP-dependent sodium/potassium ATPase (the Na+/K+ pump) is compromised. The simple, and incorrect, textbook explanation for neuronal swelling is that increased Na+ influx passively draws Cl- into the cell, with water following by osmosis via some unknown conduit. We first review the strong evidence that mammalian neurons resist volume change during acute osmotic stress. We then contrast this with their dramatic swelling during ischemia. Counter-intuitively, recent research argues that ischemic swelling of neurons is non-osmotic, involving ion/water cotransporters as well as at least one known amino acid water pump. While incompletely understood, these mechanisms argue against the dogma that neuronal swelling involves water uptake driven by an osmotic gradient with aquaporins as the conduit. Promoting clinical recovery from neuronal cytotoxic edema evoked by spreading depolarizations requires a far better understanding of molecular water pumps and ion/water cotransporters that act to rebalance water shifts during brain ischemia.
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Affiliation(s)
- Julia A Hellas
- Center for Neuroscience Studies, Queen's University, Kingston, ON, K7L 3N6, Canada.
| | - R David Andrew
- Center for Neuroscience Studies, Queen's University, Kingston, ON, K7L 3N6, Canada
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16
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Yu J, Rao P, Clark S, Mitra J, Ha T, Gouaux E. Hippocampal AMPA receptor assemblies and mechanism of allosteric inhibition. Nature 2021; 594:448-453. [PMID: 33981040 PMCID: PMC8270219 DOI: 10.1038/s41586-021-03540-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/12/2021] [Indexed: 01/28/2023]
Abstract
AMPA-selective glutamate receptors mediate the transduction of signals between the neuronal circuits of the hippocampus1. The trafficking, localization, kinetics and pharmacology of AMPA receptors are tuned by an ensemble of auxiliary protein subunits, which are integral membrane proteins that associate with the receptor to yield bona fide receptor signalling complexes2. Thus far, extensive studies of recombinant AMPA receptor-auxiliary subunit complexes using engineered protein constructs have not been able to faithfully elucidate the molecular architecture of hippocampal AMPA receptor complexes. Here we obtain mouse hippocampal, calcium-impermeable AMPA receptor complexes using immunoaffinity purification and use single-molecule fluorescence and cryo-electron microscopy experiments to elucidate three major AMPA receptor-auxiliary subunit complexes. The GluA1-GluA2, GluA1-GluA2-GluA3 and GluA2-GluA3 receptors are the predominant assemblies, with the auxiliary subunits TARP-γ8 and CNIH2-SynDIG4 non-stochastically positioned at the B'/D' and A'/C' positions, respectively. We further demonstrate how the receptor-TARP-γ8 stoichiometry explains the mechanism of and submaximal inhibition by a clinically relevant, brain-region-specific allosteric inhibitor.
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Affiliation(s)
- Jie Yu
- Vollum Institute, Oregon Health & Science University, Portland, OR, USA
| | - Prashant Rao
- Vollum Institute, Oregon Health & Science University, Portland, OR, USA
| | - Sarah Clark
- Vollum Institute, Oregon Health & Science University, Portland, OR, USA
| | - Jaba Mitra
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, USA
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Howard Hughes Medical Institute, Baltimore, MD, USA
| | - Eric Gouaux
- Vollum Institute, Oregon Health & Science University, Portland, OR, USA.
- Howard Hughes Medical Institute, Portland, OR, USA.
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