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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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2
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Yovanno RA, Chou TH, Brantley SJ, Furukawa H, Lau AY. Excitatory and inhibitory D-serine binding to the NMDA receptor. eLife 2022; 11:e77645. [PMID: 36301074 PMCID: PMC9612912 DOI: 10.7554/elife.77645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 09/09/2022] [Indexed: 01/19/2023] Open
Abstract
N-methyl-D-aspartate receptors (NMDARs) uniquely require binding of two different neurotransmitter agonists for synaptic transmission. D-serine and glycine bind to one subunit, GluN1, while glutamate binds to the other, GluN2. These agonists bind to the receptor's bi-lobed ligand-binding domains (LBDs), which close around the agonist during receptor activation. To better understand the unexplored mechanisms by which D-serine contributes to receptor activation, we performed multi-microsecond molecular dynamics simulations of the GluN1/GluN2A LBD dimer with free D-serine and glutamate agonists. Surprisingly, we observed D-serine binding to both GluN1 and GluN2A LBDs, suggesting that D-serine competes with glutamate for binding to GluN2A. This mechanism is confirmed by our electrophysiology experiments, which show that D-serine is indeed inhibitory at high concentrations. Although free energy calculations indicate that D-serine stabilizes the closed GluN2A LBD, its inhibitory behavior suggests that it either does not remain bound long enough or does not generate sufficient force for ion channel gating. We developed a workflow using pathway similarity analysis to identify groups of residues working together to promote binding. These conformation-dependent pathways were not significantly impacted by the presence of N-linked glycans, which act primarily by interacting with the LBD bottom lobe to stabilize the closed LBD.
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Affiliation(s)
- Remy A Yovanno
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Tsung Han Chou
- W.M. Keck Structural Biology Laboratory, Cold Spring Harbor LaboratoryCold Spring HarborUnited States
| | - Sarah J Brantley
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Hiro Furukawa
- W.M. Keck Structural Biology Laboratory, Cold Spring Harbor LaboratoryCold Spring HarborUnited States
| | - Albert Y Lau
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of MedicineBaltimoreUnited States
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3
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Qneibi M, Hawash M, Bdir S, Nacak Baytas S. Targeting the kinetics mechanism of AMPA receptor inhibition by 2-oxo-3H-benzoxazole derivatives. Bioorg Chem 2022; 129:106163. [PMID: 36137313 DOI: 10.1016/j.bioorg.2022.106163] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 09/11/2022] [Accepted: 09/13/2022] [Indexed: 11/02/2022]
Abstract
Ionotropic glutamate receptors are ligand-gated ion channels found in most excitatory synapses in the brain that allow for rapid information transfer. Due to their quick excitatory processes, α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid-type glutamate (AMPA) receptors have been linked to various neurodegenerative disorders, including epilepsy and Parkinson's disease. It has been critical to develop new neuroprotective compounds that inhibit AMPA-sensitive glutamate-controlled channels allosterically, and many classes of AMPA receptor-inhibiting compounds have been synthesized and evaluated. The current study focuses on thirteen 2-oxo-3H-benzoxazole derivatives (COBs) as potential AMPA receptor modulators. The whole-cell patch-clamp technique was used to assess the effects of COBs on AMPA receptor subunits (i.e., GluA1, GluA2, GluA1/2, and GluA2/3) amplitudes in the human embryonic kidney (HEK293) cells and the rates of desensitization and deactivation before and after COBs delivery. According to our findings, the COBs bind AMPA receptors allosterically and alter AMPAR characteristics in various ways. COB-1, COB-2, and COB-13 were the most effective in decreasing AMPAR currents by around 10-12 folds compared to the other COBs. Furthermore, the COBs significantly impacted AMPA receptor deactivation and desensitization rates. Of the examined homomeric and heteromeric AMPAR subunits, GluA2 was the most impacted. COB compounds appear to be a viable candidate for future study and development in regulating neurological diseases involving AMPA receptors.
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Affiliation(s)
- Mohammad Qneibi
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus, Palestine.
| | - Mohammed Hawash
- Department of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus, Palestine
| | - Sosana Bdir
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus, Palestine
| | - Sultan Nacak Baytas
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gazi University, Ankara, Turkey
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4
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Tian M, Stroebel D, Piot L, David M, Ye S, Paoletti P. GluN2A and GluN2B NMDA receptors use distinct allosteric routes. Nat Commun 2021; 12:4709. [PMID: 34354080 PMCID: PMC8342458 DOI: 10.1038/s41467-021-25058-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 07/21/2021] [Indexed: 11/17/2022] Open
Abstract
Allostery represents a fundamental mechanism of biological regulation that involves long-range communication between distant protein sites. It also provides a powerful framework for novel therapeutics. NMDA receptors (NMDARs), glutamate-gated ionotropic receptors that play central roles in synapse maturation and plasticity, are prototypical allosteric machines harboring large extracellular N-terminal domains (NTDs) that provide allosteric control of key receptor properties with impact on cognition and behavior. It is commonly thought that GluN2A and GluN2B receptors, the two predominant NMDAR subtypes in the adult brain, share similar allosteric transitions. Here, combining functional and structural interrogation, we reveal that GluN2A and GluN2B receptors utilize different long-distance allosteric mechanisms involving distinct subunit-subunit interfaces and molecular rearrangements. NMDARs have thus evolved multiple levels of subunit-specific allosteric control over their transmembrane ion channel pore. Our results uncover an unsuspected diversity in NMDAR molecular mechanisms with important implications for receptor physiology and precision drug development. NMDA receptors are glutamate-gated ion channels essential for synapse maturation and plasticity. Here the authors show that GluN2A and GluN2B NMDA receptors — the two principal subtypes NMDARs in the adult CNS — operate through distinct long range allosteric mechanisms.
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Affiliation(s)
- Meilin Tian
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Université PSL, CNRS, INSERM, Paris, France
| | - David Stroebel
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Université PSL, CNRS, INSERM, Paris, France
| | - Laura Piot
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Université PSL, CNRS, INSERM, Paris, France
| | - Mélissa David
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Université PSL, CNRS, INSERM, Paris, France
| | - Shixin Ye
- Unité INSERM U1195, Hôpital de Bicêtre, Université Paris-Saclay, Paris, Le Kremlin-Bicêtre, France.
| | - Pierre Paoletti
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Université PSL, CNRS, INSERM, Paris, France.
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5
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Conformational rearrangement of the NMDA receptor amino-terminal domain during activation and allosteric modulation. Nat Commun 2021; 12:2694. [PMID: 33976221 PMCID: PMC8113580 DOI: 10.1038/s41467-021-23024-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 04/01/2021] [Indexed: 02/07/2023] Open
Abstract
N-Methyl-D-aspartate receptors (NMDARs) are ionotropic glutamate receptors essential for synaptic plasticity and memory. Receptor activation involves glycine- and glutamate-stabilized closure of the GluN1 and GluN2 subunit ligand binding domains that is allosterically regulated by the amino-terminal domain (ATD). Using single molecule fluorescence resonance energy transfer (smFRET) to monitor subunit rearrangements in real-time, we observe a stable ATD inter-dimer distance in the Apo state and test the effects of agonists and antagonists. We find that GluN1 and GluN2 have distinct gating functions. Glutamate binding to GluN2 subunits elicits two identical, sequential steps of ATD dimer separation. Glycine binding to GluN1 has no detectable effect, but unlocks the receptor for activation so that glycine and glutamate together drive an altered activation trajectory that is consistent with ATD dimer separation and rotation. We find that protons exert allosteric inhibition by suppressing the glutamate-driven ATD separation steps, and that greater ATD separation translates into greater rotation and higher open probability. N-Methyl-D-aspartate receptors (NMDARs) activation involves closure of the GluN1 and GluN2 subunit ligand binding domains, which is regulated allosterically by the amino-terminal domain (ATD). Here, smFRET, used to monitor conformational rearrangements of the NMDAR ATD, reveals that glutamate binding to GluN2 subunits elicits two identical, sequential steps of ATD dimer separation that are regulated by protons.
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6
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Han TH, Vicidomini R, Ramos CI, Wang Q, Nguyen P, Jarnik M, Lee CH, Stawarski M, Hernandez RX, Macleod GT, Serpe M. Neto-α Controls Synapse Organization and Homeostasis at the Drosophila Neuromuscular Junction. Cell Rep 2021; 32:107866. [PMID: 32640231 PMCID: PMC7484471 DOI: 10.1016/j.celrep.2020.107866] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 02/27/2020] [Accepted: 06/16/2020] [Indexed: 02/06/2023] Open
Abstract
Glutamate receptor auxiliary proteins control receptor distribution and function, ultimately controlling synapse assembly, maturation, and plasticity. At the Drosophila neuromuscular junction (NMJ), a synapse with both pre- and postsynaptic kainate-type glutamate receptors (KARs), we show that the auxiliary protein Neto evolved functionally distinct isoforms to modulate synapse development and homeostasis. Using genetics, cell biology, and electrophysiology, we demonstrate that Neto-α functions on both sides of the NMJ. In muscle, Neto-α limits the size of the postsynaptic receptor field. In motor neurons (MNs), Neto-α controls neurotransmitter release in a KAR-dependent manner. In addition, Neto-α is both required and sufficient for the presynaptic increase in neurotransmitter release in response to reduced postsynaptic sensitivity. This KAR-independent function of Neto-α is involved in activity-induced cytomatrix remodeling. We propose that Drosophila ensures NMJ functionality by acquiring two Neto isoforms with differential expression patterns and activities.
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Affiliation(s)
- Tae Hee Han
- Cell Biology and Neurobiology Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Rosario Vicidomini
- Cell Biology and Neurobiology Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Cathy Isaura Ramos
- Cell Biology and Neurobiology Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA; Institute of Functional Genomics of Lyon, Lyon, France
| | - Qi Wang
- Cell Biology and Neurobiology Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Peter Nguyen
- Cell Biology and Neurobiology Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Michal Jarnik
- Cell Biology and Neurobiology Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Chi-Hon Lee
- Cell Biology and Neurobiology Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA; Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Michal Stawarski
- Wilkes Honors College and Department of Biology, Florida Atlantic University, Jupiter, FL, USA; Biomedical Department, University of Basel, Basel, Switzerland
| | - Roberto X Hernandez
- Wilkes Honors College and Department of Biology, Florida Atlantic University, Jupiter, FL, USA
| | - Gregory T Macleod
- Wilkes Honors College and Department of Biology, Florida Atlantic University, Jupiter, FL, USA
| | - Mihaela Serpe
- Cell Biology and Neurobiology Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA.
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7
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Glutamate-Gated NMDA Receptors: Insights into the Function and Signaling in the Kidney. Biomolecules 2020; 10:biom10071051. [PMID: 32679780 PMCID: PMC7407907 DOI: 10.3390/biom10071051] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/10/2020] [Accepted: 07/13/2020] [Indexed: 12/21/2022] Open
Abstract
N-Methyl-d-aspartate receptor (NMDAR) is a glutamate-gated ionotropic receptor that intervenes in most of the excitatory synaptic transmission within the central nervous system (CNS). Aside from being broadly distributed in the CNS and having indispensable functions in the brain, NMDAR has predominant roles in many physiological and pathological processes in a wide range of non-neuronal cells and tissues. The present review outlines current knowledge and understanding of the physiological and pathophysiological functions of NMDAR in the kidney, an essential excretory and endocrine organ responsible for the whole-body homeostasis. The review also explores the recent findings regarding signaling pathways involved in NMDAR-mediated responses in the kidney. As established from diverse lines of research reviewed here, basal levels of receptor activation within the kidney are essential for the maintenance of healthy tubular and glomerular function, while a disproportionate activation can lead to a disruption of NMDAR's downstream signaling pathways and a myriad of pathophysiological consequences.
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8
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Perszyk RE, Myers SJ, Yuan H, Gibb AJ, Furukawa H, Sobolevsky AI, Traynelis SF. Hodgkin-Huxley-Katz Prize Lecture: Genetic and pharmacological control of glutamate receptor channel through a highly conserved gating motif. J Physiol 2020; 598:3071-3083. [PMID: 32468591 DOI: 10.1113/jp278086] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/18/2020] [Indexed: 12/15/2022] Open
Abstract
Glutamate receptors are essential ligand-gated ion channels in the central nervous system that mediate excitatory synaptic transmission in response to the release of glutamate from presynaptic terminals. The structural and biophysical basis underlying the function of these receptors has been studied for decades by a wide range of approaches. However recent structural, pharmacological and genetic studies have provided new insight into the regions of this protein that are critical determinants of receptor function. Lack of variation in specific areas of the protein amino acid sequences in the human population has defined three regions in each receptor subunit that are under selective pressure, which has focused research efforts and driven new hypotheses. In addition, these three closely positioned elements reside near a cavity that is shown by multiple studies to be a likely site of action for allosteric modulators, one of which is currently in use as an FDA-approved anticonvulsant. These structural elements are capable of controlling gating of the pore, and appear to permit some modulators bound within the cavity to also alter permeation properties. This creates a new precedent whereby features of the channel pore can be modulated by exogenous drugs that bind outside the pore. The convergence of structural, genetic, biophysical and pharmacological approaches is a powerful means to gain insight into the complex biological processes defined by neurotransmitter receptor function.
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Affiliation(s)
- Riley E Perszyk
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Scott J Myers
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA.,Center for Functional Evaluation of Rare Variants (CFERV), Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Hongjie Yuan
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA.,Center for Functional Evaluation of Rare Variants (CFERV), Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Alasdair J Gibb
- Department of Neuroscience, Physiology & Pharmacology, University College London, London, UK
| | - Hiro Furukawa
- WM Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, 11724, USA
| | - Alexander I Sobolevsky
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Stephen F Traynelis
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA.,Center for Functional Evaluation of Rare Variants (CFERV), Emory University School of Medicine, Atlanta, GA, 30322, USA
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9
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The structural bases for agonist diversity in an Arabidopsis thaliana glutamate receptor-like channel. Proc Natl Acad Sci U S A 2019; 117:752-760. [PMID: 31871183 DOI: 10.1073/pnas.1905142117] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Arabidopsis thaliana glutamate receptor-like (GLR) channels are amino acid-gated ion channels involved in physiological processes including wound signaling, stomatal regulation, and pollen tube growth. Here, fluorescence microscopy and genetics were used to confirm the central role of GLR3.3 in the amino acid-elicited cytosolic Ca2+ increase in Arabidopsis seedling roots. To elucidate the binding properties of the receptor, we biochemically reconstituted the GLR3.3 ligand-binding domain (LBD) and analyzed its selectivity profile; our binding experiments revealed the LBD preference for l-Glu but also for sulfur-containing amino acids. Furthermore, we solved the crystal structures of the GLR3.3 LBD in complex with 4 different amino acid ligands, providing a rationale for how the LBD binding site evolved to accommodate diverse amino acids, thus laying the grounds for rational mutagenesis. Last, we inspected the structures of LBDs from nonplant species and generated homology models for other GLR isoforms. Our results establish that GLR3.3 is a receptor endowed with a unique amino acid ligand profile and provide a structural framework for engineering this and other GLR isoforms to investigate their physiology.
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10
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Fahim A, Rehman Z, Bhatti MF, Virk N, Ali A, Rashid A, Paracha RZ. The Route to 'Chemobrain' - Computational probing of neuronal LTP pathway. Sci Rep 2019; 9:9630. [PMID: 31270411 PMCID: PMC6610097 DOI: 10.1038/s41598-019-45883-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 06/19/2019] [Indexed: 02/08/2023] Open
Abstract
Chemotherapy causes deleterious side effects during the course of cancer management. The toxic effects may be extended to CNS chronically resulting in altered cognitive function like learning and memory. The present study follows a computational assessment of 64 chemotherapeutic drugs for their off-target interactions against the major proteins involved in neuronal long term potentiation pathway. The cancer chemo-drugs were subjected to induced fit docking followed by scoring alignment and drug-targets interaction analysis. The results were further probed by electrostatic potential computation and ligand binding affinity prediction of the top complexes. The study identified novel off-target interactions by Dactinomycin, Temsirolimus, and Everolimus against NMDA, AMPA, PKA and ERK2, while Irinotecan, Bromocriptine and Dasatinib were top interacting drugs for CaMKII. This study presents with basic foundational knowledge regarding potential chemotherapeutic interference in LTP pathway which may modulate neurotransmission and synaptic plasticity in patient receiving these chemotherapies.
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Affiliation(s)
- Ammad Fahim
- Atta ur Rahman School of Applied Biosciences, National University of Sciences and Technology (NUST), Islamabad, Pakistan.
| | - Zaira Rehman
- Atta ur Rahman School of Applied Biosciences, National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Muhammad Faraz Bhatti
- Atta ur Rahman School of Applied Biosciences, National University of Sciences and Technology (NUST), Islamabad, Pakistan.
| | - Nasar Virk
- Atta ur Rahman School of Applied Biosciences, National University of Sciences and Technology (NUST), Islamabad, Pakistan
- EBS Universität für Wirtschaft und Recht, EBS Business School, Rheingaustrasse 1, Oestrich-Winkel, 65375, Germany
| | - Amjad Ali
- Atta ur Rahman School of Applied Biosciences, National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Amir Rashid
- Department of Biochemistry, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Rehan Zafar Paracha
- Research Centre for Modeling and Simulation, National University of Sciences and Technology (NUST), Islamabad, Pakistan.
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11
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Lau AY. Enhanced sampling of glutamate receptor ligand-binding domains. Neurosci Lett 2019; 700:17-21. [DOI: 10.1016/j.neulet.2018.04.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 04/08/2018] [Accepted: 04/10/2018] [Indexed: 01/23/2023]
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12
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Wilding TJ, Huettner JE. Cadmium opens GluK2 kainate receptors with cysteine substitutions at the M3 helix bundle crossing. J Gen Physiol 2019; 151:435-451. [PMID: 30498132 PMCID: PMC6445585 DOI: 10.1085/jgp.201812234] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/01/2018] [Indexed: 02/04/2023] Open
Abstract
Kainate receptors are ligand-gated ion channels that have two major roles in the central nervous system: they mediate a postsynaptic component of excitatory neurotransmission at some glutamatergic synapses and modulate transmitter release at both excitatory and inhibitory synapses. Accumulating evidence implicates kainate receptors in a variety of neuropathologies, including epilepsy, psychiatric disorders, developmental delay, and cognitive impairment. Here, to gain a deeper understanding of the conformational changes associated with agonist binding and channel opening, we generate a series of Cys substitutions in the GluK2 kainate receptor subunit, focusing on the M3 helices that line the ion pore and form the bundle-crossing gate at the extracellular mouth of the channel. Exposure to 50 µM Cd produces direct activation of homomeric mutant channels bearing Cys substitutions in (A657C), or adjacent to (L659C), the conserved SYTANLAAF motif. Activation by Cd is occluded by modification with 2-aminoethyl MTS (MTSEA), indicating that Cd binds directly and specifically to the substituted cysteines. Cd potency for the A657C mutation (EC50 = 10 µM) suggests that binding involves at least two coordinating residues, whereas weaker Cd potency for L659C (EC50 = 2 mM) implies that activation does not require tight coordination by multiple side chains for this substitution. Experiments with heteromeric and chimeric channels indicate that activation by Cd requires Cys substitution at only two of the four subunits within a tetrameric receptor and that activation is similar for substitution within subunits in either the A/C or B/D conformations. We develop simple kinetic models for the A657C substitution that reproduce several features of Cd activation as well as the low-affinity inhibition observed at higher Cd concentrations (5-20 mM). Together, these results demonstrate rapid and reversible channel activation, independent of agonist site occupancy, upon Cd binding to Cys side chains at two specific locations along the GluK2 inner helix.
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Affiliation(s)
- Timothy J Wilding
- Department of Cell Biology and Physiology, Washington University Medical School, St. Louis, MO
| | - James E Huettner
- Department of Cell Biology and Physiology, Washington University Medical School, St. Louis, MO
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13
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Twomey EC, Yelshanskaya MV, Vassilevski AA, Sobolevsky AI. Mechanisms of Channel Block in Calcium-Permeable AMPA Receptors. Neuron 2018; 99:956-968.e4. [PMID: 30122377 PMCID: PMC6181147 DOI: 10.1016/j.neuron.2018.07.027] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 06/20/2018] [Accepted: 07/17/2018] [Indexed: 01/14/2023]
Abstract
AMPA receptors mediate fast excitatory neurotransmission and are critical for CNS development and function. Calcium-permeable subsets of AMPA receptors are strongly implicated in acute and chronic neurological disorders. However, despite the clinical importance, the therapeutic landscape for specifically targeting them, and not the calcium-impermeable AMPA receptors, remains largely undeveloped. To address this problem, we used cryo-electron microscopy and electrophysiology to investigate the mechanisms by which small-molecule blockers selectively inhibit ion channel conductance in calcium-permeable AMPA receptors. We determined the structures of calcium-permeable GluA2 AMPA receptor complexes with the auxiliary subunit stargazin bound to channel blockers, including the orb weaver spider toxin AgTx-636, the spider toxin analog NASPM, and the adamantane derivative IEM-1460. Our structures provide insights into the architecture of the blocker binding site and the mechanism of trapping, which are critical for development of small molecules that specifically target calcium-permeable AMPA receptors.
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Affiliation(s)
- Edward C Twomey
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Integrated Program in Cellular, Molecular and Biomedical Studies, Columbia University, New York, NY 10032, USA
| | - Maria V Yelshanskaya
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Alexander A Vassilevski
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow Oblast 141700, Russia
| | - Alexander I Sobolevsky
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
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14
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Gibb AJ, Ogden KK, McDaniel MJ, Vance KM, Kell SA, Butch C, Burger P, Liotta DC, Traynelis SF. A structurally derived model of subunit-dependent NMDA receptor function. J Physiol 2018; 596:4057-4089. [PMID: 29917241 PMCID: PMC6117563 DOI: 10.1113/jp276093] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 06/11/2018] [Indexed: 12/14/2022] Open
Abstract
Key points The kinetics of NMDA receptor (NMDAR) signalling are a critical aspect of the physiology of excitatory synaptic transmission in the brain. Here we develop a mechanistic description of NMDAR function based on the receptor tetrameric structure and the principle that each agonist‐bound subunit must undergo some rate‐limiting conformational change after agonist binding, prior to channel opening. By fitting this mechanism to single channel data using a new MATLAB‐based software implementation of maximum likelihood fitting with correction for limited time resolution, rate constants were derived for this mechanism that reflect distinct structural changes and predict the properties of macroscopic and synaptic NMDAR currents. The principles applied here to develop a mechanistic description of the heterotetrameric NMDAR, and the software used in this analysis, can be equally applied to other heterotetrameric glutamate receptors, providing a unifying mechanistic framework to understanding the physiology of glutamate receptor signalling in the brain.
Abstract NMDA receptors (NMDARs) are tetrameric complexes comprising two glycine‐binding GluN1 and two glutamate‐binding GluN2 subunits. Four GluN2 subunits encoded by different genes can produce up to 10 different di‐ and triheteromeric receptors. In addition, some neurological patients contain a de novo mutation or inherited rare variant in only one subunit. There is currently no mechanistic framework to describe tetrameric receptor function that can be extended to receptors with two different GluN1 or GluN2 subunits. Here we use the structural features of glutamate receptors to develop a mechanism describing both single channel and macroscopic NMDAR currents. We propose that each agonist‐bound subunit undergoes some rate‐limiting conformational change after agonist binding, prior to channel opening. We hypothesize that this conformational change occurs within a triad of interactions between a short helix preceding the M1 transmembrane helix, the highly conserved M3 motif encoded by the residues SYTANLAAF, and the linker preceding the M4 transmembrane helix of the adjacent subunit. Molecular dynamics simulations suggest that pre‐M1 helix motion is uncorrelated between subunits, which we interpret to suggest independent subunit‐specific conformational changes may influence these pre‐gating steps. According to this interpretation, these conformational changes are the main determinants of the key kinetic properties of NMDA receptor activation following agonist binding, and so these steps sculpt their physiological role. We show that this structurally derived tetrameric model describes both single channel and macroscopic data, giving a new approach to interpreting functional properties of synaptic NMDARs that provides a logical framework to understanding receptors with non‐identical subunits. The kinetics of NMDA receptor (NMDAR) signalling are a critical aspect of the physiology of excitatory synaptic transmission in the brain. Here we develop a mechanistic description of NMDAR function based on the receptor tetrameric structure and the principle that each agonist‐bound subunit must undergo some rate‐limiting conformational change after agonist binding, prior to channel opening. By fitting this mechanism to single channel data using a new MATLAB‐based software implementation of maximum likelihood fitting with correction for limited time resolution, rate constants were derived for this mechanism that reflect distinct structural changes and predict the properties of macroscopic and synaptic NMDAR currents. The principles applied here to develop a mechanistic description of the heterotetrameric NMDAR, and the software used in this analysis, can be equally applied to other heterotetrameric glutamate receptors, providing a unifying mechanistic framework to understanding the physiology of glutamate receptor signalling in the brain.
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Affiliation(s)
- Alasdair J Gibb
- Department of Neuroscience, Physiology and Pharmacology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Kevin K Ogden
- Department of Pharmacology, Emory University School of Medicine, Rollins Research Center, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Miranda J McDaniel
- Department of Pharmacology, Emory University School of Medicine, Rollins Research Center, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Katie M Vance
- Department of Pharmacology, Emory University School of Medicine, Rollins Research Center, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Steven A Kell
- Department of Chemistry, Emory University School, 1515 Dickey Drive, Atlanta, GA, 30322, USA
| | - Chris Butch
- Department of Chemistry, Emory University School, 1515 Dickey Drive, Atlanta, GA, 30322, USA
| | - Pieter Burger
- Department of Chemistry, Emory University School, 1515 Dickey Drive, Atlanta, GA, 30322, USA
| | - Dennis C Liotta
- Department of Chemistry, Emory University School, 1515 Dickey Drive, Atlanta, GA, 30322, USA
| | - Stephen F Traynelis
- Department of Pharmacology, Emory University School of Medicine, Rollins Research Center, 1510 Clifton Road, Atlanta, GA, 30322, USA
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15
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Sinitskiy AV, Pande VS. Computer Simulations Predict High Structural Heterogeneity of Functional State of NMDA Receptors. Biophys J 2018; 115:841-852. [PMID: 30029773 DOI: 10.1016/j.bpj.2018.06.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 06/18/2018] [Indexed: 01/07/2023] Open
Abstract
N-methyl-D-aspartate receptors (NMDARs)-i.e., transmembrane proteins expressed in neurons-play a central role in the molecular mechanisms of learning and memory formation. It is unclear how the known atomic structures of NMDARs determined by x-ray crystallography and electron cryomicroscopy (18 published Protein Data Bank entries) relate to the functional states of NMDARs inferred from electrophysiological recordings (multiple closed, open, preopen, etc. states). We address this problem by using molecular dynamics simulations at atomic resolution, a method successfully applied in the past to much smaller biomolecules. Our simulations predict that several conformations of NMDARs with experimentally determined geometries, including four "nonactive" electron cryomicroscopy structures, rapidly interconvert on submicrosecond timescales and therefore may correspond to the same functional state of the receptor (specifically, one of the closed states). This conclusion is not trivial because these conformational transitions involve changes in certain interatomic distances as large as tens of Å. The simulations also predict differences in the conformational dynamics of the apo and holo (i.e., agonist and coagonist bound) forms of the receptor on the microsecond timescale. To our knowledge, five new conformations of NMDARs, with geometries joining various features from different known experimental structures, are also predicted by the model. The main limitation of this work stems from its limited sampling (30 μs of aggregate length of molecular dynamics trajectories). Though this level significantly exceeds the sampling in previous simulations of parts of NMDARs, it is still much lower than the sampling recently achieved for smaller biomolecules (up to a few milliseconds), thus precluding, in particular, the observation of transitions between different functional states of NMDARs. Despite this limitation, such computational predictions may guide further experimental studies on the structure, dynamics, and function of NMDARs, for example by suggesting optimal locations of spectroscopic probes. Overall, atomic resolution simulations provide, to our knowledge, a novel perspective on the structure and dynamics of NMDARs, complementing information obtained by experimental methods.
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Affiliation(s)
- Anton V Sinitskiy
- Department of Bioengineering, Stanford University, Stanford, California.
| | - Vijay S Pande
- Department of Bioengineering, Stanford University, Stanford, California.
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16
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Yu A, Lau AY. Glutamate and Glycine Binding to the NMDA Receptor. Structure 2018; 26:1035-1043.e2. [PMID: 29887499 DOI: 10.1016/j.str.2018.05.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 03/29/2018] [Accepted: 05/08/2018] [Indexed: 02/07/2023]
Abstract
At central nervous system synapses, agonist binding to postsynaptic ionotropic glutamate receptors (iGluRs) results in signaling between neurons. N-Methyl-D-aspartic acid (NMDA) receptors are a unique family of iGluRs that activate in response to the concurrent binding of glutamate and glycine. Here, we investigate the process of agonist binding to the GluN2A (glutamate binding) and GluN1 (glycine binding) NMDA receptor subtypes using long-timescale unbiased molecular dynamics simulations. We find that positively charged residues on the surface of the GluN2A ligand-binding domain (LBD) assist glutamate binding via a "guided-diffusion" mechanism, similar in fashion to glutamate binding to the GluA2 LBD of AMPA receptors. Glutamate can also bind in an inverted orientation. Glycine, on the other hand, binds to the GluN1 LBD via an "unguided-diffusion" mechanism, whereby glycine finds its binding site primarily by random thermal fluctuations. Free energy calculations quantify the glutamate- and glycine-binding processes.
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Affiliation(s)
- Alvin Yu
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Albert Y Lau
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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17
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Krieger J, Lee JY, Greger IH, Bahar I. Activation and desensitization of ionotropic glutamate receptors by selectively triggering pre-existing motions. Neurosci Lett 2018; 700:22-29. [PMID: 29481851 PMCID: PMC6107436 DOI: 10.1016/j.neulet.2018.02.050] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 02/15/2018] [Accepted: 02/22/2018] [Indexed: 01/03/2023]
Abstract
Ionotropic glutamate receptors (iGluRs) are ligand-gated ion channels that are key players in synaptic transmission and plasticity. They are composed of four subunits, each containing four functional domains, the quaternary packing and collective structural dynamics of which are important determinants of their molecular mechanism of function. With the explosion of structural studies on different members of the family, including the structures of activated open channels, the mechanisms of action of these central signaling machines are now being elucidated. We review the current state of computational studies on two major members of the family, AMPA and NMDA receptors, with focus on molecular simulations and elastic network model analyses that have provided insights into the coupled movements of extracellular and transmembrane domains. We describe the newly emerging mechanisms of activation, allosteric signaling and desensitization, as mainly a selective triggering of pre-existing soft motions, as deduced from computational models and analyses that leverage structural data on intact AMPA and NMDA receptors in different states.
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Affiliation(s)
- James Krieger
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, 3501 Fifth Ave, Suite 3064 BST3, Pittsburgh, PA, 15260, United States
| | - Ji Young Lee
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, 3501 Fifth Ave, Suite 3064 BST3, Pittsburgh, PA, 15260, United States
| | - Ingo H Greger
- Neurobiology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, United Kingdom
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, 3501 Fifth Ave, Suite 3064 BST3, Pittsburgh, PA, 15260, United States.
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18
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Iacobucci GJ, Popescu GK. Kinetic models for activation and modulation of NMDA receptor subtypes. CURRENT OPINION IN PHYSIOLOGY 2018; 2:114-122. [PMID: 29978141 DOI: 10.1016/j.cophys.2018.02.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
NMDA receptors are a diverse family of excitatory channels with critical roles in central synaptic transmission, development, and plasticity. Controlled expression of seven subunits and their combinatorial assembly into tetrameric receptors produces a range of molecularly distinct receptor subtypes. Despite relatively similar atomic structures, each subtype has input-output functions with unique biophysical and pharmacologic profiles. Here, we briefly summarize recent advances in understanding how gating and allosteric modulation are similar or distinct across NMDA receptor isoforms and identify open questions that will focus research in this area going forward.
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19
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Biophysics of the Brain: From Molecules to Networks. Biophys J 2017; 113:E1. [PMID: 29079011 DOI: 10.1016/j.bpj.2017.10.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 10/18/2017] [Indexed: 11/22/2022] Open
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