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Ramos-Vicente D, Grant SG, Bayés À. Metazoan evolution and diversity of glutamate receptors and their auxiliary subunits. Neuropharmacology 2021; 195:108640. [PMID: 34116111 DOI: 10.1016/j.neuropharm.2021.108640] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/27/2021] [Accepted: 06/01/2021] [Indexed: 01/18/2023]
Abstract
Glutamate is the major excitatory neurotransmitter in vertebrate and invertebrate nervous systems. Proteins involved in glutamatergic neurotransmission, and chiefly glutamate receptors and their auxiliary subunits, play key roles in nervous system function. Thus, understanding their evolution and uncovering their diversity is essential to comprehend how nervous systems evolved, shaping cognitive function. Comprehensive phylogenetic analysis of these proteins across metazoans have revealed that their evolution is much more complex than what can be anticipated from vertebrate genomes. This is particularly true for ionotropic glutamate receptors (iGluRs), as their current classification into 6 classes (AMPA, Kainate, Delta, NMDA1, NMDA2 and NMDA3) would be largely incomplete. New work proposes a classification of iGluRs into 4 subfamilies that encompass 10 classes. Vertebrate AMPA, Kainate and Delta receptors would belong to one of these subfamilies, named AKDF, the NMDA subunits would constitute another subfamily and non-vertebrate iGluRs would be organised into the previously unreported Epsilon and Lambda subfamilies. Similarly, the animal evolution of metabotropic glutamate receptors has resulted in the formation of four classes of these receptors, instead of the three currently recognised. Here we review our current knowledge on the animal evolution of glutamate receptors and their auxiliary subunits. This article is part of the special issue on 'Glutamate Receptors - Orphan iGluRs'.
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Affiliation(s)
- David Ramos-Vicente
- Molecular Physiology of the Synapse Laboratory, Biomedical Research Institute Sant Pau, Barcelona, Spain; Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Seth Gn Grant
- Centre for Clinical Brain Sciences, Chancellor's Building, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, EH16 4SB, UK; Simons Initiative for the Developing Brain (SIDB), Centre for Discovery Brain Sciences, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh, EH8 9XD, UK
| | - Àlex Bayés
- Molecular Physiology of the Synapse Laboratory, Biomedical Research Institute Sant Pau, Barcelona, Spain; Universitat Autònoma de Barcelona, Barcelona, Spain.
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52
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McDaniel MJ, Ogden KK, Kell SA, Burger PB, Liotta DC, Traynelis SF. NMDA receptor channel gating control by the pre-M1 helix. J Gen Physiol 2021; 152:151592. [PMID: 32221541 PMCID: PMC7141592 DOI: 10.1085/jgp.201912362] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 08/09/2019] [Accepted: 02/14/2020] [Indexed: 01/10/2023] Open
Abstract
The NMDA receptor (NMDAR) is an ionotropic glutamate receptor formed from the tetrameric assembly of GluN1 and GluN2 subunits. Within the flexible linker between the agonist binding domain (ABD) and the M1 helix of the pore-forming transmembrane helical bundle lies a two-turn, extracellular pre-M1 helix positioned parallel to the plasma membrane and in van der Waals contact with the M3 helix thought to constitute the channel gate. The pre-M1 helix is tethered to the bilobed ABD, where agonist-induced conformational changes initiate activation. Additionally, it is a locus for de novo mutations associated with neurological disorders, is near other disease-associated de novo sites within the transmembrane domain, and is a structural determinant of subunit-selective modulators. To investigate the role of the pre-M1 helix in channel gating, we performed scanning mutagenesis across the GluN2A pre-M1 helix and recorded whole-cell macroscopic and single channel currents from HEK293 cell-attached patches. We identified two residues at which mutations perturb channel open probability, the mean open time, and the glutamate deactivation time course. We identified a subunit-specific network of aromatic amino acids located in and around the GluN2A pre-M1 helix to be important for gating. Based on these results, we are able to hypothesize about the role of the pre-M1 helix in other NMDAR subunits based on sequence and structure homology. Our results emphasize the role of the pre-M1 helix in channel gating, implicate the surrounding amino acid environment in this mechanism, and suggest unique subunit-specific contributions of pre-M1 helices to GluN1 and GluN2 gating.
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Affiliation(s)
- Miranda J McDaniel
- Department of Pharmacology, Rollins Research Center, Emory University, Atlanta, GA
| | - Kevin K Ogden
- Department of Pharmacology, Rollins Research Center, Emory University, Atlanta, GA
| | - Steven A Kell
- Department of Pharmacology, Rollins Research Center, Emory University, Atlanta, GA.,Department of Chemistry, Emory University, Atlanta, GA
| | | | | | - Stephen F Traynelis
- Department of Pharmacology, Rollins Research Center, Emory University, Atlanta, GA
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53
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Gating and modulation of a hetero-octameric AMPA glutamate receptor. Nature 2021; 594:454-458. [PMID: 34079129 PMCID: PMC7611729 DOI: 10.1038/s41586-021-03613-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 05/05/2021] [Indexed: 02/06/2023]
Abstract
AMPA receptors (AMPARs) mediate the majority of excitatory transmission in the brain and enable the synaptic plasticity that underlies learning1. A diverse array of AMPAR signalling complexes are established by receptor auxiliary subunits, which associate with the AMPAR in various combinations to modulate trafficking, gating and synaptic strength2. However, their mechanisms of action are poorly understood. Here we determine cryo-electron microscopy structures of the heteromeric GluA1-GluA2 receptor assembled with both TARP-γ8 and CNIH2, the predominant AMPAR complex in the forebrain, in both resting and active states. Two TARP-γ8 and two CNIH2 subunits insert at distinct sites beneath the ligand-binding domains of the receptor, with site-specific lipids shaping each interaction and affecting the gating regulation of the AMPARs. Activation of the receptor leads to asymmetry between GluA1 and GluA2 along the ion conduction path and an outward expansion of the channel triggers counter-rotations of both auxiliary subunit pairs, promoting the active-state conformation. In addition, both TARP-γ8 and CNIH2 pivot towards the pore exit upon activation, extending their reach for cytoplasmic receptor elements. CNIH2 achieves this through its uniquely extended M2 helix, which has transformed this endoplasmic reticulum-export factor into a powerful AMPAR modulator that is capable of providing hippocampal pyramidal neurons with their integrative synaptic properties.
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54
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Stroebel D, Mony L, Paoletti P. Glycine agonism in ionotropic glutamate receptors. Neuropharmacology 2021; 193:108631. [PMID: 34058193 DOI: 10.1016/j.neuropharm.2021.108631] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/21/2021] [Accepted: 05/23/2021] [Indexed: 12/12/2022]
Abstract
Ionotropic glutamate receptors (iGluRs) are ligand-gated ion channels that mediate the majority of excitatory neurotransmission in the vertebrate CNS. Classified as AMPA, kainate, delta and NMDA receptors, iGluRs are central drivers of synaptic plasticity widely considered as a major cellular substrate of learning and memory. Surprisingly however, five out of the eighteen vertebrate iGluR subunits do not bind glutamate but glycine, a neurotransmitter known to mediate inhibitory neurotransmission through its action on pentameric glycine receptors (GlyRs). This is the case of GluN1, GluN3A, GluN3B, GluD1 and GluD2 subunits, all also binding the D amino acid d-serine endogenously present in many brain regions. Glycine and d-serine action and affinities broadly differ between glycinergic iGluR subtypes. On 'conventional' GluN1/GluN2 NMDA receptors, glycine (or d-serine) acts in concert with glutamate as a mandatory co-agonist to set the level of receptor activity. It also regulates the receptor's trafficking and expression independently of glutamate. On 'unconventional' GluN1/GluN3 NMDARs, glycine acts as the sole agonist directly triggering opening of excitatory glycinergic channels recently shown to be physiologically relevant. On GluD receptors, d-serine on its own mediates non-ionotropic signaling involved in excitatory and inhibitory synaptogenesis, further reinforcing the concept of glutamate-insensitive iGluRs. Here we present an overview of our current knowledge on glycine and d-serine agonism in iGluRs emphasizing aspects related to molecular mechanisms, cellular function and pharmacological profile. The growing appreciation of the critical influence of glycine and d-serine on iGluR biology reshapes our understanding of iGluR signaling diversity and complexity, with important implications in neuropharmacology.
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Affiliation(s)
- David Stroebel
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Université PSL, CNRS, INSERM, F-75005, Paris, France.
| | - Laetitia Mony
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Université PSL, CNRS, INSERM, F-75005, Paris, France
| | - Pierre Paoletti
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Université PSL, CNRS, INSERM, F-75005, Paris, France.
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55
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Mayer ML. Structural biology of kainate receptors. Neuropharmacology 2021; 190:108511. [PMID: 33798545 DOI: 10.1016/j.neuropharm.2021.108511] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/16/2021] [Accepted: 02/18/2021] [Indexed: 12/31/2022]
Abstract
This review summarizes structural studies on kainate receptors that explain unique functional properties of this receptor family. A large number of structures have been solved for ligand binding domain dimer assemblies, giving insight into the subtype selective pharmacology of agonists, antagonists, and allosteric modulators. Structures and biochemical studies on the amino terminal domain reveal mechanisms that play a key role in assembly of heteromeric receptors. Surprisingly, structures of full length homomeric GluK2, GluK3 and heteromeric GluK2/GluK5, receptors reveal a novel structure for the desensitized state that is strikingly different from that for AMPA receptors.
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Affiliation(s)
- Mark L Mayer
- Porter Neuroscience Research Center, NINDS, NIH, 35A Convent Drive Room 3D 904, Bethesda, MD, 20892, USA.
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56
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Horak M, Barackova P, Langore E, Netolicky J, Rivas-Ramirez P, Rehakova K. The Extracellular Domains of GluN Subunits Play an Essential Role in Processing NMDA Receptors in the ER. Front Neurosci 2021; 15:603715. [PMID: 33796003 PMCID: PMC8007919 DOI: 10.3389/fnins.2021.603715] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 02/19/2021] [Indexed: 12/31/2022] Open
Abstract
N-methyl-D-aspartate receptors (NMDARs) belong to a family of ionotropic glutamate receptors that play essential roles in excitatory neurotransmission and synaptic plasticity in the mammalian central nervous system (CNS). Functional NMDARs consist of heterotetramers comprised of GluN1, GluN2A-D, and/or GluN3A-B subunits, each of which contains four membrane domains (M1 through M4), an intracellular C-terminal domain, a large extracellular N-terminal domain composed of the amino-terminal domain and the S1 segment of the ligand-binding domain (LBD), and an extracellular loop between M3 and M4, which contains the S2 segment of the LBD. Both the number and type of NMDARs expressed at the cell surface are regulated at several levels, including their translation and posttranslational maturation in the endoplasmic reticulum (ER), intracellular trafficking via the Golgi apparatus, lateral diffusion in the plasma membrane, and internalization and degradation. This review focuses on the roles played by the extracellular regions of GluN subunits in ER processing. Specifically, we discuss the presence of ER retention signals, the integrity of the LBD, and critical N-glycosylated sites and disulfide bridges within the NMDAR subunits, each of these steps must pass quality control in the ER in order to ensure that only correctly assembled NMDARs are released from the ER for subsequent processing and trafficking to the surface. Finally, we discuss the effect of pathogenic missense mutations within the extracellular domains of GluN subunits with respect to ER processing of NMDARs.
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Affiliation(s)
- Martin Horak
- Department of Neurochemistry, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia
| | - Petra Barackova
- Department of Neurochemistry, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia
| | - Emily Langore
- Department of Neurochemistry, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia
| | - Jakub Netolicky
- Department of Neurochemistry, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia
| | - Paula Rivas-Ramirez
- Department of Neurochemistry, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia
| | - Kristyna Rehakova
- Department of Neurochemistry, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia
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57
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Amin JB, Gochman A, He M, Certain N, Wollmuth LP. NMDA Receptors Require Multiple Pre-opening Gating Steps for Efficient Synaptic Activity. Neuron 2020; 109:488-501.e4. [PMID: 33264592 DOI: 10.1016/j.neuron.2020.11.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/06/2020] [Accepted: 11/11/2020] [Indexed: 12/27/2022]
Abstract
NMDA receptors (NMDARs) are glutamate-gated ion channels that mediate fast excitatory synaptic transmission in the nervous system. Applying glutamate to outside-out patches containing a single NMDAR, we find that agonist-bound receptors transition to the open state via two conformations, an "unconstrained pre-active" state that contributes to fast synaptic events and a "constrained pre-active" state that does not. To define how glutamate drives these conformations, we decoupled the ligand-binding domains from specific transmembrane segments for GluN1 and GluN2A. Displacements of the pore-forming M3 segments define the energy of fast opening. However, to enter the unconstrained conformation and contribute to fast signaling, the GluN2 pre-M1 helix must be displaced before the M3 segments move. This pre-M1 displacement is facilitated by the flexibility of the S2-M4 of GluN1 and GluN2A. Thus, outer structures-pre-M1 and S2-M4-work in concert to remove constraints and prime the channel for rapid opening, facilitating fast synaptic transmission.
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Affiliation(s)
- Johansen B Amin
- Graduate Program in Molecular & Cellular Pharmacology, Stony Brook University, Stony Brook, NY 11794-5230, USA; Medical Scientist Training Program (MSTP), Stony Brook University, Stony Brook, NY 11794-5230, USA
| | - Aaron Gochman
- Department of Neurobiology & Behavior, Stony Brook University, Stony Brook, NY 11794-5230, USA
| | - Miaomiao He
- Graduate Program in Biochemistry & Structural Biology, Stony Brook University, Stony Brook, NY 11794-5230, USA
| | - Noele Certain
- Graduate Program in Molecular & Cellular Pharmacology, Stony Brook University, Stony Brook, NY 11794-5230, USA
| | - Lonnie P Wollmuth
- Department of Neurobiology & Behavior, Stony Brook University, Stony Brook, NY 11794-5230, USA; Department of Biochemistry & Cell Biology, Stony Brook University, Stony Brook, NY 11794-5230, USA; Center for Nervous System Disorders, Stony Brook University, Stony Brook, NY 11794-5230, USA.
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58
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Durham RJ, Latham DR, Sanabria H, Jayaraman V. Structural Dynamics of Glutamate Signaling Systems by smFRET. Biophys J 2020; 119:1929-1936. [PMID: 33096078 PMCID: PMC7732771 DOI: 10.1016/j.bpj.2020.10.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/06/2020] [Accepted: 10/13/2020] [Indexed: 12/19/2022] Open
Abstract
Single-molecule Förster resonance energy transfer (smFRET) is a powerful technique for investigating the structural dynamics of biological macromolecules. smFRET reveals the conformational landscape and dynamic changes of proteins by building on the static structures found using cryo-electron microscopy, x-ray crystallography, and other methods. Combining smFRET with static structures allows for a direct correlation between dynamic conformation and function. Here, we discuss the different experimental setups, fluorescence detection schemes, and data analysis strategies that enable the study of structural dynamics of glutamate signaling across various timescales. We illustrate the versatility of smFRET by highlighting studies of a wide range of questions, including the mechanism of activation and transport, the role of intrinsically disordered segments, and allostery and cooperativity between subunits in biological systems responsible for glutamate signaling.
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Affiliation(s)
- Ryan J Durham
- University of Texas Health Science Center at Houston, Houston, Texas
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59
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Vu S, Singh V, Wulff H, Yarov-Yarovoy V, Zheng J. New capsaicin analogs as molecular rulers to define the permissive conformation of the mouse TRPV1 ligand-binding pocket. eLife 2020; 9:62039. [PMID: 33164749 PMCID: PMC7671684 DOI: 10.7554/elife.62039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 11/08/2020] [Indexed: 12/23/2022] Open
Abstract
The capsaicin receptor TRPV1 is an outstanding representative of ligand-gated ion channels in ligand selectivity and sensitivity. However, molecular interactions that stabilize the ligand-binding pocket in its permissive conformation, and how many permissive conformations the ligand-binding pocket may adopt, remain unclear. To answer these questions, we designed a pair of novel capsaicin analogs to increase or decrease the ligand size by about 1.5 Å without altering ligand chemistry. Together with capsaicin, these ligands form a set of molecular rulers for investigating ligand-induced conformational changes. Computational modeling and functional tests revealed that structurally these ligands alternate between drastically different binding poses but stabilize the ligand-binding pocket in nearly identical permissive conformations; functionally, they all yielded a stable open state despite varying potencies. Our study suggests the existence of an optimal ligand-binding pocket conformation for capsaicin-mediated TRPV1 activation gating, and reveals multiple ligand-channel interactions that stabilize this permissive conformation.
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Affiliation(s)
- Simon Vu
- Department of Physiology and Membrane Biology, University of California Davis, School of Medicine, Davis, United States
| | - Vikrant Singh
- Department of Pharmacology, University of California Davis, School of Medicine, Davis, United States
| | - Heike Wulff
- Department of Pharmacology, University of California Davis, School of Medicine, Davis, United States
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California Davis, School of Medicine, Davis, United States
| | - Jie Zheng
- Department of Physiology and Membrane Biology, University of California Davis, School of Medicine, Davis, United States
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60
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The pathogenic S688Y mutation in the ligand-binding domain of the GluN1 subunit regulates the properties of NMDA receptors. Sci Rep 2020; 10:18576. [PMID: 33122756 PMCID: PMC7596085 DOI: 10.1038/s41598-020-75646-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 10/16/2020] [Indexed: 02/06/2023] Open
Abstract
Although numerous pathogenic mutations have been identified in various subunits of N-methyl-D-aspartate receptors (NMDARs), ionotropic glutamate receptors that are central to glutamatergic neurotransmission, the functional effects of these mutations are often unknown. Here, we combined in silico modelling with microscopy, biochemistry, and electrophysiology in cultured HEK293 cells and hippocampal neurons to examine how the pathogenic missense mutation S688Y in the GluN1 NMDAR subunit affects receptor function and trafficking. We found that the S688Y mutation significantly increases the EC50 of both glycine and d-serine in GluN1/GluN2A and GluN1/GluN2B receptors, and significantly slows desensitisation of GluN1/GluN3A receptors. Moreover, the S688Y mutation reduces the surface expression of GluN3A-containing NMDARs in cultured hippocampal neurons, but does not affect the trafficking of GluN2-containing receptors. Finally, we found that the S688Y mutation reduces Ca2+ influx through NMDARs and reduces NMDA-induced excitotoxicity in cultured hippocampal neurons. These findings provide key insights into the molecular mechanisms that underlie the regulation of NMDAR subtypes containing pathogenic mutations.
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61
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Gangwar SP, Green MN, Michard E, Simon AA, Feijó JA, Sobolevsky AI. Structure of the Arabidopsis Glutamate Receptor-like Channel GLR3.2 Ligand-Binding Domain. Structure 2020; 29:161-169.e4. [PMID: 33027636 DOI: 10.1016/j.str.2020.09.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/21/2020] [Accepted: 09/15/2020] [Indexed: 12/20/2022]
Abstract
Glutamate receptor-like channels (GLRs) play important roles in numerous plant physiological processes. GLRs are homologous to ionotropic glutamate receptors (iGluRs) that mediate neurotransmission in vertebrates. Here we determine crystal structures of Arabidopsis thaliana GLR3.2 ligand-binding domain (LBD) in complex with glycine and methionine to 1.58- and 1.75-Å resolution, respectively. Our structures show a fold similar to that of iGluRs, but with several secondary structure elements either missing or different. The closed clamshell conformation of GLR3.2 LBD suggests that both glycine and methionine act as agonists. The mutation R133A strongly increases the constitutive activity of the channel, suggesting that the LBD mutated at the residue critical for agonist binding produces a more stable closed clamshell conformation. Furthermore, our structures explain the promiscuity of GLR activation by different amino acids, confirm evolutionary conservation of structure between GLRs and iGluRs, and predict common molecular principles of their gating mechanisms driven by bilobed clamshell-like LBDs.
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Affiliation(s)
- Shanti Pal Gangwar
- Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168(th) Street, New York, NY 10032, USA
| | - Marriah N Green
- Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168(th) Street, New York, NY 10032, USA; Training Program in Nutritional and Metabolic Biology, Institute of Human Nutrition, Columbia University Irving Medical Center, 630 West 168(th) Street, New York, NY 10032, USA
| | - Erwan Michard
- Department of Cell Biology and Molecular Genetics, University of Maryland, 0118 BioScience Research Bldg, College Park, MD 20742-5815, USA
| | - Alexander A Simon
- Department of Cell Biology and Molecular Genetics, University of Maryland, 0118 BioScience Research Bldg, College Park, MD 20742-5815, USA
| | - José A Feijó
- Department of Cell Biology and Molecular Genetics, University of Maryland, 0118 BioScience Research Bldg, College Park, MD 20742-5815, USA.
| | - Alexander I Sobolevsky
- Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168(th) Street, New York, NY 10032, USA.
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62
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Stroebel D, Paoletti P. Architecture and function of NMDA receptors: an evolutionary perspective. J Physiol 2020; 599:2615-2638. [PMID: 32786006 DOI: 10.1113/jp279028] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 07/21/2020] [Indexed: 12/20/2022] Open
Abstract
Ionotropic glutamate receptors (iGluRs) are a major class of ligand-gated ion channels that are widespread in the living kingdom. Their critical role in excitatory neurotransmission and brain function of arthropods and vertebrates has made them a compelling subject of interest for neurophysiologists and pharmacologists. This is particularly true for NMDA receptor (NMDARs), a subclass of iGluRs that act as central drivers of synaptic plasticity in the CNS. How and when the unique properties of NMDARs arose during evolution, and how they relate to the evolution of the nervous system, remain open questions. Recent years have witnessed a boom in both genomic and structural data, such that it is now possible to analyse the evolution of iGluR genes on an unprecedented scale and within a solid molecular framework. In this review, combining insights from phylogeny, atomic structure and physiological and mechanistic data, we discuss how evolution of NMDAR motifs and sequences shaped their architecture and functionalities. We trace differences and commonalities between NMDARs and other iGluRs, emphasizing a few distinctive properties of the former regarding ligand binding and gating, permeation, allosteric modulation and intracellular signalling. Finally, we speculate on how specific molecular properties of iGuRs arose to supply new functions to the evolving structure of the nervous system, from early metazoan to present mammals.
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Affiliation(s)
- David Stroebel
- Ecole Normale Supérieure, CNRS, INSERM, Institute de Biologie de l'Ecole Normale Supérieure (IBENS), Université PSL, Paris, France
| | - Pierre Paoletti
- Ecole Normale Supérieure, CNRS, INSERM, Institute de Biologie de l'Ecole Normale Supérieure (IBENS), Université PSL, Paris, France
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63
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Chin AC, Yovanno RA, Wied TJ, Gershman A, Lau AY. D-Serine Potently Drives Ligand-Binding Domain Closure in the Ionotropic Glutamate Receptor GluD2. Structure 2020; 28:1168-1178.e2. [PMID: 32735769 DOI: 10.1016/j.str.2020.07.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 06/24/2020] [Accepted: 07/10/2020] [Indexed: 12/15/2022]
Abstract
Despite their classification as ionotropic glutamate receptors, GluD receptors are not functional ligand-gated ion channels and do not bind glutamate. GluD2 receptors bind D-serine and coordinate transsynaptic complexes that regulate synaptic plasticity. Instead of opening the ion channel pore, mechanical tension produced from closure of GluD2 ligand-binding domains (LBDs) drives conformational rearrangements for non-ionotropic signaling. We report computed conformational free energy landscapes for the GluD2 LBD in apo and D-serine-bound states. Unexpectedly, the conformational free energy associated with GluD2 LBD closure upon D-serine binding is greater than that for AMPA, NMDA, and kainate receptor LBDs upon agonist binding. This excludes insufficient force generation as an explanation for lack of ion channel activity in GluD2 receptors and suggests that non-ionotropic conformational rearrangements do more work than pore opening. We also report free energy landscapes for GluD2 LBD harboring a neurodegenerative mutation and demonstrate selective stabilization of closed conformations in the apo state.
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Affiliation(s)
- Alfred C Chin
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10065, USA
| | - Remy A Yovanno
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Tyler J Wied
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ariel Gershman
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Albert Y Lau
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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64
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Frydenvang K, Pickering DS, Kshirsagar GU, Chemi G, Gemma S, Sprogøe D, Kærn AM, Brogi S, Campiani G, Butini S, Kastrup JS. Ionotropic Glutamate Receptor GluA2 in Complex with Bicyclic Pyrimidinedione-Based Compounds: When Small Compound Modifications Have Distinct Effects on Binding Interactions. ACS Chem Neurosci 2020; 11:1791-1800. [PMID: 32437601 DOI: 10.1021/acschemneuro.0c00195] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
(S)-2-Amino-3-(5-methyl-3-hydroxyisoxazol-4-yl)propanoic acid (AMPA) receptors comprise an important class of ionotropic glutamate receptors activated by glutamate in the central nervous system. These receptors have been shown to be involved in brain diseases, for example, Alzheimer's disease and epilepsy. To understand the functional role of AMPA receptors at the molecular level and their potential as targets for drugs, development of tool compounds is essential. We have previously reported the synthesis of six bicyclic pyrimidinedione-based analogues of willardiine with differences limited to the pyrimidinedione-fused five-membered rings. Despite minor molecular differences, we observed >500-fold difference in binding affinity of the compounds at full-length GluA2. Here, we report binding affinities and the binding mode of these compounds at the ligand-binding domain of GluA2 using X-ray crystallography. The structures revealed similar binding modes, with distinct differences in the interaction between GluA2 and the compounds. The methylene (2) and sulfur (3) containing compounds showed the greatest binding affinities. Changing the dihydrothiophene (3) into pyrrolidine (4), N-methyl pyrrolidine (5), or dihydrofuran (6) induced flexibility in the position of a binding-site water molecule and changes in the hydrogen-bonding network between compound, water, and GluA2. This might be essential for explaining the reduced binding affinity of these compounds. The weakest binding affinity was observed when the aliphatic oxygen containing dihydrofuran (6) was changed into an aromatic furan system (7). Molecular docking studies revealed two possible orientations of 7, whereas only one binding mode was observed for the other analogues. This could likely contribute to the weakest binding affinity of 7 at GluA2.
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Affiliation(s)
- Karla Frydenvang
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark
| | - Darryl S. Pickering
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark
| | - Giridhar U. Kshirsagar
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark
- Department of Biotechnology, Chemistry and Pharmacy (DoE 2018-2022), University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Giulia Chemi
- Department of Biotechnology, Chemistry and Pharmacy (DoE 2018-2022), University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Sandra Gemma
- Department of Biotechnology, Chemistry and Pharmacy (DoE 2018-2022), University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Desiree Sprogøe
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark
| | - Anne Mette Kærn
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark
| | - Simone Brogi
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Giuseppe Campiani
- Department of Biotechnology, Chemistry and Pharmacy (DoE 2018-2022), University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Stefania Butini
- Department of Biotechnology, Chemistry and Pharmacy (DoE 2018-2022), University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Jette Sandholm Kastrup
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark
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65
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Salazar H, Mischke S, Plested AJR. Measurements of the Timescale and Conformational Space of AMPA Receptor Desensitization. Biophys J 2020; 119:206-218. [PMID: 32559412 PMCID: PMC7335938 DOI: 10.1016/j.bpj.2020.05.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 04/06/2020] [Accepted: 05/29/2020] [Indexed: 12/19/2022] Open
Abstract
Ionotropic glutamate receptors are ligand-gated ion channels that mediate excitatory synaptic transmission in the central nervous system. Desensitization of the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid subtype after glutamate binding appears critical for brain function and involves rearrangement of the ligand binding domains (LBDs). Recently, several full-length structures of ionotropic glutamate receptors in putative desensitized states were published. These structures indicate movements of the LBDs that might be trapped by cysteine cross-links and metal bridges. We found that cysteine mutants at the interface between subunits A and C and lateral zinc bridges (between subunits C and D or A and B) can trap freely desensitizing receptors in a spectrum of states with different stabilities. Consistent with a close approach of subunits during desensitization processes, the introduction of bulky amino acids at the A-C interface produced a receptor with slow recovery from desensitization. Further, in wild-type GluA2 receptors, we detected the population of a stable desensitized state with a lifetime around 1 s. Using mutations that progressively stabilize deep desensitized states (E713T and Y768R), we were able to selectively protect receptors from cross-links at both the diagonal and lateral interfaces. Ultrafast perfusion enabled us to perform chemical modification in less than 10 ms, reporting movements associated to desensitization on this timescale within LBD dimers in resting receptors. These observations suggest that small disruptions of quaternary structure are sufficient for fast desensitization and that substantial rearrangements likely correspond to stable desensitized states that are adopted relatively slowly on a timescale much longer than physiological receptor activation.
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Affiliation(s)
- Hector Salazar
- Institute of Biology, Cellular Biophysics, Humboldt Universität zu Berlin, Berlin, Germany; Leibniz-Forschungsinstitut für Molekulare Pharmakologie Berlin, Germany; Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, and Berlin Institute of Health, NeuroCure Cluster of Excellence, Berlin, Germany
| | - Sabrina Mischke
- Institute of Biology, Cellular Biophysics, Humboldt Universität zu Berlin, Berlin, Germany; Leibniz-Forschungsinstitut für Molekulare Pharmakologie Berlin, Germany; Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, and Berlin Institute of Health, NeuroCure Cluster of Excellence, Berlin, Germany
| | - Andrew J R Plested
- Institute of Biology, Cellular Biophysics, Humboldt Universität zu Berlin, Berlin, Germany; Leibniz-Forschungsinstitut für Molekulare Pharmakologie Berlin, Germany; Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, and Berlin Institute of Health, NeuroCure Cluster of Excellence, Berlin, Germany.
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66
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Sanford L, Palmer AE. Dissociated Hippocampal Neurons Exhibit Distinct Zn 2+ Dynamics in a Stimulation-Method-Dependent Manner. ACS Chem Neurosci 2020; 11:508-514. [PMID: 32013397 PMCID: PMC7251562 DOI: 10.1021/acschemneuro.0c00006] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Ionic Zn2+ has increasingly been recognized as an important neurotransmitter and signaling ion in glutamatergic neuron pathways. Intracellular Zn2+ transiently increases as a result of neuronal excitation, and this Zn2+ signal is essential for neuron plasticity, but the source and regulation of the signal is still unclear. In this study, we rigorously quantified Zn2+, Ca2+, and pH dynamics in dissociated mouse hippocampal neurons stimulated with bath application of high KCl or glutamate. While both stimulation methods yielded Zn2+ signals, Ca2+ influx, and acidification, glutamate stimulation induced more sustained high intracellular Ca2+ and a larger increase in intracellular Zn2+. However, the stimulation-induced pH change was similar between conditions, indicating that a different cellular change is responsible for the stimulation-dependent difference in Zn2+ signal. This work provides the first robust quantification of Zn2+ dynamics in neurons using different methods of stimulation.
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Affiliation(s)
- Lynn Sanford
- Department of Biochemistry, BioFrontiers Institute , University of Colorado Boulder , Boulder , Colorado 80309 , United States
| | - Amy E Palmer
- Department of Biochemistry, BioFrontiers Institute , University of Colorado Boulder , Boulder , Colorado 80309 , United States
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67
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Kamalova A, Nakagawa T. AMPA receptor structure and auxiliary subunits. J Physiol 2020; 599:453-469. [PMID: 32004381 DOI: 10.1113/jp278701] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/28/2020] [Indexed: 11/08/2022] Open
Abstract
Fast excitatory synaptic transmission in the mammalian brain is largely mediated by AMPA-type ionotropic glutamate receptors (AMPARs), which are activated by the neurotransmitter glutamate. In synapses, the function of AMPARs is tuned by their auxiliary subunits, a diverse set of membrane proteins associated with the core pore-forming subunits of the AMPARs. Each auxiliary subunit provides distinct functional modulation of AMPARs, ranging from regulation of trafficking to shaping ion channel gating kinetics. Understanding the molecular mechanism of the function of these complexes is key to decoding synaptic modulation and their global roles in cognitive activities, such as learning and memory. Here, we review the structural and molecular complexity of AMPAR-auxiliary subunit complexes, as well as their functional diversity in different brain regions. We suggest that the recent structural information provides new insights into the molecular mechanisms underlying synaptic functions of AMPAR-auxiliary subunit complexes.
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Affiliation(s)
- Aichurok Kamalova
- Department of Molecular Physiology and Biophysics, Vanderbilt University, School of Medicine, Nashville, TN, 37232, USA.,Vanderbilt Brain Institute, Vanderbilt University, School of Medicine, Nashville, TN, 37232, USA
| | - Terunaga Nakagawa
- Department of Molecular Physiology and Biophysics, Vanderbilt University, School of Medicine, Nashville, TN, 37232, USA.,Vanderbilt Brain Institute, Vanderbilt University, School of Medicine, Nashville, TN, 37232, USA.,Center for Structural Biology, Vanderbilt University, School of Medicine, Nashville, TN, 37232, USA
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68
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Wang JX, Irvine MW, Burnell ES, Sapkota K, Thatcher RJ, Li M, Simorowski N, Volianskis A, Collingridge GL, Monaghan DT, Jane DE, Furukawa H. Structural basis of subtype-selective competitive antagonism for GluN2C/2D-containing NMDA receptors. Nat Commun 2020; 11:423. [PMID: 31969570 PMCID: PMC6976569 DOI: 10.1038/s41467-020-14321-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 12/18/2019] [Indexed: 12/15/2022] Open
Abstract
N-Methyl-D-aspartate receptors (NMDARs) play critical roles in the central nervous system. Their heterotetrameric composition generates subtypes with distinct functional properties and spatio-temporal distribution in the brain, raising the possibility for subtype-specific targeting by pharmacological means for treatment of neurological diseases. While specific compounds for GluN2A and GluN2B-containing NMDARs are well established, those that target GluN2C and GluN2D are currently underdeveloped with low potency and uncharacterized binding modes. Here, using electrophysiology and X-ray crystallography, we show that UBP791 ((2S*,3R*)-1-(7-(2-carboxyethyl)phenanthrene-2-carbonyl)piperazine-2,3-dicarboxylic acid) inhibits GluN2C/2D with 40-fold selectivity over GluN2A-containing receptors, and that a methionine and a lysine residue in the ligand binding pocket (GluN2D-Met763/Lys766, GluN2C-Met736/Lys739) are the critical molecular elements for the subtype-specific binding. These findings led to development of UBP1700 ((2S*,3R*)-1-(7-(2-carboxyvinyl)phenanthrene-2-carbonyl)piperazine-2,3-dicarboxylic acid) which shows over 50-fold GluN2C/2D-selectivity over GluN2A with potencies in the low nanomolar range. Our study shows that the L-glutamate binding site can be targeted for GluN2C/2D-specific inhibition.
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Affiliation(s)
- Jue Xiang Wang
- WM Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Mark W Irvine
- Glutamate Research Group, School of Physiology, Pharmacology and Neuroscience, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, BS8 1TD, UK
| | - Erica S Burnell
- Glutamate Research Group, School of Physiology, Pharmacology and Neuroscience, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, BS8 1TD, UK
- School of Chemistry, National University of Ireland Galway, Galway, H91TK33, Ireland
| | - Kiran Sapkota
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, 68198-5800, USA
| | - Robert J Thatcher
- Glutamate Research Group, School of Physiology, Pharmacology and Neuroscience, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, BS8 1TD, UK
| | - Minjun Li
- WM Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Noriko Simorowski
- WM Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Arturas Volianskis
- Centre for Neuroscience and Trauma, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Graham L Collingridge
- Glutamate Research Group, School of Physiology, Pharmacology and Neuroscience, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, BS8 1TD, UK
- Tanz Centre for Research in Neurodegenerative Diseases, Department of Physiology, University of Toronto, Krembil Discovery Tower, 60 Leonard Avenue, Toronto, ON, M5T 0S8, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON, M5G 1X5, Canada
| | - Daniel T Monaghan
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, 68198-5800, USA
| | - David E Jane
- Glutamate Research Group, School of Physiology, Pharmacology and Neuroscience, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, BS8 1TD, UK.
| | - Hiro Furukawa
- WM Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.
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69
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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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70
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Nakagawa T. Structures of the AMPA receptor in complex with its auxiliary subunit cornichon. Science 2019; 366:1259-1263. [DOI: 10.1126/science.aay2783] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 10/21/2019] [Indexed: 01/18/2023]
Abstract
In the brain, AMPA-type glutamate receptors (AMPARs) form complexes with their auxiliary subunits and mediate the majority of fast excitatory neurotransmission. Signals transduced by these complexes are critical for synaptic plasticity, learning, and memory. The two major categories of AMPAR auxiliary subunits are transmembrane AMPAR regulatory proteins (TARPs) and cornichon homologs (CNIHs); these subunits share little homology and play distinct roles in controlling ion channel gating and trafficking of AMPAR. Here, I report high-resolution cryo–electron microscopy structures of AMPAR in complex with CNIH3. Contrary to its predicted membrane topology, CNIH3 lacks an extracellular domain and instead contains four membrane-spanning helices. The protein-protein interaction interface that dictates channel modulation and the lipids surrounding the complex are revealed. These structures provide insights into the molecular mechanism for ion channel modulation and assembly of AMPAR/CNIH3 complexes.
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Affiliation(s)
- Terunaga Nakagawa
- Department of Molecular Physiology and Biophysics, Center for Structural Biology, and Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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71
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Lee JY, Krieger JM, Li H, Bahar I. Pharmmaker: Pharmacophore modeling and hit identification based on druggability simulations. Protein Sci 2019; 29:76-86. [PMID: 31576621 PMCID: PMC6933858 DOI: 10.1002/pro.3732] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/16/2019] [Accepted: 09/17/2019] [Indexed: 12/14/2022]
Abstract
Recent years have seen progress in druggability simulations, that is, molecular dynamics simulations of target proteins in solutions containing drug‐like probe molecules to characterize their drug‐binding abilities, if any. An important consecutive step is to analyze the trajectories to construct pharmacophore models (PMs) to use for virtual screening of libraries of small molecules. While considerable success has been observed in this type of computer‐aided drug discovery, a systematic tool encompassing multiple steps from druggability simulations to pharmacophore modeling, to identifying hits by virtual screening of libraries of compounds, has been lacking. We address this need here by developing a new tool, Pharmmaker, building on the DruGUI module of our ProDy application programming interface. Pharmmaker is composed of a suite of steps: (Step 1) identification of high affinity residues for each probe molecule type; (Step 2) selecting high affinity residues and hot spots in the vicinity of sites identified by DruGUI; (Step 3) ranking of the interactions between high affinity residues and specific probes; (Step 4) obtaining probe binding poses and corresponding protein conformations by collecting top‐ranked snapshots; and (Step 5) using those snapshots for constructing PMs. The PMs are then used as filters for identifying hits in structure‐based virtual screening. Pharmmaker, accessible online at http://prody.csb.pitt.edu/pharmmaker/, can be used in conjunction with other tools available in ProDy.
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Affiliation(s)
- Ji Young Lee
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - James M Krieger
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Hongchun Li
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
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72
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Myers SJ, Yuan H, Kang JQ, Tan FCK, Traynelis SF, Low CM. Distinct roles of GRIN2A and GRIN2B variants in neurological conditions. F1000Res 2019; 8:F1000 Faculty Rev-1940. [PMID: 31807283 PMCID: PMC6871362 DOI: 10.12688/f1000research.18949.1] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/08/2019] [Indexed: 12/12/2022] Open
Abstract
Rapid advances in sequencing technology have led to an explosive increase in the number of genetic variants identified in patients with neurological disease and have also enabled the assembly of a robust database of variants in healthy individuals. A surprising number of variants in the GRIN genes that encode N-methyl-D-aspartate (NMDA) glutamatergic receptor subunits have been found in patients with various neuropsychiatric disorders, including autism spectrum disorders, epilepsy, intellectual disability, attention-deficit/hyperactivity disorder, and schizophrenia. This review compares and contrasts the available information describing the clinical and functional consequences of genetic variations in GRIN2A and GRIN2B. Comparison of clinical phenotypes shows that GRIN2A variants are commonly associated with an epileptic phenotype but that GRIN2B variants are commonly found in patients with neurodevelopmental disorders. These observations emphasize the distinct roles that the gene products serve in circuit function and suggest that functional analysis of GRIN2A and GRIN2B variation may provide insight into the molecular mechanisms, which will allow more accurate subclassification of clinical phenotypes. Furthermore, characterization of the pharmacological properties of variant receptors could provide the first opportunity for translational therapeutic strategies for these GRIN-related neurological and psychiatric disorders.
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Affiliation(s)
- Scott J Myers
- Center for Functional Evaluation of Rare Variants (CFERV), Emory University, Atlanta, GA, USA
- Department of Pharmacology and Chemical Biology, Emory University, Atlanta, GA, USA
| | - Hongjie Yuan
- Center for Functional Evaluation of Rare Variants (CFERV), Emory University, Atlanta, GA, USA
- Department of Pharmacology and Chemical Biology, Emory University, Atlanta, GA, USA
| | - Jing-Qiong Kang
- Department of Neurology, Vanderbilt Brain Institute, Vanderbilt Kennedy Center of Human Development, Vanderbilt University, Nashville, TN, USA
| | - Francis Chee Kuan Tan
- Department of Anaesthesia, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Stephen F Traynelis
- Center for Functional Evaluation of Rare Variants (CFERV), Emory University, Atlanta, GA, USA
- Department of Pharmacology and Chemical Biology, Emory University, Atlanta, GA, USA
| | - Chian-Ming Low
- Department of Anaesthesia, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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73
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Sakakura M, Ohkubo Y, Oshima H, Re S, Ito M, Sugita Y, Takahashi H. Structural Mechanisms Underlying Activity Changes in an AMPA-type Glutamate Receptor Induced by Substitutions in Its Ligand-Binding Domain. Structure 2019; 27:1698-1709.e5. [PMID: 31585769 DOI: 10.1016/j.str.2019.09.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/24/2019] [Accepted: 09/13/2019] [Indexed: 10/25/2022]
Abstract
α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)-type glutamate receptors produce postsynaptic current by transmitting an agonist-induced structural change in the ligand-binding domain (LBD) to the transmembrane channel. Receptors carrying T686S/A substitutions in their LBDs produce weaker glutamate-evoked currents than wild-type (WT) receptors. However, the substitutions induce little differences in the crystal structures of their LBDs. To understand the structural mechanism underlying reduced activities of these AMPAR variants, we analyzed the structural dynamics of WT, T686S, and T686A variants of LBD using nuclear magnetic resonance. The HD exchange studies of the LBDs showed that the kinetic step where the ligand-binding cleft closes was changed by the substitutions, and the substitution-induced population shift from cleft-closed to cleft-open structures is responsible for the reduced activities of the variants. The chemical shift analyses revealed another structural equilibrium between cleft-locked and cleft-partially-open conformations. The substitution-induced population shift in this equilibrium may be related to slower desensitization observed for these variants.
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Affiliation(s)
- Masayoshi Sakakura
- Graduate School of Medical Life Science, Yokohama City University, Yokohama 230-0045, Japan.
| | - Yumi Ohkubo
- Graduate School of Medical Life Science, Yokohama City University, Yokohama 230-0045, Japan
| | - Hiraku Oshima
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | - Suyong Re
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | - Masahiro Ito
- Graduate School of Medical Life Science, Yokohama City University, Yokohama 230-0045, Japan
| | - Yuji Sugita
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan; Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako 351-0198, Japan; Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe 650-0047, Japan
| | - Hideo Takahashi
- Graduate School of Medical Life Science, Yokohama City University, Yokohama 230-0045, Japan.
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74
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Coombs ID, Soto D, McGee TP, Gold MG, Farrant M, Cull-Candy SG. Homomeric GluA2(R) AMPA receptors can conduct when desensitized. Nat Commun 2019; 10:4312. [PMID: 31541113 PMCID: PMC6754398 DOI: 10.1038/s41467-019-12280-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 08/28/2019] [Indexed: 11/21/2022] Open
Abstract
Desensitization is a canonical property of ligand-gated ion channels, causing progressive current decline in the continued presence of agonist. AMPA-type glutamate receptors (AMPARs), which mediate fast excitatory signaling throughout the brain, exhibit profound desensitization. Recent cryo-EM studies of AMPAR assemblies show their ion channels to be closed in the desensitized state. Here we present evidence that homomeric Q/R-edited AMPARs still allow ions to flow when the receptors are desensitized. GluA2(R) expressed alone, or with auxiliary subunits (γ-2, γ-8 or GSG1L), generates large fractional steady-state currents and anomalous current-variance relationships. Our results from fluctuation analysis, single-channel recording, and kinetic modeling, suggest that the steady-state current is mediated predominantly by conducting desensitized receptors. When combined with crystallography this unique functional readout of a hitherto silent state enabled us to examine cross-linked cysteine mutants to probe the conformation of the desensitized ligand binding domain of functioning AMPAR complexes. AMPA-type glutamate receptors, which mediate fast excitatory signaling throughout the brain, exhibit profound desensitization, causing a progressive current decline in the continued presence of agonist. Here authors show that homomeric Q/R edited AMPARs still allow ions to flow when the receptors are desensitized.
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Affiliation(s)
- Ian D Coombs
- Department of Neuroscience, Physiology and Pharmacology, University College London, Gower Street, London, WC1E 6BT, UK
| | - David Soto
- Department of Neuroscience, Physiology and Pharmacology, University College London, Gower Street, London, WC1E 6BT, UK.,Department of Biomedicine, Neurophysiology Laboratory, Medical School, Institute of Neurosciences, University of Barcelona, Casanova 143, 08036, Barcelona, Spain
| | - Thomas P McGee
- Department of Neuroscience, Physiology and Pharmacology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Matthew G Gold
- Department of Neuroscience, Physiology and Pharmacology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Mark Farrant
- Department of Neuroscience, Physiology and Pharmacology, University College London, Gower Street, London, WC1E 6BT, UK.
| | - Stuart G Cull-Candy
- Department of Neuroscience, Physiology and Pharmacology, University College London, Gower Street, London, WC1E 6BT, UK.
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75
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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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76
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Dudić A, Reiner A. Quinoxalinedione deprotonation is important for glutamate receptor binding. Biol Chem 2019; 400:927-938. [PMID: 30903748 DOI: 10.1515/hsz-2018-0464] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 03/15/2019] [Indexed: 01/27/2023]
Abstract
Quinoxalinediones are an important class of competitive antagonists at ionotropic glutamate receptors (iGluRs), where they are widely used to block α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) and kainate receptor responses. In this study we utilize two prototypic quinoxalinedione antagonists, namely DNQX and CNQX, which quench the intrinsic fluorescence of the ligand binding domain (LBD), to perform in vitro binding assays. We find that binding of DNQX and CNQX at the AMPA receptor GluA2 LBD is strongly pH dependent, whereas glutamate binding is not affected by pH. We also show that the deprotonation of DNQX, CNQX and other quinoxalinediones (NBQX and YM90K) occurs close to physiological pH, which can be explained by the lactam-lactim tautomerization of the quinoxalinedione scaffold. Analysis of our binding data indicates that quinoxalinedione deprotonation is a key requirement for binding, as we find a >100-fold higher affinity for binding of the monoanionic form compared to the neutral form. This suggests a large electrostatic contribution to the interaction with a conserved arginine residue located in the binding pocket of iGluRs. The strong pH dependence of quinoxalinedione binding, which has not previously been reported, is relevant for structure-function studies, but also for the use of quinoxalinediones in physiological experiments and envisioned therapeutic applications.
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Affiliation(s)
- Adela Dudić
- Department of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, D-44801 Bochum, Germany
| | - Andreas Reiner
- Department of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, D-44801 Bochum, Germany
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77
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On-cell coordination chemistry: Chemogenetic activation of membrane-bound glutamate receptors in living cells. Methods Enzymol 2019. [PMID: 31155063 DOI: 10.1016/bs.mie.2019.02.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Investigating functions of membrane-bound receptors provides invaluable information about cellular signaling and physiological events. Recently, chemical genetic methods to design chemical switches on the target proteins have intensely been developed for interrogation of the cellular signaling of individual receptor proteins. We recently reported coordination chemistry-based chemogenetics to allosterically activate two types of neurotransmitter receptors, ionotropic and metabotropic glutamate receptors, in living cells. Based on their well-studied structure-activity relationships, we semi-rationally incorporated two His mutations into glutamate receptors near ligand binding pockets as an allosteric site. The engineered glutamate receptors could be allosterically activated upon treatment of Pd(bpy) complex (bpy: 2,2'-bipyridine) through stabilization of the activated conformation in mammalian cells and cultured neurons. Here, we describe the detailed protocol of our approach including the receptor design and activation of the His-engineered receptors and the downstream of the signal transduction cascade in living cells.
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78
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Mechanisms of zinc modulation of olfactory bulb AMPA receptors. Neuroscience 2019; 410:160-175. [PMID: 31082537 DOI: 10.1016/j.neuroscience.2019.05.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 05/01/2019] [Accepted: 05/03/2019] [Indexed: 12/31/2022]
Abstract
The alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) subtype of ionotropic glutamate receptors mediates most fast excitatory transmission. Glutamate binding to AMPA receptors (AMPARs) causes most AMPARs to rapidly and completely desensitize, and their desensitization kinetics influence synaptic timing. Thus, factors that alter AMPAR desensitization influence synaptic transmission. Synaptically released zinc is such a factor. Zinc is a neuromodulator with effects on amino acid receptors and synaptic transmission in many brain regions, including the olfactory bulb (OB). We have previously shown in the OB that zinc potentiates AMPAR-mediated currents at low concentrations (30 μM, 100 μM) and inhibits them at a higher concentration (1 mM). It has been hypothesized that zinc potentiates AMPARs by decreasing receptor desensitization. Here, we used cyclothiazide (CTZ), a drug that blocks AMPAR desensitization, to determine whether zinc-mediated potentiation and/or inhibition of AMPA-evoked currents reflect(s) changes in AMPAR desensitization. Zinc largely had biphasic concentration-dependent effects at OB AMPARs. CTZ completely blocked potentiation by zinc but had no significant effect on inhibition. There was a significant negative correlation between the degree of potentiation of AMPAR-mediated currents by 100 μM zinc and a quantitative measure of the degree of AMPAR desensitization (the steady-state to peak [S:P] ratio of AMPA-evoked currents), but no correlation between the degree of current inhibition by 1 mM zinc and the S:P ratio. Together, these findings suggest that low zinc concentrations potentiate rat OB AMPARs by decreasing receptor desensitization, but that the inhibitory effects of higher zinc concentrations are mediated by a separate mechanism.
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79
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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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80
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Herguedas B, Watson JF, Ho H, Cais O, García-Nafría J, Greger IH. Architecture of the heteromeric GluA1/2 AMPA receptor in complex with the auxiliary subunit TARP γ8. Science 2019; 364:science.aav9011. [PMID: 30872532 PMCID: PMC6513756 DOI: 10.1126/science.aav9011] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 03/04/2019] [Indexed: 11/02/2022]
Abstract
AMPA-type glutamate receptors (AMPARs) mediate excitatory neurotransmission and are central regulators of synaptic plasticity, a molecular mechanism underlying learning and memory. Although AMPARs act predominantly as heteromers, structural studies have focused on homomeric assemblies. Here, we present a cryo-electron microscopy structure of the heteromeric GluA1/2 receptor associated with two transmembrane AMPAR regulatory protein (TARP) γ8 auxiliary subunits, the principal AMPAR complex at hippocampal synapses. Within the receptor, the core subunits arrange to give the GluA2 subunit dominant control of gating. This structure reveals the geometry of the Q/R site that controls calcium flux, suggests association of TARP-stabilized lipids, and demonstrates that the extracellular loop of γ8 modulates gating by selectively interacting with the GluA2 ligand-binding domain. Collectively, this structure provides a blueprint for deciphering the signal transduction mechanisms of synaptic AMPARs.
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Affiliation(s)
- Beatriz Herguedas
- Neurobiology Division, Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, UK.
| | - Jake F Watson
- Neurobiology Division, Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, UK
| | - Hinze Ho
- Neurobiology Division, Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, UK
| | - Ondrej Cais
- Neurobiology Division, Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, UK
| | | | - Ingo H Greger
- Neurobiology Division, Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, UK.
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81
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Sainas S, Temperini P, Farnsworth JC, Yi F, Møllerud S, Jensen AA, Nielsen B, Passoni A, Kastrup JS, Hansen KB, Boschi D, Pickering DS, Clausen RP, Lolli ML. Use of the 4-Hydroxytriazole Moiety as a Bioisosteric Tool in the Development of Ionotropic Glutamate Receptor Ligands. J Med Chem 2019; 62:4467-4482. [PMID: 30943028 DOI: 10.1021/acs.jmedchem.8b01986] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We report a series of glutamate and aspartate analogues designed using the hydroxy-1,2,3-triazole moiety as a bioisostere for the distal carboxylic acid. Compound 6b showed unprecedented selectivity among ( S)-2-amino-3-(3-hydroxy-5-methyl-4-isoxazolyl)propionic acid (AMPA) receptor subtypes, confirmed also by an unusual binding mode observed for the crystal structures in complex with the AMPA receptor GluA2 agonist-binding domain. Here, a methionine (Met729) was highly disordered compared to previous agonist-bound structures. This observation provides a possible explanation for the pharmacological profile. In the structure with 7a, an unusual organization of water molecules around the bioisostere arises compared to previous structures of ligands with other bioisosteres. Aspartate analogue 8 with the hydroxy-1,2,3-triazole moiety directly attached to glycine was unexpectedly able to activate both the glutamate and glycine agonist-binding sites of the N-methyl-d-aspartic acid receptor. These observations demonstrate novel features that arise when employing a hydroxytriazole moiety as a bioisostere for the distal carboxylic acid in glutamate receptor agonists.
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Affiliation(s)
- Stefano Sainas
- Department of Drug Science and Technology , University of Turin , via P.Giuria 9 , 10125 Turin , Italy
| | - Piero Temperini
- Department of Drug Design and Pharmacology , University of Copenhagen , 2100 Copenhagen , Denmark
| | - Jill C Farnsworth
- Department of Biomedical and Pharmaceutical Sciences, Center for Structural and Functional Neuroscience, and Center for Biomolecular Structure and Dynamics , University of Montana , Missoula , Montana 59812 , United States
| | - Feng Yi
- Department of Biomedical and Pharmaceutical Sciences, Center for Structural and Functional Neuroscience, and Center for Biomolecular Structure and Dynamics , University of Montana , Missoula , Montana 59812 , United States
| | - Stine Møllerud
- Department of Drug Design and Pharmacology , University of Copenhagen , 2100 Copenhagen , Denmark
| | - Anders A Jensen
- Department of Drug Design and Pharmacology , University of Copenhagen , 2100 Copenhagen , Denmark
| | - Birgitte Nielsen
- Department of Drug Design and Pharmacology , University of Copenhagen , 2100 Copenhagen , Denmark
| | - Alice Passoni
- Istituto di Ricerche Farmacologiche "Mario Negri" IRCCS , via La Masa 19 , 20156 Milan , Italy
| | - Jette S Kastrup
- Department of Drug Design and Pharmacology , University of Copenhagen , 2100 Copenhagen , Denmark
| | - Kasper B Hansen
- Department of Biomedical and Pharmaceutical Sciences, Center for Structural and Functional Neuroscience, and Center for Biomolecular Structure and Dynamics , University of Montana , Missoula , Montana 59812 , United States
| | - Donatella Boschi
- Department of Drug Science and Technology , University of Turin , via P.Giuria 9 , 10125 Turin , Italy
| | - Darryl S Pickering
- Department of Drug Design and Pharmacology , University of Copenhagen , 2100 Copenhagen , Denmark
| | - Rasmus P Clausen
- Department of Drug Design and Pharmacology , University of Copenhagen , 2100 Copenhagen , Denmark
| | - Marco L Lolli
- Department of Drug Science and Technology , University of Turin , via P.Giuria 9 , 10125 Turin , Italy
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82
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Developing RNA aptamers for potential treatment of neurological diseases. Future Med Chem 2019; 11:551-565. [PMID: 30912676 DOI: 10.4155/fmc-2018-0364] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
AMPA receptor antagonists are drug candidates for potential treatment of a number of CNS diseases that involve excessive receptor activation. To date, small-molecule compounds are the dominating drug candidates in the field. However, lower potency, cross activity and poor water solubility are generally associated with these compounds. Here we show the potential of RNA-based antagonists or RNA aptamers as drug candidates and some strategies to discover these aptamers from a random sequence library (∼1014 sequences). As an alternative to small molecule compounds, our aptamers exhibit higher potency and selectivity toward AMPA receptors. Because aptamers are RNA molecules, they are naturally water soluble. We also discuss the major challenges of translating RNA aptamers as lead molecules into drugs/treatment options.
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83
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Yuan C, Shi EY, Srinivasan J, Ptak CP, Oswald RE, Nowak LM. Modulation of AMPA Receptor Gating by the Anticonvulsant Drug, Perampanel. ACS Med Chem Lett 2019; 10:237-242. [PMID: 30891119 PMCID: PMC6421588 DOI: 10.1021/acsmedchemlett.8b00322] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 10/16/2018] [Indexed: 12/23/2022] Open
Abstract
Postsynaptic AMPA/glutamate receptors, essential for neuronal excitability, are important targets for anticonvulsant therapy. This single channel study of the selective noncompetitive AMPA receptor antagonist, perampanel, was performed on homotetrameric GluA3 receptor-channels that open in a stepwise manner to four distinct conductance levels through independent subunit activation. Previous structural studies show that perampanel binds to four sites located within the extracellular/transmembrane boundary of closed AMPA receptor-channel subunits. We found that channels exposed to 1 or 2 μM perampanel opened mainly to the two lower conductance levels in a dose-dependent manner. Comparison of the single channel results in the structures of the full length AMPA receptor in the closed state bound to perampanel, and the open state provide insights into the mechanism of allosteric reduction of AMPA-receptor-mediated excitation in epilepsy.
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Affiliation(s)
| | | | - Jayasri Srinivasan
- Department of Molecular Medicine, Cornell University, Ithaca, New York 14850 United States
| | - Christopher P. Ptak
- Department of Molecular Medicine, Cornell University, Ithaca, New York 14850 United States
| | - Robert E. Oswald
- Department of Molecular Medicine, Cornell University, Ithaca, New York 14850 United States
| | - Linda M. Nowak
- Department of Molecular Medicine, Cornell University, Ithaca, New York 14850 United States
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84
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Laulumaa S, Hansen KV, Masternak M, Drapier T, Francotte P, Pirotte B, Frydenvang K, Kastrup JS. Crystal Structures of Potent Dimeric Positive Allosteric Modulators at the Ligand-Binding Domain of the GluA2 Receptor. ACS Med Chem Lett 2019; 10:243-247. [PMID: 30891120 DOI: 10.1021/acsmedchemlett.8b00369] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 11/04/2018] [Indexed: 11/30/2022] Open
Abstract
The ionotropic glutamate receptor GluA2 is considered to be an attractive target for positive allosteric modulation for the development of pharmacological tools or cognitive enhancers. Here, we report a detailed structural characterization of two recently reported dimeric positive allosteric modulators, TDPAM01 and TDPAM02, with nanomolar potency at GluA2. Using X-ray crystallography, TDPAM01 and TDPAM02 were crystallized in the ligand-binding domain of the GluA2 flop isoform as well as in the flip-like mutant N775S and the preformed dimer L504Y-N775S. In all structures, one modulator molecule binds at the dimer interface with two characteristic hydrogen bonds being formed from the modulator to Pro515. Whereas the GluA2 dimers and modulator binding mode are similar when crystallized in the presence of l-glutamate, the shape of the binding site differs when no l-glutamate is present. TDPAM02 has no effect on domain closure in both apo and l-glutamate bound GluA2 dimers compared to structures without modulator.
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Affiliation(s)
- Saara Laulumaa
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark
| | - Kathrine Voigt Hansen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark
| | - Magdalena Masternak
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark
| | - Thomas Drapier
- Laboratory of Medicinal Chemistry, Center for Interdisciplinary Research on Medicines (CIRM), ULiège, Quartier Hôpital, Avenue Hippocrate,15, B36, B-4000 Liège, Belgium
| | - Pierre Francotte
- Laboratory of Medicinal Chemistry, Center for Interdisciplinary Research on Medicines (CIRM), ULiège, Quartier Hôpital, Avenue Hippocrate,15, B36, B-4000 Liège, Belgium
| | - Bernard Pirotte
- Laboratory of Medicinal Chemistry, Center for Interdisciplinary Research on Medicines (CIRM), ULiège, Quartier Hôpital, Avenue Hippocrate,15, B36, B-4000 Liège, Belgium
| | - Karla Frydenvang
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark
| | - Jette Sandholm Kastrup
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark
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85
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Structure and mechanism of AMPA receptor - auxiliary protein complexes. Curr Opin Struct Biol 2019; 54:104-111. [PMID: 30825796 DOI: 10.1016/j.sbi.2019.01.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 01/25/2019] [Accepted: 01/28/2019] [Indexed: 11/21/2022]
Abstract
Ionotropic glutamate receptors in vertebrates are composed of three major subtypes - AMPA, kainate, and NMDA receptors - and mediate the majority of fast excitatory neurotransmission at chemical synapses of the central nervous system. Among the three major families, native AMPA receptors function as complexes with a variety of auxiliary subunits, which in turn modulate receptor trafficking, gating, pharmacology, and permeation. Despite the long history of structure-mechanism studies using soluble receptor domains or intact yet isolated receptors, structures of AMPA receptor-auxiliary subunit complexes have not been available until recent breakthroughs in single-particle cryo-electron microscopy. Single particle cryo-EM studies have, in turn, provided new insights into the structure and organization of AMPA receptor - auxiliary protein complexes and into the molecular mechanisms of AMPA receptor activation and desensitization.
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86
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Piotrowska DG, Głowacka IE, Wróblewski AE, Lubowiecka L. Synthesis of nonracemic hydroxyglutamic acids. Beilstein J Org Chem 2019; 15:236-255. [PMID: 30745997 PMCID: PMC6350885 DOI: 10.3762/bjoc.15.22] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 12/22/2018] [Indexed: 11/24/2022] Open
Abstract
Glutamic acid is involved in several cellular processes though its role as the neurotransmitter is best recognized. For detailed studies of interactions with receptors a number of structural analogues of glutamic acid are required to map their active sides. This review article summarizes syntheses of nonracemic hydroxyglutamic acid analogues equipped with functional groups capable for the formation of additional hydrogen bonds, both as donors and acceptors. The majority of synthetic strategies starts from natural products and relies on application of chirons having the required configuration at the carbon atom bonded to nitrogen (e.g., serine, glutamic and pyroglutamic acids, proline and 4-hydroxyproline). Since various hydroxyglutamic acids were identified as components of complex natural products, syntheses of orthogonally protected derivatives of hydroxyglutamic acids are also covered.
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Affiliation(s)
- Dorota G Piotrowska
- Bioorganic Chemistry Laboratory, Faculty of Pharmacy, Medical University of Lodz, Muszynskiego 1, 90-151 Lodz, Poland
| | - Iwona E Głowacka
- Bioorganic Chemistry Laboratory, Faculty of Pharmacy, Medical University of Lodz, Muszynskiego 1, 90-151 Lodz, Poland
| | - Andrzej E Wróblewski
- Bioorganic Chemistry Laboratory, Faculty of Pharmacy, Medical University of Lodz, Muszynskiego 1, 90-151 Lodz, Poland
| | - Liwia Lubowiecka
- Bioorganic Chemistry Laboratory, Faculty of Pharmacy, Medical University of Lodz, Muszynskiego 1, 90-151 Lodz, Poland
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87
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Shi EY, Yuan CL, Sipple MT, Srinivasan J, Ptak CP, Oswald RE, Nowak LM. Noncompetitive antagonists induce cooperative AMPA receptor channel gating. J Gen Physiol 2019; 151:156-173. [PMID: 30622133 PMCID: PMC6363417 DOI: 10.1085/jgp.201812209] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 11/05/2018] [Accepted: 12/11/2018] [Indexed: 12/24/2022] Open
Abstract
Glutamate activates individual subunits of AMPA receptors in a stepwise manner. Shi et al. reveal that two noncompetitive antagonists disrupt this gating pattern and that their binding sites at the boundary between the transmembrane and extracellular linker domains is a tunable locus for gating. Glutamate is released from presynaptic nerve terminals in the central nervous system (CNS) and spreads excitation by binding to and activating postsynaptic iGluRs. Of the potential glutamate targets, tetrameric AMPA receptors mediate fast, transient CNS signaling. Each of the four AMPA subunits in the receptor channel complex is capable of binding glutamate at its ligand-binding domains and transmitting the energy of activation to the pore domain. Homotetrameric AMPA receptor channels open in a stepwise manner, consistent with independent activation of individual subunits, and they exhibit complex kinetic behavior that manifests as temporal shifts between four different conductance levels. Here, we investigate how two AMPA receptor-selective noncompetitive antagonists, GYKI-52466 and GYKI-53655, disrupt the intrinsic step-like gating patterns of maximally activated homotetrameric GluA3 receptors using single-channel recordings from cell-attached patches. Interactions of these 2,3-benzodiazepines with residues in the boundary between the extracellular linkers and transmembrane helical domains reorganize the gating behavior of channels. Low concentrations of modulators stabilize open and closed states to different degrees and coordinate the activation of subunits so that channels open directly from closed to higher conductance levels. Using kinetic and structural models, we provide insight into how the altered gating patterns might arise from molecular contacts within the extracellular linker-channel boundary. Our results suggest that this region may be a tunable locus for AMPA receptor channel gating.
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Affiliation(s)
- Edward Y Shi
- Department of Molecular Medicine, Cornell University, Ithaca, NY
| | - Christine L Yuan
- Department of Molecular Medicine, Cornell University, Ithaca, NY
| | - Matthew T Sipple
- Department of Molecular Medicine, Cornell University, Ithaca, NY
| | | | | | - Robert E Oswald
- Department of Molecular Medicine, Cornell University, Ithaca, NY
| | - Linda M Nowak
- Department of Molecular Medicine, Cornell University, Ithaca, NY
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88
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Song K, Zhang J, Lu S. Progress in Allosteric Database. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1163:65-87. [PMID: 31707700 DOI: 10.1007/978-981-13-8719-7_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
An allosteric mechanism refers to the biological regulation process wherein macromolecules propagate the effect of ligand binding at one site to a spatially distant orthosteric locus, thus affecting activity. The theory has remained a trending topic in biology research for over 50 years, since the understanding of allostery is fundamental for gleaning numerous biological processes and developing new drug therapies. In the past two decades, the allosteric paradigm has evolved into more descriptive models, with ever-expanding amounts of experimental data pertaining to newly identified allosteric molecules. The AlloSteric Database (ASD, accessible at http://mdl.shsmu.edu.cn/ASD ), which is a comprehensive knowledge repository, has provided the public with integrated information encompassing allosteric proteins, modulators, sites, pathways, and networks to investigate allostery since 2009. In this chapter, we introduce the history and usage of the ASD and give attention to specific applications that have benefited from the ASD.
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Affiliation(s)
- Kun Song
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Shaoyong Lu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, China.
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89
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Lee JY, Krieger J, Herguedas B, García-Nafría J, Dutta A, Shaikh SA, Greger IH, Bahar I. Druggability Simulations and X-Ray Crystallography Reveal a Ligand-Binding Site in the GluA3 AMPA Receptor N-Terminal Domain. Structure 2018; 27:241-252.e3. [PMID: 30528594 DOI: 10.1016/j.str.2018.10.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 07/25/2018] [Accepted: 10/18/2018] [Indexed: 11/19/2022]
Abstract
Ionotropic glutamate receptors (iGluRs) mediate the majority of excitatory neurotransmission in the brain. Their dysfunction is implicated in many neurological disorders, rendering iGluRs potential drug targets. Here, we performed a systematic analysis of the druggability of two major iGluR subfamilies, using molecular dynamics simulations in the presence of drug-like molecules. We demonstrate the applicability of druggability simulations by faithfully identifying known agonist and modulator sites on AMPA receptors (AMPARs) and NMDA receptors. Simulations produced the expected allosteric changes of the AMPAR ligand-binding domain in response to agonist. We also identified a novel ligand-binding site specific to the GluA3 AMPAR N-terminal domain (NTD), resulting from its unique conformational flexibility that we explored further with crystal structures trapped in vastly different states. In addition to providing an in-depth analysis into iGluR NTD dynamics, our approach identifies druggable sites and permits the determination of pharmacophoric features toward novel iGluR modulators.
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Affiliation(s)
- Ji Young Lee
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, 3501 Fifth Avenue, Suite 3064 BST3, Pittsburgh, PA 15260, USA
| | - James Krieger
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, 3501 Fifth Avenue, Suite 3064 BST3, Pittsburgh, PA 15260, USA
| | - Beatriz Herguedas
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Javier García-Nafría
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Anindita Dutta
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, 3501 Fifth Avenue, Suite 3064 BST3, Pittsburgh, PA 15260, USA
| | - Saher A Shaikh
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Ingo H Greger
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK.
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, 3501 Fifth Avenue, Suite 3064 BST3, Pittsburgh, PA 15260, USA.
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90
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Population Shift Mechanism for Partial Agonism of AMPA Receptor. Biophys J 2018; 116:57-68. [PMID: 30573176 DOI: 10.1016/j.bpj.2018.11.3122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 11/15/2018] [Accepted: 11/21/2018] [Indexed: 12/13/2022] Open
Abstract
α-amino-3-hydroxy-5-methyl-4-isoaxazolepropionic acid (AMPA) ionotropic glutamate receptors mediate fast excitatory neurotransmission in the central nervous system, and their dysfunction is associated with neurological diseases. Glutamate binding to ligand-binding domains (LBDs) of AMPA receptors induces channel opening in the transmembrane domains of the receptors. The T686A mutation reduces glutamate efficacy so that the glutamate behaves as a partial agonist. The crystal structures of wild-type and mutant LBDs are very similar and cannot account for the observed behavior. To elucidate the molecular mechanism inducing partial agonism of the T686A mutant, we computed the free-energy landscapes governing GluA2 LBD closure using replica-exchange umbrella sampling simulations. A semiclosed state, not observed in crystal structures, appears in the mutant during simulation. In this state, the LBD cleft opens slightly because of breaking of interlobe hydrogen bonds, reducing the efficiency of channel opening. The energy difference between the LBD closed and semiclosed states is small, and transitions between the two states would occur by thermal fluctuations. Evidently, glutamate binding to the T686A mutant induces a population shift from a closed to a semiclosed state, explaining the partial agonism in the AMPA receptor.
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91
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Ramos-Vicente D, Ji J, Gratacòs-Batlle E, Gou G, Reig-Viader R, Luís J, Burguera D, Navas-Perez E, García-Fernández J, Fuentes-Prior P, Escriva H, Roher N, Soto D, Bayés À. Metazoan evolution of glutamate receptors reveals unreported phylogenetic groups and divergent lineage-specific events. eLife 2018; 7:e35774. [PMID: 30465522 PMCID: PMC6307864 DOI: 10.7554/elife.35774] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 11/20/2018] [Indexed: 01/28/2023] Open
Abstract
Glutamate receptors are divided in two unrelated families: ionotropic (iGluR), driving synaptic transmission, and metabotropic (mGluR), which modulate synaptic strength. The present classification of GluRs is based on vertebrate proteins and has remained unchanged for over two decades. Here we report an exhaustive phylogenetic study of GluRs in metazoans. Importantly, we demonstrate that GluRs have followed different evolutionary histories in separated animal lineages. Our analysis reveals that the present organization of iGluRs into six classes does not capture the full complexity of their evolution. Instead, we propose an organization into four subfamilies and ten classes, four of which have never been previously described. Furthermore, we report a sister class to mGluR classes I-III, class IV. We show that many unreported proteins are expressed in the nervous system, and that new Epsilon receptors form functional ligand-gated ion channels. We propose an updated classification of glutamate receptors that includes our findings.
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Affiliation(s)
- David Ramos-Vicente
- Molecular Physiology of the Synapse LaboratoryBiomedical Research Institute Sant PauBarcelonaSpain
- Universitat Autònoma de BarcelonaBarcelonaSpain
| | - Jie Ji
- Institute of Biotechnology and Biomedicine, Department of Cell Biology, Animal Physiology and ImmunologyUniversitat Autònoma de BarcelonaBarcelonaSpain
| | - Esther Gratacòs-Batlle
- Neurophysiology Laboratory, Department of Biomedicine, Medical School, August Pi i Sunyer Biomedical Research Institute, Institute of NeurosciencesUniversitat de BarcelonaBarcelonaSpain
| | - Gemma Gou
- Molecular Physiology of the Synapse LaboratoryBiomedical Research Institute Sant PauBarcelonaSpain
- Universitat Autònoma de BarcelonaBarcelonaSpain
| | - Rita Reig-Viader
- Molecular Physiology of the Synapse LaboratoryBiomedical Research Institute Sant PauBarcelonaSpain
- Universitat Autònoma de BarcelonaBarcelonaSpain
| | - Javier Luís
- Molecular Physiology of the Synapse LaboratoryBiomedical Research Institute Sant PauBarcelonaSpain
- Universitat Autònoma de BarcelonaBarcelonaSpain
| | - Demian Burguera
- Department of Genetics, School of Biology, Institut de BiomedicinaUniversity of BarcelonaBarcelonaSpain
| | - Enrique Navas-Perez
- Department of Genetics, School of Biology, Institut de BiomedicinaUniversity of BarcelonaBarcelonaSpain
| | - Jordi García-Fernández
- Department of Genetics, School of Biology, Institut de BiomedicinaUniversity of BarcelonaBarcelonaSpain
| | - Pablo Fuentes-Prior
- Molecular Bases of DiseaseBiomedical Research Institute Sant Pau, Hospital de la Santa Creu i Sant PauBarcelonaSpain
| | - Hector Escriva
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes MarinsBanyuls-sur-MerFrance
| | - Nerea Roher
- Institute of Biotechnology and Biomedicine, Department of Cell Biology, Animal Physiology and ImmunologyUniversitat Autònoma de BarcelonaBarcelonaSpain
| | - David Soto
- Neurophysiology Laboratory, Department of Biomedicine, Medical School, August Pi i Sunyer Biomedical Research Institute, Institute of NeurosciencesUniversitat de BarcelonaBarcelonaSpain
| | - Àlex Bayés
- Molecular Physiology of the Synapse LaboratoryBiomedical Research Institute Sant PauBarcelonaSpain
- Universitat Autònoma de BarcelonaBarcelonaSpain
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92
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Xu HN, Li LX, Wang YX, Wang HG, An D, Heng B, Liu YQ. Genistein inhibits Aβ 25-35 -induced SH-SY5Y cell damage by modulating the expression of apoptosis-related proteins and Ca 2+ influx through ionotropic glutamate receptors. Phytother Res 2018; 33:431-441. [PMID: 30450837 DOI: 10.1002/ptr.6239] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 09/05/2018] [Accepted: 10/29/2018] [Indexed: 11/10/2022]
Abstract
In this study, we investigated the protective effects of genistein against SH-SY5Y cell damage induced by β-amyloid 25-35 peptide (Aβ25-35 ) and the underlying mechanisms. Aβ-induced neuronal death, apoptosis, glutamate receptor subunit expression, Ca2+ ion concentration, amino acid transmitter concentration, and apoptosis-related factor expression were evaluated to determine the effects of genistein on Aβ-induced neuronal death and apoptosis. The results showed that genistein increased the survival of SH-SY5Y cells and decreased the level of apoptosis induced by Aβ25-35 . In addition, genistein reversed the Aβ25-35 -induced changes in amino acid transmitters, α-amino-3-hydroxy-5-methyl-4-isoxazolepropionate (AMPA) receptors, and N-methyl-d-aspartate (NMDA) receptor subunits in SH-SY5Y cells. Aβ25-35 -induced changes in Ca2+ and B-cell lymphoma-2 (Bcl-2) and Bcl-2-associated X (Bax) protein and gene levels in cells were also reversed by genistein. Our data suggest that genistein protects against Aβ25-35 -induced damage in SH-SY5Y cells, possibly by regulating the expression of apoptosis-related proteins and Ca2+ influx through ionotropic glutamate receptors.
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Affiliation(s)
- Hui-Nan Xu
- College of Life Sciences, Nankai University, Tianjin, China
| | - Li-Xia Li
- College of Life Sciences, Nankai University, Tianjin, China
| | - Yu-Xiang Wang
- College of Life Sciences, Nankai University, Tianjin, China
| | - Hong-Gang Wang
- College of Life Sciences, Nankai University, Tianjin, China
| | - Di An
- College of Life Sciences, Nankai University, Tianjin, China
| | - Bin Heng
- College of Life Sciences, Nankai University, Tianjin, China
| | - Yan-Qiang Liu
- College of Life Sciences, Nankai University, Tianjin, China
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93
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Mironiuk-Puchalska E, Buchowicz W, Grześkowiak P, Wińska P, Wielechowska M, Karatsai O, Rędowicz MJ, Bretner M, Koszytkowska-Stawińska M. Potential bioisosteres of β-uracilalanines derived from 1H-1,2,3-triazole-C-carboxylic acids. Bioorg Chem 2018; 83:500-510. [PMID: 30453142 DOI: 10.1016/j.bioorg.2018.10.061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 10/16/2018] [Accepted: 10/29/2018] [Indexed: 11/19/2022]
Abstract
The 1H-1,2,3-triazole-originated derivatives of willardiine were obtained by: (i) construction of the 1H-1,2,3-triazole ring in 1,3-dipolar cycloaddition of the uracil-derived azides and the carboxylate-bearing alkynes or α-acylphosphorus ylide, or (ii) N-alkylation of the uracil derivative with the 1H-1,2,3-triazole-4-carboxylate-derived mesylate. The latter method offered: (i) reproducible results, (ii) a significant reduction of amounts of auxiliary materials, (iii) reduction in wastes and (iv) reduction in a number of manual operations required for obtaining the reaction product. Compound 6a exhibited significant binding affinity to hHS1S2I ligand-binding domain of GluR2 receptor (EC50 = 2.90 µM) and decreased viability of human astrocytoma MOG-G-CCM cells in higher extent than known AMPA antagonist GYKI 52466.
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Affiliation(s)
- Ewa Mironiuk-Puchalska
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Włodzimierz Buchowicz
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Piotr Grześkowiak
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Patrycja Wińska
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Monika Wielechowska
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Olena Karatsai
- Laboratory of Molecular Basis of Cell Motility, Nencki Institute of Experimental Biology, 3 Pasteur St., 02-093 Warsaw, Poland
| | - Maria Jolanta Rędowicz
- Laboratory of Molecular Basis of Cell Motility, Nencki Institute of Experimental Biology, 3 Pasteur St., 02-093 Warsaw, Poland
| | - Maria Bretner
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
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94
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MacLean DM, Durham RJ, Jayaraman V. Mapping the Conformational Landscape of Glutamate Receptors Using Single Molecule FRET. Trends Neurosci 2018; 42:128-139. [PMID: 30385052 DOI: 10.1016/j.tins.2018.10.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/27/2018] [Accepted: 10/02/2018] [Indexed: 10/28/2022]
Abstract
The ionotropic glutamate receptors mediate excitatory neurotransmission in the mammalian central nervous system. These receptors provide a range of temporally diverse signals which stem from subunit composition and also from the inherent ability of each member to occupy multiple functional states, the distribution of which can be altered by small molecule modulators and binding partners. Hence it becomes essential to characterize the conformational landscape of the receptors under this variety of different conditions. This has recently become possible due to single molecule fluorescence resonance energy transfer measurements, along with the rich foundation of existing structures allowing for direct correlations between conformational and functional diversity.
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Affiliation(s)
- David M MacLean
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Ryan J Durham
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Biochemistry and Cell Biology Graduate Program, Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Vasanthi Jayaraman
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
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95
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de O. Lima Filho E, da S. Ribeiro SL, Araújo RM, Menezes FG, Cavalcanti LN. Selective Synthesis of Mono- and Disubstituted Quinoxalines via Heteroaromatic Nucleophilic Substitution of 2,3-Dichloro-6,7-dinitroquinoxaline (DCDNQX) with Anilines and Phenols. ChemistrySelect 2018. [DOI: 10.1002/slct.201802582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Edson de O. Lima Filho
- Laboratório de Síntese de Heterociclos e Metodologias Aplicadas Instituto de Química; Universidade Federal do Rio Grande do Norte; Natal 59072-970 Brazil
| | - Stephany L. da S. Ribeiro
- Laboratório de Síntese de Heterociclos e Metodologias Aplicadas Instituto de Química; Universidade Federal do Rio Grande do Norte; Natal 59072-970 Brazil
| | - Renata M. Araújo
- Laboratório de Síntese de Heterociclos e Metodologias Aplicadas Instituto de Química; Universidade Federal do Rio Grande do Norte; Natal 59072-970 Brazil
| | - Fabrício G. Menezes
- Laboratório de Síntese de Heterociclos e Metodologias Aplicadas Instituto de Química; Universidade Federal do Rio Grande do Norte; Natal 59072-970 Brazil
| | - Lívia N. Cavalcanti
- Laboratório de Síntese de Heterociclos e Metodologias Aplicadas Instituto de Química; Universidade Federal do Rio Grande do Norte; Natal 59072-970 Brazil
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96
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Hansen KB, Yi F, Perszyk RE, Furukawa H, Wollmuth LP, Gibb AJ, Traynelis SF. Structure, function, and allosteric modulation of NMDA receptors. J Gen Physiol 2018; 150:1081-1105. [PMID: 30037851 PMCID: PMC6080888 DOI: 10.1085/jgp.201812032] [Citation(s) in RCA: 321] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 07/03/2018] [Indexed: 12/22/2022] Open
Abstract
Hansen et al. review recent structural data that have provided insight into the function and allosteric modulation of NMDA receptors. NMDA-type glutamate receptors are ligand-gated ion channels that mediate a Ca2+-permeable component of excitatory neurotransmission in the central nervous system (CNS). They are expressed throughout the CNS and play key physiological roles in synaptic function, such as synaptic plasticity, learning, and memory. NMDA receptors are also implicated in the pathophysiology of several CNS disorders and more recently have been identified as a locus for disease-associated genomic variation. NMDA receptors exist as a diverse array of subtypes formed by variation in assembly of seven subunits (GluN1, GluN2A-D, and GluN3A-B) into tetrameric receptor complexes. These NMDA receptor subtypes show unique structural features that account for their distinct functional and pharmacological properties allowing precise tuning of their physiological roles. Here, we review the relationship between NMDA receptor structure and function with an emphasis on emerging atomic resolution structures, which begin to explain unique features of this receptor.
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Affiliation(s)
- Kasper B Hansen
- Department of Biomedical and Pharmaceutical Sciences and Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT
| | - Feng Yi
- Department of Biomedical and Pharmaceutical Sciences and Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT
| | - Riley E Perszyk
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA
| | - Hiro Furukawa
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
| | - Lonnie P Wollmuth
- Departments of Neurobiology & Behavior and Biochemistry & Cell Biology, Stony Brook University, Stony Brook, NY
| | - Alasdair J Gibb
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK
| | - Stephen F Traynelis
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA
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97
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Rheinberger J, Gao X, Schmidpeter PA, Nimigean CM. Ligand discrimination and gating in cyclic nucleotide-gated ion channels from apo and partial agonist-bound cryo-EM structures. eLife 2018; 7:39775. [PMID: 30028291 PMCID: PMC6093708 DOI: 10.7554/elife.39775] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 07/19/2018] [Indexed: 12/11/2022] Open
Abstract
Cyclic nucleotide-modulated channels have important roles in visual signal transduction and pacemaking. Binding of cyclic nucleotides (cAMP/cGMP) elicits diverse functional responses in different channels within the family despite their high sequence and structure homology. The molecular mechanisms responsible for ligand discrimination and gating are unknown due to lack of correspondence between structural information and functional states. Using single particle cryo-electron microscopy and single-channel recording, we assigned functional states to high-resolution structures of SthK, a prokaryotic cyclic nucleotide-gated channel. The structures for apo, cAMP-bound, and cGMP-bound SthK in lipid nanodiscs, correspond to no, moderate, and low single-channel activity, respectively, consistent with the observation that all structures are in resting, closed states. The similarity between apo and ligand-bound structures indicates that ligand-binding domains are strongly coupled to pore and SthK gates in an allosteric, concerted fashion. The different orientations of cAMP and cGMP in the ‘resting’ and ‘activated’ structures suggest a mechanism for ligand discrimination. Ion channels are essential for transmitting signals in the nervous system and brain. One large group of ion channels includes members that are activated by cyclic nucleotides, small molecules used to transmit signals within cells. These cyclic nucleotide-gated channels play an important role in regulating our ability to see and smell. The activity of these ion channels has been studied for years, but scientists have only recently been able to look into their structure. Since structural biology methods require purified, well-behaved proteins, the members of this ion channel family selected for structural studies do not necessarily match those whose activity has been well established. There is a need for a good model that would allow both the structure and activity of a cyclic nucleotide-gated ion channel to be characterized. The cyclic nucleotide-gated ion channel, SthK, from bacteria called Spirochaeta thermophila, was identified as such model because both its activity and its structure are accessible. Rheinberger et al. have used cryo electron microscopy to solve several high-resolution structures of SthK channels. In two of the structures, SthK was bound to either one of two types of activating cyclic nucleotides – cAMP or cGMP – and in another structure, no cyclic nucleotides were bound. Separately recording the activity of individual channels allowed the activity states likely to be represented by these structures to be identified. Combining the results of the experiments revealed no activity from channels in an unbound state, low levels of activity for channels bound to cGMP, and moderate activity for channels bound to cAMP. Rheinberger et al. show that the channel, under the conditions experienced in cryo electron microscopy, is closed in all of the states studied. Unexpectedly, the binding of cyclic nucleotides produced no structural change even in the cyclic nucleotide-binding pocket of the channel, a region that was previously observed to undergo such changes when this region alone was crystallized. Rheinberger et al. deduce from this that the four subunits that make up the channel likely undergo the conformational change towards an open state all at once, rather than one by one. The structures and the basic functional characterization of SthK channels provide a strong starting point for future research into determining the entire opening and closing cycle for a cyclic nucleotide-gated channel. Human equivalents of the channel are likely to work in similar ways. The results presented by Rheinberger et al. could therefore be built upon to help address diseases that result from deficiencies in cyclic nucleotide-gated channels, such as loss of vision due to retinal degradation (retinitis pigmentosa or progressive cone dystrophy) and achromatopsia.
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Affiliation(s)
- Jan Rheinberger
- Departments of Anesthesiology, Weill Cornell Medical College, New York, United States
| | - Xiaolong Gao
- Departments of Anesthesiology, Weill Cornell Medical College, New York, United States
| | | | - Crina M Nimigean
- Departments of Anesthesiology, Weill Cornell Medical College, New York, United States.,Department of Physiology and Biophysics, Weill Cornell Medical College, New York, United States.,Department of Biochemistry, Weill Cornell Medical College, New York, United States
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98
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Kiyonaka S, Sakamoto S, Wakayama S, Morikawa Y, Tsujikawa M, Hamachi I. Ligand-Directed Chemistry of AMPA Receptors Confers Live-Cell Fluorescent Biosensors. ACS Chem Biol 2018; 13:1880-1889. [PMID: 29437380 DOI: 10.1021/acschembio.7b01042] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AMPA-type glutamate receptors (AMPARs) mediate fast excitatory synaptic transmission in the central nervous system. Dysregulation of AMPAR function is associated with many kinds of neurological, neurodegenerative, and psychiatric disorders. As a result, molecules capable of controlling AMPAR functions are potential therapeutic agents. Fluorescent semisynthetic biosensors have attracted considerable interest for the discovery of ligands selectively acting on target proteins. Given the large protein complex formation of AMPARs in live cells, biosensors using full-length AMPARs retaining original functionality are ideal for drug screening. Here, we demonstrate that fluorophore-labeled AMPARs prepared by ligand-directed acyl imidazole chemistry can act as turn-on fluorescent biosensors for AMPAR ligands in living cells. These biosensors selectively detect orthosteric ligands of AMPARs among the glutamate receptor family. Notably, the dissociation constants of agonists and antagonists for AMPARs were determined in live cells, which revealed that the ligand-binding properties of AMPARs to agonists are largely different in living cells, compared with noncellular conditions. We also show that these sensors can be applied to detecting allosteric modulators or subunit-selective ligands of AMPARs. Thus, our protein-based biosensors can be useful for discovering pharmaceutical agents to treat AMPAR-related neurological disorders.
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Affiliation(s)
- Shigeki Kiyonaka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Seiji Sakamoto
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Sho Wakayama
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Yuma Morikawa
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Muneo Tsujikawa
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
- CREST(Core Research for Evolutional Science and Technology, JST), Chiyodaku, Tokyo, 102-0075, Japan
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99
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Ayan M, Essiz S. The neural γ 2α 1β 2α 1β 2 gamma amino butyric acid ion channel receptor: structural analysis of the effects of the ivermectin molecule and disulfide bridges. J Mol Model 2018; 24:206. [PMID: 30008086 DOI: 10.1007/s00894-018-3739-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 06/27/2018] [Indexed: 12/21/2022]
Abstract
While ~30% of the human genome encodes membrane proteins, only a handful of structures of membrane proteins have been resolved to high resolution. Here, we studied the structure of a member of the Cys-loop ligand gated ion channel protein superfamily of receptors, human type A γ2α1β2α1β2 gamma amino butyric acid receptor complex in a lipid bilayer environment. Studying the correlation between the structure and function of the gamma amino butyric acid receptor may enhance our understanding of the molecular basis of ion channel dysfunctions linked with epilepsy, ataxia, migraine, schizophrenia and other neurodegenerative diseases. The structure of human γ2α1β2α1β2 has been modeled based on the X-ray structure of the Caenorhabditis elegans glutamate-gated chloride channel via homology modeling. The template provided the first inhibitory channel structure for the Cys-loop superfamily of ligand-gated ion channels. The only available template structure before this glutamate-gated chloride channel was a cation selective channel which had very low sequence identity with gamma aminobutyric acid receptor. Here, our aim was to study the effect of structural corrections originating from modeling on a more reliable template structure. The homology model was analyzed for structural properties via a 100 ns molecular dynamics (MD) study. Due to the structural shifts and the removal of an open channel potentiator molecule, ivermectin, from the template structure, helical packing changes were observed in the transmembrane segment. Namely removal of ivermectin molecule caused a closure around the Leu 9 position along the ion channel. In terms of the structural shifts, there are three potential disulfide bridges between the M1 and M3 helices of the γ2 and 2 α1 subunits in the model. The effect of these disulfide bridges was investigated via monitoring the differences in root mean square fluctuations (RMSF) of individual amino acids and principal component analysis of the MD trajectory of the two homology models-one with the disulfide bridge and one with protonated Cys residues. In all subunit types, RMSF of the transmembrane domain helices are reduced in the presence of disulfide bridges. Additionally, loop A, loop F and loop C fluctuations were affected in the extracellular domain. In cross-correlation analysis of the trajectory, the two model structures displayed different coupling in between the M2-M3 linker region, protruding from the membrane, and the β1-β2/D loop and cys-loop regions in the extracellular domain. Correlations of the C loop, which collapses directly over the bound ligand molecule, were also affected by differences in the packing of transmembrane helices. Finally, more localized correlations were observed in the transmembrane helices when disulfide bridges were present in the model. The differences observed in this study suggest that dynamic coupling at the interface of extracellular and ion channel domains differs from the coupling introduced by disulfide bridges in the transmembrane region. We hope that this hypothesis will be tested experimentally in the near future.
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Affiliation(s)
- Meral Ayan
- Bioinformatics and Genetics Department, Faculty of Engineering and Natural Sciences, Kadir Has University, 34083, Fatih, Istanbul, Turkey
| | - Sebnem Essiz
- Bioinformatics and Genetics Department, Faculty of Engineering and Natural Sciences, Kadir Has University, 34083, Fatih, Istanbul, Turkey.
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100
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Dual Effects of TARP γ-2 on Glutamate Efficacy Can Account for AMPA Receptor Autoinactivation. Cell Rep 2018; 20:1123-1135. [PMID: 28768197 PMCID: PMC5554777 DOI: 10.1016/j.celrep.2017.07.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 06/12/2017] [Accepted: 07/09/2017] [Indexed: 11/10/2022] Open
Abstract
Fast excitatory transmission in the CNS is mediated mainly by AMPA-type glutamate receptors (AMPARs) associated with transmembrane AMPAR regulatory proteins (TARPs). At the high glutamate concentrations typically seen during synaptic transmission, TARPs slow receptor desensitization and enhance mean channel conductance. However, their influence on channels gated by low glutamate concentrations, as encountered during delayed transmitter clearance or synaptic spillover, is poorly understood. We report here that TARP γ-2 reduces the ability of low glutamate concentrations to cause AMPAR desensitization and enhances channel gating at low glutamate occupancy. Simulations show that, by shifting the balance between AMPAR activation and desensitization, TARPs can markedly facilitate the transduction of spillover-mediated synaptic signaling. Furthermore, the dual effects of TARPs can account for biphasic steady-state glutamate concentration-response curves—a phenomenon termed “autoinactivation,” previously thought to reflect desensitization-mediated AMPAR/TARP dissociation. TARP γ-2 reduces desensitization and enhances the gating of singly liganded AMPARs This accounts for biphasic steady-state dose-response curves (autoinactivation) The effects of γ-2 are predicted to enhance synaptic spillover currents Desensitization does not lead to functional dissociation of the AMPAR/TARP complex
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