51
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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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52
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Burada AP, Vinnakota R, Kumar J. Cryo-EM structures of the ionotropic glutamate receptor GluD1 reveal a non-swapped architecture. Nat Struct Mol Biol 2020; 27:84-91. [PMID: 31925409 PMCID: PMC7025878 DOI: 10.1038/s41594-019-0359-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 11/27/2019] [Indexed: 01/06/2023]
Abstract
Ionotropic orphan delta receptors (GluD) are not gated by glutamate or
any other endogenous ligand but are grouped with ionotropic glutamate receptors
based on sequence similarity. GluD1 receptors play critical roles in
synaptogenesis, synapse maintenance and have been implicated in neuronal
disorders including schizophrenia, cognitive deficits, and cerebral ataxia. Here
we report cryo-electron microscopy structures of the rat GluD1 receptor
complexed with calcium and the ligand 7-chlorokynurenic acid, elucidating
molecular architecture and principles of receptor assembly. The structures
reveal a non-swapped architecture at the extracellular amino-terminal (ATD) and
ligand-binding domain (LBD) interface. This is in contrast to other families of
ionotropic glutamate receptors (iGluRs) where the dimer partners between the ATD
and LBD layers are swapped. Our results demonstrate that principles of
architecture and symmetry are not conserved between delta receptors and other
iGluRs and provide a molecular blueprint for understanding the functions of the
“orphan” class of iGluRs.
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Affiliation(s)
- Ananth Prasad Burada
- Laboratory of Membrane Protein Biology, National Centre for Cell Science, NCCS Complex, S. P. Pune University, Pune, Maharashtra, India
| | - Rajesh Vinnakota
- Laboratory of Membrane Protein Biology, National Centre for Cell Science, NCCS Complex, S. P. Pune University, Pune, Maharashtra, India
| | - Janesh Kumar
- Laboratory of Membrane Protein Biology, National Centre for Cell Science, NCCS Complex, S. P. Pune University, Pune, Maharashtra, India.
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53
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Litwin DB, Paudyal N, Carrillo E, Berka V, Jayaraman V. The structural arrangement and dynamics of the heteromeric GluK2/GluK5 kainate receptor as determined by smFRET. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2020; 1862:183001. [PMID: 31194959 PMCID: PMC6899175 DOI: 10.1016/j.bbamem.2019.05.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/14/2019] [Accepted: 05/31/2019] [Indexed: 01/08/2023]
Abstract
Kainate receptors, which are glutamate activated excitatory neurotransmitter receptors, predominantly exist as heteromers of GluK2 and GluK5 subunits in the mammalian central nervous system. There are currently no structures of the full-length heteromeric kainate receptors. Here, we have used single molecule FRET to determine the specific arrangement of the GluK2 and GluK5 subunits within the dimer of dimers configuration in a full-length receptor. Additionally, we have also studied the dynamics and conformational heterogeneity of the amino-terminal and agonist-binding domain interfaces associated with the resting and desensitized states of the full-length heteromeric kainate receptor using FRET-based methods. The smFRET data are compared to similar experiments performed on the homomeric kainate receptor to provide insight into the differences in conformational dynamics that distinguish the two functionally. This article is part of a Special Issue entitled: Molecular biophysics of membranes and membrane proteins.
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Affiliation(s)
- Douglas B Litwin
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, TX 77030, USA; MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Nabina Paudyal
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, TX 77030, USA; MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Elisa Carrillo
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Vladimir Berka
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, 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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54
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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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55
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Lee CH, MacKinnon R. Voltage Sensor Movements during Hyperpolarization in the HCN Channel. Cell 2019; 179:1582-1589.e7. [PMID: 31787376 DOI: 10.1016/j.cell.2019.11.006] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 10/21/2019] [Accepted: 11/01/2019] [Indexed: 12/21/2022]
Abstract
The hyperpolarization-activated cyclic nucleotide-gated (HCN) channel is a voltage-gated cation channel that mediates neuronal and cardiac pacemaker activity. The HCN channel exhibits reversed voltage dependence, meaning it closes with depolarization and opens with hyperpolarization. Different from Na+, Ca2+, and Kv1-Kv7 channels, the HCN channel does not have domain-swapped voltage sensors. We introduced a reversible, metal-mediated cross bridge into the voltage sensors to create the chemical equivalent of a hyperpolarized conformation and determined the structure using cryoelectron microscopy (cryo-EM). Unlike the depolarized HCN channel, the S4 helix is displaced toward the cytoplasm by two helical turns. Near the cytoplasm, the S4 helix breaks into two helices, one running parallel to the membrane surface, analogous to the S4-S5 linker of domain-swapped voltage-gated channels. These findings suggest a basis for allosteric communication between voltage sensors and the gate in this kind of channel. They also imply that voltage sensor movements are not the same in all voltage-gated channels.
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Affiliation(s)
- Chia-Hsueh Lee
- Laboratory of Molecular Neurobiology and Biophysics, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Roderick MacKinnon
- Laboratory of Molecular Neurobiology and Biophysics, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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56
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Tian Z, Clark BLM, Menard F. Kainic Acid-Based Agonists of Glutamate Receptors: SAR Analysis and Guidelines for Analog Design. ACS Chem Neurosci 2019; 10:4190-4198. [PMID: 31550120 DOI: 10.1021/acschemneuro.9b00349] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
A comprehensive survey of kainic acid analogs that have been tested for their biological activity is presented. Specifically, this review (1) gathers and compares over 100 kainoids according to a relative activity scale, (2) exposes structural features required to optimize affinity for kainate receptors, and (3) suggests design rules to create next-generation KA analogs. Literature SAR data are analyzed systematically and combined with the most recent crystallographic studies. In view of the renewed interest in neuroactive molecules, this review aims to help guide the efforts of organic synthesis laboratories, as well as to inform newcomers to KA/GluK research.
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Affiliation(s)
- Zhenlin Tian
- Department of Chemistry, University of British Columbia, Kelowna, BC V1V 1V7, Canada
| | - Brianna L. M. Clark
- Department of Chemistry, University of British Columbia, Kelowna, BC V1V 1V7, Canada
| | - Frederic Menard
- Department of Chemistry, University of British Columbia, Kelowna, BC V1V 1V7, Canada
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57
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Stenum-Berg C, Musgaard M, Chavez-Abiega S, Thisted CL, Barrella L, Biggin PC, Kristensen AS. Mutational Analysis and Modeling of Negative Allosteric Modulator Binding Sites in AMPA Receptors. Mol Pharmacol 2019; 96:835-850. [PMID: 31582576 DOI: 10.1124/mol.119.116871] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 10/01/2019] [Indexed: 12/16/2022] Open
Abstract
The α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs) constitute a subclass of the ionotropic glutamate receptor superfamily, which functions as glutamate-gated cation channels to mediate the majority of excitatory neurotransmission in the central nervous system. AMPARs are therapeutic targets in a range of brain disorders associated with abnormal glutamate hyperactivity. Multiple classes of AMPAR inhibitors have been developed during the past decades, including competitive antagonists, ion channel blockers, and negative allosteric modulators (NAMs). At present, the NAM is the only class of AMPAR ligands that have been developed into safe and useful drugs in humans in the form of perampanel (Fycompa), which was recently approved for treatment of epilepsy. Compared with the detailed understanding of other AMPAR ligand classes, surprisingly little information has been available regarding the molecular mechanism of perampanel and other classes of NAMs at AMPARs; including the location and structure of NAM binding pockets in the receptor complex. However, structures of the AMPAR GluA2 in complex with NAMs were recently reported that unambiguously identified the NAM binding sites. In parallel with this work, our aim with the present study was to identify specific residues involved in the formation of the NAM binding site for three prototypical AMPAR NAMs. Hence, we have performed a mutational analysis of the AMPAR region that links the four extracellular ligand-binding domains to the central ion channel in the transmembrane domain region. Furthermore, we perform computational ligand docking of the NAMs into structural models of the homomeric GluA2 receptor and optimize side chain conformations around the NAMs to model how NAMs bind in this specific site. The new insights provide potentially valuable input for structure-based drug design of new NAMs. SIGNIFICANCE STATEMENT: The α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors are glutamate-gated ion channels that mediate the majority of excitatory neurotransmission in the brain. Negative allosteric modulators of AMPA receptors are considered to have significant therapeutic potential in diseases linked to glutamate hyperactivity. The present work employs mutational analysis and molecular modeling of the binding site for prototypical NAMs to provide new molecular insight into how NAMs interact with the AMPA receptor, which is of potential use for future design of new types of NAMs.
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Affiliation(s)
- Charlotte Stenum-Berg
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (C.S.-B., S.C.-A., C.L.T., L.B., A.S.K.); and Department of Biochemistry, University of Oxford, Oxford, United Kingdom (M.M., P.C.B.)
| | - Maria Musgaard
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (C.S.-B., S.C.-A., C.L.T., L.B., A.S.K.); and Department of Biochemistry, University of Oxford, Oxford, United Kingdom (M.M., P.C.B.)
| | - Sergei Chavez-Abiega
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (C.S.-B., S.C.-A., C.L.T., L.B., A.S.K.); and Department of Biochemistry, University of Oxford, Oxford, United Kingdom (M.M., P.C.B.)
| | - Christine L Thisted
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (C.S.-B., S.C.-A., C.L.T., L.B., A.S.K.); and Department of Biochemistry, University of Oxford, Oxford, United Kingdom (M.M., P.C.B.)
| | - Lorenzo Barrella
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (C.S.-B., S.C.-A., C.L.T., L.B., A.S.K.); and Department of Biochemistry, University of Oxford, Oxford, United Kingdom (M.M., P.C.B.)
| | - Philip C Biggin
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (C.S.-B., S.C.-A., C.L.T., L.B., A.S.K.); and Department of Biochemistry, University of Oxford, Oxford, United Kingdom (M.M., P.C.B.)
| | - Anders S Kristensen
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (C.S.-B., S.C.-A., C.L.T., L.B., A.S.K.); and Department of Biochemistry, University of Oxford, Oxford, United Kingdom (M.M., P.C.B.)
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58
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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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59
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Kumari J, Vinnakota R, Kumar J. Structural and Functional Insights into GluK3-kainate Receptor Desensitization and Recovery. Sci Rep 2019; 9:10254. [PMID: 31311973 PMCID: PMC6635489 DOI: 10.1038/s41598-019-46770-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 07/02/2019] [Indexed: 12/11/2022] Open
Abstract
GluK3-kainate receptors are atypical members of the iGluR family that reside at both the pre- and postsynapse and play a vital role in the regulation of synaptic transmission. For a better understanding of structural changes that underlie receptor functions, GluK3 receptors were trapped in desensitized and resting/closed states and structures analyzed using single particle cryo-electron microscopy. While the desensitized GluK3 has domain organization as seen earlier for another kainate receptor-GluK2, antagonist bound GluK3 trapped a resting state with only two LBD domains in dimeric arrangement necessary for receptor activation. Using structures as a guide, we show that the N-linked glycans at the interface of GluK3 ATD and LBD likely mediate inter-domain interactions and attune receptor-gating properties. The mutational analysis also identified putative N-glycan interacting residues. Our results provide a molecular framework for understanding gating properties unique to GluK3 and exploring the role of N-linked glycosylation in their modulation.
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Affiliation(s)
- Jyoti Kumari
- Laboratory of Membrane Protein Biology, National Centre for Cell Science, NCCS Complex, S. P. Pune University, Maharashtra, Pune, 411007, India
| | - Rajesh Vinnakota
- Laboratory of Membrane Protein Biology, National Centre for Cell Science, NCCS Complex, S. P. Pune University, Maharashtra, Pune, 411007, India
| | - Janesh Kumar
- Laboratory of Membrane Protein Biology, National Centre for Cell Science, NCCS Complex, S. P. Pune University, Maharashtra, Pune, 411007, India.
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60
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Gating modules of the AMPA receptor pore domain revealed by unnatural amino acid mutagenesis. Proc Natl Acad Sci U S A 2019; 116:13358-13367. [PMID: 31213549 DOI: 10.1073/pnas.1818845116] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Ionotropic glutamate receptors (iGluRs) are responsible for fast synaptic transmission throughout the vertebrate nervous system. Conformational changes of the transmembrane domain (TMD) underlying ion channel activation and desensitization remain poorly understood. Here, we explored the dynamics of the TMD of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)-type iGluRs using genetically encoded unnatural amino acid (UAA) photocross-linkers, p-benzoyl-l-phenylalanine (BzF) and p-azido-l-phenylalanine (AzF). We introduced these UAAs at sites throughout the TMD of the GluA2 receptor and characterized the mutants in patch-clamp recordings, exposing them to glutamate and ultraviolet (UV) light. This approach revealed a range of optical effects on the activity of mutant receptors. We found evidence for an interaction between the Pre-M1 and the M4 TMD helix during desensitization. Photoactivation at F579AzF, a residue behind the selectivity filter in the M2 segment, had extraordinarily broad effects on gating and desensitization. This observation suggests coupling to other parts of the receptor and like in other tetrameric ion channels, selectivity filter gating.
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61
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Structural biology of glutamate receptor ion channels: towards an understanding of mechanism. Curr Opin Struct Biol 2019; 57:185-195. [PMID: 31185364 DOI: 10.1016/j.sbi.2019.05.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/03/2019] [Accepted: 05/06/2019] [Indexed: 12/21/2022]
Abstract
Ionotropic glutamate receptors (iGluRs) are tetrameric ion channels that mediate signal transmission at neuronal synapses, where they contribute centrally to the postsynaptic plasticity that underlies learning and memory. Receptor activation by l-glutamate triggers complex allosteric cascades that are transmitted through the layered and highly flexible receptor assembly culminating in opening a cation-selective pore. This process is shaped by the arrangement of the four core subunits as well as the presence of various auxiliary subunits, and is subject to regulation by an array of small molecule modulators targeting a number of sites throughout the complex. Here, we discuss recent structures of iGluR homomers and heteromers illuminating the organization and subunit arrangement of the core tetramer, co-assembled with auxiliary subunits and in complex with allosteric modulators.
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62
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Dawe GB, Kadir MF, Venskutonytė R, Perozzo AM, Yan Y, Alexander RP, Navarrete C, Santander EA, Arsenault M, Fuentes C, Aurousseau MR, Frydenvang K, Barrera NP, Kastrup JS, Edwardson JM, Bowie D. Nanoscale Mobility of the Apo State and TARP Stoichiometry Dictate the Gating Behavior of Alternatively Spliced AMPA Receptors. Neuron 2019; 102:976-992.e5. [DOI: 10.1016/j.neuron.2019.03.046] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/08/2019] [Accepted: 03/28/2019] [Indexed: 12/19/2022]
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63
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Litwin DB, Carrillo E, Shaikh SA, Berka V, Jayaraman V. The structural arrangement at intersubunit interfaces in homomeric kainate receptors. Sci Rep 2019; 9:6969. [PMID: 31061516 PMCID: PMC6502836 DOI: 10.1038/s41598-019-43360-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 04/23/2019] [Indexed: 02/02/2023] Open
Abstract
Kainate receptors are glutamate-gated cation-selective channels involved in excitatory synaptic signaling and are known to be modulated by ions. Prior functional and structural studies suggest that the dimer interface at the agonist-binding domain plays a key role in activation, desensitization, and ion modulation in kainate receptors. Here we have used fluorescence-based methods to investigate the changes and conformational heterogeneity at these interfaces associated with the resting, antagonist-bound, active, desensitized, and ion-modulated states of the receptor. These studies show that in the presence of Na+ ions the interfaces exist primarily in the coupled state in the apo, antagonist-bound and activated (open channel) states. Under desensitizing conditions, the largely decoupled dimer interface at the agonist-binding domain as seen in the cryo-EM structure is one of the states observed. However, in addition to this state there are several additional states with lower levels of decoupling. Replacing Na+ with Cs+ does not alter the FRET efficiencies of the states significantly, but shifts the population to the more decoupled states in both resting and desensitized states, which can be correlated with the lower activation seen in the presence of Cs+.
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Affiliation(s)
- Douglas B Litwin
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, Texas, 77030, USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, Texas, 77030, USA
| | - Elisa Carrillo
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, Texas, 77030, USA
| | - Sana A Shaikh
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, Texas, 77030, USA
| | - Vladimir Berka
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, Texas, 77030, USA
| | - Vasanthi Jayaraman
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, Texas, 77030, USA.
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64
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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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65
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Postsynaptic protein organization revealed by electron microscopy. Curr Opin Struct Biol 2019; 54:152-160. [PMID: 30904821 PMCID: PMC6753054 DOI: 10.1016/j.sbi.2019.02.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 02/02/2019] [Accepted: 02/18/2019] [Indexed: 11/21/2022]
Abstract
Neuronal synapses are key devices for transmitting and processing information in the nervous system. Synaptic plasticity, generally regarded as the cellular basis of learning and memory, involves changes of subcellular structures that take place at the nanoscale. High-resolution imaging methods, especially electron microscopy (EM), have allowed for quantitative analysis of such nanoscale structures in different types of synapses. In particular, the semi-ordered organization of neurotransmitter receptors and their interacting scaffolds in the postsynaptic density have been characterized for both excitatory and inhibitory synapses by studies using various EM techniques such as immuno-EM, electron tomography of high-pressure freezing and freeze-substituted samples, and cryo electron tomography. These techniques, in combination with new correlative approaches, will further facilitate our understanding of the molecular organization underlying diverse functions of neuronal synapses.
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66
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Pallesen J, Møllerud S, Frydenvang K, Pickering DS, Bornholdt J, Nielsen B, Pasini D, Han L, Marconi L, Kastrup JS, Johansen TN. N1-Substituted Quinoxaline-2,3-diones as Kainate Receptor Antagonists: X-ray Crystallography, Structure-Affinity Relationships, and in Vitro Pharmacology. ACS Chem Neurosci 2019; 10:1841-1853. [PMID: 30620174 DOI: 10.1021/acschemneuro.8b00726] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Among the ionotropic glutamate receptors, the physiological role of kainate receptors is less well understood. Although ligands with selectivity toward the kainate receptor subtype GluK1 are available, tool compounds with selectivity at the remaining kainate receptor subtypes are sparse. Here, we have synthesized a series of quinoxaline-2,3-diones with substitutions in the N1-, 6-, and 7-position to investigate the structure-activity relationship (SAR) at GluK1-3 and GluK5. Pharmacological characterization at native and recombinant kainate and AMPA receptors revealed that compound 37 had a GluK3-binding affinity ( Ki) of 0.142 μM and 8-fold preference for GluK3 over GluK1. Despite lower binding affinity of 22 at GluK3 ( Ki = 2.91 μM), its preference for GluK3 over GluK1 and GluK2 was >30-fold. Compound 37 was crystallized with the GluK1 ligand-binding domain to understand the SAR. The X-ray structure showed that 37 stabilized the protein in an open conformation, consistent with an antagonist binding mode.
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Affiliation(s)
- Jakob Pallesen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Stine Møllerud
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Karla Frydenvang
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Darryl S. Pickering
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Jan Bornholdt
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Birgitte Nielsen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Diletta Pasini
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Liwei Han
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Laura Marconi
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Jette Sandholm Kastrup
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Tommy N. Johansen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
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67
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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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68
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Zielinski MS, Vardar E, Vythilingam G, Engelhardt EM, Hubbell JA, Frey P, Larsson HM. Quantitative intrinsic auto-cathodoluminescence can resolve spectral signatures of tissue-isolated collagen extracellular matrix. Commun Biol 2019; 2:69. [PMID: 30793047 PMCID: PMC6379429 DOI: 10.1038/s42003-019-0313-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 01/18/2019] [Indexed: 11/18/2022] Open
Abstract
By analyzing isolated collagen gel samples, we demonstrated in situ detection of spectrally deconvoluted auto-cathodoluminescence signatures of specific molecular content with precise spatial localization over a maximum field of view of 300 µm. Correlation of the secondary electron and the hyperspectral images proved ~40 nm resolution in the optical channel, obtained due to a short carrier diffusion length, suppressed by fibril dimensions and poor electrical conductivity specific to their organic composition. By correlating spectrally analyzed auto-cathodoluminescence with mass spectroscopy data, we differentiated spectral signatures of two extracellular matrices, namely human fibrin complex and rat tail collagen isolate, and uncovered differences in protein distributions of isolated extracellular matrix networks of heterogeneous populations. Furthermore, we demonstrated that cathodoluminescence can monitor the progress of a human cell-mediated remodeling process, where human collagenous matrix was deposited within a rat collagenous matrix. The revealed change of the heterogeneous biological composition was confirmed by mass spectroscopy. Zielinski et al. show that quantitative label-free cathodoluminescence-scanning electron microscopy differentiates spectral signatures of two extracellular matrices. This method can monitor the progress of a smooth muscle cell-mediated remodeling process without using antibodies to enhance the optical signal.
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Affiliation(s)
| | - Elif Vardar
- Institute for Bioengineering, School of Life Sciences and School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, 1015, Switzerland.,Department of Pediatrics, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, 1011, Switzerland
| | - Ganesh Vythilingam
- Institute for Bioengineering, School of Life Sciences and School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, 1015, Switzerland.,Department of Surgery, Faculty of Medicine, University Malaya, Kuala Lumpur, 53100, Malaysia
| | - Eva-Maria Engelhardt
- Institute for Bioengineering, School of Life Sciences and School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, 1015, Switzerland
| | - Jeffrey A Hubbell
- Institute for Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA
| | - Peter Frey
- Institute for Bioengineering, School of Life Sciences and School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, 1015, Switzerland
| | - Hans M Larsson
- Institute for Bioengineering, School of Life Sciences and School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, 1015, Switzerland.
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69
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Staley EM, Jamy R, Phan AQ, Figge DA, Pham HP. N-Methyl-d-aspartate Receptor Antibody Encephalitis: A Concise Review of the Disorder, Diagnosis, and Management. ACS Chem Neurosci 2019; 10:132-142. [PMID: 30134661 DOI: 10.1021/acschemneuro.8b00304] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Anti-NMDA ( N-methyl-d-aspartate) receptor (anti-NMDAR) encephalitis is one of the most common paraneoplastic encephalitides. It occurs in both sexes, across all age ranges, and may occur in the presence or absence of an associated tumor. Its pathogenesis and clinical presentation relate to the presence of IgG1 or IgG3 antibodies targeting the NR1 subunit of the NMDA receptor, leading to a disinhibition of neuronal excitatory pathways. Initial clinical manifestations may be nonspecific, resembling a viral-like illness; however, with disease progression, symptoms can become quite severe, including prominent psychiatric features, cognitive problems, motor dysfunction, and autonomic instability. Anti-NMDAR encephalitis may even result in death in severe untreated cases. Diagnosis can be challenging, given that initial laboratory and radiographic results are typically nonspecific. The majority of patients respond to first or second-line treatments, although therapeutic options remain limited, usually consisting of tumor removal (if there is confirmation of an underlying malignancy) in conjunction with prompt initiation of immunosuppressive medications along with intravenous immunoglobulins and/or plasma exchange. Although the clinical presentation of anti-NMDAR encephalitis overlaps with several other more common neurological and psychiatric disorders, early diagnosis and treatment is essential for a positive prognosis. Here, we concisely review the pathogenesis, diagnosis, and clinical management of this disease.
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Affiliation(s)
- Elizabeth M. Staley
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, United States
| | - Rabia Jamy
- Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama 35249, United States
| | - Allan Q. Phan
- Doctor of Medicine Program, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53726, United States
| | - David A. Figge
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama 35249, United States
| | - Huy P. Pham
- Department of Pathology, Keck School of Medicine of the University of Southern California, Los Angeles, California 90033, United States
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70
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Fasipe O, Akhideno P, Owhin O, Ibiyemi-Fasipe O. Announcing the first novel class of rapid-onset antidepressants in clinical practice. JOURNAL OF MEDICAL SCIENCES 2019. [DOI: 10.4103/jmedsci.jmedsci_36_19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Baranovic J, Plested AJ. Auxiliary subunits keep AMPA receptors compact during activation and desensitization. eLife 2018; 7:40548. [PMID: 30520730 PMCID: PMC6324883 DOI: 10.7554/elife.40548] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 12/04/2018] [Indexed: 11/19/2022] Open
Abstract
Signal transduction at vertebrate excitatory synapses involves the rapid activation of AMPA (α-amino-3-hydroxy-5-methyl-4-isoxazole propionate) receptors, glutamate-gated ion channels whose four subunits assemble as a dimer-of-dimers. Technical advances in cryo-electron microscopy brought a slew of full-length structures of AMPA receptors, on their own and in combination with auxiliary subunits. These structures indicate that dimers might undergo substantial lateral motions during gating, opening up the extracellular layer along the central twofold symmetry axis. We used bifunctional methanethiosulfonate cross-linkers to calibrate the conformations found in functional AMPA receptors in the presence and absence of the auxiliary subunit Stargazin. Our data indicate that extracellular layer of AMPA receptors can get trapped in stable, opened-up conformations, especially upon long exposures to glutamate. In contrast, Stargazin limits this conformational flexibility. Thus, under synaptic conditions, where brief glutamate exposures and the presence of auxiliary proteins dominate, extracellular domains of AMPA receptors likely stay compact during gating. The nearly 100 billion neurons in our brain create a complex and intricate network that can relay information in a fraction of a second. Two neurons can communicate with each other by forming a synapse, a specialised structure where the two cells come into close contact. There, the signalling neuron releases chemicals that the receiving cell captures through dedicated receptors embedded in its membrane. For example, the AMPA receptor is a complex assemblage of different subunits that quickly transmits information by opening and closing to let ions move into the receiving cell. These receptors are some of the fastest to react to the released chemicals, allowing information to be encoded swiftly. In fact, it is increasingly clear that epilepsy and deficits in mental processes can be associated with AMPA receptors having a faulty activity. Yet, it is still unknown how exactly these proteins work. In particular, previous studies have shown that an AMPA receptor can go through dramatic changes in its structure, with the different subunits being able to spread apart widely. However, these experiments had to be conducted when the proteins were isolated from membranes and held in a cocktail of activating or deactivating molecules for hours. It is still unclear whether the results hold when AMPA receptors sit at the membrane while assembled with their partner proteins, like they normally do in the brain. Baranovic and Plested went on to investigate this question by using ‘molecular rulers’. These tiny molecules have different lengths, and they act as yardsticks: their sticky ends can attach to specific areas in the protein, helping to measure how these regions move relative to each other when the receptors are on or off. A method called patch clamp electrophysiology was used to determine how much the normal activity of the AMPA receptors was hindered by being bound by the molecular rulers. The results showed that AMPA receptors can undergo large structural changes but these movements require time and are much reduced by partner proteins. In the brain, AMPA receptors in synapses probably lack the freedom and opportunity to move so dramatically when neurons are communicating with each other. Ultimately, knowing how these receptors work and move may help grasp the changes in their activity that cause connections between neurons to become defective.
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Affiliation(s)
- Jelena Baranovic
- Institute of Biology, Cellular Biophysics, Humboldt Universität zu Berlin, Berlin, Germany.,Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany.,NeuroCure, Charité Universitätsmedizin, Berlin, Germany
| | - Andrew Jr Plested
- Institute of Biology, Cellular Biophysics, Humboldt Universität zu Berlin, Berlin, Germany.,Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany.,NeuroCure, Charité Universitätsmedizin, Berlin, Germany
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72
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Esmenjaud JB, Stroebel D, Chan K, Grand T, David M, Wollmuth LP, Taly A, Paoletti P. An inter-dimer allosteric switch controls NMDA receptor activity. EMBO J 2018; 38:embj.201899894. [PMID: 30396997 DOI: 10.15252/embj.201899894] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 10/08/2018] [Accepted: 10/10/2018] [Indexed: 11/09/2022] Open
Abstract
NMDA receptors (NMDARs) are glutamate-gated ion channels that are key mediators of excitatory neurotransmission and synaptic plasticity throughout the central nervous system. They form massive heterotetrameric complexes endowed with unique allosteric capacity provided by eight extracellular clamshell-like domains arranged as two superimposed layers. Despite an increasing number of full-length NMDAR structures, how these domains cooperate in an intact receptor to control its activity remains poorly understood. Here, combining single-molecule and macroscopic electrophysiological recordings, cysteine biochemistry, and in silico analysis, we identify a rolling motion at a yet unexplored interface between the two constitute dimers in the agonist-binding domain (ABD) layer as a key structural determinant in NMDAR activation and allosteric modulation. This rotation acts as a gating switch that tunes channel opening depending on the conformation of the membrane-distal N-terminal domain (NTD) layer. Remarkably, receptors locked in a rolled state display "super-activity" and resistance to NTD-mediated allosteric modulators. Our work unveils how NMDAR domains move in a concerted manner to transduce long-range conformational changes between layers and command receptor channel activity.
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Affiliation(s)
- Jean-Baptiste Esmenjaud
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Université PSL, CNRS, INSERM, Paris, France
| | - David Stroebel
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Université PSL, CNRS, INSERM, Paris, France
| | - Kelvin Chan
- Graduate Program in Neuroscience & Medical Scientist Training Program (MSTP), Departments of Neurobiology and Behavior & Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA
| | - Teddy Grand
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Université PSL, CNRS, INSERM, Paris, France
| | - Mélissa David
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Université PSL, CNRS, INSERM, Paris, France
| | - Lonnie P Wollmuth
- Graduate Program in Neuroscience & Medical Scientist Training Program (MSTP), Departments of Neurobiology and Behavior & Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA
| | - Antoine Taly
- Institut de Biologie Physico-Chimique (IBPC), Laboratoire de Biochimie Théorique, CNRS, Université Paris Diderot, Paris, France
| | - Pierre Paoletti
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Université PSL, CNRS, INSERM, Paris, France
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73
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Larsen AH, Dorosz J, Thorsen TS, Johansen NT, Darwish T, Midtgaard SR, Arleth L, Kastrup JS. Small-angle neutron scattering studies on the AMPA receptor GluA2 in the resting, AMPA-bound and GYKI-53655-bound states. IUCRJ 2018; 5:780-793. [PMID: 30443361 PMCID: PMC6211538 DOI: 10.1107/s2052252518012186] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 08/28/2018] [Indexed: 06/09/2023]
Abstract
The AMPA receptor GluA2 belongs to the family of ionotropic glutamate receptors, which are responsible for most of the fast excitatory neuronal signalling in the central nervous system. These receptors are important for memory and learning, but have also been associated with brain diseases such as Alzheimer's disease and epilepsy. Today, one drug is on the market for the treatment of epilepsy targeting AMPA receptors, i.e. a negative allosteric modulator of these receptors. Recently, crystal structures and cryo-electron microscopy (cryo-EM) structures of full-length GluA2 in the resting (apo), activated and desensitized states have been reported. Here, solution structures of full-length GluA2 are reported using small-angle neutron scattering (SANS) with a novel, fully matched-out detergent. The GluA2 solution structure was investigated in the resting state as well as in the presence of AMPA and of the negative allosteric modulator GYKI-53655. In solution and at neutral pH, the SANS data clearly indicate that GluA2 is in a compact form in the resting state. The solution structure resembles the crystal structure of GluA2 in the resting state, with an estimated maximum distance (D max) of 179 ± 11 Å and a radius of gyration (R g) of 61.9 ± 0.4 Å. An ab initio model of GluA2 in solution generated using DAMMIF clearly showed the individual domains, i.e. the extracellular N-terminal domains and ligand-binding domains as well as the transmembrane domain. Solution structures revealed that GluA2 remained in a compact form in the presence of AMPA or GYKI-53655. At acidic pH only, GluA2 in the presence of AMPA adopted a more open conformation of the extracellular part (estimated D max of 189 ± 5 Å and R g of 65.2 ± 0.5 Å), resembling the most open, desensitized class 3 cryo-EM structure of GluA2 in the presence of quisqualate. In conclusion, this methodological study may serve as an example for future SANS studies on membrane proteins.
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Affiliation(s)
- Andreas Haahr Larsen
- Structural Biophysics, X-ray and Neutron Science, The Niels Bohr Institute, University of Copenhagen, Denmark
| | - Jerzy Dorosz
- Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Thor Seneca Thorsen
- Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Nicolai Tidemand Johansen
- Structural Biophysics, X-ray and Neutron Science, The Niels Bohr Institute, University of Copenhagen, Denmark
| | - Tamim Darwish
- National Deuteration Facility, Australian Nuclear Science and Technology Organization, Australia
| | - Søren Roi Midtgaard
- Structural Biophysics, X-ray and Neutron Science, The Niels Bohr Institute, University of Copenhagen, Denmark
| | - Lise Arleth
- Structural Biophysics, X-ray and Neutron Science, The Niels Bohr Institute, University of Copenhagen, Denmark
| | - Jette Sandholm Kastrup
- Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
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74
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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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75
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Optimising the transient expression of GABA(A) receptors in adherent HEK293 cells. Protein Expr Purif 2018; 154:7-15. [PMID: 30248449 DOI: 10.1016/j.pep.2018.09.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/17/2018] [Accepted: 09/20/2018] [Indexed: 11/22/2022]
Abstract
Owing to their therapeutic relevance, considerable efforts are devoted to the structural characterisation of membrane proteins. Such studies are limited by the availability of high quality protein due to the difficulty of overexpression in recombinant mammalian systems. We sought to systematically optimise multiple aspects in the process of transiently transfecting HEK293 cells, to allow the rapid expression of membrane proteins, without the lengthy process of stable clone formation. We assessed the impact of medium formulation, cell line, and harvest time on the expression of GABAA receptors, as determined by [3H]muscimol binding in cell membranes. Furthermore, transfection with the use of calcium phosphate/polyethyleneimine multishell nanoparticles was optimised, and a dual vector system utilising viral enhancing elements was designed and implemented. These efforts resulted in a 40-fold improvement in GABAA α1β3 receptor expression, providing final yields of 22 fmol/cm2. The findings from this work provide a guide to the optimisation of transient expression of proteins in mammalian cells and should assist in the structural characterisation of membrane proteins.
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76
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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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77
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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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Krieger J, Lee JY, Greger IH, Bahar I. Activation and desensitization of ionotropic glutamate receptors by selectively triggering pre-existing motions. Neurosci Lett 2018; 700:22-29. [PMID: 29481851 PMCID: PMC6107436 DOI: 10.1016/j.neulet.2018.02.050] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 02/15/2018] [Accepted: 02/22/2018] [Indexed: 01/03/2023]
Abstract
Ionotropic glutamate receptors (iGluRs) are ligand-gated ion channels that are key players in synaptic transmission and plasticity. They are composed of four subunits, each containing four functional domains, the quaternary packing and collective structural dynamics of which are important determinants of their molecular mechanism of function. With the explosion of structural studies on different members of the family, including the structures of activated open channels, the mechanisms of action of these central signaling machines are now being elucidated. We review the current state of computational studies on two major members of the family, AMPA and NMDA receptors, with focus on molecular simulations and elastic network model analyses that have provided insights into the coupled movements of extracellular and transmembrane domains. We describe the newly emerging mechanisms of activation, allosteric signaling and desensitization, as mainly a selective triggering of pre-existing soft motions, as deduced from computational models and analyses that leverage structural data on intact AMPA and NMDA receptors in different states.
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Affiliation(s)
- James Krieger
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, 3501 Fifth Ave, Suite 3064 BST3, Pittsburgh, PA, 15260, United States
| | - Ji Young Lee
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, 3501 Fifth Ave, Suite 3064 BST3, Pittsburgh, PA, 15260, United States
| | - Ingo H Greger
- Neurobiology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, United Kingdom
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, 3501 Fifth Ave, Suite 3064 BST3, Pittsburgh, PA, 15260, United States.
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80
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Gupta R. Self-crowding of AMPA receptors in the excitatory postsynaptic density can effectuate anomalous receptor sub-diffusion. PLoS Comput Biol 2018; 14:e1005984. [PMID: 29444074 PMCID: PMC5812565 DOI: 10.1371/journal.pcbi.1005984] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 01/15/2018] [Indexed: 12/03/2022] Open
Abstract
AMPA receptors (AMPARs) and their associations with auxiliary transmembrane proteins are bulky structures with large steric-exclusion volumes. Hence, self-crowding of AMPARs, depending on the local density, may affect their lateral diffusion in the postsynaptic membrane as well as in the highly crowded postsynaptic density (PSD) at excitatory synapses. Earlier theoretical studies considered only the roles of transmembrane obstacles and the AMPAR-binding submembranous scaffold proteins in shaping receptor diffusion within PSD. Using lattice model of diffusion, the present study investigates the additional impacts of self-crowding on the anomalousity and effective diffusion coefficient (Deff) of AMPAR diffusion. A recursive algorithm for avoiding false self-blocking during diffusion simulation is also proposed. The findings suggest that high density of AMPARs in the obstacle-free membrane itself engenders strongly anomalous diffusion and severe decline in Deff. Adding transmembrane obstacles to the membrane accentuates the anomalousity arising from self-crowding due to the reduced free diffusion space. Contrarily, enhanced AMPAR-scaffold binding, either through increase in binding strength or scaffold density or both, ameliorates the anomalousity resulting from self-crowding. However, binding has differential impacts on Deff depending on the receptor density. Increase in binding causes consistent decrease in Deff for low and moderate receptor density. For high density, binding increases Deff as long as it reduces anomalousity associated with intense self-crowding. Given a sufficiently strong binding condition when diffusion acquires normal behavior, further increase in binding causes decrease in Deff. Supporting earlier experimental observations are mentioned and implications of present findings to the experimental observations on AMPAR diffusion are also drawn. The transmembrane AMPA receptors (AMPARs) prominently exhibit lateral diffusion in the postsynaptic membrane at excitatory synapses. Steric obstructions to AMPAR diffusion due to the crowd of other relatively static transmembrane proteins and binding of AMPARs to the submembranous scaffold proteins in the specialized region of postsynaptic density (PSD) are well known to retard receptor diffusion, which causes receptor trapping and accumulation within PSD. However, AMPARs are significantly bulky structures and may also obstruct their own diffusion paths in the presence of their high density. It is shown here that intense self-crowding of AMPARs may lead to highly obstructed and confined receptor diffusion even in the obstacle-free medium, and the presence of other obstacles further aggravates this effect. AMPAR-scaffold binding reduces confined diffusion arising from self-crowding and strong binding engenders normal diffusion even at high receptor density. However, it overall causes reduction in the effective diffusion coefficient of the receptor diffusion.
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Affiliation(s)
- Rahul Gupta
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
- * E-mail:
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81
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Tao CL, Liu YT, Sun R, Zhang B, Qi L, Shivakoti S, Tian CL, Zhang P, Lau PM, Zhou ZH, Bi GQ. Differentiation and Characterization of Excitatory and Inhibitory Synapses by Cryo-electron Tomography and Correlative Microscopy. J Neurosci 2018; 38:1493-1510. [PMID: 29311144 PMCID: PMC5815350 DOI: 10.1523/jneurosci.1548-17.2017] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 12/17/2017] [Accepted: 12/24/2017] [Indexed: 11/21/2022] Open
Abstract
As key functional units in neural circuits, different types of neuronal synapses play distinct roles in brain information processing, learning, and memory. Synaptic abnormalities are believed to underlie various neurological and psychiatric disorders. Here, by combining cryo-electron tomography and cryo-correlative light and electron microscopy, we distinguished intact excitatory and inhibitory synapses of cultured hippocampal neurons, and visualized the in situ 3D organization of synaptic organelles and macromolecules in their native state. Quantitative analyses of >100 synaptic tomograms reveal that excitatory synapses contain a mesh-like postsynaptic density (PSD) with thickness ranging from 20 to 50 nm. In contrast, the PSD in inhibitory synapses assumes a thin sheet-like structure ∼12 nm from the postsynaptic membrane. On the presynaptic side, spherical synaptic vesicles (SVs) of 25-60 nm diameter and discus-shaped ellipsoidal SVs of various sizes coexist in both synaptic types, with more ellipsoidal ones in inhibitory synapses. High-resolution tomograms obtained using a Volta phase plate and electron filtering and counting reveal glutamate receptor-like and GABAA receptor-like structures that interact with putative scaffolding and adhesion molecules, reflecting details of receptor anchoring and PSD organization. These results provide an updated view of the ultrastructure of excitatory and inhibitory synapses, and demonstrate the potential of our approach to gain insight into the organizational principles of cellular architecture underlying distinct synaptic functions.SIGNIFICANCE STATEMENT To understand functional properties of neuronal synapses, it is desirable to analyze their structure at molecular resolution. We have developed an integrative approach combining cryo-electron tomography and correlative fluorescence microscopy to visualize 3D ultrastructural features of intact excitatory and inhibitory synapses in their native state. Our approach shows that inhibitory synapses contain uniform thin sheet-like postsynaptic densities (PSDs), while excitatory synapses contain previously known mesh-like PSDs. We discovered "discus-shaped" ellipsoidal synaptic vesicles, and their distributions along with regular spherical vesicles in synaptic types are characterized. High-resolution tomograms further allowed identification of putative neurotransmitter receptors and their heterogeneous interaction with synaptic scaffolding proteins. The specificity and resolution of our approach enables precise in situ analysis of ultrastructural organization underlying distinct synaptic functions.
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Affiliation(s)
- Chang-Lu Tao
- National Laboratory for Physical Sciences at the Microscale
- School of Life Sciences
| | - Yun-Tao Liu
- National Laboratory for Physical Sciences at the Microscale
- School of Life Sciences
| | - Rong Sun
- National Laboratory for Physical Sciences at the Microscale
| | - Bin Zhang
- Chinese Academy of Sciences Key Laboratory of Brain Function and Disease
- School of Life Sciences
| | - Lei Qi
- Chinese Academy of Sciences Key Laboratory of Brain Function and Disease
- School of Life Sciences
| | - Sakar Shivakoti
- National Laboratory for Physical Sciences at the Microscale
- School of Life Sciences
| | - Chong-Li Tian
- Chinese Academy of Sciences Key Laboratory of Brain Function and Disease
- School of Life Sciences
| | - Peijun Zhang
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX37BN, United Kingdom
| | - Pak-Ming Lau
- Chinese Academy of Sciences Key Laboratory of Brain Function and Disease
- School of Life Sciences
| | - Z Hong Zhou
- National Laboratory for Physical Sciences at the Microscale,
- School of Life Sciences
- The California NanoSystems Institute, and
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, California 90095
| | - Guo-Qiang Bi
- National Laboratory for Physical Sciences at the Microscale,
- School of Life Sciences
- Chinese Academy of Sciences Center for Excellence in Brain Science and Intelligence Technology, Innovation Center for Cell Signaling Network, University of Science and Technology of China, Hefei, Anhui 230026, China
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82
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Wang Y, Bugge K, Kragelund BB, Lindorff-Larsen K. Role of protein dynamics in transmembrane receptor signalling. Curr Opin Struct Biol 2018; 48:74-82. [DOI: 10.1016/j.sbi.2017.10.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 10/16/2017] [Accepted: 10/19/2017] [Indexed: 10/18/2022]
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83
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Shimizu K, Cao W, Saad G, Shoji M, Terada T. Comparative analysis of membrane protein structure databases. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1077-1091. [PMID: 29331638 DOI: 10.1016/j.bbamem.2018.01.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 12/28/2017] [Accepted: 01/04/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND Membrane proteins play important roles in cell survival and cell communication, as they function as transporters, receptors, anchors and enzymes. They are also potential targets for drugs that block receptors or inhibit enzymes related to diseases. Although the number of known structures of membrane proteins is still small relative to the size of the proteome as a whole, many new membrane protein structures have been determined recently. SCOPE OF THE ARTICLE We compared and analyzed the widely used membrane protein databases, mpstruc, Orientations of Proteins in Membranes (OPM), and PDBTM, as well as the extended dataset of mpstruc based on sequence similarity, the PDB structures whose classification field indicates that they are "membrane proteins" and the proteins with Structural Classification of Proteins (SCOP) class-f domains. We evaluated the relationships between these databases or datasets based on the overlap in their contents and the degree of consistency in the structural, topological, and functional classifications and in the transmembrane domain assignment. MAJOR CONCLUSIONS The membrane databases differ from each other in their coverage, and in the criteria that they use for annotation and classification. To ensure the efficient use of these databases, it is important to understand their differences and similarities. The establishment of more detailed and consistent annotations for the sequence, structure, membrane association, and function of membrane proteins is still required. GENERAL SIGNIFICANCE Considering the recent growth of experimentally determined structures, a broad survey and cumulative analysis of the sum of knowledge as presented in the membrane protein structure databases can be helpful to elucidate structures and functions of membrane proteins. We also aim to provide a framework for future research and classification of membrane proteins.
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Affiliation(s)
- Kentaro Shimizu
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
| | - Wei Cao
- Faculty of Information Networking for Innovation and Design, Toyo University, Tokyo, Japan.
| | - Gull Saad
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
| | - Michiru Shoji
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
| | - Tohru Terada
- Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
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84
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Martin S, Chamberlin A, Shinde DN, Hempel M, Strom TM, Schreiber A, Johannsen J, Ousager LB, Larsen MJ, Hansen LK, Fatemi A, Cohen JS, Lemke J, Sørensen KP, Helbig KL, Lessel D, Abou Jamra R. De Novo Variants in GRIA4 Lead to Intellectual Disability with or without Seizures and Gait Abnormalities. Am J Hum Genet 2017; 101:1013-1020. [PMID: 29220673 DOI: 10.1016/j.ajhg.2017.11.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 11/13/2017] [Indexed: 01/21/2023] Open
Abstract
Using trio whole-exome sequencing, we have identified de novo heterozygous pathogenic variants in GRIA4 in five unrelated individuals with intellectual disability and other symptoms. GRIA4 encodes an AMPA receptor subunit known as GluR4, which is found on excitatory glutamatergic synapses and is important for learning and memory. Four of the variants are located in the highly conserved SYTANLAAF motif in the transmembrane protein M3, and the fifth is in an extra-cellular domain. Molecular modeling of the altered protein showed that three of the variants in the SYTANLAAF motif orient toward the center of the pore region and most likely lead to disturbance of the gating mechanism. The fourth variant in the SYTANLAAF motif most likely results in reduced permeability. The variant in the extracellular domain potentially interferes with the binding between the monomers. On the basis of clinical information and genetic results, and the fact that other subunits of the AMPA receptor have already been associated with neurodevelopmental disorders, we suggest that pathogenic de novo variants in GRIA4 lead to intellectual disability with or without seizures, gait abnormalities, problems of social behavior, and other variable features.
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85
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Shaikh SA, Dolino DM, Lee G, Chatterjee S, MacLean DM, Flatebo C, Landes CF, Jayaraman V. Stargazin Modulation of AMPA Receptors. Cell Rep 2017; 17:328-335. [PMID: 27705782 DOI: 10.1016/j.celrep.2016.09.014] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 08/08/2016] [Accepted: 09/02/2016] [Indexed: 02/03/2023] Open
Abstract
Fast excitatory synaptic signaling in the mammalian brain is mediated by AMPA-type ionotropic glutamate receptors. In neurons, AMPA receptors co-assemble with auxiliary proteins, such as stargazin, which can markedly alter receptor trafficking and gating. Here, we used luminescence resonance energy transfer measurements to map distances between the full-length, functional AMPA receptor and stargazin expressed in HEK293 cells and to determine the ensemble structural changes in the receptor due to stargazin. In addition, we used single-molecule fluorescence resonance energy transfer to study the structural and conformational distribution of the receptor and how this distribution is affected by stargazin. Our nanopositioning data place stargazin below the AMPA receptor ligand-binding domain, where it is well poised to act as a scaffold to facilitate the long-range conformational selection observations seen in single-molecule experiments. These data support a model of stargazin acting to stabilize or select conformational states that favor activation.
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Affiliation(s)
- Sana A Shaikh
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Drew M Dolino
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Biochemistry and Molecular Biology Graduate Program, Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Garam Lee
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | | | - David M MacLean
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Charlotte Flatebo
- Department of Chemistry, Rice University, Houston, TX 77251, USA; Applied Physics Graduate Program, Rice University, Houston, TX 77251, USA
| | - Christy F Landes
- Department of Chemistry, Rice University, Houston, TX 77251, USA; Department of Electrical and Computer Engineering, Rice University, Houston, TX 77251, USA; Applied Physics Graduate Program, Rice University, Houston, TX 77251, 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; Biochemistry and Molecular Biology Graduate Program, Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
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86
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Paramo T, Brown PMGE, Musgaard M, Bowie D, Biggin PC. Functional Validation of Heteromeric Kainate Receptor Models. Biophys J 2017; 113:2173-2177. [PMID: 28935133 PMCID: PMC5700254 DOI: 10.1016/j.bpj.2017.08.047] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 08/30/2017] [Accepted: 08/31/2017] [Indexed: 01/31/2023] Open
Abstract
Kainate receptors require the presence of external ions for gating. Most work thus far has been performed on homomeric GluK2 but, in vivo, kainate receptors are likely heterotetramers. Agonists bind to the ligand-binding domain (LBD) which is arranged as a dimer of dimers as exemplified in homomeric structures, but no high-resolution structure currently exists of heteromeric kainate receptors. In a full-length heterotetramer, the LBDs could potentially be arranged either as a GluK2 homomer alongside a GluK5 homomer or as two GluK2/K5 heterodimers. We have constructed models of the LBD dimers based on the GluK2 LBD crystal structures and investigated their stability with molecular dynamics simulations. We have then used the models to make predictions about the functional behavior of the full-length GluK2/K5 receptor, which we confirmed via electrophysiological recordings. A key prediction and observation is that lithium ions bind to the dimer interface of GluK2/K5 heteromers and slow their desensitization.
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Affiliation(s)
- Teresa Paramo
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Patricia M G E Brown
- Integrated Program in Neurosciences, McGill University, Montréal, Québec, Canada
| | - Maria Musgaard
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Derek Bowie
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada
| | - Philip C Biggin
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom.
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87
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Abstract
![]()
Ionotropic
glutamate receptors (iGluRs) are ligand-gated ion channels
that mediate the majority of excitatory neurotransmission in the central
nervous system. iGluRs open their ion channels in response to binding
of the neurotransmitter glutamate, rapidly depolarize the postsynaptic
neuronal membrane, and initiate signal transduction. Recent studies
using X-ray crystallography and cryo-electron microscopy have determined
full-length iGluR structures that (1) uncover the receptor architecture
in an unliganded, resting state, (2) reveal conformational changes
produced by ligands in order to activate iGluRs, open their ion channels,
and conduct ions, and (3) show how activated, glutamate-bound iGluRs
can adopt a nonconducting desensitized state. These new findings,
combined with the results of previous structural and functional experiments,
kinetic and molecular modeling, mutagenesis, and biochemical analyses,
provide new views on the structural mechanisms of iGluR gating.
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Affiliation(s)
- Edward C Twomey
- Department of Biochemistry and Molecular Biophysics and ‡Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University , 650 West 168th Street, New York, New York 10032, United States
| | - Alexander I Sobolevsky
- Department of Biochemistry and Molecular Biophysics and ‡Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University , 650 West 168th Street, New York, New York 10032, United States
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88
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Changeux JP, Christopoulos A. Allosteric modulation as a unifying mechanism for receptor function and regulation. Diabetes Obes Metab 2017; 19 Suppl 1:4-21. [PMID: 28880476 DOI: 10.1111/dom.12959] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Four major receptor families enable cells to respond to chemical and physical signals from their proximal environment. The ligand- and voltage-gated ion channels, G-protein-coupled receptors, nuclear hormone receptors and receptor tyrosine kinases are all allosteric proteins that carry multiple, spatially distinct, yet conformationally linked ligand-binding sites. Recent studies point to common mechanisms governing the allosteric transitions of these receptors, including the impact of oligomerization, pre-existing and functionally distinct conformational ensembles, intrinsically disordered regions, and the occurrence of allosteric modulatory sites. Importantly, synthetic allosteric modulators are being discovered for these receptors, providing an enriched, yet challenging, landscape for novel therapeutics.
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MESH Headings
- Allosteric Regulation/drug effects
- Allosteric Site/drug effects
- Animals
- Binding Sites/drug effects
- Dimerization
- Drug Discovery/trends
- Drugs, Investigational/chemistry
- Drugs, Investigational/pharmacology
- Humans
- Ligand-Gated Ion Channels/agonists
- Ligand-Gated Ion Channels/antagonists & inhibitors
- Ligand-Gated Ion Channels/chemistry
- Ligand-Gated Ion Channels/metabolism
- Ligands
- Models, Molecular
- Protein Conformation/drug effects
- Protein Multimerization/drug effects
- Receptor Protein-Tyrosine Kinases/agonists
- Receptor Protein-Tyrosine Kinases/antagonists & inhibitors
- Receptor Protein-Tyrosine Kinases/chemistry
- Receptor Protein-Tyrosine Kinases/metabolism
- Receptors, Cytoplasmic and Nuclear/agonists
- Receptors, Cytoplasmic and Nuclear/antagonists & inhibitors
- Receptors, Cytoplasmic and Nuclear/chemistry
- Receptors, Cytoplasmic and Nuclear/metabolism
- Receptors, G-Protein-Coupled/agonists
- Receptors, G-Protein-Coupled/antagonists & inhibitors
- Receptors, G-Protein-Coupled/chemistry
- Receptors, G-Protein-Coupled/metabolism
- Voltage-Gated Sodium Channels/chemistry
- Voltage-Gated Sodium Channels/metabolism
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Affiliation(s)
| | - Arthur Christopoulos
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, VIC 3052 Parkville, Australia
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89
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Zhang W, Eibl C, Weeks AM, Riva I, Li YJ, Plested AJR, Howe JR. Unitary Properties of AMPA Receptors with Reduced Desensitization. Biophys J 2017; 113:2218-2235. [PMID: 28863863 DOI: 10.1016/j.bpj.2017.07.030] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 07/20/2017] [Accepted: 07/25/2017] [Indexed: 01/24/2023] Open
Abstract
Wild-type AMPA receptors display a characteristic rapidly desensitizing phenotype. Many studies point to the dimer interface between pairs of extracellular ligand binding domains as the key region controlling the rate at which the receptors desensitize. However, mutations at the extracellular end of the pore-forming regions (near the putative ion channel gate) have also been shown to alter desensitization. Here we report the behavior of single GluA4 receptors carrying one of two mutations that greatly reduce desensitization at the level of ensemble currents: the dimer interface mutation L484Y and the Lurcher mutation (A623T, GluA4-Lc) in the extracellular end of M3 (the second true transmembrane helix). Analysis of unitary currents in patches with just one active receptor showed that each mutation greatly prolongs bursts of openings without prolonging the apparent duration of individual openings. Each mutation decreases the frequency with which individual receptors visit desensitized states, but both mutant receptors still desensitize multiple times per second. Cyclothiazide (CTZ) reduced desensitization of wild-type receptors and both types of mutant receptor. Analysis of shut-time distributions revealed a form of short-lived desensitization that was resistant to CTZ and was especially prominent for GluA4-Lc receptors. Despite reducing desensitization of GluA4 L484Y receptors, CTZ decreased the amplitude of ensemble currents through GluA2 and GluA4 LY receptor mutants. Single-channel analysis and comparison of the GluA2 L483Y ligand binding domain dimer in complex with glutamate with and without CTZ is consistent with the conclusion that CTZ binding to the dimer interface prevents effects of the LY mutation to modulate receptor activation, resulting in a reduction in the prevalence of large-conductance substates that accounts for the decrease in ensemble current amplitudes. Together, the results show that similar nondesensitizing AMPA-receptor phenotypes of population currents can arise from distinct underlying molecular mechanisms that produce different types of unitary activity.
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Affiliation(s)
- Wei Zhang
- Department of Pharmacology, Institution of Chinese Integrative Medicine, Hebei Medical University, Shijiazhuang, Hebei, China; Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut.
| | - Clarissa Eibl
- Leibniz-Institut für Molekulare Pharmakologie and Cluster of Excellence, NeuroCure, Charité Universitätsmedizin, Berlin, Germany; Institute of Biology, Cellular Biophysics, Humboldt Universität zu Berlin, Berlin, Germany
| | - Autumn M Weeks
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut
| | - Irene Riva
- Leibniz-Institut für Molekulare Pharmakologie and Cluster of Excellence, NeuroCure, Charité Universitätsmedizin, Berlin, Germany; Institute of Biology, Cellular Biophysics, Humboldt Universität zu Berlin, Berlin, Germany
| | - Yan-Jun Li
- Department of Pharmacology, Institution of Chinese Integrative Medicine, Hebei Medical University, Shijiazhuang, Hebei, China; State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Andrew J R Plested
- Leibniz-Institut für Molekulare Pharmakologie and Cluster of Excellence, NeuroCure, Charité Universitätsmedizin, Berlin, Germany; Institute of Biology, Cellular Biophysics, Humboldt Universität zu Berlin, Berlin, Germany
| | - James R Howe
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut.
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90
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The Challenge of Interpreting Glutamate-Receptor Ion-Channel Structures. Biophys J 2017; 113:2143-2151. [PMID: 28844473 DOI: 10.1016/j.bpj.2017.07.028] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 07/12/2017] [Accepted: 07/25/2017] [Indexed: 11/24/2022] Open
Abstract
Ion channels activated by glutamate mediate excitatory synaptic transmission in the central nervous system. Similar to other ligand-gated ion channels, their gating cycle begins with transitions from a ligand-free closed state to glutamate-bound active and desensitized states. In an attempt to reveal the molecular mechanisms underlying gating, numerous structures for glutamate receptors have been solved in complexes with agonists, antagonists, allosteric modulators, and auxiliary proteins. The embarrassingly rich library of structures emerging from this work reveals very dynamic molecules with a more complex conformational spectrum than anticipated from functional studies. Unanticipated conformations solved for complexes with competitive antagonists and a lack of understanding of the structural basis for ion channel subconductance states further highlight challenges that have yet to be addressed.
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91
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Zheng W, Wen H, Iacobucci GJ, Popescu GK. Probing the Structural Dynamics of the NMDA Receptor Activation by Coarse-Grained Modeling. Biophys J 2017. [PMID: 28636915 DOI: 10.1016/j.bpj.2017.04.043] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
N-Methyl-D-aspartate (NMDA) receptors are glutamate-gated excitatory channels that play essential roles in brain functions. High-resolution structures have been solved for an allosterically inhibited and agonist-bound form of a functional NMDA receptor; however, other key functional states (particularly the active open-channel state) were only resolved at moderate resolutions by cryo-electron microscopy (cryo-EM). To decrypt the mechanism of the NMDA receptor activation, structural modeling is essential to provide presently missing information about structural dynamics. We performed systematic coarse-grained modeling using an elastic network model and related modeling/analysis tools (e.g., normal mode analysis, flexibility and hotspot analysis, cryo-EM flexible fitting, and transition pathway modeling) based on an active-state cryo-EM map. We observed extensive conformational changes that allosterically couple the extracellular regulatory and agonist-binding domains to the pore-forming trans-membrane domain (TMD), and validated these, to our knowledge, new observations against known mutational and functional studies. Our results predict two key modes of collective motions featuring shearing/twisting of the extracellular domains relative to the TMD, reveal subunit-specific flexibility profiles, and identify functional hotspot residues at key domain-domain interfaces. Finally, by examining the conformational transition pathway between the allosterically inhibited form and the active form, we predict a discrete sequence of domain motions, which propagate from the extracellular domains to the TMD. In summary, our results offer rich structural and dynamic information, which is consistent with the literature on structure-function relationships in NMDA receptors, and will guide in-depth studies on the activation dynamics of this important neurotransmitter receptor.
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Affiliation(s)
- Wenjun Zheng
- Department of Physics, State University of New York at Buffalo, Buffalo, New York.
| | - Han Wen
- Department of Physics, State University of New York at Buffalo, Buffalo, New York
| | - Gary J Iacobucci
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, New York
| | - Gabriela K Popescu
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, New York
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92
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Activation and Desensitization Mechanism of AMPA Receptor-TARP Complex by Cryo-EM. Cell 2017; 170:1234-1246.e14. [PMID: 28823560 DOI: 10.1016/j.cell.2017.07.045] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 06/08/2017] [Accepted: 07/25/2017] [Indexed: 11/21/2022]
Abstract
AMPA receptors mediate fast excitatory neurotransmission in the mammalian brain and transduce the binding of presynaptically released glutamate to the opening of a transmembrane cation channel. Within the postsynaptic density, however, AMPA receptors coassemble with transmembrane AMPA receptor regulatory proteins (TARPs), yielding a receptor complex with altered gating kinetics, pharmacology, and pore properties. Here, we elucidate structures of the GluA2-TARP γ2 complex in the presence of the partial agonist kainate or the full agonist quisqualate together with a positive allosteric modulator or with quisqualate alone. We show how TARPs sculpt the ligand-binding domain gating ring, enhancing kainate potency and diminishing the ensemble of desensitized states. TARPs encircle the receptor ion channel, stabilizing M2 helices and pore loops, illustrating how TARPs alter receptor pore properties. Structural and computational analysis suggests the full agonist and modulator complex harbors an ion-permeable channel gate, providing the first view of an activated AMPA receptor.
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93
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Yonkunas M, Buddhadev M, Flores Canales JC, Kurnikova MG. Configurational Preference of the Glutamate Receptor Ligand Binding Domain Dimers. Biophys J 2017; 112:2291-2300. [PMID: 28591602 DOI: 10.1016/j.bpj.2017.04.042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 04/11/2017] [Accepted: 04/24/2017] [Indexed: 01/26/2023] Open
Abstract
Ionotropic glutamate receptors are a family of tetrameric ion channels with functional states consisting of nonconducting, conducting, and desensitized states that are starting to become well characterized by electrophysiological and biophysical studies. However, the structure and relative energetics of these states beyond the general structure of the receptor are still not well understood. It is known that the interface between monomeric subunits of the tetramer plays a major role in distinguishing these functional states. We have used umbrella sampling and multimicrosecond molecular dynamics simulations of the GluA2 AMPA subtype glutamate receptor ligand-binding domain (LBD) dimers to characterize a natural propensity of the LBD dimers for various configurational states. Our results show a proposed desensitized conformation of the LBD dimer is a highly preferable conformation of the LBD dimer without the influence of other receptor domains or crystallographic conditions. This has been demonstrated by both free protein simulations of 5 μs duration, as well as by computed free energy difference between the active and desensitized states. At the same time, the simulations performed using the same protocols revealed that for the LBD mutant L483Y, known to lack desensitization, the postulated active state of the LBD dimer is indeed the preferred configurational state, which remained stable in the simulations. Our findings pave the path for developing more detailed hypotheses of the full receptor activation mechanism. Combined with the energetics of glutamate binding to the LBD and the energy required to open the transmembrane pore helices, our results strongly support a hypothesis that the low absolute free-energy state is the desensitized state of the intact AMPA receptor.
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Affiliation(s)
- Michael Yonkunas
- Chemistry Department, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Maiti Buddhadev
- Chemistry Department, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | | | - Maria G Kurnikova
- Chemistry Department, Carnegie Mellon University, Pittsburgh, Pennsylvania.
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94
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Channel opening and gating mechanism in AMPA-subtype glutamate receptors. Nature 2017; 549:60-65. [PMID: 28737760 PMCID: PMC5743206 DOI: 10.1038/nature23479] [Citation(s) in RCA: 169] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 07/14/2017] [Indexed: 01/03/2023]
Abstract
AMPA-subtype ionotropic glutamate receptors mediate fast excitatory neurotransmission throughout the central nervous system. Gated by the neurotransmitter glutamate, AMPA receptors are critical for synaptic strength and dysregulation of AMPA receptor-mediated signaling is linked to numerous neurological diseases. Here, we use cryo-electron microscopy to solve the structures of AMPA receptor-auxiliary subunit complexes in the apo, antagonist and agonist-bound states and elucidate the iris-like mechanism of ion channel opening. The ion channel selectivity filter is formed by the extended portions of the re-entrant M2 loops, while the helical portions of M2 contribute to extensive hydrophobic interfaces between AMPA receptor subunits in the ion channel. We show how the permeation pathway changes upon channel opening and identify conformational changes throughout the entire AMPA receptor that accompany activation and desensitization. Our findings provide a framework for understanding gating across the family of ionotropic glutamate receptors and the role of AMPA receptors in excitatory neurotransmission.
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95
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Dai J, Zhou HX. Semiclosed Conformations of the Ligand-Binding Domains of NMDA Receptors during Stationary Gating. Biophys J 2017; 111:1418-1428. [PMID: 27705765 DOI: 10.1016/j.bpj.2016.08.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 08/02/2016] [Accepted: 08/12/2016] [Indexed: 12/26/2022] Open
Abstract
NMDA receptors are tetrameric ligand-gated ion channels. In the continuous presence of saturating agonists, NMDA receptors undergo stationary gating, in which the channel stochastically switches between an open state that permits ion conductance and a closed state that prevents permeation. The ligand-binding domains (LBDs) of the four subunits are expected to have closed clefts in the channel-open state. On the other hand, there is little knowledge about the conformational status of the LBDs in the channel-closed state during stationary gating. To probe the latter conformational status, Kussius and Popescu engineered interlobe disulfide cross-links in NMDA receptors and found that the cross-linking produced stationary gating kinetics that differed only subtly from that produced by agonist binding. These authors assumed that the cross-linking immobilized the LBDs in cleft-closed conformations, and consequently concluded that throughout stationary gating, agonist-bound LBDs also stayed predominantly in cleft-closed conformations and made only infrequent excursions to cleft-open conformations. Here, by calculating the conformational free energies of cross-linked and agonist-bound LBDs, we assess whether cross-linking actually traps the LBDs in cleft-closed conformations and delineate semiclosed conformations of agonist-bound LBDs that may potentially be thermodynamically and kinetically important during stationary gating. Our free-energy results show that the cross-linked LBDs are not locked in the fully closed form; rather, they sample semiclosed conformations almost as readily as the agonist-bound LBDs. Several lines of reasoning suggest that LBDs are semiclosed in the channel-closed state during stationary gating. Our free-energy simulations suggest possible structural details of such semiclosed LBD conformations, including intra- and intermolecular interactions that serve as alternatives to those in the cleft-closed conformations.
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Affiliation(s)
- Jian Dai
- Department of Physics, Florida State University, Tallahassee, Florida; Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida
| | - Huan-Xiang Zhou
- Department of Physics, Florida State University, Tallahassee, Florida; Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida.
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96
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Structural mechanisms of activation and desensitization in neurotransmitter-gated ion channels. Nat Struct Mol Biol 2017; 23:494-502. [PMID: 27273633 DOI: 10.1038/nsmb.3214] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 03/29/2016] [Indexed: 12/31/2022]
Abstract
Ion channels gated by neurotransmitters are present across metazoans, in which they are essential for brain function, sensation and locomotion; closely related homologs are also found in bacteria. Structures of eukaryotic pentameric cysteine-loop (Cys-loop) receptors and tetrameric ionotropic glutamate receptors in multiple functional states have recently become available. Here, I describe how these studies relate to established ideas regarding receptor activation and how they have enabled decades' worth of functional work to be pieced together, thus allowing previously puzzling aspects of receptor activity to be understood.
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97
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Iacobucci GJ, Popescu GK. NMDA receptors: linking physiological output to biophysical operation. Nat Rev Neurosci 2017; 18:236-249. [PMID: 28303017 DOI: 10.1038/nrn.2017.24] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
NMDA receptors are preeminent neurotransmitter-gated channels in the CNS, which respond to glutamate in a manner that integrates multiple external and internal cues. They belong to the ionotropic glutamate receptor family and fulfil unique and crucial roles in neuronal development and function. These roles depend on characteristic response kinetics, which reflect the operation of the receptors. Here, we review biologically salient features of the NMDA receptor signal and its mechanistic origins. Knowledge of distinctive NMDA receptor biophysical properties, their structural determinants and physiological roles is necessary to understand the physiological and neurotoxic actions of glutamate and to design effective therapeutics.
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Affiliation(s)
- Gary J Iacobucci
- Department of Biochemistry, University of Buffalo, State University of New York (SUNY), 144 Farber Hall, 3435 Main street, Buffalo, New York 14214, USA
| | - Gabriela K Popescu
- Department of Biochemistry, University of Buffalo, State University of New York (SUNY), 144 Farber Hall, 3435 Main street, Buffalo, New York 14214, USA
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98
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Tobi D. Dynamical differences of hemoglobin and the ionotropic glutamate receptor in different states revealed by a new dynamics alignment method. Proteins 2017; 85:1507-1517. [PMID: 28459140 DOI: 10.1002/prot.25311] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 04/02/2017] [Accepted: 04/24/2017] [Indexed: 12/26/2022]
Abstract
A new algorithm for comparison of protein dynamics is presented. Compared protein structures are superposed and their modes of motions are calculated using the anisotropic network model. The obtained modes are aligned using the dynamic programming algorithm of Needleman and Wunsch, commonly used for sequence alignment. Dynamical comparison of hemoglobin in the T and R2 states reveals that the dynamics of the allosteric effector 2,3-bisphosphoglycerate binding site is different in the two states. These differences can contribute to the selectivity of the effector to the T state. Similar comparison of the ionotropic glutamate receptor in the kainate+(R,R)-2b and ZK bound states reveals that the kainate+(R,R)-2b bound states slow modes describe upward motions of ligand binding domain and the transmembrane domain regions. Such motions may lead to the opening of the receptor. The upper lobes of the LBDs of the ZK bound state have a smaller interface with the amino terminal domains above them and have a better ability to move together. The present study exemplifies the use of dynamics comparison as a tool to study protein function. Proteins 2017; 85:1507-1517. © 2014 Wiley Periodicals, Inc.
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Affiliation(s)
- Dror Tobi
- Department of Computer Sciences, Ariel University, Ariel, 40700, Israel.,Department of Molecular Biology, Ariel University, Ariel, 40700, Israel
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99
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Twomey EC, Yelshanskaya MV, Grassucci RA, Frank J, Sobolevsky AI. Structural Bases of Desensitization in AMPA Receptor-Auxiliary Subunit Complexes. Neuron 2017; 94:569-580.e5. [PMID: 28472657 PMCID: PMC5492975 DOI: 10.1016/j.neuron.2017.04.025] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 04/10/2017] [Accepted: 04/17/2017] [Indexed: 02/09/2023]
Abstract
Fast excitatory neurotransmission is mediated by AMPA-subtype ionotropic glutamate receptors (AMPARs). AMPARs, localized at post-synaptic densities, are regulated by transmembrane auxiliary subunits that modulate AMPAR assembly, trafficking, gating, and pharmacology. Aberrancies in AMPAR-mediated signaling are associated with numerous neurological disorders. Here, we report cryo-EM structures of an AMPAR in complex with the auxiliary subunit GSG1L in the closed and desensitized states. GSG1L favors the AMPAR desensitized state, where channel closure is facilitated by profound structural rearrangements in the AMPAR extracellular domain, with ligand-binding domain dimers losing their local 2-fold rotational symmetry. Our structural and functional experiments suggest that AMPAR auxiliary subunits share a modular architecture and use a common transmembrane scaffold for distinct extracellular modules to differentially regulate AMPAR gating. By comparing the AMPAR-GSG1L complex structures, we map conformational changes accompanying AMPAR recovery from desensitization and reveal structural bases for regulation of synaptic transmission by auxiliary subunits.
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Affiliation(s)
- Edward C Twomey
- Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168(th) Street, New York, NY 10032, USA; Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, 650 West 168(th) Street, New York, NY 10032, USA
| | - Maria V Yelshanskaya
- Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168(th) Street, New York, NY 10032, USA
| | - Robert A Grassucci
- Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168(th) Street, New York, NY 10032, USA; Howard Hughes Medical Institute, 650 West 168(th) Street, New York, NY 10032, USA
| | - Joachim Frank
- Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168(th) Street, New York, NY 10032, USA; Department of Biological Sciences, Columbia University, 650 West 168(th) Street, New York, NY 10032, USA; Howard Hughes Medical Institute, 650 West 168(th) Street, New York, NY 10032, 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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100
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Greger IH, Watson JF, Cull-Candy SG. Structural and Functional Architecture of AMPA-Type Glutamate Receptors and Their Auxiliary Proteins. Neuron 2017; 94:713-730. [DOI: 10.1016/j.neuron.2017.04.009] [Citation(s) in RCA: 169] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 04/04/2017] [Accepted: 04/05/2017] [Indexed: 12/20/2022]
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