1
|
Sasmal DK, Yadav R, Lu HP. Single-Molecule Patch-Clamp FRET Anisotropy Microscopy Studies of NMDA Receptor Ion Channel Activation and Deactivation under Agonist Ligand Binding in Living Cells. J Am Chem Soc 2016; 138:8789-801. [DOI: 10.1021/jacs.6b03496] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Dibyendu Kumar Sasmal
- Center for Photochemical
Sciences, Department of Chemistry, Bowling Green State University, Bowling
Green, Ohio 43403, United States
| | - Rajeev Yadav
- Center for Photochemical
Sciences, Department of Chemistry, Bowling Green State University, Bowling
Green, Ohio 43403, United States
| | - H. Peter Lu
- Center for Photochemical
Sciences, Department of Chemistry, Bowling Green State University, Bowling
Green, Ohio 43403, United States
| |
Collapse
|
2
|
Cooper DR, Dolino DM, Jaurich H, Shuang B, Ramaswamy S, Nurik CE, Chen J, Jayaraman V, Landes CF. Conformational transitions in the glycine-bound GluN1 NMDA receptor LBD via single-molecule FRET. Biophys J 2016; 109:66-75. [PMID: 26153703 PMCID: PMC4572502 DOI: 10.1016/j.bpj.2015.05.025] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 05/15/2015] [Accepted: 05/18/2015] [Indexed: 12/30/2022] Open
Abstract
The N-methyl-D-aspartate receptor (NMDAR) is a member of the glutamate receptor family of proteins and is responsible for excitatory transmission. Activation of the receptor is thought to be controlled by conformational changes in the ligand binding domain (LBD); however, glutamate receptor LBDs can occupy multiple conformations even in the activated form. This work probes equilibrium transitions among NMDAR LBD conformations by monitoring the distance across the glycine-bound LBD cleft using single-molecule Förster resonance energy transfer (smFRET). Recent improvements in photoprotection solutions allowed us to monitor transitions among the multiple conformations. Also, we applied a recently developed model-free algorithm called "step transition and state identification" to identify the number of states, their smFRET efficiencies, and their interstate kinetics. Reversible interstate conversions, corresponding to transitions among a wide range of cleft widths, were identified in the glycine-bound LBD, on much longer timescales compared to channel opening. These transitions were confirmed to be equilibrium in nature by shifting the distribution reversibly via denaturant. We found that the NMDAR LBD proceeds primarily from one adjacent smFRET state to the next under equilibrium conditions, consistent with a cleft-opening/closing mechanism. Overall, by analyzing the state-to-state transition dynamics and distributions, we achieve insight into specifics of long-lived LBD equilibrium structural dynamics, as well as obtain a more general description of equilibrium folding/unfolding in a conformationally dynamic protein. The relationship between such long-lived LBD dynamics and channel function in the full receptor remains an open and interesting question.
Collapse
Affiliation(s)
- David R Cooper
- Department of Chemistry, Rice University, Houston, Texas
| | - Drew M Dolino
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, Graduate School of Biomedical Sciences, University of Texas Health Science Center, Houston, Texas
| | | | - Bo Shuang
- Department of Chemistry, Rice University, Houston, Texas
| | - Swarna Ramaswamy
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, Graduate School of Biomedical Sciences, University of Texas Health Science Center, Houston, Texas
| | - Caitlin E Nurik
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, Graduate School of Biomedical Sciences, University of Texas Health Science Center, Houston, Texas
| | - Jixin Chen
- Department of Chemistry, Rice University, Houston, Texas
| | - Vasanthi Jayaraman
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, Graduate School of Biomedical Sciences, University of Texas Health Science Center, Houston, Texas.
| | - Christy F Landes
- Department of Chemistry, Rice University, Houston, Texas; Department of Electrical and Computer Engineering, Rice University, Houston, Texas.
| |
Collapse
|
3
|
Sasmal D, Lu HP. Single-molecule patch-clamp FRET microscopy studies of NMDA receptor ion channel dynamics in living cells: revealing the multiple conformational states associated with a channel at its electrical off state. J Am Chem Soc 2014; 136:12998-3005. [PMID: 25148304 PMCID: PMC4183623 DOI: 10.1021/ja506231j] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Indexed: 01/10/2023]
Abstract
Conformational dynamics plays a critical role in the activation, deactivation, and open-close activities of ion channels in living cells. Such conformational dynamics is often inhomogeneous and extremely difficult to be directly characterized by ensemble-averaged spectroscopic imaging or only by single channel patch-clamp electric recording methods. We have developed a new and combined technical approach, single-molecule patch-clamp FRET microscopy, to probe ion channel conformational dynamics in living cell by simultaneous and correlated measurements of real-time single-molecule FRET spectroscopic imaging with single-channel electric current recording. Our approach is particularly capable of resolving ion channel conformational change rate process when the channel is at its electrically off states and before the ion channel is activated, the so-called "silent time" when the electric current signals are at zero or background. We have probed NMDA (N-methyl-D-aspartate) receptor ion channel in live HEK-293 cell, especially, the single ion channel open-close activity and its associated protein conformational changes simultaneously. Furthermore, we have revealed that the seemingly identical electrically off states are associated with multiple conformational states. On the basis of our experimental results, we have proposed a multistate clamshell model to interpret the NMDA receptor open-close dynamics.
Collapse
Affiliation(s)
- Dibyendu
Kumar Sasmal
- Department
of Chemistry and
Center for Photochemical Sciences, Bowling
Green State University, Bowling
Green, Ohio 43403, United States
| | - H. Peter Lu
- Department
of Chemistry and
Center for Photochemical Sciences, Bowling
Green State University, Bowling
Green, Ohio 43403, United States
| |
Collapse
|
4
|
Middendorp SJ, Hurni E, Schönberger M, Stein M, Pangerl M, Trauner D, Sigel E. Relative positioning of classical benzodiazepines to the γ2-subunit of GABAA receptors. ACS Chem Biol 2014; 9:1846-53. [PMID: 24918742 DOI: 10.1021/cb500186a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
GABAA receptors are the major inhibitory neurotransmitter receptors in the brain. Benzodiazepine exert their action via a high affinity-binding site at the α/γ subunit interface on some of these receptors. Diazepam has sedative, hypnotic, anxiolytic, muscle relaxant, and anticonvulsant effects. It acts by potentiating the current evoked by the agonist GABA. Understanding specific interaction of benzodiazepines in the binding pocket of different GABAA receptor isoforms might help to separate these divergent effects. As a first step, we characterized the interaction between diazepam and the major GABAA receptor isoform α1β2γ2. We mutated several amino acid residues on the γ2-subunit assumed to be located near or in the benzodiazepine binding pocket individually to cysteine and studied the interaction with three ligands that are modified with a cysteine-reactive isothiocyanate group (-NCS). When the reactive NCS group is in apposition to the cysteine residue this leads to a covalent reaction. In this way, three amino acid residues, γ2Tyr58, γ2Asn60, and γ2Val190 were located relative to classical benzodiazepines in their binding pocket on GABAA receptors.
Collapse
Affiliation(s)
- Simon J. Middendorp
- Institute
of Biochemistry and Molecular Medicine, University of Bern, CH-3012 Bern, Switzerland
| | - Evelyn Hurni
- Institute
of Biochemistry and Molecular Medicine, University of Bern, CH-3012 Bern, Switzerland
| | - Matthias Schönberger
- Department
of Chemistry, Ludwig-Maximilians-Universität München and Center of Integrated Protein Science, 81377 Munich, Germany
| | - Marco Stein
- Department
of Chemistry, Ludwig-Maximilians-Universität München and Center of Integrated Protein Science, 81377 Munich, Germany
| | - Michael Pangerl
- Department
of Chemistry, Ludwig-Maximilians-Universität München and Center of Integrated Protein Science, 81377 Munich, Germany
| | - Dirk Trauner
- Department
of Chemistry, Ludwig-Maximilians-Universität München and Center of Integrated Protein Science, 81377 Munich, Germany
| | - Erwin Sigel
- Institute
of Biochemistry and Molecular Medicine, University of Bern, CH-3012 Bern, Switzerland
| |
Collapse
|
5
|
Lemoine D, Jiang R, Taly A, Chataigneau T, Specht A, Grutter T. Ligand-gated ion channels: new insights into neurological disorders and ligand recognition. Chem Rev 2012; 112:6285-318. [PMID: 22988962 DOI: 10.1021/cr3000829] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Damien Lemoine
- Laboratoire de Biophysicochimie des Récepteurs Canaux, UMR 7199 CNRS, Conception et Application de Molécules Bioactives, Faculté de Pharmacie, Université de Strasbourg , 67400 Illkirch, France
| | | | | | | | | | | |
Collapse
|
6
|
Abstract
ATP-gated P2X receptors are trimeric ion channels, as recently confirmed by X-ray crystallography. However, the structure was solved without ATP and even though extracellular intersubunit cavities surrounded by conserved amino acid residues previously shown to be important for ATP function were proposed to house ATP, the localization of the ATP sites remains elusive. Here we localize the ATP-binding sites by creating, through a proximity-dependent "tethering" reaction, covalent bonds between a synthesized ATP-derived thiol-reactive P2X2 agonist (NCS-ATP) and single cysteine mutants engineered in the putative binding cavities of the P2X2 receptor. By combining whole-cell and single-channel recordings, we report that NCS-ATP covalently and specifically labels two previously unidentified positions N140 and L186 from two adjacent subunits separated by about 18 Å in a P2X2 closed state homology model, suggesting the existence of at least two binding modes. Tethering reaction at both positions primes subsequent agonist binding, yet with distinct functional consequences. Labeling of one position impedes subsequent ATP function, which results in inefficient gating, whereas tethering of the other position, although failing to produce gating by itself, enhances subsequent ATP function. Our results thus define a large and dynamic intersubunit ATP-binding pocket and suggest that receptors trapped in covalently agonist-bound states differ in their ability to gate the ion channel.
Collapse
|
7
|
Charon S, Taly A, Rodrigo J, Perret P, Goeldner M. Binding modes of noncompetitive GABA-channel blockers revisited using engineered affinity-labeling reactions combined with new docking studies. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2011; 59:2803-2807. [PMID: 20839772 DOI: 10.1021/jf102468n] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The binding modes of noncompetitive GABA(A)-channel blockers were re-examined taking into account the recent description of the 3D structure of prokaryotic pentameric ligand-gated ion channels, which provided access to new mammalian or insect GABA receptor models, emphasizing their transmembrane portion. Two putative binding modes were deciphered for this class of compounds, including the insecticide fipronil, located nearby either the intra- or the extracellular part of the membrane, respectively. These results are in full agreement with previously described affinity-labeling reactions performed with GABA(A) noncompetitive blockers (Perret et al. J. Biol. Chem.1999, 274, 25350-25354).
Collapse
Affiliation(s)
- Sébastien Charon
- Laboratoire de Chimie Bioorganique, CNRS-UMR 7199, Faculté de Pharmacie, Université de Strasbourg, Strasbourg, France
| | | | | | | | | |
Collapse
|
8
|
Rai A, Singh AK, Singh P, Yadav LDS. Stereoselective cascade reactions for construction of polyfunctionalised octahydroquinolines via [2C+2C+1C,1N] cyclisation. Tetrahedron Lett 2011. [DOI: 10.1016/j.tetlet.2011.01.079] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
9
|
Tan KR, Baur R, Charon S, Goeldner M, Sigel E. Relative positioning of diazepam in the benzodiazepine-binding-pocket of GABA receptors. J Neurochem 2009; 111:1264-73. [PMID: 19804380 DOI: 10.1111/j.1471-4159.2009.06419.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
GABA(A) receptors are the major inhibitory neurotransmitter receptors in the brain. Some of them are targets of benzodiazepines that are widely used in clinical practice for their sedative/hypnotic, anxiolytic, muscle relaxant and anticonvulsant effects. In order to rationally separate these different drug actions, we need to understand the interaction of such compounds with the benzodiazepine-binding pocket. With this aim, we mutated residues located in the benzodiazepine-binding site individually to cysteine. These mutated receptors were combined with benzodiazepine site ligands carrying a cysteine reactive group in a defined position. Proximal apposition of reaction partners will lead to a covalent reaction. We describe here such proximity-accelerated chemical coupling reactions of alpha(1)S205C and alpha(1)T206C with a diazepam derivative modified at the C-3 position with a reactive isothiocyanate group (-NCS). We also provide new data that identify alpha(1)H101C and alpha(1)N102C as exclusive sites of the reaction of a diazepam derivative where the -Cl atom is replaced by a -NCS group. Based on these observations we propose a relative positioning of diazepam within the benzodiazepine-binding site of alpha(1)beta(2)gamma(2) receptors.
Collapse
Affiliation(s)
- Kelly R Tan
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse, Switzerland
| | | | | | | | | |
Collapse
|
10
|
Mony L, Krzaczkowski L, Leonetti M, Le Goff A, Alarcon K, Neyton J, Bertrand HO, Acher F, Paoletti P. Structural basis of NR2B-selective antagonist recognition by N-methyl-D-aspartate receptors. Mol Pharmacol 2008; 75:60-74. [PMID: 18923063 DOI: 10.1124/mol.108.050971] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
N-Methyl-D-aspartate receptors (NMDARs) are ionotropic glutamate receptors endowed with unique pharmacological and functional properties. In particular, their high permeability to calcium ions confers on NMDARs a central role in triggering long term changes in synaptic strength. Under excitotoxic pathological conditions, such as those occurring during brain trauma, stroke, or Parkinson's or Huntington's diseases, calcium influx through NMDAR channels can also lead to neuronal injury. This argues for the use of NMDAR antagonists as potential therapeutic agents. To date, the most promising NMDAR antagonists are ifenprodil and derivatives, compounds that act as noncompetitive inhibitors selective for NMDARs containing the NR2B subunit. Recent studies have identified the large N-terminal domain (NTD) of NR2B as the region controlling ifenprodil sensitivity of NMDARs. We present here a detailed characterization of the ifenprodil binding site using both experimental and computational approaches. 3D homology modeling reveals that ifenprodil fits well in a closed cleft conformation of the NRB NTD; however, ifenprodil can adopt either of two possible binding orientations of opposite direction. By studying the effects of cleft mutations, we show that only the orientation in which the phenyl moiety points deep toward the NTD hinge is functionally relevant. Moreover, based on our model, we identify novel NTD NR2B residues that are crucial for conferring ifenprodil sensitivity and provide functional evidence that these residues directly interact with the ifenprodil molecule. This work provides a general insight into the origin of the subunit-selectivity of NMDAR noncompetitive antagonists and offer clues for the discovery of novel NR2B-selective antagonists.
Collapse
Affiliation(s)
- Laetitia Mony
- Laboratoire de Neurobiologie, Centre National de Recherche Scientifique (CNRS) Unité Mixte de Recherche 8544, Ecole Normale Supérieure, Paris, France
| | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Alarcon K, Martz A, Mony L, Neyton J, Paoletti P, Goeldner M, Foucaud B. Reactive derivatives for affinity labeling in the ifenprodil site of NMDA receptors. Bioorg Med Chem Lett 2008; 18:2765-70. [PMID: 18434149 DOI: 10.1016/j.bmcl.2008.04.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2008] [Revised: 04/07/2008] [Accepted: 04/08/2008] [Indexed: 10/22/2022]
Abstract
To prepare thiol-reactive ifenprodil derivatives designed as potential probes for cysteine-substituted NR2B containing NMDA receptors, electrophilic centers were introduced in different areas of the ifenprodil structure. Intermediates and final compounds were evaluated by binding studies and by electrophysiology to determine the structural requirements for their selectivity. The reactive compounds were further tested for their stability and for their reactivity in model reactions; some were found suitable as structural probes to investigate the binding site and the docking mode of ifenprodil in the NR2B subunit.
Collapse
Affiliation(s)
- Karine Alarcon
- Laboratoire de Chimie Bioorganique, CNRS UMR 7175, Faculté de Pharmacie, Université Louis Pasteur de Strasbourg, 74 Route du Rhin, F-67401 Illkirch, France.
| | | | | | | | | | | | | |
Collapse
|
12
|
Martineau M, Baux G, Mothet JP. D-serine signalling in the brain: friend and foe. Trends Neurosci 2006; 29:481-91. [PMID: 16806506 DOI: 10.1016/j.tins.2006.06.008] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2005] [Revised: 04/10/2006] [Accepted: 06/08/2006] [Indexed: 01/08/2023]
Abstract
Neurons and glia talk to each other at synapses. Glia sense the level of synaptic activity and consequently regulate its efficacy via the release of neuromodulators. One such glia-derived modulator is D-serine, an amino acid that serves as an endogenous ligand for the strychnine-insensitive glycine-binding site of NMDA glutamate receptors. Here, we provide an overview of recent findings on the mechanisms of its synthesis, release and clearance at synapses, with an emphasis on the dichotomy of behaviour of this novel messenger in the brain. The discovery of the good and ugly faces of this gliotransmitter is an important issue of modern neuroscience that has repercussions for the treatment of brain disorders.
Collapse
Affiliation(s)
- Magalie Martineau
- Laboratoire de Neurobiologie Morphofonctionnelle, INSERM U378, 146 Rue Léo Saignat, 33077 Bordeaux, France
| | | | | |
Collapse
|
13
|
Mayer ML, Ghosal A, Dolman NP, Jane DE. Crystal structures of the kainate receptor GluR5 ligand binding core dimer with novel GluR5-selective antagonists. J Neurosci 2006; 26:2852-61. [PMID: 16540562 PMCID: PMC6673968 DOI: 10.1523/jneurosci.0123-06.2005] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2006] [Revised: 01/30/2006] [Accepted: 01/31/2006] [Indexed: 12/31/2022] Open
Abstract
Glutamate receptor (GluR) ion channels mediate fast synaptic transmission in the mammalian CNS. Numerous crystallographic studies, the majority on the GluR2-subtype AMPA receptor, have revealed the structural basis for binding of subtype-specific agonists. In contrast, because there are far fewer antagonist-bound structures, the mechanisms for antagonist binding are much less well understood, particularly for kainate receptors that exist as multiple subtypes with a distinct biology encoded by the GluR5-7, KA1, and KA2 genes. We describe here high-resolution crystal structures for the GluR5 ligand-binding core complex with UBP302 and UBP310, novel GluR5-selective antagonists. The crystal structures reveal the structural basis for the high selectivity for GluR5 observed in radiolabel displacement assays for the isolated ligand binding cores of the GluR2, GluR5, and GluR6 subunits and during inhibition of glutamate-activated currents in studies on full-length ion channels. The antagonists bind via a novel mechanism and do not form direct contacts with the E723 side chain as occurs in all previously solved AMPA and kainate receptor agonist and antagonist complexes. This results from a hyperextension of the ligand binding core compared with previously solved structures. As a result, in dimer assemblies, there is a 22 A extension of the ion channel linkers in the transition from antagonist- to glutamate-bound forms. This large conformational change is substantially different from that described for AMPA receptors, was not possible to predict from previous work, and suggests that glutamate receptors are capable of much larger movements than previously thought.
Collapse
Affiliation(s)
- Mark L Mayer
- Porter Neuroscience Research Center, National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20892, USA.
| | | | | | | |
Collapse
|
14
|
Levitsky K, Boersma MD, Ciolli CJ, Belshaw PJ. Exo-mechanism proximity-accelerated alkylations: investigations of linkers, electrophiles and surface mutations in engineered cyclophilin-cyclosporin systems. Chembiochem 2006; 6:890-9. [PMID: 15832403 DOI: 10.1002/cbic.200400383] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Investigations on the scope and utility of exo-mechanism proximity-accelerated reactions in engineered receptor-ligand systems are reported. We synthesized a series of electrophilic cyclosporin (CsA) derivatives by varying electrophiles and linker lengths, prepared a series of nucleophilic cysteine mutations on the surface of cyclophilin A (Cyp), and examined their reactivity and specificity in proximity-accelerated reactions. Acrylamide and epoxide electrophiles afforded useful reactivity and high specificity for alkylation of engineered receptors in Jurkat cell extracts. We found that remote cysteines (>17 A from the ligand) could be alkylated with useful rates under physiological conditions. The results from mutations of the receptor surface suggest that the dominant factors governing the rates of proximity-accelerated reactions are related to the local environment of the reactive group on the protein surface. This study defines several parameters affecting reactivity in exo-mechanism proximity-accelerated reactions and provides guidance for the design of experiments for biological investigations involving proximity-accelerated reactions.
Collapse
Affiliation(s)
- Konstantin Levitsky
- Department of Biochemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | | | | | | |
Collapse
|
15
|
Abstract
Glutamate receptor ion channels mediate excitatory responses at the majority of CNS synapses. They are the only ligand-gated ion channels for which multiple high-resolution crystal structures have been solved. Highlights of information gained from mechanistic studies based on the crystal structures of their ligand-binding domains include explanations for strikingly diverse phenomena. These include the basis for subtype-specific agonist selectivity; mechanisms for desensitization and allosteric modulation; and mechanisms for partial agonist activity. In addition, multiple lines of evidence, including low-resolution electron microscopic studies, suggest that native AMPA receptors combine with an auxiliary subunit which regulates activity and trafficking. Functional studies suggest that glutamate receptor gating is distinct from that of structurally related voltage-gated ion channels.
Collapse
Affiliation(s)
- Mark L Mayer
- Laboratory of Cellular and Molecular Neurophysiology, Porter Neuroscience Research Center, Building 35 Room 3B 1002 MSC 3712, 35 Lincoln Drive, Bethesda, MD 20892-3712, USA.
| |
Collapse
|
16
|
Blaise MC, Sowdhamini R, Pradhan N. Comparative analysis of different competitive antagonists interaction with NR2A and NR2B subunits of N-methyl-D-aspartate (NMDA) ionotropic glutamate receptor. J Mol Model 2005; 11:489-502. [PMID: 15928921 DOI: 10.1007/s00894-005-0258-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2004] [Accepted: 02/22/2005] [Indexed: 10/25/2022]
Abstract
The antagonist-bound conformation of the NR2A and NR2B subunits of N-methyl-D-aspartate (NMDA) ionotropic glutamate receptor are modeled using the crystal structure of the DCKA (5,7-dichloro-kynurenic acid)-bound form of the NR1 subunit ligand-binding core (S1S2). Five different competitive NMDA receptor antagonists [(1) DL-AP5; (2) DL-AP7; (3) CGP-37847; (4) CGP 39551; (5) (RS)-CPP] have been docked into both NR2A and NR2B subunits. Experimental studies report NR2A and NR2B subunits having dissimilar interactions and affinities towards the antagonists. However, the molecular mechanism of this difference remains unexplored. The distinctive features in the antagonist's interaction with these two different but closely related (approximately 80% sequence identity at this region) subunits are analyzed from the patterns of their hydrogen bonding. The regions directly involved in the antagonist binding have been classified into seven different interaction sites. Two conserved hydrophilic pockets located at both the S1 and S2 domains are found to be crucial for antagonist binding. The positively charged (Lys) residues present at the second interaction site and the invariant residue (Arg) located at the fourth interaction site are seen to influence ligand binding. The geometry of the binding pockets of NR2A and NR2B subunits have been determined from the distance between the C-alpha atoms in the residues interacting with the ligands. The binding pockets are found to be different for NR2A and NR2B. There are gross dissimilarities in competitive antagonist binding between these two subunits. The binding pocket geometry identified in this study may have the potential for future development of selective antagonists for the NR2A or NR2B subunit.
Collapse
Affiliation(s)
- Mathias-Costa Blaise
- Department of Psychopharmacology, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bangalore, 560029, India
| | | | | |
Collapse
|
17
|
Laube B, Schemm R, Betz H. Molecular determinants of ligand discrimination in the glutamate-binding pocket of the NMDA receptor. Neuropharmacology 2004; 47:994-1007. [PMID: 15555634 DOI: 10.1016/j.neuropharm.2004.07.041] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2004] [Revised: 06/22/2004] [Accepted: 07/28/2004] [Indexed: 11/27/2022]
Abstract
Binding of glutamate to ionotropic glutamate receptors occurs within a bilobate binding pocket built from conserved S1 and S2 domains. Using the crystal structure of the binding region of the (RS)-2-amino-3-(3-hydroxy-5-methyl-4-isoxazolyl)-propionic acid (AMPA)-selective GluR2 subunit, we identified determinants of ligand selectivity and efficacy within the glutamate-binding pocket of the NR2B subunit of the N-methyl-D-aspartate (NMDA) receptor by site-directed mutagenesis. Electrophysiological analyses of mutated NR2B polypeptides revealed drastic effects on the affinity of L-glutamate but not of the co-agonist glycine. With seven out of 19 substitutions, we found differences in the potency of the full agonist L-glutamate and the partial agonist NMDA. In particular, substitutions located at the interface between the S1 and S2 domains resulted in changes of agonist efficacy, suggesting a role in transducing the ligand-binding signal. Inhibition by the competitive antagonist D-AP5 was highly sensitive to replacement of residues involved in stabilization of the closed conformation of the binding pocket, consistent with antagonists preventing closure of the binding pocket. In addition, we identified residues predicted to be important for liganding the methyl group of NMDA. Collectively our data describe specific side chain interactions that determine ligand efficacy and pharmacology at the glutamate site of the NMDA receptor.
Collapse
Affiliation(s)
- Bodo Laube
- Department of Neurochemistry, Max-Planck-Institute for Brain Research, Deutschordenstrasse 46, 60528 Frankfurt, Germany.
| | | | | |
Collapse
|
18
|
Barth A, Nguyen LB, Barth L, Newell DW. Glycine-induced neurotoxicity in organotypic hippocampal slice cultures. Exp Brain Res 2004; 161:351-7. [PMID: 15490133 DOI: 10.1007/s00221-004-2079-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2004] [Accepted: 07/27/2004] [Indexed: 10/26/2022]
Abstract
The role of the neutral amino acid glycine in excitotoxic neuronal injury is unclear. Glycine coactivates glutamate N-methyl-D-aspartate (NMDA) receptors by binding to a distinct recognition site on the NR1 subunit. Purely excitatory glycine receptors composed of NR1 and NR3/NR4 NMDA receptor subunits have recently been described, raising the possibility of excitotoxic effects mediated by glycine alone. We have previously shown that exposure to high concentrations of glycine causes extensive neurotoxicity in organotypic hippocampal slice cultures by activation of NMDA receptors. In the present study, we investigated further properties of in vitro glycine-mediated toxicity. Agonists of the glycine recognition site of NMDA receptors (D-serine and D-alanine) did not have any toxic effect in hippocampal cultures, whereas competitive blockade of the glycine site by 7-chlorokynurenic acid was neuroprotective. Stimulation (taurine, beta-alanine) or inhibition (strychnine) of the inhibitory strychnine-sensitive glycine receptors did not produce any neurotoxicity. The toxic effects of high-dose glycine were comparable in extent to those produced by the excitatory amino acid glutamate in our model. When combined with sublethal hypoxia/hypoglycemia, the threshold of glycine toxicity was decreased to less than 1 mM, which corresponds to the range of concentrations of excitatory amino acids measured during in vivo cerebral ischemia. Taken together, these results further support the assumption of an active role of glycine in excitotoxic neuronal injury.
Collapse
Affiliation(s)
- A Barth
- Department of Neurological Surgery, University of Washington, School of Medicine, Seattle, WA, USA.
| | | | | | | |
Collapse
|
19
|
Schell MJ. The N-methyl D-aspartate receptor glycine site and D-serine metabolism: an evolutionary perspective. Philos Trans R Soc Lond B Biol Sci 2004; 359:943-64. [PMID: 15306409 PMCID: PMC1693380 DOI: 10.1098/rstb.2003.1399] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The N-methyl D-aspartate (NMDA) type of glutamate receptor requires two distinct agonists to operate. Glycine is assumed to be the endogenous ligand for the NMDA receptor glycine site, but this notion has been challenged by the discovery of high levels of endogenous d-serine in the mammalian forebrain. I have outlined an evolutionary framework for the appearance of a glycine site in animals and the metabolic events leading to high levels of D-serine in brain. Sequence alignments of the glycine-binding regions, along with the scant experimental data available, suggest that the properties of invertebrate NMDA receptor glycine sites are probably different from those in vertebrates. The synthesis of D-serine in brain is due to a pyridoxal-5'-phosphate (B(6))-requiring serine racemase in glia. Although it remains unknown when serine racemase first evolved, data concerning the evolution of B(6) enzymes, along with the known occurrences of serine racemases in animals, point to D-serine synthesis arising around the divergence time of arthropods. D-Serine catabolism occurs via the ancient peroxisomal enzyme d-amino acid oxidase (DAO), whose ontogenetic expression in the hindbrain of mammals is delayed until the postnatal period and absent from the forebrain. The phylogeny of D-serine metabolism has relevance to our understanding of brain ontogeny, schizophrenia and neurotransmitter dynamics.
Collapse
Affiliation(s)
- Michael J Schell
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK.
| |
Collapse
|
20
|
Abstract
A vast number of proteins are involved in synaptic function. Many have been cloned and their functional role defined with varying degrees of success, but their number and complexity currently defy any molecular understanding of the physiology of synapses. A beacon of success in this medieval era of synaptic biology is an emerging understanding of the mechanisms underlying the activity of the neurotransmitter receptors for glutamate. Largely as a result of structural studies performed in the past three years we now have a mechanistic explanation for the activation of channel gating by agonists and partial agonists; the process of desensitization, and its block by allosteric modulators, is also mostly explained; and the basis of receptor subtype selectivity is emerging with clarity as more and more structures are solved. In the space of months we have gone from cartoons of postulated mechanisms to hard fact. It is anticipated that this level of understanding will emerge for other synaptic proteins in the coming decade.
Collapse
Affiliation(s)
- Mark L Mayer
- Laboratory of Cellular and Molecular Neurophysiology, Building 36, Room 2B28, NICHD, NIH, DHHS, Bethesda, Maryland 20892, USA.
| | | |
Collapse
|
21
|
Berezhnoy D, Nyfeler Y, Gonthier A, Schwob H, Goeldner M, Sigel E. On the benzodiazepine binding pocket in GABAA receptors. J Biol Chem 2003; 279:3160-8. [PMID: 14612433 DOI: 10.1074/jbc.m311371200] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Benzodiazepines are used for their sedative/hypnotic, anxiolytic, muscle relaxant, and anticonvulsive effects. They exert their actions through a specific high affinity binding site on the major inhibitory neurotransmitter receptor, the gamma-aminobutyric acid, type A (GABA(A)) receptor channel, where they act as positive allosteric modulators. To start to elucidate the relative positioning of benzodiazepine binding site ligands in their binding pocket, GABA(A) receptor residues thought to reside in the site were individually mutated to cysteine and combined with benzodiazepine analogs carrying substituents reactive to cysteine. Direct apposition of such reactive partners is expected to lead to an irreversible site-directed reaction. We describe here the covalent interaction of alpha(1)H101C with a reactive group attached to the C-7 position of diazepam. This interaction was studied at the level of radioactive ligand binding and at the functional level using electrophysiological methods. Covalent reaction occurs concomitantly with occupancy of the binding pocket. It stabilizes the receptor in its allosterically stimulated conformation. Covalent modification is not observed in wild type receptors or when using mutated alpha(1)H101C-containing receptors in combination with the reactive ligand pre-reacted with a sulfhydryl group, and the modification rate is reduced by the binding site ligand Ro15-1788. We present in addition evidence that gamma(2)Ala-79 is probably located in the access pathway of the ligand to its binding pocket.
Collapse
Affiliation(s)
- Dmytro Berezhnoy
- Department of Pharmacology, University of Bern, CH-3010 Bern, Switzerland
| | | | | | | | | | | |
Collapse
|