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Ramos-Vicente D, Grant SG, Bayés À. Metazoan evolution and diversity of glutamate receptors and their auxiliary subunits. Neuropharmacology 2021; 195:108640. [PMID: 34116111 DOI: 10.1016/j.neuropharm.2021.108640] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/27/2021] [Accepted: 06/01/2021] [Indexed: 01/18/2023]
Abstract
Glutamate is the major excitatory neurotransmitter in vertebrate and invertebrate nervous systems. Proteins involved in glutamatergic neurotransmission, and chiefly glutamate receptors and their auxiliary subunits, play key roles in nervous system function. Thus, understanding their evolution and uncovering their diversity is essential to comprehend how nervous systems evolved, shaping cognitive function. Comprehensive phylogenetic analysis of these proteins across metazoans have revealed that their evolution is much more complex than what can be anticipated from vertebrate genomes. This is particularly true for ionotropic glutamate receptors (iGluRs), as their current classification into 6 classes (AMPA, Kainate, Delta, NMDA1, NMDA2 and NMDA3) would be largely incomplete. New work proposes a classification of iGluRs into 4 subfamilies that encompass 10 classes. Vertebrate AMPA, Kainate and Delta receptors would belong to one of these subfamilies, named AKDF, the NMDA subunits would constitute another subfamily and non-vertebrate iGluRs would be organised into the previously unreported Epsilon and Lambda subfamilies. Similarly, the animal evolution of metabotropic glutamate receptors has resulted in the formation of four classes of these receptors, instead of the three currently recognised. Here we review our current knowledge on the animal evolution of glutamate receptors and their auxiliary subunits. This article is part of the special issue on 'Glutamate Receptors - Orphan iGluRs'.
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Affiliation(s)
- David Ramos-Vicente
- Molecular Physiology of the Synapse Laboratory, Biomedical Research Institute Sant Pau, Barcelona, Spain; Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Seth Gn Grant
- Centre for Clinical Brain Sciences, Chancellor's Building, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, EH16 4SB, UK; Simons Initiative for the Developing Brain (SIDB), Centre for Discovery Brain Sciences, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh, EH8 9XD, UK
| | - Àlex Bayés
- Molecular Physiology of the Synapse Laboratory, Biomedical Research Institute Sant Pau, Barcelona, Spain; Universitat Autònoma de Barcelona, Barcelona, Spain.
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Bledsoe D, Vacca B, Laube B, Klein BG, Costa B. Ligand binding domain interface: A tipping point for pharmacological agents binding with GluN1/2A subunit containing NMDA receptors. Eur J Pharmacol 2019; 844:216-224. [PMID: 30553788 DOI: 10.1016/j.ejphar.2018.12.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 12/11/2018] [Accepted: 12/12/2018] [Indexed: 10/27/2022]
Abstract
N-methyl D-aspartate (NMDA) receptors play a crucial role in normal brain function, pathogenesis of neurodegenerative and psychiatric disorders. Functional tetra-heteromeric NMDA receptor contains two obligatory GluN1 subunits and two identical or different non-GluN1 subunits that evolve from six different genes including four GluN2 (A-D) and two GluN3 (A-B) subunits. Since NMDA receptors confer varied physiological properties and spatiotemporal distributions in the brain, pharmacological agents that target NMDA receptors with specific GluN2 subunits have significant potential for therapeutic applications. In the present work, by using electrophysiology techniques, we have studied the role of ligand binding domain (LBD) interactions in determining the effect of well-characterized pharmacological agents including agonists, competitive antagonists, channel blockers and an allosteric modulator. Remarkably, point mutations at the distal end (site-II&III) of GluN1 LBD interface increased memantine potency up to sevenfold when co-expressed with wild type GluN2A receptors but exhibit no effect on Mg2+ activity. Conversely, mutations at the proximal end (site-I) of the LBD interface did not affect the memantine but altered Zn2+ and Mg2+ potency towards opposite directions. These results indicate that GluN1/2A LBD interface interactions play a key role in determining channel function. Further, subtle changes in LBD interaction can be readily translated to the downstream extracellular vestibule of channel pore to adopt a conformation that may affect memantine, Zn2+ and Mg2+ binding. Further studies on NMDA receptor LBD to transmembrane domain signal propagation mechanisms will help develop GluN2 subunit selective biomolecules that can be used for the treatment of neurological and psychiatric disorders.
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Affiliation(s)
- Douglas Bledsoe
- Edward Via Virginia College of Osteopathic Medicine, Blacksburg, VA, USA
| | - Bryanna Vacca
- Edward Via Virginia College of Osteopathic Medicine, Blacksburg, VA, USA
| | - Bodo Laube
- Department of Neurophysiology and Neurosensory Systems, Technical University, Darmstadt, Germany
| | - Bradley G Klein
- Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, USA; School of Neuroscience, Virginia Tech, Blacksburg, VA, USA
| | - Blaise Costa
- Edward Via Virginia College of Osteopathic Medicine, Blacksburg, VA, USA; Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, USA; School of Neuroscience, Virginia Tech, Blacksburg, VA, USA.
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Bledsoe D, Tamer C, Mesic I, Madry C, Klein BG, Laube B, Costa BM. Positive Modulatory Interactions of NMDA Receptor GluN1/2B Ligand Binding Domains Attenuate Antagonists Activity. Front Pharmacol 2017; 8:229. [PMID: 28536523 PMCID: PMC5423295 DOI: 10.3389/fphar.2017.00229] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 04/11/2017] [Indexed: 01/03/2023] Open
Abstract
N-methyl D-aspartate receptors (NMDAR) play crucial role in normal brain function and pathogenesis of neurodegenerative and psychiatric disorders. Functional tetra-heteromeric NMDAR contains two obligatory GluN1 subunits and two identical or different non-GluN1 subunits that include six different gene products; four GluN2 (A–D) and two GluN3 (A–B) subunits. The heterogeneity of subunit combination facilities the distinct function of NMDARs. All GluN subunits contain an extracellular N-terminal Domain (NTD) and ligand binding domain (LBD), transmembrane domain (TMD) and an intracellular C-terminal domain (CTD). Interaction between the GluN1 and co-assembling GluN2/3 subunits through the LBD has been proven crucial for defining receptor deactivation mechanisms that are unique for each combination of NMDAR. Modulating the LBD interactions has great therapeutic potential. In the present work, by amino acid point mutations and electrophysiology techniques, we have studied the role of LBD interactions in determining the effect of well-characterized pharmacological agents including agonists, competitive antagonists, and allosteric modulators. The results reveal that agonists (glycine and glutamate) potency was altered based on mutant amino acid sidechain chemistry and/or mutation site. Most antagonists inhibited mutant receptors with higher potency; interestingly, clinically used NMDAR channel blocker memantine was about three-fold more potent on mutated receptors (N521A, N521D, and K531A) than wild type receptors. These results provide novel insights on the clinical pharmacology of memantine, which is used for the treatment of mild to moderate Alzheimer's disease. In addition, these findings demonstrate the central role of LBD interactions that can be exploited to develop novel NMDAR based therapeutics.
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Affiliation(s)
- Douglas Bledsoe
- Edward Via College of Osteopathic MedicineBlacksburg, VA, USA
| | - Ceyhun Tamer
- Department of Neurophysiology and Neurosensory Systems, Technische Universität DarmstadtDarmstadt, Germany
| | - Ivana Mesic
- Department of Neurophysiology and Neurosensory Systems, Technische Universität DarmstadtDarmstadt, Germany
| | - Christian Madry
- Department of Neuroscience, Physiology and Pharmacology, University College LondonLondon, UK
| | - Bradley G Klein
- Department of Biomedical Sciences & Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia TechBlacksburg, VA, USA
| | - Bodo Laube
- Department of Neurophysiology and Neurosensory Systems, Technische Universität DarmstadtDarmstadt, Germany
| | - Blaise M Costa
- Edward Via College of Osteopathic MedicineBlacksburg, VA, USA.,School of Neuroscience, Virginia TechBlacksburg, VA, USA
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Kane LT, Costa BM. Identification of novel allosteric modulator binding sites in NMDA receptors: A molecular modeling study. J Mol Graph Model 2015; 61:204-13. [PMID: 26280688 DOI: 10.1016/j.jmgm.2015.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 06/16/2015] [Accepted: 06/18/2015] [Indexed: 12/31/2022]
Abstract
The dysfunction of N-methyl-d-Aspartate receptors (NMDARs), a subtype of glutamate receptors, is correlated with schizophrenia, stroke, and many other neuropathological disorders. However, not all NMDAR subtypes equally contribute towards these disorders. Since NMDARs composed of different GluN2 subunits (GluN2A-D) confer varied physiological properties and have different distributions in the brain, pharmacological agents that target NMDARs with specific GluN2 subunits have significant potential for therapeutic applications. In our previous research, we have identified a family of novel allosteric modulators that differentially potentiate and/or inhibit NMDARs of differing GluN2 subunit composition. To further elucidate their molecular mechanisms, in the present study, we have identified four potential binding sites for novel allosteric modulators by performing molecular modeling, docking, and in silico mutations. The molecular determinants of the modulator binding sites (MBS), analysis of particular MBS electrostatics, and the specific loss or gain of binding after mutations have revealed modulators that have strong potential affinities for specific MBS on given subunits and the role of key amino acids in either promoting or obstructing modulator binding. These findings will help design higher affinity GluN2 subunit-selective pharmaceuticals, which are currently unavailable to treat psychiatric and neurological disorders.
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Affiliation(s)
- Lucas T Kane
- Edward Via Virginia College of Osteopathic Medicine, Blacksburg, VA 24060, USA
| | - Blaise M Costa
- Edward Via Virginia College of Osteopathic Medicine, Blacksburg, VA 24060, USA; Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg VA, 24061, USA.
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Cloning and characterization of the N-methyl-D-aspartate receptor subunit NR1 gene from chum salmon, Oncorhynchus keta (Walbaum, 1792). SPRINGERPLUS 2014; 3:9. [PMID: 24422186 PMCID: PMC3884082 DOI: 10.1186/2193-1801-3-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 12/23/2013] [Indexed: 01/12/2023]
Abstract
Here, we report the information about molecular and expression characterization of NR1 gene in chum salmon for the first time. The complete NR1 subunit showed a large open-reading frame of 2844 bp in the total length of 3193 bp, and this cDNA contained a coding region encoding 948 amino acids and a stop codon. The organization of the NR1 subunit of chum salmon were similar of most other fishes, except C’ terminal. The expression of NR1 subunit was to show higher in the natal river near to the hatchery than near to the coast. We expect that the information reported herein may facilitate further investigations on the relationship between memory factors of natal rivers and homing mechanisms in Salmonidae.
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Sangadala S, Rao Metpally RP, B. Reddy BV. Molecular Interaction Between Smurfl WW2 Domain and PPXY Motifs of Smadl, Smad5, and Smad6—Modeling and Analysis. J Biomol Struct Dyn 2007; 25:11-23. [DOI: 10.1080/07391102.2007.10507151] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Chen PE, Wyllie DJA. Pharmacological insights obtained from structure-function studies of ionotropic glutamate receptors. Br J Pharmacol 2007; 147:839-53. [PMID: 16474411 PMCID: PMC1760717 DOI: 10.1038/sj.bjp.0706689] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Ionotropic glutamate receptors mediate the vast majority of fast excitatory synaptic transmission in the CNS. Elucidating the structure of these proteins is central to understanding their overall function and in the last few years a tremendous amount of knowledge has been gained from the crystal structures of the ligand-binding domains of the receptor protein. These efforts have enabled us to unravel the possible mechanisms of partial agonism, agonist selectivity and desensitization. This review summarizes recent data obtained from structural studies of the binding pockets of the GluR2, GluR5/6, NR1 and NR2A subunits and discusses these studies together with homology modelling and molecular dynamics simulations that have suggested possible binding modes for full and partial agonists as well as antagonists within the binding pocket of various ionotropic glutamate receptor subunits. Comparison of the ligand-binding pockets suggests that the ligand-binding mechanisms may be conserved throughout the glutamate receptor family, although agonist selectivity may be explained by a number of features inherent to the AMPA, kainate and NMDA receptor-binding pockets such as steric occlusion, cavity size and the contribution of water-bridged interactions.
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Affiliation(s)
- Philip E Chen
- Division of Neuroscience, University of Edinburgh, 1 George Square, Edinburgh EH8 9JZ
| | - David J A Wyllie
- Division of Neuroscience, University of Edinburgh, 1 George Square, Edinburgh EH8 9JZ
- Author for correspondence:
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Nilsson A, Duan J, Mo-Boquist LL, Benedikz E, Sundström E. Characterisation of the human NMDA receptor subunit NR3A glycine binding site. Neuropharmacology 2006; 52:1151-9. [PMID: 17320117 DOI: 10.1016/j.neuropharm.2006.12.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2006] [Revised: 12/05/2006] [Accepted: 12/07/2006] [Indexed: 11/20/2022]
Abstract
In this study, we characterise the binding site of the human N-methyl-d-aspartate (NMDA) receptor subunit NR3A. Saturation radioligand binding of the NMDA receptor agonists [(3)H]-glycine and [(3)H]-glutamate showed that only glycine binds to human NR3A (hNR3A) with high affinity (K(d)=535nM (277-793nM)). Eight amino acids, which correspond to amino acids that are critical for ligand binding to other NMDA receptor subunits, situated within the S1S2 predicted ligand binding domain of hNR3A were mutated, which resulted in complete or near complete loss of [(3)H]-glycine binding to hNR3A. The NMDA NR1 glycine site agonist d-serine and partial agonist HA-966 (3-amino-1-hydroxypyrrolid-2-one), similarly to glycine displaced [(3)H]-glycine monophasically, suggesting a single common binding site. However, neither the partial agonist d-cycloserine nor the antagonist 7-chlorokynurenic acid displaced [(3)H]-glycine. Using homology modelling, a model of the NR3A binding pocket was generated which we suggest can be used to identify candidate agonists and antagonists. Our data show that glycine is a ligand, and most probably the endogenous ligand, for native NR3A at a binding site with unique pharmacological characteristics.
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Affiliation(s)
- A Nilsson
- Division of Neurodegeneration and Neuroinflammation, Department of Neurobiology, Caring Sciences and Society, Karolinska Institutet, Novum, S-141 86 Stockholm, Sweden.
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Ye K, Lameijer EWM, Beukers MW, Ijzerman AP. A two-entropies analysis to identify functional positions in the transmembrane region of class A G protein-coupled receptors. Proteins 2006; 63:1018-30. [PMID: 16532452 DOI: 10.1002/prot.20899] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Residues in the transmembrane region of G protein-coupled receptors (GPCRs) are important for ligand binding and activation, but the function of individual positions is poorly understood. Using a sequence alignment of class A GPCRs (grouped in subfamilies), we propose a so-called "two-entropies analysis" to determine the potential role of individual positions in the transmembrane region of class A GPCRs. In our approach, such positions appear scattered, while largely clustered according to their biological function. Our method appears superior when compared to other bioinformatics approaches, such as the evolutionary trace method, entropy-variability plot, and correlated mutation analysis, both qualitatively and quantitatively.
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Affiliation(s)
- Kai Ye
- Division of Medicinal Chemistry, Leiden/Amsterdam Center for Drug Research, Leiden University, Leiden, The Netherlands
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