1
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Thompson JRE, Beaudoin CA, Lummis SCR. Modelling and Molecular Dynamics Predict the Structure and Interactions of the Glycine Receptor Intracellular Domain. Biomolecules 2023; 13:1757. [PMID: 38136628 PMCID: PMC10741472 DOI: 10.3390/biom13121757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/28/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
Glycine receptors (GlyRs) are glycine-gated inhibitory pentameric ligand-gated ion channels composed of α or α + β subunits. A number of structures of these proteins have been reported, but to date, these have only revealed details of the extracellular and transmembrane domains, with the intracellular domain (ICD) remaining uncharacterised due to its high flexibility. The ICD is a region that can modulate function in addition to being critical for receptor localisation and clustering via proteins such as gephyrin. Here, we use modelling and molecular dynamics (MD) to reveal details of the ICDs of both homomeric and heteromeric GlyR. At their N and C ends, both the α and β subunit ICDs have short helices, which are major sites of stabilising interactions; there is a large flexible loop between them capable of forming transient secondary structures. The α subunit can affect the β subunit ICD structure, which is more flexible in a 4α2:1β than in a 4α1:1β GlyR. We also explore the effects of gephyrin binding by creating GlyR models bound to the gephyrin E domain; MD simulations suggest these are more stable than the unbound forms, and again there are α subunit-dependent differences, despite the fact the gephyrin binds to the β subunit. The bound models also suggest that gephyrin causes compaction of the ICD. Overall, the data expand our knowledge of this important receptor protein and in particular clarify features of the underexplored ICD.
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Affiliation(s)
| | | | - Sarah C. R. Lummis
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
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2
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Martinez M, Petit J, Leyva A, Sogues A, Megrian D, Rodriguez A, Gaday Q, Ben Assaya M, Portela MM, Haouz A, Ducret A, Grangeasse C, Alzari PM, Durán R, Wehenkel AM. Eukaryotic-like gephyrin and cognate membrane receptor coordinate corynebacterial cell division and polar elongation. Nat Microbiol 2023; 8:1896-1910. [PMID: 37679597 PMCID: PMC10522489 DOI: 10.1038/s41564-023-01473-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 08/11/2023] [Indexed: 09/09/2023]
Abstract
The order Corynebacteriales includes major industrial and pathogenic Actinobacteria such as Corynebacterium glutamicum or Mycobacterium tuberculosis. These bacteria have multi-layered cell walls composed of the mycolyl-arabinogalactan-peptidoglycan complex and a polar growth mode, thus requiring tight coordination between the septal divisome, organized around the tubulin-like protein FtsZ, and the polar elongasome, assembled around the coiled-coil protein Wag31. Here, using C. glutamicum, we report the discovery of two divisome members: a gephyrin-like repurposed molybdotransferase (Glp) and its membrane receptor (GlpR). Our results show how cell cycle progression requires interplay between Glp/GlpR, FtsZ and Wag31, showcasing a crucial crosstalk between the divisome and elongasome machineries that might be targeted for anti-mycobacterial drug discovery. Further, our work reveals that Corynebacteriales have evolved a protein scaffold to control cell division and morphogenesis, similar to the gephyrin/GlyR system that mediates synaptic signalling in higher eukaryotes through network organization of membrane receptors and the microtubule cytoskeleton.
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Affiliation(s)
- Mariano Martinez
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
| | - Julienne Petit
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
| | - Alejandro Leyva
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Adrià Sogues
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
- Structural and Molecular Microbiology, VIB-VUB Center for Structural Biology, VIB, Vrije Universiteit Brussel, Brussels, Belgium
| | - Daniela Megrian
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
| | - Azalia Rodriguez
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Quentin Gaday
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
| | - Mathildeb Ben Assaya
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
| | - Maria Magdalena Portela
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Ahmed Haouz
- Plate-forme de cristallographie, C2RT-Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
| | - Adrien Ducret
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086, Université de Lyon, Lyon, France
| | - Christophe Grangeasse
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086, Université de Lyon, Lyon, France
| | - Pedro M Alzari
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
| | - Rosario Durán
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay.
| | - Anne Marie Wehenkel
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France.
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3
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Martinez M, Petit J, Leyva A, Sogues A, Megrian D, Rodriguez A, Gaday Q, Ben Assaya M, Portela M, Haouz A, Ducret A, Grangeasse C, Alzari PM, Durán R, Wehenkel A. Eukaryotic-like gephyrin and cognate membrane receptor coordinate corynebacterial cell division and polar elongation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.01.526586. [PMID: 36778425 PMCID: PMC9915583 DOI: 10.1101/2023.02.01.526586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The order Corynebacteriales includes major industrial and pathogenic actinobacteria such as Corynebacterium glutamicum or Mycobacterium tuberculosis . Their elaborate multi-layered cell wall, composed primarily of the mycolyl-arabinogalactan-peptidoglycan complex, and their polar growth mode impose a stringent coordination between the septal divisome, organized around the tubulin-like protein FtsZ, and the polar elongasome, assembled around the tropomyosin-like protein Wag31. Here, we report the identification of two new divisome members, a gephyrin-like repurposed molybdotransferase (GLP) and its membrane receptor (GLPR). We show that the interplay between the GLPR/GLP module, FtsZ and Wag31 is crucial for orchestrating cell cycle progression. Our results provide a detailed molecular understanding of the crosstalk between two essential machineries, the divisome and elongasome, and reveal that Corynebacteriales have evolved a protein scaffold to control cell division and morphogenesis similar to the gephyrin/GlyR system that in higher eukaryotes mediates synaptic signaling through network organization of membrane receptors and the microtubule cytoskeleton.
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Affiliation(s)
- M. Martinez
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, F-75015 Paris, France
| | - J. Petit
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, F-75015 Paris, France
| | - A. Leyva
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - A. Sogues
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, F-75015 Paris, France
| | - D. Megrian
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, F-75015 Paris, France
| | - A. Rodriguez
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Q. Gaday
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, F-75015 Paris, France
| | - M. Ben Assaya
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, F-75015 Paris, France
| | - M. Portela
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - A. Haouz
- Plate-forme de cristallographie, C2RT-Institut Pasteur, CNRS, UMR 3528, Université Paris Cité, F-75015 Paris, France
| | - A. Ducret
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086, Université de Lyon, 7 passage du Vercors, 69367 Lyon, France
| | - C. Grangeasse
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086, Université de Lyon, 7 passage du Vercors, 69367 Lyon, France
| | - P. M. Alzari
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, F-75015 Paris, France
| | - R. Durán
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - A. Wehenkel
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, F-75015 Paris, France
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4
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Schulte C, Soldà A, Spänig S, Adams N, Bekić I, Streicher W, Heider D, Strasser R, Maric HM. Multivalent binding kinetics resolved by fluorescence proximity sensing. Commun Biol 2022; 5:1070. [PMID: 36207490 PMCID: PMC9546861 DOI: 10.1038/s42003-022-03997-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 09/14/2022] [Indexed: 11/12/2022] Open
Abstract
Multivalent protein interactors are an attractive modality for probing protein function and exploring novel pharmaceutical strategies. The throughput and precision of state-of-the-art methodologies and workflows for the effective development of multivalent binders is currently limited by surface immobilization, fluorescent labelling and sample consumption. Using the gephyrin protein, the master regulator of the inhibitory synapse, as benchmark, we exemplify the application of Fluorescence proximity sensing (FPS) for the systematic kinetic and thermodynamic optimization of multivalent peptide architectures. High throughput synthesis of +100 peptides with varying combinatorial dimeric, tetrameric, and octameric architectures combined with direct FPS measurements resolved on-rates, off-rates, and dissociation constants with high accuracy and low sample consumption compared to three complementary technologies. The dataset and its machine learning-based analysis deciphered the relationship of specific architectural features and binding kinetics and thereby identified binders with unprecedented protein inhibition capacity; thus, highlighting the value of FPS for the rational engineering of multivalent inhibitors.
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Affiliation(s)
- Clemens Schulte
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of Wuerzburg, Josef-Schneider-Str. 2, Germany, 97080, Wuerzburg, Germany
| | - Alice Soldà
- Dynamic Biosensors GmbH Germany, Lochhamer Strasse 15, 82152, Martinsried/Planegg, Germany
| | - Sebastian Spänig
- Department of Bioinformatics, Faculty of Mathematics and Computer Science, Philipps-University of Marburg, Hans-Meerwein-Strasse 6, 35043, Marburg, Germany
| | - Nathan Adams
- Nanotemper Technologies GmbH, Flößergasse 4, 81369, Munich, Germany
| | - Ivana Bekić
- Nanotemper Technologies GmbH, Flößergasse 4, 81369, Munich, Germany
| | - Werner Streicher
- Nanotemper Technologies GmbH, Flößergasse 4, 81369, Munich, Germany
| | - Dominik Heider
- Department of Bioinformatics, Faculty of Mathematics and Computer Science, Philipps-University of Marburg, Hans-Meerwein-Strasse 6, 35043, Marburg, Germany
| | - Ralf Strasser
- Dynamic Biosensors GmbH Germany, Lochhamer Strasse 15, 82152, Martinsried/Planegg, Germany
| | - Hans Michael Maric
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of Wuerzburg, Josef-Schneider-Str. 2, Germany, 97080, Wuerzburg, Germany.
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5
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Avraham O, Bayer EA, Livnah O. Wilavidin* - a novel member of the avidin family that forms unique biotin-binding hexamers. FEBS J 2021; 289:1700-1714. [PMID: 34726340 DOI: 10.1111/febs.16259] [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: 09/01/2021] [Revised: 10/20/2021] [Accepted: 11/01/2021] [Indexed: 11/28/2022]
Abstract
Nature's optimization of protein functions is a highly intricate evolutionary process. In addition to optimal tertiary folding, the intramolecular recognition among the monomers that generate higher-order quaternary arrangements is driven by stabilizing interactions that have a pivotal role for ideal activity. Homotetrameric avidin and streptavidin are regularly utilized in many applications, whereby their ultra-high affinity toward biotin is dependent on their quaternary arrangements. In recent years, a new subfamily of avidins was discovered that comprises homodimers rather than tetramers, in which the high affinity toward biotin is maintained. Intriguingly, several of the respective dimers have been shown to assemble into higher-order cylindrical hexamers or octamers that dissociate into dimers upon biotin binding. Here, we present wilavidin, a newly discovered member of the dimeric subfamily, forming hexamers in the apo form, which are uniquely maintained upon biotin binding with six high-affinity binding sites. Removal of the short C-terminal segment of wilavidin resulted in the presence of the dimer only, thus emphasizing the role of this segment in stabilizing the hexamer. Utilization of a hexavalent biotin-binding form of avidin would be beneficial for expanding the biotechnological toolbox. Additionally, this unique family of dimeric avidins and their propensity to oligomerize to hexamers or octamers can serve as a basis for protein oligomerization and intermonomeric recognition as well as cumulative interactions that determine molecular assemblies.
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Affiliation(s)
- Orly Avraham
- The Wolfson Centre for Applied Structural Biology, Department of Biological Chemistry, Alexander Silverman Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel.,Department of Life Sciences, National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Oded Livnah
- The Wolfson Centre for Applied Structural Biology, Department of Biological Chemistry, Alexander Silverman Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
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6
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George S, Chiou TT, Kanamalla K, De Blas AL. Recruitment of Plasma Membrane GABA-A Receptors by Submembranous Gephyrin/Collybistin Clusters. Cell Mol Neurobiol 2021; 42:1585-1604. [PMID: 33547626 DOI: 10.1007/s10571-021-01050-1] [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: 08/20/2020] [Accepted: 01/23/2021] [Indexed: 11/29/2022]
Abstract
It has been shown that subunit composition is the main determinant of the synaptic or extrasynaptic localization of GABAA receptors (GABAARs). Synaptic and extrasynaptic GABAARs are involved in phasic and tonic inhibition, respectively. It has been proposed that synaptic GABAARs bind to the postsynaptic gephyrin/collybistin (Geph/CB) lattice, but not the typically extrasynaptic GABAARs. Nevertheless, there are no studies of the direct binding of various types of GABAARs with the submembranous Geph/CB lattice in the absence of other synaptic proteins, some of which are known to interact with GABAARs. We have reconstituted GABAARs of various subunit compositions, together with the Geph/CB scaffold, in HEK293 cells, and have investigated the recruitment of surface GABAARs by submembranous Geph/CB clusters. Results show that the typically synaptic α1β3γ2 GABAARs were trapped by submembranous Geph/CB clusters. The α5β3γ2 GABAARs, which are both synaptic and extrasynaptic, were also trapped by Geph/CB clusters. Extrasynaptic α4β3δ GABAARs consistently showed little or no trapping by the Geph/CB clusters. However, the extrasynaptic α6β3δ, α1β3, α6β3 (and less α4β3) GABAARs were highly trapped by the Geph/CB clusters. AMPA and NMDA glutamate receptors were not trapped. The results suggest: (I) in the absence of other synaptic molecules, the Geph/CB lattice has the capacity to trap not only synaptic but also several typically extrasynaptic GABAARs; (II) the Geph/CB lattice is important but does not play a decisive role in the synaptic localization of GABAARs; and (III) in neurons there must be mechanisms preventing the trapping of several typically extrasynaptic GABAARs by the postsynaptic Geph/CB lattice.
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Affiliation(s)
- Shanu George
- Department of Physiology and Neurobiology, University of Connecticut, 75 North Eagleville Road, U-3156, Storrs, CT, 06269-3156, USA
| | - Tzu-Ting Chiou
- Department of Physiology and Neurobiology, University of Connecticut, 75 North Eagleville Road, U-3156, Storrs, CT, 06269-3156, USA
| | - Karthik Kanamalla
- Department of Physiology and Neurobiology, University of Connecticut, 75 North Eagleville Road, U-3156, Storrs, CT, 06269-3156, USA
| | - Angel L De Blas
- Department of Physiology and Neurobiology, University of Connecticut, 75 North Eagleville Road, U-3156, Storrs, CT, 06269-3156, USA.
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7
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Kasaragod VB, Schindelin H. Structure of Heteropentameric GABA A Receptors and Receptor-Anchoring Properties of Gephyrin. Front Mol Neurosci 2019; 12:191. [PMID: 31440140 PMCID: PMC6693554 DOI: 10.3389/fnmol.2019.00191] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 07/22/2019] [Indexed: 12/20/2022] Open
Abstract
γ-Aminobutyric acid type A receptors (GABAARs) mediate the majority of fast synaptic inhibition in the central nervous system (CNS). GABAARs belong to the Cys-loop superfamily of pentameric ligand-gated ion channels (pLGIC) and are assembled from 19 different subunits. As dysfunctional GABAergic neurotransmission manifests itself in neurodevelopmental disorders including epilepsy and anxiety, GABAARs are key drug targets. The majority of synaptic GABAARs are anchored at the inhibitory postsynaptic membrane by the principal scaffolding protein gephyrin, which acts as the central organizer in maintaining the architecture of the inhibitory postsynaptic density (iPSD). This interaction is mediated by the long intracellular loop located in between transmembrane helices 3 and 4 (M3–M4 loop) of the receptors and a universal receptor-binding pocket residing in the C-terminal domain of gephyrin. In 2014, the crystal structure of the β3-homopentameric GABAAR provided crucial information regarding the architecture of the receptor; however, an understanding of the structure and assembly of heteropentameric receptors at the atomic level was lacking. This review article will highlight recent advances in understanding the structure of heteropentameric synaptic GABAARs and how these structures have provided fundamental insights into the assembly of these multi-subunit receptors as well as their modulation by diverse ligands including the physiological agonist GABA. We will further discuss the role of gephyrin in the anchoring of synaptic GABAARs and glycine receptors (GlyRs), which are crucial for maintaining the architecture of the iPSD. Finally, we will also summarize how anti-malarial artemisinin drugs modulate gephyrin-mediated inhibitory neurotransmission.
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Affiliation(s)
- Vikram Babu Kasaragod
- Institute of Structural Biology, Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - Hermann Schindelin
- Institute of Structural Biology, Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
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Kasaragod VB, Hausrat TJ, Schaefer N, Kuhn M, Christensen NR, Tessmer I, Maric HM, Madsen KL, Sotriffer C, Villmann C, Kneussel M, Schindelin H. Elucidating the Molecular Basis for Inhibitory Neurotransmission Regulation by Artemisinins. Neuron 2019; 101:673-689.e11. [DOI: 10.1016/j.neuron.2019.01.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 10/11/2018] [Accepted: 12/27/2018] [Indexed: 02/06/2023]
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9
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Brissonnet Y, Araoz R, Sousa R, Percevault L, Brument S, Deniaud D, Servent D, Le Questel JY, Lebreton J, Gouin SG. Di- and heptavalent nicotinic analogues to interfere with α7 nicotinic acetylcholine receptors. Bioorg Med Chem 2019; 27:700-707. [PMID: 30692022 DOI: 10.1016/j.bmc.2019.01.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/07/2019] [Accepted: 01/13/2019] [Indexed: 12/11/2022]
Abstract
In the field of nicotinic acetylcholine receptors (nAChRs), recognized as important therapeutic targets, much effort has been dedicated to the development of nicotinic analogues to agonize or antagonize distinct homo- and heteropentamers nAChR subtypes, selectively. In this work we developed di- and heptavalent nicotinic derivatives based on ethylene glycol (EG) and cyclodextrin cores, respectively. The compounds showed a concentration dependent inhibition of acetylcholine-induced currents on α7 nAChR expressed by Xenopus oocytes. Interesting features were observed with the divalent nicotinic derivatives, acting as antagonists with varied inhibitory concentrations (IC50) in function of the spacer arm length. The best divalent compounds showed a 16-fold lowered IC50 compared to the monovalent reference (12 vs 195 µM). Docking investigations provide guidelines to rationalize these experimental findings.
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Affiliation(s)
- Yoan Brissonnet
- Université de Nantes, CEISAM, Chimie Et Interdisciplinarité, Synthèse, Analyse, Modélisation, UMR CNRS 6230, UFR des Sciences et des Techniques, 2, rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Romulo Araoz
- CNRS, Neuro-PSI, UMR9197, 91191 Gif-Sur-Yvette, France; CEA/DRF/JOLIOT/SIMOPRO/Toxines Récepteur et Canaux Ioniques, F-91191 Gif-Sur-Yvette, France.
| | - Rui Sousa
- Université de Nantes, CEISAM, Chimie Et Interdisciplinarité, Synthèse, Analyse, Modélisation, UMR CNRS 6230, UFR des Sciences et des Techniques, 2, rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Lucie Percevault
- Université de Nantes, CEISAM, Chimie Et Interdisciplinarité, Synthèse, Analyse, Modélisation, UMR CNRS 6230, UFR des Sciences et des Techniques, 2, rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Sami Brument
- Université de Nantes, CEISAM, Chimie Et Interdisciplinarité, Synthèse, Analyse, Modélisation, UMR CNRS 6230, UFR des Sciences et des Techniques, 2, rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - David Deniaud
- Université de Nantes, CEISAM, Chimie Et Interdisciplinarité, Synthèse, Analyse, Modélisation, UMR CNRS 6230, UFR des Sciences et des Techniques, 2, rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Denis Servent
- CEA/DRF/JOLIOT/SIMOPRO/Toxines Récepteur et Canaux Ioniques, F-91191 Gif-Sur-Yvette, France
| | - Jean-Yves Le Questel
- Université de Nantes, CEISAM, Chimie Et Interdisciplinarité, Synthèse, Analyse, Modélisation, UMR CNRS 6230, UFR des Sciences et des Techniques, 2, rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France.
| | - Jacques Lebreton
- Université de Nantes, CEISAM, Chimie Et Interdisciplinarité, Synthèse, Analyse, Modélisation, UMR CNRS 6230, UFR des Sciences et des Techniques, 2, rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Sébastien G Gouin
- Université de Nantes, CEISAM, Chimie Et Interdisciplinarité, Synthèse, Analyse, Modélisation, UMR CNRS 6230, UFR des Sciences et des Techniques, 2, rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France.
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10
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Specht CG. Fractional occupancy of synaptic binding sites and the molecular plasticity of inhibitory synapses. Neuropharmacology 2019; 169:107493. [PMID: 30648560 DOI: 10.1016/j.neuropharm.2019.01.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 12/01/2018] [Accepted: 01/09/2019] [Indexed: 01/20/2023]
Abstract
The postsynaptic density (PSD) at inhibitory synapses is a complex molecular assembly that serves as a platform for the interaction of neurotransmitter receptors, scaffold and adapter proteins, cytoskeletal elements and signalling molecules. The stability of the PSD depends on a multiplicity of interactions linking individual components. At the same time the PSD retains a substantial degree of flexibility. The continuous exchange of synaptic molecules and the preferential addition or removal of certain components induce plastic changes in the synaptic structure. This property necessarily implies that interactors are in dynamic equilibrium and that not all synaptic binding sites are occupied simultaneously. This review discusses the molecular plasticity of inhibitory synapses in terms of the connectivity of their components. Whereas stable protein complexes are marked by stoichiometric relationships between subunits, the majority of synaptic interactions have fractional occupancy, which is here defined as the non-saturation of synaptic binding sites. Fractional occupancy can have several causes: reduced kinetic or thermodynamic stability of the interactions, an imbalance in the concentrations or limited spatio-temporal overlap of interacting proteins, negative cooperativity or mutually exclusive binding. The role of fractional occupancy in the regulation of synaptic structure and function is explored based on recent data about the connectivity of inhibitory receptors and scaffold proteins. I propose that the absolute quantification of interactors and their stoichiometry at identified synapses can provide new mechanistic insights into the dynamic properties of inhibitory PSDs at the molecular level. This article is part of the special issue entitled 'Mobility and trafficking of neuronal membrane proteins'.
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Affiliation(s)
- Christian G Specht
- École Normale Supérieure, PSL Research University, CNRS, Inserm, Institute of Biology (IBENS), Paris, 75005, France.
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11
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Kasaragod VB, Schindelin H. Structure-Function Relationships of Glycine and GABA A Receptors and Their Interplay With the Scaffolding Protein Gephyrin. Front Mol Neurosci 2018; 11:317. [PMID: 30258351 PMCID: PMC6143783 DOI: 10.3389/fnmol.2018.00317] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 08/16/2018] [Indexed: 12/03/2022] Open
Abstract
Glycine and γ-aminobutyric acid (GABA) are the major determinants of inhibition in the central nervous system (CNS). These neurotransmitters target glycine and GABAA receptors, respectively, which both belong to the Cys-loop superfamily of pentameric ligand-gated ion channels (pLGICs). Interactions of the neurotransmitters with the cognate receptors result in receptor opening and a subsequent influx of chloride ions, which, in turn, leads to hyperpolarization of the membrane potential, thus counteracting excitatory stimuli. The majority of glycine receptors and a significant fraction of GABAA receptors (GABAARs) are recruited and anchored to the post-synaptic membrane by the central scaffolding protein gephyrin. This ∼93 kDa moonlighting protein is structurally organized into an N-terminal G-domain (GephG) connected to a C-terminal E-domain (GephE) via a long unstructured linker. Both inhibitory neurotransmitter receptors interact via a short peptide motif located in the large cytoplasmic loop located in between transmembrane helices 3 and 4 (TM3-TM4) of the receptors with a universal receptor-binding epitope residing in GephE. Gephyrin engages in nearly identical interactions with the receptors at the N-terminal end of the peptide motif, and receptor-specific interaction toward the C-terminal region of the peptide. In addition to its receptor-anchoring function, gephyrin also interacts with a rather large collection of macromolecules including different cytoskeletal elements, thus acting as central scaffold at inhibitory post-synaptic specializations. Dysfunctions in receptor-mediated or gephyrin-mediated neurotransmission have been identified in various severe neurodevelopmental disorders. Although biochemical, cellular and electrophysiological studies have helped to understand the physiological and pharmacological roles of the receptors, recent high resolution structures of the receptors have strengthened our understanding of the receptors and their gating mechanisms. Besides that, multiple crystal structures of GephE in complex with receptor-derived peptides have shed light into receptor clustering by gephyrin at inhibitory post-synapses. This review will highlight recent biochemical and structural insights into gephyrin and the GlyRs as well as GABAA receptors, which provide a deeper understanding of the molecular machinery mediating inhibitory neurotransmission.
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Affiliation(s)
- Vikram B Kasaragod
- Institute of Structural Biology, Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - Hermann Schindelin
- Institute of Structural Biology, Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
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Sequences Flanking the Gephyrin-Binding Site of GlyRβ Tune Receptor Stabilization at Synapses. eNeuro 2018; 5:eN-NWR-0042-17. [PMID: 29464196 PMCID: PMC5818551 DOI: 10.1523/eneuro.0042-17.2018] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 12/26/2017] [Accepted: 01/15/2018] [Indexed: 12/18/2022] Open
Abstract
The efficacy of synaptic transmission is determined by the number of neurotransmitter receptors at synapses. Their recruitment depends upon the availability of postsynaptic scaffolding molecules that interact with specific binding sequences of the receptor. At inhibitory synapses, gephyrin is the major scaffold protein that mediates the accumulation of heteromeric glycine receptors (GlyRs) via the cytoplasmic loop in the β-subunit (β-loop). This binding involves high- and low-affinity interactions, but the molecular mechanism of this bimodal binding and its implication in GlyR stabilization at synapses remain unknown. We have approached this question using a combination of quantitative biochemical tools and high-density single molecule tracking in cultured rat spinal cord neurons. The high-affinity binding site could be identified and was shown to rely on the formation of a 310-helix C-terminal to the β-loop core gephyrin-binding motif. This site plays a structural role in shaping the core motif and represents the major contributor to the synaptic confinement of GlyRs by gephyrin. The N-terminal flanking sequence promotes lower affinity interactions by occupying newly identified binding sites on gephyrin. Despite its low affinity, this binding site plays a modulatory role in tuning the mobility of the receptor. Together, the GlyR β-loop sequences flanking the core-binding site differentially regulate the affinity of the receptor for gephyrin and its trapping at synapses. Our experimental approach thus bridges the gap between thermodynamic aspects of receptor-scaffold interactions and functional receptor stabilization at synapses in living cells.
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Maric HM, Hausrat TJ, Neubert F, Dalby NO, Doose S, Sauer M, Kneussel M, Strømgaard K. Gephyrin-binding peptides visualize postsynaptic sites and modulate neurotransmission. Nat Chem Biol 2016; 13:153-160. [DOI: 10.1038/nchembio.2246] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 09/15/2016] [Indexed: 11/09/2022]
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Alvarez FJ. Gephyrin and the regulation of synaptic strength and dynamics at glycinergic inhibitory synapses. Brain Res Bull 2016; 129:50-65. [PMID: 27612963 DOI: 10.1016/j.brainresbull.2016.09.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 08/23/2016] [Accepted: 09/05/2016] [Indexed: 01/23/2023]
Abstract
Glycinergic synapses predominate in brainstem and spinal cord where they modulate motor and sensory processing. Their postsynaptic mechanisms have been considered rather simple because they lack a large variety of glycine receptor isoforms and have relatively simple postsynaptic densities at the ultrastructural level. However, this simplicity is misleading being their postsynaptic regions regulated by a variety of complex mechanisms controlling the efficacy of synaptic inhibition. Early studies suggested that glycinergic inhibitory strength and dynamics depend largely on structural features rather than on molecular complexity. These include regulation of the number of postsynaptic glycine receptors, their localization and the amount of co-localized GABAA receptors and GABA-glycine co-transmission. These properties we now know are under the control of gephyrin. Gephyrin is the first postsynaptic scaffolding protein ever discovered and it was recently found to display a large degree of variation and regulation by splice variants, posttranslational modifications, intracellular trafficking and interactions with the underlying cytoskeleton. Many of these mechanisms are governed by converging excitatory activity and regulate gephyrin oligomerization and receptor binding, the architecture of the postsynaptic density (and by extension the whole synaptic complex), receptor retention and stability. These newly uncovered molecular mechanisms define the size and number of gephyrin postsynaptic regions and the numbers and proportions of glycine and GABAA receptors contained within. All together, they control the emergence of glycinergic synapses of different strength and temporal properties to best match the excitatory drive received by each individual neuron or local dendritic compartment.
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Affiliation(s)
- Francisco J Alvarez
- Department of Physiology, Emory University, Atlanta, GA 30322-3110, United States.
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Kasaragod VB, Schindelin H. Structural Framework for Metal Incorporation during Molybdenum Cofactor Biosynthesis. Structure 2016; 24:782-788. [PMID: 27112598 DOI: 10.1016/j.str.2016.02.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 02/15/2016] [Accepted: 02/21/2016] [Indexed: 11/16/2022]
Abstract
The molybdenum cofactor (Moco) is essential for the catalytic activity of all molybdenum-containing enzymes with the exception of nitrogenase. Moco biosynthesis follows an evolutionarily highly conserved pathway and genetic deficiencies in the corresponding human enzymes result in Moco deficiency, which manifests itself in severe neurological symptoms and death in childhood. In humans the final steps of Moco biosynthesis are catalyzed by gephyrin, specifically the penultimate adenylation of molybdopterin (MPT) by its N-terminal G domain (GephG) and the final metal incorporation by its C-terminal E domain (GephE). To better understand the poorly defined molecular framework of this final step, we determined high-resolution crystal structures of GephE in the apo state and in complex with ADP, AMP, and molybdate. Our data provide novel insights into the catalytic steps leading to final Moco maturation, namely deadenylation as well as molybdate binding and insertion.
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Affiliation(s)
- Vikram Babu Kasaragod
- Rudolf Virchow Center for Experimental Biomedicine, Institute of Structural Biology, University of Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany
| | - Hermann Schindelin
- Rudolf Virchow Center for Experimental Biomedicine, Institute of Structural Biology, University of Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany.
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Molecular basis of the alternative recruitment of GABAA versus glycine receptors through gephyrin. Nat Commun 2014; 5:5767. [DOI: 10.1038/ncomms6767] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 11/04/2014] [Indexed: 01/17/2023] Open
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Petrini EM, Barberis A. Diffusion dynamics of synaptic molecules during inhibitory postsynaptic plasticity. Front Cell Neurosci 2014; 8:300. [PMID: 25294987 PMCID: PMC4171989 DOI: 10.3389/fncel.2014.00300] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 09/05/2014] [Indexed: 12/24/2022] Open
Abstract
The plasticity of inhibitory transmission is expected to play a key role in the modulation of neuronal excitability and network function. Over the last two decades, the investigation of the determinants of inhibitory synaptic plasticity has allowed distinguishing presynaptic and postsynaptic mechanisms. While there has been a remarkable progress in the characterization of presynaptically-expressed plasticity of inhibition, the postsynaptic mechanisms of inhibitory long-term synaptic plasticity only begin to be unraveled. At postsynaptic level, the expression of inhibitory synaptic plasticity involves the rearrangement of the postsynaptic molecular components of the GABAergic synapse, including GABAA receptors, scaffold proteins and structural molecules. This implies a dynamic modulation of receptor intracellular trafficking and receptor surface lateral diffusion, along with regulation of the availability and distribution of scaffold proteins. This Review will focus on the mechanisms of the multifaceted molecular reorganization of the inhibitory synapse during postsynaptic plasticity, with special emphasis on the key role of protein dynamics to ensure prompt and reliable activity-dependent adjustments of synaptic strength.
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Affiliation(s)
- Enrica Maria Petrini
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia Genoa, Italy
| | - Andrea Barberis
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia Genoa, Italy
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