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609 results on '"Centre de Biochimie Structurale [Montpellier] (CBS)"'

1. Two-dimensional mass spectrometry: new perspectives for tandem mass spectrometry

Author: Christian Rolando, Maria A. van Agthoven, Peter B. O’Connor, Marc-André Delsuc, Yuko P. Y. Lam, Miniaturisation pour la Synthèse, l’Analyse et la Protéomique - USR 3290 (MSAP), Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Centre de Biochimie Structurale [Montpellier] (CBS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Miniaturisation pour la Synthèse, l’Analyse et la Protéomique - UAR 3290 (MSAP), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Miniaturisation pour la Synthèse, l’Analyse et la Protéomique - UAR 3290 [MSAP], and Centre de Biochimie Structurale [Montpellier] [CBS]
Subjects: 0301 basic medicine, 030103 biophysics, Technical Primer, Biophysics, Analytical chemistry, Mass spectrometry, Tandem mass spectrometry, Fourier transform ion cyclotron resonance, Ion, 03 medical and health sciences, symbols.namesake, Fragmentation (mass spectrometry), [CHIM.ANAL]Chemical Sciences/Analytical chemistry, Tandem Mass Spectrometry, Two dimensional, [CHIM]Chemical Sciences, Fourier Analysis, Chemistry, General Medicine, Cyclotrons, Fourier transform, Fourier transform ion cyclotron resonance mass spectrometry, 030104 developmental biology, Mass spectrum, symbols
Abstract: International audience; Fourier transform ion cyclotron resonance mass analysers (FT-ICR MS) can offer the highest resolutions and mass accuracies in mass spectrometry. Mass spectra acquired in an FT-ICR MS can yield accurate elemental compositions of all compounds in a complex sample. Fragmentation caused by ion-neutral, ion-electron, or ion-photon interactions leads to more detailed structural information on compounds. The most often used method to correlate compounds and their fragment ions is to isolate the precursor ions from the sample before fragmentation. Two-dimensional mass spectrometry (2D MS) offers a method to correlate precursor and fragment ions without requiring precursor isolation. 2D MS therefore enables easy access to the fragmentation patterns of all compounds from complex samples. In this article, the principles of FT-ICR MS are reviewed and the 2D MS experiment is explained. Data processing for 2D MS is detailed, and the interpretation of 2D mass spectra is described.
Published: 2019
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2. Biological Fate of Fe3O4 Core-Shell Mesoporous Silica Nanoparticles Depending on Particle Surface Chemistry

Author: Jean-Marie Devoisselle, Wei Liu, Joséphine Lai-Kee-Him, Yannick Guari, Mélanie Auffan, Afitz Da Silva, Magali Gary-Bobo, Estelle Rascol, Morgane Daurat, Patrick Bron, Bernard Angeletti, Clarence Charnay, Marie Maynadier, Christophe Dorandeu, Joël Chopineau, Marcel Garcia, Institut Charles Gerhardt Montpellier - Institut de Chimie Moléculaire et des Matériaux de Montpellier (ICGM), Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Institut de Chimie du CNRS (INC)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut des Biomolécules Max Mousseron [Pôle Chimie Balard] (IBMM), NanoMedSyn (NMS), Centre de Biochimie Structurale [Montpellier] (CBS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Nîmes (UNIMES), Institut Charles Gerhardt, Université Montpellier 2 - Sciences et Techniques ( UM2 ), Institut des Biomolécules Max Mousseron [Pôle Chimie Balard] ( IBMM ), Ecole Nationale Supérieure de Chimie de Montpellier ( ENSCM ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), Institut Charles Gerhardt Montpellier - Institut de Chimie Moléculaire et des Matériaux de Montpellier ( ICGM ICMMM ), Université Montpellier 1 ( UM1 ) -Université Montpellier 2 - Sciences et Techniques ( UM2 ) -Ecole Nationale Supérieure de Chimie de Montpellier ( ENSCM ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), Institut de recherche en cancérologie de Montpellier ( IRCM ), Université Montpellier 1 ( UM1 ) -CRLCC Val d'Aurelle - Paul Lamarque-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université de Montpellier ( UM ), Centre de Biochimie Structurale [Montpellier] ( CBS ), Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), Interactions cellulaires et moléculaires ( ICM ), Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -IFR140-Centre National de la Recherche Scientifique ( CNRS ), Centre européen de recherche et d'enseignement de géosciences de l'environnement ( CEREGE ), Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Collège de France ( CdF ) -Institut National de la Recherche Agronomique ( INRA ) -Institut national des sciences de l'Univers ( INSU - CNRS ), School of Computer [Chine], National University of Defense Technology [Changsha], Chimie moléculaire et organisation du solide ( CMOS ), Université Montpellier 2 - Sciences et Techniques ( UM2 ) -Centre National de la Recherche Scientifique ( CNRS ), Institut Charles Gerhardt Montpellier - Institut de Chimie Moléculaire et des Matériaux de Montpellier (ICGM ICMMM), Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), NanoMedSyn, Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Collège de France (CdF)-Institut national des sciences de l'Univers (INSU - CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut de Chimie du CNRS (INC), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Montpellier (UM)-Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Collège de France (CdF (institution))-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), and Beaussier, Catherine
Subjects: safety, General Chemical Engineering, Nanoparticle, [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, Nanotechnology, nanoparticles, surface coating, cell-membrane interactions, biodistribution, 02 engineering and technology, Polyethylene glycol, 010402 general chemistry, 01 natural sciences, Article, Cell membrane, chemistry.chemical_compound, PEG ratio, medicine, General Materials Science, [INFO.INFO-BT]Computer Science [cs]/Biotechnology, Lipid bilayer, Chemistry, technology, industry, and agriculture, Mesoporous silica, 021001 nanoscience & nanotechnology, 0104 chemical sciences, Surface coating, [INFO.INFO-BT] Computer Science [cs]/Biotechnology, medicine.anatomical_structure, Membrane, Chemical engineering, [SDU.STU] Sciences of the Universe [physics]/Earth Sciences, 0210 nano-technology, [ INFO.INFO-BT ] Computer Science [cs]/Biotechnology
Abstract: International audience; The biological fate of nanoparticles (NPs) for biomedical applications is highly dependent of their size and charge, their aggregation state and their surface chemistry. The chemical composition of the NPs surface influences their stability in biological fluids, their interaction with proteins, and their attraction to the cell membranes. In this work, core-shell magnetic mesoporous silica nanoparticles (Fe 3 O 4 @MSN), that are considered as potential theranostic candidates, are coated with polyethylene glycol (PEG) or 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipid bilayer. Their biological fate is studied in comparison to the native NPs. The physicochemical properties of these three types of NPs and their suspension behavior in different media are investigated. The attraction to a membrane model is also evaluated using a supported lipid bilayer. The surface composition of NPs strongly influences their dispersion in biological fluids mimics, protein binding and their interaction with cell membrane. While none of these types of NPs is found to be toxic on mice four days after intravenous injection of a dose of 40 mg kg 1 of NPs, their surface coating nature influences the in vivo biodistribution. Importantly, NP coated with DMPC exhibit a strong accumulation in liver and a very low accumulation in lung in comparison with nude or PEG ones.
Published: 2017
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3. Sustainable computational science: the ReScience initiative

Author: Rougier, Nicolas P, Hinsen, Konrad, Alexandre, Frederic, Arildsen, Thomas, Barba, Lorena A, Benureau, Fabien C.Y, Brown, C. Titus, deBuy, Pierre, Caglayan, Ozan, Davison, Andrew P., Delsuc, Marc-Andre, Detorakis, Georgios, Diem, Alexandra, Drix, Damien, Enel, Pierre, Girard, Benoit, Guest, Olivia, Hall, Matt G, Henriques, Rafael N, Hinaut, Xavier, Jaron, Kamil S, Khamassi, Mehdi, Klein, Almar, Manninen, Tiina, Marchesi, Pietro, McGlinn, Daniel, Metzner, Christoph, Petchey, Owen, Plesser, Hans Ekkehard, Poisot, Timothee, Ram, Karthik, Ram, Yoav, Roesch, Etienne, Rossant, Cyrille, Rostami, Vahid, Shifman, Aaron, Stachelek, Joseph, Stimberg, Marcel, Stollmeier, Frank, Vaggi, Federico, Viejo, Guillaume, Vitay, Julien, Vostinar, Anya E, Yurchak, Roman, Zito, Tiziano, Mnemonic Synergy ( Mnemosyne ), Laboratoire Bordelais de Recherche en Informatique ( LaBRI ), Centre National de la Recherche Scientifique ( CNRS ) -École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique ( CNRS ) -École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut des Maladies Neurodégénératives [Bordeaux] ( IMN ), Université de Bordeaux ( UB ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Bordeaux ( UB ) -Centre National de la Recherche Scientifique ( CNRS ), Centre de biophysique moléculaire ( CBM ), Université d'Orléans ( UO ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Department of Electronic Systems - Aalborg University, Aalborg University [Denmark] ( AAU ), Washington State University ( WSU ), CIM - Communication, Information, Médias - EA 1484 ( CIM ), Université Sorbonne Nouvelle - Paris 3, Université Libre de Bruxelles [Bruxelles] ( ULB ), Laboratoire d'Informatique de l'Université du Mans ( LIUM ), Le Mans Université ( UM ), Ecole des Neurosciences de Paris Île de France ( ENP ), Ecole des Neurosciences de Paris, Centre de Biochimie Structurale [Montpellier] ( CBS ), Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire des signaux et systèmes ( L2S ), Université Paris-Sud - Paris 11 ( UP11 ) -CentraleSupélec-Centre National de la Recherche Scientifique ( CNRS ), University of Southampton [Southampton], Humboldt Universität zu Berlin, Institut cellule souche et cerveau / Stem Cell and Brain Research Institute ( SBRI ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale ( INSERM ), Laboratoire de Physiologie de la Perception et de l'Action ( LPPA ), Collège de France ( CdF ) -Centre National de la Recherche Scientifique ( CNRS ), Institut des Systèmes Intelligents et de Robotique ( ISIR ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ), University of Oxford [Oxford], University College of London [London] ( UCL ), Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Knowledge Technology group [Hamburg] ( KT ), Department of Informatics [Hamburg], Universität Hamburg ( UHH ) -Universität Hamburg ( UHH ), Université de Lausanne ( UNIL ), National Coalition of Independent Scholar ( NCIS ), Finnish Meteorological Institute ( FMI ), Vrije Universiteit Amsterdam [Amsterdam] ( VU ), Department of Biology [Charleston], College of Charleston, Universität Zürich [Zürich] ( UZH ), University of Zürich [Zürich] ( UZH ), Institute of Neuroscience and Medicine [Jülich] ( INM-1 ), Université de Montréal, University of California [Berkeley], Department of Biological Sciences [Stanford], Stanford University [Stanford], Department of Psychology, University of Geneva [Switzerland], Swiss Center for Affective Sciences, University of Ottawa [Ottawa], Michigan State University [East Lansing], Institut de la Vision, Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Institut d'études de la cognition ( IEC ), Département d'Etudes Cognitives - ENS Paris ( DEC ), École normale supérieure - Paris ( ENS Paris ) -École normale supérieure - Paris ( ENS Paris ), Max Planck Institute of Experimental Medicine [Göttingen] ( MPI ), Statistical Machine Learning and Parsimony ( SIERRA ), Département d'informatique de l'École normale supérieure ( DI-ENS ), École normale supérieure - Paris ( ENS Paris ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Centre National de la Recherche Scientifique ( CNRS ) -École normale supérieure - Paris ( ENS Paris ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Centre National de la Recherche Scientifique ( CNRS ) -Centre National de la Recherche Scientifique ( CNRS ) -Inria de Paris, Institut National de Recherche en Informatique et en Automatique ( Inria ), Chemnitz University of Technology, Grinnell College, Laboratoire pour l'utilisation des lasers intenses ( LULI ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -École polytechnique ( X ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Eberhard Karls Universität Tübingen, Mnemonic Synergy (Mnemosyne), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut des Maladies Neurodégénératives [Bordeaux] (IMN), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre de biophysique moléculaire (CBM), Université d'Orléans (UO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Aalborg University [Denmark] (AAU), Washington State University (WSU), University of California [Davis] (UC Davis), University of California (UC), Université libre de Bruxelles (ULB), Laboratoire d'Informatique de l'Université du Mans (LIUM), Le Mans Université (UM), Ecole des Neurosciences de Paris Île de France (ENP), Centre de Biochimie Structurale [Montpellier] (CBS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des signaux et systèmes (L2S), Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), University of Southampton, Humboldt University Of Berlin, Institut cellule souche et cerveau (SBRI), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de Physiologie de la Perception et de l'Action (LPPA), Collège de France (CdF (institution))-Centre National de la Recherche Scientifique (CNRS), Institut des Systèmes Intelligents et de Robotique (ISIR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), AMAC, Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), University of Oxford, University College of London [London] (UCL), Instituto de Medicina Molecular (iMM), Faculdade de Medicina [Lisboa], Universidade de Lisboa = University of Lisbon (ULISBOA)-Universidade de Lisboa = University of Lisbon (ULISBOA), Knowledge Technology group [Hamburg] (KT), University of Hamburg-University of Hamburg, Université de Lausanne = University of Lausanne (UNIL), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), National Coalition of Independent Scholar (NCIS), Finnish Meteorological Institute (FMI), Vrije Universiteit Amsterdam [Amsterdam] (VU), Universität Zürich [Zürich] = University of Zurich (UZH), Institute of Neuroscience and Medicine [Jülich] (INM-1), Université de Montréal (UdeM), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Department of Biology [Stanford], Stanford University, Université de Genève = University of Geneva (UNIGE), Swiss Center for Affective Sciences (CISA), Michigan State University System, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Labex Institut d'étude de la cognition (IEC), Département d'Etudes Cognitives - ENS Paris (DEC), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Max Planck Institute of Experimental Medicine [Göttingen] (MPI), Max-Planck-Gesellschaft, Statistical Machine Learning and Parsimony (SIERRA), Département d'informatique - ENS Paris (DI-ENS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Inria de Paris, Institut National de Recherche en Informatique et en Automatique (Inria), Chemnitz University of Technology / Technische Universität Chemnitz, Laboratoire pour l'utilisation des lasers intenses (LULI), Université Pierre et Marie Curie - Paris 6 (UPMC)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Inria Bordeaux - Sud-Ouest, Université d'Orléans (UO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), University of California, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Humboldt-Universität zu Berlin, Institut cellule souche et cerveau (U846 Inserm - UCBL1), Universidade de Lisboa (ULISBOA)-Universidade de Lisboa (ULISBOA), Université de Lausanne (UNIL), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Inria de Paris, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC), Département d'informatique de l'École normale supérieure (DI-ENS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), and Rougier, Nicolas P.
Subjects: FOS: Computer and information sciences, Technology, Journal, lcsh:QA75.5-76.95, Computational Science, GitHub, Scientific Computing and Simulation, Social Computing, Open Science, Replicability, REPRODUCIBLE RESEARCH, [INFO.INFO-DL]Computer Science [cs]/Digital Libraries [cs.DL], Open peer-review, Digital Libraries (cs.DL), Computational science, Open science, Publication, Reproducible, Replicable, Sustainable, GitHub, Open peer-review, [ INFO.INFO-DL ] Computer Science [cs]/Digital Libraries [cs.DL], Science & Technology, Computer Science, Information Systems, Data Science, Computational science, bepress|Physical Sciences and Mathematics|Computer Sciences, Computer Science - Digital Libraries, Sustainable, Reproducibility, Networking and Information Technology R&D (NITRD), Digital Libraries, Computer Science, Reproducible, Publication, Open science, lcsh:Electronic computers. Computer science, [INFO.INFO-DL] Computer Science [cs]/Digital Libraries [cs.DL], Replicable
Abstract: Computer science offers a large set of tools for prototyping, writing, running, testing, validating, sharing and reproducing results, however computational science lags behind. In the best case, authors may provide their source code as a compressed archive and they may feel confident their research is reproducible. But this is not exactly true. James Buckheit and David Donoho proposed more than two decades ago that an article about computational results is advertising, not scholarship. The actual scholarship is the full software environment, code, and data that produced the result. This implies new workflows, in particular in peer-reviews. Existing journals have been slow to adapt: source codes are rarely requested, hardly ever actually executed to check that they produce the results advertised in the article. ReScience is a peer-reviewed journal that targets computational research and encourages the explicit replication of already published research, promoting new and open-source implementations in order to ensure that the original research can be replicated from its description. To achieve this goal, the whole publishing chain is radically different from other traditional scientific journals. ReScience resides on GitHub where each new implementation of a computational study is made available together with comments, explanations, and software tests., 8 pages, 1 figure
Published: 2017
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4. Prioritizing targets for structural biology through the lens of proteomics: The archaeal protein TGAM_1934 from Thermococcus gammatolerans

Author: Valérie Aloin, Fabrice Confalonieri, Alain Dedieu, Karine de Guillen, Bernard Fernandez, Jean-Baptiste Boyer, Arnaud Lagorce, Jean Armengaud, Christian Roumestand, Yinshan Yang, Centre de Biochimie Structurale [Montpellier] (CBS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de Biochimie des Systèmes Perturbés (LBSP), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Radiorésistance des bactéries et des archées (RBA), Département Biologie des Génomes (DBG), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Centre de Biochimie Structurale [Montpellier] ( CBS ), Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Biochimie des Systèmes Perturbés ( LBSP ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), Institut de génétique et microbiologie [Orsay] ( IGM ), Université Paris-Sud - Paris 11 ( UP11 ) -Centre National de la Recherche Scientifique ( CNRS ), Radiorésistance des bactéries et des archées ( RBA ), Département Biologie des Génomes ( DBG ), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ) -Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Models, Molecular, Proteomics, Protein Conformation, Archaeal Proteins, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Quantitative proteomics, High-throughput proteomics, Computational biology, Biochemistry, Microbiology, Protein structure, Iron-Binding Proteins, Amino Acid Sequence, Nuclear Magnetic Resonance, Biomolecular, Molecular Biology, Peptide sequence, biology, [ SDV ] Life Sciences [q-bio], Genome project, computer.file_format, ORFan, biology.organism_classification, Protein Data Bank, Molecular biology, Thermococcus, Structural biology, Protein evolution, NMR structure, computer, Genome annotation
Abstract: International audience; ORFans are hypothetical proteins lacking any significant sequence similarity with other proteins. Here, we highlighted by quantitative proteomics the TGAM_1934 ORFan from the hyperradioresistant Thermococcus gammatolerans archaeon as one of the most abundant hypothetical proteins. This protein has been selected as a priority target for structure determination on the basis of its abundance in three cellular conditions. Its solution structure has been determined using multidimensional heteronuclear NMR spectroscopy. TGAM_1934 displays an original fold, although sharing some similarities with the 3D structure of the bacterial ortholog of frataxin, CyaY, a protein conserved in bacteria and eukaryotes and involved in iron-sulfur cluster biogenesis. These results highlight the potential of structural proteomics in prioritizing ORFan targets for structure determination based on quantitative proteomics data. The proteomic data and structure coordinates have been deposited to the ProteomeXchange with identifier PXD000402 (http://proteomecentral.proteomexchange.org/dataset/PXD000402) and Protein Data Bank under the accession number 2mcf, respectively.
Published: 2015
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5. Functional analyses of phosphatidylserine/PI(4)P exchangers with diverse lipid species and membrane contexts reveal unanticipated rules on lipid transfer

Author: Maud Magdeleine, Nicolas Fuggetta, Nicolas-Frédéric Lipp, Vanessa Delfosse, William Bourguet, Guillaume Drin, Souade Ikhlef, Institut de pharmacologie moléculaire et cellulaire (IPMC), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA), Centre de Biochimie Structurale [Montpellier] (CBS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Malbec, Odile, Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Physiology, QH301-705.5, [SDV]Life Sciences [q-bio], Plant Science, Phosphatidylserines, Saccharomyces cerevisiae, Biology, Phosphoinositide, Endoplasmic Reticulum, Ligands, General Biochemistry, Genetics and Molecular Biology, Fluorescence, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Structural Biology, Organelle, Pi, Humans, Biology (General), Phosphatidylserine, Ecology, Evolution, Behavior and Systematics, Lipid Transport, 030304 developmental biology, 0303 health sciences, Degree of unsaturation, Endoplasmic reticulum, Cell Membrane, Cell Biology, Lipid transport, [SDV] Life Sciences [q-bio], Sterols, Kinetics, Membrane, chemistry, Biophysics, General Agricultural and Biological Sciences, Plant lipid transfer proteins, 030217 neurology & neurosurgery, Developmental Biology, Biotechnology, Research Article, Plasma membrane
Abstract: Background Lipid species are accurately distributed in the eukaryotic cell so that organelle and plasma membranes have an adequate lipid composition to support numerous cellular functions. In the plasma membrane, a precise regulation of the level of lipids such as phosphatidylserine, PI(4)P, and PI(4,5)P2, is critical for maintaining the signaling competence of the cell. Several lipid transfer proteins of the ORP/Osh family contribute to this fine-tuning by delivering PS, synthesized in the endoplasmic reticulum, to the plasma membrane in exchange for PI(4)P. To get insights into the role of these PS/PI(4)P exchangers in regulating plasma membrane features, we question how they selectively recognize and transfer lipid ligands with different acyl chains, whether these proteins exchange PS exclusively for PI(4)P or additionally for PI(4,5)P2, and how sterol abundance in the plasma membrane impacts their activity. Results We measured in vitro how the yeast Osh6p and human ORP8 transported PS and PI(4)P subspecies of diverse length and unsaturation degree between membranes by fluorescence-based assays. We established that the exchange activity of Osh6p and ORP8 strongly depends on whether these ligands are saturated or not, and is high with representative cellular PS and PI(4)P subspecies. Unexpectedly, we found that the speed at which these proteins individually transfer lipid ligands between membranes is inversely related to their affinity for them and that high-affinity ligands must be exchanged to be transferred more rapidly. Next we determined that Osh6p and ORP8 cannot use PI(4,5)P2 for exchange processes, because it is a low-affinity ligand, and do not transfer more PS into sterol-rich membranes. Conclusions Our study provides new insights into PS/PI(4)P exchangers by indicating the degree to which they can regulate the acyl chain composition of the PM, and how they control PM phosphoinositide levels. Moreover, we establish general rules on how the activity of lipid transfer proteins relates to their affinity for ligands.
Published: 2021
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6. Allosteric modulators enhance agonist efficacy by increasing the residence time of a GPCR in the active state

Author: Emmanuel Margeat, Robert B. Quast, Anne-Marinette Cao, Philippe Rondard, Fataneh Fatemi, Jean-Philippe Pin, Centre de Biochimie Structurale [Montpellier] (CBS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Ecole Polytechnique Fédérale de Lausanne (EPFL), Shahid Beheshti University, Institut de Génomique Fonctionnelle (IGF), Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 1 (UM1)-Université de Montpellier (UM), Guerineau, Nathalie C., Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), and Margeat, Emmanuel
Subjects: [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Protein Conformation, cooperativity, [SDV]Life Sciences [q-bio], Gene Expression, General Physics and Astronomy, Molecular neuroscience, insights, Disaccharides, Receptors, Metabotropic Glutamate, taste, 0302 clinical medicine, G protein-coupled receptors, Glucosides, Catalytic Domain, Fluorescence Resonance Energy Transfer, Amino Acids, Receptor, Micelles, 0303 health sciences, Multidisciplinary, Chemistry, Glutamate receptor, Molecular conformation, Recombinant Proteins, Single Molecule Imaging, stabilization, 3. Good health, protein-coupled receptors, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, [SDV] Life Sciences [q-bio], Transmembrane domain, Indans, single-molecule fret, Cholesterol Esters, Allosteric Site, Protein Binding, Agonist, Allosteric modulator, Octoxynol, medicine.drug_class, Science, Gi alpha subunit, Allosteric regulation, mechanism, [SDV.BBM.BP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Glutamic Acid, Diosgenin, Article, General Biochemistry, Genetics and Molecular Biology, Bridged Bicyclo Compounds, 03 medical and health sciences, Single-molecule biophysics, Allosteric Regulation, medicine, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Humans, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, 030304 developmental biology, G protein-coupled receptor, Biphenyl Compounds, Cell Membrane, General Chemistry, Bridged Bicyclo Compounds, Heterocyclic, [SDV.BIO] Life Sciences [q-bio]/Biotechnology, HEK293 Cells, Xanthenes, Metabotropic glutamate receptor, Biophysics, activation, Glycolipids, Protein Multimerization, 030217 neurology & neurosurgery
Abstract: Here, the authors use smFRET to assess the structural dynamics of metabotropic glutamate receptor mGlu2 and show that a positive allosteric modulator or the Gi protein stabilize mGlu2 in the glutamate-induced active state, leading to the full activation of the receptor., Much hope in drug development comes from the discovery of positive allosteric modulators (PAM) that display target subtype selectivity and act by increasing agonist potency and efficacy. How such compounds can allosterically influence agonist action remains unclear. Metabotropic glutamate receptors (mGlu) are G protein-coupled receptors that represent promising targets for brain diseases, and for which PAMs acting in the transmembrane domain have been developed. Here, we explore the effect of a PAM on the structural dynamics of mGlu2 in optimized detergent micelles using single molecule FRET at submillisecond timescales. We show that glutamate only partially stabilizes the extracellular domains in the active state. Full activation is only observed in the presence of a PAM or the G(i) protein. Our results provide important insights on the role of allosteric modulators in mGlu activation, by stabilizing the active state of a receptor that is otherwise rapidly oscillating between active and inactive states.
Published: 2021
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7. Analysis of spontaneous tumor-specific CD4 T-cell immunity in lung cancer using promiscuous HLA-DR telomerase-derived epitopes: potential synergistic effect with chemotherapy response

Author: Xavier Pivot, Françoise Le Pimpec-Barthes, Patrice Ravel, Christophe Borg, Michele Lamuraglia, Eric Tartour, Nadine Benhamouda, Philippe Saas, Aurélie Cazes, Magalie Dosset, Yann Godet, Bernard Maillere, Emeline Levionnois, Olivier Adotevi, Pierre Langlade-Demoyen, Elizabeth Fabre, Béatrice Gaugler, Interactions hôte-greffon-tumeur, ingénierie cellulaire et génique - UFC (UMR INSERM 1098) (RIGHT), Institut National de la Santé et de la Recherche Médicale (INSERM)-Etablissement français du sang [Bourgogne-Franche-Comté] (EFS BFC)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Paris-Centre de Recherche Cardiovasculaire (PARCC - UMR-S U970), Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire d'Imagerie Paramétrique (LIP), Université Pierre et Marie Curie - Paris 6 (UPMC)-IFR58-Centre National de la Recherche Scientifique (CNRS), Centre de Biochimie Structurale [Montpellier] (CBS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Invectys, BioTop Institut Pasteur, Service d'Oncologie Médicale [CHRU Besançon], Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon)-Université de Franche-Comté (UFC), Institut de Biologie et de Technologies de Saclay (IBITECS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Etablissement français du sang [Bourgogne-Franche-Comté] (EFS [Bourgogne-Franche-Comté]), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Interactions hôte-greffon-tumeur, ingénierie cellulaire et génique - UFC (UMR INSERM 1098) ( HOTE GREFFON ), Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Etablissement français du sang [Bourgogne-France-Comté] ( EFS [Bourgogne-France-Comté] ) -Université de Franche-Comté ( UFC ), Paris-Centre de Recherche Cardiovasculaire ( PARCC - U970 ), Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Hôpital Européen Georges Pompidou [APHP] ( HEGP ), Laboratoire d'Imagerie Paramétrique ( LIP ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -IFR58-Centre National de la Recherche Scientifique ( CNRS ), Centre de Biochimie Structurale [Montpellier] ( CBS ), Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), Service d'oncologie Médicale, Centre Hospitalier Régional Universitaire [Besançon] ( CHRU Besançon ) -Hôpital Jean Minjoz, Institut de Biologie et de Technologies de Saclay ( IBITECS ), Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), Saas, Philippe, and Institut National de la Santé et de la Recherche Médicale (INSERM)-Etablissement français du sang [Bourgogne-Franche-Comté] (EFS [Bourgogne-Franche-Comté])-Université de Franche-Comté (UFC)
Subjects: CD4-Positive T-Lymphocytes, Male, Cancer Research, Telomerase, Enzyme-Linked Immunospot Assay, Lung Neoplasms, MESH : Stimulation, Chemical, medicine.medical_treatment, MESH: Apomorphine, Lymphocyte Activation, Epitope, Epitopes, 0302 clinical medicine, Carcinoma, Non-Small-Cell Lung, [ SDV.IMM ] Life Sciences [q-bio]/Immunology, MESH: Animals, Cells, Cultured, 0303 health sciences, MESH : Rats, ELISPOT, MESH : Lysergic Acid Diethylamide, MESH: Motor Activity, 3. Good health, MESH: Limbic System, MESH: Lysergic Acid Diethylamide, MESH : Apomorphine, MESH : Limbic System, Oncology, 030220 oncology & carcinogenesis, [SDV.IMM]Life Sciences [q-bio]/Immunology, Female, MESH: Hydroxydopamines, [SDV.IMM] Life Sciences [q-bio]/Immunology, MESH : Dopamine, MESH: Rats, MESH : Male, MESH: Dopamine, MESH : Septal Nuclei, 03 medical and health sciences, Interferon-gamma, MESH: Pimozide, MESH: Receptors, Drug, MESH: Stimulation, Chemical, HLA-DR, medicine, Carcinoma, Humans, Lung cancer, 030304 developmental biology, Aged, Chemotherapy, MESH : Receptors, Drug, business.industry, MESH : Hydroxydopamines, Cancer, MESH : Pimozide, HLA-DR Antigens, medicine.disease, MESH: Male, Immunology, Cancer research, MESH: Septal Nuclei, MESH : Animals, business, MESH : Motor Activity
Abstract: Purpose: To investigate the presence and impact of spontaneous telomerase-specific CD4 T-cell responses in cancer patients. Experimental Design: A multistep approach was used to design novel pan-HLA-DR–restricted peptides from telomerase. T-cell clones isolated from cancer patients were used to characterize the polarization of telomerase-specific CD4 response. The presence of spontaneous CD4 T-cell response against telomerase was monitored in 84 metastatic non–small cell lung cancer (NSCLC) patients before first-line chemotherapy (CT) using IFN-γ ELISPOT assay. Then we analyzed the impact of the pretherapeutic telomerase-specific CD4 T immunity on clinical outcome in patients according to their respective response to CT. Results: We described four novel telomerase-derived CD4 epitopes referred as universal cancer peptides (UCP) that effectively bind to most commonly found human MHC class II alleles. UCP-specific CD4 T-cell repertoire is present in human and UCP-specific CD4 T-cell clones generated from cancer patients exhibited high avidity and are Th1 polarized. Significant frequency (38%) of naturally occurring UCP-specific T-cell responses were detected before CT in advanced NSCLC but not in healthy volunteers. This response was shown to significantly increase overall survival (OS) of patients responding to CT (Median OS: 53 vs. 40 weeks, P = 0.034). Conclusions: These results show for the first time a potential synergistic effect of telomerase-specific CD4 T-cell response with CT response in NSCLC and underline the potential role of tumor-specific CD4 T-cell response on the efficiency of conventional anticancer therapy. Clin Cancer Res; 18(10); 2943–53. ©2012 AACR.
Published: 2012
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8. Cocaine-Induced Psychotic Symptoms in French Cocaine Addicts

Author: Philippe Coeuru, Eric Guillem, Lucia Romo, Vanessa Bloch, Laetitia Bellais, Florence Vorspan, Georges Brousse, Jean-Pierre Lépine, Neuropsychopharmacologie des addictions. Vulnérabilité et variabilité expérimentale et clinique (NAVVEC - UM 81 (UMR 8206/ U705)), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Descartes - Paris 5 (UPD5)-Institut des sciences du Médicament -Toxicologie - Chimie - Environnement (IFR71), Institut National de la Santé et de la Recherche Médicale (INSERM)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Paris Descartes - Paris 5 (UPD5)-Université Paris Diderot - Paris 7 (UPD7), Faculté de Médecine - Clermont-Ferrand, Université d'Auvergne - Clermont-Ferrand I (UdA), Centre de Biochimie Structurale [Montpellier] (CBS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Clinique, Psychanalyse, Développement (CliPsyD), Université Paris Nanterre (UPN), Institut National de la Santé et de la Recherche Médicale (INSERM)-Ecole Nationale Supérieure de Chimie de Paris- Chimie ParisTech-PSL (ENSCP)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Ecole Nationale Supérieure de Chimie de Paris- Chimie ParisTech-PSL (ENSCP)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Paris Descartes - Paris 5 (UPD5)-Université Paris Diderot - Paris 7 (UPD7), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Université Paris Diderot - Paris 7 (UPD7)-Institut des sciences du Médicament -Toxicologie - Chimie - Environnement (IFR71), Institut de Recherche pour le Développement (IRD)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Neuropsychopharmacologie des addictions. Vulnérabilité et variabilité expérimentale et clinique ( NAVVEC (UM 81) ), Université Paris Diderot - Paris 7 ( UPD7 ) -Institut des sciences du Médicament -Toxicologie - Chimie - Environnement ( IFR71 ), Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Ecole Nationale Supérieure de Chimie de Paris- Chimie ParisTech-PSL ( ENSCP ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Ecole Nationale Supérieure de Chimie de Paris- Chimie ParisTech-PSL ( ENSCP ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Université d'Auvergne - Clermont-Ferrand I ( UdA ), Centre de Biochimie Structurale [Montpellier] ( CBS ), Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), Clinique, Psychanalyse, Développement ( CliPsyD ), and Université Paris Nanterre ( UPN )
Subjects: Adult, Male, Questionnaires, Psychosis, medicine.medical_specialty, media_common.quotation_subject, education, Lifetime prevalence, [SHS.PSY]Humanities and Social Sciences/Psychology, [ SCCO.PSYC ] Cognitive science/Psychology, Cocaine related disorders, Substance-Induced, Psychoses, Substance-Induced, [ SDV.NEU.PC ] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Psychology and behavior, [ SHS.PSY ] Humanities and Social Sciences/Psychology, 03 medical and health sciences, Cocaine-Related Disorders, 0302 clinical medicine, Cocaine, Surveys and Questionnaires, medicine, Prevalence, Humans, Psychiatry, Biological Psychiatry, media_common, Retrospective Studies, Psychiatric Status Rating Scales, Induced psychosis, [SDV.NEU.PC]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Psychology and behavior, Addiction, Psychoses, Retrospective cohort study, Middle Aged, medicine.disease, 030227 psychiatry, 3. Good health, Psychiatry and Mental health, Psychiatric status rating scales, [SCCO.PSYC]Cognitive science/Psychology, Cocaine use, Female, France, Psychology, 030217 neurology & neurosurgery
Abstract: International audience; Cocaine use is known to induce transient psychotic symptoms. We evaluated retrospectively the lifetime prevalence of cocaine-induced psychotic symptoms in 105 cocaine addicts with the French version of the Scale for Assessment of Positive Symptoms-Cocaine Induced Psychosis (SAPS-CIP) in a clinical setting. Most patients (86.5%) described such symptoms.
Published: 2012
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9. The Obsessive-Compulsive Cocaine Scale (OCCS): A Pilot Study of a New Questionnaire for Assessing Cocaine Craving

Author: Vorspan, Florence, Bellais, Laetitia, Romo, Lucia, Bloch, Vanessa, Neira, Ramon, Lépine, Jean-Pierre, Neuropsychopharmacologie des addictions. Vulnérabilité et variabilité expérimentale et clinique (NAVVEC - UM 81 (UMR 8206/ U705)), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Descartes - Paris 5 (UPD5)-Institut des sciences du Médicament -Toxicologie - Chimie - Environnement (IFR71), Institut National de la Santé et de la Recherche Médicale (INSERM)-Ecole Nationale Supérieure de Chimie de Paris- Chimie ParisTech-PSL (ENSCP)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Ecole Nationale Supérieure de Chimie de Paris- Chimie ParisTech-PSL (ENSCP)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Paris Descartes - Paris 5 (UPD5)-Université Paris Diderot - Paris 7 (UPD7), Clinique, Psychanalyse, Développement (CliPsyD), Université Paris Nanterre (UPN), Centre de Biochimie Structurale [Montpellier] (CBS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Paris Descartes - Paris 5 (UPD5)-Université Paris Diderot - Paris 7 (UPD7), Neuropsychopharmacologie des addictions. Vulnérabilité et variabilité expérimentale et clinique ( NAVVEC (UM 81) ), Université Paris Diderot - Paris 7 ( UPD7 ) -Institut des sciences du Médicament -Toxicologie - Chimie - Environnement ( IFR71 ), Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Ecole Nationale Supérieure de Chimie de Paris- Chimie ParisTech-PSL ( ENSCP ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Ecole Nationale Supérieure de Chimie de Paris- Chimie ParisTech-PSL ( ENSCP ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Clinique, Psychanalyse, Développement ( CliPsyD ), Université Paris Nanterre ( UPN ), Centre de Biochimie Structurale [Montpellier] ( CBS ), Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), Université Paris Diderot - Paris 7 (UPD7)-Institut des sciences du Médicament -Toxicologie - Chimie - Environnement (IFR71), Institut de Recherche pour le Développement (IRD)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Adult, Male, Questionnaires, Principal Component Analysis, [SDV.NEU.PC]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Psychology and behavior, [SHS.PSY]Humanities and Social Sciences/Psychology, [ SCCO.PSYC ] Cognitive science/Psychology, Pilot Projects, Middle Aged, [ SDV.NEU.PC ] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Psychology and behavior, [ SHS.PSY ] Humanities and Social Sciences/Psychology, Cocaine-Related Disorders, mental disorders, [SCCO.PSYC]Cognitive science/Psychology, Compulsive Behavior, Crack Cocaine, Feasibility Studies, Humans, Female, Prospective Studies, Obsessive Behavior
Abstract: International audience; This study aimed to develop a scale (Obsessive-Compulsive Cocaine Scale [OCCS]) for measuring cocaine craving based on the Obsessive Compulsive Drinking Scale (OCDS). We tested the scale on 116 French-speaking cocaine users. The scale was reliable (Cronbach's α= 0.93). It was significantly correlated with a visual analogue scale of craving (r = 0.641, p textless .001) and discriminated between cocaine-dependant subjects (score 36 ± 11) and abusers (score 17 ± 9, p textless .001). Prospective tests on a sample of 20 subjects showed that the OCCS score changed over 3 weeks of treatment and was significantly correlated with the visual analogue scale of craving (r = 0.492, p = .038). Principal component analysis identified three factors: resistance, intensity, and interference. The OCCS questionnaire could be used to repeatedly assess cocaine craving in prospective studies in cocaine addicts. (Am J Addict 2012;00:1-7).
Published: 2012
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10. Montpellier Infectious Diseases (MID): 1st Annual Meeting (2011)

Author: Marc Sitbon, Martine Biard-Piechaczyk, Vincent Robert, Laurence Briant, Stephan Köhler, Gilles Labesse, Christian Devaux, Institut de Génétique Moléculaire de Montpellier ( IGMM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de Montpellier ( UM ), Institut de Recherche en Infectiologie de Montpellier ( IRIM ), Laboratoire de chimie quantique et de modélisation moléculaire ( LCQMM ), Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Chimie - UMR5182 ( LC ), École normale supérieure - Lyon ( ENS Lyon ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique ( CNRS ), Centre de Biochimie Structurale [Montpellier] ( CBS ), Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), Institut de Génétique Moléculaire de Montpellier (IGMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de chimie quantique et de modélisation moléculaire (LCQMM), Centre National de la Recherche Scientifique (CNRS), Laboratoire de Chimie - UMR5182 (LC), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École normale supérieure - Lyon (ENS Lyon)-Institut de Chimie du CNRS (INC), Centre de Biochimie Structurale [Montpellier] (CBS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Microbiology (medical), 0303 health sciences, 030306 microbiology, Microbiology, [ SDV.MP.VIR ] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, 3. Good health, 03 medical and health sciences, Infectious Diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Genetics, Molecular Biology, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology
Abstract: International audience; no abstract available
Published: 2011
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11. Capture in the metabolic arena: co-selection of gamma and deltaretrovirus envelope glycoproteins and their receptors

Author: Lydie Nadal-Desbarats, Nicolas Manel, Donatella Giovannini, Hiroyuki Abe, Felix J. Kim, Jawida Touhami, Valérie Courgnaud, Karine de Guillen, Marc Sitbon, Jean-Luc Battini, Wiliam M Switzer, Madakasira Lavanya, Pierre Castelnau, Emmanuelle Lagrue, Christian Roumestand, Institut de Génétique Moléculaire de Montpellier ( IGMM ), Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), Centers for Disease Control and Prevention [Atlanta] ( CDC ), Centers for Disease Control and Prevention, Service de Neurologie et Neurochirurgie Pédiatrique, CHRU Tours-Centre de Pédiatrie Gatien-de-Clocheville, Imagerie et cerveau, Université de Tours-Institut National de la Santé et de la Recherche Médicale ( INSERM ), Centre de Biochimie Structurale [Montpellier] ( CBS ), Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), Institut de Génétique Moléculaire de Montpellier (IGMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Centers for Disease Control and Prevention [Atlanta] (CDC), Centre Hospitalier Régional Universitaire de Tours (CHRU Tours)-Centre de Pédiatrie Gatien-de-Clocheville, Imagerie et cerveau (iBrain - Inserm U1253 - UNIV Tours ), Université de Tours (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de Biochimie Structurale [Montpellier] (CBS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), BMC, Ed., Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), and Université de Tours-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: lcsh:Immunologic diseases. Allergy, viruses, Retrotransposon, Biology, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Viral envelope, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Virology, Gene, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Gammaretrovirus, Genetics, chemistry.chemical_classification, 0303 health sciences, Invited Speaker Presentation, virus diseases, biology.organism_classification, Deltaretrovirus, 3. Good health, [ SDV.MHEP.MI ] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Infectious Diseases, chemistry, Capsid, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, 030211 gastroenterology & hepatology, Glycoprotein, lcsh:RC581-607, DNA
Abstract: Although all infectious and replication-competent retroviruses harbor an env gene, the origin of env remains unknown except for that of a few invertebrate retroviruses. It is generally admitted that infectious retroviruses have evolved from endogenous viral retrotransposons by insertion of an ''external'' gene that encodes for a fusion glycoprotein (env capture). In 2000, Malik et al. provided the first formal evidence for the origin of env in several invertebrate retroviruses. For instance, they showed that env of Gypsy, an infectious Drosophila retrotransposon, has been ''captured'' from a fusion protein-encoding gene of a baculovirus, a totally unrelated large DNA enveloped virus. Vertebrate retroviruses cover 7 genera distinguished by their gag (capsid encoding) and pol (enzyme encoding) genes. The gammaretroviruses (murine leukemia viruses, MLV as a prototype) and deltaretroviruses (the human T cell leukemia virus, HTLV as a prototype) are the most distant genera according to their pol genes. However, we reported that HTLV env is most closely related to MLV env, sharing similar modular organization and motifs even within the receptor-binding domain (RBD), the Env most variable sequence. Accordingly, swapping the RBD-encoding regions between the two types of Env yielded functional chimeras. We argued that this common ancestry between the env of remotely related retroviruses is also in favor of an env capture scenario by vertebrate retroviruses. Nonetheless, the origin of these env, and more specifically their RBD, remains unknown. Based on the gammaretrovirus Env modular organization, we derived soluble RBD domains of different gamma and deltaretroviruses. This has been instrumental to the identification of Glut1, the major glucose transporter, as the cognate receptor of HTLV-1 and 2 Env. We further showed that Glut1 binds all known HTLV or S(imian)TLV types and that intracellular interaction of HTLV or STLV RBD with Glut1 modulates glucose transport and glycolysis. Of most interest is that, like Glut1, all of the receptors identified so far for gammaretrovirus Env belong to the family of multimembrane-spanning molecules and that those for which a function has been determined are all metabolite transporters (amino acids, inorganic phosphate, vitamins, etc.). The selection as Env receptors of metabolite transporters that shuttles from cytoplasmic pools to the cell surface and the cytoplasmic interaction between RBD and their cognate receptors have us to postulate that gamma and deltaretrovirus Env, and more particularly their RBD modules, are related to transporter chaperone molecules that modulate their cell surface translocation.
Published: 2009
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12. Single-particle tracking photoactivated localization microscopy of membrane proteins in living plant tissues

Author: Alexandre Martinière, Yvon Jaillais, Matthieu Pierre Platre, Marcelo Nollmann, Claire Burny, Vincent Bayle, Jean-Bernard Fiche, Reproduction et développement des plantes (RDP), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre de Biochimie Structurale [Montpellier] (CBS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut für Populationsgenetik [Vienna], Veterinärmedizinische Universität Wien, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-18-CE13-0025,caLIPSO,Mécanismes du pattern lipidique du réseau trans-Golgien (trans-Golgi Network) et rôles dans le tri des protéines, la polarité cellulaire et le développement des plantes(2018), and ANR-19-CE20-0008,CellOsmo,Nanodomain membranaire: un role dans la signalisation osmotique(2019)
Subjects: Fluorescence-lifetime imaging microscopy, Computer science, [SDV]Life Sciences [q-bio], single particle tracking, Arabidopsis, Total internal reflection microscopy, Fluorescence correlation spectroscopy, total internal reflection fluorescence microscopy, General Biochemistry, Genetics and Molecular Biology, Diffusion, molecular diffusion, 03 medical and health sciences, 0302 clinical medicine, Plant Cells, super-resolution microscopy, Microscopy, Photoactivated localization microscopy, 030304 developmental biology, 0303 health sciences, plants, Super-resolution microscopy, sptPALM, Optical Imaging, photo-activated localization microscopy, Rho GTPase, Membrane Proteins, Fluorescence recovery after photobleaching, root, Single Molecule Imaging, Autofluorescence, Spectrometry, Fluorescence, Microscopy, Fluorescence, single molecule localization microscopy, auxin, Biological system, 030217 neurology & neurosurgery, Fluorescence Recovery After Photobleaching
Abstract: Super-resolution microscopy techniques have pushed the limit of optical imaging to unprecedented spatial resolutions. However, one of the frontiers in nanoscopy is its application to intact living organisms. Here we describe the implementation and application of super-resolution single-particle tracking photoactivated localization microscopy (sptPALM) to probe single-molecule dynamics of membrane proteins in live roots of the model plant Arabidopsis thaliana. We first discuss the advantages and limitations of sptPALM for studying the diffusion properties of membrane proteins and compare this to fluorescence recovery after photobleaching (FRAP) and fluorescence correlation spectroscopy (FCS). We describe the technical details for handling and imaging the samples for sptPALM, with a particular emphasis on the specificity of imaging plant cells, such as their thick cell walls or high degree of autofluorescence. We then provide a practical guide from data collection to image analyses. In particular, we introduce our sptPALM_viewer software and describe how to install and use it for analyzing sptPALM experiments. Finally, we report an R statistical analysis pipeline to analyze and compare sptPALM experiments. Altogether, this protocol should enable plant researchers to perform sptPALM using a benchmarked reproducible protocol. Routinely, the procedure takes 3–4 h of imaging followed by 3–4 d of image processing and data analysis. This protocol describes how to perform single-particle tracking photoactivated localization microscopy (sptPALM) of membrane proteins in living plant tissues. The procedure covers all stages, from sample preparation to data analysis.
Published: 2021
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13. The diversity of molecular interactions involving intrinsically disordered proteins: A molecular modeling perspective

Author: Ilinka, Clerc, Amin, Sagar, Alessandro, Barducci, Nathalie, Sibille, Pau, Bernadó, Juan, Cortés, Équipe Robotique et InteractionS (LAAS-RIS), Laboratoire d'analyse et d'architecture des systèmes (LAAS), Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées, Centre de Biochimie Structurale [Montpellier] (CBS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), ANR-17-CE11-0022,GPCteR,Mécanismes moléculaires des régions C-terminales désordonnées et fonctionnelles des RCPG et impact sur les voies de la signalisation cellulaire dépendantes de l'arrestine(2017), ANR-14-ACHN-0016,M4,Modélisation Multi-échelle des Machines bioMoléculaires(2014), ANR-19-P3IA-0004,ANITI,Artificial and Natural Intelligence Toulouse Institute(2019), Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Liquid-liquid phase separation, Intrinsically disordered proteins, Molecular dynamics simulations, Molecular recognition elements, Molecular interactions, Review Article, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], TP248.13-248.65, Conformational sampling, Biotechnology
Abstract: International audience; Intrinsically Disordered Proteins and Regions (IDPs/IDRs) are key components of a multitude of biological processes. Conformational malleability enables IDPs/IDRs to perform very specialized functions that cannot be accomplished by globular proteins. The functional role for most of these proteins is related to the recognition of other biomolecules to regulate biological processes or as a part of signaling pathways. Depending on the extent of disorder, the number of interacting sites and the type of partner, very different architectures for the resulting assemblies are possible. More recently, molecular condensates with liquid-like properties composed of multiple copies of IDPs and nucleic acids have been proven to regulate key processes in eukaryotic cells. The structural and kinetic details of disordered biomolecular complexes are difficult to unveil experimentally due to their inherent conformational heterogeneity. Computational approaches, alone or in combination with experimental data, have emerged as unavoidable tools to understand the functional mechanisms of this elusive type of assemblies. The level of description used, all-atom or coarse-grained, strongly depends on the size of the molecular systems and on the timescale of the investigated mechanism. In this mini-review, we describe the most relevant architectures found for molecular interactions involving IDPs/IDRs and the computational strategies applied for their investigation.
Published: 2021
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14. The H-NS dimerization domain defines a new fold contributing to DNA recognition

Author: Vanessa Bloch, Marie Thérèse Augé, Bruno Robert, Stefan T. Arold, Yinshan Yang, Sylvie Rimsky, Emmanuel Margeat, Alain Chavanieu, Michel Kochoyan, Centre de Biochimie Structurale [Montpellier] ( CBS ), Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire Bioénergétique, Métalloprotéines et Stress ( LBMS ), Département Biochimie, Biophysique et Biologie Structurale ( B3S ), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Biologie et de Pharmacologie Appliquée ( LBPA ), École normale supérieure - Cachan ( ENS Cachan ) -Centre National de la Recherche Scientifique ( CNRS ), Centre de Biochimie Structurale [Montpellier] (CBS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire Bioénergétique Membranaire et Stress (LBMS), Département Biochimie, Biophysique et Biologie Structurale (B3S), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie et de Pharmacologie Appliquée (LBPA), Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Cachan (ENS Cachan), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), and École normale supérieure - Cachan (ENS Cachan)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Models, Molecular, Protein Folding, Magnetic Resonance Spectroscopy, MESH : Molecular Sequence Data, Protein Conformation, MESH : DNA, MESH: Amino Acid Sequence, MESH: Protein Structure, Tertiary, chemistry.chemical_compound, MESH: Protein Conformation, Structural Biology, MESH : Bacterial Proteins, MESH: Peptide Fragments, MESH: Bacterial Proteins, Conserved Sequence, MESH : Protein Conformation, 0303 health sciences, MESH: Conserved Sequence, MESH : Amino Acid Sequence, MESH: DNA, DNA-Binding Proteins, Biochemistry, MESH : Dimerization, MESH : DNA-Binding Proteins, MESH : Mutation, Dimerization, MESH : Protein Structure, Tertiary, MESH: Models, Molecular, Binding domain, MESH : Protein Folding, MESH: Mutation, HMG-box, MESH : Models, Molecular, MESH: Protein Folding, Molecular Sequence Data, Fluorescence Polarization, Computational biology, Biology, DNA-binding protein, 03 medical and health sciences, Bacterial Proteins, MESH : Conserved Sequence, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Amino Acid Sequence, B3 domain, Molecular Biology, Gene, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, 030304 developmental biology, MESH: Fluorescence Polarization, MESH: Molecular Sequence Data, MESH: Magnetic Resonance Spectroscopy, 030306 microbiology, Circular bacterial chromosome, MESH : Peptide Fragments, DNA, Peptide Fragments, Protein Structure, Tertiary, MESH: Dimerization, Heteronuclear molecule, chemistry, Mutation, MESH : Fluorescence Polarization, MESH : Magnetic Resonance Spectroscopy, MESH: DNA-Binding Proteins
Abstract: International audience; H-NS, a protein found in Gram-negative bacteria, is involved in structuring the bacterial chromosome and acts as a global regulator for the expression of a wide variety of genes. These functions are correlated with both its DNA-binding and oligomerization properties. We have identified the minimal dimerization domain of H-NS, a 46 amino acid-long N-terminal fragment, and determined its structure using heteronuclear NMR spectroscopy. The highly intertwined structure of the dimer, reminiscent of a handshake, defines a new structural fold, which may offer a possibility for discriminating prokaryotic from eukaryotic proteins in drug design. Using mutational analysis, we also show that this N-terminal domain actively contributes to DNA binding, conversely to the current paradigm. Together, our data allows us to propose a model for the action of full length H-NS.
Published: 2003
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15. TAT-RasGAP 317-326 kills cells by targeting inner-leaflet–enriched phospholipids

Author: Christian Widmann, Filip Stojceski, Pierre-Emmanuel Milhiet, Gabriel Ichim, Gianvito Grasso, Robyn Roth, Cédric Godefroy, Kushal Kumar Das, Andrea Danani, Marc Serulla, Tim Schober, Ana J. García-Sáez, Sergii Afonin, Mathieu Heulot, Milhiet, Pierre-Emmanuel, Université de Lausanne = University of Lausanne (UNIL), Centre de Recherche en Cancérologie de Lyon (UNICANCER/CRCL), Centre Léon Bérard [Lyon]-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Istituto Dalle Molle di Studi sull'Intelligenza Artificiale (IDSIA), Università della Svizzera italiana = University of Italian Switzerland (USI)-Scuola universitaria professionale della Svizzera italiana = University of Applied Sciences and Arts of Southern Switzerland [Manno] (SUPSI), Karlsruhe Institute of Technology (KIT), Karlsruher Institut für Technologie (KIT), Washington University School of Medicine [Saint Louis, MO], Centre de Biochimie Structurale [Montpellier] (CBS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, University of Lausanne (UNIL), Università della Svizzera italiana = University of Italian Switzerland (USI)-Scuola universitaria professionale della Svizzera italiana [Manno] (SUPSI), Washington University School of Medecine [Saint Louis, MO], Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Interfaculty Institute of Biochemistry (IFIB), University of Tübingen, 72076, Tübingen, Germany
Subjects: Phosphatidylinositol 4,5-Diphosphate, 0301 basic medicine, Programmed cell death, Necrosis, [SDV.BBM.BP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Peptide, CHO Cells, Phosphatidylserines, Molecular Dynamics Simulation, 03 medical and health sciences, chemistry.chemical_compound, Cricetulus, 0302 clinical medicine, Neoplasms, medicine, Animals, Humans, Nuclear Magnetic Resonance, Biomolecular, chemistry.chemical_classification, Multidisciplinary, Cell Death, Chemistry, Cell Membrane, GTPase-Activating Proteins, Phosphatidylserine, Biological Sciences, Peptide Fragments, Cell biology, Point mutant, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Microscopy, Electron, Cytosol, 030104 developmental biology, Membrane, 030220 oncology & carcinogenesis, Liposomes, Cancer cell, lipids (amino acids, peptides, and proteins), medicine.symptom, HeLa Cells
Abstract: International audience; TAT-RasGAP 317–326 is a cell-penetrating peptide-based construct with anticancer and antimicrobial activities. This peptide kills a subset of cancer cells in a manner that does not involve known programmed cell death pathways. Here we have elucidated the mode of action allowing TAT-RasGAP 317–326 to kill cells. This peptide binds and disrupts artificial membranes containing lipids typically enriched in the inner leaflet of the plasma membrane, such as phosphatidylinositol-bisphosphate (PIP 2 ) and phosphatidylserine (PS). Decreasing the amounts of PIP 2 in cells renders them more resistant to TAT-RasGAP 317–326 , while reducing the ability of cells to repair their plasma membrane makes them more sensitive to the peptide. The W317A TAT-RasGAP 317–326 point mutant, known to have impaired killing activities, has reduced abilities to bind and permeabilize PIP 2 - and PS-containing membranes and to translocate through biomembranes, presumably because of a higher propensity to adopt an α-helical state. This work shows that TAT-RasGAP 317–326 kills cells via a form of necrosis that relies on the physical disruption of the plasma membrane once the peptide targets specific phospholipids found on the cytosolic side of the plasma membrane.
Published: 2020
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16. Rational programming of history-dependent logic in cellular populations

Author: Ana Zúñiga, Pauline Mayonove, Z. Ben Meriem, Miguel Camacho, Violaine Moreau, Pascal Hersen, Jerome Bonnet, Luca Ciandrini, Sarah Guiziou, Bodescot, Myriam, Infrastructure Française pour la Biologie Structurale Intégrée - - FRISBI2010 - ANR-10-INBS-0005 - INBS - VALID, Centre de Biochimie Structurale [Montpellier] (CBS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), University of Washington [Seattle], Matière et Systèmes Complexes (MSC (UMR_7057)), Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Laboratoire Charles Coulomb (L2C), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Physico-Chimie Curie [Institut Curie] (PCC), Institut Curie [Paris]-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Support was provided by an ERC Starting Grant 'Compucell,' the INSERM Atip-Avenir program and the Bettencourt-Schueller Foundation. S.G. was supported by a Ph.D. fellowship from the French Ministry of Research and the French Foundation for Medical Research (FRM) FDT20170437282. Z.B.M. and P.H. were supported by an ERC Consolidator grant 'Smartcells.' The CBS acknowledges support from the French Infrastructure for Integrated Structural Biology (FRISBI) ANR-10-INSB-05-01., ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)
Subjects: Logic, Computer science, Science, Population, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, ENCODE, Article, Cell Physiological Phenomena, Workflow, Recombinases, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Biomanufacturing, education, lcsh:Science, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, Gene, 030304 developmental biology, 0303 health sciences, education.field_of_study, Models, Genetic, Molecular engineering, business.industry, DNA, Modular design, Programming language, Multicellular organism, chemistry, Scalability, Synthetic Biology, lcsh:Q, Software engineering, business, Software, 030217 neurology & neurosurgery, Biotechnology
Abstract: Genetic programs operating in a history-dependent fashion are ubiquitous in nature and govern sophisticated processes such as development and differentiation. The ability to systematically and predictably encode such programs would advance the engineering of synthetic organisms and ecosystems with rich signal processing abilities. Here we implement robust, scalable history-dependent programs by distributing the computational labor across a cellular population. Our design is based on standardized recombinase-driven DNA scaffolds expressing different genes according to the order of occurrence of inputs. These multicellular computing systems are highly modular, do not require cell-cell communication channels, and any program can be built by differential composition of strains containing well-characterized logic scaffolds. We developed automated workflows that researchers can use to streamline program design and optimization. We anticipate that the history-dependent programs presented here will support many applications using cellular populations for material engineering, biomanufacturing and healthcare., Automated frameworks to systematically implement robust history-dependent genetic programs in cellular populations.
Published: 2020
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17. STEEP mediates STING ER exit and activation of signaling

Author: Chiranjeevi Bodda, Søren B. Jensen, Carsten Scavenius, Anne Troldborg, Christine Doucet, Cheng long Sun, Ramya Nandakumar, Anders Laustsen, Thaneas Prabakaran, Zong liang Gao, Samuel J. Windross, Harald Stenmark, Zheng Guo, Line S. Reinert, Sonia Assil, Rune Hartmann, Søren R. Paludan, Jinrong Huang, Martin K. Thomsen, Yan Zhang, Ryo Narita, Jan J. Enghild, Bao cun Zhang, Zhijian J. Chen, Raphaela Goldbach-Mansky, Takeshi Noda, David Olagnier, Rasmus O. Bak, Cong gang Zhang, Martin F. Berthelsen, Yujia Cai, Department of Biomedicine Aarhus, Department of Clinical Medicine (Aarhus University), Department of Chemistry and Interdisciplinary Nanoscience Center, Aarhus University, Department of Molecular Biology, University of Aarhus, Institute for Cancer Research [Oslo], Oslo University Hospital [Oslo], Centre de Biochimie Structurale [Montpellier] (CBS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Graduate School of Frontier Biosciences [Osaka], Osaka University [Osaka], National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), The Novo Nordisk Foundation (NNF18OC0030274) and the Lundbeck Foundation (R198-2015-171, R268-2016-3927), B.-c.Z. is funded by a postdoctoral grant from the Danish Council for Independent Research, Medical Sciences (5053-00083B), the postdoctoral salary to S.A. was funded by the European Union under the Horizon 2020 Research and Innovation Program and Marie Skłodowska-Curie Actions (MSCA) – international fellowship (PathAutoBio 796840), the PhD scholarship to S.J.W. was funded by the European Union under the Horizon 2020 Research and Innovation Program and the MSCA-Innovative Training Networks Programme MSCA-ITN (EDGE, 675278), the postdoctoral grant to A.T. was funded by the Lundbeck Foundation (R264-2017-3344)., and European Project: 786602,ENVISION
Subjects: 0301 basic medicine, cGAS-STING pathway, [SDV]Life Sciences [q-bio], Regulator, DNA VIRUSES, Stimulation, Endoplasmic Reticulum, ADAPTER, Mice, 0302 clinical medicine, Gene expression, Lupus Erythematosus, Systemic, Immunology and Allergy, SYNTHASE, PHOSPHORYLATION, Chemistry, Nuclear Proteins, 3. Good health, Cell biology, TRANSLOCATION, Protein Transport, Membrane curvature, symbols, 2ND-MESSENGER, AUTOPHAGY, Innate immunology, medicine.symptom, Signal Transduction, DNA sensing, intracellular trafficking, Immunology, Nerve Tissue Proteins, Inflammation, Article, 03 medical and health sciences, symbols.namesake, medicine, Animals, Humans, Endoplasmic reticulum, Membrane Proteins, CYCLIC GMP-AMP, Golgi apparatus, eye diseases, Sting, 030104 developmental biology, SAVI, Gene Expression Regulation, INNATE IMMUNITY, 030215 immunology
Abstract: STING is essential for control of infections and for tumor immunosurveillance, but it can also drive pathological inflammation. STING resides on the endoplasmic reticulum (ER) and traffics following stimulation to the ERGIC/Golgi, where signaling occurs. Although STING ER exit is the rate-limiting step in STING signaling, the mechanism that drives this process is not understood. Here we identify STEEP as a positive regulator of STING signaling. STEEP was associated with STING and promoted trafficking from the ER. This was mediated through stimulation of phosphatidylinositol-3-phosphate (PtdIns(3)P) production and ER membrane curvature formation, thus inducing COPII-mediated ER-to-Golgi trafficking of STING. Depletion of STEEP impaired STING-driven gene expression in response to virus infection in brain tissue and in cells from patients with STING-associated diseases. Interestingly, STING gain-of-function mutants from patients interacted strongly with STEEP, leading to increased ER PtdIns(3)P levels and membrane curvature. Thus, STEEP enables STING signaling by promoting ER exit. STING ER exit is the rate-limiting step in STING signaling, but the mechanism that drives this process is not understood. Paludan and colleagues identify CxORF56, called STEEP here, as a positive regulator of STING signaling.
Published: 2020
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18. Relaxation time asymmetry in stator dynamics of the bacterial flagellar motor

Author: Jerome Dorignac, Jean-Charles Walter, Andrea Parmeggiani, María-José Franco-Oñate, Nils-Ole Walliser, Ashley L. Nord, Fred Geniet, John Palmeri, Ruben Perez-Carrasco, Department of Life Sciences, Imperial College London, Laboratoire Charles Coulomb (L2C), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Centre de Biochimie Structurale [Montpellier] (CBS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Centre de Biologie Structurale [Montpellier] (CBS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), and Nord, Ashley
Subjects: Stator, media_common.quotation_subject, [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], Flagellum, 010402 general chemistry, 01 natural sciences, Asymmetry, law.invention, 03 medical and health sciences, Bacterial Proteins, law, Molecular motor, Torque, Ion channel, 030304 developmental biology, media_common, Physics, 0303 health sciences, Multidisciplinary, [PHYS.PHYS.PHYS-BIO-PH] Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], Bacteria, Rotor (electric), Molecular Motor Proteins, Dynamics (mechanics), 0104 chemical sciences, Flagella, Biophysics
Abstract: The bacterial flagellar motor (BFM) is the membrane-embedded rotary molecular motor which turns the flagellum that provides thrust to many bacterial species. This large multimeric complex, composed of a few dozen constituent proteins, has emerged as a hallmark of dynamic subunit exchange. The stator units are inner-membrane ion channels which dynamically bind and unbind to the peptidoglycan at the rotor periphery, consuming the ion motive force (IMF) and applying torque to the rotor when bound. The dynamic exchange is known to be a function of the viscous load on the flagellum, allowing the bacterium to dynamically adapt to its local viscous environment, but the molecular mechanisms of exchange and mechanosensitivity remain to be revealed. Here, by actively perturbing the steady-state stator stoichiometry of individual motors, we reveal a stoichiometry-dependent asymmetry in stator remodeling kinetics. We interrogate the potential effect of next-neighbor interactions and local stator unit depletion and find that neither can explain the observed asymmetry. We then simulate and fit two mechanistically diverse models which recapitulate the asymmetry, finding stator assembly dynamics to be particularly well described by a two-state catch-bond mechanism.
Published: 2022
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19. Viro-fluidics: Real-time analysis of virus production kinetics at the singlecell level

Author: Joëlle Eid, Marius Socol, Antoine Naillon, Jérôme Feuillard, Luca Ciandrini, Emmanuel Margeat, Benoit Charlot, Marylène Mougel, Institut de Recherche en Infectiologie de Montpellier (IRIM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Laboratoire sols, solides, structures - risques [Grenoble] (3SR), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), Centre de Biologie Structurale [Montpellier] (CBS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institut d’Electronique et des Systèmes (IES), Gibier, François, and Centre de Biochimie Structurale [Montpellier] (CBS)
Subjects: [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, [SPI.NANO] Engineering Sciences [physics]/Micro and nanotechnologies/Microelectronics, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.BBM.BP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, [SPI.NANO]Engineering Sciences [physics]/Micro and nanotechnologies/Microelectronics, [SDV.BIO] Life Sciences [q-bio]/Biotechnology
Abstract: International audience; Real-time visualization and quantification of viruses released by a cell are crucial to further decipher infection processes. Kinetics studies at the single-cell level will circumvent the limitations of bulk assays with asynchronous virus replication. We have implemented a "viro-fluidic" method, which combines microfluidics and virology at single-cell and single-virus resolutions. As an experimental model, we used standard cell lines producing fluorescent HIV-like particles (VLPs). First, to scale the strategy to the single-cell level, we validated a sensitive flow virometry system to detect VLPs in low concentration samples (≥ 10 4 VLPs/mL). Then, this system was coupled to a single-cell trapping device to monitor in real-time the VLPs released, one at a time, from single cells under cell culture conditions. Our results revealed an average production rate of 50 VLPs/h/cell similar to the rate estimated for the same cells grown in population. Thus, the virus-producing capacities of the trapped cells were preserved and its real-time monitoring was accurate. Moreover, single-cell analysis revealed a release of VLPs with stochastic bursts with typical-time intervals of few minutes, revealing the existence of limiting step(s) in the virus biogenesis process. Our tools can be applied to other pathogens or to extracellular vesicles to elucidate the dissemination mechanisms of these biological nanoparticles. WHY IT MATTERS We are frequently exposed to viruses, but some of them, like HIV, cause fatal diseases and pandemics. We have developed a simple viro-fluidic system that requires only fluorescent labeling of viral particles and allows direct observation of viruses exiting a cell, one by one, under cell culture conditions. The system operates in real-time and at single cell and single viral particle resolutions. Our results reveal HIV production at a moderate frequency which was not predicted for optimal virus dissemination. Importantly, the viro-fluidic tool is remarkably easy for biologists to access and is transposable to other pathogens or extracellular vesicles.
Published: 2022
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20. Discovery of a cryptic site at the interface 2 of TEAD – Towards a new family of YAP/TAZ-TEAD inhibitors

Author: Jean-François Guichou, Manon Sturbaut, Romain Magnez, Marie-Christine Chartier-Harlin, Patricia Melnyk, Martine Pugnière, Maxime Liberelle, Pasquale Sileo, Philippe Cotelle, Xavier Thuru, Muriel Gelin, Fabrice Bailly, Mathilde Coevoet, Frédéric Allemand, Lille Neurosciences & Cognition - U 1172 (LilNCog (ex-JPARC)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Institut de Recherche en Cancérologie de Montpellier (IRCM - U1194 Inserm - UM), CRLCC Val d'Aurelle - Paul Lamarque-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Cancer Heterogeneity, Plasticity and Resistance to Therapies - UMR 9020 - U 1277 (CANTHER), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), Centre de Biochimie Structurale [Montpellier] (CBS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centrale Lille, This work was financially supported by grants from le Ministère de l’Education et de la Recherche and the University of Lille (M. S. and P.S.) and fundings from le Cancéropôle Nord-Ouest (Mobility Support Program for Young Researchers, M. S.). This work was also supported by the French Infrastructure for Integrated Structural Biology (FRISBI) ANR-10-INSB-05-01., ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010), Lille Neurosciences & Cognition - U 1172 (LilNCog), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Models, Molecular, TEAD cryptic binding pocket, Hippo pathway, Antineoplastic Agents, Cell Cycle Proteins, Ligands, TEAD inhibition, 03 medical and health sciences, Structure-Activity Relationship, 0302 clinical medicine, Transcription (biology), Drug Discovery, Humans, [CHIM]Chemical Sciences, Tissue homeostasis, Binding assays, 030304 developmental biology, Cell Proliferation, Pharmacology, 0303 health sciences, Hippo signaling pathway, Dose-Response Relationship, Drug, Molecular Structure, Chemistry, Cell growth, Organic Chemistry, HEK 293 cells, TEA Domain Transcription Factors, General Medicine, Interface 2, 3. Good health, Cell biology, HEK293 Cells, 030220 oncology & carcinogenesis, Transcriptional Coactivator with PDZ-Binding Motif Proteins, Phosphorylation, Pyrazoles, Nuclear transport, Cellular model, Drug Screening Assays, Antitumor, Transcription Factors
Abstract: International audience; The Hippo pathway is involved in organ size control and tissue homeostasis by regulating cell growth, proliferation and apoptosis. It controls the phosphorylation of the transcription co-activator YAP (Yes associated protein) and TAZ (Transcriptional coactivator with PDZ-binding motif) in order to control their nuclear import and their interaction with TEAD (Transcriptional Enhanced Associated Domain). YAP, TAZ and TEADs are dysregulated in several cancers making YAP/TAZ-TEAD interaction a new emerging anti-cancer target. We report the synthesis of a set of trisubstituted pyrazoles which bind to hTEAD2 at the interface 2 revealing for the first time a cryptic pocket created by the movement of the phenol ring of Y382. Compound 6 disrupts YAP/TAZ-TEAD interaction in HEK293T cells and inhibits TEAD target genes and cell proliferation in MDA-MB-231 cells. Compound 6 is therefore the first inhibitor of YAP/TAZ-TEAD targeting interface 2. This molecule could serve with other pan-TEAD inhibitors such as interface 3 ligands, for the delineation of the relative importance of VGLL vs YAP/TAZ in a given cellular model.
Published: 2021
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21. Structure and assembly of nuclear pore complexes by correlative AFM and super-resolution microscopy

Author: Vial, Anthony, Centre de Biochimie Structurale [Montpellier] (CBS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Université Montpellier, Pierre-Emmanuel Milhiet, and STAR, ABES
Subjects: Nuclear pore complex, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, [SDV.SA] Life Sciences [q-bio]/Agricultural sciences, Pore nucléaire, Microscopie de super-Résolution, Membrane curvature, Super-Resolution microscopy, Afm, Courbure membranaire
Abstract: A characteristic feature of eukaryotic cells is the physical isolation of the genetic material by the nuclear envelope (NE), a double lipid bilayer composed of an inner and outer nuclear membrane separated by a lumen. Across this barrier are the nuclear pore complexes (NPCs), the only gateways between the nucleus and cytoplasm. They are made of multiple copies of around 30 proteins called nucleoporins. During interphase, proliferating cells have to duplicate their genetic material, organelles, membranes and enzymatic tools, to split them between daughter cells. While DNA replication is widely studied, duplication of other materials is largely unexplored. In most cases, this is just a matter of protein and lipid synthesis, yet NPC replication is a complex process involving macromolecular assembly combined with membrane remodelling. Moreover, the nuclear permeability barrier must remain intact during the whole process, underlining that protein assembly and membrane fusion must be tightly coordinated. Interphase pore assembly occurs by de novo insertion of new pore units in the NE, which requires the local fusion of the inner and outer nuclear membranes. The fusion process must involve the close apposition of the two membranes, generating locally a complex combination of positive and negative curvature in the bilayers.A recent study showed that interphase assembly of the NPC is a directional process that initiates at the inner nuclear membrane. That a highly symmetrical protein complex assembles in an asymmetric manner is extremely intriguing. We wanted to elucidate the precise evolution of the protein structure and membrane topography during this process. In this context, the goal of my thesis was to investigate the detailed sequence of events of NPC assembly at the molecular and topographic level. Atomic Force Microscopy (AFM) is a technique of choice for this, as it produces high-resolution topographies from single nano-objects. Moreover, correlative Single Molecule Localization Microscopy (SMLM) can add compositional information, with a similar resolution. As AFM is a contact technique, I first had to develop a protocol to purify and open human cell nuclei in a manner that does not affect the structure of NPCs and surrounding NE. Then I measured for the first time the topography and mechanical properties of human NPC nucleoplasmic side, together with SMLM images of the main basket component Tpr. My results demonstrate a large range of flexibility in the conformations of this structure which questioned the usually admitted protruding structure of the basket.Then, I used differential immuno-labelling to discriminate mature NPCs from intermediates, and record their topography. In addition, SMLM on POM121, an early player in interphase assembly, revealed that this transmembrane nucleoporin acts as a seeding point in early intermediates. POM121 concentration then increases at this seeding point and grows, to finally be segregated towards a ring structure in NPC interphase intermediates.Finally, using quantitative measurements of NPC structure based on Stimulated Emission Depletion Microscopy combined with small-interferent RNA treatments against a set of nucleoporins, I have been able to characterize the contribution of several nucleoporins to the kinetics of assembly and structure of NPC interphase intermediates.Taken together, these results demonstrated how AFM can be used as a nanotool to investigate the inner nuclear membrane of human cells and especially NPCs. They also reveal the high variability of NPC basket structure and bring new information to understand the complex process of NPC interphase assembly., Les pores nucléaires (NPC) sont les seules passerelles entre le noyau et le cytoplasme. Ils sont constitués de plusieurs copies d'une trentaine de protéines appelées nucléoporines. Pendant l'interphase, les cellules en prolifération doivent dupliquer leur matériel génétique, organelles, membranes et outils enzymatiques, pour les répartir entre les cellules filles. Dans la plupart des cas, il s'agit simplement d'une question de synthèse de protéines et de lipides, or la réplication du NPC est un processus complexe impliquant un assemblage macromoléculaire combiné à un remodelage membranaire. De plus, la barrière de perméabilité nucléaire doit rester intacte pendant tout le processus, ce qui souligne que l'assemblage des protéines et la fusion des membranes doivent être étroitement coordonnés. L'assemblage des pores en interphase se produit par l'insertion de novo de nouveaux pores dans l’EN, ce qui nécessite la fusion locale des membranes nucléaires interne et externe. Le processus de fusion doit impliquer l'apposition étroite des deux membranes, générant localement une combinaison complexe de courbures positive et négative dans les bicouches.Une étude récente a montré que l'assemblage du NPC en interphase est un processus directionnel qui commence au niveau de la membrane nucléaire interne. Le fait qu'un complexe protéique hautement symétrique s'assemble de manière asymétrique est extrêmement intriguant. Nous avons voulu comprendre l'évolution précise de la structure protéique et de la topographie de la membrane au cours de ce processus. Dans ce contexte, le but de ma thèse était d'étudier la séquence détaillée des événements d’assemblage du NPC au niveau moléculaire et topographique. La microscopie à force atomique (AFM) est une technique de choix pour cela, car elle produit des images topographiques à haute résolution d’objets nanoscopiques. De plus, la corrélation avec la microscopie de localisation de molécules uniques (SMLM) peut ajouter des informations sur la composition, avec une résolution similaire. L'AFM étant une technique nécessitant d’entrer en contact avec l’échantillon, j'ai d'abord dû mettre au point un protocole pour purifier et ouvrir les noyaux de cellules humaines d'une manière qui n'affecte pas la structure des NPCs et de l’EN autour. Ensuite, j'ai mesuré pour la première fois la topographie et les propriétés mécaniques de la face nucléoplasmique de NPCs humains, ainsi que des images SMLM du composant principal du panier, Tpr. Mes résultats démontrent une large gamme de flexibilité dans les conformations de cette structure, ce qui remet en question la structure protubérante du panier habituellement admise.Ensuite, j'ai utilisé l'immunomarquage différentiel pour discriminer les NPCs matures des intermédiaires, et enregistrer leur topographie. De plus, le SMLM sur POM121, un acteur précoce de l'assemblage en interphase, a révélé que cette nucléoporine transmembranaire agit comme un point d'ancrage dans les intermédiaires précoces. La concentration de POM121 augmente ensuite à ce point d'ancrage et croît, pour finalement être ségrégée vers une structure en anneau dans les intermédiaires de l'interphase du NPC.Enfin, en utilisant des mesures quantitatives de la structure des NPC basées sur la microscopie à déplétion par émission stimulée, combinées à des traitements par ARN interférent contre un ensemble de nucléoporines, j'ai pu caractériser la contribution de plusieurs nucléoporines à la cinétique d'assemblage et à la structure en interphase des intermédiaires de NPCs.Pris ensemble, ces résultats ont démontré comment l'AFM peut être utilisé comme un nano-outil pour étudier la membrane nucléaire interne des cellules humaines et en particulier des NPCs. Ils révèlent également la grande variabilité de la structure du panier des NPC et apportent de nouvelles informations pour comprendre l'assemblage en l'interphase des NPC.
Published: 2021

22. Study of Polycomb target genes architecture in Drosophila using multiplexed optical microscopy

Author: Gurgo, Julián Roberto, Centre de Biochimie Structurale [Montpellier] (CBS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Université Montpellier, Marcelo Nollmann, Frédéric Bantignies, and STAR, ABES
Subjects: Polycomb group proteins, Régulation génique, Multiplexed FISH, Protéines du groupe Polycomb, Chromatin 3D organization, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Organisation 3D de la chromatine, [SDV.BBM.BM] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Gene regulation
Abstract: Chromatin organization is related to many biological processes. Chromosome confor-mation capture techniques revealed that chromatin is organized in domains enriched inchromatin interactions, called Topologically Associating Domains (TADs). In Drosophila,TADs coincide with active and repressed chromatin marks, and are classified according totheir epigenetic states. One of these TAD types, known as Polycomb TADs, are bound byPolycomb group proteins (PcG proteins), a family of factors conserved in most eukaryoticorganisms, and crucial for the regulation of gene repression. Evidence from microscopyand chromosome conformation capture techniques shows that PcG targets tend to pref-erentially interact with each other, suggesting that they form repressive compartments.However, little is known about the nature of these interactions, or if several PcG genesare associated in 3D to form compartments.In this work, we investigate the role of Polycomb group proteins in the formationof repressive compartments during Drosophila development by applying Hi-M, a novelimaging-based method that enables the reconstruction of chromatin conformation whilepreserving spatial information. We first extended Hi-M to enable imaging of thick,multi-layered samples by combining a fluidics handling robot to a confocal microscopeand adapting existing analysis pipelines. Next, we applied this method to the studythe chromosome-wide organization of Polycomb target genes in different segments of adeveloping Drosophila embryo. We show that spatial co-localization of distant intra-chromosomal Polycomb targets is infrequent, and that these interactions are predom-inantly pairwise. We also observe that long-range interactions are acquired after theemergence of TADs at NC14, concomitantly with the enrichment of PcG foci. These re-sults were supported by polymer modelling showing that a microphase-separated polymerin the globule regime captures the experimental behaviour of Polycomb domains. Ourexperiments and simulations suggest that Polycomb repressive compartments form byinfrequent pairwise associations of Polycomb domains. Finally, we show that interactionfrequencies between Polycomb targets are modulated by both transcriptional repressionand activation. Overall our results shed light into the chromosome-wide organization ofPc target genes, and constrain future models for the formation of Pc compartments., L’organisation de la chromatine est liée à de nombreux processus biologiques. Les techniques de capture de conformation des chromosomes ont révélé que la chromatine est organisée en domaines enrichis en interactions chromatiniennes, appelés Topologi-cally Associating Domains (TADs). Chez la drosophile, les TADs coïncident avec les marques chromatiniennes actives et réprimées, et sont classés en fonction de leurs états épigénétiques. L’un de ces types de TAD, connu sous le nom de TADs Polycomb, est lié aux protéines du groupe Polycomb (protéines PcG), une famille de facteurs conservés dans la plupart des organismes eucaryotes, et cruciaux pour la régulation de la répression des gènes. Des preuves issues de la microscopie et des techniques de capture de la conformation des chromosomes montrent que les cibles PcG ont tendance à interagir préférentiellement les unes avec les autres, ce qui suggère qu’elles forment des compartiments de répression. Cependant, on sait peu de choses sur la nature de ces interactions, ou si plusieurs gènes PcG sont associés en 3D pour former des compartiments. Dans ce travail, nous étudions le rôle des protéines du groupe Polycomb dans la formation de compartiments répressifs au cours du développement de la drosophile en appliquant Hi-M, une nouvelle méthode basée sur l’imagerie qui permet la reconstruction de la conformation de la chromatine tout en préservant l’information spatiale. Nous avons d’abord étendu Hi-M pour permettre l’imagerie d’échantillons épais et multicouches en combinant un robot de manipulation fluidique à un microscope confocal et en adaptant les pipelines d’analyse existants. Ensuite, nous avons appliqué cette méthode pour étudie rl’organisation chromosomique des gènes cibles de Polycomb dans différents segments d’une mbryon de drosophile en développement. Nous montrons que la co-localisation spatiale de cibles Polycomb intra-chromosomiques distantes est peu fréquente, et que ces inter-actions sont principalement par paires. Nous observons également que les interactions à longue portée sont acquises après l’émergence des TADs à NC14, de façon concomitante avec l’enrichissement des foyers de PcG. Ces résultats ont été soutenus par la modélisation du polymère montrant qu’un polymère séparé en microphase dans le régime des globules capture le comportement expérimental des domaines Polycomb. Nos expériences et simulations suggèrent que les compartiments répressifs Polycomb se forment par des associations par paires peu fréquentes de domaines Polycomb. Enfin, nous montrons que les fréquences d’interaction entre les cibles Polycomb sont modulées à la fois par la répression et l’activation transcriptionnelle. Dans l’ensemble, nos résultats éclairent l’organisation des gènes cibles de Pc à l’échelle du chromosome, et contraignent les futurs modèles de formation des compartiments de Pc.
Published: 2021

23. Structures of the archaerhodopsin-3 transporter reveal that disordering of internal water networks underpins receptor sensitization

Author: Carol V. Robinson, Hsin-Yung Yen, Juan F. Bada Juarez, Kin Kuan Hoi, Igor Schapiro, Danny Axford, Anthony Vial, Anthony Watts, Isabel Moraes, Suliman Adam, James M. Birch, J. Vinals, Tristan O. C. Kwan, Pierre-Emmanuel Milhiet, Peter J. Judge, Department of Biochemistry [Oxford], University of Oxford [Oxford], The Fritz Haber Research Center for Molecular Dynamics [Jerusalem], The Hebrew University of Jerusalem (HUJ), DIAMOND Light source, Diamond Light Source Limited [Didcot, UK], Harwell Science and Innovation Campus [Didcot, UK], Rutherford Appleton Laboratory, Research Complex at Harwell, Chemistry Research Laboratory [Oxford, UK], Omas therapeutics, Centre de Biochimie Structurale [Montpellier] (CBS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), University of Oxford, Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), and Milhiet, Pierre-Emmanuel
Subjects: 0301 basic medicine, [SDV.BBM.BS] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Science, Archaeal Proteins, Molecular Conformation, General Physics and Astronomy, Electrons, Optogenetics, Crystallography, X-Ray, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, chemistry.chemical_compound, Computational biophysics, Membrane biophysics, 0302 clinical medicine, Isomerism, Membrane proteins, Receptor, X-ray crystallography, Membrane potential, Multidisciplinary, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Membrane Transport Proteins, Water, Retinal, Hydrogen Bonding, General Chemistry, Chromophore, Lipids, 030104 developmental biology, chemistry, Biophysics, Retinaldehyde, Bacterial rhodopsins, sense organs, Protons, Ground state, Isomerization, Protein Processing, Post-Translational, 030217 neurology & neurosurgery
Abstract: Many transmembrane receptors have a desensitized state, in which they are unable to respond to external stimuli. The family of microbial rhodopsin proteins includes one such group of receptors, whose inactive or dark-adapted (DA) state is established in the prolonged absence of light. Here, we present high-resolution crystal structures of the ground (light-adapted) and DA states of Archaerhodopsin-3 (AR3), solved to 1.1 Å and 1.3 Å resolution respectively. We observe significant differences between the two states in the dynamics of water molecules that are coupled via H-bonds to the retinal Schiff Base. Supporting QM/MM calculations reveal how the DA state permits a thermodynamic equilibrium between retinal isomers to be established, and how this same change is prevented in the ground state in the absence of light. We suggest that the different arrangement of internal water networks in AR3 is responsible for the faster photocycle kinetics compared to homologs., Archaerhodopsin-3 (AR3) mutants are commonly used in optogenetics for neuron silencing and membrane voltage sensing. High-resolution crystal structures show that desensitization of the AR3 photoreceptor occurs when internal hydrogen-bonded water networks are modified in response to changes in chromophore isomerization.
Published: 2021
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24. Δ133p53β isoform pro-invasive activity is regulated through an aggregation-dependent mechanism in cancer cells

Author: Gilles Gadea, Frédéric Allemand, Nikola Arsic, Sylvain de Rossi, Pierre Roux, Marina Kazantseva, Sunali Mehta, Serge Urbach, Andrey V. Kajava, Martial Séveno, Antony W. Braithwaite, Aurélie Fournet, Nathalie Sibille, Etienne Villain, Pau Bernadó, Jean-Christophe Bourdon, Tania L. Slatter, Centre de recherche en Biologie Cellulaire (CRBM), Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), University of Otago [Dunedin, Nouvelle-Zélande], Université de La Réunion (UR), Cyclotron Réunion Océan Indien (CYROI), Université de La Réunion (UR)-Centre Hospitalier Universitaire de La Réunion (CHU La Réunion), Centre de Biochimie Structurale [Montpellier] (CBS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), BioCampus Montpellier (BCM), Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut de Génomique Fonctionnelle (IGF), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Ninewells Hospital and Medical School [Dundee], Institut de Biologie Computationnelle (IBC), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre de recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), BioCampus (BCM), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM), and Prigent, Claude
Subjects: Gene isoform, Models, Molecular, Cell biology, Protein Conformation, Science, General Physics and Astronomy, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Protein Aggregation, Pathological, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, Mice, Protein Aggregates, 0302 clinical medicine, Cell Line, Tumor, Neoplasms, medicine, Animals, Humans, Protein Isoforms, Neoplasm Invasiveness, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, 030304 developmental biology, Protein Unfolding, Cancer, Cell invasion, 0303 health sciences, Multidisciplinary, Chemistry, Mechanism (biology), General Chemistry, medicine.disease, Gene Expression Regulation, Neoplastic, 030220 oncology & carcinogenesis, Cancer cell, Mutation, MCF-7 Cells, Chaperone complex, sense organs, Tumor Suppressor Protein p53, Intracellular
Abstract: The p53 isoform, Δ133p53β, is critical in promoting cancer. Here we report that Δ133p53β activity is regulated through an aggregation-dependent mechanism. Δ133p53β aggregates were observed in cancer cells and tumour biopsies. The Δ133p53β aggregation depends on association with interacting partners including p63 family members or the CCT chaperone complex. Depletion of the CCT complex promotes accumulation of Δ133p53β aggregates and loss of Δ133p53β dependent cancer cell invasion. In contrast, association with p63 family members recruits Δ133p53β from aggregates increasing its intracellular mobility. Our study reveals novel mechanisms of cancer progression for p53 isoforms which are regulated through sequestration in aggregates and recruitment upon association with specific partners like p63 isoforms or CCT chaperone complex, that critically influence cancer cell features like EMT, migration and invasion., p53 isoform Δ133p53β is reported to promote intrinsic oncogenic functions. Here the authors show Δ133p53β is sequestered as aggregates in an inactive form, while association with interacting partners including p63 isoforms and the CCT chaperone complex promotes Δ133p53β activity, resulting in enhanced cancer cell migration and invasion.
Published: 2021
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25. Stress response in dissociation and conversion disorders: A systematic review

Author: Philippe Courtet, Jorge Lopez-Castroman, Stéphane Mouchabac, Mocrane Abbar, Eric Thouvenot, Emilie Olié, Charlotte Boulet, Ismael Conejero, Centre Hospitalier Universitaire de Nîmes (CHU Nîmes), Institut de Génomique Fonctionnelle (IGF), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Service de Psychiatrie adultes [CHU Saint-Antoine], CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Institut du Cerveau et de la Moëlle Epinière = Brain and Spine Institute (ICM), Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Centre de Biochimie Structurale [Montpellier] (CBS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service de psychiatrie adulte [CHU Saint-Antoine], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), and Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Hypothalamo-Hypophyseal System, medicine.drug_class, Cognitive Neuroscience, [SDV]Life Sciences [q-bio], MEDLINE, Pituitary-Adrenal System, Dissociative Disorders, Autonomic Nervous System, Dissociative, Dissociation (psychology), Cortisol, Stress Disorders, Post-Traumatic, 03 medical and health sciences, Behavioral Neuroscience, 0302 clinical medicine, Psychiatric history, medicine, Humans, Dissociative disorders, Conversion disorder, Stress regulation, Autonomous nervous system, business.industry, HPA axis, medicine.disease, 030227 psychiatry, 3. Good health, Dissociative disorder, Autonomic nervous system, Neuropsychology and Physiological Psychology, Systematic review, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], medicine.symptom, business, 030217 neurology & neurosurgery, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Clinical psychology
Abstract: International audience; Dissociative disorders (DD) and conversion disorders (CD) are frequent in general and psychiatric populations. Some evidence suggest that the hypothalamic-pituitary axis (HPA) and autonomic nervous system (ANS) are dysregulated in both disorders. We carried out a systematic review of the literature to summarize the existing knowledge on the stress response, via HPA and/or ANS, in patients with DD, CD, or dissociative symptoms. We systematically searched Medline and Web of Science using the Medical Subject Headings related to stress axis, CD, DD, and dissociative symptoms following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Results suggest that in participants without psychiatric history, high cortisol secretion is related to high dissociation scores. Conversely the stress system might be blunted in patients with post-traumatic stress disorder who develop dissociative symptoms. Stress response changes seem to be associated with the emergence and persistence of dissociative and conversion disorders. Hence, monitoring the stress response and examining closely the history of stress exposure in DD and CD should be encouraged in future larger studies.
Published: 2021
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26. A Mycobacterium tuberculosis effector targets mitochondrion, controls energy metabolism and limits cytochrome c exit

Author: Marianne Martin, Angelique deVisch, Yves-Marie Boudehen, Philippe Barthe, Claude Gutierrez, Obolbek Turapov, Talip Aydogan, Laurène Heriaud, Jerome Gracy, Olivier Neyrolles, Galina V. Mukamolova, François Letourneur, Martin Cohen-Gonsaud, LPHI - Laboratory of Pathogen Host Interactions (LPHI), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Centre de Biochimie Structurale [Montpellier] (CBS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), University of Leicester, MARTIN LAVERRAT, Marianne, and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Microbiology (medical), 0303 health sciences, biology, General Immunology and Microbiology, Ecology, 030306 microbiology, Effector, Mitochondrial intermembrane space, Physiology, Cytochrome c, [SDV]Life Sciences [q-bio], Oxidative phosphorylation, Cell Biology, Mitochondrion, 3. Good health, Cell biology, [SDV] Life Sciences [q-bio], 03 medical and health sciences, Immune system, Infectious Diseases, Apoptosis, biology.protein, Genetics, Reprogramming, 030304 developmental biology
Abstract: Host metabolism reprogramming is a key feature of Mycobacterium tuberculosis (Mtb) infection that enables the survival of this pathogen within phagocytic cells and modulates the immune response facilitating the spread of the tuberculosis disease. Here, we demonstrate that a previously uncharacterized secreted protein from Mtb, Rv1813c manipulates the host metabolism by targeting mitochondria. When expressed in eukaryotic cells, the protein is delivered to the mitochondrial intermembrane space and promotes the enhancement of host ATP production by boosting the oxidative phosphorylation metabolic pathway. Furthermore, the release of cytochrome c from mitochondria, an early apoptotic event in response to short-term oxidative stress, is delayed in Rv1813c expressing cells. This study reveals a novel class of mitochondria targeting effectors from Mtb which might participate in host cells metabolic reprogramming and apoptosis control during Mtb infections.
Published: 2021

27. A nanobody activating metabotropic glutamate receptor 4 discriminates between homo- and heterodimers

Author: Joan Font, Robert B. Quast, Patrick Chames, Jordi Haubrich, Anne Goupil-Lamy, Damien Nevoltris, Jean-Philippe Pin, Pauline Scholler, Philippe Rondard, Francine Acher, Laurent Prézeau, Institut de Génomique Fonctionnelle (IGF), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Centre de Biochimie Structurale [Montpellier] (CBS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Dassault Systèmes, Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC), Université de Paris (UP), ANR-18-CE11-0004,DynaMuR2,Dynamique structurale d'un RCPG dimérique en molécule unique(2018), ANR-10-LABX-0053,MAbImprove,Optimization of therapeutic monoclonal antibodies development Better antibodies, better developed AND better used(2010), ANR-15-CE18-0020,nanoGluAct,Modulation de la synapse glutamatergique à l'aide de nanobodies(2015), ANR-10-INBS-0004,France-BioImaging,Développment d'une infrastructure française distribuée coordonnée(2010), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU), Université Paris Cité - UFR Sciences du Vivant [Sciences] (UPCité - UFR SDV), Université Paris Cité (UPCité), Centre de Recherche en Cancérologie de Marseille (CRCM), Aix Marseille Université (AMU)-Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Guerineau, Nathalie C., Laboratoires d'excellence - Optimization of therapeutic monoclonal antibodies development Better antibodies, better developed AND better used - - MAbImprove2010 - ANR-10-LABX-0053 - LABX - VALID, Modulation de la synapse glutamatergique à l'aide de nanobodies - - nanoGluAct2015 - ANR-15-CE18-0020 - AAPG2015 - VALID, Développment d'une infrastructure française distribuée coordonnée - - France-BioImaging2010 - ANR-10-INBS-0004 - INBS - VALID, APPEL À PROJETS GÉNÉRIQUE 2018 - Dynamique structurale d'un RCPG dimérique en molécule unique - - DynaMuR22018 - ANR-18-CE11-0004 - AAPG2018 - VALID, Université de Paris - UFR Sciences du Vivant [Sciences] (UP - UFR SDV), and UFR Sciences du Vivant [Sciences] - Université Paris Cité (UFR SDV UPCité)
Subjects: Allosteric modulator, Protein Conformation, [SDV]Life Sciences [q-bio], Allosteric regulation, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Receptors, Metabotropic Glutamate, Models, Biological, 03 medical and health sciences, 0302 clinical medicine, Humans, Receptor, agonist, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, single-domain antibody, 030304 developmental biology, G protein-coupled receptor, 0303 health sciences, Multidisciplinary, Chemistry, Metabotropic glutamate receptor 4, Glutamate receptor, Glutamate binding, Single-Domain Antibodies, Biological Sciences, activation mechanism, 3. Good health, Cell biology, [SDV] Life Sciences [q-bio], Metabotropic receptor, Gene Expression Regulation, G protein–coupled receptor, Mutation, 030217 neurology & neurosurgery, Protein Binding
Abstract: International audience; There is growing interest in developing biologics due to their high target selectivity. The G protein-coupled homo- and heterodimeric metabotropic glutamate (mGlu) receptors regulate many synapses and are promising targets for the treatment of numerous brain diseases. Although subtype-selective allosteric small molecules have been reported, their effects on the recently discovered heterodimeric receptors are often not known. Here, we describe a nanobody that specifically and fully activates homodimeric human mGlu4 receptors. Molecular modeling and mutagenesis studies revealed that the nanobody acts by stabilizing the closed active state of the glutamate binding domain by interacting with both lobes. In contrast, this nanobody does not activate the heterodimeric mGlu2-4 but acts as a pure positive allosteric modulator. These data further reveal how an antibody can fully activate a class C receptor and bring further evidence that nanobodies represent an alternative way to specifically control mGlu receptor subtypes.
Published: 2021
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28. Agonists and allosteric modulators promote signaling from different metabotropic glutamate receptor 5 conformations

Author: François Hoh, Julie Kniazeff, Juan Lorenzo Catena, Cyril Goudet, Jean-Philippe Pin, Xavier Gómez-Santacana, Anaëlle Dumazer, Jean-Louis Banères, Ludovic Berto, Fanny Malhaire, Amadeu Llebaria, Robert B. Quast, Alice E. Berizzi, Giuseppe Cannone, Kutti R. Vinothkumar, Chia-Ying Huang, Chady Nasrallah, Guillaume Lebon, Julie Briot, Joan Font-Ingles, Karine Rottier, Institut de Génomique Fonctionnelle (IGF), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), MRC Laboratory of Molecular Biology [Cambridge, UK] (LMB), University of Cambridge [UK] (CAM)-Medical Research Council, Paul Scherrer Institute (PSI), Centre de Biochimie Structurale [Montpellier] (CBS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut des Biomolécules Max Mousseron [Pôle Chimie Balard] (IBMM), Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Institut de Chimie du CNRS (INC)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Laboratory of Medicinal Chemistry, Institute for Advanced Chemistry of Catalonia (MCS (IQAC-CSIC)), Tata Institute for Fundamental Research (TIFR), Ministerio de Ciencia e Innovación (España), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Guerineau, Nathalie C., MRC, Lab Mol Biol, Cambridge, England, Partenaires INRAE, The Swiss Light Source (SLS) (SLS-PSI), Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut de Química Avançada de Catalunya (IQAC), Consejo Superior de Investigaciones Científicas [Spain] (CSIC), and National Centre for Biological Sciences [TIFR] (NCBS)
Subjects: Models, Molecular, Allosteric modulators, [SDV]Life Sciences [q-bio], G-protein-coupled receptors, Signal transduction, Crystallography, X-Ray, photochromic ligands, Excitatory Amino Acid Agonists, Receptor, Cryo-EM, 0303 health sciences, Metabotropic glutamate receptor 5, Chemistry, Protein Stability, 030302 biochemistry & molecular biology, metabotropic glutamate receptor 5, Glutamate receptor, 3. Good health, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, [SDV] Life Sciences [q-bio], allosteric modulators, Glutamate, signal transduction, Protein Binding, Agonist, animal structures, medicine.drug_class, Receptor, Metabotropic Glutamate 5, Allosteric regulation, glutamate, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, Structure-Activity Relationship, medicine, [CHIM.CRIS]Chemical Sciences/Cristallography, Humans, Protein Interaction Domains and Motifs, [CHIM.CRIS] Chemical Sciences/Cristallography, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, 030304 developmental biology, G protein-coupled receptor, X-ray crystallography, Cryoelectron Microscopy, Protein Subunits, HEK293 Cells, Metabotropic glutamate receptor, Photochromic ligands, Biophysics, cryo-EM, Excitatory Amino Acid Antagonists
Abstract: Summary Metabotropic glutamate receptors (mGluRs) are dimeric G-protein-coupled receptors activated by the main excitatory neurotransmitter, L-glutamate. mGluR activation by agonists binding in the venus flytrap domain is regulated by positive (PAM) or negative (NAM) allosteric modulators binding to the 7-transmembrane domain (7TM). We report the cryo-electron microscopy structures of fully inactive and intermediate-active conformations of mGlu5 receptor bound to an antagonist and a NAM or an agonist and a PAM, respectively, as well as the crystal structure of the 7TM bound to a photoswitchable NAM. The agonist induces a large movement between the subunits, bringing the 7TMs together and stabilizing a 7TM conformation structurally similar to the inactive state. Using functional approaches, we demonstrate that the PAM stabilizes a 7TM active conformation independent of the conformational changes induced by agonists, representing an alternative mode of mGlu activation. These findings provide a structural basis for different mGluR activation modes., Graphical abstract, Highlights • Cryo-EM analysis of thermostabilized mGlu5 receptor bound to inhibitors or activators • X-ray structure of trans-Alloswitch-1 bound to thermostable mGlu5 7TMs • Photopharmacology provides insight into allosteric regulation of mGlu5 7TMs • Multiple conformations of mGlu5 receptor activate G protein, Nasrallah et al. present cryo-EM structures of thermostabilized mGlu5 dimer bound to inhibitors and activators as well as an X-ray structure of mGlu5 7TM-bound photoswitchable ligand alloswitch-1. The structural and functional analyses reveal different modes of mGLu5 receptor activation and provide a structural basis for mGlu receptor activation mechanism.
Published: 2021
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29. Ligands and DNA in the allosteric control of retinoid receptors function

Author: Natacha Rochel, William Bourguet, Pierre Germain, Centre de Biochimie Structurale [Montpellier] (CBS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Rochel, Natacha
Subjects: retinoids, Receptors, Retinoic Acid, medicine.drug_class, [SDV]Life Sciences [q-bio], Allosteric regulation, Retinoic acid, retinoic acid receptor, Retinoid X receptor, Ligands, Biochemistry, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, medicine, Animals, Retinoid, Receptor, Molecular Biology, Transcription factor, 030304 developmental biology, 0303 health sciences, Promoter, DNA, allosteric regulation, Cell biology, [SDV] Life Sciences [q-bio], Retinoic acid receptor, Retinoid X Receptors, chemistry, transcription, 030217 neurology & neurosurgery
Abstract: Retinoids are a family of compounds that include both vitamin A (all-trans retinol) and its naturally occurring metabolites such as retinoic acids (e.g. all-trans retinoic acid) as well as synthetic analogs. They are critically involved in the regulation of a wide variety of essential biological processes, such as embryogenesis and organogenesis, apoptosis, reproduction, vision, and the growth and differentiation of normal and neoplastic cells in vertebrates. The ability of these small molecules to control the expression of several hundred genes through binding to nuclear ligand-dependent transcription factors accounts for most of their functions. Three retinoic acid receptor (RARα,β,γ) and three retinoid X receptor (RXRα,β,γ) subtypes form a variety of RXR–RAR heterodimers that have been shown to mediate the pleiotropic effects of retinoids through the recruitment of high-molecular weight co-regulatory complexes to response-element DNA sequences found in the promoter region of their target genes. Hence, heterodimeric retinoid receptors are multidomain entities that respond to various incoming signals, such as ligand and DNA binding, by allosteric structural alterations which are the basis of further signal propagation. Here, we provide an overview of the current state of knowledge with regard to the structural mechanisms by which retinoids and DNA response elements act as allosteric effectors that may combine to finely tune RXR–RAR heterodimers activity.
Published: 2021
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30. The impact of space and time on the functional output of the nucleus

Author: Nollmann, Marcelo, Bennabi, Isma, Götz, Markus, Gregor, Thomas, Centre de Biochimie Structurale [Montpellier] (CBS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Physique des fonctions biologiques / Physics of Biological Functions, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Department of Physics, Princeton University (DPPU), Princeton University, Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Nollmann, Marcelo, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Ana Pombo, Martin Hetzer, Tom Misteli, and Gregor, Thomas
Subjects: [SDV] Life Sciences [q-bio], [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV]Life Sciences [q-bio], [SDV.BDD] Life Sciences [q-bio]/Development Biology, [SDV.BC.BC] Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.BDD]Life Sciences [q-bio]/Development Biology, [SDV.BBM.BC] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM]
Abstract: Article également paru le 6 juillet 2021 dans Cold Spring Harbor Perspectives in Biology, DOI 10.1101/cshperspect.a040378; International audience; Over the past two decades, it has become clear that the multi-scale spatial and temporal organization of the genome has important implications for nuclear function. This chapter centers on insights gained from recent advances in light microscopy on our understanding of transcription. Particular focus is given to the genomic scales where most functional interactions occur, namely kb-Mb. We discuss the relevant spatial and temporal scales that shape nuclear order and their consequences on regulatory components and function. The emerging picture is that spatiotemporal constraints increase the complexity in transcriptional regulation. This brings new challenges to the fore, such as uncertainty about how information travels from factors through the genome and space to generate a functional output.
Published: 2021
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31. A Novel Approach to the Facile Growth and Organization of Photothermal Prussian Blue Nanocrystals on Different Surfaces

Author: Yannick Guari, Luca Costa, Christophe Dorandeu, Gautier Félix, Pierre-Emmanuel Milhiet, Jean-Marie Devoisselle, Giang Ngo, Joël Chopineau, Joulia Larionova, Institut Charles Gerhardt Montpellier - Institut de Chimie Moléculaire et des Matériaux de Montpellier (ICGM ICMMM), Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut de Chimie du CNRS (INC), Centre de Biochimie Structurale [Montpellier] (CBS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Félix, Gautier, Institut Charles Gerhardt Montpellier - Institut de Chimie Moléculaire et des Matériaux de Montpellier (ICGM), Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Institut de Chimie du CNRS (INC)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Materials science, Nanostructure, General Chemical Engineering, supported lipid bilayers, Nanoparticle, 02 engineering and technology, 010402 general chemistry, 01 natural sciences, Article, chemistry.chemical_compound, surface growth, Homogeneity (physics), nanostructures, General Materials Science, Laser power scaling, Lipid bilayer, QD1-999, Prussian blue, [CHIM.MATE] Chemical Sciences/Material chemistry, atomic force microscopy, [CHIM.MATE]Chemical Sciences/Material chemistry, gold surface, Photothermal therapy, 021001 nanoscience & nanotechnology, 0104 chemical sciences, Chemistry, Chemical engineering, chemistry, Nanocrystal, films, 0210 nano-technology
Abstract: We report here a novel “one-pot” approach for the controlled growth and organization of Prussian blue nanostructures on three different surfaces: pure Au0, cysteamine-functionalized Au0, and SiO2-supported lipid bilayers with different natures of lipids. We demonstrate that fine control over the size, morphology, and the degree and homogeneity of the surface coverage by Prussian Blue (PB) nanostructures may be achieved by manipulating different parameters, which are the precursor concentration, the nature of the functional groups or the nature of lipids on the surfaces. This allows the growth of isolated PB nanopyramids and nanocubes or the design of thin dense films over centimeter square surfaces. The formation of unusual Prussian blue nanopyramids is discussed. Finally, we demonstrate, by using experimental techniques and theoretical modeling, that PB nanoparticles deposited on the gold surface exhibit strong photothermal properties, permitting a rapid temperature increase up to 90 °C with a conversion of the laser power of almost 50% for power source heat.
Published: 2021
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32. Arginine multivalency stabilizes protein/RNA condensates

Author: Matteo Paloni, Alessandro Barducci, Giovanni Bussi, Centre de Biochimie Structurale [Montpellier] (CBS), and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: Poly U, Arginine, Full‐Length Papers, Lysine, Stacking, RNA/protein interaction, 010402 general chemistry, Biochemistry, 01 natural sciences, Settore FIS/03 - Fisica della Materia, 03 medical and health sciences, Molecular dynamics, RNA-Protein Interaction, Polylysine, Molecular Biology, ComputingMilieux_MISCELLANEOUS, coacervates, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, Oligonucleotide, Chemistry, Hydrogen bond, Biomolecule, 030302 biochemistry & molecular biology, RNA, liquid-liquid phase separation, molecular dynamics simulations, 0104 chemical sciences, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Biophysics, Peptides
Abstract: Biomolecular condensates assembled through liquid-liquid phase separation (LLPS) of proteins and RNAs are currently recognized to play an important role in cellular organization. Their assembly depends on the formation of a network of transient, multivalent interactions between flexible scaffold biomolecules. Understanding how protein and RNA sequences determine these interactions and ultimately regulate the phase separation is an open key challenge. Recent in vitro studies have revealed that arginine and lysine residues, which are enriched in most cellular condensates, have markedly distinct propensities to drive the LLPS of protein/RNA mixtures. Here, we employ explicit-solvent atomistic Molecular Dynamics (MD) simulations to shed light on the microscopic origin of this difference by investigating mixtures of polyU oligonucleotides with either polyR/polyK peptides. In agreement with experiments, our simulations indicate that arginine has a higher affinity for polyU than lysine both in highly diluted conditions and in concentrated solutions with a biomolecular density comparable to cellular condensate. The analysis of intermolecular contacts suggests that this differential behavior is due to the propensity of arginine side chains to simultaneously form a higher number of specific interactions with oligonucleotides, including hydrogen bonds and stacking interactions. Our results provide a molecular description of how the multivalency of the guanidinium group enables the coordination of multiple RNA groups by a single arginine residue, thus ultimately stabilizing protein/RNA condensates.
Published: 2021
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33. Comparative Assessment of NMR Probes for the Experimental Description of Protein Folding Pathways with High-Pressure NMR

Author: Yinshan Yang, Vincent Van Deuren, Christian Roumestand, Catherine Anne Royer, Philippe Barthe, Cécile Dubois, Karine de Guillen, Centre de Biochimie Structurale [Montpellier] (CBS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Rensselaer Polytechnic Institute (RPI), ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010), BARTHE, Philippe, and Infrastructure Française pour la Biologie Structurale Intégrée - - FRISBI2010 - ANR-10-INBS-0005 - INBS - VALID
Subjects: Life Sciences & Biomedicine - Other Topics, DYNAMICS, 0301 basic medicine, [SDV.BBM.BS] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], STAPHYLOCOCCAL NUCLEASE, Stereochemistry, QH301-705.5, [SDV]Life Sciences [q-bio], Hydrostatic pressure, Sequence (biology), Biology, 010402 general chemistry, SEQUENCE, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, chemistry.chemical_compound, Amide, protein folding, Molecule, Biology (General), ENERGY LANDSCAPE, Science & Technology, SPECTROSCOPY, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], STABILITY, General Immunology and Microbiology, high hydrostatic pressure, NMR, 0104 chemical sciences, Folding (chemistry), 030104 developmental biology, STATES, chemistry, Yield (chemistry), thermodynamic stability, Chemical stability, Protein folding, General Agricultural and Biological Sciences, Life Sciences & Biomedicine
Abstract: Simple Summary During the last decade, high-pressure multidimensional NMR has emerged as a very powerful tool to describe the folding landscapes of proteins. This is (i) because pressure is a gentle perturbation, the effects of which originate from local properties of the folded state, contrary to chemical or thermal denaturation, and (ii) because multidimensional NMR intrinsically provides multiple probes strategically scattered on the three-dimensional structure of the protein, allowing a quasi-atomic resolution to describe the folding pathway. Residue-specific information obtained from these probes can be used to describe protein folding pathways through the calculation of NMR-derived fractional probabilities of contact at increasing pressure. Here, we used this strategy to evaluate and compare the results obtained from NH amide, CαHα, and CH3 groups when used as NMR probes to explore the folding pathway of the model protein ∆+PHS Staphylococcal Nuclease. Abstract Multidimensional NMR intrinsically provides multiple probes that can be used for deciphering the folding pathways of proteins: NH amide and CαHα groups are strategically located on the backbone of the protein, while CH3 groups, on the side-chain of methylated residues, are involved in important stabilizing interactions in the hydrophobic core. Combined with high hydrostatic pressure, these observables provide a powerful tool to explore the conformational landscapes of proteins. In the present study, we made a comparative assessment of the NH, CαHα, and CH3 groups for analyzing the unfolding pathway of ∆+PHS Staphylococcal Nuclease. These probes yield a similar description of the folding pathway, with virtually identical thermodynamic parameters for the unfolding reaction, despite some notable differences. Thus, if partial unfolding begins at identical pressure for these observables (especially in the case of backbone probes) and concerns similar regions of the molecule, the residues involved in contact losses are not necessarily the same. In addition, an unexpected slight shift toward higher pressure was observed in the sequence of the scenario of unfolding with CαHα when compared to amide groups.
Published: 2021
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34. Small-Molecule Inhibitors of Cyclophilins Block Opening of the Mitochondrial Permeability Transition Pore and Protect Mice From Hepatic Ischemia/Reperfusion Injury

Author: Muriel Gelin, Fred Allemand, Cong Trung Nguyen, Mathieu Panel, Abdelhakim Ahmed-Belkacem, Bijan Ghaleh, Rozenn Brillet, Isaac Ruiz, Julien Calderaro, Fouad Lafdil, Jean-François Guichou, Fatima Teixeira-Clerc, Didier Morin, Jean-Michel Pawlotsky, Institut Mondor de Recherche Biomédicale (IMRB), Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR10-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Centre de Biochimie Structurale [Montpellier] (CBS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), morin, didier, and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: Male, 0301 basic medicine, Isomerase activity, [SDV.MHEP.CHI] Life Sciences [q-bio]/Human health and pathology/Surgery, Ischemia, Mitochondria, Liver, [SDV.MHEP.CHI]Life Sciences [q-bio]/Human health and pathology/Surgery, Pharmacology, Mitochondrion, Mitochondrial Membrane Transport Proteins, Mouse model, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, medicine, Animals, Humans, Calcium Signaling, Enzyme Inhibitors, Inner mitochondrial membrane, Cells, Cultured, Mice, Knockout, Hepatology, Mitochondrial Permeability Transition Pore, Chemistry, Liver Diseases, MPTP, Gastroenterology, PPIF, [SDV.MHEP.HEG]Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, medicine.disease, [SDV.MHEP.HEG] Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, 3. Good health, PPIase activity, Mice, Inbred C57BL, Disease Models, Animal, 030104 developmental biology, Liver, Mitochondrial permeability transition pore, Cytoprotection, [SDV.SP.PHARMA] Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, Reperfusion Injury, [SDV.SP.PHARMA]Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, 030211 gastroenterology & hepatology, Drug, Mitochondrial Swelling, Reperfusion injury, Cyclophilin D, Signal Transduction
Abstract: International audience; Background & Aims: Hepatic ischemia-reperfusion injury is a complication of liver surgery that involves mitochondrial dysfunction resulting from mitochondrial permeability transition pore (mPTP) opening. Cyclophilin D (PPIF or CypD) is a peptidyl-prolyl cis-trans isomerase that regulates mPTP opening in the inner mitochondrial membrane. We investigated whether and how recently created small-molecule inhibitors of CypD prevent opening of the mPTP in hepatocytes and the resulting effects in cell models and livers of mice undergoing ischemia/reperfusion injuryMethods: We measured the activity of 9 small-molecule inhibitors of cyclophilins in an assay of CypD activity. The effects of the small-molecule CypD inhibitors or vehicle on mPTP opening were assessed by measuring mitochondrial swelling and calcium retention in isolated liver mitochondria from C57BL/6J (wild-type) and Ppif–/– (CypD knockout) mice and in primary mouse and human hepatocytes by fluorescence microscopy. We induced ischemia/reperfusion injury in livers of mice given a small-molecule CypD inhibitor or vehicle before and during reperfusion and collected samples of blood and liver for histologic analysis.Results: The compounds inhibited peptidyl-prolyl isomerase activity (half maximal inhibitory concentration values, 0.2–16.2 μmol/L) and, as a result, calcium-induced mitochondrial swelling, by preventing mPTP opening (half maximal inhibitory concentration values, 1.4–132 μmol/L) in a concentration-dependent manner. The most potent inhibitor (C31) bound CypD with high affinity and inhibited swelling in mitochondria from livers of wild-type and Ppif–/– mice (indicating an additional, CypD-independent effect on mPTP opening) and in primary human and mouse hepatocytes. Administration of C31 in mice with ischemia/reperfusion injury before and during reperfusion restored hepatic calcium retention capacity and oxidative phosphorylation parameters and reduced liver damage compared with vehicle.Conclusions:Recently created small-molecule inhibitors of CypD reduced calcium-induced swelling in mitochondria from mouse and human liver tissues. Administration of these compounds to mice during ischemia/reperfusion restored hepatic calcium retention capacity and oxidative phosphorylation parameters and reduced liver damage. These compounds might be developed to protect patients from ischemia/reperfusion injury after liver surgery or for other hepatic or nonhepatic disorders related to abnormal mPTP opening.
Published: 2019
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35. Mammalian Mechanoelectrical Transduction: Structure and Function of Force-Gated Ion Channels

Author: Dominique Douguet, Eric Honoré, Centre de Biochimie Structurale [Montpellier] (CBS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de pharmacologie moléculaire et cellulaire (IPMC), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Université Nice Sophia Antipolis (1965 - 2019) (UNS), and Honoré, Eric
Subjects: 0303 health sciences, [SDV]Life Sciences [q-bio], PIEZO1, Mechanoelectrical transduction, Depolarization, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Gating, Biology, General Biochemistry, Genetics and Molecular Biology, Autonomic regulation, Structure and function, [SDV] Life Sciences [q-bio], 03 medical and health sciences, 0302 clinical medicine, [SDV.BC.BC] Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Mechanosensitive channels, Neuroscience, ComputingMilieux_MISCELLANEOUS, 030217 neurology & neurosurgery, Ion channel, 030304 developmental biology
Abstract: The conversion of force into an electrical cellular signal is mediated by the opening of different types of mechanosensitive ion channels (MSCs), including TREK/TRAAK K2P channels, Piezo1/2, TMEM63/OSCA, and TMC1/2. Mechanoelectrical transduction plays a key role in hearing, balance, touch, and proprioception and is also implicated in the autonomic regulation of blood pressure and breathing. Thus, dysfunction of MSCs is associated with a variety of inherited and acquired disease states. Significant progress has recently been made in identifying these channels, solving their structure, and understanding the gating of both hyperpolarizing and depolarizing MSCs. Besides prototypical activation by membrane tension, additional gating mechanisms involving channel curvature and/or tethered elements are at play.
Published: 2019
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36. Insights into the activation mechanism of human estrogen-related receptor γ by environmental endocrine disruptors

Author: Erwan Thouennon, Vanessa Delfosse, Rémy Bailly, Pauline Blanc, Abdelhay Boulahtouf, Marina Grimaldi, Alessandro Barducci, William Bourguet, Patrick Balaguer, Institut de Recherche en Cancérologie de Montpellier (IRCM - U1194 Inserm - UM), CRLCC Val d'Aurelle - Paul Lamarque-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Centre de Biochimie Structurale [Montpellier] (CBS), and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: Transcriptional Activation, Estrogen-related receptor γ, Molecular Dynamics Simulation, Crystallography, X-Ray, Ligands, 03 medical and health sciences, Cellular and Molecular Neuroscience, 0302 clinical medicine, Phenols, Cell Line, Tumor, Humans, Benzhydryl Compounds, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Endocrine disruptors, Molecular Biology, 030304 developmental biology, Pharmacology, 0303 health sciences, Binding Sites, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Xenoestrogens, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Cell Biology, Recombinant Proteins, Protein Structure, Tertiary, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Receptors, Estrogen, Thermodynamics, Molecular Medicine, Protein–ligand interaction, 030217 neurology & neurosurgery, Protein Binding
Abstract: International audience; The estrogen-related receptor γ (ERRγ, NR3B3) is a constitutively active nuclear receptor which has been proposed to act as a mediator of the low-dose effects of a number of environmental endocrine-disrupting chemicals (EDCs) such as the xenoestrogen bisphenol-A (BPA). To better characterize the ability of exogenous compounds to bind and activate ERRγ, we used a combination of cell-based, biochemical, structural and computational approaches. A purposely created stable cell line allowed for the determination of the EC50s for over 30 environmental ERRγ ligands, including previously unknown ones. Interestingly, affinity constants (Kds) of the most potent compounds measured by isothermal titration calorimetry were in the 50–500 nM range, in agreement with their receptor activation potencies. Crystallographic analysis of the interaction between the ERRγ ligand-binding domain (LBD) and compounds of the bisphenol, alkylphenol and naphthol families revealed a partially shared binding mode and minimal alterations of the receptor conformation upon ligand binding. Further biophysical characterizations coupled to molecular dynamics simulations suggested a mechanism through which ERRγ ligands would exhibit their agonistic properties by preserving the transcriptionally active form of the receptor while rigidifying some loop regions with associated functions. This unique mechanism contrasts with the classical one involving a ligand-induced repositioning and stabilization of the C-terminal activation helix H12.
Published: 2019
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37. Osmotic Stress Activates Two Reactive Oxygen Species Pathways with Distinct Effects on Protein Nanodomains and Diffusion

Author: Yvon Jaillais, Stéphane Mari, Jean-Bernard Fiche, Xavier Dumont, Marija Smokvarska, Alexandre Martinière, Christophe Maurel, Carine Alcon, Marcelo Nollmann, Kian Hématy, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Centre de Biochimie Structurale [Montpellier] (CBS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Reproduction et développement des plantes (RDP), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Baracco, Chantal, Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: 0106 biological sciences, Osmotic shock, Physiology, [SDV]Life Sciences [q-bio], Arabidopsis, Aquaporin, Plant Science, Aquaporins, Endocytosis, 01 natural sciences, Protein Domains, Osmotic Pressure, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Arabidopsis thaliana, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, chemistry.chemical_classification, Reactive oxygen species, biology, Arabidopsis Proteins, Chemistry, Cell Biology, biology.organism_classification, Cell biology, [SDV] Life Sciences [q-bio], Second messenger system, Signal transduction, Reactive Oxygen Species, Signal Transduction, 010606 plant biology & botany
Abstract: Physiological acclimation of plants to an everchanging environment is governed by complex combinatorial signaling networks that perceive and transduce various abiotic and biotic stimuli. Reactive oxygen species (ROS) serve as one of the second messengers in plant responses to hyperosmotic stress. The molecular bases of ROS production and the primary cellular processes that they target were investigated in the Arabidopsis (Arabidopsis thaliana) root. Combined pharmacological and genetic approaches showed that the RESPIRATORY BURST OXIDASE HOMOLOG (RBOH) pathway and an additional pathway involving apoplastic ascorbate and iron can account for ROS production upon hyperosmotic stimulation. The two pathways determine synergistically the rate of membrane internalization, within minutes after activation. Live superresolution microscopy revealed at single-molecule scale how ROS control specific diffusion and nano-organization of membrane cargo proteins. In particular, ROS generated by RBOHs initiated clustering of the PLASMA MEMBRANE INTRINSIC PROTEIN2;1 aquaporin and its removal from the plasma membrane. This process is contributed to by clathrin-mediated endocytosis, with a positive role of RBOH-dependent ROS, specifically under hyperosmotic stress.
Published: 2019
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38. Disentangling the complexity of low complexity proteins

Author: Mier, Pablo, Bernadó, Pau, Gáspári, Zoltán, Ouzounis, Christos A., Promponas, Vasilis J., Kajava, Andrey V., Hancock, John M., Tosatto, Silvio C. E., Dosztanyi, Zsuzsanna, Andrade-Navarro, Miguel A., Paladin, Lisanna, Tamana, Stella, Petrosian, Sophia, Hajdu-Soltész, Borbála, Urbanek, Annika, Gruca, Aleksandra, Plewczynski, Dariusz, Grynberg, Marcin, Promponas, Vasilis J. [0000-0003-3352-4831], University Medical Center of the Johannes Gutenberg-University Mainz, Azienda Ospedaliera di Padova, University of Cyprus [Nicosia], Eötvös Loránd University (ELTE), Centre de Biochimie Structurale [Montpellier] (CBS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Silesian University of Technology, Warsaw University of Technology [Warsaw], Pázmány Péter Catholic University, Centre de recherche en Biologie Cellulaire (CRBM), Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), National Research University of Information Technologies, Mechanics and Optics [St. Petersburg] (ITMO), Earlham Institute [Norwich], and Department of Chemical Sciences University of Padova and Institute on Membrane Technology, Unit of Padova, via F. Marzolo 1, Padova, 35131
Subjects: Protein Conformation, Computer science, Review Article, Computational biology, Measure (mathematics), Evolution, Molecular, Low complexity, 03 medical and health sciences, Protein Domains, Amino Acid Sequence, structure, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Databases, Protein, Molecular Biology, 030304 developmental biology, Structure (mathematical logic), 0303 health sciences, Sequence, [SCCO.NEUR]Cognitive science/Neuroscience, composition bias, 030302 biochemistry & molecular biology, Proteins, disorder, low complexity regions, Structure and function, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Algorithms, Information Systems
Abstract: There are multiple definitions for low complexity regions (LCRs) in protein sequences, with all of them broadly considering LCRs as regions with fewer amino acid types compared to an average composition. Following this view, LCRs can also be defined as regions showing composition bias. In this critical review, we focus on the definition of sequence complexity of LCRs and their connection with structure. We present statistics and methodological approaches that measure low complexity (LC) and related sequence properties. Composition bias is often associated with LC and disorder, but repeats, while compositionally biased, might also induce ordered structures. We illustrate this dichotomy, and more generally the overlaps between different properties related to LCRs, using examples. We argue that statistical measures alone cannot capture all structural aspects of LCRs and recommend the combined usage of a variety of predictive tools and measurements. While the methodologies available to study LCRs are already very advanced, we foresee that a more comprehensive annotation of sequences in the databases will enable the improvement of predictions and a better understanding of the evolution and the connection between structure and function of LCRs. This will require the use of standards for the generation and exchange of data describing all aspects of LCRs. Short abstract There are multiple definitions for low complexity regions (LCRs) in protein sequences. In this critical review, we focus on the definition of sequence complexity of LCRs and their connection with structure. We present statistics and methodological approaches that measure low complexity (LC) and related sequence properties. Composition bias is often associated with LC and disorder, but repeats, while compositionally biased, might also induce ordered structures. We illustrate this dichotomy, plus overlaps between different properties related to LCRs, using examples.
Published: 2019
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39. A revisited version of the apo structure of the ligand-binding domain of the human nuclear receptor retinoic X receptor α

Author: Jérôme Eberhardt, Alastair G. McEwen, William Bourguet, Dino Moras, Annick Dejaegere, univOAK, Archive ouverte, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre de Biochimie Structurale [Montpellier] (CBS), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Models, Molecular, Protein Conformation, [CHIM.THER] Chemical Sciences/Medicinal Chemistry, Biophysics, nuclear receptors, [CHIM.THER]Chemical Sciences/Medicinal Chemistry, Crystallography, X-Ray, Ligands, Biochemistry, Research Communications, 03 medical and health sciences, Protein Domains, Structural Biology, retinoic acid, Genetics, Humans, Amino Acid Sequence, 030304 developmental biology, 0303 health sciences, Binding Sites, Retinoid X Receptor alpha, 030302 biochemistry & molecular biology, retinoic X receptor α, Condensed Matter Physics, ligand binding domains, Apoproteins, Crystallization, Protein Binding
Abstract: The retinoic X receptor (RXR) plays a crucial role in the superfamily of nuclear receptors (NRs) by acting as an obligatory partner of several nuclear receptors; its role as a transcription factor is thus critical in many signalling pathways, such as metabolism, cell development, differentiation and cellular death. The first published structure of the apo ligand-binding domain (LBD) of RXRα, which is still used as a reference today, contained inaccuracies. In the present work, these inaccuracies were corrected using modern crystallographic tools. The most important correction concerns the presence of a π-bulge in helix H7, which was originally built as a regular α-helix. The presence of several CHAPS molecules, which are visible for the first time in the electron-density map and which stabilize the H1–H3 loop, which contains helix H2, are also revealed. The apo RXR structure has played an essential role in deciphering the molecular mode of action of NR ligands and is still used in numerous biophysical studies. This refined structure should be used preferentially in the future in interpreting experiments as well as for modelling and structural dynamics studies of the apo RXRα LBD.
Published: 2019
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40. Nanoscale organization of tetraspanins during HIV-1 budding by correlative dSTORM/AFM

Author: Laurent Fernandez, Antoine Le Gall, Eric Rubinstein, Célia Chamontin, Marylène Mougel, Pierre-Emmanuel Milhiet, Selma Dahmane, Patrice Dosset, Florent Murcy, Marcelo Nollmann, Desiree Salas, Christine Doucet, Mougel, Marylene, Centre de Biochimie Structurale [Montpellier] (CBS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Modèles de Cellules Souches Malignes et Thérapeutiques, Université Paris-Sud - Paris 11 (UP11)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre d'Immunologie et des Maladies Infectieuses (CIMI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: Viral protein, [SDV]Life Sciences [q-bio], viruses, Cell, 02 engineering and technology, Microscopy, Atomic Force, 010402 general chemistry, medicine.disease_cause, gag Gene Products, Human Immunodeficiency Virus, 01 natural sciences, Tetraspanin 29, Tetraspanin 28, Flow cytometry, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, medicine, Humans, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, General Materials Science, Budding, medicine.diagnostic_test, Chemistry, Super-resolution microscopy, Virus Assembly, Cell Membrane, Flow Cytometry, 021001 nanoscience & nanotechnology, 3. Good health, 0104 chemical sciences, Cell biology, [SDV] Life Sciences [q-bio], Membrane, medicine.anatomical_structure, Viral replication, embryonic structures, HIV-1, 0210 nano-technology, HeLa Cells, CD81
Abstract: International audience; Membrane partition and remodeling play a key role in numerous cell mechanisms, especially in viral replication cycles where viruses subvert the plasma membrane to enter and escape from the host cell. Specifically assembly and release of HIV-1 particles require specific cellular components, which are recruited to the egress site by the viral protein Gag. We previously demonstrated that HIV-1 assembly alters both partitioning and dynamics of the tetraspanins CD9 and CD81, which are key players in many infectious processes, forming enriched areas where the virus buds. In this study we correlated super resolution microscopy mapping of tetraspanins with membrane topography delineated by atomic force microscopy (AFM) in Gag-expressing cells. We revealed that CD9 is specifically trapped within the nascent viral particles, especially at buds tips, suggesting that Gag mediates CD9 and CD81 depletion from the plasma membrane. In addition, we showed that CD9 is organized as small membrane assemblies of few tens of nanometers that can coalesce upon Gag expression.
Published: 2019
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41. Mechanical Control of Cell Migration by the Metastasis Suppressor Tetraspanin CD82/KAI1

Author: Diala Kantar, Luca Costa, Fedor Berditchevski, Laurent Fernandez, Lucie Chauvin, Christopher Chevillard, Elena Odintsova, Laura Ordas, Patrice Dosset, Lisa Heron-Milhavet, Anthony Lozano, Alexia Calovoulos, Christine Benistant, Christine Doucet, Pierre-Emmanuel Milhiet, Centre de Biochimie Structurale [Montpellier] (CBS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut de Génétique Moléculaire de Montpellier (IGMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Institut de Recherche en Cancérologie de Montpellier (IRCM - U1194 Inserm - UM), CRLCC Val d'Aurelle - Paul Lamarque-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Acides Nucléiques : Régulations Naturelle et Artificielle (ARNA), Université de Bordeaux (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Institute of Cancer and Genomic Sciences, University of Birmingham, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), and Milhiet, Pierre-Emmanuel
Subjects: cell migration, QH301-705.5, Cell, Caveolin 1, [SDV.BBM.BP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, [SDV.CAN]Life Sciences [q-bio]/Cancer, Kangai-1 Protein, plasma membrane, Mechanotransduction, Cellular, Article, Cell Line, Focal adhesion, 03 medical and health sciences, 0302 clinical medicine, [SDV.CAN] Life Sciences [q-bio]/Cancer, Tetraspanin, Cell Movement, Caveolae, Cell Line, Tumor, Neoplasms, Stress Fibers, Caveolin, medicine, Cell Adhesion, Humans, Biology (General), Mechanotransduction, Neoplasm Metastasis, 030304 developmental biology, caveolins, mechanotransduction, 0303 health sciences, Chemistry, Cell Membrane, Membrane Proteins, Cell migration, General Medicine, focal adhesions, Cell biology, tetraspanins, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, medicine.anatomical_structure, 030220 oncology & carcinogenesis, YAP, CD82, actin, Signal Transduction, Transcription Factors
Abstract: International audience; The plasma membrane is a key actor of cell migration. For instance, its tension controls persistent cell migration and cell surface caveolae integrity. Then, caveolae constituents such as caveolin-1 can initiate a mechanotransduction loop that involves actin- and focal adhesion-dependent control of the mechanosensor YAP to finely tune cell migration. Tetraspanin CD82 (also named KAI-1) is an integral membrane protein and a metastasis suppressor. Its expression is lost in many cancers including breast cancer. It is a strong inhibitor of cell migration by a little-known mechanism. We demonstrated here that CD82 controls persistent 2D migration of EGF-induced single cells, stress fibers and focal adhesion sizes and dynamics. Mechanistically, we found that CD82 regulates membrane tension, cell surface caveolae abundance and YAP nuclear translocation in a caveolin-1-dependent manner. Altogether, our data show that CD82 controls 2D cell migration using membrane-driven mechanics involving caveolin and the YAP pathway.
Published: 2021
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42. The study of the determinants controlling Arpp19 phosphatase-inhibitory activity reveals an Arpp19/PP2A-B55 feedback loop

Author: Jean-Claude Labbé, Sylvain Roque, Francisca Mechali, Cindy Genoud, Suzanne Vigneron, Anna Castro, Thierry Lorca, Martin Cohen-Gonsaud, Gilles Labesse, Perle Robert, Perrine Goguet-Rubio, Phillipe Barthe, Centre de recherche en Biologie Cellulaire (CRBM), Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), Centre de Biochimie Structurale [Montpellier] (CBS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Lorca, Thierry, Centre de recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), and Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, inorganic chemicals, Cell division, Xenopus, Science, [SDV]Life Sciences [q-bio], Phosphatase, Cyclin B, General Physics and Astronomy, Mitosis, macromolecular substances, Xenopus Proteins, environment and public health, General Biochemistry, Genetics and Molecular Biology, Article, Feedback, Dephosphorylation, 03 medical and health sciences, Xenopus laevis, 0302 clinical medicine, CDC2 Protein Kinase, Phosphoprotein Phosphatases, Animals, Protein Phosphatase 2, Phosphorylation, Cyclin-dependent kinase 1, Multidisciplinary, biology, Chemistry, Kinase, General Chemistry, Protein phosphatase 2, Phosphoproteins, 3. Good health, Cell biology, [SDV] Life Sciences [q-bio], Meiosis, enzymes and coenzymes (carbohydrates), 030104 developmental biology, biology.protein, bacteria, Female, Carboxylic Ester Hydrolases, 030217 neurology & neurosurgery
Abstract: Arpp19 is a potent PP2A-B55 inhibitor that regulates this phosphatase to ensure the stable phosphorylation of mitotic/meiotic substrates. At G2-M, Arpp19 is phosphorylated by the Greatwall kinase on S67. This phosphorylated Arpp19 form displays a high affinity to PP2A-B55 and a slow dephosphorylation rate, acting as a competitor of PP2A-B55 substrates. The molecular determinants conferring slow dephosphorylation kinetics to S67 are unknown. PKA also phosphorylates Arpp19. This phosphorylation performed on S109 is essential to maintain prophase I-arrest in Xenopus oocytes although the underlying signalling mechanism is elusive. Here, we characterize the molecular determinants conferring high affinity and slow dephosphorylation to S67 and controlling PP2A-B55 inhibitory activity of Arpp19. Moreover, we show that phospho-S109 restricts S67 phosphorylation by increasing its catalysis by PP2A-B55. Finally, we discover a double feed-back loop between these two phospho-sites essential to coordinate the temporal pattern of Arpp19-dependent PP2A-B55 inhibition and Cyclin B/Cdk1 activation during cell division., Progression of the cell division cycle requires feedback loops including those of phosphorylation and dephosphorylation; however the precise regulation of phosphorylation kinetics of Arpp19, an inhibitor of protein phosphatase 2A, is unclear. Here, the authors report that feedback between phosphorylation states of Ser67 and Ser109 of Arpp19 coordinates Arpp19-dependent inhibition of PP2A-B55 and Cyclin B activation during cell cycle progression.
Published: 2021
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43. Pharmacological activation of PIEZO1 in human red blood cells prevents Plasmodium falciparum invasion

Author: Rachel Cerdan, Dominique Douguet, Laurence Berry, Hélène Guizouarn, Roberto Bernal, Jordy Le Guet, Rakhee Lohia, Manouk Abkarian, Eric Honoré, Kai Wengelnik, LPHI - Laboratory of Pathogen Host Interactions (LPHI), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Valrose (IBV), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Universidad de Santiago de Chile [Santiago] (USACH), Centre de Biochimie Structurale [Montpellier] (CBS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de pharmacologie moléculaire et cellulaire (IPMC), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA), Institut National de la Santé et de la Recherche Médicale (INSERM), Wengelnik, Kai, Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)
Subjects: 0303 health sciences, biology, Chemistry, Activator (genetics), PIEZO1, Plasmodium falciparum, Parasitemia, medicine.disease, biology.organism_classification, 3. Good health, Microbiology, 03 medical and health sciences, Red blood cell, 0302 clinical medicine, medicine.anatomical_structure, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, parasitic diseases, medicine, Mechanosensitive channels, Receptor, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, 030217 neurology & neurosurgery, Intracellular, 030304 developmental biology
Abstract: An inherited gain-of–function variant (E756 del) in the mechanosensitive cationic channel PIEZO1 was recently shown to confer a significant protection against severe malaria. Here, we demonstrate in vitro that human red blood cell (RBC) infection by Plasmodium falciparum is prevented by the pharmacological activation of PIEZO1. The PIEZO1 activator Yoda1 inhibits RBC invasion, without affecting parasite intraerythrocytic growth, division or egress. RBC dehydration, echinocytosis and intracellular Na+/K+ imbalance are unrelated to the mechanism of protection. Inhibition of invasion is maintained, even after a prolonged wash out of Yoda1. Similarly, the chemically unrelated activators Jedi1 and Jedi2 potently inhibit parasitemia, further indicating a PIEZO1-dependent mechanism. Notably, Yoda1 treatment significantly reduced RBC surface receptors of P. falciparum, and decreased merozoite attachment and subsequent RBC deformation. Altogether these data indicate that the pharmacological activation of Piezo1 in human RBCs inhibits malaria infection by impairing P. falciparum invasion.
Published: 2021

44. Molecular structure of the intact bacterial flagellar basal body

Author: Joseph J. E. Caesar, Ashley L. Nord, Justin C. Deme, Emily Furlong, Fabienne F. V. Chevance, Susan M. Lea, Kelly T. Hughes, Richard M. Berry, Steven Johnson, Sir William Dunn School of Pathology [Oxford], University of Oxford [Oxford], Center for Structural Biology (CCR, NCI), Central Oxford Structural Molecular Imaging Centre, University of Oxford, Centre de Biochimie Structurale [Montpellier] (CBS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), University of Utah, Department of Biology, University of Oxford, Department of Physics, University of Oxford, Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), and Nord, Ashley
Subjects: Microbiology (medical), [SDV.BBM.BS] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Immunology, Flagellum, Rotation, Applied Microbiology and Biotechnology, Microbiology, Article, law.invention, Cell wall, 03 medical and health sciences, Bacterial Proteins, Salmonella, law, Genetics, Inner membrane, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], 030306 microbiology, Chemistry, Cryoelectron Microscopy, Cell Biology, Basal Bodies, Molecular machine, Membrane, Flagella, Bushing, Drive shaft, Biophysics, Bacterial outer membrane
Abstract: The bacterial flagellum is a macromolecular protein complex that enables motility in many species. Bacterial flagella self-assemble a strong, multicomponent drive shaft that couples rotation in the inner membrane to the micrometre-long flagellar filament that powers bacterial swimming in viscous fluids1–3. Here, we present structures of the intact Salmonella flagellar basal body4, encompassing the inner membrane rotor, drive shaft and outer-membrane bushing, solved using cryo-electron microscopy to resolutions of 2.2–3.7 A. The structures reveal molecular details of how 173 protein molecules of 13 different types assemble into a complex spanning two membranes and a cell wall. The helical drive shaft at one end is intricately interwoven with the rotor component with both the export gate complex and the proximal rod forming interactions with the MS-ring. At the other end, the drive shaft distal rod passes through the LP-ring bushing complex, which functions as a molecular bearing anchored in the outer membrane through interactions with the lipopolysaccharide. The in situ structure of a protein complex capping the drive shaft provides molecular insights into the assembly process of this molecular machine. The in situ cryo-electron microscopy structure of the intact Salmonella flagellar basal body—including the inner membrane rotor, drive shaft and outer membrane bushing complex—elucidates the mechanisms of assembly of this complex macromolecular structure that enables bacterial motility.
Published: 2021
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45. Resolving the activation mechanism of the D99N antiterminator LicT protein

Author: Jérôme Gracy, Hélène Déméné, Nathalie Declerck, Yinshan Yang, Centre de Biochimie Structurale [Montpellier] (CBS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Département Microbiologie et Chaîne Alimentaire - INRAE (MICA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Déméné, Hélène
Subjects: Models, Molecular, [SDV]Life Sciences [q-bio], Mutant, medicine.disease_cause, antitermination protein, 03 medical and health sciences, Bacterial Proteins, Protein Domains, Structural Biology, medicine, Point Mutation, Nuclear Magnetic Resonance, Biomolecular, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Mutation, Binding Sites, Effector, Chemistry, 030302 biochemistry & molecular biology, RNA, activation mechanism, NMR, Cell biology, [SDV] Life Sciences [q-bio], RNA, Bacterial, Antitermination, Phosphorylation, BglG, Protein Multimerization, Linker, Function (biology), signal transduction, Bacillus subtilis, Transcription Factors
Abstract: International audience; LicT is an antiterminator protein of the BglG family whose members are key players in the control of carbohydrate catabolism in bacteria. These antiterminators are generally composed of three modules, an N-terminal RNA-binding domain (CAT) followed by two homologous regulation modules (PRD1 and PRD2) that control the RNA binding activity of the effector domain via phosphorylation on conserved histidines. Although several structures of isolated domains of BglG-like proteins have been described, no structure containing CAT and at least one PRD simultaneously has yet been reported in an active state, precluding detailed understanding of signal transduction between modules. To fulfill this gap, we recently reported the complete NMR sequence assignment of a constitutively active mutant (D99N) CAT-PRD1*, which contains the effector domain and the first regulation domain of LicT. As a follow-up, we have determined and report here the 3D solution structure of this active, dimeric LicT construct (40 kDa). The structure reveals how the mutation constrains the PRD1 regulation domain into an active conformation which is transduced to CAT via a network of negatively charged residues belonging to PRD1 dimeric interface and to the linker region. In addition, our data support a model where BglG-type antitermination regulatory modules can only adopt a single conformation compatible with the active structure of the effector domain, regardless of whether activation is mediated by mutation on the first or second PRD. The linker between the effector and regulation modules appears to function as an adaptable hinge tuning the position of the functional modules.
Published: 2021
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46. Melanotransferrin is efficiently sorted on the surface of exosomes secreted by melanoma cells

Author: Gaëtan Bellot, Nesrine Aissaoui, Laurent Henry, Marie Morille, Michel Vidal, Anne Bonhoure, Pierre-Emmanuel Stoebner, Dynamique des interactions membranaires normales et pathologiques (DIMNP), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université Montpellier 1 (UM1), Institut des Biomolécules Max Mousseron [Pôle Chimie Balard] (IBMM), Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Institut de Chimie du CNRS (INC)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut Charles Gerhardt Montpellier - Institut de Chimie Moléculaire et des Matériaux de Montpellier (ICGM ICMMM), Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut de Chimie du CNRS (INC), Groupe Hospitalier Saint Louis - Lariboisière - Fernand Widal [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Centre de Biochimie Structurale [Montpellier] (CBS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Centre National de la Recherche Scientifique (CNRS)
Subjects: Cancer Research, Skin Neoplasms, Dermatology, Exosomes, Mice, Melanoma Biomarker, medicine, Animals, Humans, [CHIM]Chemical Sciences, Melanoma, neoplasms, ComputingMilieux_MISCELLANEOUS, Membrane Glycoproteins, CD63, biology, Chemistry, medicine.disease, Microvesicles, 3. Good health, Oncology, Cutaneous melanoma, Cancer cell, biology.protein, Cancer research, Melanotransferrin, Antibody
Abstract: Cutaneous melanoma is the most lethal type of skin cancer. Early detection is crucial to improve the outcome of melanoma patients. The identification of noninvasive prognostic biomarkers for the follow-up of melanoma patients is still in demand for clinical use. We show here that exosomal melanotransferrin fulfills the biomarker characteristics required to meet this demand. Melanotransferrin is typically overexpressed in melanoma cells compared to other cell types - including cancer cells - and is efficiently sorted and secreted with nanovesicles, or so-called exosomes, due to its membrane-anchoring by a glycosylphosphatidylinositol. Melanotransferrin is exposed on the surface of exosomes and is accessible for antibody recognition. An ELISA was set up to quantify melanotransferrin after immobilization of nanovesicles through the exosomal constituent tetraspanins CD63. Melanotransferrin was detected using a low number of exosomes purified from melanoma cell line cultures, and melanotransferrin detection was abolished by phosphatidylinositol-specific phospholipase C treatment. This exosomal melanotransferrin ELISA was able to discriminate an equal number of assayed exosomes purified from two different melanoma cell lines (A-375 vs. SK-MEL-28). Moreover, plasma samples from patients with melanoma and noncancer disease were assayed using this ELISA and elevated levels of exosomal melanotransferrin were seen in the plasma of patients with melanoma. We propose that exosomal melanotransferrin should be assessed as a potential melanoma biomarker.
Published: 2021
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47. Development of novel correlative AFM-Fluorescent methods for the study of biological samples

Author: Saavedra V., Oscar, Centre de Biochimie Structurale [Montpellier] (CBS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Université Montpellier, Pierre-Emmanuel Milhiet, and STAR, ABES
Subjects: Rupture forces, Microscopies corrélatives, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, [SDV.SA] Life Sciences [q-bio]/Agricultural sciences, Correlative microscopies, Miet, Microscopie à force atomique, Membranes biologiques, Forces de rupture, Compression, Atomic Force Microscopy (AFM), Biological membranes, Metal Induced Energy Transfer (MIET)
Abstract: Biological membranes are flexibles barriers that ensure cell permeability, delineating the cell boundaries and the intracellular compartments to organelles within the cell. They are composed mainly by phospholipids and proteins. Those components are the main ones responsible for membrane remodeling. The latter process is highly dynamic and requires observation at high spatial and temporal resolution. This thesis work focused on two main challenges in the study of membranes: i) Softness of biological membranes and their mechanical properties. Membranes are very soft and fragile materials, and determine their real morphology is highly complicated due to their softness. We have studied the maximal force exerted by an AFM tip that supported lipid bilayers can withstand before rupture, as well as their Young’s modulus, both as a function of the tip size. ii) Chemical sensitivity and molecular recognition in microscopy. AFM can achieve the topography of the membrane. However, this technique cannot distinguish the molecule below the AFM tip. In order to overcome this barrier, we worked on developing a new fluorescence super-resolution technique combining AFM and confocal microscopies. First, we developed a correlated and synchronous confocal Fluorescence-lifetime imaging microscope (FLIM)-AFM setup. Finally, we developed a Metal Induced Energy Transfer (MIET)-AFM setup in order to measure molecular recognition, topography, and mechanical properties of biological samples simultaneously., Les membranes biologiques sont des barrières flexibles qui assurent la perméabilité des cellules, délimitant les frontières cellulaires et les compartiments intracellulaires aux organites à l'intérieur de la cellule. Elles sont composées principalement de phospholipides et de protéines. Ces composants sont les principaux responsables du remodelage des membranes. Ce dernier processus est très dynamique et nécessite une observation à haute résolution latérale et temporelle. Ce travail de thèse s'est concentré sur deux défis principaux dans l'étude des membranes : i) Les propriétés mécaniques. Les membranes sont des matériaux très mous et fragiles, et déterminer leur morphologie réelle est très compliqué en raison de leur mollesse. Nous avons étudié la force maximale exercée par une pointe AFM que les bicouches lipidiques supportées peuvent supporter avant la rupture, ainsi que leur module d'Young, tous deux en fonction de la taille de la pointe. ii) Sensibilité chimique lors de l'imagerie des membranes. L'AFM permet d'obtenir la topographie de la membrane. Cependant, cette technique ne peut pas distinguer la molécule située sous la pointe de l'AFM. Afin de surmonter cet obstacle, nous avons travaillé à la mise au point d'une nouvelle technique de fluorescence à super-résolution combinant l'AFM et les microscopies confocales. Tout d'abord, nous avons mis au point un microscope confocal synchrone et corrélé d'imagerie de fluorescence à vie (FLIM)-AFM. Enfin, nous avons mis au point un dispositif de transfert d'énergie induit par les métaux (MIET)-AFM afin de mesurer simultanément la reconnaissance moléculaire, la topographie et les propriétés mécaniques des échantillons biologiques.
Published: 2021

48. Développement de nouvelles approches de microscopie correlative AFM-Fluorescence pour l'analyse d'échantillons biologiques

Author: Saavedra V., Oscar, Centre de Biochimie Structurale [Montpellier] (CBS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Montpellier, and Pierre-Emmanuel Milhiet
Subjects: Rupture forces, Microscopies corrélatives, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Correlative microscopies, Miet, Microscopie à force atomique, Membranes biologiques, Forces de rupture, Compression, Atomic Force Microscopy (AFM), Biological membranes, Metal Induced Energy Transfer (MIET)
Abstract: Biological membranes are flexibles barriers that ensure cell permeability, delineating the cell boundaries and the intracellular compartments to organelles within the cell. They are composed mainly by phospholipids and proteins. Those components are the main ones responsible for membrane remodeling. The latter process is highly dynamic and requires observation at high spatial and temporal resolution. This thesis work focused on two main challenges in the study of membranes: i) Softness of biological membranes and their mechanical properties. Membranes are very soft and fragile materials, and determine their real morphology is highly complicated due to their softness. We have studied the maximal force exerted by an AFM tip that supported lipid bilayers can withstand before rupture, as well as their Young’s modulus, both as a function of the tip size. ii) Chemical sensitivity and molecular recognition in microscopy. AFM can achieve the topography of the membrane. However, this technique cannot distinguish the molecule below the AFM tip. In order to overcome this barrier, we worked on developing a new fluorescence super-resolution technique combining AFM and confocal microscopies. First, we developed a correlated and synchronous confocal Fluorescence-lifetime imaging microscope (FLIM)-AFM setup. Finally, we developed a Metal Induced Energy Transfer (MIET)-AFM setup in order to measure molecular recognition, topography, and mechanical properties of biological samples simultaneously.; Les membranes biologiques sont des barrières flexibles qui assurent la perméabilité des cellules, délimitant les frontières cellulaires et les compartiments intracellulaires aux organites à l'intérieur de la cellule. Elles sont composées principalement de phospholipides et de protéines. Ces composants sont les principaux responsables du remodelage des membranes. Ce dernier processus est très dynamique et nécessite une observation à haute résolution latérale et temporelle. Ce travail de thèse s'est concentré sur deux défis principaux dans l'étude des membranes : i) Les propriétés mécaniques. Les membranes sont des matériaux très mous et fragiles, et déterminer leur morphologie réelle est très compliqué en raison de leur mollesse. Nous avons étudié la force maximale exercée par une pointe AFM que les bicouches lipidiques supportées peuvent supporter avant la rupture, ainsi que leur module d'Young, tous deux en fonction de la taille de la pointe. ii) Sensibilité chimique lors de l'imagerie des membranes. L'AFM permet d'obtenir la topographie de la membrane. Cependant, cette technique ne peut pas distinguer la molécule située sous la pointe de l'AFM. Afin de surmonter cet obstacle, nous avons travaillé à la mise au point d'une nouvelle technique de fluorescence à super-résolution combinant l'AFM et les microscopies confocales. Tout d'abord, nous avons mis au point un microscope confocal synchrone et corrélé d'imagerie de fluorescence à vie (FLIM)-AFM. Enfin, nous avons mis au point un dispositif de transfert d'énergie induit par les métaux (MIET)-AFM afin de mesurer simultanément la reconnaissance moléculaire, la topographie et les propriétés mécaniques des échantillons biologiques.
Published: 2021

49. Cryo–electron microscopy structure of the antidiuretic hormone arginine-vasopressin V2 receptor signaling complex

Author: Patrick Bron, Stefano Trapani, Hélène Orcel, Julien Bous, Nicolas Floquet, Remy Sounier, Cedric Leyrat, Aurelie Ancelin, Julie Saint-Paul, Sébastien Granier, Gérald Gaibelet, Joséphine Lai-Kee-Him, Hélène Déméné, Bernard Mouillac, Maxime Louet, Institut de Génomique Fonctionnelle (IGF), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Centre de Biochimie Structurale [Montpellier] (CBS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut des Biomolécules Max Mousseron [Pôle Chimie Balard] (IBMM), Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Institut de Chimie du CNRS (INC)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), and Guerineau, Nathalie C.
Subjects: endocrine system, Gs alpha subunit, Cryo-electron microscopy, Protein subunit, [SDV]Life Sciences [q-bio], 01 natural sciences, 03 medical and health sciences, Structural Biology, Arginine vasopressin receptor 2, 0103 physical sciences, Receptor, Ternary complex, Research Articles, 030304 developmental biology, G protein-coupled receptor, 0303 health sciences, Multidisciplinary, 010304 chemical physics, Chemistry, urogenital system, SciAdv r-articles, 3. Good health, [SDV] Life Sciences [q-bio], Biophysics, hormones, hormone substitutes, and hormone antagonists, Antidiuretic, Research Article, Signal Transduction
Abstract: Structures of the AVP-V2R-Gs protein complex provide molecular insights into the function of this clinically relevant target., The antidiuretic hormone arginine-vasopressin (AVP) forms a signaling complex with the V2 receptor (V2R) and the Gs protein, promoting kidney water reabsorption. Molecular mechanisms underlying activation of this critical G protein–coupled receptor (GPCR) signaling system are still unknown. To fill this gap of knowledge, we report here the cryo–electron microscopy structure of the AVP-V2R-Gs complex. Single-particle analysis revealed the presence of three different states. The two best maps were combined with computational and nuclear magnetic resonance spectroscopy constraints to reconstruct two structures of the ternary complex. These structures differ in AVP and Gs binding modes. They reveal an original receptor-Gs interface in which the Gαs subunit penetrates deep into the active V2R. The structures help to explain how V2R R137H or R137L/C variants can lead to two severe genetic diseases. Our study provides important structural insights into the function of this clinically relevant GPCR signaling complex.
Published: 2021
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50. Folding of phosphodiester-linked donor-acceptor oligomers into supramolecular nanotubes in water

Author: Gérard Vergoten, Michael Smietana, Jean-Jacques Vasseur, Kévan Pérez de Carvasal, Nesrine Aissaoui, François Morvan, Gaëtan Bellot, Institut des Biomolécules Max Mousseron [Pôle Chimie Balard] (IBMM), Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Institut de Chimie du CNRS (INC)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Centre de Biochimie Structurale [Montpellier] (CBS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institute for Translational Research in Inflammation - U 1286 (INFINITE (Ex-Liric)), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)
Subjects: Phosphoramidite, 010405 organic chemistry, Stereochemistry, [CHIM.ORGA]Chemical Sciences/Organic chemistry, Metals and Alloys, Supramolecular chemistry, General Chemistry, [CHIM.THER]Chemical Sciences/Medicinal Chemistry, Random hexamer, 010402 general chemistry, 01 natural sciences, Acceptor, Catalysis, 0104 chemical sciences, Surfaces, Coatings and Films, Electronic, Optical and Magnetic Materials, Folding (chemistry), chemistry.chemical_compound, chemistry, Diimide, Phosphodiester bond, Materials Chemistry, Ceramics and Composites, Solvophobic
Abstract: International audience; Inspired by the automated synthesis of DNA on solid support, electron-rich dialkxoynaphthalene dialkoxynaphthalene (DAN) donor and electron-deficient-naphthalene-tetracarboxylic diimide (NDI) acceptor, amphiphilic foldamers have been synthesised from their respective phosphoramidite building blocks. The folding of the phosphodiester-linked hexamer (DAN-NDI)3 revealed in water the formation in water of regular supramolecular nanotubes resulting from the self-assembly of multiple hexamers stabilized by donor/acceptor interactions and solvophobic effect.
Published: 2021
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