12 results on '"Gisele Cardoso de Amorim"'
Search Results
2. Structural and molecular determinants for the interaction of ExbB from Serratia marcescens and HasB, a TonB paralog
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Valérie Biou, Ricardo Jorge Diogo Adaixo, Mohamed Chami, Pierre-Damien Coureux, Benoist Laurent, Véronique Yvette Ntsogo Enguéné, Gisele Cardoso de Amorim, Nadia Izadi-Pruneyre, Christian Malosse, Julia Chamot-Rooke, Henning Stahlberg, and Philippe Delepelaire
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Biology (General) ,QH301-705.5 - Abstract
Cryo-EM structures of the ExbB and ExbB-ExbD membrane protein complexes in the Gram-negative bacteria Serratia marcescens reveal insights into inner membrane machinery and interactions specific to the Has system.
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- 2022
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3. Large-Scale Recombinant Production of the SARS-CoV-2 Proteome for High-Throughput and Structural Biology Applications
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Nadide Altincekic, Sophie Marianne Korn, Nusrat Shahin Qureshi, Marie Dujardin, Martí Ninot-Pedrosa, Rupert Abele, Marie Jose Abi Saad, Caterina Alfano, Fabio C. L. Almeida, Islam Alshamleh, Gisele Cardoso de Amorim, Thomas K. Anderson, Cristiane D. Anobom, Chelsea Anorma, Jasleen Kaur Bains, Adriaan Bax, Martin Blackledge, Julius Blechar, Anja Böckmann, Louis Brigandat, Anna Bula, Matthias Bütikofer, Aldo R. Camacho-Zarco, Teresa Carlomagno, Icaro Putinhon Caruso, Betül Ceylan, Apirat Chaikuad, Feixia Chu, Laura Cole, Marquise G. Crosby, Vanessa de Jesus, Karthikeyan Dhamotharan, Isabella C. Felli, Jan Ferner, Yanick Fleischmann, Marie-Laure Fogeron, Nikolaos K. Fourkiotis, Christin Fuks, Boris Fürtig, Angelo Gallo, Santosh L. Gande, Juan Atilio Gerez, Dhiman Ghosh, Francisco Gomes-Neto, Oksana Gorbatyuk, Serafima Guseva, Carolin Hacker, Sabine Häfner, Bing Hao, Bruno Hargittay, K. Henzler-Wildman, Jeffrey C. Hoch, Katharina F. Hohmann, Marie T. Hutchison, Kristaps Jaudzems, Katarina Jović, Janina Kaderli, Gints Kalniņš, Iveta Kaņepe, Robert N. Kirchdoerfer, John Kirkpatrick, Stefan Knapp, Robin Krishnathas, Felicitas Kutz, Susanne zur Lage, Roderick Lambertz, Andras Lang, Douglas Laurents, Lauriane Lecoq, Verena Linhard, Frank Löhr, Anas Malki, Luiza Mamigonian Bessa, Rachel W. Martin, Tobias Matzel, Damien Maurin, Seth W. McNutt, Nathane Cunha Mebus-Antunes, Beat H. Meier, Nathalie Meiser, Miguel Mompeán, Elisa Monaca, Roland Montserret, Laura Mariño Perez, Celine Moser, Claudia Muhle-Goll, Thais Cristtina Neves-Martins, Xiamonin Ni, Brenna Norton-Baker, Roberta Pierattelli, Letizia Pontoriero, Yulia Pustovalova, Oliver Ohlenschläger, Julien Orts, Andrea T. Da Poian, Dennis J. Pyper, Christian Richter, Roland Riek, Chad M. Rienstra, Angus Robertson, Anderson S. Pinheiro, Raffaele Sabbatella, Nicola Salvi, Krishna Saxena, Linda Schulte, Marco Schiavina, Harald Schwalbe, Mara Silber, Marcius da Silva Almeida, Marc A. Sprague-Piercy, Georgios A. Spyroulias, Sridhar Sreeramulu, Jan-Niklas Tants, Kaspars Tārs, Felix Torres, Sabrina Töws, Miguel Á. Treviño, Sven Trucks, Aikaterini C. Tsika, Krisztina Varga, Ying Wang, Marco E. Weber, Julia E. Weigand, Christoph Wiedemann, Julia Wirmer-Bartoschek, Maria Alexandra Wirtz Martin, Johannes Zehnder, Martin Hengesbach, and Andreas Schlundt
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COVID-19 ,SARS-CoV-2 ,nonstructural proteins ,structural proteins ,accessory proteins ,intrinsically disordered region ,Biology (General) ,QH301-705.5 - Abstract
The highly infectious disease COVID-19 caused by the Betacoronavirus SARS-CoV-2 poses a severe threat to humanity and demands the redirection of scientific efforts and criteria to organized research projects. The international COVID19-NMR consortium seeks to provide such new approaches by gathering scientific expertise worldwide. In particular, making available viral proteins and RNAs will pave the way to understanding the SARS-CoV-2 molecular components in detail. The research in COVID19-NMR and the resources provided through the consortium are fully disclosed to accelerate access and exploitation. NMR investigations of the viral molecular components are designated to provide the essential basis for further work, including macromolecular interaction studies and high-throughput drug screening. Here, we present the extensive catalog of a holistic SARS-CoV-2 protein preparation approach based on the consortium’s collective efforts. We provide protocols for the large-scale production of more than 80% of all SARS-CoV-2 proteins or essential parts of them. Several of the proteins were produced in more than one laboratory, demonstrating the high interoperability between NMR groups worldwide. For the majority of proteins, we can produce isotope-labeled samples of HSQC-grade. Together with several NMR chemical shift assignments made publicly available on covid19-nmr.com, we here provide highly valuable resources for the production of SARS-CoV-2 proteins in isotope-labeled form.
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- 2021
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4. Interaction of a partially disordered antisigma factor with its partner, the signaling domain of the TonB-dependent transporter HasR.
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Idir Malki, Catherine Simenel, Halina Wojtowicz, Gisele Cardoso de Amorim, Ada Prochnicka-Chalufour, Sylviane Hoos, Bertrand Raynal, Patrick England, Alain Chaffotte, Muriel Delepierre, Philippe Delepelaire, and Nadia Izadi-Pruneyre
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Medicine ,Science - Abstract
Bacteria use diverse signaling pathways to control gene expression in response to external stimuli. In Gram-negative bacteria, the binding of a nutrient is sensed by an outer membrane transporter. This signal is then transmitted to an antisigma factor and subsequently to the cytoplasm where an ECF sigma factor induces expression of genes related to the acquisition of this nutrient. The molecular interactions involved in this transmembrane signaling are poorly understood and structural data on this family of antisigma factor are rare. Here, we present the first structural study of the periplasmic domain of an antisigma factor and its interaction with the transporter. The study concerns the signaling in the heme acquisition system (Has) of Serratia marcescens. Our data support unprecedented partially disordered periplasmic domain of an anti-sigma factor HasS in contact with a membrane-mimicking environment. We solved the 3D structure of the signaling domain of HasR transporter and identified the residues at the HasS-HasR interface. Their conservation in several bacteria suggests wider significance of the proposed model for the understanding of bacterial transmembrane signaling.
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- 2014
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5. The structure of HasB reveals a new class of TonB protein fold.
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Gisele Cardoso de Amorim, Ada Prochnicka-Chalufour, Philippe Delepelaire, Julien Lefèvre, Catherine Simenel, Cécile Wandersman, Muriel Delepierre, and Nadia Izadi-Pruneyre
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Medicine ,Science - Abstract
TonB is a key protein in active transport of essential nutrients like vitamin B12 and metal sources through the outer membrane transporters of Gram-negative bacteria. This inner membrane protein spans the periplasm, contacts the outer membrane receptor by its periplasmic domain and transduces energy from the cytoplasmic membrane pmf to the receptor allowing nutrient internalization. Whereas generally a single TonB protein allows the acquisition of several nutrients through their cognate receptor, in some species one particular TonB is dedicated to a specific system. Despite a considerable amount of data available, the molecular mechanism of TonB-dependent active transport is still poorly understood. In this work, we present a structural study of a TonB-like protein, HasB dedicated to the HasR receptor. HasR acquires heme either free or via an extracellular heme transporter, the hemophore HasA. Heme is used as an iron source by bacteria. We have solved the structure of the HasB periplasmic domain of Serratia marcescens and describe its interaction with a critical region of HasR. Some important differences are observed between HasB and TonB structures. The HasB fold reveals a new structural class of TonB-like proteins. Furthermore, we have identified the structural features that explain the functional specificity of HasB. These results give a new insight into the molecular mechanism of nutrient active transport through the bacterial outer membrane and present the first detailed structural study of a specific TonB-like protein and its interaction with the receptor.
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- 2013
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6. Insights into the specificity for the interaction of the promiscuous SARS-CoV-2 nucleocapsid protein N-terminal domain with deoxyribonucleic acids
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Icaro Putinhon Caruso, Vitor dos Santos Almeida, Mariana Juliani do Amaral, Guilherme Caldas de Andrade, Gabriela Rocha de Araújo, Talita Stelling de Araújo, Jéssica Moreira de Azevedo, Glauce Moreno Barbosa, Leonardo Bartkevihi, Peter Reis Bezerra, Katia Maria dos Santos Cabral, Isabella Otênio de Lourenço, Clara L.F. Malizia-Motta, Aline de Luna Marques, Nathane Cunha Mebus-Antunes, Thais Cristtina Neves-Martins, Jéssica Maróstica de Sá, Karoline Sanches, Marcos Caique Santana-Silva, Ariana Azevedo Vasconcelos, Marcius da Silva Almeida, Gisele Cardoso de Amorim, Cristiane Dinis Anobom, Andrea T. Da Poian, Francisco Gomes-Neto, Anderson S. Pinheiro, Fabio C.L. Almeida, Federal University of Rio de Janeiro, Universidade Estadual Paulista (UNESP), Multidisciplinary Center for Research in Biology (NUMPEX), Oswaldo Cruz Foundation (FIOCRUZ), and Rio BioNMR Network
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Gene Expression Regulation, Viral ,Models, Molecular ,Binding Sites ,SARS-CoV-2 ,Spectrum Analysis ,COVID-19 ,Hydrogen Bonding ,General Medicine ,DNA ,Nucleocapsid Proteins ,DNA/RNA binding protein ,Biochemistry ,Article ,Binding specificity ,Structure-Activity Relationship ,SARS-CoV-2 nucleocapsid protein ,Structural Biology ,Nucleic Acids ,Host-Pathogen Interactions ,Humans ,RNA ,Protein Interaction Domains and Motifs ,Molecular Biology ,Protein Binding - Abstract
Made available in DSpace on 2022-04-28T19:50:20Z (GMT). No. of bitstreams: 0 Previous issue date: 2022-04-01 Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) The SARS-CoV-2 nucleocapsid protein (N) is a multifunctional promiscuous nucleic acid-binding protein, which plays a major role in nucleocapsid assembly and discontinuous RNA transcription, facilitating the template switch of transcriptional regulatory sequences (TRS). Here, we dissect the structural features of the N protein N-terminal domain (N-NTD) and N-NTD plus the SR-rich motif (N-NTD-SR) upon binding to single and double-stranded TRS DNA, as well as their activities for dsTRS melting and TRS-induced liquid-liquid phase separation (LLPS). Our study gives insights on the specificity for N-NTD(-SR) interaction with TRS. We observed an approximation of the triple-thymidine (TTT) motif of the TRS to β-sheet II, giving rise to an orientation difference of ~25° between dsTRS and non-specific sequence (dsNS). It led to a local unfavorable energetic contribution that might trigger the melting activity. The thermodynamic parameters of binding of ssTRSs and dsTRS suggested that the duplex dissociation of the dsTRS in the binding cleft is entropically favorable. We showed a preference for TRS in the formation of liquid condensates when compared to NS. Moreover, our results on DNA binding may serve as a starting point for the design of inhibitors, including aptamers, against N, a possible therapeutic target essential for the virus infectivity. Institute of Medical Biochemistry Federal University of Rio de Janeiro Multiuser Center for Biomolecular Innovation (CMIB) Department of Physics São Paulo State University (UNESP) National Center of Nuclear Magnetic Resonance (CNRMN) CENABIO Federal University of Rio de Janeiro Faculty of Pharmacy Federal University of Rio de Janeiro Protein Advanced Biochemistry (PAB) CENABIO Federal University of Rio de Janeiro Department of Biochemistry Institute of Chemistry Federal University of Rio de Janeiro Multidisciplinary Center for Research in Biology (NUMPEX) Campus Duque de Caxias Federal University of Rio de Janeiro Laboratory of Toxinology Oswaldo Cruz Foundation (FIOCRUZ) Rio BioNMR Network Multiuser Center for Biomolecular Innovation (CMIB) Department of Physics São Paulo State University (UNESP) FAPERJ: 202.279/2018 FAPERJ: 204.432/2014 FAPERJ: 210.361/2015 FAPERJ: 239.229/2018 FAPERJ: 255.940/2020 CNPq: 309564/2017-4 CNPq: 439306/2018-3
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- 2021
7. Structure and Assembly of the Enterohemorrhagic Escherichia coli Type 4 Pilus
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Michael Nilges, Gisele Cardoso de Amorim, Nadia Izadi-Pruneyre, Edward H. Egelman, Weili Zheng, Camille Jollivet, Olivera Francetic, Areli Luna Rico, Ingrid Guilvout, Benjamin Bardiaux, Bioinformatique structurale - Structural Bioinformatics, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Résonance Magnétique Nucléaire des Biomolécules, Biochimie des Interactions Macromoléculaires / Biochemistry of Macromolecular Interactions, Université Paris Diderot - Paris 7 (UPD7), University of Virginia [Charlottesville], This work was funded by the Institut Pasteur, the Centre National de la Recherche Scientifique (CNRS), the French Agence Nationale de la Recherche (ANR-14-CE09-0004 to O.F.), the Fondation pour la Recherche Médicale (Equipe FRM 2017M.DEQ20170839114 to M.N.), the European Union FP7-IDEAS-ERC 294809 (to M.N.), and the NIH R35GM122510 (to E.H.E.). A.L.R. was funded by the Pasteur Paris University (PPU) international PhD program., We are grateful to Muriel Delepierre and Daniel Ladant for support and interest in this work., ANR-14-CE09-0004,FiberSpace,Pili de type IV et pseudopili: structure, dynamique, assemblage et fonction moléculaire(2014), European Project: 294809,EC:FP7:ERC,ERC-2011-ADG_20110310,BAYCELLS(2012), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and University of Virginia
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Protein Conformation, alpha-Helical ,Pilus assembly ,Gene Expression ,medicine.disease_cause ,Pilus ,hemorrhagic coli pilus (HCP) ,Structural Biology ,Cloning, Molecular ,0303 health sciences ,Type II secretion system ,biology ,[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM] ,Chemistry ,Escherichia coli Proteins ,030302 biochemistry & molecular biology ,pilus assembly ,[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] ,Recombinant Proteins ,Cell biology ,Molecular Docking Simulation ,Enterohemorrhagic Escherichia coli ,Thermodynamics ,pilin structure ,Fimbriae Proteins ,Protein Binding ,Protein subunit ,Genetic Vectors ,Static Electricity ,Article ,type 4 pili ,03 medical and health sciences ,type II secretion system ,medicine ,Escherichia coli ,Protein Interaction Domains and Motifs ,Amino Acid Sequence ,Cell adhesion ,Molecular Biology ,Nuclear Magnetic Resonance, Biomolecular ,030304 developmental biology ,Binding Sites ,Sequence Homology, Amino Acid ,molecular modeling ,Cryoelectron Microscopy ,Periplasmic space ,biochemical phenomena, metabolism, and nutrition ,[SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology ,NMR ,Kinetics ,Pilin ,Fimbriae, Bacterial ,Mutation ,biology.protein ,bacteria ,EHEC ,cryo-EM ,Protein Conformation, beta-Strand ,Sequence Alignment - Abstract
International audience; Bacterial type 4a pili are dynamic surface filaments that promote bacterial adherence, motility, and macromolecular transport. Their genes are highly conserved among enterobacteria and their expression in enterohemorrhagic Escherichia coli (EHEC) promotes adhesion to intestinal epithelia and pro-inflammatory signaling. To define the molecular basis of EHEC pilus assembly, we determined the structure of the periplasmic domain of its major subunit PpdD (PpdDp), a prototype of an enterobacterial pilin subfamily containing two disulfide bonds. The structure of PpdDp, determined by NMR, was then docked into the density envelope of purified EHEC pili obtained by cryoelectron microscopy (cryo-EM). Cryo-EM reconstruction of EHEC pili at ∼8 Å resolution revealed extremely high pilus flexibility correlating with a large extended region of the pilin stem. Systematic mutagenesis combined with functional and interaction analyses identified charged residues essential for pilus assembly. Structural information on exposed regions and interfaces between EHEC pilins is relevant for vaccine and drug discovery.
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- 2019
8. Structural basis of the signalling through a bacterial membrane receptor HasR deciphered by an integrative approach
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Philippe Delepelaire, Gisele Cardoso de Amorim, Rémi Fronzes, Javier Pérez, Catherine Simenel, Gérard Pehau-Arnaudet, Muriel Delepierre, Idir Malki, Olga Roudenko, Alexandros Koutsioubas, Francesca Gubellini, Nadia Izadi-Pruneyre, Halina Wójtowicz, Ada Prochnicka-Chalufour, Résonance Magnétique Nucléaire des Biomolécules, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Synchrotron SOLEIL (SSOLEIL), Centre National de la Recherche Scientifique (CNRS), Centre de Recherche et Innovation Technologique (CITECH), Institut Pasteur [Paris] (IP), Biologie Structurale de la Sécrétion Bactérienne, Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association-Helmholtz-Gemeinschaft = Helmholtz Association, Institut de biologie physico-chimique (IBPC (FR_550)), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), This work was funded by the Institut Pasteur, the Centre National de la Recherche Scientifique (CNRS), two grants from the ANR (Agence Nationale de la Recherche) [grant numbers HEMESTOCKEXCHANGE 12-BSV3-0022-01 and HEMETRANS 08-BLAN-0160], Equipement d'Excellence CACSICE and SOLEIL [grant number 2013448]. H.W. was funded by postdoctoral fellowships from the Mairie de Paris [grant number 2012-209]., We thank Emmanuel Frachon, from the Platform of Recombinant Protein of the Institut Pasteur, for bacterial cell production. We thank Dominique Durand and Patrice Vachette for the first SAXS measurements on HasR. We thank Florence Cordier and Bertrand Raynal for helpful discussions., ANR-12-BSV3-0022,HEMESTOCKEXCHANGE,Hème et porphyrine chez des bactéries modèle: des fonctions aux mécanismes(2012), ANR-08-BLAN-0160,HEMETRANS,Transfert et transport d'hème entre protéines et signalisation transmembranaire(2008), ANR-11-EQPX-0008,CACSICE,Centre d'analyse de systèmes complexes dans les environnements complexes(2011), ANR-12-BS08-0020,SynchroKin,Mise en place d'une technique expérimentale pour la mesure de données cinétiques et mécanistiques utilisant la radiation synchrotron SOLEIL(2012), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Institut Pasteur [Paris], and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
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0301 basic medicine ,Magnetic Resonance Spectroscopy ,transmembrane signalling ,Heme ,Biology ,Crystallography, X-Ray ,Biochemistry ,03 medical and health sciences ,Bacterial Proteins ,Cell surface receptor ,bacterial nutrient transporter ,HasR ,Gene expression ,[SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM] ,Molecular Biology ,Gene ,Research Articles ,Serratia marcescens ,[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM] ,digestive, oral, and skin physiology ,Membrane Transport Proteins ,haem ,Transporter ,Cell Biology ,Periplasmic space ,[SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology ,Cell biology ,[SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics ,Microscopy, Electron ,[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology ,030104 developmental biology ,Signalling ,Cytoplasm ,Signal transduction ,integrative approach ,Research Article ,Protein Binding ,Signal Transduction - Abstract
In bacteria, some scarce nutrients are sensed, bound and internalized by their specific transporter. In the present study, using an integrative structural approach, we study HasR, a bacterial haem transporter in both its free and its loaded forms., Bacteria use diverse signalling pathways to adapt gene expression to external stimuli. In Gram-negative bacteria, the binding of scarce nutrients to membrane transporters triggers a signalling process that up-regulates the expression of genes of various functions, from uptake of nutrient to production of virulence factors. Although proteins involved in this process have been identified, signal transduction through this family of transporters is not well understood. In the present study, using an integrative approach (EM, SAXS, X-ray crystallography and NMR), we have studied the structure of the haem transporter HasR captured in two stages of the signalling process, i.e. before and after the arrival of signalling activators (haem and its carrier protein). We show for the first time that the HasR domain responsible for signal transfer: (i) is highly flexible in two stages of signalling; (ii) extends into the periplasm at approximately 70–90 Å (1 Å=0.1 nm) from the HasR β-barrel; and (iii) exhibits local conformational changes in response to the arrival of signalling activators. These features would favour the signal transfer from HasR to its cytoplasmic membrane partners.
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- 2016
9. 1H, 15N and 13C resonance assignments of PpdD, a type IV pilin from enterohemorrhagic Escherichia coli
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Nadia Izadi-Pruneyre, David A. Cisneros, Gisele Cardoso de Amorim, Muriel Delepierre, and Olivera Francetic
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biology ,Fimbria ,medicine.disease_cause ,Biochemistry ,Pilus ,Transduction (genetics) ,chemistry.chemical_compound ,chemistry ,Structural Biology ,Pilin ,medicine ,biology.protein ,Twitching motility ,Escherichia coli ,DNA - Abstract
Bacterial type 4 pili (T4P) are long flexible fibers involved in adhesion, DNA uptake, phage transduction, aggregation and a flagella-independent movement called "twitching motility". T4P comprise ...
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- 2012
10. (1)H, (13)C and (15)N resonance assignments of the periplasmic signalling domain of HasR, a TonB-dependent outer membrane heme transporter
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Nadia Izadi-Pruneyre, Catherine Simenel, Muriel Delepierre, Idir Malki, Ada Prochnicka-Chalufour, and Gisele Cardoso de Amorim
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biology ,Membrane transport protein ,Cell ,Membrane Transport Proteins ,Transporter ,Periplasmic space ,biology.organism_classification ,Biochemistry ,Cell biology ,Protein Structure, Tertiary ,chemistry.chemical_compound ,medicine.anatomical_structure ,chemistry ,Bacterial Proteins ,Structural Biology ,Cytoplasm ,Serratia marcescens ,Periplasm ,biology.protein ,medicine ,bacteria ,Bacterial outer membrane ,Heme ,Nuclear Magnetic Resonance, Biomolecular - Abstract
TonB-dependent transporters (TBDTs) are bacterial outer membrane proteins that internalize nutrients such as vitamin B12, metal complexes, heme, some carbohydrates, etc. In addition to their transport activity, several TBDTs are also involved in a signalling cascade from the cell surface into the cytoplasm, via their periplasmic signalling domain. Here we report the backbone and side chain resonance assignments of the signalling domain of HasR, a TonB-dependent outer membrane heme transporter from Serratia marcescens as a first step towards its structural study.
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- 2012
11. The Structure of HasB Reveals a New Class of TonB Protein Fold
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Nadia Izadi-Pruneyre, Muriel Delepierre, Julien Lefèvre, Gisele Cardoso de Amorim, Ada Prochnicka-Chalufour, Catherine Simenel, Cécile Wandersman, and Philippe Delepelaire
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Macromolecular Assemblies ,Models, Molecular ,Signal peptide ,Protein Structure ,Protein Folding ,Protein Conformation ,Molecular Sequence Data ,Biophysics ,lcsh:Medicine ,Plasma protein binding ,Biology ,Biochemistry ,Microbiology ,Protein Structure, Secondary ,Transmembrane Transport Proteins ,Protein structure ,Bacterial Proteins ,Macromolecular Structure Analysis ,polycyclic compounds ,Inner membrane ,Amino Acid Sequence ,Biomacromolecule-Ligand Interactions ,Amino Acids ,lcsh:Science ,Binding Sites ,Multidisciplinary ,lcsh:R ,Proteins ,Computational Biology ,Membrane Proteins ,Bacteriology ,Periplasmic space ,biochemical phenomena, metabolism, and nutrition ,Cell biology ,Membrane protein ,bacteria ,lcsh:Q ,Protein folding ,Peptides ,Bacterial outer membrane ,Sequence Alignment ,Research Article ,Protein Binding - Abstract
TonB is a key protein in active transport of essential nutrients like vitamin B12 and metal sources through the outer membrane transporters of Gram-negative bacteria. This inner membrane protein spans the periplasm, contacts the outer membrane receptor by its periplasmic domain and transduces energy from the cytoplasmic membrane pmf to the receptor allowing nutrient internalization. Whereas generally a single TonB protein allows the acquisition of several nutrients through their cognate receptor, in some species one particular TonB is dedicated to a specific system. Despite a considerable amount of data available, the molecular mechanism of TonB-dependent active transport is still poorly understood. In this work, we present a structural study of a TonB-like protein, HasB dedicated to the HasR receptor. HasR acquires heme either free or via an extracellular heme transporter, the hemophore HasA. Heme is used as an iron source by bacteria. We have solved the structure of the HasB periplasmic domain of Serratia marcescens and describe its interaction with a critical region of HasR. Some important differences are observed between HasB and TonB structures. The HasB fold reveals a new structural class of TonB-like proteins. Furthermore, we have identified the structural features that explain the functional specificity of HasB. These results give a new insight into the molecular mechanism of nutrient active transport through the bacterial outer membrane and present the first detailed structural study of a specific TonB-like protein and its interaction with the receptor.
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- 2013
12. Comprehensive Fragment Screening of the SARS‐CoV‐2 Proteome Explores Novel Chemical Space for Drug Development
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Hannes Berg, Maria A. Wirtz Martin, Nadide Altincekic, Islam Alshamleh, Jasleen Kaur Bains, Julius Blechar, Betül Ceylan, Vanessa de Jesus, Karthikeyan Dhamotharan, Christin Fuks, Santosh L. Gande, Bruno Hargittay, Katharina F. Hohmann, Marie T. Hutchison, Sophie Marianne Korn, Robin Krishnathas, Felicitas Kutz, Verena Linhard, Tobias Matzel, Nathalie Meiser, Anna Niesteruk, Dennis J. Pyper, Linda Schulte, Sven Trucks, Kamal Azzaoui, Marcel J. J. Blommers, Yojana Gadiya, Reagon Karki, Andrea Zaliani, Philip Gribbon, Marcius da Silva Almeida, Cristiane Dinis Anobom, Anna L. Bula, Matthias Bütikofer, Ícaro Putinhon Caruso, Isabella Caterina Felli, Andrea T. Da Poian, Gisele Cardoso de Amorim, Nikolaos K. Fourkiotis, Angelo Gallo, Dhiman Ghosh, Francisco Gomes‐Neto, Oksana Gorbatyuk, Bing Hao, Vilius Kurauskas, Lauriane Lecoq, Yunfeng Li, Nathane Cunha Mebus‐Antunes, Miguel Mompeán, Thais Cristtina Neves‐Martins, Martí Ninot‐Pedrosa, Anderson S. Pinheiro, Letizia Pontoriero, Yulia Pustovalova, Roland Riek, Angus J. Robertson, Marie Jose Abi Saad, Miguel Á. Treviño, Aikaterini C. Tsika, Fabio C. L. Almeida, Ad Bax, Katherine Henzler‐Wildman, Jeffrey C. Hoch, Kristaps Jaudzems, Douglas V. Laurents, Julien Orts, Roberta Pierattelli, Georgios A. Spyroulias, Elke Duchardt‐Ferner, Jan Ferner, Boris Fürtig, Martin Hengesbach, Frank Löhr, Nusrat Qureshi, Christian Richter, Krishna Saxena, Andreas Schlundt, Sridhar Sreeramulu, Anna Wacker, Julia E. Weigand, Julia Wirmer‐Bartoschek, Jens Wöhnert, Harald Schwalbe, State of Hesse, German Research Foundation, European Commission, Ministero dell'Istruzione, dell'Università e della Ricerca, Agence Nationale de la Recherche (France), Centre National de la Recherche Scientifique (France), National Institutes of Health (US), National Science Foundation (US), Latvian Council of Science, Berg, Hannes, Wirtz Martin, Maria A., Altincekic, Nadide, Alshamleh, Islam, Dhamotharan, Karthikeyan, Marianne Korn, Sophie, Schulte, Linda, da Silva Almeida, Marcius, Caterina Felli, Isabella, Fourkiotis, Nikolaos K., Gallo, Angelo, Ninot-Pedrosa, Martí, Pontoriero, Letizia, Treviño, Miguel A., Tsika, Aikaterini C., Almeida, Fabio C.L., Bax, Ad, Henzler-Wildman, Katherine, Hoch, Jeffrey C., Jaudzems, Kristaps, Laurents, D.V., Ferner, Jan, Hengesbach, Martin, Löhr, Frank, Qureshi, Nusrat, Richter, Christian, Schlundt, Andreas, Weigand, Julia E., Wirmer-Bartoschek, Julia, Schwalbe, Harald, and Publica
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Proteome ,SARS-CoV-2 ,Protein ,COVID19-NMR ,General Medicine ,General Chemistry ,Ligands ,NMR Spectroscopy ,Catalysis ,COVID-19 Drug Treatment ,Fragment Screening ,Drug Design ,Drug Discovery ,Humans ,COVID19 * drug discovery * fragment screening * NMR spectroscopy * SARS-CoV-2 - Abstract
12 pags., 4 figs., 3 tabs., SARS-CoV-2 (SCoV2) and its variants of concern pose serious challenges to the public health. The variants increased challenges to vaccines, thus necessitating for development of new intervention strategies including anti-virals. Within the international Covid19-NMR consortium, we have identified binders targeting the RNA genome of SCoV2. We established protocols for the production and NMR characterization of more than 80 % of all SCoV2 proteins. Here, we performed an NMR screening using a fragment library for binding to 25 SCoV2 proteins and identified hits also against previously unexplored SCoV2 proteins. Computational mapping was used to predict binding sites and identify functional moieties (chemotypes) of the ligands occupying these pockets. Striking consensus was observed between NMR-detected binding sites of the main protease and the computational procedure. Our investigation provides novel structural and chemical space for structure-based drug design against the SCoV2 proteome., Work at BMRZ is supported by the state of Hesse. Work in Covid19-NMR was supported by the Goethe Corona Funds, by the IWBEFRE-program 20007375 of state of Hesse, the DFG through CRC902: “Molecular Principles of RNA-based regulation.” and through infrastructure funds (project numbers: 277478796, 277479031, 392682309, 452632086, 70653611) and by European Union’s Horizon 2020 research and innovation program iNEXT-discovery under grant agreement No 871037. BY-COVID receives funding from the European Union’s Horizon Europe Research and Innovation Programme under grant agreement number 101046203. “INSPIRED” (MIS 5002550) project, implemented under the Action “Reinforcement of the Research and Innovation Infrastructure,” funded by the Operational Program “Competitiveness, Entrepreneurship and Innovation” (NSRF 2014–2020) and co-financed by Greece and the EU (European Regional Development Fund) and the FP7 REGPOT CT-2011-285950—“SEE-DRUG” project (purchase of UPAT’s 700 MHz NMR equipment). The support of the CERM/CIRMMP center of Instruct-ERIC is gratefully acknowledged. This work has been funded in part by a grant of the Italian Ministry of University and Research (FISR2020IP_02112, ID-COVID) and by Fondazione CR Firenze. A.S. is supported by the Deutsche Forschungsgemeinschaft [SFB902/B16, SCHL2062/2-1] and the Johanna Quandt Young Academy at Goethe [2019/AS01]. M.H. and C.F. thank SFB902 and the Stiftung Polytechnische Gesellschaft for the Scholarship. L.L. work was supported by the French National Research Agency (ANR, NMR-SCoV2-ORF8), the Fondation de la Recherche Médicale (FRM, NMR-SCoV2-ORF8), FINOVI and the IR-RMN-THC Fr3050 CNRS. Work at UConn Health was supported by grants from the US National Institutes of Health (R01 GM135592 to B.H., P41 GM111135 and R01 GM123249 to J.C.H.) and the US National Science Foundation (DBI 2030601 to J.C.H.). Latvian Council of Science Grant No. VPP-COVID-2020/1-0014. National Science Foundation EAGER MCB-2031269. This work was supported by the grant Krebsliga KFS-4903-08-2019 and SNF-311030_192646 to J.O. P.G. (ITMP) The EOSC Future project is co-funded by the European Union Horizon Programme call INFRAEOSC-03-2020—Grant Agreement Number 101017536. Open Access funding enabled and organized by Projekt DEAL
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