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Rossotti M, Arceri D, Mansuelle P, Bornet O, Durand A, Ouchane S, Launay H, Dorlet P. The green cupredoxin CopI is a multicopper protein able to oxidize Cu(I). J Inorg Biochem 2024; 254:112503. [PMID: 38364337 DOI: 10.1016/j.jinorgbio.2024.112503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 02/18/2024]
Abstract
Anthropogenic activities in agriculture and health use the antimicrobial properties of copper. This has led to copper accumulation in the environment and contributed to the emergence of copper resistant microorganisms. Understanding bacterial copper homeostasis diversity is therefore highly relevant since it could provide valuable targets for novel antimicrobial treatments. The periplasmic CopI protein is a monodomain cupredoxin comprising several copper binding sites and is directly involved in copper resistance in bacteria. However, its structure and mechanism of action are yet to be determined. To study the different binding sites for cupric and cuprous ions and to understand their possible interactions, we have used mutants of the putative copper binding modules of CopI and spectroscopic methods to characterize their properties. We show that CopI is able to bind a cuprous ion in its central histidine/methionine-rich region and oxidize it thanks to its cupredoxin center. The resulting cupric ion can bind to a third site at the N-terminus of the protein. Nuclear magnetic resonance spectroscopy revealed that the central histidine/methionine-rich region exhibits a dynamic behavior and interacts with the cupredoxin binding region. CopI is therefore likely to participate in copper resistance by detoxifying the cuprous ions from the periplasm.
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Affiliation(s)
- Melanie Rossotti
- CNRS, Aix Marseille Univ, BIP, Institut de Microbiologie de la Méditerranée (IMM), Marseille, France
| | - Diletta Arceri
- CNRS, Aix Marseille Univ, BIP, Institut de Microbiologie de la Méditerranée (IMM), Marseille, France
| | - Pascal Mansuelle
- CNRS, FR3479, Institut de Microbiologie de la Méditerranée (IMM), Plateforme Protéomique, Marseille Protéomique (MaP), IbiSA Labelled, Aix Marseille Univ, Marseille, France
| | - Olivier Bornet
- CNRS, Aix Marseille Univ, Institut de Microbiologie de la Méditerranée (IMM), Marseille, France
| | - Anne Durand
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Soufian Ouchane
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Hélène Launay
- CNRS, Aix Marseille Univ, BIP, Institut de Microbiologie de la Méditerranée (IMM), Marseille, France
| | - Pierre Dorlet
- CNRS, Aix Marseille Univ, BIP, Institut de Microbiologie de la Méditerranée (IMM), Marseille, France.
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Sahaka M, Bornet O, Marchand A, Lafont D, Gontero B, Carrière F, Launay H. Monitoring galactolipid digestion and simultaneous changes in lipid-bile salt micellar organization by real-time NMR spectroscopy. Chem Phys Lipids 2024; 258:105361. [PMID: 37981224 DOI: 10.1016/j.chemphyslip.2023.105361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/08/2023] [Accepted: 11/10/2023] [Indexed: 11/21/2023]
Abstract
The use of Nuclear Magnetic Resonance spectroscopy for studying lipid digestion in vitro most often consists of quantifying lipolysis products after they have been extracted from the reaction medium using organic solvents. However, the current sensitivity level of NMR spectrometers makes possible to avoid the extraction step and continuously quantify the lipids directly in the reaction medium. We used real-time 1H NMR spectroscopy and guinea pig pancreatic lipase-related protein 2 (GPLRP2) as biocatalyst to monitor in situ the lipolysis of monogalactosyl diacylglycerol (MGDG) in the form of mixed micelles with the bile salt sodium taurodeoxycholate (NaTDC). Residual substrate and lipolysis products (monogalactosyl monoacylglycerol (MGMG); monogalactosylglycerol (MGG) and octanoic acid (OA) were simultaneously quantified throughout the reaction thanks to specific proton resonances. Lipolysis was complete with the release of all MGDG fatty acids. These results were confirmed by thin layer chromatography (TLC) and densitometry after lipid extraction at different reaction times. Using diffusion-ordered NMR spectroscopy (DOSY), we could also estimate the diffusion coefficients of all the reaction compounds and deduce the hydrodynamic radius of the lipid aggregates in which they were present. It was shown that MGDG-NaTDC mixed micelles with an initial hydrodynamic radius rH of 7.3 ± 0.5 nm were changed into smaller micelles of NaTDC-MGDG-MGMG of 2.3 ± 0.5 nm in the course of the lipolysis reaction, and finally into NaTDC-OA mixed micelles (rH of 2.9 ± 0.5 nm) and water soluble MGG. These results provide a better understanding of the digestion of galactolipids by PLRP2, a process that leads to the complete micellar solubilisation of their fatty acids and renders their intestinal absorption possible.
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Affiliation(s)
- Moulay Sahaka
- Aix Marseille Univ, CNRS, UMR7281 Bioénergétique et Ingénierie des Protéines, 31 Chemin Joseph Aiguier, 13009 Marseille, France
| | - Olivier Bornet
- NMR Platform, Institut de Microbiologie de la Méditerranée, Aix Marseille Univ, 13009 Marseille, France
| | - Achille Marchand
- Aix Marseille Univ, CNRS, UMR7281 Bioénergétique et Ingénierie des Protéines, 31 Chemin Joseph Aiguier, 13009 Marseille, France
| | - Dominique Lafont
- Laboratoire de Chimie Organique 2-GLYCO, ICBMS UMR 5246, CNRS-Université Claude Bernard Lyon 1, Université de Lyon, bâtiment Lederer, 1 rue Victor Grignard, 69622 Villeurbanne Cedex, France
| | - Brigitte Gontero
- Aix Marseille Univ, CNRS, UMR7281 Bioénergétique et Ingénierie des Protéines, 31 Chemin Joseph Aiguier, 13009 Marseille, France
| | - Frédéric Carrière
- Aix Marseille Univ, CNRS, UMR7281 Bioénergétique et Ingénierie des Protéines, 31 Chemin Joseph Aiguier, 13009 Marseille, France.
| | - Hélène Launay
- Aix Marseille Univ, CNRS, UMR7281 Bioénergétique et Ingénierie des Protéines, 31 Chemin Joseph Aiguier, 13009 Marseille, France.
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3
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Jensen UT, Rohner D, Bornet O, Carron D, Garner P, Loupi D, Antonakis J. Combating COVID-19 with charisma: Evidence on governor speeches in the United States. Leadersh Q 2023:101702. [PMID: 37361053 PMCID: PMC10201331 DOI: 10.1016/j.leaqua.2023.101702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 04/22/2023] [Accepted: 05/02/2023] [Indexed: 06/28/2023]
Abstract
Using field and laboratory data, we show that leader charisma can affect COVID-related mitigating behaviors. We coded a panel of U.S. governor speeches for charisma signaling using a deep neural network algorithm. The model explains variation in stay-at-home behavior of citizens based on their smart phone data movements, showing a robust effect of charisma signaling: stay-at-home behavior increased irrespective of state-level citizen political ideology or governor party allegiance. Republican governors with a particularly high charisma signaling score impacted the outcome more relative to Democratic governors in comparable conditions. Our results also suggest that one standard deviation higher charisma signaling in governor speeches could potentially have saved 5,350 lives during the study period (02/28/2020-05/14/2020). Next, in an incentivized laboratory experiment we found that politically conservative individuals are particularly prone to believe that their co-citizens will follow governor appeals to distance or stay at home when exposed to a speech that is high in charisma; these beliefs in turn drive their preference to engage in those behaviors. These results suggest that political leaders should consider additional "soft-power" levers like charisma-which can be learned-to complement policy interventions for pandemics or other public heath crises, especially with certain populations who may need a "nudge."
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Affiliation(s)
- Ulrich Thy Jensen
- Center for Organization Research and Design, School of Public Affairs, Arizona State University, United States
- Crown Prince Frederik Center for Public Leadership, Aarhus University, Denmark
| | - Dominic Rohner
- Faculty of Business and Economics (HEC Lausanne), University of Lausanne & E4S, Centre for Economic Policy Research (CEPR), Switzerland
| | | | | | | | | | - John Antonakis
- Faculty of Business and Economics (HEC Lausanne), University of Lausanne & E4S, Switzerland
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Attia B, Serrano B, Bornet O, Guerlesquin F, My L, Castaing JP, Mignot T, Elantak L. 1H, 13C and 15N chemical shift assignments of the ZnR and GYF cytoplasmic domains of the GltJ protein from Myxococcus xanthus. Biomol NMR Assign 2022; 16:219-223. [PMID: 35445965 DOI: 10.1007/s12104-022-10083-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/30/2022] [Indexed: 06/14/2023]
Abstract
Bacterial cell motility is essential for a range of physiological phenomena such as nutrient sensing, predation, biofilm formation and pathogenesis. One of the most intriguing motilities is bacterial gliding, which is defined as the ability of some bacteria to move across surfaces without an external appendage. In Myxococcus xanthus, gliding motility depends on the assembly of focal adhesion complexes (FAC) which include the Glt mutiprotein complex and allow directional movement of individual cells (A-motility). Within the Glt multiprotein complex, GltJ is one of the key proteins involved in FAC assembly. In this work we report complete backbone and side chain 1H, 13C and 15N chemical shifts of the two cytoplasmic domains of GltJ, GltJ-ZnR (BMRB No. 51104) and GltJ-GYF (BMRB No. 51096). These data provide the first step toward the first high resolution structures of protein domains from the Glt machinery and the atomic level characterization of GltJ cytoplasmic activity during FAC assembly.
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Affiliation(s)
- Bouchra Attia
- Laboratoire d'Ingénierie Des Systèmes Macromoléculaires, Centre National de La Recherche Scientifique (CNRS), Aix-Marseille Université, UMR7255, 13009, Marseille, France
| | - Bastien Serrano
- Laboratoire d'Ingénierie Des Systèmes Macromoléculaires, Centre National de La Recherche Scientifique (CNRS), Aix-Marseille Université, UMR7255, 13009, Marseille, France
| | - Olivier Bornet
- Centre National de La Recherche Scientifique (CNRS), Institut de Microbiologie de La Méditerranée, FR3479, 13009, Marseille, France
| | - Françoise Guerlesquin
- Laboratoire d'Ingénierie Des Systèmes Macromoléculaires, Centre National de La Recherche Scientifique (CNRS), Aix-Marseille Université, UMR7255, 13009, Marseille, France
| | - Laetitia My
- Laboratoire de Chimie Bactérienne, Centre National de La Recherche Scientifique (CNRS), Aix-Marseille Université, UMR7283, 13009, Marseille, France
| | - Jean-Philippe Castaing
- Laboratoire de Chimie Bactérienne, Centre National de La Recherche Scientifique (CNRS), Aix-Marseille Université, UMR7283, 13009, Marseille, France
| | - Tâm Mignot
- Laboratoire de Chimie Bactérienne, Centre National de La Recherche Scientifique (CNRS), Aix-Marseille Université, UMR7283, 13009, Marseille, France
| | - Latifa Elantak
- Laboratoire d'Ingénierie Des Systèmes Macromoléculaires, Centre National de La Recherche Scientifique (CNRS), Aix-Marseille Université, UMR7255, 13009, Marseille, France.
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5
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Launay H, Shao H, Bornet O, Cantrelle FX, Lebrun R, Receveur-Brechot V, Gontero B. Flexibility of Oxidized and Reduced States of the Chloroplast Regulatory Protein CP12 in Isolation and in Cell Extracts. Biomolecules 2021; 11:biom11050701. [PMID: 34066751 PMCID: PMC8151241 DOI: 10.3390/biom11050701] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/03/2021] [Accepted: 05/04/2021] [Indexed: 12/12/2022] Open
Abstract
In the chloroplast, Calvin–Benson–Bassham enzymes are active in the reducing environment created in the light by electrons from the photosystems. In the dark, these enzymes are inhibited, mainly caused by oxidation of key regulatory cysteine residues. CP12 is a small protein that plays a role in this regulation with four cysteine residues that undergo a redox transition. Using amide-proton exchange with solvent, measured by nuclear magnetic resonance (NMR) and mass-spectrometry, we confirmed that reduced CP12 is intrinsically disordered. Using real-time NMR, we showed that the oxidation of the two disulfide bridges is simultaneous. In oxidized CP12, the C23–C31 pair is in a region that undergoes a conformational exchange in the NMR-intermediate timescale. The C66–C75 pair is in the C-terminus that folds into a stable helical turn. We confirmed that these structural states exist in a physiologically relevant environment: a cell extract from Chlamydomonas reinhardtii. Consistent with these structural equilibria, the reduction is slower for the C66–C75 pair than for the C23–C31 pair. The redox mid-potentials for the two cysteine pairs differ and are similar to those found for glyceraldehyde 3-phosphate dehydrogenase and phosphoribulokinase, consistent with the regulatory role of CP12.
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Affiliation(s)
- Helene Launay
- Aix Marseille Univ, CNRS, BIP, UMR7281, F-13402 Marseille, France; (H.S.); (V.R.-B.)
- Correspondence: (H.L.); (B.G.)
| | - Hui Shao
- Aix Marseille Univ, CNRS, BIP, UMR7281, F-13402 Marseille, France; (H.S.); (V.R.-B.)
| | - Olivier Bornet
- NMR Platform, Institut de Microbiologie de la Méditerranée, Aix Marseille Univ, F-13009 Marseille, France;
| | - Francois-Xavier Cantrelle
- CNRS, ERL9002, Integrative Structural Biology, Univ. Lille, F-59658 Lille, France;
- U1167, INSERM, CHU Lille, Institut Pasteur de Lille, F-59019 Lille, France
| | - Regine Lebrun
- Plate-forme Protéomique, Marseille Protéomique (MaP), IMM FR 3479, 31 Chemin Joseph Aiguier, F-13009 Marseille, France;
| | | | - Brigitte Gontero
- Aix Marseille Univ, CNRS, BIP, UMR7281, F-13402 Marseille, France; (H.S.); (V.R.-B.)
- Correspondence: (H.L.); (B.G.)
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6
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Roblin C, Chiumento S, Bornet O, Nouailler M, Müller CS, Jeannot K, Basset C, Kieffer-Jaquinod S, Couté Y, Torelli S, Le Pape L, Schünemann V, Olleik H, De La Villeon B, Sockeel P, Di Pasquale E, Nicoletti C, Vidal N, Poljak L, Iranzo O, Giardina T, Fons M, Devillard E, Polard P, Maresca M, Perrier J, Atta M, Guerlesquin F, Lafond M, Duarte V. The unusual structure of Ruminococcin C1 antimicrobial peptide confers clinical properties. Proc Natl Acad Sci U S A 2020; 117:19168-19177. [PMID: 32719135 PMCID: PMC7431081 DOI: 10.1073/pnas.2004045117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The emergence of superbugs developing resistance to antibiotics and the resurgence of microbial infections have led scientists to start an antimicrobial arms race. In this context, we have previously identified an active RiPP, the Ruminococcin C1, naturally produced by Ruminococcus gnavus E1, a symbiont of the healthy human intestinal microbiota. This RiPP, subclassified as a sactipeptide, requires the host digestive system to become active against pathogenic Clostridia and multidrug-resistant strains. Here we report its unique compact structure on the basis of four intramolecular thioether bridges with reversed stereochemistry introduced posttranslationally by a specific radical-SAM sactisynthase. This structure confers to the Ruminococcin C1 important clinical properties including stability to digestive conditions and physicochemical treatments, a higher affinity for bacteria than simulated intestinal epithelium, a valuable activity at therapeutic doses on a range of clinical pathogens, mediated by energy resources disruption, and finally safety for human gut tissues.
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Affiliation(s)
- Clarisse Roblin
- Aix-Marseille Université, CNRS, Centrale Marseille, Institut des Sciences Moléculaires de Marseille (iSm2), 13013 Marseille, France
- ADISSEO France SAS, Centre d'Expertise et de Recherche en Nutrition, 03600 Commentry, France
| | - Steve Chiumento
- Université Grenoble Alpes, Commissariat à l'Energie Atomique et aux énergies alternatives (CEA), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Chimie et Biologie des Métaux (CBM), CNRS UMR 5249, 38054 Grenoble, France
| | - Olivier Bornet
- NMR Platform, Institut de Microbiologie de la Méditerranée, CNRS, Aix-Marseille Université, 13009 Marseille, France;
| | - Matthieu Nouailler
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR 7255, Institut de Microbiologie de la Méditerranée, CNRS, Aix-Marseille Université, 13009 Marseille, France
| | - Christina S Müller
- Fachbereich Physik, Technische Universität Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Katy Jeannot
- Centre National de Référence de la Résistance aux Antibiotiques, Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Besançon, 25030 Besançon, France
- UMR 6249 Chrono-Environnement, Unité de Formation et de Recherche (UFR) Santé, Université de Bourgogne-Franche-Comté, 25030 Besançon, France
| | - Christian Basset
- Université Grenoble Alpes, Commissariat à l'Energie Atomique et aux énergies alternatives (CEA), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Chimie et Biologie des Métaux (CBM), CNRS UMR 5249, 38054 Grenoble, France
| | - Sylvie Kieffer-Jaquinod
- Université Grenoble Alpes, CEA, INSERM, IRIG, Biologie à Grande Echelle (BGE), 38054 Grenoble, France
| | - Yohann Couté
- Université Grenoble Alpes, CEA, INSERM, IRIG, Biologie à Grande Echelle (BGE), 38054 Grenoble, France
| | - Stéphane Torelli
- Université Grenoble Alpes, Commissariat à l'Energie Atomique et aux énergies alternatives (CEA), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Chimie et Biologie des Métaux (CBM), CNRS UMR 5249, 38054 Grenoble, France
| | - Laurent Le Pape
- Université Grenoble Alpes, Commissariat à l'Energie Atomique et aux énergies alternatives (CEA), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Chimie et Biologie des Métaux (CBM), CNRS UMR 5249, 38054 Grenoble, France
| | - Volker Schünemann
- Fachbereich Physik, Technische Universität Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Hamza Olleik
- Aix-Marseille Université, CNRS, Centrale Marseille, Institut des Sciences Moléculaires de Marseille (iSm2), 13013 Marseille, France
| | - Bruno De La Villeon
- Department of Digestive, Endocrine and Metabolic Surgery, Hôpital Laveran, Military Health Service, 13013 Marseille, France
| | - Philippe Sockeel
- Department of Digestive, Endocrine and Metabolic Surgery, Hôpital Laveran, Military Health Service, 13013 Marseille, France
| | - Eric Di Pasquale
- Institut de NeuroPhysioPathologie, Faculté de Médecine, Aix Marseille Université, 13397 Marseille, France
| | - Cendrine Nicoletti
- Aix-Marseille Université, CNRS, Centrale Marseille, Institut des Sciences Moléculaires de Marseille (iSm2), 13013 Marseille, France
| | - Nicolas Vidal
- Yelen Analytics, Institut de Chimie Radicalaire, Aix-Marseille Université, 13013 Marseille, France
| | - Leonora Poljak
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative, Université de Toulouse, CNRS, Université Paul Sabatier (UPS), 31400 Toulouse, France
| | - Olga Iranzo
- Aix-Marseille Université, CNRS, Centrale Marseille, Institut des Sciences Moléculaires de Marseille (iSm2), 13013 Marseille, France
| | - Thierry Giardina
- Aix-Marseille Université, CNRS, Centrale Marseille, Institut des Sciences Moléculaires de Marseille (iSm2), 13013 Marseille, France
| | - Michel Fons
- Laboratoire de Bioénergétique et Ingénierie des Protéines, UMR 7281, Institut de Microbiologie de la Méditerranée, CNRS, Aix-Marseille Université, 13009 Marseille, France
| | - Estelle Devillard
- ADISSEO France SAS, Centre d'Expertise et de Recherche en Nutrition, 03600 Commentry, France
| | - Patrice Polard
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative, Université de Toulouse, CNRS, Université Paul Sabatier (UPS), 31400 Toulouse, France
| | - Marc Maresca
- Aix-Marseille Université, CNRS, Centrale Marseille, Institut des Sciences Moléculaires de Marseille (iSm2), 13013 Marseille, France
| | - Josette Perrier
- Aix-Marseille Université, CNRS, Centrale Marseille, Institut des Sciences Moléculaires de Marseille (iSm2), 13013 Marseille, France
| | - Mohamed Atta
- Université Grenoble Alpes, Commissariat à l'Energie Atomique et aux énergies alternatives (CEA), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Chimie et Biologie des Métaux (CBM), CNRS UMR 5249, 38054 Grenoble, France
| | - Françoise Guerlesquin
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR 7255, Institut de Microbiologie de la Méditerranée, CNRS, Aix-Marseille Université, 13009 Marseille, France
| | - Mickael Lafond
- Aix-Marseille Université, CNRS, Centrale Marseille, Institut des Sciences Moléculaires de Marseille (iSm2), 13013 Marseille, France;
| | - Victor Duarte
- Université Grenoble Alpes, Commissariat à l'Energie Atomique et aux énergies alternatives (CEA), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Chimie et Biologie des Métaux (CBM), CNRS UMR 5249, 38054 Grenoble, France;
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7
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Canestrari MJ, Serrano B, Bartoli J, Prima V, Bornet O, Puppo R, Bouveret E, Guerlesquin F, Viala JP. Deciphering the specific interaction between the acyl carrier protein IacP and the T3SS‐major hydrophobic translocator SipB from
Salmonella. FEBS Lett 2019; 594:251-265. [DOI: 10.1002/1873-3468.13593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 08/13/2019] [Accepted: 08/28/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Mickaël J. Canestrari
- LISM Institut de Microbiologie de la Méditerranée CNRS and Aix‐Marseille University France
| | - Bastien Serrano
- LISM Institut de Microbiologie de la Méditerranée CNRS and Aix‐Marseille University France
| | - Julia Bartoli
- LISM Institut de Microbiologie de la Méditerranée CNRS and Aix‐Marseille University France
| | - Valérie Prima
- LISM Institut de Microbiologie de la Méditerranée CNRS and Aix‐Marseille University France
| | - Olivier Bornet
- NMR Platform Institut de Microbiologie de la Méditerranée CNRS and Aix‐Marseille University France
| | - Rémy Puppo
- Proteomics Platform‐ IBISA2 Institut de Microbiologie de la Méditerranée CNRS and Aix‐Marseille University France
| | - Emmanuelle Bouveret
- LISM Institut de Microbiologie de la Méditerranée CNRS and Aix‐Marseille University France
| | - Françoise Guerlesquin
- LISM Institut de Microbiologie de la Méditerranée CNRS and Aix‐Marseille University France
| | - Julie P. Viala
- LISM Institut de Microbiologie de la Méditerranée CNRS and Aix‐Marseille University France
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8
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Chiumento S, Roblin C, Kieffer-Jaquinod S, Tachon S, Leprètre C, Basset C, Aditiyarini D, Olleik H, Nicoletti C, Bornet O, Iranzo O, Maresca M, Hardré R, Fons M, Giardina T, Devillard E, Guerlesquin F, Couté Y, Atta M, Perrier J, Lafond M, Duarte V. Ruminococcin C, a promising antibiotic produced by a human gut symbiont. Sci Adv 2019; 5:eaaw9969. [PMID: 31579822 PMCID: PMC6760926 DOI: 10.1126/sciadv.aaw9969] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 08/27/2019] [Indexed: 05/12/2023]
Abstract
A major public health challenge today is the resurgence of microbial infections caused by multidrug-resistant strains. Consequently, novel antimicrobial molecules are actively sought for development. In this context, the human gut microbiome is an under-explored potential trove of valuable natural molecules, such as the ribosomally-synthesized and post-translationally modified peptides (RiPPs). The biological activity of the sactipeptide subclass of RiPPs remains under-characterized. Here, we characterize an antimicrobial sactipeptide, Ruminococcin C1, purified from the caecal contents of rats mono-associated with Ruminococcus gnavus E1, a human symbiont. Its heterologous expression and post-translational maturation involving a specific sactisynthase establish a thioether network, which creates a double-hairpin folding. This original structure confers activity against pathogenic Clostridia and multidrug-resistant strains but no toxicity towards eukaryotic cells. Therefore, the Ruminococcin C1 should be considered as a valuable candidate for drug development and its producer strain R. gnavus E1 as a relevant probiotic for gut health enhancement.
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Affiliation(s)
- Steve Chiumento
- Univ. Grenoble Alpes, CEA, CNRS, CBM-UMR5249, 38000 Grenoble, France
| | - Clarisse Roblin
- Aix-Marseille Univ., CNRS, Centrale Marseille, iSm2, Marseille, France
- ADISSEO France SAS, Centre d’Expertise et de Recherche en Nutrition, Commentry, France
| | | | - Sybille Tachon
- Aix-Marseille Univ., CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Chloé Leprètre
- Univ. Grenoble Alpes, CEA, CNRS, CBM-UMR5249, 38000 Grenoble, France
| | - Christian Basset
- Univ. Grenoble Alpes, CEA, CNRS, CBM-UMR5249, 38000 Grenoble, France
| | - Dwi Aditiyarini
- Univ. Grenoble Alpes, CEA, CNRS, CBM-UMR5249, 38000 Grenoble, France
| | - Hamza Olleik
- Aix-Marseille Univ., CNRS, Centrale Marseille, iSm2, Marseille, France
| | | | | | - Olga Iranzo
- Aix-Marseille Univ., CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Marc Maresca
- Aix-Marseille Univ., CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Renaud Hardré
- Aix-Marseille Univ., CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Michel Fons
- Unité de Bioénergétique et Ingénierie des Protéines UMR7281, Institut de Microbiologie de la Méditerranée, Aix-Marseille Univ., CNRS, Marseille, France
| | - Thierry Giardina
- Aix-Marseille Univ., CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Estelle Devillard
- ADISSEO France SAS, Centre d’Expertise et de Recherche en Nutrition, Commentry, France
| | | | - Yohann Couté
- Univ. Grenoble Alpes, CEA, INSERM, BGE U1038, 38000 Grenoble, France
| | - Mohamed Atta
- Univ. Grenoble Alpes, CEA, CNRS, CBM-UMR5249, 38000 Grenoble, France
| | - Josette Perrier
- Aix-Marseille Univ., CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Mickael Lafond
- Aix-Marseille Univ., CNRS, Centrale Marseille, iSm2, Marseille, France
- Corresponding author. (M.L.); (V.D.)
| | - Victor Duarte
- Univ. Grenoble Alpes, CEA, CNRS, CBM-UMR5249, 38000 Grenoble, France
- Corresponding author. (M.L.); (V.D.)
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9
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ELANTAK L, Touarin P, Bornet O, Chen Q, Scott LG, Guerlesquin F. Deciphering a novel mechanism regulating galectin‐glycoprotein lattice assembly/disassembly during cell‐cell interactions. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.544.18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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10
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Ali-Ahmad A, Fadel F, Sebban-Kreuzer C, Ba M, Pélissier GD, Bornet O, Guerlesquin F, Bourne Y, Bordi C, Vincent F. Structural and functional insights into the periplasmic detector domain of the GacS histidine kinase controlling biofilm formation in Pseudomonas aeruginosa. Sci Rep 2017; 7:11262. [PMID: 28900144 PMCID: PMC5595915 DOI: 10.1038/s41598-017-11361-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 08/17/2017] [Indexed: 11/15/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogenic bacterium responsible for both acute and chronic infections and has developed resistance mechanisms due to its ability to promote biofilm formation and evade host adaptive immune responses. Here, we investigate the functional role of the periplasmic detector domain (GacSPD) from the membrane-bound GacS histidine kinase, which is one of the key players for biofilm formation and coordination of bacterial lifestyles. A gacS mutant devoid of the periplasmic detector domain is severely defective in biofilm formation. Functional assays indicate that this effect is accompanied by concomitant changes in the expression of the two RsmY/Z small RNAs that control activation of GacA-regulated genes. The solution NMR structure of GacSPD reveals a distinct PDC/PAS α/β fold characterized by a three-stranded β-sheet flanked by α-helices and an atypical major loop. Point mutations in a putative ligand binding pocket lined by positively-charged residues originating primarily from the major loop impaired biofilm formation. These results demonstrate the functional role of GacSPD, evidence critical residues involved in GacS/GacA signal transduction system that regulates biofilm formation, and document the evolutionary diversity of the PDC/PAS domain fold in bacteria.
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Affiliation(s)
| | - Firas Fadel
- CNRS, Aix Marseille Univ, AFMB, Marseille, France
- LISM, IMM, Aix-Marseille Univ and CNRS, Marseille, 13402, France
| | | | - Moly Ba
- LISM, IMM, Aix-Marseille Univ and CNRS, Marseille, 13402, France
| | | | - Olivier Bornet
- LISM, IMM, Aix-Marseille Univ and CNRS, Marseille, 13402, France
| | | | - Yves Bourne
- CNRS, Aix Marseille Univ, AFMB, Marseille, France
| | - Christophe Bordi
- LISM, IMM, Aix-Marseille Univ and CNRS, Marseille, 13402, France.
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11
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Ali-Ahmad A, Bornet O, Fadel F, Bourne Y, Vincent F, Bordi C, Guerlesquin F, Sebban-Kreuzer C. NMR assignments of the GacS histidine-kinase periplasmic detection domain from Pseudomonas aeruginosa PAO1. Biomol NMR Assign 2017; 11:25-28. [PMID: 27714507 DOI: 10.1007/s12104-016-9714-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 10/01/2016] [Indexed: 06/06/2023]
Abstract
Pseudomonas aeruginosa is a highly adaptable opportunistic pathogen. It can infect vulnerable patients such as those with cystic fibrosis or hospitalized in intensive care units where it is responsible for both acute and chronic infection. The switch between these infections is controlled by a complex regulatory system involving the central GacS/GacA two-component system that activates the production of two small non-coding RNAs. GacS is a histidine kinase harboring one periplasmic detection domain, two inner-membrane helices and three H1/D1/H2 cytoplasmic domains. By detecting a yet unknown signal, the GacS histidine-kinase periplasmic detection domain (GacSp) is predicted to play a key role in activating the GacS/GacA pathway. Here, we present the chemical shift assignment of 96 % of backbone atoms (HN, N, C, Cα, Cβ and Hα), 88 % aliphatic hydrogen atoms and 90 % of aliphatic carbon atoms of this domain. The NMR-chemical shift data, on the basis of Talos server secondary structure predictions, reveal that GacSp consists of 3 β-strands, 3 α-helices and a major loop devoid of secondary structures.
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Affiliation(s)
| | - Olivier Bornet
- LISM, IMM, CNRS, Aix-Marseille Univ, 13402, Marseille, France
| | - Firas Fadel
- AFMB, CNRS, Aix Marseille Univ, Marseille, France
- LISM, IMM, CNRS, Aix-Marseille Univ, 13402, Marseille, France
| | - Yves Bourne
- AFMB, CNRS, Aix Marseille Univ, Marseille, France
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12
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Navarro R, Bornet O, Houot L, Lloubes R, Guerlesquin F, Nouailler M. (1)H, (15)N and (13)C resonance assignments of the C-terminal domain of Vibrio cholerae TolA protein. Biomol NMR Assign 2016; 10:311-313. [PMID: 27436120 DOI: 10.1007/s12104-016-9690-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 06/22/2016] [Indexed: 06/06/2023]
Abstract
Vibrio cholerae is the bacterial causative agent of the human disease cholera. Non-pathogenic bacterium can be converted to pathogenic following infection by a filamentous phage, CTXΦ, that carries the cholera toxin encoding genes. A crucial step during phage infection requires a direct interaction between the CTXΦ minor coat protein (pIII(CTX)) and the C-terminal domain of V. cholerae TolA protein (TolAIIIvc). In order to get a better understanding of TolA function during the infection process, we have initiated a study of the V. cholerae TolAIII domain by 2D and 3D heteronuclear NMR. With the exception of the His-tag (H123-H128), 97 % of backbone (1)H, (15)N and (13)C resonances were assigned and the side chain assignments for 92 % of the protein were obtained (BMRB deposit with accession number 25689).
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Affiliation(s)
- Romain Navarro
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR 7255, CNRS, Aix-Marseille Université, Marseille, France
| | - Olivier Bornet
- Institut de Microbiologie de la Méditerranée, FR 3479, CNRS, Aix-Marseille Université, Marseille, France
| | - Laetitia Houot
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR 7255, CNRS, Aix-Marseille Université, Marseille, France
| | - Roland Lloubes
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR 7255, CNRS, Aix-Marseille Université, Marseille, France
| | - Françoise Guerlesquin
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR 7255, CNRS, Aix-Marseille Université, Marseille, France
| | - Matthieu Nouailler
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR 7255, CNRS, Aix-Marseille Université, Marseille, France.
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13
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Garcin EB, Bornet O, Elantak L, Nouailler M, Guerlesquin F, Sebban-Kreuzer C. ¹H, ¹³C and ¹⁵N backbone and side-chain chemical shift assignments for reduced unusual thioredoxin Patrx2 of Pseudomonas aeruginosa. Biomol NMR Assign 2014; 8:247-250. [PMID: 23771858 DOI: 10.1007/s12104-013-9493-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 06/03/2013] [Indexed: 06/02/2023]
Abstract
The gram-negative organism Pseudomonas aeruginosa is an opportunistic human pathogen and a leading cause of hospital-acquired infections. In P. aeruginosa PAO1, three cytoplasmic thioredoxins have been identified. An unusual thioredoxin (Patrx2) (108 amino acids) encoded by the PA2694 gene, is identified as a new thioredoxin-like protein based on sequence homology. Thioredoxin is a ubiquitous protein, which serves as a general protein disulfide oxidoreductase. Patrx2 present an atypical active site CGHC. We report the nearly complete (1)H, (13)C and (15)N resonance assignments of reduced Patrx2. 2D and 3D heteronuclear NMR experiments were performed with uniformly (15)N-, (13)C-labelled Patrx2, resulting in 97.2% backbone and 92.5% side-chain (1)H, (13)C and (15)N resonance assignments for the reduced form. (BMRB deposits with accession number 18130).
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Affiliation(s)
- Edwige B Garcin
- LISM, IMM, CNRS, Aix-Marseille Université, Marseille, France
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14
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Elantak L, Espeli M, Boned A, Bornet O, Bonzi J, Gauthier L, Feracci M, Roche P, Guerlesquin F, Schiff C. Structural basis for galectin-1-dependent pre-B cell receptor (pre-BCR) activation. J Biol Chem 2012; 287:44703-13. [PMID: 23124203 DOI: 10.1074/jbc.m112.395152] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
During B cell differentiation in the bone marrow, the expression and activation of the pre-B cell receptor (pre-BCR) constitute crucial checkpoints for B cell development. Both constitutive and ligand-dependent pre-BCR activation modes have been described. The pre-BCR constitutes an immunoglobulin heavy chain (Igμ) and a surrogate light chain composed of the invariant λ5 and VpreB proteins. We previously showed that galectin-1 (GAL1), produced by bone marrow stromal cells, is a pre-BCR ligand that induces receptor clustering, leading to efficient pre-BII cell proliferation and differentiation. GAL1 interacts with the pre-BCR via the unique region of λ5 (λ5-UR). Here, we investigated the solution structure of a minimal λ5-UR motif that interacts with GAL1. This motif adopts a stable helical conformation that docks onto a GAL1 hydrophobic surface adjacent to its carbohydrate binding site. We identified key hydrophobic residues from the λ5-UR as crucial for the interaction with GAL1 and for pre-BCR clustering. These residues involved in GAL1-induced pre-BCR activation are different from those essential for autonomous receptor activation. Overall, our results indicate that constitutive and ligand-induced pre-BCR activation could occur in a complementary manner.
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Affiliation(s)
- Latifa Elantak
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, CNRS UMR7255, Aix-Marseille Université, 13402 Marseille cedex 20, France
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15
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Garcin EB, Bornet O, Elantak L, Vita N, Pieulle L, Guerlesquin F, Sebban-Kreuzer C. Structural and mechanistic insights into unusual thiol disulfide oxidoreductase. J Biol Chem 2011; 287:1688-97. [PMID: 22128175 DOI: 10.1074/jbc.m111.288316] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cytoplasmic desulfothioredoxin (Dtrx) from the anaerobe Desulfovibrio vulgaris Hildenborough has been identified as a new member of the thiol disulfide oxidoreductase family. The active site of Dtrx contains a particular consensus sequence, CPHC, never seen in the cytoplasmic thioredoxins and generally found in periplasmic oxidases. Unlike canonical thioredoxins (Trx), Dtrx does not present any disulfide reductase activity, but it presents instead an unusual disulfide isomerase activity. We have used NMR spectroscopy to gain insights into the structure and the catalytic mechanism of this unusual Dtrx. The redox potential of Dtrx (-181 mV) is significantly less reducing than that of canonical Trx. A pH dependence study allowed the determination of the pK(a) of all protonable residues, including the cysteine and histidine residues. Thus, the pK(a) values for the thiol group of Cys(31) and Cys(34) are 4.8 and 11.3, respectively. The His(33) pK(a) value, experimentally determined for the first time, differs notably as a function of the redox states, 7.2 for the reduced state and 4.6 for the oxidized state. These data suggest an important role for His(33) in the molecular mechanism of Dtrx catalysis that is confirmed by the properties of mutant DtrxH33G protein. The NMR structure of Dtrx shows a different charge repartition compared with canonical Trx. The results presented are likely indicative of the involvement of this protein in the catalysis of substrates specific of the anaerobe cytoplasm of DvH. The study of Dtrx is an important step toward revealing the molecular details of the thiol-disulfide oxidoreductase catalytic mechanism.
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Affiliation(s)
- Edwige B Garcin
- IMR, IFR88, CNRS, Aix-Marseille Université, Marseille 13402, France
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16
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Garcin EB, Bornet O, Pieulle L, Guerlesquin F, Sebban-Kreuzer C. 1H, 13C and 15N chemical shift assignments of the thioredoxin from the obligate anaerobe Desulfovibrio vulgaris Hildenborough. Biomol NMR Assign 2011; 5:177-179. [PMID: 21287302 DOI: 10.1007/s12104-011-9294-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Accepted: 01/21/2011] [Indexed: 05/30/2023]
Abstract
Thioredoxins are ubiquitous key antioxidant enzymes which play an essential role in cell defense against oxidative stress. They maintain the redox homeostasis owing to the regulation of thiol-disulfide exchange. In the present paper, we report the full resonance assignments of (1)H, (13)C and (15)N atoms for the reduced and oxidized forms of Desulfovibrio vulgaris Hildenborough thioredoxin 1 (Trx1). 2D and 3D heteronuclear NMR experiments were performed using uniformly (15)N-, (13)C-labelled Trx1. Chemical shifts of 97% of the backbone and 90% of the side chain atoms were obtained for the oxidized and reduced form (BMRB deposits with accession number 17299 and 17300, respectively).
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Affiliation(s)
- Edwige B Garcin
- IMR-IFR88, CNRS; Aix-Marseille Université, Marseille, France
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17
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Feracci M, Pimentel C, Bornet O, Roche P, Salaun D, Badache A, Guerlesquin F. MEMO associated with an ErbB2 receptor phosphopeptide reveals a new phosphotyrosine motif. FEBS Lett 2011; 585:2688-92. [PMID: 21840311 DOI: 10.1016/j.febslet.2011.07.048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Revised: 07/15/2011] [Accepted: 07/28/2011] [Indexed: 02/01/2023]
Abstract
Tyrosine phosphorylations are essential in signal transduction. Recently, a new type of phosphotyrosine binding protein, MEMO (Mediator of ErbB2-driven cell motility), has been reported to bind specifically to an ErbB2-derived phosphorylated peptide encompassing Tyr-1227 (PYD). Structural and functional analyses of variants of this peptide revealed the minimum sequence required for MEMO recognition. Using a docking approach we have generated a structural model for MEMO/PYD complex and compare this new phosphotyrosine motif to SH2 and PTB phosphotyrosine motives.
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18
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Garcin EB, Bornet O, Pieulle L, Guerlesquin F, Sebban-Kreuzer C. 1H, 13C and 15N backbone and side-chain chemical shift assignments for oxidized and reduced desulfothioredoxin. Biomol NMR Assign 2010; 4:135-137. [PMID: 20390383 DOI: 10.1007/s12104-010-9226-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2010] [Accepted: 03/30/2010] [Indexed: 05/29/2023]
Abstract
Based on sequence homology, desulfothioredoxin (DTrx) from Desulfovibrio vulgaris Hildenborough has been identified as a new member of the thioredoxin superfamily. Desulfothioredoxin (104 amino acids) contains a particular active site consensus sequence, CPHC probably correlated to the anaerobic metabolism of these bacteria. We report the full 1H, 13C and 15N resonance assignments of the reduced and the oxidized form of desulfothioredoxin (DTrx). 2D and 3D heteronuclear NMR experiments were performed using uniformly 15N-, 13C-labelled DTrx. More than 98% backbone and 96% side-chain 1H, 13C and 15N resonance assignments were obtained. (BMRB deposits with accession number 16712 and 16713).
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Affiliation(s)
- Edwige B Garcin
- IMR-IFR88, CNRS, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France
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19
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Dermoun Z, Foulon A, Miller MD, Harrington DJ, Deacon AM, Sebban-Kreuzer C, Roche P, Lafitte D, Bornet O, Wilson IA, Dolla A. TM0486 from the hyperthermophilic anaerobe Thermotoga maritima is a thiamin-binding protein involved in response of the cell to oxidative conditions. J Mol Biol 2010; 400:463-76. [PMID: 20471400 DOI: 10.1016/j.jmb.2010.05.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Revised: 04/28/2010] [Accepted: 05/07/2010] [Indexed: 11/28/2022]
Abstract
The COG database was used for a comparative genome analysis with genomes from anaerobic and aerobic microorganisms with the aim of identifying proteins specific to the anaerobic way of life. A total of 33 COGs were identified, five of which correspond to proteins of unknown function. We focused our study on TM0486 from Thermotoga maritima, which belongs to one of these COGs of unknown function, namely COG0011. The crystal structure of the protein was determined at 2 A resolution. The structure adopts a beta alpha beta beta alpha beta ferredoxin-like fold and assembles as a homotetramer. The structure also revealed the presence of a pocket in each monomer that bound an unidentified ligand. NMR and calorimetry revealed that TM0486 specifically bound thiamin with a K(d) of 1.58 microM, but not hydroxymethyl pyrimidine (HMP), which has been implicated as a potential ligand. We demonstrated that the TM0486 gene belongs to the same multicistronic unit as TM0483, TM0484 and TM0485. Although these three genes have been assigned to the transport of HMP, with TM0484 being the periplasmic thiamin/HMP-binding protein and TM0485 and TM0483 the transmembrane and the ATPase components, respectively, our results led us to conclude that this operon encodes an ABC transporter dedicated to thiamin, with TM0486 transporting charged thiamin in the cytoplasm. Given that this transcriptional unit was up-regulated when T. maritima was exposed to oxidative conditions, we propose that, by chelating cytoplasmic thiamin, TM0486 and, by extension, proteins belonging to COG0011 are involved in the response mechanism to stress that could arise during aerobic conditions.
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Affiliation(s)
- Zorah Dermoun
- IMR-CNRS, IFR88, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France.
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20
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Nouailler M, Morelli X, Bornet O, Chetrit B, Dermoun Z, Guerlesquin F. Solution structure of HndAc: a thioredoxin-like domain involved in the NADP-reducing hydrogenase complex. Protein Sci 2006; 15:1369-78. [PMID: 16731971 PMCID: PMC2242533 DOI: 10.1110/ps.051916606] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The NADP-reducing hydrogenase complex from Desulfovibrio fructosovorans is a heterotetramer encoded by the hndABCD operon. Sequence analysis indicates that the HndC subunit (52 kDa) corresponds to the NADP-reducing unit, and the HndD subunit (63.5 kDa) is homologous to Clostridium pasteurianum hydrogenase. The role of HndA and HndB subunits (18.8 kDa and 13.8 kDa, respectively) in the complex remains unknown. The HndA subunit belongs to the [2Fe-2S] ferredoxin family typified by C. pasteurianum ferredoxin. HndA is organized into two independent structural domains, and we report in the present work the NMR structure of its C-terminal domain, HndAc. HndAc has a thioredoxin-like fold consisting in four beta-strands and two relatively long helices. The [2Fe-2S] cluster is located near the surface of the protein and bound to four cysteine residues particularly well conserved in this class of proteins. Electron exchange between the HndD N-terminal [2Fe-2S] domain (HndDN) and HndAc has been previously evidenced, and in the present studies we have mapped the binding site of the HndDN domain on HndAc. A structural analysis of HndB indicates that it is a FeS subunit with 41% similarity with HndAc and it contains a possible thioredoxin-like fold. Our data let us propose that HndAc and HndB can form a heterodimeric intermediate in the electron transfer between the hydrogenase (HndD) active site and the NADP reduction site in HndC.
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Affiliation(s)
- Matthieu Nouailler
- Unité de Bioénergétique et Ingénierie des Protéines, IBSM-CNRS, Marseille Cedex 20, France
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21
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ElAntak L, Morelli X, Bornet O, Hatchikian C, Czjzek M, Dolla A, Guerlesquin F. The cytochrome c3-[Fe]-hydrogenase electron-transfer complex: structural model by NMR restrained docking. FEBS Lett 2003; 548:1-4. [PMID: 12885397 DOI: 10.1016/s0014-5793(03)00718-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Cytochrome c(3) (M(r) 13000) is a low redox potential cytochrome specific of the anaerobic metabolism in sulfate-reducing bacteria. This tetrahemic cytochrome is an intermediate between the [Fe]-hydrogenase and the cytochrome Hmc in Desulfovibrio vulgaris Hildenborough strain. The present work describes the structural model of the cytochrome c(3)-[Fe]-hydrogenase complex obtained by nuclear magnetic resonance restrained docking. This model connects the distal cluster of the [Fe]-hydrogenase to heme 4 of the cytochrome, the same heme found in the interaction with cytochrome Hmc. This result gives evidence that cytochrome c(3) is an electron shuttle between the periplasmic hydrogenase and the Hmc membrane-bound complex.
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Affiliation(s)
- Latifa ElAntak
- Unité de Bioénergétique et Ingénierie des Protéines, IBSM-CNRS, 31 chemin Joseph Aiguier, 13402 Cedex 20, Marseille, France.
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22
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Renisio JG, Pérez J, Czisch M, Guenneugues M, Bornet O, Frenken L, Cambillau C, Darbon H. Solution structure and backbone dynamics of an antigen-free heavy chain variable domain (VHH) from Llama. Proteins 2002; 47:546-55. [PMID: 12001233 DOI: 10.1002/prot.10096] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Camelids, (dromedaries, camels, and llamas) produce heavy-chains antibodies, with their antigen recognition sites composed of a single VH-like domain, referred to as VHH. The solution structure of one of these VHHs domains (VHH-H14), raised against the alpha subunit of the human chorionic gonadotropin hormone (hCG), has been determined by (15)N heteronuclear three-dimensional NMR spectroscopy. The framework is well resolved within the set of 20 best-calculated NMR structures and is close to that of classical VH domains from vertebrate antibodies, consisting of two antiparallel beta-sheets organized in a beta-barrel. Loops display a lower precision, especially the Complementarity Determining Regions (CDRs), involved in antigen recognition. Comparison of the three-dimensional VHH-H14 solution structure with its previously solved crystal structure (Spinelli et al., Nature Struct. Biol. 1996;3:752-757) reveals a high similarity to the framework, whereas significant conformational differences occur on CDRs, leading to the assumption that the antigen recognition site is a more mobile part. In order to deepen our insights into the dynamics of VHH-H14 in solution, (15)N relaxation was measured with longitudinal R1 and transverse R2 self-relaxation rates, and (15)N steady-state heteronuclear nuclear Overhauser enhancements (NOE), making it possible to probe picosecond-to-millisecond internal motions. Determination of dynamic parameters (S(2), tau(e), and Rex) through the Lipari-Szabo Model-free approach enables the identification of several regions with enhanced dynamics. Especially, the mobility measurements from NMR confirm that the antigen recognition site is the most mobile part of the VHH-H14 domain on picosecond-to-nanosecond fast time scales. Several residues belonging to the three CDRs are submitted to chemical exchange processes occurring on slow microsecond-to-millisecond time scales, suggesting that the formation of the VHH/antigen complex should be accompanied by structural changes.
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Affiliation(s)
- Jean-Guillaume Renisio
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098, CNRS and Universités d'Aix-Marseille I and II, Marseille, France
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Mosbah A, Tardif C, Bornet O, Valette O, Henrissat B, Darbon H. Assignment of the 1H, 13C, and 15N resonances of the 22,5 kDa CBM28 module of the cellulase Cel5I of Clostridium cellulolyticum. J Biomol NMR 2002; 23:157-158. [PMID: 12153043 DOI: 10.1023/a:1016354623398] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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Elantak L, Bornet O, Morelli X, Dolla A, Guerlesquin F. Sequential NMR assignment of the ferri-cytochrome c3 from Desulfovibrio vulgaris Hildenborough. J Biomol NMR 2002; 23:69-70. [PMID: 12061720 DOI: 10.1023/a:1015365012019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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Czjzek M, Bolam DN, Mosbah A, Allouch J, Fontes CM, Ferreira LM, Bornet O, Zamboni V, Darbon H, Smith NL, Black GW, Henrissat B, Gilbert HJ. The location of the ligand-binding site of carbohydrate-binding modules that have evolved from a common sequence is not conserved. J Biol Chem 2001; 276:48580-7. [PMID: 11673472 DOI: 10.1074/jbc.m109142200] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Polysaccharide-degrading enzymes are generally modular proteins that contain non-catalytic carbohydrate-binding modules (CBMs), which potentiate the activity of the catalytic module. CBMs have been grouped into sequence-based families, and three-dimensional structural data are available for half of these families. Clostridium thermocellum xylanase 11A is a modular enzyme that contains a CBM from family 6 (CBM6), for which no structural data are available. We have determined the crystal structure of this module to a resolution of 2.1 A. The protein is a beta-sandwich that contains two potential ligand-binding clefts designated cleft A and B. The CBM interacts primarily with xylan, and NMR spectroscopy coupled with site-directed mutagenesis identified cleft A, containing Trp-92, Tyr-34, and Asn-120, as the ligand-binding site. The overall fold of CBM6 is similar to proteins in CBM families 4 and 22, although surprisingly the ligand-binding site in CBM4 and CBM22 is equivalent to cleft B in CBM6. These structural data define a superfamily of CBMs, comprising CBM4, CBM6, and CBM22, and demonstrate that, although CBMs have evolved from a relatively small number of ancestors, the structural elements involved in ligand recognition have been assembled at different locations on the ancestral scaffold.
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Affiliation(s)
- M Czjzek
- Laboratoire d'Architecture et de Fonction des Macromolécules Biologiques, IBSM, CNRS Marseille and University Aix-Marseille I & II, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France.
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Campanacci V, Mosbah A, Bornet O, Wechselberger R, Jacquin-Joly E, Cambillau C, Darbon H, Tegoni M. Chemosensory protein from the moth Mamestra brassicae. Expression and secondary structure from 1H and 15N NMR. Eur J Biochem 2001; 268:4731-9. [PMID: 11532009 DOI: 10.1046/j.1432-1327.2001.02398.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A group of ubiquitous small proteins (average 13 kDa) has been isolated from several sensory organs of a wide range of insect species. They are believed to be involved in chemical communication and perception (olfaction or taste) and have therefore been called chemo-sensory proteins (CSPs). Several CSPs have been identified in the antennae and proboscis of the moth Mamestra brassicae. We have expressed one of the antennal proteins (CSPMbraA6) in large quantities as a soluble recombinant protein in Escherichia coli periplasm. This 112-residue protein is a highly soluble monomer of 13 072 Da with a pI of 5.5. NMR data (1H and 15N) indicate that CSPMbraA6 is well folded and contains seven alpha helices (59 amino acids) and two short extended structures (12 amino acids) from positions 5 to 10 and from 107 to 112. Thirty-seven amino acids are involved in beta turns and coiled segments and four amino acids are not assigned in the NMR spectra (the N-terminus and the residue 52 in the loop 48-53), probably due to their mobility. This is the first report on the expression and structural characterization of a recombinant CSP.
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Affiliation(s)
- V Campanacci
- AFMB, UMR 6098-CNRS and Universités d'Aix-Marseille I and II, Marseille, France
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Mosbah A, Belaïch A, Bornet O, Belaïch JP, Henrissat B, Darbon H. Solution structure of the module X2 1 of unknown function of the cellulosomal scaffolding protein CipC of Clostridium cellulolyticum. J Mol Biol 2000; 304:201-17. [PMID: 11080456 DOI: 10.1006/jmbi.2000.4192] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Multidimensional, homo- and heteronuclear magnetic resonance spectroscopy combined with dynamical annealing has been used to determine the structure of a 94 residue module (X2 1) of the scaffolding protein CipC from the anaerobic bacterium Clostridium cellulolyticum. An experimental data set comprising 1647 nuclear Overhauser effect-derived restraints, 105 hydrogen bond restraints and 66 phi torsion angle restraints was used to calculate 20 converging final solutions. The calculated structures have an average rmsd about the mean structure of 0.55(+/-0.11) A for backbone atoms and 1.40(+/-0.11) A for all heavy atoms when fitted over the secondary structural elements. The X2 1 module has an immunoglobulin-like fold with two beta-sheets packed against each other. One sheet contains three strands, the second contains four strands. An additional strand is intercalated between the beta-sandwich, as well as two turns of a 3(.10) helix. X2 1 has a surprising conformational stability and may act as a conformational linker and solubility enhancer within the scaffolding protein. The fold of X2 1 is very similar to that of telokin, titin Ig domain, hemolin D2 domain, twitchin immunoglobulin domain and the first four domains of the IgSF portion of transmembrane cell adhesion molecule. As a consequence, the X2 1 module is the first prokaryotic member assigned to the I set of the immunoglobulin superfamily even though no sequence similarity with any member of this superfamily could be detected.
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Affiliation(s)
- A Mosbah
- Architecture et Fonction des Macromolécules Biologiques, CNRS UPR 9039, 31 Chemin Joseph-Aiguier, Marseille, Cedex 20, 13402, France
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Dominguez C, Sebban-Kreuzer C, Bornet O, Kerfelec B, Chapus C, Guerlesquin F. Interactions of bile salt micelles and colipase studied through intermolecular nOes. FEBS Lett 2000; 482:109-12. [PMID: 11018532 DOI: 10.1016/s0014-5793(00)02034-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Colipase is a small protein (10 kDa), which acts as a protein cofactor for the pancreatic lipase. Various models of the activated ternary complex (lipase-colipase-bile salt micelles) have been proposed using detergent micelles, but no structural information has been established with bile salt micelles. We have investigated the organization of sodium taurodeoxycholate (NaTDC) micelles and their interactions with pig and horse colipases by homonuclear nuclear magnetic resonance (NMR) spectroscopy. The NMR data supply evidence that the folding of horse colipase is similar to that already described for pig colipase. Intermolecular nuclear Overhauser effects have shown that two conserved aromatic residues interact with NaTDC micelles.
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Affiliation(s)
- C Dominguez
- Unité de Bioénergétique et Ingénierie des Protéines, IBSM-CNRS, 31 chemin Joseph Aiguier, 13204 Marseille Cedex 20, France
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Morelli X, Czjzek M, Hatchikian CE, Bornet O, Fontecilla-Camps JC, Palma NP, Moura JJ, Guerlesquin F. Structural model of the Fe-hydrogenase/cytochrome c553 complex combining transverse relaxation-optimized spectroscopy experiments and soft docking calculations. J Biol Chem 2000; 275:23204-10. [PMID: 10748163 DOI: 10.1074/jbc.m909835199] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Fe-hydrogenase is a 54-kDa iron-sulfur enzyme essential for hydrogen cycling in sulfate-reducing bacteria. The x-ray structure of Desulfovibrio desulfuricans Fe-hydrogenase has recently been solved, but structural information on the recognition of its redox partners is essential to understand the structure-function relationships of the enzyme. In the present work, we have obtained a structural model of the complex of Fe-hydrogenase with its redox partner, the cytochrome c(553), combining docking calculations and NMR experiments. The putative models of the complex demonstrate that the small subunit of the hydrogenase has an important role in the complex formation with the redox partner; 50% of the interacting site on the hydrogenase involves the small subunit. The closest contact between the redox centers is observed between Cys-38, a ligand of the distal cluster of the hydrogenase and Cys-10, a ligand of the heme in the cytochrome. The electron pathway from the distal cluster of the Fe-hydrogenase to the heme of cytochrome c(553) was investigated using the software Greenpath and indicates that the observed cysteine/cysteine contact has an essential role. The spatial arrangement of the residues on the interface of the complex is very similar to that already described in the ferredoxin-cytochrome c(553) complex, which therefore, is a very good model for the interacting domain of the Fe-hydrogenase-cytochrome c(553).
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Affiliation(s)
- X Morelli
- Unité de Bioénergétique et Ingénierie des Protéines, IBSM-CNRS, Marseille Cedex 20, France
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Abstract
BmKTX is a toxin recently purified from the venom of Buthus Martensi, which belongs to the kaliotoxin family. We have determined its solution structure by use of conventional two-dimensional NMR techniques followed by distance-geometry and energy minimization. The calculated structure is composed of a short alpha-helix (residues 14 to 20) connected by a tight turn to a two-stranded antiparallel beta-sheet (sequences 25-27 and 32-34). The beta-turn connecting these strands belongs to type I. The N-terminal segment (sequence 1 to 8) runs parallel to the beta-sheet although it cannot be considered as a third strand. Comparison of the conformation of BmKTX and toxins of the kaliotoxin family clearly demonstrates that they are highly related. Therefore, analysis of the residues belonging to the interacting surface of those toxins allows us to propose a functional map of BmKTX slightly different from the one of KTX and AgTX2, which may explain the variations in affinities of these toxins towards the Kv1.3 channels.
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Affiliation(s)
- J G Renisio
- AFMB, CNRS UPR 9039, IFR1, Marseille, France
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31
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Abstract
The new concept of slaved pulses is evaluated in the context of the study of protein hydration. The inversion properties of these pulses are shown to be superior in quality to the previously published schemes. High-quality water selective homonuclear 2D 1H NOESY-NOESY and NOESY-TOCSY experiments were recorded on horse heart ferrocytochrome c.
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Affiliation(s)
- O Bornet
- IBSM-CNRS, 31, chemin Joseph Aiguier, Marseille Cedex 20, F-13402, France
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32
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Abstract
Lq2 is a unique scorpion toxin. Acting from the extracellular side, Lq2 blocks the ion conduction pore in not only the voltage- and Ca2+ -activated channels, but also the inward-rectifier K+ channels. This finding argues that the three-dimensional structures of the pores in these K+ channels are similar. However, the amino acid sequences that form the external part of the pore are minimally conserved among the various classes of K+ channels. Because Lq2 can bind to all the three classes of K+ channels, we can use Lq2 as a structural probe to examine how the non-conserved pore-forming sequences are arranged in space to form similar pore structures. In the present study, we determined the three-dimensional structure of Lq2 using nuclear magnetic resonance (NMR) techniques. Lq2 consists of an alpha-helix (residues S10 to L20) and a beta-sheet, connected by an alphabeta3 loop (residues N22 to N24). The beta-sheet has two well-defined anti-parallel strands (residues G26 to M29 and residues K32 to C35), which are connected by a type I' beta-turn centered between residues N30 and K31. The N-terminal segment (residues Z1 to T8) appears to form a quasi-third strand of the beta-sheet.
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Affiliation(s)
- J G Renisio
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, UPR 9039, Marseille, France
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Blanc E, Romi-Lebrun R, Bornet O, Nakajima T, Darbon H. Solution structure of two new toxins from the venom of the Chinese scorpion Buthus martensi Karsch blockers of potassium channels. Biochemistry 1998; 37:12412-8. [PMID: 9730813 DOI: 10.1021/bi9809371] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The solution structure of BmTX2 purified from the venom of the Chinese Buthid Buthus martensi has been determined by 2D NMR spectroscopy techniques which led to the description of its 3D conformation. The structure consists of a triple-stranded beta-sheet connected to a helical structure. This helix encompasses 10 residues, from 11 to 20, begins with a turn of 310 helix, and ends with an alpha helix. The three strands of beta sheet comprise residues 2-6, with a bulge covering residues 4 and 5, 26-29, and 32-35, with a type I' beta turn centered on residues 30-31. We also characterized the solution structure of BmTX1. The two toxins which are potent blockers of both large-conductance calcium-activated potassium channels (BKCa channels) and voltage-gated potassium channels (Kv1. 3) are highly superimposable and possess the same structural characteristics. Analysis of these structures allows us to hypothesize that, besides the main surface of interaction described by the functional map of charybdotoxin, one can expect that the binding of scorpion toxins on BKCa channels may involve residues on the edge of this surface.
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Affiliation(s)
- E Blanc
- AFMB, CNRS UPR 9039, IFR1, 31, Marseille, France
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Bornet O, Prévost C, Vovelle F, Chassignol M, Thuong NT, Lancelot G. Solution structure of oligonucleotides covalently linked to a psoralen derivative. Nucleic Acids Res 1995; 23:788-95. [PMID: 7708495 PMCID: PMC306761 DOI: 10.1093/nar/23.5.788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Psoralen (pso) was attached via its C-5 position to the 5'-phosphate group of an oligodeoxynucleotide d(TAAGCCG) by a hexamethylene linker (m6). Complex formation between pso-m6-d(TAAGCCG) and the complementary strands d(CGGCTTA)[7-7mer] or d(CGGCTTAT)[7-8mer] was investigated by nuclear magnetic resonance in aqueous solution. Structural informations derived from DQF-COSY and NOESY maps, revealed that the mini double helix adopts a B-form conformation and that the deoxyriboses preferentially adopt a C2'-endo conformation. The nOe connectivities observed between the protons of the bases or the sugars in each duplex, and the protons of the psoralen and the hexamethylene chain, led us to propose a model involving an equilibrium between two conformations due to different locations of the psoralen. Upon UV-irradiation, the psoralen moiety cross-linked the two DNA strands at the level of 5'TpA3' sequences. NMR studies of the single major photo-cross-linked duplex pso-m6-d(TAAGCCG) and d(CGGCTTA) were performed. The stereochemistry of the diadduct is indeed cis-syn at both cyclobutane rings. In addition, the effects of this diadduct on the helical structure are analyzed in detail.
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Affiliation(s)
- O Bornet
- Centre de Biophysique Moléculaire, CNRS, Orléans, France
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Abstract
The three-dimensional structure of an intramolecular triple helix whose three strands have been linked by a hexaethylene glycol chain, and selectively 13C-enriched in position C1' on the third strand was investigated by NMR spectroscopy and constrained molecular mechanics calculations. Starting from different initial conformations, we show that the NOE constraints determined by the complete relaxation matrix calculation and iterative back-calculations allowed us to reach the same final restrained triple helix, taking into account implicitly the solvent effect. We conclude that this triplex adopted a B-type conformation rather than a A-type. The sugar pucker was found predominantly in the S-type conformation, in the range of C2'-endo geometry.
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Affiliation(s)
- O Bornet
- Centre de Biophysique Moléculaire, CNRS, Orléans, France
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Bornet O, Lancelot G, Chanteloup L, Nguyen TT, Beau JM. Selectively 13C-enriched DNA: 13C and 1H assignments of a triple helix by two-dimensional relayed HMQC experiments. J Biomol NMR 1994; 4:575-580. [PMID: 8075542 DOI: 10.1007/bf00156621] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We present NMR studies of an intramolecular triple helix, the three strands of which have been linked by a hexaethylene glycol chain. To overcome the generally encountered difficulties of assignment in the homo-pyrimidine strands, the carbon Cl' of the pyrimidines were selectively 13C-enriched. Assignments of the aromatic and sugar protons were obtained from NOESY-HMQC and TOCSY-HMQC spectra. We show that the recognition of a DNA duplex by a third strand via triplex formation is easily carried out in solution by observing the changes of the 1Hl'-13Cl' connectivities as a function of pH. Furthermore, the conformation of the sugars has been found to be C2'-endo, on the basis of the coupling constant values directly measured in an HSQC spectrum.
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Affiliation(s)
- O Bornet
- Centre de Biophysique Moléculaire, CNRS, Orléans, France
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