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Nedvědová Š, De Stefano D, Walker O, Hologne M, Miele AE. Revisiting Schistosoma mansoni Micro-Exon Gene (MEG) Protein Family: A Tour into Conserved Motifs and Annotation. Biomolecules 2023; 13:1275. [PMID: 37759676 PMCID: PMC10526429 DOI: 10.3390/biom13091275] [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: 07/20/2023] [Revised: 08/15/2023] [Accepted: 08/18/2023] [Indexed: 09/29/2023] Open
Abstract
Genome sequencing of the human parasite Schistosoma mansoni revealed an interesting gene superfamily, called micro-exon gene (meg), that encodes secreted MEG proteins. The genes are composed of short exons (3-81 base pairs) regularly interspersed with long introns (up to 5 kbp). This article recollects 35 S. mansoni specific meg genes that are distributed over 7 autosomes and one pair of sex chromosomes and that code for at least 87 verified MEG proteins. We used various bioinformatics tools to produce an optimal alignment and propose a phylogenetic analysis. This work highlighted intriguing conserved patterns/motifs in the sequences of the highly variable MEG proteins. Based on the analyses, we were able to classify the verified MEG proteins into two subfamilies and to hypothesize their duplication and colonization of all the chromosomes. Together with motif identification, we also proposed to revisit MEGs' common names and annotation in order to avoid duplication, to help the reproducibility of research results and to avoid possible misunderstandings.
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Affiliation(s)
- Štěpánka Nedvědová
- UMR 5280 Institute of Analytical Sciences, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, 69100 Villeurbanne, France; (Š.N.); (O.W.); (M.H.)
- Department of Chemistry, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, 16500 Prague, Czech Republic
- Department of Zoology and Fisheries, Center of Infectious Animal Diseases, Czech University of Life Sciences, 16500 Prague, Czech Republic
| | - Davide De Stefano
- UMR 5280 Institute of Analytical Sciences, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, 69100 Villeurbanne, France; (Š.N.); (O.W.); (M.H.)
| | - Olivier Walker
- UMR 5280 Institute of Analytical Sciences, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, 69100 Villeurbanne, France; (Š.N.); (O.W.); (M.H.)
| | - Maggy Hologne
- UMR 5280 Institute of Analytical Sciences, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, 69100 Villeurbanne, France; (Š.N.); (O.W.); (M.H.)
| | - Adriana Erica Miele
- UMR 5280 Institute of Analytical Sciences, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, 69100 Villeurbanne, France; (Š.N.); (O.W.); (M.H.)
- Department of Biochemical Sciences, Sapienza University of Rome, 00185 Rome, Italy
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Nedvedova S, Guillière F, Miele AE, Cantrelle FX, Dvorak J, Walker O, Hologne M. Divide, conquer and reconstruct: How to solve the 3D structure of recalcitrant Micro-Exon Gene (MEG) protein from Schistosoma mansoni. PLoS One 2023; 18:e0289444. [PMID: 37535563 PMCID: PMC10399815 DOI: 10.1371/journal.pone.0289444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 07/19/2023] [Indexed: 08/05/2023] Open
Abstract
Micro-Exon Genes are a widespread class of genes known for their high variability, widespread in the genome of parasitic trematodes such as Schistosoma mansoni. In this study, we present a strategy that allowed us to solve the structures of three alternatively spliced isoforms from the Schistoma mansoni MEG 2.1 family for the first time. All isoforms are hydrophobic, intrinsically disordered, and recalcitrant to be expressed in high yield in heterologous hosts. We resorted to the chemical synthesis of shorter pieces, before reconstructing the entire sequence. Here, we show that isoform 1 partially folds in a-helix in the presence of trifluoroethanol while isoform 2 features two rigid elbows, that maintain the peptide as disordered, preventing any structuring. Finally, isoform 3 is dominated by the signal peptide, which folds into a-helix. We demonstrated that combining biophysical techniques, like circular dichroism and nuclear magnetic resonance at natural abundance, with in silico molecular dynamics simulation for isoform 1 only, was the key to solve the structure of MEG 2.1. Our results provide a crucial piece to the puzzle of this elusive and highly variable class of proteins.
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Affiliation(s)
- Stepanka Nedvedova
- Université de Lyon, CNRS, UCB Lyon1, Institut des Sciences Analytiques, UMR5280, 5 rue de la Doua, Villeurbanne, France
- Department of Chemistry, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
- Department of Zoology and Fisheries, Center of Infectious Animal Diseases, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Florence Guillière
- Université de Lyon, CNRS, UCB Lyon1, Institut des Sciences Analytiques, UMR5280, 5 rue de la Doua, Villeurbanne, France
| | - Adriana Erica Miele
- Université de Lyon, CNRS, UCB Lyon1, Institut des Sciences Analytiques, UMR5280, 5 rue de la Doua, Villeurbanne, France
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - François-Xavier Cantrelle
- Université de Lille, CNRS, UMR8576 -UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Jan Dvorak
- Department of Zoology and Fisheries, Center of Infectious Animal Diseases, Czech University of Life Sciences Prague, Prague, Czech Republic
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czechia
- Faculty of Environmental Sciences, Center of Infectious Animal Diseases, Czech University of Life Sciences in Prague, Prague, Czech Republic
| | - Olivier Walker
- Université de Lyon, CNRS, UCB Lyon1, Institut des Sciences Analytiques, UMR5280, 5 rue de la Doua, Villeurbanne, France
| | - Maggy Hologne
- Université de Lyon, CNRS, UCB Lyon1, Institut des Sciences Analytiques, UMR5280, 5 rue de la Doua, Villeurbanne, France
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3
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Arrault C, Monneau YR, Martin M, Cantrelle FX, Boll E, Chirot F, Comby Zerbino C, Walker O, Hologne M. The battle for silver binding: How the interplay between the SilE, SilF, and SilB proteins contributes to the silver efflux pump mechanism. J Biol Chem 2023; 299:105004. [PMID: 37394004 PMCID: PMC10407283 DOI: 10.1016/j.jbc.2023.105004] [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: 04/07/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/04/2023] Open
Abstract
The resistance of gram-negative bacteria to silver ions is mediated by a silver efflux pump, which mainly relies on a tripartite efflux complex SilCBA, a metallochaperone SilF and an intrinsically disordered protein SilE. However, the precise mechanism by which silver ions are extruded from the cell and the different roles of SilB, SilF, and SilE remain poorly understood. To address these questions, we employed nuclear magnetic resonance and mass spectrometry to investigate the interplay between these proteins. We first solved the solution structures of SilF in its free and Ag+-bound forms, and we demonstrated that SilB exhibits two silver binding sites in its N and C termini. Conversely to the homologous Cus system, we determined that SilF and SilB interact without the presence of silver ions and that the rate of silver dissociation is eight times faster when SilF is bound to SilB, indicating the formation of a SilF-Ag-SilB intermediate complex. Finally, we have shown that SilE does not bind to either SilF or SilB, regardless of the presence or absence of silver ions, further corroborating that it merely acts as a regulator that prevents the cell from being overloaded with silver. Collectively, we have provided further insights into protein interactions within the sil system that contribute to bacterial resistance to silver ions.
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Affiliation(s)
- Cyrielle Arrault
- Université de Lyon, CNRS, UCB Lyon1, Institut des Sciences Analytiques, UMR5280, Villeurbanne, France
| | - Yoan Rocky Monneau
- Université de Lyon, CNRS, UCB Lyon1, Institut des Sciences Analytiques, UMR5280, Villeurbanne, France; Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Marie Martin
- Université de Lyon, CNRS, UCB Lyon1, Institut des Sciences Analytiques, UMR5280, Villeurbanne, France
| | - François-Xavier Cantrelle
- Université de Lille, CNRS, UMR8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Emmanuelle Boll
- Université de Lille, CNRS, UMR8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Fabien Chirot
- Univ Lyon 1, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, UMR5306, Cité Lyonnaise de l'Environnement et de l'Analyse, Villeurbanne, France
| | - Clothilde Comby Zerbino
- Univ Lyon 1, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, UMR5306, Cité Lyonnaise de l'Environnement et de l'Analyse, Villeurbanne, France
| | - Olivier Walker
- Université de Lyon, CNRS, UCB Lyon1, Institut des Sciences Analytiques, UMR5280, Villeurbanne, France
| | - Maggy Hologne
- Université de Lyon, CNRS, UCB Lyon1, Institut des Sciences Analytiques, UMR5280, Villeurbanne, France.
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Monneau Y, Arrault C, Duroux C, Martin M, Chirot F, Mac Aleese L, Girod M, Comby-Zerbino C, Hagège A, Walker O, Hologne M. Structural and dynamical insights into SilE silver binding from combined analytical probes. Phys Chem Chem Phys 2023; 25:3061-3071. [PMID: 36617868 DOI: 10.1039/d2cp04206a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Silver has been used for its antimicrobial properties to fight infection for thousands of years. Unfortunately, some Gram-negative bacteria have developed silver resistance causing the death of patients in a burn unit. The genes responsible for silver resistance have been designated as the sil operon. Among the proteins of the sil operon, SilE has been shown to play a key role in bacterial silver resistance. Based on the limited information available, it has been depicted as an intrinsically disordered protein that folds into helices upon silver ion binding. Herein, this work demonstrates that SilE is composed of 4 clearly identified helical segments in the presence of several silver ions. The combination of analytical and biophysical techniques (NMR spectroscopy, CD, SAXS, HRMS, CE-ICP-MS, and IM-MS) reveals that SilE harbors four strong silver binding sites among the eight sites available. We have also further evidenced that SilE does not adopt a globular structure but rather samples a large conformational space from elongated to more compact structures. This particular structural organization facilitates silver binding through much higher accessibility of the involved His and Met residues. These valuable results will advance our current understanding of the role of SilE in the silver efflux pump complex mechanism and will help in the future rational design of inhibitors to fight bacterial silver resistance.
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Affiliation(s)
- Yoan Monneau
- Université de Lyon, CNRS, UCB Lyon1, Institut des Sciences Analytiques, UMR5280, 5 rue de la Doua, Villeurbanne 69100, France.
| | - Cyrielle Arrault
- Université de Lyon, CNRS, UCB Lyon1, Institut des Sciences Analytiques, UMR5280, 5 rue de la Doua, Villeurbanne 69100, France.
| | - Coraline Duroux
- Université de Lyon, CNRS, UCB Lyon1, Institut des Sciences Analytiques, UMR5280, 5 rue de la Doua, Villeurbanne 69100, France.
| | - Marie Martin
- Université de Lyon, CNRS, UCB Lyon1, Institut des Sciences Analytiques, UMR5280, 5 rue de la Doua, Villeurbanne 69100, France.
| | - Fabien Chirot
- Univ Lyon 1, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, UMR5306, Cité Lyonnaise de l'Environnement et de l'Analyse, 5 rue de la Doua, Villeurbanne 69100, France
| | - Luke Mac Aleese
- Univ Lyon 1, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, UMR5306, Cité Lyonnaise de l'Environnement et de l'Analyse, 5 rue de la Doua, Villeurbanne 69100, France
| | - Marion Girod
- Université de Lyon, CNRS, UCB Lyon1, Institut des Sciences Analytiques, UMR5280, 5 rue de la Doua, Villeurbanne 69100, France.
| | - Clothilde Comby-Zerbino
- Univ Lyon 1, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, UMR5306, Cité Lyonnaise de l'Environnement et de l'Analyse, 5 rue de la Doua, Villeurbanne 69100, France
| | - Agnès Hagège
- Université de Lyon, CNRS, UCB Lyon1, Institut des Sciences Analytiques, UMR5280, 5 rue de la Doua, Villeurbanne 69100, France.
| | - Olivier Walker
- Université de Lyon, CNRS, UCB Lyon1, Institut des Sciences Analytiques, UMR5280, 5 rue de la Doua, Villeurbanne 69100, France.
| | - Maggy Hologne
- Université de Lyon, CNRS, UCB Lyon1, Institut des Sciences Analytiques, UMR5280, 5 rue de la Doua, Villeurbanne 69100, France.
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5
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Niu T, De Rosny C, Chautard S, Rey A, Patoli D, Groslambert M, Cosson C, Lagrange B, Zhang Z, Visvikis O, Hacot S, Hologne M, Walker O, Wong J, Wang P, Ricci R, Henry T, Boyer L, Petrilli V, Py BF. NLRP3 phosphorylation in its LRR domain critically regulates inflammasome assembly. Nat Commun 2021; 12:5862. [PMID: 34615873 PMCID: PMC8494922 DOI: 10.1038/s41467-021-26142-w] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 09/17/2021] [Indexed: 11/16/2022] Open
Abstract
NLRP3 controls the secretion of inflammatory cytokines IL-1β/18 and pyroptosis by assembling the inflammasome. Upon coordinated priming and activation stimuli, NLRP3 recruits NEK7 within hetero-oligomers that nucleate ASC and caspase-1 filaments, but the apical molecular mechanisms underlying inflammasome assembly remain elusive. Here we show that NEK7 recruitment to NLRP3 is controlled by the phosphorylation status of NLRP3 S803 located within the interaction surface, in which NLRP3 S803 is phosphorylated upon priming and later dephosphorylated upon activation. Phosphomimetic substitutions of S803 abolish NEK7 recruitment and inflammasome activity in macrophages in vitro and in vivo. In addition, NLRP3-NEK7 binding is also essential for NLRP3 deubiquitination by BRCC3 and subsequently inflammasome assembly, with NLRP3 phosphomimetic mutants showing enhanced ubiquitination and degradation than wildtype NLRP3. Finally, we identify CSNK1A1 as the kinase targeting NLRP3 S803. Our findings thus reveal NLRP3 S803 phosphorylation status as a druggable apical molecular mechanism controlling inflammasome assembly. Nlrp3 inflammasome activation requires Nek7 recruitment to drive ASC speck formation. Here the authors show how Nlrp3 phosphorylation events control this Nek7 recruitment.
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Affiliation(s)
- Tingting Niu
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France.,Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, 500 Dongchuan Road, 200241, Shanghai, China
| | - Charlotte De Rosny
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Séverine Chautard
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Amaury Rey
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Danish Patoli
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Marine Groslambert
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Camille Cosson
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Brice Lagrange
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Zhirong Zhang
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, UMR7104, Inserm, U964, Université de Strasbourg, Illkirch, France
| | - Orane Visvikis
- Université Côte d'Azur, Inserm, C3M, F-06204, Nice, France
| | - Sabine Hacot
- CRCL, Centre de Recherche en Cancérologie de Lyon, INSERM U1052, CNRS UMR5286, Université de Lyon, Université Lyon 1, Centre Léon Bérard, Lyon, France
| | - Maggy Hologne
- Institut des Sciences Analytiques (ISA), Univ Lyon, CNRS, CNRS UMR5280, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Olivier Walker
- Institut des Sciences Analytiques (ISA), Univ Lyon, CNRS, CNRS UMR5280, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Jeimin Wong
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, 500 Dongchuan Road, 200241, Shanghai, China
| | - Ping Wang
- Shanghai Tenth People's Hospital of Tongji University, Tongji Cancer Center, School of Medicine, Tongji University, 200092, Shanghai, China
| | - Roméo Ricci
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, UMR7104, Inserm, U964, Université de Strasbourg, Illkirch, France
| | - Thomas Henry
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Laurent Boyer
- Université Côte d'Azur, Inserm, C3M, F-06204, Nice, France
| | - Virginie Petrilli
- CRCL, Centre de Recherche en Cancérologie de Lyon, INSERM U1052, CNRS UMR5286, Université de Lyon, Université Lyon 1, Centre Léon Bérard, Lyon, France
| | - Bénédicte F Py
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France.
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Babel L, Nguyen MH, Mittelheisser C, Martin M, Fromm KM, Walker O, Hologne M. NMR reveals the interplay between SilE and SilB model peptides in the context of silver resistance. Chem Commun (Camb) 2021; 57:8726-8729. [PMID: 34396382 PMCID: PMC8686694 DOI: 10.1039/d1cc02597j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
SilE and SilB are both proteins involved in the silver efflux pump found in Gram-negative bacteria such as S. typhimurium. Using model peptides along with NMR and CD experiments, we show how SilE may store silver ions prior to delivery and we hypothesize for the first time the interplay between SilB and SilE. Illustrative sketch representative of the interplay between the SilB and SilE proteins in the context of silver bacteria resistance. In case of an excess of silver, SilE plays the role of a regulator and avoids a collapse of the silver efflux pump.![]()
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Affiliation(s)
- Lucille Babel
- University of Fribourg, Department of Chemistry, chemin du musée 9, Fribourg 1700, Switzerland
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7
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Marcellini M, Nguyen MH, Martin M, Hologne M, Walker O. Accurate Prediction of Protein NMR Spin Relaxation by Means of Polarizable Force Fields. Application to Strongly Anisotropic Rotational Diffusion. J Phys Chem B 2020; 124:5103-5112. [DOI: 10.1021/acs.jpcb.0c01922] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Moreno Marcellini
- Institut des Sciences Analytiques (ISA), Univ Lyon, CNRS, UMR5280, Université Claude Bernard Lyon1, Lyon, France
| | - Minh-Ha Nguyen
- Institut des Sciences Analytiques (ISA), Univ Lyon, CNRS, UMR5280, Université Claude Bernard Lyon1, Lyon, France
| | - Marie Martin
- Institut des Sciences Analytiques (ISA), Univ Lyon, CNRS, UMR5280, Université Claude Bernard Lyon1, Lyon, France
| | - Maggy Hologne
- Institut des Sciences Analytiques (ISA), Univ Lyon, CNRS, UMR5280, Université Claude Bernard Lyon1, Lyon, France
| | - Olivier Walker
- Institut des Sciences Analytiques (ISA), Univ Lyon, CNRS, UMR5280, Université Claude Bernard Lyon1, Lyon, France
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8
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Chen PC, Hologne M, Walker O, Hennig J. Ab-Initio Prediction of NMR Spin-Relaxation Parameters from MD Simulations. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.2860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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9
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Bottinelli C, Revelut K, Hologne M, Gaillard Y, Bévalot F. GC-MS, GC-QTOF and NMR analyses to elucidate composition of 41 powders from an NPS collector. Toxicologie Analytique et Clinique 2019. [DOI: 10.1016/j.toxac.2019.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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10
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Bloyet LM, Schramm A, Lazert C, Raynal B, Hologne M, Walker O, Longhi S, Gerlier D. Regulation of measles virus gene expression by P protein coiled-coil properties. Sci Adv 2019; 5:eaaw3702. [PMID: 31086822 PMCID: PMC6506246 DOI: 10.1126/sciadv.aaw3702] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 04/01/2019] [Indexed: 05/18/2023]
Abstract
The polymerase of negative-stranded RNA viruses consists of the large protein (L) and the phosphoprotein (P), the latter serving both as a chaperon and a cofactor for L. We mapped within measles virus (MeV) P the regions responsible for binding and stabilizing L and showed that the coiled-coil multimerization domain (MD) of P is required for gene expression. MeV MD is kinked as a result of the presence of a stammer. Both restoration of the heptad regularity and displacement of the stammer strongly decrease or abrogate activity in a minigenome assay. By contrast, P activity is rather tolerant of substitutions within the stammer. Single substitutions at the "a" or "d" hydrophobic anchor positions with residues of variable hydrophobicity revealed that P functionality requires a narrow range of cohesiveness of its MD. Results collectively indicate that, beyond merely ensuring P oligomerization, the MD finely tunes viral gene expression through its cohesiveness.
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Affiliation(s)
- Louis-Marie Bloyet
- CIRI, International Center for Infectiology Research, INSERM, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Univ Lyon, Lyon, France
| | - Antoine Schramm
- Aix-Marseille University, CNRS, Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Marseille, France
| | - Carine Lazert
- CIRI, International Center for Infectiology Research, INSERM, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Univ Lyon, Lyon, France
| | - Bertrand Raynal
- Institut Pasteur, Plateforme de Biophysique Moléculaire, Paris, France
| | - Maggy Hologne
- Institut des Sciences Analytiques (ISA), Univ Lyon, CNRS, UMR5280, Université Claude Bernard Lyon 1, Lyon France
| | - Olivier Walker
- Institut des Sciences Analytiques (ISA), Univ Lyon, CNRS, UMR5280, Université Claude Bernard Lyon 1, Lyon France
| | - Sonia Longhi
- Aix-Marseille University, CNRS, Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Marseille, France
| | - Denis Gerlier
- CIRI, International Center for Infectiology Research, INSERM, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Univ Lyon, Lyon, France
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11
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Chabert V, Hologne M, Sénèque O, Walker O, Fromm KM. Alpha-helical folding of SilE models upon Ag(His)(Met) motif formation. Chem Commun (Camb) 2018; 54:10419-10422. [PMID: 30132476 DOI: 10.1039/c8cc03784a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The SilE protein is suspected to have a prominent role in Ag+ detoxification of silver resistant bacteria. Using model peptides, we elucidated both qualitative and quantitative aspects of the Ag+-induced α-helical structuring role of His- and Met-rich sequences of SilE, improving our understanding of its function within the Sil system.
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Affiliation(s)
- Valentin Chabert
- University of Fribourg, Department of Chemistry, Chemin du Musée 9, 1700 Fribourg, Switzerland.
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12
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Chen PC, Hologne M, Walker O, Hennig J. Ab Initio Prediction of NMR Spin Relaxation Parameters from Molecular Dynamics Simulations. J Chem Theory Comput 2018; 14:1009-1019. [PMID: 29294268 DOI: 10.1021/acs.jctc.7b00750] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
1H-15N NMR spin relaxation and relaxation dispersion experiments can reveal the time scale and extent of protein motions across the ps-ms range, where the ps-ns dynamics revealed by fundamental quantities R1, R2, and heteronuclear NOE can be well-sampled by molecular dynamics simulations (MD). Although the principles of relaxation prediction from simulations are well-established, numerous NMR-MD comparisons have hitherto focused upon the aspect of order parameters S2 due to common artifacts in the prediction of transient dynamics. We therefore summarize here all necessary components and highlight existing and proposed solutions, such as the inclusion of quantum mechanical zero-point vibrational corrections and separate MD convergence of global and local motions in coarse-grained and all-atom force fields, respectively. For the accuracy of the MD prediction to be tested, two model proteins GB3 and Ubiquitin are used to validate five atomistic force fields against published NMR data supplemented by the coarse-grained force field MARTINI+EN. In Amber and CHARMM-type force fields, quantitative agreement was achieved for structured elements with minimum adjustment of global parameters. Deviations from experiment occur in flexible loops and termini, indicating differences in both the extent and time scale of backbone motions. The lack of systematic patterns and water model dependence suggests that modeling of the local environment limits prediction accuracy. Nevertheless, qualitative accuracy in a 2 μs CHARMM36m Stam2 VHS domain simulation demonstrates the potential of MD-based interpretation in combination with NMR-measured dynamics, increasing the utility of spin relaxation in integrative structural biology.
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Affiliation(s)
- Po-Chia Chen
- Structural and Computational Biology Unit, EMBL Heidelberg , Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Maggy Hologne
- Université de Lyon, CNRS, Université Claude Bernard Lyon1, Ens de Lyon, Institut des Sciences Analytiques, UMR 5280 , 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Olivier Walker
- Université de Lyon, CNRS, Université Claude Bernard Lyon1, Ens de Lyon, Institut des Sciences Analytiques, UMR 5280 , 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Janosch Hennig
- Structural and Computational Biology Unit, EMBL Heidelberg , Meyerhofstrasse 1, 69117 Heidelberg, Germany
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13
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Boughougal A, Cherchali FZ, Messai A, Attik N, Decoret D, Hologne M, Sanglar C, Pilet G, Tommasino JB, Luneau D. New model of metalloantibiotic: synthesis, structure and biological activity of a zinc(ii) mononuclear complex carrying two enrofloxacin and sulfadiazine antibiotics. NEW J CHEM 2018. [DOI: 10.1039/c8nj01774c] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Synthesis of a new model of the Zn-based complex with two complementary antibiotics (sulfonamide and quinolone).
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Affiliation(s)
- Amina Boughougal
- Université de Lyon
- Laboratoire des Multimatériaux et Interfaces (LMI) UMR 5615 CNRS – Université Claude Bernard Lyon 1
- 69622 Villeurbanne Cedex
- France
- Laboratoire d’Ingénierie et Sciences des Matériaux Avancés (ISMA)
| | - Fatma Zohra Cherchali
- Université de Lyon
- Laboratoire des Multimatériaux et Interfaces (LMI) UMR 5615 CNRS – Université Claude Bernard Lyon 1
- 69622 Villeurbanne Cedex
- France
- Laboratoire d’Etudes Physico-Chimiques des Matériaux
| | - Amel Messai
- Laboratoire d’Ingénierie et Sciences des Matériaux Avancés (ISMA)
- Institut des Sciences et Technologie
- Abbès Laghrour University
- Khenchela 40000
- Algeria
| | - Nina Attik
- Université de Lyon
- Laboratoire des Multimatériaux et Interfaces (LMI) UMR 5615 CNRS – Université Claude Bernard Lyon 1
- 69622 Villeurbanne Cedex
- France
| | | | - Maggy Hologne
- Univ. Lyon
- CNRS, UCB Lyon 1
- Institut des Sciences Analytiques
- 69100 Villeurbanne
- France
| | - Corinne Sanglar
- Univ. Lyon
- CNRS, UCB Lyon 1
- Institut des Sciences Analytiques
- 69100 Villeurbanne
- France
| | - Guillaume Pilet
- Université de Lyon
- Laboratoire des Multimatériaux et Interfaces (LMI) UMR 5615 CNRS – Université Claude Bernard Lyon 1
- 69622 Villeurbanne Cedex
- France
| | - Jean Bernard Tommasino
- Université de Lyon
- Laboratoire des Multimatériaux et Interfaces (LMI) UMR 5615 CNRS – Université Claude Bernard Lyon 1
- 69622 Villeurbanne Cedex
- France
| | - Dominique Luneau
- Université de Lyon
- Laboratoire des Multimatériaux et Interfaces (LMI) UMR 5615 CNRS – Université Claude Bernard Lyon 1
- 69622 Villeurbanne Cedex
- France
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14
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Chen PC, Hologne M, Walker O. Computing the Rotational Diffusion of Biomolecules via Molecular Dynamics Simulation and Quaternion Orientations. J Phys Chem B 2017; 121:1812-1823. [DOI: 10.1021/acs.jpcb.6b11703] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Po-chia Chen
- Université de Lyon, CNRS, Université Claude Bernard Lyon1, Ens de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Maggy Hologne
- Université de Lyon, CNRS, Université Claude Bernard Lyon1, Ens de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Olivier Walker
- Université de Lyon, CNRS, Université Claude Bernard Lyon1, Ens de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
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15
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Chabert V, Hologne M, Sénèque O, Crochet A, Walker O, Fromm KM. Model peptide studies of Ag+ binding sites from the silver resistance protein SilE. Chem Commun (Camb) 2017; 53:6105-6108. [DOI: 10.1039/c7cc02630g] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A model peptide study characterizes several Ag+-binding sites of the bacterial silver resistant protein SilE, providing new insights into its physiological role.
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Affiliation(s)
- V. Chabert
- Univ. Fribourg
- Department of Chemistry
- 1700 Fribourg
- Switzerland
| | - M. Hologne
- Univ. Lyon
- CNRS
- UCB Lyon 1
- ENS-Lyon
- Institut des Sciences Analytiques
| | - O. Sénèque
- Univ. Grenoble Alpes
- CNRS
- CEA, LCBM (UMR 5249)
- F-38000 Grenoble
- France
| | - A. Crochet
- Univ. Fribourg
- Fribourg Center for Nanomaterials
- FriMat
- 1700 Fribourg
- Switzerland
| | - O. Walker
- Univ. Lyon
- CNRS
- UCB Lyon 1
- ENS-Lyon
- Institut des Sciences Analytiques
| | - K. M. Fromm
- Univ. Fribourg
- Department of Chemistry
- 1700 Fribourg
- Switzerland
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16
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Ladroue V, Stemmelen A, Besacier F, Hologne M. Les NPS en vogue en région Rhône-Alpes : rapport de cas. Toxicologie Analytique et Clinique 2016. [DOI: 10.1016/j.toxac.2016.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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17
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Hologne M, Cantrelle FX, Riviere G, Guillière F, Trivelli X, Walker O. NMR Reveals the Interplay among the AMSH SH3 Binding Motif, STAM2, and Lys63-Linked Diubiquitin. J Mol Biol 2016; 428:4544-4558. [PMID: 27725184 DOI: 10.1016/j.jmb.2016.10.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 09/30/2016] [Accepted: 10/01/2016] [Indexed: 01/31/2023]
Abstract
AMSH [associated molecule with a Src homology 3 domain of signal transducing adaptor molecule (STAM)] is one of the deubiquitinating enzymes associated in the regulation of endocytic cargo trafficking. It shows an exquisite selectivity for Lys63-linked polyubiquitin chains that are the main chains involved in cargo sorting. The first step requires the ESCRT-0 complex that comprises the STAM and hepatocyte growth factor-regulated substrate (Hrs) proteins. Previous studies have shown that the presence of the STAM protein increases the efficiency of Lys63-linked polyubiquitin chain cleavage by AMSH, one of the deubiquitinating enzyme involved in lysosomal degradation. In the present study, we are seeking to understand if a particular structural organization among these three key players is responsible for the stimulation of the catalytic activity of AMSH. To address this question, we first monitored the interaction between the ubiquitin interacting motif (UIM)-SH3 construct of STAM2 and the Lys63-linked diubiquitin (Lys63-Ub2) chains by means of NMR. We show that Lys63-Ub2 is able to bind either the UIM or the SH3 domain without any selectivity. We further demonstrate that the SH3 binding motif (SBM) of AMSH (AMSH-SBM) outcompetes Lys63-Ub2 for binding SH3. Additionally, we show how different AMSH-SBM variants, modified by their sequence and length, exhibit similar equilibrium dissociation constants when binding SH3 but significantly differ in their dissociation rate constants. Finally, we report the solution NMR structure of the AMSH-SBM/SH3 complex and propose a structural organization where the AMSH-SBM interacts with the STAM2-SH3 domain and contributes to the correct positioning of AMSH prior to polyubiquitin chains' cleavage.
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Affiliation(s)
- Maggy Hologne
- Université de Lyon, CNRS, Université Claude Bernard Lyon1, Ens de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - François-Xavier Cantrelle
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| | - Gwladys Riviere
- Université de Lyon, CNRS, Université Claude Bernard Lyon1, Ens de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Florence Guillière
- Université de Lyon, CNRS, Université Claude Bernard Lyon1, Ens de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Xavier Trivelli
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| | - Olivier Walker
- Université de Lyon, CNRS, Université Claude Bernard Lyon1, Ens de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France.
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18
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Rigard M, Bröms JE, Mosnier A, Hologne M, Martin A, Lindgren L, Punginelli C, Lays C, Walker O, Charbit A, Telouk P, Conlan W, Terradot L, Sjöstedt A, Henry T. Francisella tularensis IglG Belongs to a Novel Family of PAAR-Like T6SS Proteins and Harbors a Unique N-terminal Extension Required for Virulence. PLoS Pathog 2016; 12:e1005821. [PMID: 27602570 PMCID: PMC5014421 DOI: 10.1371/journal.ppat.1005821] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 07/20/2016] [Indexed: 12/12/2022] Open
Abstract
The virulence of Francisella tularensis, the etiological agent of tularemia, relies on an atypical type VI secretion system (T6SS) encoded by a genomic island termed the Francisella Pathogenicity Island (FPI). While the importance of the FPI in F. tularensis virulence is clearly established, the precise role of most of the FPI-encoded proteins remains to be deciphered. In this study, using highly virulent F. tularensis strains and the closely related species F. novicida, IglG was characterized as a protein featuring a unique α-helical N-terminal extension and a domain of unknown function (DUF4280), present in more than 250 bacterial species. Three dimensional modeling of IglG and of the DUF4280 consensus protein sequence indicates that these proteins adopt a PAAR-like fold, suggesting they could cap the T6SS in a similar way as the recently described PAAR proteins. The newly identified PAAR-like motif is characterized by four conserved cysteine residues, also present in IglG, which may bind a metal atom. We demonstrate that IglG binds metal ions and that each individual cysteine is required for T6SS-dependent secretion of IglG and of the Hcp homologue, IglC and for the F. novicida intracellular life cycle. In contrast, the Francisella-specific N-terminal α-helical extension is not required for IglG secretion, but is critical for F. novicida virulence and for the interaction of IglG with another FPI-encoded protein, IglF. Altogether, our data suggest that IglG is a PAAR-like protein acting as a bi-modal protein that may connect the tip of the Francisella T6SS with a putative T6SS effector, IglF. Francisella tularensis is a highly pathogenic bacterium causing tularemia. Its ability to cause disease is linked to its ability to replicate in the macrophage cytosol. The intracellular life cycle of Francisella is controlled by a type VI secretion system (T6SS), which is thought to inject effectors into the host cell to allow bacterial escape into the host cytosol. The molecular mechanisms behind this process are still largely unclear. In this work, we identify IglG as a protein with two important domains, one conserved in proteins from more than 250 bacterial species (DUF4280, renamed here as PAAR-like domain) and one specific for the Francisella genus. Using protein sequence analysis and three-dimensional structure predictions, comparative modeling and biochemistry approaches, our data demonstrate that IglG is a metal-binding protein that based on its PAAR-like domain might cap the VgrG spike of the T6SS and act as a membrane-puncturing protein. Furthermore, we identified that the Francisella-specific domain is directly involved in forming a protein complex with another virulence protein, IglF. This work, in addition to enhancing the molecular understanding of the Francisella T6SS, defines the features of the conserved DUF4280, a novel PAAR-like domain involved in type VI secretion (T6S) of many bacterial species.
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Affiliation(s)
- Mélanie Rigard
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS, UMR5308, Lyon, France
- University of Lyon, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
| | - Jeanette E. Bröms
- Department of Clinical Microbiology, Clinical Bacteriology, and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Amandine Mosnier
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS, UMR5308, Lyon, France
- University of Lyon, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
| | - Maggy Hologne
- Institut des Sciences Analytiques, CNRS, UMR 5280, Université de Lyon, Université Claude Bernard Lyon 1, ENS de Lyon, Villeurbanne, France
| | - Amandine Martin
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS, UMR5308, Lyon, France
- University of Lyon, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
| | - Lena Lindgren
- Department of Clinical Microbiology, Clinical Bacteriology, and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Claire Punginelli
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS, UMR5308, Lyon, France
- University of Lyon, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
| | - Claire Lays
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS, UMR5308, Lyon, France
- University of Lyon, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
| | - Olivier Walker
- Institut des Sciences Analytiques, CNRS, UMR 5280, Université de Lyon, Université Claude Bernard Lyon 1, ENS de Lyon, Villeurbanne, France
| | - Alain Charbit
- Université Paris Descartes, Sorbonne Paris Cité, Bâtiment Leriche, Paris, France
- Institut Necker-Enfants Malades, Equipe 11: Pathogénie des Infections Systémiques, Paris, France
| | - Philippe Telouk
- University of Lyon, Lyon, France
- Laboratoire de Geologie de Lyon; Ecole Normale Supérieure de Lyon, Lyon, France
| | - Wayne Conlan
- National Research Council Canada, Human Health Therapeutics Portfolio, Ottawa, Ontario, Canada
| | - Laurent Terradot
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS-Université de Lyon, Institut de Biologie et Chimie des Protéines, Lyon, France
- * E-mail: (LT); (AS); (TH)
| | - Anders Sjöstedt
- Department of Clinical Microbiology, Clinical Bacteriology, and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
- * E-mail: (LT); (AS); (TH)
| | - Thomas Henry
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS, UMR5308, Lyon, France
- University of Lyon, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- * E-mail: (LT); (AS); (TH)
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19
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Chabert V, Hologne M, Walker O, Fromm KM. Bacterial resistance to silver: the role of SilE protein. Acta Crystallogr A Found Adv 2016. [DOI: 10.1107/s2053273316099204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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20
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Hologne M, Gaubert A, Sanglar C, Bordes C, Casabianca H. New validation of molecular mass measurements by means of 2D DOSY 1H NMR experiments: Application to surfactants. CR CHIM 2015. [DOI: 10.1016/j.crci.2014.05.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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21
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Ladroue V, Besacier F, Hologne M. Découverte d’un laboratoire de conditionnement de nouveaux produits de synthèse en France. ACTA ACUST UNITED AC 2014. [DOI: 10.1051/ata/2013052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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22
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Lange A, Ismail MB, Rivière G, Hologne M, Lacabanne D, Guillière F, Lancelin JM, Krimm I, Walker O. Competitive binding of UBPY and ubiquitin to the STAM2 SH3 domain revealed by NMR. FEBS Lett 2012; 586:3379-84. [PMID: 22841719 DOI: 10.1016/j.febslet.2012.07.047] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 07/15/2012] [Accepted: 07/17/2012] [Indexed: 10/28/2022]
Abstract
To date, the signal transducing adaptor molecule 2 (STAM2) was shown to harbour two ubiquitin binding domains (UBDs) known as the VHS and UIM domains, while the SH3 domain of STAM2 was reported to interact with deubiquitinating enzymes (DUBs) like UBPY and AMSH. In the present study, NMR evidences the interaction of the STAM2 SH3 domain with ubiquitin, demonstrating that SH3 constitutes the third UBD of STAM2. Furthermore, we show that a UBPY-derived peptide can outcompete ubiquitin for SH3 binding and vice versa. These results suggest that the SH3 domain of STAM2 plays versatile roles in the context of ubiquitin mediated receptor sorting.
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Affiliation(s)
- Anja Lange
- Université de Lyon, Université Claude Bernard Lyon1, CNRS, UMR 5280 Institut des Sciences Analytiques, Villeurbanne, France
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23
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Rivière G, Hologne M, Marcillat O, Lancelin JM. Dynamical properties of the loop 320s of substrate-free and substrate-bound muscle creatine kinase by NMR: evidence for independent subunits. FEBS J 2012; 279:2863-75. [PMID: 22715856 DOI: 10.1111/j.1742-4658.2012.08667.x] [Citation(s) in RCA: 2] [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: 11/30/2022]
Abstract
Muscle creatine kinase (MCK; EC2.7.3.2) is a 86 kDa homodimer that belongs to the family of guanidino kinases. MCK has been intensively studied for several decades, but it is still not known why it is a dimer because this quaternary structure does not translate into obvious structural or functional advantages over the homologous monomeric arginine kinase. In particular, it remains to be demonstrated whether MCK subunits are independent. Here, we describe NMR chemical-shift perturbation and relaxation experiments designed to study the active site 320s flexible loop of this enzyme. The analysis was performed with the enzyme in its ligand-free and MgADP-complexed forms, as well as with the transition-state analogue abortive complex (MCK-Mg-ADP-creatine-nitrate ion). Our data indicate that each subunit can bind substrates independently.
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Affiliation(s)
- Gwladys Rivière
- Institut des Sciences Analytiques, Université de Lyon, Université Claude Bernard Lyon 1, Villeurbanne, France
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24
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Chung JS, Noguera-Mazon V, Lancelin JM, Kim SK, Hirasawa M, Hologne M, Leustek T, Knaff DB. Interaction domain on thioredoxin for Pseudomonas aeruginosa 5'-adenylylsulfate reductase. J Biol Chem 2009; 284:31181-9. [PMID: 19744922 DOI: 10.1074/jbc.m109.035634] [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
NMR spectroscopy has been used to map the interaction domain on Escherichia coli thioredoxin for the thioredoxin- dependent 5'-adenylylsulfate reductase from Pseudomonas aeruginosa (PaAPR). Seventeen thioredoxin amino acids, all clustered around Cys-32 (the more surface-exposed of the two active-site cysteines), have been located at the PaAPR binding site. The center of the binding domain is dominated by nonpolar amino acids, with a smaller number of charged and polar amino acids located on the periphery of the site. Twelve of the amino acids detected by NMR have non-polar, hydrophobic side chains, including one aromatic amino acid (Trp-31). Four of the thioredoxin amino acids at the PaAPR binding site have polar side chains (Lys-36, Asp-61, Gln-62 and Arg-73), with three of the four having charged side chains. Site-directed mutagenesis experiments have shown that replacement of Lys-36, Asp-61, and Arg-73 and of the absolutely conserved Trp-31 significantly decreases the V(max) for the PaAPR-catalyzed reduction of 5'-adenylylsulfate, with E. coli thioredoxin serving as the electron donor. The most dramatic effect was observed with the W31A variant, which showed no activity as a donor to PaAPR. Although the thiol of the active-site Cys-256 of PaAPR is the point of the initial nucleophilic attack by reduced thioredoxin, mutagenic replacement of Cys-256 by serine has no effect on thioredoxin binding to PaAPR.
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Affiliation(s)
- Jung-Sung Chung
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, USA
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25
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Reif B, Xue Y, Agarwal V, Pavlova MS, Hologne M, Diehl A, Ryabov YE, Skrynnikov NR. Protein Side-Chain Dynamics Observed by Solution- and Solid-State NMR: Comparative Analysis of Methyl 2H Relaxation Data. J Am Chem Soc 2006; 128:12354-5. [PMID: 16984151 DOI: 10.1021/ja062808a] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [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
Rapid advances in solid-state MAS NMR made it possible to probe protein dynamics on a per-residue basis, similar to solution experiments. In this work we compare methyl 2H relaxation rates measured in the solid and liquid samples of alpha-spectrin SH3 domain. The solution data are treated using a model-free approach to separate the contributions from the overall molecular tumbling and fast internal motion. The latter part forms the basis for comparison with the solid-state data. Although the accuracy of solid-state measurements is limited by deuterium spin diffusion, the results suggest a significant similarity between methyl dynamics in the two samples. This is a potentially important observation, preparing the ground for combined analysis of the dynamics data by solid- and solution-state NMR.
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Affiliation(s)
- Bernd Reif
- Forschunginstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany
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26
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Hologne M, Chen Z, Reif B. Characterization of dynamic processes using deuterium in uniformly 2H,13C,15N enriched peptides by MAS solid-state NMR. J Magn Reson 2006; 179:20-8. [PMID: 16289962 DOI: 10.1016/j.jmr.2005.10.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2005] [Revised: 09/29/2005] [Accepted: 10/24/2005] [Indexed: 05/05/2023]
Abstract
We present in this paper 2H,13C MAS correlation experiments that are performed on a uniformly 2H,13C,15N labeled sample of Nac-Val, and on the uniformly 2H,15N labeled dipeptide Nac-Val-Leu-OH. The experiments involve the measurement of 2H T1 relaxation times at two different magnetic fields, as well as the measurement of the 2H tensor parameters by evolution of the 2H chemical shift. The data are interpreted quantitatively to differentiate between different side chain motional models.
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Affiliation(s)
- Maggy Hologne
- Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Str. 10 13125 Berlin, Germany
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Hologne M, Raya J, Hirschinger J. 13C/15N distance determination by CPMAS NMR in uniformly 13C labeled molecules. Magn Reson Chem 2006; 44:174-7. [PMID: 16358305 DOI: 10.1002/mrc.1744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The REDOR and CPMAS techniques are applied for measuring 13C-15N dipolar coupling constants in glycine. It is shown that the selective CP or SPECIFIC CP technique removes the coherent evolution of the spin system under homonuclear 13C-13C J couplings. While the large coupling constant (approximately 900 Hz) is readily determined because of the presence of large oscillations in the CPMAS dynamics, their absence precludes the measurement of the small coupling constant (approximately 200 Hz). The experimental results and numerical simulations demonstrate that the determination of 13C-15N coupling constants of medium size (<1 kHz) by the CPMAS technique is mainly limited by the strength of the 1H decoupling field and the size of the 13C and 15N chemical shift anisotropies.
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Affiliation(s)
- Maggy Hologne
- Institut de Chimie, FRE 2446 CNRS, Université Louis Pasteur, BP 296, 67008 Strasbourg Cedex, France
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Abstract
We show in this communication that dynamic information for uniformly 2H,13C,15N isotopically enriched, crystalline proteins can be obtained by MAS solid-state NMR spectroscopy. The experiments make use of the deuterium quadrupolar tensor, which is the dominant interaction mechanism. Dynamic properties are accessed by measurement of the size of the quadrupolar coupling constant, Cq, and the value of the asymmetry parameter, eta, via evolution of the deuterium chemical shift, as well as by measurement of deuterium T1 relaxation times. Three-dimensional experiments are performed in order to obtain site-specific resolution. Due to proton dilution, no proton decoupling is required in the carbon evolution periods at MAS rotation frequencies of 10 kHz.
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Affiliation(s)
- Maggy Hologne
- Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
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Hologne M, Bertani P, Azaïs T, Bonhomme C, Hirschinger J. 1H/31P distance determination by solid state NMR in multiple-spin systems. Solid State Nucl Magn Reson 2005; 28:50-6. [PMID: 15899581 DOI: 10.1016/j.ssnmr.2005.04.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2005] [Revised: 04/19/2005] [Accepted: 04/20/2005] [Indexed: 05/02/2023]
Abstract
The results of two techniques of dipolar recoupling, REDOR and CPMAS, are compared in the case of a coupled multiple-spin system. A fundamentally different behavior is observed for these two techniques. In REDOR, the terms associated with each interaction S-I(k) commute with each other and no truncation takes place so that each addition of spin I(k) causes a splitting with its dipolar frequency. In CPMAS, the flip-flop terms of the dipolar Hamiltonian do not commute with the dominant term from the strongly coupled spin pair so that the weak coupling terms from the neighboring spin I(k) are effectively truncated by the dominant pair interaction. Spin dynamics calculations are in agreement with the experimental data in a cubane shaped cluster.
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Affiliation(s)
- Maggy Hologne
- Institut de Chimie, FRE 2446 CNRS, Université Louis Pasteur, BP 296, 67008 Strasbourg Cedex, France
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Hologne M, Hirschinger JJ. Molecular dynamics as studied by static-powder and magic-angle spinning 2H NMR. Solid State Nucl Magn Reson 2004; 26:1-10. [PMID: 15157533 DOI: 10.1016/s0926-2040(03)00062-6] [Citation(s) in RCA: 20] [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] [Subscribe] [Scholar Register] [Received: 05/19/2003] [Indexed: 05/24/2023]
Abstract
The 2H NMR magic-angle spinning (MAS) technique is compared to the static-powder quadrupole echo (QE) and Jeener-Brockaert (JB) pulse sequences for a quantitative investigation of molecular dynamics in solids. The linewidth of individual spinning sidebands of the one-dimensional MAS spectra are observed to be characteristic of the correlation time from approximately 10(-2) to approximately 10(-8) s so that the dynamic range is increased by approximately three orders of magnitude when compared to the QE experiment. As a consequence, MAS 2H NMR is found to be more sensitive to the presence of an inhomogeneous distribution of correlation times than the QE and JB experiments which rely upon lineshape distortions due to anisotropic T2 and T1Q relaxation, respectively. All these results are demonstrated experimentally and numerically using the two-site flip motion of dimethyl sulfone and of the nitrobenzene guest in the alpha-p-tert-butylcalix[4]arene-nitrobenzene inclusion compound.
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Affiliation(s)
- Maggy Hologne
- Institut de Chimie, FRE 2446 CNRS, Université Louis Pasteur, BP 296, 67008 Strasbourg, Cedex, France
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