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Maity A, Wulffelé J, Ayala I, Favier A, Adam V, Bourgeois D, Brutscher B. Structural Heterogeneity in a Phototransformable Fluorescent Protein Impacts its Photochemical Properties. Adv Sci (Weinh) 2024; 11:e2306272. [PMID: 38146132 PMCID: PMC10933604 DOI: 10.1002/advs.202306272] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/29/2023] [Indexed: 12/27/2023]
Abstract
Photoconvertible fluorescent proteins (PCFP) are important cellular markers in advanced imaging modalities such as photoactivatable localization microscopy (PALM). However, their complex photophysical and photochemical behavior hampers applications such as quantitative and single-particle-tracking PALM. This work employs multidimensional NMR combined with ensemble fluorescence measurements to show that the popular mEos4b in its Green state populates two conformations (A and B), differing in side-chain protonation of the conserved residues E212 and H62, altering the hydrogen-bond network in the chromophore pocket. The interconversion (protonation/deprotonation) between these two states, which occurs on the minutes time scale in the dark, becomes strongly accelerated in the presence of UV light, leading to a population shift. This work shows that the reversible photoswitching and Green-to-Red photoconversion properties differ between the A and B states. The chromophore in the A-state photoswitches more efficiently and is proposed to be more prone to photoconversion, while the B-state shows a higher level of photobleaching. Altogether, this data highlights the central role of conformational heterogeneity in fluorescent protein photochemistry.
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Affiliation(s)
- Arijit Maity
- CEACNRSInstitut de Biologie Structurale (IBS)Université Grenoble Alpes71 avenue des Martyrs, Cedex 9Grenoble38044France
| | - Jip Wulffelé
- CEACNRSInstitut de Biologie Structurale (IBS)Université Grenoble Alpes71 avenue des Martyrs, Cedex 9Grenoble38044France
| | - Isabel Ayala
- CEACNRSInstitut de Biologie Structurale (IBS)Université Grenoble Alpes71 avenue des Martyrs, Cedex 9Grenoble38044France
| | - Adrien Favier
- CEACNRSInstitut de Biologie Structurale (IBS)Université Grenoble Alpes71 avenue des Martyrs, Cedex 9Grenoble38044France
| | - Virgile Adam
- CEACNRSInstitut de Biologie Structurale (IBS)Université Grenoble Alpes71 avenue des Martyrs, Cedex 9Grenoble38044France
| | - Dominique Bourgeois
- CEACNRSInstitut de Biologie Structurale (IBS)Université Grenoble Alpes71 avenue des Martyrs, Cedex 9Grenoble38044France
| | - Bernhard Brutscher
- CEACNRSInstitut de Biologie Structurale (IBS)Université Grenoble Alpes71 avenue des Martyrs, Cedex 9Grenoble38044France
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2
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Lethier M, Huard K, Hons M, Favier A, Brutscher B, Boeri Erba E, Abbott DW, Cusack S, Pellegrini E. Structure shows that the BIR2 domain of E3 ligase XIAP binds across the RIPK2 kinase dimer interface. Life Sci Alliance 2023; 6:e202201784. [PMID: 37673444 PMCID: PMC10485824 DOI: 10.26508/lsa.202201784] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 08/09/2023] [Accepted: 08/09/2023] [Indexed: 09/08/2023] Open
Abstract
RIPK2 is an essential adaptor for NOD signalling and its kinase domain is a drug target for NOD-related diseases, such as inflammatory bowel disease. However, recent work indicates that the phosphorylation activity of RIPK2 is dispensable for signalling and that inhibitors of both RIPK2 activity and RIPK2 ubiquitination prevent the essential interaction between RIPK2 and the BIR2 domain of XIAP, the key RIPK2 ubiquitin E3 ligase. Moreover, XIAP BIR2 antagonists also block this interaction. To reveal the molecular mechanisms involved, we combined native mass spectrometry, NMR, and cryo-electron microscopy to determine the structure of the RIPK2 kinase BIR2 domain complex and validated the interface with in cellulo assays. The structure shows that BIR2 binds across the RIPK2 kinase antiparallel dimer and provides an explanation for both inhibitory mechanisms. It also highlights why phosphorylation of the kinase activation loop is dispensable for signalling while revealing the structural role of RIPK2-K209 residue in the RIPK2-XIAP BIR2 interaction. Our results clarify the features of the RIPK2 conformation essential for its role as a scaffold protein for ubiquitination.
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Affiliation(s)
- Mathilde Lethier
- https://ror.org/01zjc6908 European Molecular Biology Laboratory, Grenoble, France
| | - Karine Huard
- https://ror.org/01zjc6908 European Molecular Biology Laboratory, Grenoble, France
| | - Michael Hons
- https://ror.org/01zjc6908 European Molecular Biology Laboratory, Grenoble, France
| | - Adrien Favier
- University Grenoble Alpes, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
| | - Bernhard Brutscher
- University Grenoble Alpes, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
| | - Elisabetta Boeri Erba
- University Grenoble Alpes, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
| | - Derek W Abbott
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Stephen Cusack
- https://ror.org/01zjc6908 European Molecular Biology Laboratory, Grenoble, France
| | - Erika Pellegrini
- https://ror.org/01zjc6908 European Molecular Biology Laboratory, Grenoble, France
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3
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Vallet A, Martin-Laffon J, Favier A, Revel B, Bonnot T, Vidaud C, Armengaud J, Gaillard JC, Delangle P, Devime F, Figuet S, Serre NBC, Erba EB, Brutscher B, Ravanel S, Bourguignon J, Alban C. The plasma membrane-associated cation-binding protein PCaP1 of Arabidopsis thaliana is a uranyl-binding protein. J Hazard Mater 2023; 446:130668. [PMID: 36608581 DOI: 10.1016/j.jhazmat.2022.130668] [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: 10/17/2022] [Revised: 12/14/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Uranium (U) is a naturally-occurring radionuclide that is toxic to living organisms. Given that proteins are primary targets of U(VI), their identification is an essential step towards understanding the mechanisms of radionuclide toxicity, and possibly detoxification. Here, we implemented a chromatographic strategy including immobilized metal affinity chromatography to trap protein targets of uranyl in Arabidopsis thaliana. This procedure allowed the identification of 38 uranyl-binding proteins (UraBPs) from root and shoot extracts. Among them, UraBP25, previously identified as plasma membrane-associated cation-binding protein 1 (PCaP1), was further characterized as a protein interacting in vitro with U(VI) and other metals using spectroscopic and structural approaches, and in planta through analyses of the fate of U(VI) in Arabidopsis lines with altered PCaP1 gene expression. Our results showed that recombinant PCaP1 binds U(VI) in vitro with affinity in the nM range, as well as Cu(II) and Fe(III) in high proportions, and that Ca(II) competes with U(VI) for binding. U(VI) induces PCaP1 oligomerization through binding at the monomer interface, at both the N-terminal structured domain and the C-terminal flexible region. Finally, U(VI) translocation in Arabidopsis shoots was affected in pcap1 null-mutant, suggesting a role for this protein in ion trafficking in planta.
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Affiliation(s)
- Alicia Vallet
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, IBS, 38000 Grenoble, France
| | | | - Adrien Favier
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, IBS, 38000 Grenoble, France
| | - Benoît Revel
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, 38000 Grenoble, France
| | - Titouan Bonnot
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, 38000 Grenoble, France
| | - Claude Vidaud
- BIAM, CEA, CNRS, Univ. Aix-Marseille, 13108 Saint-Paul-lez-Durance, France
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, F-F-30200 Bagnols-sur-Cèze, France
| | - Jean-Charles Gaillard
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, F-F-30200 Bagnols-sur-Cèze, France
| | - Pascale Delangle
- Univ. Grenoble Alpes, CEA, CNRS, GRE-INP, IRIG, SyMMES, 38000 Grenoble, France
| | - Fabienne Devime
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, 38000 Grenoble, France
| | - Sylvie Figuet
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, 38000 Grenoble, France
| | - Nelson B C Serre
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, 38000 Grenoble, France
| | | | | | - Stéphane Ravanel
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, 38000 Grenoble, France
| | | | - Claude Alban
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, 38000 Grenoble, France.
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4
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Henot F, Rioual E, Favier A, Macek P, Crublet E, Josso P, Brutscher B, Frech M, Gans P, Loison C, Boisbouvier J. Visualizing the transiently populated closed-state of human HSP90 ATP binding domain. Nat Commun 2022; 13:7601. [PMID: 36494347 PMCID: PMC9734131 DOI: 10.1038/s41467-022-35399-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 11/29/2022] [Indexed: 12/13/2022] Open
Abstract
HSP90 are abundant molecular chaperones, assisting the folding of several hundred client proteins, including substrates involved in tumor growth or neurodegenerative diseases. A complex set of large ATP-driven structural changes occurs during HSP90 functional cycle. However, the existence of such structural rearrangements in apo HSP90 has remained unclear. Here, we identify a metastable excited state in the isolated human HSP90α ATP binding domain. We use solution NMR and mutagenesis to characterize structures of both ground and excited states. We demonstrate that in solution the HSP90α ATP binding domain transiently samples a functionally relevant ATP-lid closed state, distant by more than 30 Å from the ground state. NMR relaxation enables to derive information on the kinetics and thermodynamics of this interconversion, while molecular dynamics simulations establish that the ATP-lid in closed conformation is a metastable exited state. The precise description of the dynamics and structures sampled by human HSP90α ATP binding domain provides information for the future design of new therapeutic ligands.
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Affiliation(s)
- Faustine Henot
- grid.4444.00000 0001 2112 9282Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71, avenue des martyrs, F-38044 Grenoble, France
| | - Elisa Rioual
- grid.4444.00000 0001 2112 9282Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71, avenue des martyrs, F-38044 Grenoble, France ,grid.7849.20000 0001 2150 7757Institut Lumière Matière, University of Lyon, Université Claude Bernard Lyon 1, CNRS, F-69622 Villeurbanne, France
| | - Adrien Favier
- grid.4444.00000 0001 2112 9282Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71, avenue des martyrs, F-38044 Grenoble, France
| | - Pavel Macek
- grid.4444.00000 0001 2112 9282Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71, avenue des martyrs, F-38044 Grenoble, France ,NMR-Bio, 5 place Robert Schuman, F-38025 Grenoble, France
| | - Elodie Crublet
- NMR-Bio, 5 place Robert Schuman, F-38025 Grenoble, France
| | - Pierre Josso
- grid.7849.20000 0001 2150 7757Institut Lumière Matière, University of Lyon, Université Claude Bernard Lyon 1, CNRS, F-69622 Villeurbanne, France
| | - Bernhard Brutscher
- grid.4444.00000 0001 2112 9282Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71, avenue des martyrs, F-38044 Grenoble, France
| | - Matthias Frech
- grid.39009.330000 0001 0672 7022Discovery Technologies, Merck KGaA, Frankfurter Straße 250, 64293 Darmstadt, Germany
| | - Pierre Gans
- grid.4444.00000 0001 2112 9282Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71, avenue des martyrs, F-38044 Grenoble, France
| | - Claire Loison
- grid.7849.20000 0001 2150 7757Institut Lumière Matière, University of Lyon, Université Claude Bernard Lyon 1, CNRS, F-69622 Villeurbanne, France
| | - Jerome Boisbouvier
- grid.4444.00000 0001 2112 9282Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71, avenue des martyrs, F-38044 Grenoble, France
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5
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Blake H, Carlisle S, Fothergill L, Hassard J, Favier A, Corner J, Ball JK, Denning C. Process evaluation of a university residence-based SARS-CoV-2 testing programme in the UK. Eur J Public Health 2022. [DOI: 10.1093/eurpub/ckac131.046] [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: 11/14/2022] Open
Abstract
Abstract
Background
Regular testing for SARS-CoV-2 is an important strategy for controlling virus outbreaks on university campuses during the COVID-19 pandemic but testing participation can be low. The Residence-Based Testing Participation Pilot (RB-TPP) was a novel 4-week intervention implemented at two student residences on a UK university campus, aiming to increase asymptomatic testing frequency and normalise university life through relaxed social restrictions onsite.
Methods
Mixed-methods process evaluation determined whether RB-TPP was implemented as planned and identified implementation barriers and facilitators. Data were collected from meeting records, university students (online survey: n = 152; focus groups: n = 30), and staff (interviews, n = 13). Barriers and facilitators to implementation were mapped to the ‘Capability, Opportunity, Motivation-Behaviour’ (COM-B) behaviour change framework.
Results
Uptake was high (n = 464 students opted-in; 98% of those living onsite). Implementation was broadly as planned, with adjustments due to national escalation of the COVID-19 Delta variant. Majority engaged in testing (88%); 46% (52% of testers) were fully compliant with pre-determined testing frequency. Most felt positively towards relaxed social distancing (97.9%). Implementation was facilitated by convenience and efficiency of testing and reduced negative impacts of isolation through opportunities for students to socialise. Barriers to implementation were mixed-messages about the rules, ambivalent attitudes, and lack of adherence to COVID-19 protective measures in the minority.
Conclusions
This is the first process evaluation of the implementation of asymptomatic SARS-CoV-2 testing in university residences. Testing participation increased and student mental wellbeing improved. Rapid adaptions to the changing pandemic context generated complexity and challenge. Findings have global relevance for outbreak prevention and management strategies in higher education settings.
Key messages
• Delivery of asymptomatic SARS-CoV-2 testing and relaxation of social distancing within residences led to high rates of testing participation and benefits for student mental wellbeing.
• This is the first process evaluation of the implementation of asymptomatic SARS-CoV-2 testing in university residences with global relevance for outbreak prevention in higher education settings.
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Affiliation(s)
- H Blake
- School of Health Sciences, University of Nottingham , Nottingham, UK
- NIHR Nottingham Biomedical Research Centre, University of Nottingham , Nottingham, UK
| | - S Carlisle
- School of Health Sciences, University of Nottingham , Nottingham, UK
| | - L Fothergill
- School of Health Sciences, University of Nottingham , Nottingham, UK
| | - J Hassard
- School of Medicine, University of Nottingham , Nottingham, UK
| | - A Favier
- Faculty of Registrars, University of Nottingham , Nottingham, UK
| | - J Corner
- Executive Office, University of Nottingham , Nottingham, UK
| | - JK Ball
- School of Life Sciences, University of Nottingham , Nottingham, UK
- Biodiscovery Institute, University of Nottingham , Nottingham, UK
| | - C Denning
- School of Medicine, University of Nottingham , Nottingham, UK
- Biodiscovery Institute, University of Nottingham , Nottingham, UK
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6
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Blake H, Carlisle S, Fothergill L, Hassard J, Favier A, Corner J, Ball JK, Denning C. Mixed-methods process evaluation of a residence-based SARS-CoV-2 testing participation pilot on a UK university campus during the COVID-19 pandemic. BMC Public Health 2022; 22:1470. [PMID: 35915479 PMCID: PMC9343222 DOI: 10.1186/s12889-022-13792-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 06/10/2022] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Regular testing for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is an important strategy for controlling virus outbreaks on university campuses during the COVID-19 pandemic but testing participation rates can be low. The Residence-Based Testing Participation Pilot (RB-TPP) was a novel intervention implemented at two student residences on a large UK university campus over 4 weeks. The aim of the pilot was to increase the frequency of asymptomatic SARS-CoV-2 saliva testing onsite. This process evaluation aimed to determine whether RB-TPP was implemented as planned and identify implementation barriers and facilitators. METHODS A mixed-methods process evaluation was conducted alongside the RB-TPP. Evaluation participants were students (opting in, or out of RB-TPP) and staff with a role in service provision or student support. Monitoring data were collected from the intervention delivery team and meeting records. Data were collected from students via online survey (n = 152) and seven focus groups (n = 30), and from staff via individual interviews (n = 13). Quantitative data were analysed descriptively and qualitative data thematically. Barriers and facilitators to implementation were mapped to the 'Capability, Opportunity, Motivation-Behaviour' (COM-B) behaviour change framework. RESULTS Four hundred sixty-four students opted to participate in RB-TPP (98% of students living onsite). RB-TPP was implemented broadly as planned but relaxed social distancing was terminated early due to concerns relating to national escalation of the COVID-19 Delta variant, albeit testing continued. Most students (97.9%) perceived the period of relaxed social distancing within residences positively. The majority engaged in asymptomatic testing (88%); 46% (52% of testers) were fully compliant with pre-determined testing frequency. Implementation was facilitated by convenience and efficiency of testing, and reduction in the negative impacts of isolation through opportunities for students to socialise. Main barriers to implementation were perceived mixed-messages about the rules, ambivalent attitudes, and lack of adherence to COVID-19 protective measures in the minority. CONCLUSIONS This process evaluation identifies factors that help or hinder the success of university residence-based outbreak prevention and management strategies. RB-TPP led to increased rates of SARS-CoV-2 testing participation among students in university residences. Perceived normalisation of university life significantly enhanced student mental wellbeing. The complexity and challenge generated by multiple lines of communication and rapid adaptions to a changing pandemic context was evident. TRIAL REGISTRATION NUMBER UKAS 307727-02-01; Pre-results. CLINICALTRIALS gov Identifier: NCT05045989 ; post-results (first posted, 16/09/21). ETHICAL APPROVAL Faculty of Medicine & Health Sciences Research Ethics Committee, University of Nottingham (Ref: FMHS 96-0920).
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Affiliation(s)
- H Blake
- School of Health Sciences, University of Nottingham, Nottingham, UK.
- NIHR Nottingham Biomedical Research Centre, Nottingham, UK.
| | - S Carlisle
- School of Medicine, University of Nottingham, Nottingham, UK
| | - L Fothergill
- School of Health Sciences, University of Nottingham, Nottingham, UK
| | - J Hassard
- School of Medicine, University of Nottingham, Nottingham, UK
| | - A Favier
- Faculty of Registrars, University of Nottingham, Nottingham, UK
| | - J Corner
- Faculty of Registrars, University of Nottingham, Nottingham, UK
| | - J K Ball
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - C Denning
- School of Medicine, University of Nottingham, Nottingham, UK
- Biodiscovery Institute, University of Nottingham, Nottingham, UK
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7
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Helissey C, Guitard N, Théry H, Goulinet S, Mauduit P, Girleanu M, Favier A, Drouet M, Chargari C, Cavallero S. Mesenchymal Stem/Stromal Cells: TWO NEW POTENTIAL THERAPEUTIC APPROACHES IN RADIATION CYSTITIS DERIVED FROM MESENCHYMAL STEM CELLS: EXTRACELLULAR VESICLES AND CONDITIONED MEDIUM. Cytotherapy 2022. [DOI: 10.1016/s1465-3249(22)00214-6] [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: 11/03/2022]
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8
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Botter C, Favier A, Aubry G, Canlorbe G, Méningaud JP, Belghiti J, Hersant B. [How I do…to repair posterior perineal tissue loss with a posterior vaginal mucosa flap after vulvectomy]. Gynecol Obstet Fertil Senol 2022; 50:333-337. [PMID: 34871787 DOI: 10.1016/j.gofs.2021.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 11/26/2021] [Accepted: 11/27/2021] [Indexed: 06/13/2023]
Affiliation(s)
- C Botter
- Department of maxillofacial and plastic, reconstructive, and aesthetic surgery, Henri-Mondor hospital, Créteil, France
| | - A Favier
- Department of gynecological and breast surgery and oncology, Pitié-Salpêtrière university hospital, Paris, France.
| | - G Aubry
- Department of gynecological and breast surgery and oncology, Pitié-Salpêtrière university hospital, Paris, France
| | - G Canlorbe
- Department of gynecological and breast surgery and oncology, Pitié-Salpêtrière university hospital, Paris, France
| | - J-P Méningaud
- Department of maxillofacial and plastic, reconstructive, and aesthetic surgery, Henri-Mondor hospital, Créteil, France
| | - J Belghiti
- Department of gynecological and breast surgery and oncology, Pitié-Salpêtrière university hospital, Paris, France
| | - B Hersant
- Department of maxillofacial and plastic, reconstructive, and aesthetic surgery, Henri-Mondor hospital, Créteil, France
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Liu B, Chan H, Bauda E, Contreras-Martel C, Bellard L, Villard AM, Mas C, Neumann E, Fenel D, Favier A, Serrano M, Henriques AO, Rodrigues CDA, Morlot C. Structural insights into ring-building motif domains involved in bacterial sporulation. J Struct Biol 2021; 214:107813. [PMID: 34808342 DOI: 10.1016/j.jsb.2021.107813] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 09/21/2021] [Revised: 10/29/2021] [Accepted: 11/15/2021] [Indexed: 02/06/2023]
Abstract
Components of specialized secretion systems, which span the inner and outer membranes in Gram-negative bacteria, include ring-forming proteins whose oligomerization was proposed to be promoted by domains called RBM for "Ring-Building Motifs". During spore formation in Gram-positive bacteria, a transport system called the SpoIIIA-SpoIIQ complex also assembles in the double membrane that surrounds the forespore following its endocytosis by the mother cell. The presence of RBM domains in some of the SpoIIIA proteins led to the hypothesis that they would assemble into rings connecting the two membranes and form a conduit between the mother cell and forespore. Among them, SpoIIIAG forms homo-oligomeric rings in vitro but the oligomerization of other RBM-containing SpoIIIA proteins, including SpoIIIAH, remains to be demonstrated. In this work, we identified RBM domains in the YhcN/YlaJ family of proteins that are not related to the SpoIIIA-SpoIIQ complex. We solved the crystal structure of YhcN from Bacillus subtilis, which confirmed the presence of a RBM fold, flanked by additional secondary structures. As the protein did not show any oligomerization ability in vitro, we investigated the structural determinants of ring formation in SpoIIIAG, SpoIIIAH and YhcN. We showed that in vitro, the conserved core of RBM domains alone is not sufficient for oligomerization while the β-barrel forming region in SpoIIIAG forms rings on its own. This work suggests that some RBMs might indeed participate in the assembly of homomeric rings but others might have evolved toward other functions.
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Affiliation(s)
- Bowen Liu
- Univ. Grenoble Alpes, CNRS, CEA, IBS, 38000 Grenoble, France
| | - Helena Chan
- The ithree institute, University of Technology Sydney, 2007 Ultimo, NSW, Australia
| | - Elda Bauda
- Univ. Grenoble Alpes, CNRS, CEA, IBS, 38000 Grenoble, France
| | | | - Laure Bellard
- Univ. Grenoble Alpes, CNRS, CEA, IBS, 38000 Grenoble, France
| | | | - Caroline Mas
- Univ. Grenoble Alpes, CNRS, CEA, IBS, 38000 Grenoble, France
| | | | - Daphna Fenel
- Univ. Grenoble Alpes, CNRS, CEA, IBS, 38000 Grenoble, France
| | - Adrien Favier
- Univ. Grenoble Alpes, CNRS, CEA, IBS, 38000 Grenoble, France
| | - Monica Serrano
- Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Adriano O Henriques
- Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa, Oeiras, Portugal
| | | | - Cecile Morlot
- Univ. Grenoble Alpes, CNRS, CEA, IBS, 38000 Grenoble, France.
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10
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Favier A, Boinon D, Salviat F, Mazouni C, De Korvin B, Tunon C, Salomon AV, Doutriaux-Dumoulin I, Vaysse C, Marchal F, Boulanger L, Chabbert-Buffet N, Zilberman S, Coutant C, Espié M, Cortet M, Boussion V, Cohen M, Fermeaux V, Mathelin C, Michiels S, Delaloge S, Uzan C, Charles C. [Surgery or not on an atypical breast lesion? Taking anxiety into account in shared decision support from a prospective cohort of 300 patients]. ACTA ACUST UNITED AC 2021; 50:142-150. [PMID: 34562643 DOI: 10.1016/j.gofs.2021.09.010] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Indexed: 11/27/2022]
Abstract
INTRODUCTION Organized and individual breast screening have been accompanied by an increase in the detection of "atypical breast lesions (ABL)". Recently, the NOMAT multicenter study proposed a predictive model of the risk of developing breast cancer after detection of an ABL in order to avoid surgical removal of "low-risk" lesions. It also aimed to provide information on psychological experience, in particularly anxiety, to assist in the shared medical decision process. METHODS Three hundred women undergoing surgery for ABL were included between 2015 and 2018 at 18 French centers. Women completed questionnaires before and after surgery assessing their level of anxiety (STAI-State, STAI-Trait), their level of tolerance to uncertainty, their perceived risk of developing a breast cancer, and their satisfaction with the management care. RESULTS One hundred nighty nine patients completed the STAI-Status before and after surgery. Overall, a decrease in anxiety level (35.4 vs 42.7, P<0.001) was observed. Anxious temperament and greater intolerance to uncertainty were significantly associated swith decreased anxiety (33%), whereas younger age was associated with increased anxiety (8%). CONCLUSION Surgery for ABL seems to be associated with only a few cases with an increase in anxiety and seems to increase the perception of the risk of developing breast cancer. Taking into account the psychological dimension remains in all cases essential in the process of shared therapeutic decision.
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Affiliation(s)
- A Favier
- AP-HP (Assistance Publique des hôpitaux de Paris), department of gynecological and breast surgery and oncology, Pitié-Salpêtrière University Hospital, Paris, France.
| | - D Boinon
- Psycho-oncology unit, Gustave-Roussy, université Paris-Saclay, Villejuif, France; Université de Paris, LPPS, 92100 Boulogne Billancourt, France
| | - F Salviat
- Service de biostatistique et d'épidémiologie, Gustave-Roussy, Villejuif, France; CESP Inserm U1018, université Paris-Saclay, université Paris-Saclay, Villejuif, France
| | | | - B De Korvin
- Radiology center, centre Eugène-Marquis, CLCC, Rennes, France
| | - C Tunon
- Institut Bergonié, Bordeaux, France
| | - A-V Salomon
- Institut Curie, université Paris-Sciences Lettres, Inserm U934, département de médecine diagnostique et théranostique, Paris, France
| | | | - C Vaysse
- Département de chirurgie, CHU-Toulouse, institut universitaire du cancer de Toulouse-Oncopole, Toulouse, France
| | - F Marchal
- Institut de cancérologie de Lorraine, Vandœuvre-lès-Nancy, France
| | | | | | - S Zilberman
- Hôpital Tenon, Sorbonne university, Paris, France
| | - C Coutant
- Centre Georges François Leclerc, Dijon, France
| | - M Espié
- University of Paris, Breast Unit, hôpital Saint-Louis, AP-HP, Paris, France
| | - M Cortet
- Service de gynécologie-obstétrique, hôpital de la Croix Rousse, Hospices Civils de Lyon, Lyon, France
| | - V Boussion
- Centre Jean-Perrin, Clermont-Ferrand, France
| | - M Cohen
- Institut Paoli Calmettes, Marseille, France
| | - V Fermeaux
- Service de pathologie, CHU Dupuytren, Limoges, France
| | - C Mathelin
- Les Hôpitaux universitaires de Strasbourg, Strasbourg, France
| | - S Michiels
- Service de biostatistique et d'épidémiologie, Gustave-Roussy, Villejuif, France; CESP Inserm U1018, université Paris-Saclay, université Paris-Saclay, Villejuif, France
| | | | - C Uzan
- AP-HP (Assistance Publique des hôpitaux de Paris), department of gynecological and breast surgery and oncology, Pitié-Salpêtrière University Hospital, Paris, France; Sorbonne University, Inserm UMR_S_938, "Cancer Biology and Therapeutics", centre de recherche Saint-Antoine (CRSA), Paris, France; Institut universitaire de cancérologie (IUC), Paris, France
| | - C Charles
- Université de Bordeaux, Bordeaux Population Health (U1219), équipe méthodes pour la recherche interventionnelle en santé des populations (MéRISP), Bordeaux, France
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11
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Denarier E, Ecklund KH, Berthier G, Favier A, O'Toole ET, Gory-Fauré S, De Macedo L, Delphin C, Andrieux A, Markus SM, Boscheron C. Modeling a disease-correlated tubulin mutation in budding yeast reveals insight into MAP-mediated dynein function. Mol Biol Cell 2021; 32:ar10. [PMID: 34379441 PMCID: PMC8684761 DOI: 10.1091/mbc.e21-05-0237] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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] [Indexed: 11/22/2022] Open
Abstract
Mutations in the genes that encode α- and β-tubulin underlie many neurological diseases, most notably malformations in cortical development. In addition to revealing the molecular basis for disease etiology, studying such mutations can provide insight into microtubule function and the role of the large family of microtubule effectors. In this study, we use budding yeast to model one such mutation—Gly436Arg in α-tubulin, which is causative of malformations in cortical development—in order to understand how it impacts microtubule function in a simple eukaryotic system. Using a combination of in vitro and in vivo methodologies, including live cell imaging and electron tomography, we find that the mutant tubulin is incorporated into microtubules, causes a shift in α-tubulin isotype usage, and dramatically enhances dynein activity, which leads to spindle-positioning defects. We find that the basis for the latter phenotype is an impaired interaction between She1—a dynein inhibitor—and the mutant microtubules. In addition to revealing the natural balance of α-tubulin isotype utilization in cells, our results provide evidence of an impaired interaction between microtubules and a dynein regulator as a consequence of a tubulin mutation and sheds light on a mechanism that may be causative of neurodevelopmental diseases.
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Affiliation(s)
- E Denarier
- Univ. Grenoble Alpes, CEA, CNRS, GIN, IBS, Inserm, IRIG, F-38000 Grenoble, France
| | - K H Ecklund
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States
| | - G Berthier
- Univ. Grenoble Alpes, CEA, CNRS, GIN, IBS, Inserm, IRIG, F-38000 Grenoble, France
| | - A Favier
- Univ. Grenoble Alpes, CEA, CNRS, GIN, IBS, Inserm, IRIG, F-38000 Grenoble, France
| | - E T O'Toole
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Boulder, Colorado, United States
| | - S Gory-Fauré
- Univ. Grenoble Alpes, CEA, CNRS, GIN, IBS, Inserm, IRIG, F-38000 Grenoble, France
| | - L De Macedo
- Univ. Grenoble Alpes, CEA, CNRS, GIN, IBS, Inserm, IRIG, F-38000 Grenoble, France
| | - C Delphin
- Univ. Grenoble Alpes, CEA, CNRS, GIN, IBS, Inserm, IRIG, F-38000 Grenoble, France
| | - A Andrieux
- Univ. Grenoble Alpes, CEA, CNRS, GIN, IBS, Inserm, IRIG, F-38000 Grenoble, France
| | - S M Markus
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States
| | - C Boscheron
- Univ. Grenoble Alpes, CEA, CNRS, GIN, IBS, Inserm, IRIG, F-38000 Grenoble, France
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12
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Giachin G, Jessop M, Bouverot R, Acajjaoui S, Saïdi M, Chretien A, Bacia‐Verloop M, Signor L, Mas PJ, Favier A, Borel Meneroud E, Hons M, Hart DJ, Kandiah E, Boeri Erba E, Buisson A, Leonard G, Gutsche I, Soler‐Lopez M. Assembly of The Mitochondrial Complex I Assembly Complex Suggests a Regulatory Role for Deflavination. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202011548] [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: 11/05/2022]
Affiliation(s)
- Gabriele Giachin
- Structural Biology Group European Synchrotron Radiation Facility (ESRF) 71 avenue des Martyrs 38043 Grenoble France
| | - Matthew Jessop
- Institut de Biologie Structurale (IBS) CNRS, CEA Université Grenoble Alpes 71 avenue des Martyrs 38044 Grenoble France
| | - Romain Bouverot
- Structural Biology Group European Synchrotron Radiation Facility (ESRF) 71 avenue des Martyrs 38043 Grenoble France
| | - Samira Acajjaoui
- Structural Biology Group European Synchrotron Radiation Facility (ESRF) 71 avenue des Martyrs 38043 Grenoble France
| | - Melissa Saïdi
- Structural Biology Group European Synchrotron Radiation Facility (ESRF) 71 avenue des Martyrs 38043 Grenoble France
| | - Anaïs Chretien
- Structural Biology Group European Synchrotron Radiation Facility (ESRF) 71 avenue des Martyrs 38043 Grenoble France
| | - Maria Bacia‐Verloop
- Institut de Biologie Structurale (IBS) CNRS, CEA Université Grenoble Alpes 71 avenue des Martyrs 38044 Grenoble France
| | - Luca Signor
- Institut de Biologie Structurale (IBS) CNRS, CEA Université Grenoble Alpes 71 avenue des Martyrs 38044 Grenoble France
| | - Philippe J. Mas
- Integrated Structural Biology Grenoble (ISBG) CNRS CEA, Université Grenoble Alpes 71 avenue des Martyrs 38042 Grenoble France
| | - Adrien Favier
- Institut de Biologie Structurale (IBS) CNRS, CEA Université Grenoble Alpes 71 avenue des Martyrs 38044 Grenoble France
| | - Eve Borel Meneroud
- Grenoble Institut des Neurosciences (GIN) Centre Inserm U1216 Equipe Neuropathologies et Dysfonctions Synaptiques Université Grenoble Alpes 31 Chemin Fortuné Ferrini 38700 La Tronche France
| | - Michael Hons
- European Molecular Biology Laboratory (EMBL) Grenoble Outstation 71 avenue des Martyrs 38042 Grenoble France
| | - Darren J. Hart
- Institut de Biologie Structurale (IBS) CNRS, CEA Université Grenoble Alpes 71 avenue des Martyrs 38044 Grenoble France
| | - Eaazhisai Kandiah
- Structural Biology Group European Synchrotron Radiation Facility (ESRF) 71 avenue des Martyrs 38043 Grenoble France
| | - Elisabetta Boeri Erba
- Institut de Biologie Structurale (IBS) CNRS, CEA Université Grenoble Alpes 71 avenue des Martyrs 38044 Grenoble France
| | - Alain Buisson
- Grenoble Institut des Neurosciences (GIN) Centre Inserm U1216 Equipe Neuropathologies et Dysfonctions Synaptiques Université Grenoble Alpes 31 Chemin Fortuné Ferrini 38700 La Tronche France
| | - Gordon Leonard
- Structural Biology Group European Synchrotron Radiation Facility (ESRF) 71 avenue des Martyrs 38043 Grenoble France
| | - Irina Gutsche
- Institut de Biologie Structurale (IBS) CNRS, CEA Université Grenoble Alpes 71 avenue des Martyrs 38044 Grenoble France
| | - Montserrat Soler‐Lopez
- Structural Biology Group European Synchrotron Radiation Facility (ESRF) 71 avenue des Martyrs 38043 Grenoble France
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13
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Giachin G, Jessop M, Bouverot R, Acajjaoui S, Saïdi M, Chretien A, Bacia-Verloop M, Signor L, Mas PJ, Favier A, Borel Meneroud E, Hons M, Hart DJ, Kandiah E, Boeri Erba E, Buisson A, Leonard G, Gutsche I, Soler-Lopez M. Assembly of The Mitochondrial Complex I Assembly Complex Suggests a Regulatory Role for Deflavination. Angew Chem Int Ed Engl 2021; 60:4689-4697. [PMID: 33320993 PMCID: PMC7986633 DOI: 10.1002/anie.202011548] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Indexed: 01/01/2023]
Abstract
Fatty acid β‐oxidation (FAO) and oxidative phosphorylation (OXPHOS) are mitochondrial redox processes that generate ATP. The biogenesis of the respiratory Complex I, a 1 MDa multiprotein complex that is responsible for initiating OXPHOS, is mediated by assembly factors including the mitochondrial complex I assembly (MCIA) complex. However, the organisation and the role of the MCIA complex are still unclear. Here we show that ECSIT functions as the bridging node of the MCIA core complex. Furthermore, cryo‐electron microscopy together with biochemical and biophysical experiments reveal that the C‐terminal domain of ECSIT directly binds to the vestigial dehydrogenase domain of the FAO enzyme ACAD9 and induces its deflavination, switching ACAD9 from its role in FAO to an MCIA factor. These findings provide the structural basis for the MCIA complex architecture and suggest a unique molecular mechanism for coordinating the regulation of the FAO and OXPHOS pathways to ensure an efficient energy production.
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Affiliation(s)
- Gabriele Giachin
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 71 avenue des Martyrs, 38043, Grenoble, France
| | - Matthew Jessop
- Institut de Biologie Structurale (IBS), CNRS, CEA, Université Grenoble Alpes, 71 avenue des Martyrs, 38044, Grenoble, France
| | - Romain Bouverot
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 71 avenue des Martyrs, 38043, Grenoble, France
| | - Samira Acajjaoui
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 71 avenue des Martyrs, 38043, Grenoble, France
| | - Melissa Saïdi
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 71 avenue des Martyrs, 38043, Grenoble, France
| | - Anaïs Chretien
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 71 avenue des Martyrs, 38043, Grenoble, France
| | - Maria Bacia-Verloop
- Institut de Biologie Structurale (IBS), CNRS, CEA, Université Grenoble Alpes, 71 avenue des Martyrs, 38044, Grenoble, France
| | - Luca Signor
- Institut de Biologie Structurale (IBS), CNRS, CEA, Université Grenoble Alpes, 71 avenue des Martyrs, 38044, Grenoble, France
| | - Philippe J Mas
- Integrated Structural Biology Grenoble (ISBG) CNRS, CEA, Université Grenoble Alpes, 71 avenue des Martyrs, 38042, Grenoble, France
| | - Adrien Favier
- Institut de Biologie Structurale (IBS), CNRS, CEA, Université Grenoble Alpes, 71 avenue des Martyrs, 38044, Grenoble, France
| | - Eve Borel Meneroud
- Grenoble Institut des Neurosciences (GIN), Centre Inserm U1216, Equipe Neuropathologies et Dysfonctions Synaptiques, Université Grenoble Alpes, 31 Chemin Fortuné Ferrini, 38700, La Tronche, France
| | - Michael Hons
- European Molecular Biology Laboratory (EMBL), Grenoble Outstation, 71 avenue des Martyrs, 38042, Grenoble, France
| | - Darren J Hart
- Institut de Biologie Structurale (IBS), CNRS, CEA, Université Grenoble Alpes, 71 avenue des Martyrs, 38044, Grenoble, France
| | - Eaazhisai Kandiah
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 71 avenue des Martyrs, 38043, Grenoble, France
| | - Elisabetta Boeri Erba
- Institut de Biologie Structurale (IBS), CNRS, CEA, Université Grenoble Alpes, 71 avenue des Martyrs, 38044, Grenoble, France
| | - Alain Buisson
- Grenoble Institut des Neurosciences (GIN), Centre Inserm U1216, Equipe Neuropathologies et Dysfonctions Synaptiques, Université Grenoble Alpes, 31 Chemin Fortuné Ferrini, 38700, La Tronche, France
| | - Gordon Leonard
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 71 avenue des Martyrs, 38043, Grenoble, France
| | - Irina Gutsche
- Institut de Biologie Structurale (IBS), CNRS, CEA, Université Grenoble Alpes, 71 avenue des Martyrs, 38044, Grenoble, France
| | - Montserrat Soler-Lopez
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 71 avenue des Martyrs, 38043, Grenoble, France
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14
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Favier A, Gans P, Boeri Erba E, Signor L, Muthukumar SS, Pfannschmidt T, Blanvillain R, Cobessi D. The Plastid-Encoded RNA Polymerase-Associated Protein PAP9 Is a Superoxide Dismutase With Unusual Structural Features. Front Plant Sci 2021; 12:668897. [PMID: 34276730 PMCID: PMC8278866 DOI: 10.3389/fpls.2021.668897] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/28/2021] [Indexed: 05/09/2023]
Abstract
In Angiosperms, the plastid-encoded RNA polymerase (PEP) is a multimeric enzyme, essential for the proper expression of the plastid genome during chloroplast biogenesis. It is especially required for the light initiated expression of photosynthesis genes and the subsequent build-up of the photosynthetic apparatus. The PEP complex is composed of a prokaryotic-type core of four plastid-encoded subunits and 12 nuclear-encoded PEP-associated proteins (PAPs). Among them, there are two iron superoxide dismutases, FSD2/PAP9 and FSD3/PAP4. Superoxide dismutases usually are soluble enzymes not bound into larger protein complexes. To investigate this unusual feature, we characterized PAP9 using molecular genetics, fluorescence microscopy, mass spectrometry, X-ray diffraction, and solution-state NMR. Despite the presence of a predicted nuclear localization signal within the sequence of the predicted chloroplast transit peptide, PAP9 was mainly observed within plastids. Mass spectrometry experiments with the recombinant Arabidopsis PAP9 suggested that monomers and dimers of PAP9 could be associated to the PEP complex. In crystals, PAP9 occurred as a dimeric enzyme that displayed a similar fold to that of the FeSODs or manganese SOD (MnSODs). A zinc ion, instead of the expected iron, was found to be penta-coordinated with a trigonal-bipyramidal geometry in the catalytic center of the recombinant protein. The metal coordination involves a water molecule and highly conserved residues in FeSODs. Solution-state NMR and DOSY experiments revealed an unfolded C-terminal 34 amino-acid stretch in the stand-alone protein and few internal residues interacting with the rest of the protein. We hypothesize that this C-terminal extension had appeared during evolution as a distinct feature of the FSD2/PAP9 targeting it to the PEP complex. Close vicinity to the transcriptional apparatus may allow for the protection against the strongly oxidizing aerial environment during plant conquering of terrestrial habitats.
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Affiliation(s)
- Adrien Favier
- Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Pierre Gans
- Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | | | - Luca Signor
- Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | | | | | - Robert Blanvillain
- Université Grenoble-Alpes, CNRS, CEA, INRA, IRIG-LPCV, Grenoble, France
- *Correspondence: Robert Blanvillain,
| | - David Cobessi
- Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
- David Cobessi,
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15
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Vallet A, Favier A, Brutscher B, Schanda P. ssNMRlib: a comprehensive library and tool box for acquisition of solid-state nuclear magnetic resonance experiments on Bruker spectrometers. Magn Reson (Gott) 2020; 1:331-345. [PMID: 37904819 PMCID: PMC10500710 DOI: 10.5194/mr-1-331-2020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 11/16/2020] [Indexed: 11/01/2023]
Abstract
We introduce ssNMRlib, a comprehensive suite of pulse sequences and jython scripts for user-friendly solid-state nuclear magnetic resonance (NMR) data acquisition, parameter optimization and storage on Bruker spectrometers. ssNMRlib allows the straightforward setup of even highly complex multi-dimensional solid-state NMR experiments with a few clicks from an intuitive graphical interface directly from the Bruker Topspin acquisition software. ssNMRlib allows the setup of experiments in a magnetic-field-independent manner and thus facilitates the workflow in a multi-spectrometer setting with a centralized library. Safety checks furthermore assist the user in experiment setup. Currently hosting more than 140 1D to 4D experiments, primarily for biomolecular solid-state NMR, the library can be easily customized and new experiments are readily added as new templates. ssNMRlib is part of the previously introduced NMRlib library, which comprises many solution-NMR pulse sequences and macros.
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Affiliation(s)
- Alicia Vallet
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, 38044 Grenoble, France
| | - Adrien Favier
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, 38044 Grenoble, France
| | - Bernhard Brutscher
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, 38044 Grenoble, France
| | - Paul Schanda
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, 38044 Grenoble, France
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16
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Liebers M, Gillet FX, Israel A, Pounot K, Chambon L, Chieb M, Chevalier F, Ruedas R, Favier A, Gans P, Boeri Erba E, Cobessi D, Pfannschmidt T, Blanvillain R. Nucleo-plastidic PAP8/pTAC6 couples chloroplast formation with photomorphogenesis. EMBO J 2020; 39:e104941. [PMID: 33001465 DOI: 10.15252/embj.2020104941] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 03/09/2020] [Revised: 09/02/2020] [Accepted: 09/09/2020] [Indexed: 12/29/2022] Open
Abstract
The initial greening of angiosperms involves light activation of photoreceptors that trigger photomorphogenesis, followed by the development of chloroplasts. In these semi-autonomous organelles, construction of the photosynthetic apparatus depends on the coordination of nuclear and plastid gene expression. Here, we show that the expression of PAP8, an essential subunit of the plastid-encoded RNA polymerase (PEP) in Arabidopsis thaliana, is under the control of a regulatory element recognized by the photomorphogenic factor HY5. PAP8 protein is localized and active in both plastids and the nucleus, and particularly required for the formation of late photobodies. In the pap8 albino mutant, phytochrome-mediated signalling is altered, degradation of the chloroplast development repressors PIF1/PIF3 is disrupted, HY5 is not stabilized, and the expression of the photomorphogenesis regulator GLK1 is impaired. PAP8 translocates into plastids via its targeting pre-sequence, interacts with the PEP and eventually reaches the nucleus, where it can interact with another PEP subunit pTAC12/HMR/PAP5. Since PAP8 is required for the phytochrome B-mediated signalling cascade and the reshaping of the PEP activity, it may coordinate nuclear gene expression with PEP-driven chloroplastic gene expression during chloroplast biogenesis.
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Affiliation(s)
- Monique Liebers
- CNRS, CEA, INRA, IRIG-LPCV, Univ. Grenoble-Alpes, Grenoble, France
| | | | - Abir Israel
- CNRS, CEA, INRA, IRIG-LPCV, Univ. Grenoble-Alpes, Grenoble, France
| | - Kevin Pounot
- CNRS, CEA, INRA, IRIG-LPCV, Univ. Grenoble-Alpes, Grenoble, France
| | - Louise Chambon
- CNRS, CEA, INRA, IRIG-LPCV, Univ. Grenoble-Alpes, Grenoble, France
| | - Maha Chieb
- CNRS, CEA, INRA, IRIG-LPCV, Univ. Grenoble-Alpes, Grenoble, France
| | - Fabien Chevalier
- CNRS, CEA, INRA, IRIG-LPCV, Univ. Grenoble-Alpes, Grenoble, France
| | - Rémi Ruedas
- CEA, CNRS, IBS, Univ. Grenoble Alpes, Grenoble, France
| | - Adrien Favier
- CEA, CNRS, IBS, Univ. Grenoble Alpes, Grenoble, France
| | - Pierre Gans
- CEA, CNRS, IBS, Univ. Grenoble Alpes, Grenoble, France
| | | | - David Cobessi
- CEA, CNRS, IBS, Univ. Grenoble Alpes, Grenoble, France
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Favier A, Owen C, Jayot A, Ilenko A, Daraï E, Bendifallah S. [How I do…to perfom a laparoscopic colorectal discoid resection for endometriosis]. ACTA ACUST UNITED AC 2019; 47:698-699. [PMID: 31352144 DOI: 10.1016/j.gofs.2019.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Indexed: 11/17/2022]
Affiliation(s)
- A Favier
- Service de chirurgie gynécologique, hôpital Tenon, 4, rue de la Chine, 75012 Paris, France.
| | - C Owen
- Service de chirurgie gynécologique, hôpital Tenon, 4, rue de la Chine, 75012 Paris, France
| | - A Jayot
- Service de chirurgie gynécologique, hôpital Tenon, 4, rue de la Chine, 75012 Paris, France
| | - A Ilenko
- Service de chirurgie gynécologique, hôpital Tenon, 4, rue de la Chine, 75012 Paris, France
| | - E Daraï
- Service de chirurgie gynécologique, hôpital Tenon, 4, rue de la Chine, 75012 Paris, France
| | - S Bendifallah
- Service de chirurgie gynécologique, hôpital Tenon, 4, rue de la Chine, 75012 Paris, France
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18
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Gauto DF, Estrozi LF, Schwieters CD, Effantin G, Macek P, Sounier R, Sivertsen AC, Schmidt E, Kerfah R, Mas G, Colletier JP, Güntert P, Favier A, Schoehn G, Schanda P, Boisbouvier J. Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex. Nat Commun 2019; 10:2697. [PMID: 31217444 PMCID: PMC6584647 DOI: 10.1038/s41467-019-10490-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [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: 03/19/2019] [Accepted: 05/10/2019] [Indexed: 12/14/2022] Open
Abstract
Atomic-resolution structure determination is crucial for understanding protein function. Cryo-EM and NMR spectroscopy both provide structural information, but currently cryo-EM does not routinely give access to atomic-level structural data, and, generally, NMR structure determination is restricted to small (<30 kDa) proteins. We introduce an integrated structure determination approach that simultaneously uses NMR and EM data to overcome the limits of each of these methods. The approach enables structure determination of the 468 kDa large dodecameric aminopeptidase TET2 to a precision and accuracy below 1 Å by combining secondary-structure information obtained from near-complete magic-angle-spinning NMR assignments of the 39 kDa-large subunits, distance restraints from backbone amides and ILV methyl groups, and a 4.1 Å resolution EM map. The resulting structure exceeds current standards of NMR and EM structure determination in terms of molecular weight and precision. Importantly, the approach is successful even in cases where only medium-resolution cryo-EM data are available. NMR structure determination is challenging for proteins with a molecular weight above 30 kDa and atomic-resolution structure determination from cryo-EM data is currently not the rule. Here the authors describe an integrated structure determination approach that simultaneously uses NMR and EM data and allows them to determine the structure of the 468 kDa dodecameric aminopeptidase TET2 complex.
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Affiliation(s)
- Diego F Gauto
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, 71, Avenue des Martyrs, F-38044, Grenoble, France
| | - Leandro F Estrozi
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, 71, Avenue des Martyrs, F-38044, Grenoble, France.
| | - Charles D Schwieters
- Laboratory of Imaging Sciences, Center for Information Technology, National Institutes of Health, 12 South Drive, MSC 5624, Bethesda, MD, 20892, USA
| | - Gregory Effantin
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, 71, Avenue des Martyrs, F-38044, Grenoble, France
| | - Pavel Macek
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, 71, Avenue des Martyrs, F-38044, Grenoble, France.,NMR-Bio, 5 Place Robert Schuman, F-38025, Grenoble, France
| | - Remy Sounier
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, 71, Avenue des Martyrs, F-38044, Grenoble, France.,Institut de Génomique Fonctionnelle, CNRS UMR-5203, INSERM U1191, University of Montpellier, F-34000, Montpellier, France
| | - Astrid C Sivertsen
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, 71, Avenue des Martyrs, F-38044, Grenoble, France
| | - Elena Schmidt
- Institute of Biophysical Chemistry, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - Rime Kerfah
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, 71, Avenue des Martyrs, F-38044, Grenoble, France.,NMR-Bio, 5 Place Robert Schuman, F-38025, Grenoble, France
| | - Guillaume Mas
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, 71, Avenue des Martyrs, F-38044, Grenoble, France.,Biozentrum University of Basel, Klingelbergstrasse 70, 4056, Basel, Switzerland
| | - Jacques-Philippe Colletier
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, 71, Avenue des Martyrs, F-38044, Grenoble, France
| | - Peter Güntert
- Institute of Biophysical Chemistry, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany.,Laboratory of Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland.,Graduate School of Science, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Adrien Favier
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, 71, Avenue des Martyrs, F-38044, Grenoble, France.
| | - Guy Schoehn
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, 71, Avenue des Martyrs, F-38044, Grenoble, France
| | - Paul Schanda
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, 71, Avenue des Martyrs, F-38044, Grenoble, France.
| | - Jerome Boisbouvier
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, 71, Avenue des Martyrs, F-38044, Grenoble, France
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19
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Favier A, Brutscher B. NMRlib: user-friendly pulse sequence tools for Bruker NMR spectrometers. J Biomol NMR 2019; 73:199-211. [PMID: 31076970 DOI: 10.1007/s10858-019-00249-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [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: 03/13/2019] [Accepted: 04/25/2019] [Indexed: 06/09/2023]
Abstract
We present NMRlib, a suite of jython-based tools designed for Bruker spectrometers (TopSpin versions 3.2-4.0) that allow easy setup, management, and exchange of NMR experiments. A NMR experiment can be set up and executed in a few clicks by navigating through the NMRlib GUI tree structure, without any further parameter adjustment. NMRlib is magnetic-field independent, and thus particularly helpful for laboratories operating multiple NMR spectrometers. NMRlib is easily personalized by adding, deleting, or reorganizing experiments. Additional tools are provided for data processing, visualization, and analysis. In particular, NMRlib contains all the polarization-enhanced fast-pulsing NMR experiments (SOFAST, BEST, HADAMAC,…) developed in our laboratory over the last decade. We also discuss some specific features that have been implemented to make these experiments most efficient and user friendly.
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Affiliation(s)
- Adrien Favier
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000, Grenoble, France.
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20
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Vallet A, Favier A, Brutscher B. Aromatic SOFAST-HMBC for proteins at natural 13C abundance. J Magn Reson 2019; 300:95-102. [PMID: 30721859 DOI: 10.1016/j.jmr.2019.01.009] [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: 12/17/2018] [Revised: 01/11/2019] [Accepted: 01/18/2019] [Indexed: 06/09/2023]
Abstract
We propose here SOFAST-HMBC as a new complementary NMR tool for aromatic side chain assignment of protein samples at natural 13C abundance. The characteristic peak patterns detected in SOFAST-HMBC for each aromatic side chain allow straightforward assignment of all protons and carbons (including quaternary ones) of the aromatic ring, and for tyrosine and phenylalanine, connection to the CB of the aliphatic chain. The performance of SOFAST-HMBC is demonstrated for three small proteins (7-14 kDa) at millimolar sample concentration using modern high-field NMR instruments equipped with cryogenically cooled probes. Despite the low amount of NMR-active 13C nuclei in these samples, 1H-13C multiple-bond correlation spectra of good quality were obtained in reasonable experimental times of typically less than 24 h.
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Affiliation(s)
- Alicia Vallet
- Univ. Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | - Adrien Favier
- Univ. Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
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21
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Duret D, Haftek-Terreau Z, Carretier M, Berki T, Ladavière C, Monier K, Bouvet P, Marvel J, Leverrier Y, Charreyre MT, Favier A. Labeling of native proteins with fluorescent RAFT polymer probes: application to the detection of a cell surface protein using flow cytometry. Polym Chem 2018. [DOI: 10.1039/c7py02064c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Fluorescent RAFT polymer probes with an activated ester reactive end-group can be advantageously used to label native proteins.
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Affiliation(s)
- D. Duret
- Univ Lyon
- Université Lyon 1
- INSA de Lyon
- CNRS
- Laboratoire Ingénierie des Matériaux Polymères
| | | | - M. Carretier
- Univ Lyon
- Université Lyon 1
- INSA de Lyon
- CNRS
- Laboratoire Ingénierie des Matériaux Polymères
| | - T. Berki
- Univ Lyon
- Université Lyon 1
- INSA de Lyon
- CNRS
- Laboratoire Ingénierie des Matériaux Polymères
| | - C. Ladavière
- Univ Lyon
- Université Lyon 1
- INSA de Lyon
- CNRS
- Laboratoire Ingénierie des Matériaux Polymères
| | - K. Monier
- Univ Lyon
- ENS de Lyon
- CNRS
- Laboratoire Joliot-Curie
- USR3010
| | - P. Bouvet
- Univ Lyon
- ENS de Lyon
- CNRS
- Laboratoire Joliot-Curie
- USR3010
| | - J. Marvel
- Univ Lyon
- INSERM
- ENS de Lyon
- CNRS
- Université Lyon 1
| | | | - M.-T. Charreyre
- Univ Lyon
- Université Lyon 1
- INSA de Lyon
- CNRS
- Laboratoire Ingénierie des Matériaux Polymères
| | - A. Favier
- Univ Lyon
- Université Lyon 1
- INSA de Lyon
- CNRS
- Laboratoire Ingénierie des Matériaux Polymères
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22
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Rennella E, Sára T, Juen M, Wunderlich C, Imbert L, Solyom Z, Favier A, Ayala I, Weinhäupl K, Schanda P, Konrat R, Kreutz C, Brutscher B. RNA binding and chaperone activity of the E. coli cold-shock protein CspA. Nucleic Acids Res 2017; 45:4255-4268. [PMID: 28126922 PMCID: PMC5397153 DOI: 10.1093/nar/gkx044] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [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: 11/14/2016] [Accepted: 01/17/2017] [Indexed: 11/14/2022] Open
Abstract
Ensuring the correct folding of RNA molecules in the cell is of major importance for a large variety of biological functions. Therefore, chaperone proteins that assist RNA in adopting their functionally active states are abundant in all living organisms. An important feature of RNA chaperone proteins is that they do not require an external energy source to perform their activity, and that they interact transiently and non-specifically with their RNA targets. So far, little is known about the mechanistic details of the RNA chaperone activity of these proteins. Prominent examples of RNA chaperones are bacterial cold shock proteins (Csp) that have been reported to bind single-stranded RNA and DNA. Here, we have used advanced NMR spectroscopy techniques to investigate at atomic resolution the RNA-melting activity of CspA, the major cold shock protein of Escherichia coli, upon binding to different RNA hairpins. Real-time NMR provides detailed information on the folding kinetics and folding pathways. Finally, comparison of wild-type CspA with single-point mutants and small peptides yields insights into the complementary roles of aromatic and positively charged amino-acid side chains for the RNA chaperone activity of the protein.
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Affiliation(s)
- Enrico Rennella
- Institut de Biologie Structurale, Université Grenoble 1, 71 avenue des Martyrs, 38044 Grenoble Cedex 9, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France.,Centre National de Recherche Scientifique (CNRS), Grenoble, France
| | - Tomáš Sára
- Department of Computational & Structural Biology, Max F. Perutz Laboratories, Campus, Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Michael Juen
- Institute of Organic Chemistry, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Christoph Wunderlich
- Institute of Organic Chemistry, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Lionel Imbert
- Institut de Biologie Structurale, Université Grenoble 1, 71 avenue des Martyrs, 38044 Grenoble Cedex 9, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France.,Centre National de Recherche Scientifique (CNRS), Grenoble, France
| | - Zsofia Solyom
- Institut de Biologie Structurale, Université Grenoble 1, 71 avenue des Martyrs, 38044 Grenoble Cedex 9, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France.,Centre National de Recherche Scientifique (CNRS), Grenoble, France
| | - Adrien Favier
- Institut de Biologie Structurale, Université Grenoble 1, 71 avenue des Martyrs, 38044 Grenoble Cedex 9, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France.,Centre National de Recherche Scientifique (CNRS), Grenoble, France
| | - Isabel Ayala
- Institut de Biologie Structurale, Université Grenoble 1, 71 avenue des Martyrs, 38044 Grenoble Cedex 9, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France.,Centre National de Recherche Scientifique (CNRS), Grenoble, France
| | - Katharina Weinhäupl
- Institut de Biologie Structurale, Université Grenoble 1, 71 avenue des Martyrs, 38044 Grenoble Cedex 9, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France.,Centre National de Recherche Scientifique (CNRS), Grenoble, France
| | - Paul Schanda
- Institut de Biologie Structurale, Université Grenoble 1, 71 avenue des Martyrs, 38044 Grenoble Cedex 9, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France.,Centre National de Recherche Scientifique (CNRS), Grenoble, France
| | - Robert Konrat
- Department of Computational & Structural Biology, Max F. Perutz Laboratories, Campus, Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Bernhard Brutscher
- Institut de Biologie Structurale, Université Grenoble 1, 71 avenue des Martyrs, 38044 Grenoble Cedex 9, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France.,Centre National de Recherche Scientifique (CNRS), Grenoble, France
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23
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Franco R, Favier A, Schanda P, Brutscher B. Optimized fast mixing device for real-time NMR applications. J Magn Reson 2017; 281:125-129. [PMID: 28595119 PMCID: PMC5542027 DOI: 10.1016/j.jmr.2017.05.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 05/29/2017] [Indexed: 05/03/2023]
Abstract
We present an improved fast mixing device based on the rapid mixing of two solutions inside the NMR probe, as originally proposed by Hore and coworkers (J. Am. Chem. Soc. 125 (2003) 12484-12492). Such a device is important for off-equilibrium studies of molecular kinetics by multidimensional real-time NMR spectrsocopy. The novelty of this device is that it allows removing the injector from the NMR detection volume after mixing, and thus provides good magnetic field homogeneity independently of the initial sample volume placed in the NMR probe. The apparatus is simple to build, inexpensive, and can be used without any hardware modification on any type of liquid-state NMR spectrometer. We demonstrate the performance of our fast mixing device in terms of improved magnetic field homogeneity, and show an application to the study of protein folding and the structural characterization of transiently populated folding intermediates.
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Affiliation(s)
- Rémi Franco
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 71 avenue des Martyrs, 38044 Grenoble Cedex 9, France
| | - Adrien Favier
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 71 avenue des Martyrs, 38044 Grenoble Cedex 9, France
| | - Paul Schanda
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 71 avenue des Martyrs, 38044 Grenoble Cedex 9, France
| | - Bernhard Brutscher
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 71 avenue des Martyrs, 38044 Grenoble Cedex 9, France.
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24
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Franco R, Gil-Caballero S, Ayala I, Favier A, Brutscher B. Probing Conformational Exchange Dynamics in a Short-Lived Protein Folding Intermediate by Real-Time Relaxation–Dispersion NMR. J Am Chem Soc 2017; 139:1065-1068. [DOI: 10.1021/jacs.6b12089] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Rémi Franco
- Institut
de Biologie Structurale, Université Grenoble Alpes, 71 Avenue
des Martyrs, 38044 Grenoble Cedex 9, France
- Commissariat à
l’Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France
- Centre National
de Recherche Scientifique (CNRS), Grenoble, France
| | | | - Isabel Ayala
- Institut
de Biologie Structurale, Université Grenoble Alpes, 71 Avenue
des Martyrs, 38044 Grenoble Cedex 9, France
- Commissariat à
l’Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France
- Centre National
de Recherche Scientifique (CNRS), Grenoble, France
| | - Adrien Favier
- Institut
de Biologie Structurale, Université Grenoble Alpes, 71 Avenue
des Martyrs, 38044 Grenoble Cedex 9, France
- Commissariat à
l’Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France
- Centre National
de Recherche Scientifique (CNRS), Grenoble, France
| | - Bernhard Brutscher
- Institut
de Biologie Structurale, Université Grenoble Alpes, 71 Avenue
des Martyrs, 38044 Grenoble Cedex 9, France
- Commissariat à
l’Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France
- Centre National
de Recherche Scientifique (CNRS), Grenoble, France
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25
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Coudray C, Boucher F, Hida H, Tirard V, de Leiris J, Favier A. Selenium supplementation decreases the pro-oxidant and cardiotoxicity effects of adriamycin in the rat. Redox Rep 2016; 2:323-32. [DOI: 10.1080/13510002.1996.11747068] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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26
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Rohac R, Amara P, Benjdia A, Martin L, Ruffié P, Favier A, Berteau O, Mouesca JM, Fontecilla-Camps JC, Nicolet Y. Carbon–sulfur bond-forming reaction catalysed by the radical SAM enzyme HydE. Nat Chem 2016; 8:491-500. [DOI: 10.1038/nchem.2490] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 02/25/2016] [Indexed: 11/09/2022]
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27
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Balakirev MY, Mullally JE, Favier A, Assard N, Sulpice E, Lindsey DF, Rulina AV, Gidrol X, Wilkinson KD. Wss1 metalloprotease partners with Cdc48/Doa1 in processing genotoxic SUMO conjugates. eLife 2015; 4. [PMID: 26349035 PMCID: PMC4559962 DOI: 10.7554/elife.06763] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 08/06/2015] [Indexed: 12/11/2022] Open
Abstract
Sumoylation during genotoxic stress regulates the composition of DNA repair complexes. The yeast metalloprotease Wss1 clears chromatin-bound sumoylated proteins. Wss1 and its mammalian analog, DVC1/Spartan, belong to minigluzincins family of proteases. Wss1 proteolytic activity is regulated by a cysteine switch mechanism activated by chemical stress and/or DNA binding. Wss1 is required for cell survival following UV irradiation, the smt3-331 mutation and Camptothecin-induced formation of covalent topoisomerase 1 complexes (Top1cc). Wss1 forms a SUMO-specific ternary complex with the AAA ATPase Cdc48 and an adaptor, Doa1. Upon DNA damage Wss1/Cdc48/Doa1 is recruited to sumoylated targets and catalyzes SUMO chain extension through a newly recognized SUMO ligase activity. Activation of Wss1 results in metalloprotease self-cleavage and proteolysis of associated proteins. In cells lacking Tdp1, clearance of topoisomerase covalent complexes becomes SUMO and Wss1-dependent. Upon genotoxic stress, Wss1 is vacuolar, suggesting a link between genotoxic stress and autophagy involving the Doa1 adapter.
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Affiliation(s)
- Maxim Y Balakirev
- Institut de recherches en technologies et sciences pour le vivant-Biologie à Grande Echelle, Commissariat a l'Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France
| | - James E Mullally
- Department of Biochemistry, Emory University, Atlanta, United States
| | - Adrien Favier
- Institut de Biologie Structurale, University Grenoble Alpes, Grenoble, France
| | - Nicole Assard
- Institut de recherches en technologies et sciences pour le vivant-Biologie à Grande Echelle, Commissariat a l'Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France
| | - Eric Sulpice
- Institut de recherches en technologies et sciences pour le vivant-Biologie à Grande Echelle, Commissariat a l'Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France
| | - David F Lindsey
- Department of Biological Sciences, Walla Walla University, College Place, United States
| | - Anastasia V Rulina
- Institut de recherches en technologies et sciences pour le vivant-Biologie à Grande Echelle, Commissariat a l'Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France
| | - Xavier Gidrol
- Institut de recherches en technologies et sciences pour le vivant-Biologie à Grande Echelle, Commissariat a l'Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France
| | - Keith D Wilkinson
- Department of Biochemistry, Emory University, Atlanta, United States
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28
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Gil-Caballero S, Favier A, Brutscher B. HNCA+, HNCO+, and HNCACB+ experiments: improved performance by simultaneous detection of orthogonal coherence transfer pathways. J Biomol NMR 2014; 60:1-9. [PMID: 25056271 DOI: 10.1007/s10858-014-9847-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 07/07/2014] [Indexed: 06/03/2023]
Abstract
Three experiments, BEST-TROSY HNCA+, HNCO+ and HNCACB+ are presented for sequential backbone resonance assignment of (13)C, (15)N labelled proteins. The novelty of these experiments with respect to conventional pulse sequences is the detection of additional orthogonal coherence transfer pathways that results in enhanced sensitivity for sequential correlations without significantly compromising the intensity of intra-residue correlation peaks. In addition, a 2-step phase cycle separates peaks originating from the orthogonal coherence transfer pathways in 2 sub-spectra, thus providing similar information as obtained from performing a pair of sequential and intra-residue correlation experiments.
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Affiliation(s)
- Sergio Gil-Caballero
- Institut de Biologie Structurale, Université Grenoble 1, 71 Avenue des Martyrs, 38044, Grenoble Cedex 9, France
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29
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Navarro JRG, Lerouge F, Micouin G, Cepraga C, Favier A, Charreyre MT, Blanchard NP, Lermé J, Chaput F, Focsan M, Kamada K, Baldeck PL, Parola S. Plasmonic bipyramids for fluorescence enhancement and protection against photobleaching. Nanoscale 2014; 6:5138-5145. [PMID: 24643337 DOI: 10.1039/c3nr06425e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A great number of studies focus their interest on the photophysical properties of fluorescent hybrid gold nanoparticles for potential applications in biotechnologies such as imaging and/or treatment. Spherical gold nanoparticles are known to quench a chromophore fluorescent signal, when moieties are located in their close vicinity. The use of a polymer spacer on such a system allowed only partial recovery of the dye emission by controlling the surface to dye distance. Gold-based anisotropic sharp nanostructures appear to exhibit more interesting features due to the strong electric field generated at their edges and tips. In this paper, a complete study of hybrid fluorescent bipyramidal-like gold nanostructures is presented. We describe the chemical synthesis of gold bipyramids functionalized with fluorescent water-soluble polymers and their photophysics both in solution and on a single object. We show that the use of a bipyramidal shape instead of a spherical one leads to total recovery of the fluorescence and even to an enhancement of the emission of the dyes by a factor of 1.4.
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Affiliation(s)
- J R G Navarro
- Ecole Normale Supérieure de Lyon, CNRS, Université Lyon 1, Laboratoire de Chimie UMR 5182, 46, allée d'Italie, F-69364, Lyon Cedex 07, France.
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30
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Bersch B, Bougault C, Roux L, Favier A, Vernet T, Durmort C. New insights into histidine triad proteins: solution structure of a Streptococcus pneumoniae PhtD domain and zinc transfer to AdcAII. PLoS One 2013; 8:e81168. [PMID: 24312273 PMCID: PMC3842936 DOI: 10.1371/journal.pone.0081168] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [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: 06/07/2013] [Accepted: 10/09/2013] [Indexed: 12/18/2022] Open
Abstract
Zinc (Zn2+) homeostasis is critical for pathogen host colonization and invasion. Polyhistidine triad (Pht) proteins, located at the surface of various streptococci, have been proposed to be involved in Zn2+ homeostasis. The phtD gene, coding for a Zn2+-binding protein, is organized in an operon with adcAII coding for the extracellular part of a Zn2+ transporter. In the present work, we investigate the relationship between PhtD and AdcAII using biochemical and structural biology approaches. Immuno-precipitation experiments on purified membranes of Streptococcus pneumoniae (S. pneumoniae) demonstrate that native PhtD and AdcAII interact in vivo confirming our previous in vitro observations. NMR was used to demonstrate Zn2+ transfer from the Zn2+-bound form of a 137 amino acid N-terminal domain of PhtD (t-PhtD) to AdcAII. The high resolution NMR structure of t-PhtD shows that Zn2+ is bound in a tetrahedral site by histidines 83, 86, and 88 as well as by glutamate 63. Comparison of the NMR parameters measured for apo- and Zn2+-t-PhtD shows that the loss of Zn2+ leads to a diminished helical propensity at the C-terminus and increases the local dynamics and overall molecular volume. Structural comparison with the crystal structure of a 55-long fragment of PhtA suggests that Pht proteins are built from short repetitive units formed by three β-strands containing the conserved HxxHxH motif. Taken together, these results support a role for S. pneumoniae PhtD as a Zn2+ scavenger for later release to the surface transporter AdcAII, leading to Zn2+ uptake.
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Affiliation(s)
- Beate Bersch
- Institut de Biologie Structurale, Université Grenoble Alpes, Grenoble, France ; Institut de Biologie Structurale, Direction des Sciences du Vivant, Commissariat à l'Energie Atomique et aux Energies Alternatives, Grenoble, France ; Institut de Biologie Structurale, Centre National de la Recherche Scientifique, Grenoble, France
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Erkekoğlu P, Rachidi W, Yüzügüllü O, Giray B, Oztürk M, Favier A, Hıncal F. Corrigendum to “Induction of ROS, p53, p21 in DEHP- and MEHP-exposed LNCaP cells-protection by selenium compounds” [Food Chem. Toxicol. 49 (2011) 1565–1567]. Food Chem Toxicol 2013. [DOI: 10.1016/j.fct.2013.07.066] [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: 11/25/2022]
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Lutje Hulsik D, Liu YY, Strokappe NM, Battella S, El Khattabi M, McCoy LE, Sabin C, Hinz A, Hock M, Macheboeuf P, Bonvin AMJJ, Langedijk JPM, Davis D, Forsman Quigley A, Aasa-Chapman MMI, Seaman MS, Ramos A, Poignard P, Favier A, Simorre JP, Weiss RA, Verrips CT, Weissenhorn W, Rutten L. A gp41 MPER-specific llama VHH requires a hydrophobic CDR3 for neutralization but not for antigen recognition. PLoS Pathog 2013; 9:e1003202. [PMID: 23505368 PMCID: PMC3591319 DOI: 10.1371/journal.ppat.1003202] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [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: 09/25/2012] [Accepted: 01/07/2013] [Indexed: 01/28/2023] Open
Abstract
The membrane proximal external region (MPER) of the HIV-1 glycoprotein gp41 is targeted by the broadly neutralizing antibodies 2F5 and 4E10. To date, no immunization regimen in animals or humans has produced HIV-1 neutralizing MPER-specific antibodies. We immunized llamas with gp41-MPER proteoliposomes and selected a MPER-specific single chain antibody (VHH), 2H10, whose epitope overlaps with that of mAb 2F5. Bi-2H10, a bivalent form of 2H10, which displayed an approximately 20-fold increased affinity compared to the monovalent 2H10, neutralized various sensitive and resistant HIV-1 strains, as well as SHIV strains in TZM-bl cells. X-ray and NMR analyses combined with mutagenesis and modeling revealed that 2H10 recognizes its gp41 epitope in a helical conformation. Notably, tryptophan 100 at the tip of the long CDR3 is not required for gp41 interaction but essential for neutralization. Thus bi-2H10 is an anti-MPER antibody generated by immunization that requires hydrophobic CDR3 determinants in addition to epitope recognition for neutralization similar to the mode of neutralization employed by mAbs 2F5 and 4E10.
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Affiliation(s)
- David Lutje Hulsik
- Unit of Virus Host Cell Interactions (UVHCI), UMI 3265, Université Joseph Fourier-EMBL-CNRS, Grenoble, France
| | - Ying-ying Liu
- Biomolecular Imaging (BMI), Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Nika M. Strokappe
- Biomolecular Imaging (BMI), Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Simone Battella
- Biomolecular Imaging (BMI), Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Mohamed El Khattabi
- Biomolecular Imaging (BMI), Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Laura E. McCoy
- MRC/UCL Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London, London, United Kingdom
| | - Charles Sabin
- Unit of Virus Host Cell Interactions (UVHCI), UMI 3265, Université Joseph Fourier-EMBL-CNRS, Grenoble, France
| | - Andreas Hinz
- Unit of Virus Host Cell Interactions (UVHCI), UMI 3265, Université Joseph Fourier-EMBL-CNRS, Grenoble, France
| | - Miriam Hock
- Unit of Virus Host Cell Interactions (UVHCI), UMI 3265, Université Joseph Fourier-EMBL-CNRS, Grenoble, France
| | - Pauline Macheboeuf
- Unit of Virus Host Cell Interactions (UVHCI), UMI 3265, Université Joseph Fourier-EMBL-CNRS, Grenoble, France
| | - Alexandre M. J. J. Bonvin
- Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | | | - David Davis
- Department of Virology, Biomedical Primate Research Centre (BPRC), Rijswijk, The Netherlands
| | - Anna Forsman Quigley
- MRC/UCL Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London, London, United Kingdom
| | - Marlén M. I. Aasa-Chapman
- MRC/UCL Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London, London, United Kingdom
| | - Michael S. Seaman
- Division of Viral Pathogenesis, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Alejandra Ramos
- Department of Immunology and Microbial Science, International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
| | - Pascal Poignard
- Department of Immunology and Microbial Science, International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- International AIDS Vaccine Initiative, New York, New York, United States of America
| | - Adrien Favier
- CNRS, Institut de Biologie Structurale-Jean-Pierre Ebel, Grenoble Cedex, France
- CEA, Institut de Biologie Structurale-Jean-Pierre Ebel, Grenoble Cedex, France
- UJF-Grenoble-1, Institut de Biologie Structurale-Jean-Pierre Ebel, Grenoble Cedex, France
| | - Jean-Pierre Simorre
- CNRS, Institut de Biologie Structurale-Jean-Pierre Ebel, Grenoble Cedex, France
- CEA, Institut de Biologie Structurale-Jean-Pierre Ebel, Grenoble Cedex, France
- UJF-Grenoble-1, Institut de Biologie Structurale-Jean-Pierre Ebel, Grenoble Cedex, France
| | - Robin A. Weiss
- MRC/UCL Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London, London, United Kingdom
| | - C. Theo Verrips
- Biomolecular Imaging (BMI), Faculty of Science, Utrecht University, Utrecht, The Netherlands
- QVQ BV, Utrecht, The Netherlands
| | - Winfried Weissenhorn
- Unit of Virus Host Cell Interactions (UVHCI), UMI 3265, Université Joseph Fourier-EMBL-CNRS, Grenoble, France
- * E-mail: (WW); (LR)
| | - Lucy Rutten
- Biomolecular Imaging (BMI), Faculty of Science, Utrecht University, Utrecht, The Netherlands
- * E-mail: (WW); (LR)
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Feuerstein S, Solyom Z, Aladag A, Favier A, Schwarten M, Hoffmann S, Willbold D, Brutscher B. Transient structure and SH3 interaction sites in an intrinsically disordered fragment of the hepatitis C virus protein NS5A. J Mol Biol 2012; 420:310-23. [PMID: 22543239 DOI: 10.1016/j.jmb.2012.04.023] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 04/21/2012] [Indexed: 12/01/2022]
Abstract
Understanding the molecular mechanisms involved in virus replication and particle assembly is of primary fundamental and biomedical importance. Intrinsic conformational disorder plays a prominent role in viral proteins and their interaction with other viral and host cell proteins via transiently populated structural elements. Here, we report on the results of an investigation of an intrinsically disordered 188-residue fragment of the hepatitis C virus non-structural protein 5A (NS5A), which contains a classical poly-proline Src homology 3 (SH3) binding motif, using sensitivity- and resolution-optimized multidimensional NMR methods, complemented by small-angle X-ray scattering data. Our study provides detailed atomic-resolution information on transient local and long-range structure, as well as fast time scale dynamics in this NS5A fragment. In addition, we could characterize two distinct interaction modes with the SH3 domain of Bin1 (bridging integrator protein 1), a pro-apoptotic tumor suppressor. Despite being largely disordered, the protein contains three regions that transiently adopt α-helical structures, partly stabilized by long-range tertiary interactions. Two of these transient α-helices form a noncanonical SH3-binding motif, which allows low-affinity SH3 binding. Our results contribute to a better understanding of the role of the NS5A protein during hepatitis C virus infection. The present work also highlights the power of NMR spectroscopy to characterize multiple binding events including short-lived transient interactions between globular and highly disordered proteins.
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Affiliation(s)
- Sophie Feuerstein
- Institut de Biologie Structurale, Université Grenoble 1, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France
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Salvatore DB, Duraffourg N, Favier A, Persson BA, Lund M, Delage MM, Silvers R, Schwalbe H, Croguennec T, Bouhallab S, Forge V. Investigation at Residue Level of the Early Steps during the Assembly of Two Proteins into Supramolecular Objects. Biomacromolecules 2011; 12:2200-10. [DOI: 10.1021/bm200285e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [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)
- Delphine B. Salvatore
- Laboratoire de Chimie et Biologie des Métaux (UMR 5249), CEA−Grenoble, 17, rue des Martyrs, F-38057 Grenoble, France
- UMR 1253, INRA, Agrocampus Ouest, Science et Technologie du Lait et de l’Oeuf, 65 rue de Saint-Brieuc, F-35000 Rennes, France
| | - Nicolas Duraffourg
- Laboratoire de Chimie et Biologie des Métaux (UMR 5249), CEA−Grenoble, 17, rue des Martyrs, F-38057 Grenoble, France
| | - Adrien Favier
- Laboratoire de Résonance Magnétique Nucléaire, Institut de Biologie Structurale Jean-Pierre Ebel, 41, rue Jules Horowitz, F-38027 Grenoble, France
| | - Björn A. Persson
- Department of Theoretical Chemistry, University of Lund, POB 124, S-22100 Lund, Sweden
| | - Mikael Lund
- Department of Theoretical Chemistry, University of Lund, POB 124, S-22100 Lund, Sweden
| | - Marie-Madeleine Delage
- UMR 1253, INRA, Agrocampus Ouest, Science et Technologie du Lait et de l’Oeuf, 65 rue de Saint-Brieuc, F-35000 Rennes, France
| | - Robert Silvers
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany
| | - Thomas Croguennec
- UMR 1253, INRA, Agrocampus Ouest, Science et Technologie du Lait et de l’Oeuf, 65 rue de Saint-Brieuc, F-35000 Rennes, France
| | - Saïd Bouhallab
- UMR 1253, INRA, Agrocampus Ouest, Science et Technologie du Lait et de l’Oeuf, 65 rue de Saint-Brieuc, F-35000 Rennes, France
| | - Vincent Forge
- Laboratoire de Chimie et Biologie des Métaux (UMR 5249), CEA−Grenoble, 17, rue des Martyrs, F-38057 Grenoble, France
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Favier A, Brutscher B. Recovering lost magnetization: polarization enhancement in biomolecular NMR. J Biomol NMR 2011; 49:9-15. [PMID: 21190063 DOI: 10.1007/s10858-010-9461-5] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Accepted: 11/26/2010] [Indexed: 05/03/2023]
Abstract
Experimental sensitivity remains a major drawback for the application of NMR spectroscopy to fragile and low concentrated biomolecular samples. Here we describe an efficient polarization enhancement mechanism in longitudinal-relaxation enhanced fast-pulsing triple-resonance experiments. By recovering undetectable (1)H polarization originating from longitudinal relaxation during the pulse sequence, the steady-state (15)N polarization becomes enhanced by up to a factor of ~5 with respect to thermal equilibrium yielding significant sensitivity improvements compared to conventional schemes. The benefits of BEST-TROSY experiments at high magnetic field strength are illustrated for various protein applications, but they will be equally useful for other protonated macromolecular systems.
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Affiliation(s)
- Adrien Favier
- IBS, Institut de Biologie Structurale Jean-Pierre Ebel, 41 rue Jules Horowitz, 38027 Grenoble, France
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Sarret G, Favier A, Covès J, Hazemann JL, Mergeay M, Bersch B. CopK from Cupriavidus metallidurans CH34 binds Cu(I) in a tetrathioether site: characterization by X-ray absorption and NMR spectroscopy. J Am Chem Soc 2010; 132:3770-7. [PMID: 20192263 DOI: 10.1021/ja9083896] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cupriavidus metallidurans CH34 is a bacterium that is resistant to high metal concentrations in the environment. Increased copper resistance is associated with the cop cluster on the large plasmid pMOL30 that is composed of at least 21 genes. The copK gene encodes a 74 residue periplasmic protein whose expression is strongly upregulated in the presence of copper. CopK was previously shown to cooperatively bind Cu(I) and Cu(II) in distinct, specific sites. The solution structure of Cu(I)-CopK and the characterization of the Cu(I) site by X-ray absorption spectroscopy and NMR are reported here. EXAFS spectra are in agreement with a tetrathioether Cu(I) site, providing so far unique spectral information on a 4S-coordinated Cu(I) in a protein. The methionine residues forming the Cu(I) site, M28, M38, M44, and M54, are identified by NMR. We propose the chemical shift of the methionine C(epsilon) as a new and sensitive probe for the detection of Cu(I) bound to thioether groups. The solution structure of Cu(I)-CopK demonstrates that Cu(I) binding induces a complete structural modification with the disruption of the second beta-sheet and a rotation of the C-terminal part of nearly 180 degrees around a hinge formed by asparagine 57. This conformational change is directly related to the loss of the dimer interface and most probably to the formation of the Cu(II) site involving histidine 70. The solution structure of Cu(I)-CopK therefore provides the molecular basis for the understanding of the Cu(I)/Cu(II) binding cooperativity.
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Affiliation(s)
- Géraldine Sarret
- Environmental Geochemistry Group, LGIT, UMR 5559, Université Joseph Fourier and CNRS, BP 53, 38041 Grenoble, France
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Erkekoglu P, Rachidi W, Yuzugullu OG, Giray B, Ozturk M, Favier A, Hincal F. Evaluation of the effects of phthalates on antioxidant status, p53 expression and oxidative DNA damage in Leydig carcinoma cells and protection by selenium compounds. Toxicol Lett 2010. [DOI: 10.1016/j.toxlet.2010.03.559] [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: 10/19/2022]
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Bardiaux B, Favier A, Etzkorn M, Baldus M, Böckmann A, Nilges M, Malliavin TE. Simultaneous use of solution, solid-state NMR and X-ray crystallography to study the conformational landscape of the Crh protein during oligomerization and crystallization. Adv Appl Bioinform Chem 2010; 3:25-38. [PMID: 21918624 PMCID: PMC3170007 DOI: 10.2147/aabc.s8715] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We explore, using the Crh protein dimer as a model, how information from solution NMR, solid-state NMR and X-ray crystallography can be combined using structural bioinformatics methods, in order to get insights into the transition from solution to crystal. Using solid-state NMR chemical shifts, we filtered intra-monomer NMR distance restraints in order to keep only the restraints valid in the solid state. These filtered restraints were added to solid-state NMR restraints recorded on the dimer state to sample the conformational landscape explored during the oligomerization process. The use of non-crystallographic symmetries then permitted the extraction of converged conformers subsets. Ensembles of NMR and crystallographic conformers calculated independently display similar variability in monomer orientation, which supports a funnel shape for the conformational space explored during the solution-crystal transition. Insights into alternative conformations possibly sampled during oligomerization were obtained by analyzing the relative orientation of the two monomers, according to the restraint precision. Molecular dynamics simulations of Crh confirmed the tendencies observed in NMR conformers, as a paradoxical increase of the distance between the two β1a strands, when the structure gets closer to the crystallographic structure, and the role of water bridges in this context.
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Affiliation(s)
- Benjamin Bardiaux
- Unité de Bioinformatique Structurale, CNRS URA 2185, Institut Pasteur, Paris, France
- Campus Berlin- Buch, Berlin, Germany
| | - Adrien Favier
- Institut de Biologie Structurale Jean-Pierre Ebel CEACNRS- Université Joseph Fourier, Grenoble, France
| | - Manuel Etzkorn
- Max Planck Institute Biophysical Chemistry, Göttingen, Germany
| | - Marc Baldus
- Bijvoet Center for Biomolecular Research Faculty of Science, Utrecht University Utrecht, The Netherlands
| | - Anja Böckmann
- Institut de Biologie et Chimie des Proteines, UMR 5086 CNRS/Université de Lyon 1, Lyon, France
| | - Michael Nilges
- Unité de Bioinformatique Structurale, CNRS URA 2185, Institut Pasteur, Paris, France
| | - Thérèse E Malliavin
- Unité de Bioinformatique Structurale, CNRS URA 2185, Institut Pasteur, Paris, France
- Correspondence: Thérèse E Malliavin, Unité de Bioinformatique Structurale, CNRS URA 2185, Institut Pasteur 25-28 rue du Dr Roux, F-75724 Paris, Cedex 15, France, Tel (33) 1 40 61 34 75, Fax (33) 1 45 68 87 19, Email
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Raynal M, Ceruse P, Girard B, Rakotovao F, Rakoto FA, Favier A, Coupat C, Aiss D. [Management of ear, nose, and throat diseases in district hospital centers in Madagascar]. Med Trop (Mars) 2010; 70:13-17. [PMID: 20337109] [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] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The purpose of this report is to describe the experience of a specialized medico-surgical ENT team sent to hospital centers in Atalaha and Tulear, Madagascar by a nonprofit organization called "Terre rouge" from the Reunion Island. In three separate short-term missions, a total of 93 patients received care. Discussion focuses on the particular pathological, cultural, and pedagogical features of the Island and on the resources that were deployed during the missions. Providing ENT care in district hospitals in Madagascar requires adaptation to the difficult climatic conditions, poor hospital facilities (infrastructure, equip ment, and personnel), and advanced stage of diseases. To ensure continuous access to ENT care, it will be necessary to provide practical and didactic training for healthcare personnel in the country.
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Affiliation(s)
- M Raynal
- Service d'ORL et de chirurgie cervico-faciale, HIA Percy, Clamart.
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Pelus E, Arnaud J, Ducros V, Faure H, Favier A, Roussel AM. Trace element (Cu, Zn, Fe, Mn, Se) intakes of a group of French men using the duplicate diet technique. Int J Food Sci Nutr 2009. [DOI: 10.3109/09637489409167018] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Coudray C, Richard MJ, Laporte F, Faure P, Roussel AM, Favier A. Superoxide Dismutase Activity and Zinc Status: a Study in Animals and Man. ACTA ACUST UNITED AC 2009. [DOI: 10.3109/13590849208997956] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Chater S, Douki T, Favier A, Sakly M, Abdelmelek H. Changes in antioxidant status and biochemical parameters after orally cadmium administration in females rats. Acta Biol Hung 2009; 60:79-88. [PMID: 19378926 DOI: 10.1556/abiol.60.2009.1.8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [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: 11/19/2022]
Abstract
The research was conducted to investigate the toxic effects of cadmium chloride (CdCl2), administered during gestation period on female Wistar rats. Pregnant rats received CdCl2 (20 mg/l, orally) from Day 6 to Day 19 of pregnancy. Results showed that Cd treatment induced a decrease in body weight gain. The relative liver weight increased significantly, with a marked decrease of glycogen and total lipids content. The administration of Cd induced hepatotoxicity as indicated by elevations in plasma alanine aminotransferase (ALT), aspartate aminotransferase and lactate dehydrogenase (LDH) activities (p < 0.05). Treatment with CdCl2 caused a significant (p < 0.05) increase in glucose. A significant increase was observed in the level of MDA and 8-oxodGuo tissues in the cadmium-exposed group compared to the control group (p < 0.05). Results showed that cadmium given to dams led to an oxidative stress and DNA damage in tissues of pregnant rats.
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Affiliation(s)
- S Chater
- Laboratoire de Physiologie Intégrée, Faculté des Sciences de Bizerte, 7021 Jarzouna, Tunisia.
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Amara S, Douki T, Gare C, Favier A, Sakly M, Rhouma K, Abdelmelek H. Effects of static magnetic field exposure on antioxidative enzymes activity and DNA in rat brain. Gen Physiol Biophys 2009; 28:260-5. [DOI: 10.4149/gpb_2009_03_260] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Amara S, Garrel C, Favier A, Rhouma K, Sakly M, Abdelmelek H. Effect of static magnetic field and/or cadmium in the antioxidant enzymes activity in rat heart and skeletal muscle. Gen Physiol Biophys 2009; 28:414-9. [DOI: 10.4149/gpb_2009_04_414] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Millau JF, Raffin AL, Caillat S, Claudet C, Arras G, Ugolin N, Douki T, Ravanat JL, Breton J, Oddos T, Dumontet C, Sarasin A, Chevillard S, Favier A, Sauvaigo S. A microarray to measure repair of damaged plasmids by cell lysates. Lab Chip 2008; 8:1713-1722. [PMID: 18813395 DOI: 10.1039/b806634e] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
DNA repair mechanisms constitute major defences against agents that cause cancer, degenerative disease and aging. Different repair systems cooperate to maintain the integrity of genetic information. Investigations of DNA repair involvement in human pathology require an efficient tool that takes into account the variety and complexity of repair systems. We have developed a highly sensitive damaged plasmid microarray to quantify cell lysate excision/synthesis (ES) capacities using small amounts of proteins. This microsystem is based on efficient immobilization and conservation on hydrogel coated glass slides of plasmid DNA damaged with a panel of genotoxic agents. Fluorescent signals are generated from incorporation of labelled dNTPs by DNA excision-repair synthesis mechanisms at plasmid sites. Highly precise DNA repair phenotypes i.e. simultaneous quantitative measures of ES capacities toward seven lesions repaired by distinct repair pathways, are obtained. Applied to the characterization of xeroderma pigmentosum (XP) cells at basal level and in response to a low dose of UVB irradiation, the assay showed the multifunctional role of different XP proteins in cell protection against all types of damage. On the other hand, measurement of the ES of peripheral blood mononuclear cells from six donors revealed significant diversity between individuals. Our results illustrate the power of such a parallelized approach with high potential for several applications including the discovery of new cancer biomarkers and the screening of chemical agents modulating DNA repair systems.
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Affiliation(s)
- J-F Millau
- Laboratoire des Lésions des Acides Nucléiques, LCIB (UMR-E 3 CEA-UJF), INAC, CEA Grenoble, 38054, Grenoble cedex 9, France
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Corne C, Fiche JB, Cunin V, Buhot A, Fuchs J, Calemczuk R, Favier A, Livache T, Gasparutto D. SPR-imaging based assays on an oligonucleotide-array to analyze DNA lesions recognition and excision by repair proteins. ACTA ACUST UNITED AC 2008:249-50. [DOI: 10.1093/nass/nrn126] [Citation(s) in RCA: 3] [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: 11/13/2022]
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Ribeiro EA, Favier A, Gerard FCA, Leyrat C, Brutscher B, Blondel D, Ruigrok RWH, Blackledge M, Jamin M. Solution structure of the C-terminal nucleoprotein-RNA binding domain of the vesicular stomatitis virus phosphoprotein. J Mol Biol 2008; 382:525-38. [PMID: 18657547 DOI: 10.1016/j.jmb.2008.07.028] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2008] [Accepted: 07/07/2008] [Indexed: 10/21/2022]
Abstract
Beyond common features in their genome organization and replication mechanisms, the evolutionary relationships among viruses of the Rhabdoviridae family are difficult to decipher because of the great variability in the amino acid sequence of their proteins. The phosphoprotein (P) of vesicular stomatitis virus (VSV) is an essential component of the RNA transcription and replication machinery; in particular, it contains binding sites for the RNA-dependent RNA polymerase and for the nucleoprotein. Here, we devised a new method for defining boundaries of structured domains from multiple disorder prediction algorithms, and we identified an autonomous folding C-terminal domain in VSV P (P(CTD)). We show that, like the C-terminal domain of rabies virus (RV) P, VSV P(CTD) binds to the viral nucleocapsid (nucleoprotein-RNA complex). We solved the three-dimensional structure of VSV P(CTD) by NMR spectroscopy and found that the topology of its polypeptide chain resembles that of RV P(CTD). The common part of both proteins could be superimposed with a backbone RMSD from mean atomic coordinates of 2.6 A. VSV P(CTD) has a shorter N-terminal helix (alpha(1)) than RV P(CTD); it lacks two alpha-helices (helices alpha(3) and alpha(6) of RV P), and the loop between strands beta(1) and beta(2) is longer than that in RV. Dynamical properties measured by NMR relaxation revealed the presence of fast motions (below the nanosecond timescale) in loop regions (amino acids 209-214) and slower conformational exchange in the N- and C-terminal helices. Characterization of a longer construct indicated that P(CTD) is preceded by a flexible linker. The results presented here support a modular organization of VSV P, with independent folded domains separated by flexible linkers, which is conserved among different genera of Rhabdoviridae and is similar to that proposed for the P proteins of the Paramyxoviridae.
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Affiliation(s)
- Euripedes A Ribeiro
- UJF-EMBL-CNRS-UMR 5233-Unit of Virus Host Cell Interactions, 6 rue Jules Horowitz, 38042 Grenoble Cedex 9, France
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Bersch B, Favier A, Schanda P, van Aelst S, Vallaeys T, Covès J, Mergeay M, Wattiez R. Molecular Structure and Metal-binding Properties of the Periplasmic CopK Protein Expressed in Cupriavidus metallidurans CH34 During Copper Challenge. J Mol Biol 2008; 380:386-403. [DOI: 10.1016/j.jmb.2008.05.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2008] [Revised: 05/06/2008] [Accepted: 05/08/2008] [Indexed: 11/16/2022]
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Sauvaigo S, Bonnet-Duquennoy M, Odin F, Hazane F, Kurfürst R, Favier A. Sensitivity to oxidative damage and DNA repair capacity of Japanese skin. Int J Cosmet Sci 2008. [DOI: 10.1111/j.1467-2494.2004.00254_18.x] [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: 11/29/2022]
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Faure P, Tamisier R, Baguet JP, Favier A, Halimi S, Lévy P, Pépin JL. Impairment of serum albumin antioxidant properties in obstructive sleep apnoea syndrome. Eur Respir J 2008; 31:1046-53. [PMID: 18256067 DOI: 10.1183/09031936.00062707] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Antioxidant counteraction of oxidative stress has been poorly explored in obstructive sleep apnoea (OSA). Serum albumin is a major antioxidant agent and structural modifications induced by glucose or free radicals impair its antioxidant properties. The aim of the present study was to compare antioxidant capacities and structural changes of albumin in nonobese OSA patients and healthy volunteers. Albumin structural changes were studied by quenching of fluorescence in the presence of acrylamide. Albumin thiols and fructosamines, reflecting oxidation- and glycation-induced changes in serum albumin, respectively, were assessed. Albumin structural changes were demonstrated by a significant decrease in quenching of fluorescence in OSA patients. Oxidation, resulting in a significant decrease in thiol groups (3.7+/-0.7 versus 2.3+/-0.4 micromol x g(-1) protein), and glycation, associated with a significant increase in fructosamines (226.6+/-27 versus 286+/-44.4 micromol x L(-1)), were found when comparing healthy volunteers with OSA patients. There was a significant relationship between both parameters and sleep apnoea severity. After continuous positive airway pressure intervention, albumin thiol groups were reassessed in seven of the 16 OSA patients and increased significantly from 2.25+/-0.39 to 2.79+/-0.31 micromol x g(-1) protein. Obstructive sleep apnoea patients demonstrated a reduction in serum albumin antioxidant properties that may aggravate oxidative stress and, thus, contribute to cardiovascular and metabolic morbidities.
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Affiliation(s)
- P Faure
- Dept of Integrated Biology, University Hospital Grenoble, Grenoble Cedex 09, France
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