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Structural insights into the catalytic cycle of a bacterial multidrug ABC efflux pump. J Mol Biol 2022; 434:167541. [DOI: 10.1016/j.jmb.2022.167541] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/02/2022] [Accepted: 03/09/2022] [Indexed: 12/19/2022]
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Chaptal V, Zampieri V, Wiseman B, Orelle C, Martin J, Nguyen KA, Gobet A, Di Cesare M, Magnard S, Javed W, Eid J, Kilburg A, Peuchmaur M, Marcoux J, Monticelli L, Hogbom M, Schoehn G, Jault JM, Boumendjel A, Falson P. Substrate-bound and substrate-free outward-facing structures of a multidrug ABC exporter. SCIENCE ADVANCES 2022; 8:eabg9215. [PMID: 35080979 DOI: 10.1101/2021.03.12.435132] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Multidrug ABC transporters translocate drugs across membranes by a mechanism for which the molecular features of drug release are so far unknown. Here, we resolved three ATP-Mg2+-bound outward-facing conformations of the Bacillus subtilis (homodimeric) BmrA by x-ray crystallography and single-particle cryo-electron microscopy (EM) in detergent solution, one of them with rhodamine 6G (R6G), a substrate exported by BmrA when overexpressed in B. subtilis. Two R6G molecules bind to the drug-binding cavity at the level of the outer leaflet, between transmembrane (TM) helices 1-2 of one monomer and TM5'-6' of the other. They induce a rearrangement of TM1-2, highlighting a local flexibility that we confirmed by hydrogen/deuterium exchange and molecular dynamics simulations. In the absence of R6G, simulations show a fast postrelease occlusion of the cavity driven by hydrophobicity, while when present, R6G can move within the cavity, maintaining it open.
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Affiliation(s)
- Vincent Chaptal
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Veronica Zampieri
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Benjamin Wiseman
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
| | - Cédric Orelle
- Bacterial Nucleotide-Binding Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Juliette Martin
- Modeling Biological Macromolecules Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Kim-Anh Nguyen
- University of Grenoble Alpes, INSERM, LRB, 38000 Grenoble, France
| | - Alexia Gobet
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Margot Di Cesare
- Bacterial Nucleotide-Binding Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Sandrine Magnard
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Waqas Javed
- Bacterial Nucleotide-Binding Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Jad Eid
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Arnaud Kilburg
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Marine Peuchmaur
- University of Grenoble Alpes, CNRS, DPM UMR 5063, 38041 Grenoble, France
| | - Julien Marcoux
- Institut de Pharmacologie et de Biologie Structurale (IPBS), UMR 5089, Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Luca Monticelli
- Modeling Biological Macromolecules Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Martin Hogbom
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
| | - Guy Schoehn
- University of Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Jean-Michel Jault
- Bacterial Nucleotide-Binding Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | | | - Pierre Falson
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
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Chaptal V, Zampieri V, Wiseman B, Orelle C, Martin J, Nguyen KA, Gobet A, Di Cesare M, Magnard S, Javed W, Eid J, Kilburg A, Peuchmaur M, Marcoux J, Monticelli L, Hogbom M, Schoehn G, Jault JM, Boumendjel A, Falson P. Substrate-bound and substrate-free outward-facing structures of a multidrug ABC exporter. SCIENCE ADVANCES 2022; 8:eabg9215. [PMID: 35080979 PMCID: PMC8791611 DOI: 10.1126/sciadv.abg9215] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Multidrug ABC transporters translocate drugs across membranes by a mechanism for which the molecular features of drug release are so far unknown. Here, we resolved three ATP-Mg2+-bound outward-facing conformations of the Bacillus subtilis (homodimeric) BmrA by x-ray crystallography and single-particle cryo-electron microscopy (EM) in detergent solution, one of them with rhodamine 6G (R6G), a substrate exported by BmrA when overexpressed in B. subtilis. Two R6G molecules bind to the drug-binding cavity at the level of the outer leaflet, between transmembrane (TM) helices 1-2 of one monomer and TM5'-6' of the other. They induce a rearrangement of TM1-2, highlighting a local flexibility that we confirmed by hydrogen/deuterium exchange and molecular dynamics simulations. In the absence of R6G, simulations show a fast postrelease occlusion of the cavity driven by hydrophobicity, while when present, R6G can move within the cavity, maintaining it open.
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Affiliation(s)
- Vincent Chaptal
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Veronica Zampieri
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Benjamin Wiseman
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
| | - Cédric Orelle
- Bacterial Nucleotide-Binding Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Juliette Martin
- Modeling Biological Macromolecules Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Kim-Anh Nguyen
- University of Grenoble Alpes, INSERM, LRB, 38000 Grenoble, France
| | - Alexia Gobet
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Margot Di Cesare
- Bacterial Nucleotide-Binding Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Sandrine Magnard
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Waqas Javed
- Bacterial Nucleotide-Binding Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Jad Eid
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Arnaud Kilburg
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Marine Peuchmaur
- University of Grenoble Alpes, CNRS, DPM UMR 5063, 38041 Grenoble, France
| | - Julien Marcoux
- Institut de Pharmacologie et de Biologie Structurale (IPBS), UMR 5089, Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Luca Monticelli
- Modeling Biological Macromolecules Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Martin Hogbom
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
| | - Guy Schoehn
- University of Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Jean-Michel Jault
- Bacterial Nucleotide-Binding Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | | | - Pierre Falson
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
- Corresponding author.
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Di Cesare M, Diagne AM, Bourgey B, Jault JM, Orelle C. Functional Overexpression of Membrane Proteins in E. coli: The Good, the Bad, and the Ugly. Methods Mol Biol 2022; 2507:41-58. [PMID: 35773576 DOI: 10.1007/978-1-0716-2368-8_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Overexpression of properly folded membrane proteins is a mandatory step for their functional and structural characterization. One of the most used expression systems for the production of proteins is Escherichia coli. Many advantageous strains combined with T7 expression systems have been developed over the years. Recently, we showed that the choice of the strain is critical for the functionality of membrane proteins, even when the proteins are successfully incorporated in the membrane (Mathieu et al. Sci Rep. 2019; 9(1):2654). Notably, the amount and/or activity of the T7-RNA polymerase, which drives the transcription of the genes of interest, may indirectly affect the folding and functionality of overexpressed membrane proteins. Moreover, we reported a general trend in which mild detergents mainly extract the population of active membrane proteins, whereas a harsher detergent like Fos-choline 12 could solubilize them irrespectively of their functionality. Based on these observations, we provide some guidelines to optimize the quality of membrane proteins overexpressed in E. coli.
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Affiliation(s)
- Margot Di Cesare
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Aissatou Maty Diagne
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Benjamin Bourgey
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Jean-Michel Jault
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/University of Lyon, Lyon, France.
| | - Cédric Orelle
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/University of Lyon, Lyon, France.
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Birch J, Cheruvara H, Gamage N, Harrison PJ, Lithgo R, Quigley A. Changes in Membrane Protein Structural Biology. BIOLOGY 2020; 9:E401. [PMID: 33207666 PMCID: PMC7696871 DOI: 10.3390/biology9110401] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/11/2020] [Accepted: 11/12/2020] [Indexed: 12/21/2022]
Abstract
Membrane proteins are essential components of many biochemical processes and are important pharmaceutical targets. Membrane protein structural biology provides the molecular rationale for these biochemical process as well as being a highly useful tool for drug discovery. Unfortunately, membrane protein structural biology is a difficult area of study due to low protein yields and high levels of instability especially when membrane proteins are removed from their native environments. Despite this instability, membrane protein structural biology has made great leaps over the last fifteen years. Today, the landscape is almost unrecognisable. The numbers of available atomic resolution structures have increased 10-fold though advances in crystallography and more recently by cryo-electron microscopy. These advances in structural biology were achieved through the efforts of many researchers around the world as well as initiatives such as the Membrane Protein Laboratory (MPL) at Diamond Light Source. The MPL has helped, provided access to and contributed to advances in protein production, sample preparation and data collection. Together, these advances have enabled higher resolution structures, from less material, at a greater rate, from a more diverse range of membrane protein targets. Despite this success, significant challenges remain. Here, we review the progress made and highlight current and future challenges that will be overcome.
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Affiliation(s)
- James Birch
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Harish Cheruvara
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Nadisha Gamage
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Peter J. Harrison
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Ryan Lithgo
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, Leicestershire, UK
| | - Andrew Quigley
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
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Kanonenberg K, Royes J, Kedrov A, Poschmann G, Angius F, Solgadi A, Spitz O, Kleinschrodt D, Stühler K, Miroux B, Schmitt L. Shaping the lipid composition of bacterial membranes for membrane protein production. Microb Cell Fact 2019; 18:131. [PMID: 31400768 PMCID: PMC6689329 DOI: 10.1186/s12934-019-1182-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 07/30/2019] [Indexed: 12/29/2022] Open
Abstract
Background The overexpression and purification of membrane proteins is a bottleneck in biotechnology and structural biology. E. coli remains the host of choice for membrane protein production. To date, most of the efforts have focused on genetically tuning of expression systems and shaping membrane composition to improve membrane protein production remained largely unexplored. Results In E. coli C41(DE3) strain, we deleted two transporters involved in fatty acid metabolism (OmpF and AcrB), which are also recalcitrant contaminants crystallizing even at low concentration. Engineered expression hosts presented an enhanced fitness and improved folding of target membrane proteins, which correlated with an altered membrane fluidity. We demonstrated the scope of this approach by overproducing several membrane proteins (4 different ABC transporters, YidC and SecYEG). Conclusions In summary, E. coli membrane engineering unprecedentedly increases the quality and yield of membrane protein preparations. This strategy opens a new field for membrane protein production, complementary to gene expression tuning. Electronic supplementary material The online version of this article (10.1186/s12934-019-1182-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kerstin Kanonenberg
- Institute of Biochemistry, Heinrich-Heine-University Duesseldorf, Universitaetsstr. 1, 40225, Duesseldorf, Germany.,CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry", Université de Lyon, 7 Passage du vercors, 69007, Lyon, France
| | - Jorge Royes
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR7099, CNRS, IBPC, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Alexej Kedrov
- Institute of Biochemistry, Heinrich-Heine-University Duesseldorf, Universitaetsstr. 1, 40225, Duesseldorf, Germany
| | - Gereon Poschmann
- Molecular Proteomics Laboratory, Biologisch Medizinisches Forschungszentrum (BMFZ), Heinrich-Heine-University Duesseldorf, Duesseldorf, Germany
| | - Federica Angius
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR7099, CNRS, IBPC, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005, Paris, France.,Department of Microbiology, Institute for Water and Wetland Research, Heyendaalseweg 135, 6525, Nijmegen, The Netherlands
| | - Audrey Solgadi
- Institut Paris Saclay d'Innovation Thérapeutique, INSERM, CNRS, - Plateforme SAMM, Université Paris-Saclay, Châtenay-Malabry, France
| | - Olivia Spitz
- Institute of Biochemistry, Heinrich-Heine-University Duesseldorf, Universitaetsstr. 1, 40225, Duesseldorf, Germany
| | - Diana Kleinschrodt
- Institute of Biochemistry, Heinrich-Heine-University Duesseldorf, Universitaetsstr. 1, 40225, Duesseldorf, Germany
| | - Kai Stühler
- Molecular Proteomics Laboratory, Biologisch Medizinisches Forschungszentrum (BMFZ), Heinrich-Heine-University Duesseldorf, Duesseldorf, Germany
| | - Bruno Miroux
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR7099, CNRS, IBPC, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005, Paris, France.
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich-Heine-University Duesseldorf, Universitaetsstr. 1, 40225, Duesseldorf, Germany.
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Breyton C, Javed W, Vermot A, Arnaud CA, Hajjar C, Dupuy J, Petit-Hartlein I, Le Roy A, Martel A, Thépaut M, Orelle C, Jault JM, Fieschi F, Porcar L, Ebel C. Assemblies of lauryl maltose neopentyl glycol (LMNG) and LMNG-solubilized membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:939-957. [PMID: 30776334 DOI: 10.1016/j.bbamem.2019.02.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 02/08/2019] [Accepted: 02/08/2019] [Indexed: 12/11/2022]
Abstract
Laurylmaltose neopentylglycol (LMNG) bears two linked hydrophobic chains of equal length and two hydrophilic maltoside groups. It arouses a strong interest in the field of membrane protein biochemistry, since it was shown to efficiently solubilize and stabilize membrane proteins often better than the commonly used dodecylmaltopyranoside (DDM), and to allow structure determination of some challenging membrane proteins. However, LMNG was described to form large micelles, which could be unfavorable for structural purposes. We thus investigated its auto-assemblies and the association state of different membrane proteins solubilized in LMNG by analytical ultracentrifugation, size exclusion chromatography coupled to light scattering, centrifugation on sucrose gradient and/or small angle scattering. At high concentrations (in the mM range), LMNG forms long rods, and it stabilized the membrane proteins investigated herein, i.e. a bacterial multidrug transporter, BmrA; a prokaryotic analogous of the eukaryotic NADPH oxidases, SpNOX; an E. coli outer membrane transporter, FhuA; and the halobacterial bacteriorhodopsin, bR. BmrA, in the Apo and the vanadate-inhibited forms showed reduced kinetics of limited proteolysis in LMNG compared to DDM. Both SpNOX and BmrA display an increased specific activity in LMNG compared to DDM. The four proteins form LMNG complexes with their usual quaternary structure and with usual amount of bound detergent. No heterogeneous complexes related to the large micelle size of LMNG alone were observed. In conditions where LMNG forms assemblies of large size, FhuA crystals diffracting to 4.0 Å were obtained by vapor diffusion. LMNG large micelle size thus does not preclude membrane protein homogeneity and crystallization.
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Affiliation(s)
- Cécile Breyton
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France
| | - Waqas Javed
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France; University of Lyon, CNRS, UMR5086, Molecular Microbiology and Structural Biochemistry, IBCP, Lyon 69367, France
| | - Annelise Vermot
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France
| | - Charles-Adrien Arnaud
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France
| | - Christine Hajjar
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France
| | - Jérôme Dupuy
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France
| | - Isabelle Petit-Hartlein
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France
| | - Aline Le Roy
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France
| | - Anne Martel
- Institut Max Von Laue Paul Langevin, 38042 Grenoble, France
| | - Michel Thépaut
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France
| | - Cédric Orelle
- University of Lyon, CNRS, UMR5086, Molecular Microbiology and Structural Biochemistry, IBCP, Lyon 69367, France
| | - Jean-Michel Jault
- University of Lyon, CNRS, UMR5086, Molecular Microbiology and Structural Biochemistry, IBCP, Lyon 69367, France
| | - Franck Fieschi
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France
| | - Lionel Porcar
- Institut Max Von Laue Paul Langevin, 38042 Grenoble, France
| | - Christine Ebel
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France.
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Nguyen KA, Peuchmaur M, Magnard S, Haudecoeur R, Boyère C, Mounien S, Benammar I, Zampieri V, Igonet S, Chaptal V, Jawhari A, Boumendjel A, Falson P. Glycosyl-Substituted Dicarboxylates as Detergents for the Extraction, Overstabilization, and Crystallization of Membrane Proteins. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201713395] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Kim-Anh Nguyen
- DPM UMR 5063; Univ Grenoble-Alpes/CNRS; 38041 Grenoble France
| | | | - Sandrine Magnard
- DRMP group, IBCP UMR 5086 (MMSB); CNRS/Lyon I University; 69367 Lyon France
| | | | - Cédric Boyère
- DPM UMR 5063; Univ Grenoble-Alpes/CNRS; 38041 Grenoble France
| | | | - Ikram Benammar
- DPM UMR 5063; Univ Grenoble-Alpes/CNRS; 38041 Grenoble France
| | - Veronica Zampieri
- DRMP group, IBCP UMR 5086 (MMSB); CNRS/Lyon I University; 69367 Lyon France
| | | | - Vincent Chaptal
- DRMP group, IBCP UMR 5086 (MMSB); CNRS/Lyon I University; 69367 Lyon France
| | | | | | - Pierre Falson
- DRMP group, IBCP UMR 5086 (MMSB); CNRS/Lyon I University; 69367 Lyon France
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9
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Nguyen KA, Peuchmaur M, Magnard S, Haudecoeur R, Boyère C, Mounien S, Benammar I, Zampieri V, Igonet S, Chaptal V, Jawhari A, Boumendjel A, Falson P. Glycosyl-Substituted Dicarboxylates as Detergents for the Extraction, Overstabilization, and Crystallization of Membrane Proteins. Angew Chem Int Ed Engl 2018; 57:2948-2952. [DOI: 10.1002/anie.201713395] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Kim-Anh Nguyen
- DPM UMR 5063; Univ Grenoble-Alpes/CNRS; 38041 Grenoble France
| | | | - Sandrine Magnard
- DRMP group, IBCP UMR 5086 (MMSB); CNRS/Lyon I University; 69367 Lyon France
| | | | - Cédric Boyère
- DPM UMR 5063; Univ Grenoble-Alpes/CNRS; 38041 Grenoble France
| | | | - Ikram Benammar
- DPM UMR 5063; Univ Grenoble-Alpes/CNRS; 38041 Grenoble France
| | - Veronica Zampieri
- DRMP group, IBCP UMR 5086 (MMSB); CNRS/Lyon I University; 69367 Lyon France
| | | | - Vincent Chaptal
- DRMP group, IBCP UMR 5086 (MMSB); CNRS/Lyon I University; 69367 Lyon France
| | | | | | - Pierre Falson
- DRMP group, IBCP UMR 5086 (MMSB); CNRS/Lyon I University; 69367 Lyon France
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10
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Orelle C, Durmort C, Mathieu K, Duchêne B, Aros S, Fenaille F, André F, Junot C, Vernet T, Jault JM. A multidrug ABC transporter with a taste for GTP. Sci Rep 2018; 8:2309. [PMID: 29396536 PMCID: PMC5797166 DOI: 10.1038/s41598-018-20558-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 01/19/2018] [Indexed: 01/26/2023] Open
Abstract
During the evolution of cellular bioenergetics, many protein families have been fashioned to match the availability and replenishment in energy supply. Molecular motors and primary transporters essentially need ATP to function while proteins involved in cell signaling or translation consume GTP. ATP-Binding Cassette (ABC) transporters are one of the largest families of membrane proteins gathering several medically relevant members that are typically powered by ATP hydrolysis. Here, a Streptococcus pneumoniae ABC transporter responsible for fluoroquinolones resistance in clinical settings, PatA/PatB, is shown to challenge this concept. It clearly favors GTP as the energy supply to expel drugs. This preference is correlated to its ability to hydrolyze GTP more efficiently than ATP, as found with PatA/PatB reconstituted in proteoliposomes or nanodiscs. Importantly, the ATP and GTP concentrations are similar in S. pneumoniae supporting the physiological relevance of GTP as the energy source of this bacterial transporter.
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Affiliation(s)
- Cédric Orelle
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 7 Passage du Vercors, F-69367, Lyon, France
| | - Claire Durmort
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38044, Grenoble, France.
| | - Khadija Mathieu
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 7 Passage du Vercors, F-69367, Lyon, France
| | - Benjamin Duchêne
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38044, Grenoble, France
| | - Sandrine Aros
- CEA, Institut Joliot, Service de Pharmacologie et d'Immunoanalyse, UMR 0496, Laboratoire d'Etude du Métabolisme des Médicaments, MetaboHUB-Paris, Université Paris Saclay, F-91191, Gif-sur-Yvette cedex, France
| | - François Fenaille
- CEA, Institut Joliot, Service de Pharmacologie et d'Immunoanalyse, UMR 0496, Laboratoire d'Etude du Métabolisme des Médicaments, MetaboHUB-Paris, Université Paris Saclay, F-91191, Gif-sur-Yvette cedex, France
| | - François André
- Laboratoire Stress Oxydant et Détoxication (LSOD), Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, F-91198, Gif-sur-Yvette cedex, France
| | - Christophe Junot
- CEA, Institut Joliot, Service de Pharmacologie et d'Immunoanalyse, UMR 0496, Laboratoire d'Etude du Métabolisme des Médicaments, MetaboHUB-Paris, Université Paris Saclay, F-91191, Gif-sur-Yvette cedex, France
| | - Thierry Vernet
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38044, Grenoble, France
| | - Jean-Michel Jault
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 7 Passage du Vercors, F-69367, Lyon, France.
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11
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Aduri NG, Ernst HA, Prabhala BK, Bhatt S, Boesen T, Gajhede M, Mirza O. Human proton coupled folic acid transporter is a monodisperse oligomer in the lauryl maltose neopentyl glycol solubilized state. Biochem Biophys Res Commun 2017; 495:1738-1743. [PMID: 29208467 DOI: 10.1016/j.bbrc.2017.12.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 12/01/2017] [Indexed: 01/23/2023]
Abstract
The human proton coupled folic acid transporter PCFT is the major import route for dietary folates. Mutations in the gene encoding PCFT cause hereditary folic acid malabsorption, which manifests itself by compromised folate absorption from the intestine and also in impaired folate transport into the central nervous system. Since its recent discovery, PCFT has been the subject of numerous biochemical studies aiming at understanding its structure and mechanism. One major focus has been its oligomeric state, with some reports supporting oligomers and others a monomer. Here, we report the overexpression and purification of recombinant PCFT. Following detergent screening, n-Dodecyl β-D-maltoside (DDM) and lauryl maltose neopentyl glycol (LMNG) were chosen for further work as they exhibited the most optimal solubilization. We found that purified detergent solubilized PCFT was able to bind folic acid, thus indicating a functionally active protein. Size exclusion chromatography showed that PCFT in DDM was polydisperse; the LMNG preparation was clearly monodisperse but with shorter retention time than the major DDM peak. To assess the oligomeric state negative stain electron microscopy was performed which showed a particle with the size of a PCFT dimer.
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Affiliation(s)
- Nanda G Aduri
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Heidi A Ernst
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bala K Prabhala
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Shweta Bhatt
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Boesen
- Interdisciplinary Nanoscience Center, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark
| | - Michael Gajhede
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Osman Mirza
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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12
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Abeyrathne PD, Grigorieff N. Expression, purification, and contaminant detection for structural studies of Ralstonia metallidurance ClC protein rm1. PLoS One 2017; 12:e0180163. [PMID: 28692650 PMCID: PMC5503242 DOI: 10.1371/journal.pone.0180163] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/09/2017] [Indexed: 11/19/2022] Open
Abstract
Single-particle electron cryo-microscopy (cryo-EM) has become a popular method for high-resolution study of the structural and functional properties of proteins. However, sufficient expression and purification of membrane proteins holds many challenges. We describe methods to overcome these obstacles using ClC-rm1, a prokaryotic chloride channel (ClC) family protein from Ralstonia metallidurans, overexpressed in Escherichia coli (E. coli) BL21(DE3) strain. Mass spectrometry and electron microscopy analyses of purified samples revealed multiple contaminants that can obfuscate results of subsequent high-resolution structural analysis. Here we describe the systematic optimization of sample preparation procedures, including expression systems, solubilization techniques, purification protocols, and contamination detection. We found that expressing ClC-rm1 in E. coli BL21(DE3) and using n-dodecyl-β-D-maltopyranoside as a detergent for solubilization and purification steps resulted in the highest quality samples of those we tested. However, although protein yield, sample stability, and the resolution of structural detail were improved following these changes, we still detected contaminants including Acriflavine resistant protein AcrB. AcrB was particularly difficult to remove as it co-purified with ClC-rm1 due to four intrinsic histidine residues at its C-terminus that bind to affinity resins. We were able to obtain properly folded pure ClC-rm1 by adding eGFP to the C-terminus and overexpressing the protein in the ΔacrB variant of the JW0451-2 E. coli strain.
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Affiliation(s)
- Priyanka D. Abeyrathne
- Howard Hughes Medical Institute, Janelia Research Campus, Helix Drive, Ashburn, VA, United States of America
| | - Nikolaus Grigorieff
- Howard Hughes Medical Institute, Janelia Research Campus, Helix Drive, Ashburn, VA, United States of America
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13
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Quantification of Detergents Complexed with Membrane Proteins. Sci Rep 2017; 7:41751. [PMID: 28176812 PMCID: PMC5297245 DOI: 10.1038/srep41751] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 12/23/2016] [Indexed: 01/20/2023] Open
Abstract
Most membrane proteins studies require the use of detergents, but because of the lack of a general, accurate and rapid method to quantify them, many uncertainties remain that hamper proper functional and structural data analyses. To solve this problem, we propose a method based on matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS) that allows quantification of pure or mixed detergents in complex with membrane proteins. We validated the method with a wide variety of detergents and membrane proteins. We automated the process, thereby allowing routine quantification for a broad spectrum of usage. As a first illustration, we show how to obtain information of the amount of detergent in complex with a membrane protein, essential for liposome or nanodiscs reconstitutions. Thanks to the method, we also show how to reliably and easily estimate the detergent corona diameter and select the smallest size, critical for favoring protein-protein contacts and triggering/promoting membrane protein crystallization, and to visualize the detergent belt for Cryo-EM studies.
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14
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Overexpression, Membrane Preparation, and Purification of a Typical Multidrug ABC Transporter BmrA. Methods Mol Biol 2016. [PMID: 27485334 DOI: 10.1007/978-1-4939-3637-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The production and purification is normally the first step in any biophysical or biochemical study of a new target protein. For membrane proteins, due to their generally low expression levels and hydrophobic properties this is often a major hurdle. Some multidrug transporters are members of one of the largest families of membrane proteins, the ABC ("ATP-binding cassette"), and are responsible for the uptake and export of a wide variety of molecules. This can lead to resistance when those molecules are antibiotics or chemotherapy drugs. To better understand their role in multidrug resistance pure and active protein is required. Here we outline a protocol to produce a highly pure and functionally active multidrug transporter BmrA that is suitable for use in biophysical and biochemical studies. We show that BmrA can be heterologously overexpressed in huge amount in E. coli and extracted from the membrane in a functionally active form.
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15
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Detergents in Membrane Protein Purification and Crystallisation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 922:13-28. [PMID: 27553232 DOI: 10.1007/978-3-319-35072-1_2] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Detergents play a significant role in structural and functional characterisation of integral membrane proteins (IMPs). IMPs reside in the biological membranes and exhibit a great variation in their structural and physical properties. For in vitro biophysical studies, structural and functional analyses, IMPs need to be extracted from the membrane lipid bilayer environment in which they are found and purified to homogeneity while maintaining a folded and functionally active state. Detergents are capable of successfully solubilising and extracting the IMPs from the membrane bilayers. A number of detergents with varying structure and physicochemical properties are commercially available and can be applied for this purpose. Nevertheless, it is important to choose a detergent that is not only able to extract the membrane protein but also provide an optimal environment while retaining the correct structural and physical properties of the protein molecule. Choosing the best detergent for this task can be made possible by understanding the physical and chemical properties of the different detergents and their interaction with the IMPs. In addition, understanding the mechanism of membrane solubilisation and protein extraction along with crystallisation requirements, if crystallographic studies are going to be undertaken, can help in choosing the best detergent for the purpose. This chapter aims to present the fundamental properties of detergents and highlight information relevant to IMP crystallisation. The first section of the chapter reviews the physicochemical properties of detergents and parameters essential for predicting their behaviour in solution. The second section covers the interaction of detergents with the biologic membranes and proteins followed by their role in membrane protein crystallisation. The last section will briefly cover the types of detergent and their properties focusing on custom designed detergents for membrane protein studies.
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16
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Chaptal V, Kilburg A, Flot D, Wiseman B, Aghajari N, Jault JM, Falson P. Two different centered monoclinic crystals of the E. coli outer-membrane protein OmpF originate from the same building block. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:326-32. [PMID: 26620074 DOI: 10.1016/j.bbamem.2015.11.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 11/17/2015] [Accepted: 11/21/2015] [Indexed: 11/17/2022]
Abstract
Macromolecule crystal formation can be divided in two major steps: 1. the formation of a nucleus and 2. the growth of this nucleus into a full mature crystal. The latter is well described and understood, while the former remains elusive due to the difficulty to study it and is described by nucleation theories. Here we report the structure of the Escherichia coli outer membrane porin OmpF in two centered monoclinic space groups. Strikingly, the two crystals originate from the same building block, made of two trimers of OmpF interacting via their rough side. The different crystallization conditions trigger the formation of distinct arrangement of these building blocks, leading to the formation of translational non-crystallographic symmetry (tNCS) in one case, made possible by the loose lateral packing mediated by detergents. In light of nucleation theories, these results allow us to speculate that these two crystals originate from nuclei made of either clusters of building blocks, or already forming columns that later associate laterally using detergents as glue.
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Affiliation(s)
- Vincent Chaptal
- Drug Resistance Mechanism and Modulation team, Institut de Biologie et Chimie des Protéines (IBCP), UMR5086 CNRS/Université Lyon 1, 7 passage du Vercors, F-69367 Lyon, France.
| | - Arnaud Kilburg
- Drug Resistance Mechanism and Modulation team, Institut de Biologie et Chimie des Protéines (IBCP), UMR5086 CNRS/Université Lyon 1, 7 passage du Vercors, F-69367 Lyon, France
| | - David Flot
- ESRF - The European Synchrotron 71, Avenue des Martyrs Grenoble, France
| | - Benjamin Wiseman
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), 6 rue Jules Horowitz, Grenoble, F-38027 cedex-1, France; CEA, DSV, IBS, F-38000 Grenoble, France; CNRS UMR 5075, IBS, F-38000 Grenoble, France
| | - Nushin Aghajari
- Biocrystallography and Structural Biology of Therapeutic Targets team, Institut de Biologie et Chimie des Protéines (IBCP), UMR5086 CNRS/Université Lyon 1, 7 passage du Vercors, F-69367 Lyon, France
| | - Jean-Michel Jault
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), 6 rue Jules Horowitz, Grenoble, F-38027 cedex-1, France; CEA, DSV, IBS, F-38000 Grenoble, France; CNRS UMR 5075, IBS, F-38000 Grenoble, France
| | - Pierre Falson
- Drug Resistance Mechanism and Modulation team, Institut de Biologie et Chimie des Protéines (IBCP), UMR5086 CNRS/Université Lyon 1, 7 passage du Vercors, F-69367 Lyon, France
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