1
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Flores-Ibarra A, Maia RNA, Olasz B, Church JR, Gotthard G, Schapiro I, Heberle J, Nogly P. Light-Oxygen-Voltage (LOV)-sensing Domains: Activation Mechanism and Optogenetic Stimulation. J Mol Biol 2024; 436:168356. [PMID: 37944792 DOI: 10.1016/j.jmb.2023.168356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 10/11/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023]
Abstract
The light-oxygen-voltage (LOV) domains of phototropins emerged as essential constituents of light-sensitive proteins, helping initiate blue light-triggered responses. Moreover, these domains have been identified across all kingdoms of life. LOV domains utilize flavin nucleotides as co-factors and undergo structural rearrangements upon exposure to blue light, which activates an effector domain that executes the final output of the photoreaction. LOV domains are versatile photoreceptors that play critical roles in cellular signaling and environmental adaptation; additionally, they can noninvasively sense and control intracellular processes with high spatiotemporal precision, making them ideal candidates for use in optogenetics, where a light signal is linked to a cellular process through a photoreceptor. The ongoing development of LOV-based optogenetic tools, driven by advances in structural biology, spectroscopy, computational methods, and synthetic biology, has the potential to revolutionize the study of biological systems and enable the development of novel therapeutic strategies.
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Affiliation(s)
- Andrea Flores-Ibarra
- Dioscuri Center for Structural Dynamics of Receptors, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Raiza N A Maia
- Department of Chemistry, The University of Texas at Austin, 78712-1224 Austin, TX, USA
| | - Bence Olasz
- Dioscuri Center for Structural Dynamics of Receptors, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Jonathan R Church
- Institute of Chemistry, The Hebrew University of Jerusalem, 91905 Jerusalem, Israel
| | | | - Igor Schapiro
- Institute of Chemistry, The Hebrew University of Jerusalem, 91905 Jerusalem, Israel
| | - Joachim Heberle
- Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Przemyslaw Nogly
- Dioscuri Center for Structural Dynamics of Receptors, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland.
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2
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Gruhl T, Weinert T, Rodrigues MJ, Milne CJ, Ortolani G, Nass K, Nango E, Sen S, Johnson PJM, Cirelli C, Furrer A, Mous S, Skopintsev P, James D, Dworkowski F, Båth P, Kekilli D, Ozerov D, Tanaka R, Glover H, Bacellar C, Brünle S, Casadei CM, Diethelm AD, Gashi D, Gotthard G, Guixà-González R, Joti Y, Kabanova V, Knopp G, Lesca E, Ma P, Martiel I, Mühle J, Owada S, Pamula F, Sarabi D, Tejero O, Tsai CJ, Varma N, Wach A, Boutet S, Tono K, Nogly P, Deupi X, Iwata S, Neutze R, Standfuss J, Schertler G, Panneels V. Ultrafast structural changes direct the first molecular events of vision. Nature 2023; 615:939-944. [PMID: 36949205 PMCID: PMC10060157 DOI: 10.1038/s41586-023-05863-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 02/17/2023] [Indexed: 03/24/2023]
Abstract
Vision is initiated by the rhodopsin family of light-sensitive G protein-coupled receptors (GPCRs)1. A photon is absorbed by the 11-cis retinal chromophore of rhodopsin, which isomerizes within 200 femtoseconds to the all-trans conformation2, thereby initiating the cellular signal transduction processes that ultimately lead to vision. However, the intramolecular mechanism by which the photoactivated retinal induces the activation events inside rhodopsin remains experimentally unclear. Here we use ultrafast time-resolved crystallography at room temperature3 to determine how an isomerized twisted all-trans retinal stores the photon energy that is required to initiate the protein conformational changes associated with the formation of the G protein-binding signalling state. The distorted retinal at a 1-ps time delay after photoactivation has pulled away from half of its numerous interactions with its binding pocket, and the excess of the photon energy is released through an anisotropic protein breathing motion in the direction of the extracellular space. Notably, the very early structural motions in the protein side chains of rhodopsin appear in regions that are involved in later stages of the conserved class A GPCR activation mechanism. Our study sheds light on the earliest stages of vision in vertebrates and points to fundamental aspects of the molecular mechanisms of agonist-mediated GPCR activation.
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Affiliation(s)
- Thomas Gruhl
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Tobias Weinert
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Matthew J Rodrigues
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Christopher J Milne
- Photon Science Division, Laboratory for Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
- European XFEL, Schenefeld, Germany
| | - Giorgia Ortolani
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Karol Nass
- Photon Science Division, Laboratory for Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Eriko Nango
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Japan
- RIKEN SPring-8 Center, Hyogo, Japan
| | - Saumik Sen
- Condensed Matter Theory Group, Laboratory for Theoretical and Computational Physics, Division of Scientific Computing, Theory and Data, Paul Scherrer Institute, Villigen PSI, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Philip J M Johnson
- Photon Science Division, Laboratory for Nonlinear Optics, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Claudio Cirelli
- Photon Science Division, Laboratory for Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Antonia Furrer
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- Biologics Center, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Sandra Mous
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Petr Skopintsev
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Daniel James
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- Department of Physics, Utah Valley University, Orem, UT, USA
| | - Florian Dworkowski
- Photon Science Division, Laboratory for Macromolecules and Bioimaging, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Petra Båth
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Demet Kekilli
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Dmitry Ozerov
- Division Scientific Computing, Theory and Data, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Rie Tanaka
- RIKEN SPring-8 Center, Hyogo, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hannah Glover
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Camila Bacellar
- Photon Science Division, Laboratory for Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Steffen Brünle
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | | | - Azeglio D Diethelm
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Dardan Gashi
- Photon Science Division, Laboratory for Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Guillaume Gotthard
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Ramon Guixà-González
- Condensed Matter Theory Group, Laboratory for Theoretical and Computational Physics, Division of Scientific Computing, Theory and Data, Paul Scherrer Institute, Villigen PSI, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Yasumasa Joti
- Japan Synchrotron Radiation Research Institute, Hyogo, Japan
| | - Victoria Kabanova
- Photon Science Division, Laboratory for Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
- Laboratory for Ultrafast X-ray Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Gregor Knopp
- Photon Science Division, Laboratory for Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Elena Lesca
- Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Pikyee Ma
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Isabelle Martiel
- Photon Science Division, Laboratory for Macromolecules and Bioimaging, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Jonas Mühle
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Shigeki Owada
- RIKEN SPring-8 Center, Hyogo, Japan
- Japan Synchrotron Radiation Research Institute, Hyogo, Japan
| | - Filip Pamula
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Daniel Sarabi
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Oliver Tejero
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Ching-Ju Tsai
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Niranjan Varma
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Anna Wach
- Institute of Nuclear Physics Polish Academy of Sciences, Kraców, Poland
- Operando X-ray Spectroscopy, Energy and Environment Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, Hyogo, Japan
| | - Przemyslaw Nogly
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
- Dioscuri Center For Structural Dynamics of Receptors, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Kraków, Poland
| | - Xavier Deupi
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- Condensed Matter Theory Group, Laboratory for Theoretical and Computational Physics, Division of Scientific Computing, Theory and Data, Paul Scherrer Institute, Villigen PSI, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - So Iwata
- RIKEN SPring-8 Center, Hyogo, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Jörg Standfuss
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Gebhard Schertler
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland.
- Department of Biology, ETH Zurich, Zurich, Switzerland.
| | - Valerie Panneels
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland.
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3
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Aumonier S, Engilberge S, Caramello N, von Stetten D, Gotthard G, Leonard GA, Mueller-Dieckmann C, Royant A. Slow protein dynamics probed by time-resolved oscillation crystallography at room temperature. IUCrJ 2022; 9:756-767. [PMID: 36381146 PMCID: PMC9634615 DOI: 10.1107/s2052252522009150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/14/2022] [Indexed: 05/23/2023]
Abstract
The development of serial crystallography over the last decade at XFELs and synchrotrons has produced a renaissance in room-temperature macromolecular crystallography (RT-MX), and fostered many technical and methodological breakthroughs designed to study phenomena occurring in proteins on the picosecond-to-second timescale. However, there are components of protein dynamics that occur in much slower regimes, of which the study could readily benefit from state-of-the-art RT-MX. Here, the room-temperature structural study of the relaxation of a reaction intermediate at a synchrotron, exploiting a handful of single crystals, is described. The intermediate in question is formed in microseconds during the photoreaction of the LOV2 domain of phototropin 2 from Arabidopsis thaliana, which then decays in minutes. This work monitored its relaxation in the dark using a fast-readout EIGER X 4M detector to record several complete oscillation X-ray diffraction datasets, each of 1.2 s total exposure time, at different time points in the relaxation process. Coupled with in crystallo UV-Vis absorption spectroscopy, this RT-MX approach allowed the authors to follow the relaxation of the photoadduct, a thio-ether covalent bond between the chromophore and a cysteine residue. Unexpectedly, the return of the chromophore to its spectroscopic ground state is followed by medium-scale protein rearrangements that trigger a crystal phase transition and hinder the full recovery of the structural ground state of the protein. In addition to suggesting a hitherto unexpected role of a conserved tryptophan residue in the regulation of the photocycle of LOV2, this work provides a basis for performing routine time-resolved protein crystallography experiments at synchrotrons for phenomena occurring on the second-to-hour timescale.
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Affiliation(s)
- Sylvain Aumonier
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs CS 40220, Grenoble 38043, France
| | - Sylvain Engilberge
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs CS 40220, Grenoble 38043, France
| | - Nicolas Caramello
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs CS 40220, Grenoble 38043, France
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - David von Stetten
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs CS 40220, Grenoble 38043, France
| | - Guillaume Gotthard
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs CS 40220, Grenoble 38043, France
| | - Gordon A. Leonard
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs CS 40220, Grenoble 38043, France
| | - Christoph Mueller-Dieckmann
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs CS 40220, Grenoble 38043, France
| | - Antoine Royant
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs CS 40220, Grenoble 38043, France
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71 avenue des Martyrs, Grenoble 38044, France
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4
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Caramello N, Engilberge S, Aumonier S, Von Stetten D, Gotthard G, Leonard G, Mueller-Dieckmann C, Royant A. Protein dynamics probed by time-resolved crystallography on the second to hour time scale. Acta Cryst Sect A 2022. [DOI: 10.1107/s2053273322093639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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5
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Mous S, Gotthard G, Ehrenberg D, Sen S, Weinert T, Johnson PJM, James D, Nass K, Furrer A, Kekilli D, Ma P, Brünle S, Casadei CM, Martiel I, Dworkowski F, Gashi D, Skopintsev P, Wranik M, Knopp G, Panepucci E, Panneels V, Cirelli C, Ozerov D, Schertler GFX, Wang M, Milne C, Standfuss J, Schapiro I, Heberle J, Nogly P. Dynamics and mechanism of a light-driven chloride pump. Science 2022; 375:845-851. [PMID: 35113649 DOI: 10.1126/science.abj6663] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Chloride transport by microbial rhodopsins is an essential process for which molecular details such as the mechanisms that convert light energy to drive ion pumping and ensure the unidirectionality of the transport have remained elusive. We combined time-resolved serial crystallography with time-resolved spectroscopy and multiscale simulations to elucidate the molecular mechanism of a chloride-pumping rhodopsin and the structural dynamics throughout the transport cycle. We traced transient anion-binding sites, obtained evidence for how light energy is used in the pumping mechanism, and identified steric and electrostatic molecular gates ensuring unidirectional transport. An interaction with the π-electron system of the retinal supports transient chloride ion binding across a major bottleneck in the transport pathway. These results allow us to propose key mechanistic features enabling finely controlled chloride transport across the cell membrane in this light-powered chloride ion pump.
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Affiliation(s)
- Sandra Mous
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Guillaume Gotthard
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Zürich, Switzerland.,Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - David Ehrenberg
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Berlin, Germany
| | - Saumik Sen
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tobias Weinert
- Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Philip J M Johnson
- Laboratory of Nonlinear Optics, Photon Science Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Daniel James
- Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Karol Nass
- Laboratory of Femtochemistry, Photon Science Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Antonia Furrer
- Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Demet Kekilli
- Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Pikyee Ma
- Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Steffen Brünle
- Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Cecilia Maria Casadei
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Zürich, Switzerland.,Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Isabelle Martiel
- Laboratory for Macromolecules and Bioimaging, Photon Science Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Florian Dworkowski
- Laboratory for Macromolecules and Bioimaging, Photon Science Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Dardan Gashi
- Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland.,Laboratory of Femtochemistry, Photon Science Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Petr Skopintsev
- Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Maximilian Wranik
- Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Gregor Knopp
- Laboratory of Femtochemistry, Photon Science Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Ezequiel Panepucci
- Laboratory for Macromolecules and Bioimaging, Photon Science Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Valerie Panneels
- Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Claudio Cirelli
- Laboratory of Femtochemistry, Photon Science Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Dmitry Ozerov
- Science IT, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Gebhard F X Schertler
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Zürich, Switzerland.,Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Meitian Wang
- Laboratory for Macromolecules and Bioimaging, Photon Science Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Chris Milne
- Laboratory of Femtochemistry, Photon Science Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Joerg Standfuss
- Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Joachim Heberle
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Berlin, Germany
| | - Przemyslaw Nogly
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Zürich, Switzerland
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6
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Lafaye C, Aumonier S, Torra J, Signor L, von Stetten D, Noirclerc-Savoye M, Shu X, Ruiz-González R, Gotthard G, Royant A, Nonell S. Riboflavin-binding proteins for singlet oxygen production. Photochem Photobiol Sci 2022; 21:1545-1555. [PMID: 35041199 DOI: 10.1007/s43630-021-00156-1] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 12/07/2021] [Indexed: 12/27/2022]
Abstract
miniSOG, developed as the first fully genetically encoded singlet oxygen photosensitiser, has found various applications in cell imaging and functional studies. Yet, miniSOG has suboptimal properties, including a low yield of singlet oxygen generation, which can nevertheless be improved tenfold upon blue light irradiation. In a previous study, we showed that this improvement was due to the photolysis of the miniSOG chromophore, flavin mononucleotide (FMN), into lumichrome, with concomitant removal of the phosphoribityl tail, thereby improving oxygen access to the alloxazine ring. We thus reasoned that a chromophore with a shorter tail would readily improve the photosensitizing properties of miniSOG. In this work, we show that the replacement of FMN by riboflavin (RF), which lacks the bulky phosphate group, significantly improves the singlet oxygen quantum yield (ΦΔ). We then proceeded to mutagenize the residues stabilizing the phosphate group of FMN to alter the chromophore specificity. We identified miniSOG-R57Q as a flavoprotein that selectively binds RF in cellulo, with a modestly improved ΦΔ. Our results show that it is possible to modify the flavin specificity of a given flavoprotein, thus providing a new option to tune its photophysical properties, including those leading to photosensitization. We also determined the structure of miniSOG-Q103L, a mutant with a much increased ΦΔ, which allowed us to postulate the existence of another access channel to FMN for molecular oxygen.
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Affiliation(s)
- Céline Lafaye
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, 38044, Grenoble Cedex 9, France
| | - Sylvain Aumonier
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38043, Grenoble Cedex 9, France
| | - Joaquim Torra
- Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017, Barcelona, Spain
| | - Luca Signor
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, 38044, Grenoble Cedex 9, France
| | - David von Stetten
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38043, Grenoble Cedex 9, France
| | - Marjolaine Noirclerc-Savoye
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, 38044, Grenoble Cedex 9, France
| | - Xiaokun Shu
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, CA, 94158-9001, USA.,Cardiovascular Research Institute, University of California-San Francisco, San Francisco, CA, 94158-9001, USA
| | - Rubén Ruiz-González
- Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017, Barcelona, Spain
| | - Guillaume Gotthard
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38043, Grenoble Cedex 9, France
| | - Antoine Royant
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, 38044, Grenoble Cedex 9, France. .,European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38043, Grenoble Cedex 9, France.
| | - Santi Nonell
- Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017, Barcelona, Spain.
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7
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Wilhelm J, Kühn S, Tarnawski M, Gotthard G, Tünnermann J, Tänzer T, Karpenko J, Mertes N, Xue L, Uhrig U, Reinstein J, Hiblot J, Johnsson K. Kinetic and Structural Characterization of the Self-Labeling Protein Tags HaloTag7, SNAP-tag, and CLIP-tag. Biochemistry 2021; 60:2560-2575. [PMID: 34339177 PMCID: PMC8388125 DOI: 10.1021/acs.biochem.1c00258] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/23/2021] [Indexed: 01/16/2023]
Abstract
The self-labeling protein tags (SLPs) HaloTag7, SNAP-tag, and CLIP-tag allow the covalent labeling of fusion proteins with synthetic molecules for applications in bioimaging and biotechnology. To guide the selection of an SLP-substrate pair and provide guidelines for the design of substrates, we report a systematic and comparative study of the labeling kinetics and substrate specificities of HaloTag7, SNAP-tag, and CLIP-tag. HaloTag7 reaches almost diffusion-limited labeling rate constants with certain rhodamine substrates, which are more than 2 orders of magnitude higher than those of SNAP-tag for the corresponding substrates. SNAP-tag labeling rate constants, however, are less affected by the structure of the label than those of HaloTag7, which vary over 6 orders of magnitude for commonly employed substrates. Determining the crystal structures of HaloTag7 and SNAP-tag labeled with fluorescent substrates allowed us to rationalize their substrate preferences. We also demonstrate how these insights can be exploited to design substrates with improved labeling kinetics.
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Affiliation(s)
- Jonas Wilhelm
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
| | - Stefanie Kühn
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
| | - Miroslaw Tarnawski
- Protein
Expression and Characterization Facility, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Guillaume Gotthard
- Structural
Biology Group, European Synchrotron Radiation
Facility (ESRF), 38043 Grenoble, France
| | - Jana Tünnermann
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
| | - Timo Tänzer
- Institute
of Chemical Sciences and Engineering, École
Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Julie Karpenko
- Institute
of Chemical Sciences and Engineering, École
Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Nicole Mertes
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
| | - Lin Xue
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
| | - Ulrike Uhrig
- Chemical
Biology Core Facility, European Molecular
Biology Laboratory, 69117 Heidelberg, Germany
| | - Jochen Reinstein
- Department
of Biomolecular Mechanisms, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
| | - Julien Hiblot
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
- Institute
of Chemical Sciences and Engineering, École
Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Kai Johnsson
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
- Institute
of Chemical Sciences and Engineering, École
Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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8
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Sorigué D, Hadjidemetriou K, Blangy S, Gotthard G, Legrand P, Nurizzo D, Royant A, Berthomieu C, Weik M, Domratcheva T, Brettel K, Vos MH, Schlichting I, Müller P, Beisson F, Arnoux P. High-resolution structure and reaction cycle of fatty acid photodecarboxylase: anatomy of a crime scene. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321094356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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9
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Sorigué D, Hadjidemetriou K, Blangy S, Gotthard G, Bonvalet A, Coquelle N, Samire P, Aleksandrov A, Antonucci L, Benachir A, Boutet S, Byrdin M, Cammarata M, Carbajo S, Cuiné S, Doak RB, Foucar L, Gorel A, Grünbein M, Hartmann E, Hienerwadel R, Hilpert M, Kloos M, Lane TJ, Légeret B, Legrand P, Li-Beisson Y, Moulin SLY, Nurizzo D, Peltier G, Schirò G, Shoeman RL, Sliwa M, Solinas X, Zhuang B, Barends TRM, Colletier JP, Joffre M, Royant A, Berthomieu C, Weik M, Domratcheva T, Brettel K, Vos MH, Schlichting I, Arnoux P, Müller P, Beisson F. Mechanism and dynamics of fatty acid photodecarboxylase. Science 2021; 372:372/6538/eabd5687. [PMID: 33833098 DOI: 10.1126/science.abd5687] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 02/17/2021] [Indexed: 12/21/2022]
Abstract
Fatty acid photodecarboxylase (FAP) is a photoenzyme with potential green chemistry applications. By combining static, time-resolved, and cryotrapping spectroscopy and crystallography as well as computation, we characterized Chlorella variabilis FAP reaction intermediates on time scales from subpicoseconds to milliseconds. High-resolution crystal structures from synchrotron and free electron laser x-ray sources highlighted an unusual bent shape of the oxidized flavin chromophore. We demonstrate that decarboxylation occurs directly upon reduction of the excited flavin by the fatty acid substrate. Along with flavin reoxidation by the alkyl radical intermediate, a major fraction of the cleaved carbon dioxide unexpectedly transformed in 100 nanoseconds, most likely into bicarbonate. This reaction is orders of magnitude faster than in solution. Two strictly conserved residues, R451 and C432, are essential for substrate stabilization and functional charge transfer.
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Affiliation(s)
- D Sorigué
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - K Hadjidemetriou
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, 38000 Grenoble, France
| | - S Blangy
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - G Gotthard
- European Synchrotron Radiation Facility, 38043 Grenoble, France
| | - A Bonvalet
- LOB, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - N Coquelle
- Large-Scale Structures Group, Institut Laue Langevin, 38042 Grenoble Cedex 9, France
| | - P Samire
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France.,Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - A Aleksandrov
- LOB, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - L Antonucci
- LOB, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - A Benachir
- LOB, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - S Boutet
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - M Byrdin
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, 38000 Grenoble, France
| | - M Cammarata
- Department of Physics, UMR UR1-CNRS 6251, University of Rennes 1, F-Rennes, France.
| | - S Carbajo
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - S Cuiné
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - R B Doak
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - L Foucar
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - A Gorel
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - M Grünbein
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - E Hartmann
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - R Hienerwadel
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - M Hilpert
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - M Kloos
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany.
| | - T J Lane
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - B Légeret
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - P Legrand
- Synchrotron SOLEIL. L'Orme des Merisiers Saint-Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - Y Li-Beisson
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - S L Y Moulin
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - D Nurizzo
- European Synchrotron Radiation Facility, 38043 Grenoble, France
| | - G Peltier
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - G Schirò
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, 38000 Grenoble, France
| | - R L Shoeman
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - M Sliwa
- Univ. Lille, CNRS, UMR 8516, LASIRE, LAboratoire de Spectroscopie pour les Interactions, la Réactivité et l'Environnement, 59000 Lille, France
| | - X Solinas
- LOB, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - B Zhuang
- LOB, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France.,Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - T R M Barends
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - J-P Colletier
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, 38000 Grenoble, France
| | - M Joffre
- LOB, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - A Royant
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, 38000 Grenoble, France.,European Synchrotron Radiation Facility, 38043 Grenoble, France
| | - C Berthomieu
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France.
| | - M Weik
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, 38000 Grenoble, France.
| | - T Domratcheva
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany. .,Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - K Brettel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - M H Vos
- LOB, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France.
| | - I Schlichting
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany.
| | - P Arnoux
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France.
| | - P Müller
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - F Beisson
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France.
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10
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Lambert GG, Depernet H, Gotthard G, Schultz DT, Navizet I, Lambert T, Adams SR, Torreblanca-Zanca A, Chu M, Bindels DS, Levesque V, Nero Moffatt J, Salih A, Royant A, Shaner NC. Aequorea's secrets revealed: New fluorescent proteins with unique properties for bioimaging and biosensing. PLoS Biol 2020; 18:e3000936. [PMID: 33137097 PMCID: PMC7660908 DOI: 10.1371/journal.pbio.3000936] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/12/2020] [Accepted: 10/15/2020] [Indexed: 11/21/2022] Open
Abstract
Using mRNA sequencing and de novo transcriptome assembly, we identified, cloned, and characterized 9 previously undiscovered fluorescent protein (FP) homologs from Aequorea victoria and a related Aequorea species, with most sequences highly divergent from A. victoria green fluorescent protein (avGFP). Among these FPs are the brightest green fluorescent protein (GFP) homolog yet characterized and a reversibly photochromic FP that responds to UV and blue light. Beyond green emitters, Aequorea species express purple- and blue-pigmented chromoproteins (CPs) with absorbances ranging from green to far-red, including 2 that are photoconvertible. X-ray crystallography revealed that Aequorea CPs contain a chemically novel chromophore with an unexpected crosslink to the main polypeptide chain. Because of the unique attributes of several of these newly discovered FPs, we expect that Aequorea will, once again, give rise to an entirely new generation of useful probes for bioimaging and biosensing.
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Affiliation(s)
- Gerard G. Lambert
- Department of Neurosciences, Center for Research in Biological Systems, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Hadrien Depernet
- Structural Biology Group, European Synchrotron Radiation Facility, Grenoble, France
| | - Guillaume Gotthard
- Structural Biology Group, European Synchrotron Radiation Facility, Grenoble, France
| | - Darrin T. Schultz
- University of California Santa Cruz, Santa Cruz, California, United States of America
- Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America
| | - Isabelle Navizet
- Laboratoire Modélisation et Simulation Multi-Echelle, Université Gustave Eiffel, Université Paris Est Creteil, Marne-la-Vallée, France
| | - Talley Lambert
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Stephen R. Adams
- Department of Pharmacology, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Albertina Torreblanca-Zanca
- Department of Neurosciences, Center for Research in Biological Systems, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Meihua Chu
- Department of Neurosciences, Center for Research in Biological Systems, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Daphne S. Bindels
- Nikon Imaging Center, University of California San Diego, La Jolla, California, United States of America
| | - Vincent Levesque
- Birch Aquarium at Scripps, La Jolla, California, United States of America
| | | | - Anya Salih
- Confocal Facility, Western Sydney University, Penrith, New South Wales, Australia
| | - Antoine Royant
- Structural Biology Group, European Synchrotron Radiation Facility, Grenoble, France
- Institut de Biologie Structurale, Université Grenoble Alpes, CNRS, CEA, Grenoble, France
| | - Nathan C. Shaner
- Department of Neurosciences, Center for Research in Biological Systems, University of California San Diego School of Medicine, La Jolla, California, United States of America
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11
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Aumonier S, Santoni G, Gotthard G, von Stetten D, Leonard GA, Royant A. Millisecond time-resolved serial oscillation crystallography of a blue-light photoreceptor at a synchrotron. IUCrJ 2020; 7:728-736. [PMID: 32695419 PMCID: PMC7340269 DOI: 10.1107/s2052252520007411] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 06/03/2020] [Indexed: 05/23/2023]
Abstract
The recent development of serial crystallography has popularized time-resolved crystallography as a technique to determine the structure of protein-reaction intermediate states. However, most approaches rely on the availability of thousands to millions of microcrystals. A method is reported here, using monochromatic synchrotron radiation, for the room-temperature collection, processing and merging of X-ray oscillation diffraction data from <100 samples in order to observe the build up of a photoreaction intermediate species. Using this method, we monitored with a time resolution of 63 ms how the population of a blue-light photoreceptor domain in a crystal progressively photoconverts from the dark to the light state. The series of resulting snapshots allows us to visualize in detail the gradual rearrangement of both the protein and chromophore during this process.
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Affiliation(s)
- Sylvain Aumonier
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble Cedex 9, 38043, France
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, 71 avenue des Martyrs, Grenoble Cedex 9, 38044, France
| | - Gianluca Santoni
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble Cedex 9, 38043, France
| | - Guillaume Gotthard
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble Cedex 9, 38043, France
| | - David von Stetten
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble Cedex 9, 38043, France
| | - Gordon A. Leonard
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble Cedex 9, 38043, France
| | - Antoine Royant
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble Cedex 9, 38043, France
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, 71 avenue des Martyrs, Grenoble Cedex 9, 38044, France
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12
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De Zitter E, Ridard J, Thédié D, Adam V, Lévy B, Byrdin M, Gotthard G, Van Meervelt L, Dedecker P, Demachy I, Bourgeois D. Mechanistic Investigations of Green mEos4b Reveal a Dynamic Long-Lived Dark State. J Am Chem Soc 2020; 142:10978-10988. [PMID: 32463688 DOI: 10.1021/jacs.0c01880] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Green-to-red photoconvertible fluorescent proteins (PCFPs) are key players in advanced microscopy schemes such as photoactivated localization microscopy (PALM). Whereas photoconversion and red-state blinking in PCFPs have been studied intensively, their green-state photophysical behavior has received less attention. Yet dark states in green PCFPs can become strongly populated in PALM schemes and exert an indirect but considerable influence on the quality of data recorded in the red channel. Furthermore, green-state photoswitching in PCFPs can be used directly for PALM and has been engineered to design highly efficient reversibly switchable fluorescent proteins (RSFPs) amenable to various nanoscopy schemes. Here, we demonstrate that green mEos4b efficiently switches to a long-lived dark state through cis-trans isomerization of its chromophore, as do most RSFPs. However, by combining kinetic crystallography, molecular dynamics simulations, and Raman spectroscopy, we find that the dark state in green mEos4b is much more dynamic than that seen in switched-off green IrisFP, a biphotochromic PCFP engineered from the common EosFP parent. Our data suggest that H-bonding patterns maintained by the chromophore in green PCFPs and RSFPs in both their on- and off-states collectively control photoswitching quantum yields. The reduced number of H-bonds maintained by the dynamic dark chromophore in green mEos4b thus largely accounts for the observed lower switching contrast as compared to that of IrisFP. We also compare the long-lived dark states reached from green and red mEos4b, on the basis of their X-ray structures and Raman signatures. Altogether, these data provide a unifying picture of the complex photophysics of PCFPs and RSFPs.
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Affiliation(s)
- Elke De Zitter
- Department of Chemistry, KU Leuven, Heverlee 3001, Belgium
| | - Jacqueline Ridard
- Institut de Chimie Physique UMR8000, Université Paris-Saclay, CNRS, Orsay 91405, France
| | - Daniel Thédié
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble 38044, France
| | - Virgile Adam
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble 38044, France
| | - Bernard Lévy
- Institut de Chimie Physique UMR8000, Université Paris-Saclay, CNRS, Orsay 91405, France
| | - Martin Byrdin
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble 38044, France
| | - Guillaume Gotthard
- Structural Biology Group, European Synchrotron Radiation Facility, Grenoble 38000, France
| | | | - Peter Dedecker
- Department of Chemistry, KU Leuven, Heverlee 3001, Belgium
| | - Isabelle Demachy
- Institut de Chimie Physique UMR8000, Université Paris-Saclay, CNRS, Orsay 91405, France
| | - Dominique Bourgeois
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble 38044, France
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13
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Gonzalez D, Rihani K, Neiers F, Poirier N, Fraichard S, Gotthard G, Chertemps T, Maïbèche M, Ferveur JF, Briand L. The Drosophila odorant-binding protein 28a is involved in the detection of the floral odour ß-ionone. Cell Mol Life Sci 2019; 77:2565-2577. [PMID: 31564000 DOI: 10.1007/s00018-019-03300-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 09/03/2019] [Accepted: 09/16/2019] [Indexed: 11/27/2022]
Abstract
Odorant-binding proteins (OBPs) are small soluble proteins that are thought to transport hydrophobic odorants across the aqueous sensillar lymph to olfactory receptors. A recent study revealed that OBP28a, one of the most abundant Drosophila OBPs, is not required for odorant transport, but acts in buffering rapid odour variation in the odorant environment. To further unravel and decipher its functional role, we expressed recombinant OBP28a and characterized its binding specificity. Using a fluorescent binding assay, we found that OBP28a binds a restricted number of floral-like chemicals, including ß-ionone, with an affinity in the micromolar range. We solved the X-ray crystal structure of OBP28a, which showed extensive conformation changes upon ligand binding. Mutant flies genetically deleted for the OBP28a gene showed altered responses to ß-ionone at a given concentration range, supporting its essential role in the detection of specific compounds present in the natural environment of the fly.
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Affiliation(s)
- Daniel Gonzalez
- AgroSup Dijon, CNRS, INRA, Université de Bourgogne-Franche Comté, Centre des Sciences du Goût et de l'Alimentation, 21000, Dijon, France
| | - Karen Rihani
- AgroSup Dijon, CNRS, INRA, Université de Bourgogne-Franche Comté, Centre des Sciences du Goût et de l'Alimentation, 21000, Dijon, France
| | - Fabrice Neiers
- AgroSup Dijon, CNRS, INRA, Université de Bourgogne-Franche Comté, Centre des Sciences du Goût et de l'Alimentation, 21000, Dijon, France
| | - Nicolas Poirier
- AgroSup Dijon, CNRS, INRA, Université de Bourgogne-Franche Comté, Centre des Sciences du Goût et de l'Alimentation, 21000, Dijon, France
| | - Stéphane Fraichard
- AgroSup Dijon, CNRS, INRA, Université de Bourgogne-Franche Comté, Centre des Sciences du Goût et de l'Alimentation, 21000, Dijon, France
| | | | - Thomas Chertemps
- Sorbonne Université, INRA, CNRS, IRD, UPEC, Institut d'Ecologie et des Sciences de l'Environnement de Paris, 75005, Paris, France
| | - Martine Maïbèche
- Sorbonne Université, INRA, CNRS, IRD, UPEC, Institut d'Ecologie et des Sciences de l'Environnement de Paris, 75005, Paris, France
| | - Jean-François Ferveur
- AgroSup Dijon, CNRS, INRA, Université de Bourgogne-Franche Comté, Centre des Sciences du Goût et de l'Alimentation, 21000, Dijon, France
| | - Loïc Briand
- AgroSup Dijon, CNRS, INRA, Université de Bourgogne-Franche Comté, Centre des Sciences du Goût et de l'Alimentation, 21000, Dijon, France.
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14
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Gotthard G, Aumonier S, De Sanctis D, Leonard G, von Stetten D, Royant A. Specific radiation damage is a lesser concern at room temperature. IUCrJ 2019; 6:665-680. [PMID: 31316810 PMCID: PMC6608634 DOI: 10.1107/s205225251900616x] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/02/2019] [Indexed: 05/22/2023]
Abstract
Carrying out macromolecular crystallography (MX) experiments at cryogenic temperatures significantly slows the rate of global radiation damage, thus facilitating the solution of high-resolution crystal structures of macromolecules. However, cryo-MX experiments suffer from the early onset of so-called specific radiation damage that affects certain amino-acid residues and, in particular, the active sites of many proteins. Here, a series of MX experiments are described which suggest that specific and global radiation damage are much less decoupled at room temperature than they are at cryogenic temperatures. The results reported here demonstrate the interest in reviving the practice of collecting MX diffraction data at room temperature and allow structural biologists to favourably envisage the development of time-resolved MX experiments at synchrotron sources.
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Affiliation(s)
| | - Sylvain Aumonier
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
| | | | - Gordon Leonard
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
| | | | - Antoine Royant
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
- Université Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale), F-38000 Grenoble, France
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15
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Gozzi GJ, Gonzalez D, Boudesco C, Dias AMM, Gotthard G, Uyanik B, Dondaine L, Marcion G, Hermetet F, Denis C, Hardy L, Suzanne P, Douhard R, Jego G, Dubrez L, Demidov ON, Neiers F, Briand L, Sopková-de Oliveira Santos J, Voisin-Chiret AS, Garrido C. Selecting the first chemical molecule inhibitor of HSP110 for colorectal cancer therapy. Cell Death Differ 2019; 27:117-129. [PMID: 31068676 DOI: 10.1038/s41418-019-0343-4] [Citation(s) in RCA: 20] [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: 10/25/2018] [Revised: 04/04/2019] [Accepted: 04/12/2019] [Indexed: 01/10/2023] Open
Abstract
Pro-survival stress-inducible chaperone HSP110 is the only HSP for which a mutation has been found in a cancer. Multicenter clinical studies demonstrated a direct association between HSP110 inactivating mutation presence and excellent prognosis in colorectal cancer patients. Here, we have combined crystallographic studies on human HSP110 and in silico modeling to identify HSP110 inhibitors that could be used in colorectal cancer therapy. Two molecules (foldamers 33 and 52), binding to the same cleft of HSP110 nucleotide-binding domain, were selected from a chemical library (by co-immunoprecipitation, AlphaScreening, Interference-Biolayer, Duo-link). These molecules block HSP110 chaperone anti-aggregation activity and HSP110 association to its client protein STAT3, thereby inhibiting STAT3 phosphorylation and colorectal cancer cell growth. These effects were strongly decreased in HSP110 knockdown cells. Foldamer's 33 ability to inhibit tumor growth was confirmed in two colorectal cancer animal models. Although tumor cell death (apoptosis) was noted after treatment of the animals with foldamer 33, no apparent toxicity was observed, notably in epithelial cells from intestinal crypts. Taken together, we identified the first HSP110 inhibitor, a possible drug-candidate for colorectal cancer patients whose unfavorable outcome is associated to HSP110.
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Affiliation(s)
- Gustavo J Gozzi
- INSERM UMR1231, Laboratory of Excellence LipSTIC and label Ligue Nationale contre le Cancer, Dijon, France.,University of Burgundy Franche-Comté, Dijon, France
| | - Daniel Gonzalez
- INSERM UMR1231, Laboratory of Excellence LipSTIC and label Ligue Nationale contre le Cancer, Dijon, France.,University of Burgundy Franche-Comté, Dijon, France
| | - Christophe Boudesco
- INSERM UMR1231, Laboratory of Excellence LipSTIC and label Ligue Nationale contre le Cancer, Dijon, France.,University of Burgundy Franche-Comté, Dijon, France
| | - Alexandre M M Dias
- INSERM UMR1231, Laboratory of Excellence LipSTIC and label Ligue Nationale contre le Cancer, Dijon, France.,University of Burgundy Franche-Comté, Dijon, France
| | | | - Burhan Uyanik
- INSERM UMR1231, Laboratory of Excellence LipSTIC and label Ligue Nationale contre le Cancer, Dijon, France.,University of Burgundy Franche-Comté, Dijon, France
| | - Lucile Dondaine
- INSERM UMR1231, Laboratory of Excellence LipSTIC and label Ligue Nationale contre le Cancer, Dijon, France.,University of Burgundy Franche-Comté, Dijon, France
| | - Guillaume Marcion
- INSERM UMR1231, Laboratory of Excellence LipSTIC and label Ligue Nationale contre le Cancer, Dijon, France.,University of Burgundy Franche-Comté, Dijon, France
| | - François Hermetet
- INSERM UMR1231, Laboratory of Excellence LipSTIC and label Ligue Nationale contre le Cancer, Dijon, France.,University of Burgundy Franche-Comté, Dijon, France
| | - Camille Denis
- Normandie Université, UNICAEN, EA 4258 CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie) - FR CNRS INC3M, Boulevard Becquerel, 14032, Caen, France
| | - Laurianne Hardy
- Normandie Université, UNICAEN, EA 4258 CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie) - FR CNRS INC3M, Boulevard Becquerel, 14032, Caen, France
| | - Peggy Suzanne
- Normandie Université, UNICAEN, EA 4258 CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie) - FR CNRS INC3M, Boulevard Becquerel, 14032, Caen, France
| | - Romain Douhard
- INSERM UMR1231, Laboratory of Excellence LipSTIC and label Ligue Nationale contre le Cancer, Dijon, France.,University of Burgundy Franche-Comté, Dijon, France
| | - Gaetan Jego
- INSERM UMR1231, Laboratory of Excellence LipSTIC and label Ligue Nationale contre le Cancer, Dijon, France.,University of Burgundy Franche-Comté, Dijon, France
| | - Laurence Dubrez
- INSERM UMR1231, Laboratory of Excellence LipSTIC and label Ligue Nationale contre le Cancer, Dijon, France.,University of Burgundy Franche-Comté, Dijon, France
| | - Oleg N Demidov
- INSERM UMR1231, Laboratory of Excellence LipSTIC and label Ligue Nationale contre le Cancer, Dijon, France.,University of Burgundy Franche-Comté, Dijon, France
| | - Fabrice Neiers
- University of Burgundy Franche-Comté, Dijon, France.,Centre des Sciences du Goût et de l'Alimentation, INRA, CNRS, Dijon, France
| | - Loïc Briand
- University of Burgundy Franche-Comté, Dijon, France.,Centre des Sciences du Goût et de l'Alimentation, INRA, CNRS, Dijon, France
| | - Jana Sopková-de Oliveira Santos
- Normandie Université, UNICAEN, EA 4258 CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie) - FR CNRS INC3M, Boulevard Becquerel, 14032, Caen, France
| | - Anne-Sophie Voisin-Chiret
- Normandie Université, UNICAEN, EA 4258 CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie) - FR CNRS INC3M, Boulevard Becquerel, 14032, Caen, France
| | - Carmen Garrido
- INSERM UMR1231, Laboratory of Excellence LipSTIC and label Ligue Nationale contre le Cancer, Dijon, France. .,University of Burgundy Franche-Comté, Dijon, France. .,Georges François Leclerc Center (CGFL), Dijon, France.
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16
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Golub M, Guillon V, Gotthard G, Zeller D, Martinez N, Seydel T, Koza MM, Lafaye C, Clavel D, von Stetten D, Royant A, Peters J. Dynamics of a family of cyan fluorescent proteins probed by incoherent neutron scattering. J R Soc Interface 2019; 16:20180848. [PMID: 30836899 DOI: 10.1098/rsif.2018.0848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Cyan fluorescent proteins (CFPs) are variants of green fluorescent proteins in which the central tyrosine of the chromophore has been replaced by a tryptophan. The increased bulk of the chromophore within a compact protein and the change in the positioning of atoms capable of hydrogen bonding have made it difficult to optimize their fluorescence properties, which took approximately 15 years between the availability of the first useable CFP, enhanced cyan fluorescent protein (ECFP), and that of a variant with almost perfect fluorescence efficiency, mTurquoise2. To understand the molecular bases of the progressive improvement in between these two CFPs, we have studied by incoherent neutron scattering the dynamics of five different variants exhibiting progressively increased fluorescence efficiency along the evolution pathway. Our results correlate well with the analysis of the previously determined X-ray crystallographic structures, which show an increase in flexibility between ECFP and the second variant, Cerulean, which is then hindered in the three later variants, SCFP3A (Super Cyan Fluorescent Protein 3A), mTurquoise and mTurquoise2. This confirms that increasing the rigidity of the direct environment of the fluorescent chromophore is not the sole parameter leading to brighter fluorescent proteins and that increased flexibility in some cases may be helpful.
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Affiliation(s)
- Maksym Golub
- 1 Institut Laue Langevin , 71 avenue des Martyrs, 38042 Grenoble Cedex 9 , France.,2 Univ. Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale) , 38000 Grenoble , France
| | - Virginia Guillon
- 2 Univ. Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale) , 38000 Grenoble , France
| | | | - Dominik Zeller
- 1 Institut Laue Langevin , 71 avenue des Martyrs, 38042 Grenoble Cedex 9 , France.,4 Laboratoire Interdisciplinaire de Physique, Univ. Grenoble Alpes, CNRS , 38000 Grenoble , France
| | - Nicolas Martinez
- 1 Institut Laue Langevin , 71 avenue des Martyrs, 38042 Grenoble Cedex 9 , France.,2 Univ. Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale) , 38000 Grenoble , France
| | - Tilo Seydel
- 1 Institut Laue Langevin , 71 avenue des Martyrs, 38042 Grenoble Cedex 9 , France
| | - Michael M Koza
- 1 Institut Laue Langevin , 71 avenue des Martyrs, 38042 Grenoble Cedex 9 , France
| | - Céline Lafaye
- 2 Univ. Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale) , 38000 Grenoble , France
| | - Damien Clavel
- 2 Univ. Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale) , 38000 Grenoble , France
| | | | - Antoine Royant
- 2 Univ. Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale) , 38000 Grenoble , France.,3 European Synchrotron Radiation Facility , 38043 Grenoble , France
| | - Judith Peters
- 1 Institut Laue Langevin , 71 avenue des Martyrs, 38042 Grenoble Cedex 9 , France.,4 Laboratoire Interdisciplinaire de Physique, Univ. Grenoble Alpes, CNRS , 38000 Grenoble , France
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17
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Hutin S, Santoni G, Zander U, Foos N, Aumonier S, Gotthard G, Royant A, Mueller-Dieckmann C, Leonard G. Structure Solution of the Fluorescent Protein Cerulean Using MeshAndCollect. J Vis Exp 2019. [PMID: 30958477 DOI: 10.3791/58594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
X-ray crystallography is the major technique used to obtain high resolution information concerning the 3-dimensional structures of biological macromolecules. Until recently, a major requirement has been the availability of relatively large, well diffracting crystals, which are often challenging to obtain. However, the advent of serial crystallography and a renaissance in multi-crystal data collection methods has meant that the availability of large crystals need no longer be a limiting factor. Here, we illustrate the use of the automated MeshAndCollect protocol, which first identifies the positions of many small crystals mounted on the same sample holder and then directs the collection from the crystals of a series of partial diffraction data sets for subsequent merging and use in structure determination. MeshAndCollect can be applied to any type of micro-crystals, even if weakly diffracting. As an example, we present here the use of the technique to solve the crystal structure of the Cyan Fluorescent Protein (CFP) Cerulean.
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Affiliation(s)
- Stephanie Hutin
- European Synchrotron Radiation Facility, Structural Biology Group;
| | - Gianluca Santoni
- European Synchrotron Radiation Facility, Structural Biology Group
| | | | - Nicolas Foos
- European Synchrotron Radiation Facility, Structural Biology Group
| | - Sylvain Aumonier
- European Synchrotron Radiation Facility, Structural Biology Group
| | | | - Antoine Royant
- European Synchrotron Radiation Facility, Structural Biology Group; Univ. Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale)
| | | | - Gordon Leonard
- European Synchrotron Radiation Facility, Structural Biology Group
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18
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Torra J, Lafaye C, Signor L, Aumonier S, Flors C, Shu X, Nonell S, Gotthard G, Royant A. Tailing miniSOG: structural bases of the complex photophysics of a flavin-binding singlet oxygen photosensitizing protein. Sci Rep 2019; 9:2428. [PMID: 30787421 PMCID: PMC6382843 DOI: 10.1038/s41598-019-38955-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [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: 08/02/2018] [Accepted: 01/11/2019] [Indexed: 11/15/2022] Open
Abstract
miniSOG is the first flavin-binding protein that has been developed with the specific aim of serving as a genetically-encodable light-induced source of singlet oxygen (1O2). We have determined its 1.17 Å resolution structure, which has allowed us to investigate its mechanism of photosensitization using an integrated approach combining spectroscopic and structural methods. Our results provide a structural framework to explain the ability of miniSOG to produce 1O2 as a competition between oxygen- and protein quenching of its triplet state. In addition, a third excited-state decay pathway has been identified that is pivotal for the performance of miniSOG as 1O2 photosensitizer, namely the photo-induced transformation of flavin mononucleotide (FMN) into lumichrome, which increases the accessibility of oxygen to the flavin FMN chromophore and makes protein quenching less favourable. The combination of the two effects explains the increase in the 1O2 quantum yield by one order of magnitude upon exposure to blue light. Besides, we have identified several surface electron-rich residues that are progressively photo-oxidized, further contributing to facilitate the production of 1O2. Our results help reconcile the apparent poor level of 1O2 generation by miniSOG and its excellent performance in correlative light and electron microscopy experiments.
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Affiliation(s)
- Joaquim Torra
- Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, Barcelona, 08017, Spain
| | - Céline Lafaye
- Univ. Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale), F-38000, Grenoble, France
| | - Luca Signor
- Univ. Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale), F-38000, Grenoble, France
| | - Sylvain Aumonier
- European Synchrotron Radiation Facility, F-38043, Grenoble, France
| | - Cristina Flors
- Madrid Institute for Advanced Studies in Nanoscience (IMDEA Nanoscience), Ciudad Universitaria de Cantoblanco, C/Faraday 9, 28049, Madrid, Spain.,Nanobiotechnology Unit Associated to the National Center for Biotechnology (CNB-CSIC-IMDEA), Ciudad Universitaria de Cantoblanco, 28049, Madrid, Spain
| | - Xiaokun Shu
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California, 94158-9001, United States.,Cardiovascular Research Institute, University of California-San Francisco, San Francisco, California, 94158-9001, United States
| | - Santi Nonell
- Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, Barcelona, 08017, Spain.
| | | | - Antoine Royant
- Univ. Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale), F-38000, Grenoble, France. .,European Synchrotron Radiation Facility, F-38043, Grenoble, France.
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19
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Kalms J, Schmidt A, Frielingsdorf S, Utesch T, Gotthard G, von Stetten D, van der Linden P, Royant A, Mroginski MA, Carpentier P, Lenz O, Scheerer P. Tracking the route of molecular oxygen in O 2-tolerant membrane-bound [NiFe] hydrogenase. Proc Natl Acad Sci U S A 2018; 115:E2229-E2237. [PMID: 29463722 PMCID: PMC5877991 DOI: 10.1073/pnas.1712267115] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
[NiFe] hydrogenases catalyze the reversible splitting of H2 into protons and electrons at a deeply buried active site. The catalytic center can be accessed by gas molecules through a hydrophobic tunnel network. While most [NiFe] hydrogenases are inactivated by O2, a small subgroup, including the membrane-bound [NiFe] hydrogenase (MBH) of Ralstonia eutropha, is able to overcome aerobic inactivation by catalytic reduction of O2 to water. This O2 tolerance relies on a special [4Fe3S] cluster that is capable of releasing two electrons upon O2 attack. Here, the O2 accessibility of the MBH gas tunnel network has been probed experimentally using a "soak-and-freeze" derivatization method, accompanied by protein X-ray crystallography and computational studies. This combined approach revealed several sites of O2 molecules within a hydrophobic tunnel network leading, via two tunnel entrances, to the catalytic center of MBH. The corresponding site occupancies were related to the O2 concentrations used for MBH crystal derivatization. The examination of the O2-derivatized data furthermore uncovered two unexpected structural alterations at the [4Fe3S] cluster, which might be related to the O2 tolerance of the enzyme.
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Affiliation(s)
- Jacqueline Kalms
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, D-10117 Berlin, Germany
| | - Andrea Schmidt
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, D-10117 Berlin, Germany
| | | | - Tillmann Utesch
- Institut für Chemie, Technische Universität Berlin, D-10623 Berlin, Germany
| | | | | | - Peter van der Linden
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
- Partnership for Soft Condensed Matter (PSCM), F-38043 Grenoble, France
| | - Antoine Royant
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), F-38000 Grenoble, France
| | | | - Philippe Carpentier
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biosciences et Biotechnologies de Grenoble (BIG)-Laboratoire Chimie et Biologie des Métaux (LCBM), F-38000 Grenoble, France
| | - Oliver Lenz
- Institut für Chemie, Technische Universität Berlin, D-10623 Berlin, Germany
| | - Patrick Scheerer
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, D-10117 Berlin, Germany;
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20
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Jacquet P, Hiblot J, Daudé D, Bergonzi C, Gotthard G, Armstrong N, Chabrière E, Elias M. Rational engineering of a native hyperthermostable lactonase into a broad spectrum phosphotriesterase. Sci Rep 2017; 7:16745. [PMID: 29196634 PMCID: PMC5711954 DOI: 10.1038/s41598-017-16841-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [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: 08/29/2017] [Accepted: 11/16/2017] [Indexed: 11/13/2022] Open
Abstract
The redesign of enzyme active sites to alter their function or specificity is a difficult yet appealing challenge. Here we used a structure-based design approach to engineer the lactonase SsoPox from Sulfolobus solfataricus into a phosphotriesterase. The five best variants were characterized and their structure was solved. The most active variant, αsD6 (V27A-Y97W-L228M-W263M) demonstrates a large increase in catalytic efficiencies over the wild-type enzyme, with increases of 2,210-fold, 163-fold, 58-fold, 16-fold against methyl-parathion, malathion, ethyl-paraoxon, and methyl-paraoxon, respectively. Interestingly, the best mutants are also capable of degrading fensulfothion, which is reported to be an inhibitor for the wild-type enzyme, as well as others that are not substrates of the starting template or previously reported W263 mutants. The broad specificity of these engineered variants makes them promising candidates for the bioremediation of organophosphorus compounds. Analysis of their structures reveals that the increase in activity mainly occurs through the destabilization of the active site loop involved in substrate binding, and it has been observed that the level of disorder correlates with the width of the enzyme specificity spectrum. This finding supports the idea that active site conformational flexibility is essential to the acquisition of broader substrate specificity.
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Affiliation(s)
- Pauline Jacquet
- CNRS UMR 7278, IRD198, INSERM U1095, APHM, Institut Hospitalier Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Julien Hiblot
- CNRS UMR 7278, IRD198, INSERM U1095, APHM, Institut Hospitalier Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Bd Jean Moulin, 13005, Marseille, France
- MPI for Medical Research, Chemical Biology department (EPFL), Heidelberg, Germany
| | - David Daudé
- Gene&GreenTK, IHU Méditerranée Infection, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Céline Bergonzi
- CNRS UMR 7278, IRD198, INSERM U1095, APHM, Institut Hospitalier Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Bd Jean Moulin, 13005, Marseille, France
- University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics & Biotechnology Institute, St. Paul, MN, 55108, USA
| | - Guillaume Gotthard
- CNRS UMR 7278, IRD198, INSERM U1095, APHM, Institut Hospitalier Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Nicholas Armstrong
- CNRS UMR 7278, IRD198, INSERM U1095, APHM, Institut Hospitalier Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Eric Chabrière
- CNRS UMR 7278, IRD198, INSERM U1095, APHM, Institut Hospitalier Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Bd Jean Moulin, 13005, Marseille, France.
| | - Mikael Elias
- University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics & Biotechnology Institute, St. Paul, MN, 55108, USA.
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21
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Gotthard G, von Stetten D, Clavel D, Noirclerc-Savoye M, Royant A. Chromophore Isomer Stabilization Is Critical to the Efficient Fluorescence of Cyan Fluorescent Proteins. Biochemistry 2017; 56:6418-6422. [PMID: 29148725 DOI: 10.1021/acs.biochem.7b01088] [Citation(s) in RCA: 11] [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: 11/30/2022]
Abstract
ECFP, the first usable cyan fluorescent protein (CFP), was obtained by adapting the tyrosine-based chromophore environment in green fluorescent protein to that of a tryptophan-based one. This first-generation CFP was superseded by the popular Cerulean, CyPet, and SCFP3A that were engineered by rational and random mutagenesis, yet the latter CFPs still exhibit suboptimal properties of pH sensitivity and reversible photobleaching behavior. These flaws were serendipitously corrected in the third-generation CFP mTurquoise and its successors without an obvious rationale. We show here that the evolution process had unexpectedly remodeled the chromophore environment in second-generation CFPs so they would accommodate a different isomer, whose formation is favored by acidic pH or light irradiation and which emits fluorescence much less efficiently. Our results illustrate how fluorescent protein engineering based solely on fluorescence efficiency optimization may affect other photophysical or physicochemical parameters and provide novel insights into the rational evolution of fluorescent proteins with a tryptophan-based chromophore.
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Affiliation(s)
| | | | - Damien Clavel
- Univ. Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale), F-38000 Grenoble, France
| | | | - Antoine Royant
- European Synchrotron Radiation Facility , F-38043 Grenoble, France.,Univ. Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale), F-38000 Grenoble, France
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22
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Abstract
Mimivirus was the first discovered amoebal giant virus. The Mimivirus virions are covered by a dense layer of approximately 130 nm-long fibers, the length and shape of which diverge from those of other viruses. Here, we aimed at expressing the L725 protein to further confirm and study its role as a fiber-associated protein. We report Escherichia coli expression of the L725 protein, which is encoded by a Mimivirus ORFan, was previously identified by proteomics in purified viral fibers and demonstrated to be a fiber-associated protein by RNA-silencing experiments. The expressed protein was recognized by anti-Mimivirus fiber or anti-Mimivirus L725 polyclonal antibodies. This study is the only expression, to our knowledge, of a product from a Mimiviral ORFan gene.
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23
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Bindels DS, Haarbosch L, van Weeren L, Postma M, Wiese KE, Mastop M, Aumonier S, Gotthard G, Royant A, Hink MA, Gadella TWJ. mScarlet: a bright monomeric red fluorescent protein for cellular imaging. Nat Methods 2017; 14:53-56. [PMID: 27869816 DOI: 10.1038/nmeth.4074] [Citation(s) in RCA: 587] [Impact Index Per Article: 83.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 10/20/2016] [Indexed: 12/24/2022]
Abstract
We report the engineering of mScarlet, a truly monomeric red fluorescent protein with record brightness, quantum yield (70%) and fluorescence lifetime (3.9 ns). We developed mScarlet starting with a consensus synthetic template and using improved spectroscopic screening techniques; mScarlet's crystal structure reveals a planar and rigidified chromophore. mScarlet outperforms existing red fluorescent proteins as a fusion tag, and it is especially useful as a Förster resonance energy transfer (FRET) acceptor in ratiometric imaging.
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Affiliation(s)
- Daphne S Bindels
- Section of Molecular Cytology and van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Lindsay Haarbosch
- Section of Molecular Cytology and van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Laura van Weeren
- Section of Molecular Cytology and van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Marten Postma
- Section of Molecular Cytology and van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Katrin E Wiese
- Section of Molecular Cytology and van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Marieke Mastop
- Section of Molecular Cytology and van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Sylvain Aumonier
- European Synchrotron Radiation Facility, Grenoble, France
- Institut de Biologie Structurale, Université Grenoble Alpes, CNRS, CEA, Grenoble, F-38044, France
| | - Guillaume Gotthard
- European Synchrotron Radiation Facility, Grenoble, France
- Institut de Biologie Structurale, Université Grenoble Alpes, CNRS, CEA, Grenoble, F-38044, France
| | - Antoine Royant
- European Synchrotron Radiation Facility, Grenoble, France
- Institut de Biologie Structurale, Université Grenoble Alpes, CNRS, CEA, Grenoble, F-38044, France
| | - Mark A Hink
- Section of Molecular Cytology and van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Theodorus W J Gadella
- Section of Molecular Cytology and van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
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Clavel D, Gotthard G, von Stetten D, De Sanctis D, Pasquier H, Lambert GG, Shaner NC, Royant A. Structural analysis of the bright monomeric yellow-green fluorescent protein mNeonGreen obtained by directed evolution. Acta Crystallogr D Struct Biol 2016; 72:1298-1307. [PMID: 27917830 PMCID: PMC5137226 DOI: 10.1107/s2059798316018623] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 11/21/2016] [Indexed: 11/10/2022] Open
Abstract
Until recently, genes coding for homologues of the autofluorescent protein GFP had only been identified in marine organisms from the phyla Cnidaria and Arthropoda. New fluorescent-protein genes have now been found in the phylum Chordata, coding for particularly bright oligomeric fluorescent proteins such as the tetrameric yellow fluorescent protein lanYFP from Branchiostoma lanceolatum. A successful monomerization attempt led to the development of the bright yellow-green fluorescent protein mNeonGreen. The structures of lanYFP and mNeonGreen have been determined and compared in order to rationalize the directed evolution process leading from a bright, tetrameric to a still bright, monomeric fluorescent protein. An unusual discolouration of crystals of mNeonGreen was observed after X-ray data collection, which was investigated using a combination of X-ray crystallography and UV-visible absorption and Raman spectroscopies, revealing the effects of specific radiation damage in the chromophore cavity. It is shown that X-rays rapidly lead to the protonation of the phenolate O atom of the chromophore and to the loss of its planarity at the methylene bridge.
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Affiliation(s)
- Damien Clavel
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
- CNRS, Laboratoire de Chimie Physique, UMR 8000 and Université Paris-Sud, F-91405 Orsay, France
| | | | | | | | - Hélène Pasquier
- CNRS, Laboratoire de Chimie Physique, UMR 8000 and Université Paris-Sud, F-91405 Orsay, France
| | - Gerard G. Lambert
- Department of Photobiology and Bioimaging, The Scintillon Institute, San Diego, California, USA
| | - Nathan C. Shaner
- Department of Photobiology and Bioimaging, The Scintillon Institute, San Diego, California, USA
| | - Antoine Royant
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
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25
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Colletier JP, Sliwa M, Gallat FX, Sugahara M, Guillon V, Schirò G, Coquelle N, Woodhouse J, Roux L, Gotthard G, Royant A, Uriarte LM, Ruckebusch C, Joti Y, Byrdin M, Mizohata E, Nango E, Tanaka T, Tono K, Yabashi M, Adam V, Cammarata M, Schlichting I, Bourgeois D, Weik M. Serial Femtosecond Crystallography and Ultrafast Absorption Spectroscopy of the Photoswitchable Fluorescent Protein IrisFP. J Phys Chem Lett 2016; 7:882-887. [PMID: 26866390 DOI: 10.1021/acs.jpclett.5b02789] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [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: 06/05/2023]
Abstract
Reversibly photoswitchable fluorescent proteins find growing applications in cell biology, yet mechanistic details, in particular on the ultrafast photochemical time scale, remain unknown. We employed time-resolved pump-probe absorption spectroscopy on the reversibly photoswitchable fluorescent protein IrisFP in solution to study photoswitching from the nonfluorescent (off) to the fluorescent (on) state. Evidence is provided for the existence of several intermediate states on the pico- and microsecond time scales that are attributed to chromophore isomerization and proton transfer, respectively. Kinetic modeling favors a sequential mechanism with the existence of two excited state intermediates with lifetimes of 2 and 15 ps, the second of which controls the photoswitching quantum yield. In order to support that IrisFP is suited for time-resolved experiments aiming at a structural characterization of these ps intermediates, we used serial femtosecond crystallography at an X-ray free electron laser and solved the structure of IrisFP in its on state. Sample consumption was minimized by embedding crystals in mineral grease, in which they remain photoswitchable. Our spectroscopic and structural results pave the way for time-resolved serial femtosecond crystallography aiming at characterizing the structure of ultrafast intermediates in reversibly photoswitchable fluorescent proteins.
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Affiliation(s)
| | - Michel Sliwa
- Université de Lille , CNRS, UMR 8516, LASIR, Laboratoire de Spectrochimie Infrarouge et Raman, F59 000 Lille, France
| | - François-Xavier Gallat
- Institut de Biologie Structurale , Université de Grenoble Alpes, CEA, CNRS, F-38044 Grenoble, France
| | - Michihiro Sugahara
- RIKEN SPring-8 Center , 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Virginia Guillon
- Institut de Biologie Structurale , Université de Grenoble Alpes, CEA, CNRS, F-38044 Grenoble, France
| | - Giorgio Schirò
- Institut de Biologie Structurale , Université de Grenoble Alpes, CEA, CNRS, F-38044 Grenoble, France
| | - Nicolas Coquelle
- Institut de Biologie Structurale , Université de Grenoble Alpes, CEA, CNRS, F-38044 Grenoble, France
| | - Joyce Woodhouse
- Institut de Biologie Structurale , Université de Grenoble Alpes, CEA, CNRS, F-38044 Grenoble, France
| | - Laure Roux
- Institut de Biologie Structurale , Université de Grenoble Alpes, CEA, CNRS, F-38044 Grenoble, France
| | - Guillaume Gotthard
- Institut de Biologie Structurale , Université de Grenoble Alpes, CEA, CNRS, F-38044 Grenoble, France
- The European Synchrotron Radiation Facility (ESRF) , 6 rue Jules Horowitz, BP 220, 38043 Grenoble Cedex, France
| | - Antoine Royant
- Institut de Biologie Structurale , Université de Grenoble Alpes, CEA, CNRS, F-38044 Grenoble, France
- The European Synchrotron Radiation Facility (ESRF) , 6 rue Jules Horowitz, BP 220, 38043 Grenoble Cedex, France
| | - Lucas Martinez Uriarte
- Université de Lille , CNRS, UMR 8516, LASIR, Laboratoire de Spectrochimie Infrarouge et Raman, F59 000 Lille, France
| | - Cyril Ruckebusch
- Université de Lille , CNRS, UMR 8516, LASIR, Laboratoire de Spectrochimie Infrarouge et Raman, F59 000 Lille, France
| | - Yasumasa Joti
- Japan Synchrotron Radiation Research Institute , 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Martin Byrdin
- Institut de Biologie Structurale , Université de Grenoble Alpes, CEA, CNRS, F-38044 Grenoble, France
| | - Eiichi Mizohata
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University , Osaka 565-0871, Japan
| | - Eriko Nango
- RIKEN SPring-8 Center , 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Tomoyuki Tanaka
- RIKEN SPring-8 Center , 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute , 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Makina Yabashi
- RIKEN SPring-8 Center , 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Virgile Adam
- Institut de Biologie Structurale , Université de Grenoble Alpes, CEA, CNRS, F-38044 Grenoble, France
| | - Marco Cammarata
- Department of Physics, UMR UR1-CNRS 6251, University of Rennes 1 , Rennes, France
| | - Ilme Schlichting
- Max-Planck-Institut für medizinische Forschung , Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Dominique Bourgeois
- Institut de Biologie Structurale , Université de Grenoble Alpes, CEA, CNRS, F-38044 Grenoble, France
| | - Martin Weik
- Institut de Biologie Structurale , Université de Grenoble Alpes, CEA, CNRS, F-38044 Grenoble, France
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Huynh HTT, Gotthard G, Terras J, Aboudharam G, Drancourt M, Chabrière E. Surface plasmon resonance imaging of pathogens: the Yersinia pestis paradigm. BMC Res Notes 2015; 8:259. [PMID: 26105071 PMCID: PMC4479326 DOI: 10.1186/s13104-015-1236-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [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] [Received: 09/04/2014] [Accepted: 06/17/2015] [Indexed: 11/26/2022] Open
Abstract
Background Yersinia pestis, causing deadly plague, is classified as a group A bioterrorism bacterium. Some recent DNA-based methods were used for detection of bioterrorism agents. Results Y. pestis was used as a model organism to develop an immunosensor based on surface plasmon resonance imaging (SPRi) using monoclonal antibody against Y. pestis F1 antigen. The experimental approach included step-by-step detection of Y. pestis membrane proteins, lysed bacteria, intact bacteria, mock-infected powder and mock-infected clinical specimens. SPRi detected on average 106 intact Y. pestis organisms in buffer, in mock-infected powder and in a 1:4 mixture with HEL cells. Conclusions This study offers the proof-of-concept of the SPRi-based detection of a human pathogen in both environmental and clinical specimens.
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Affiliation(s)
- Hong T T Huynh
- Faculté de médecine, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UMR CNRS 7278, IRD 198, INSERM 1095, 27, Boulevard Jean Moulin-Cedex 5, Marseille, France.
| | - Guillaume Gotthard
- Faculté de médecine, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UMR CNRS 7278, IRD 198, INSERM 1095, 27, Boulevard Jean Moulin-Cedex 5, Marseille, France.
| | - Jérome Terras
- Faculté de médecine, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UMR CNRS 7278, IRD 198, INSERM 1095, 27, Boulevard Jean Moulin-Cedex 5, Marseille, France.
| | - Gérard Aboudharam
- Faculté de médecine, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UMR CNRS 7278, IRD 198, INSERM 1095, 27, Boulevard Jean Moulin-Cedex 5, Marseille, France.
| | - Michel Drancourt
- Faculté de médecine, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UMR CNRS 7278, IRD 198, INSERM 1095, 27, Boulevard Jean Moulin-Cedex 5, Marseille, France.
| | - Eric Chabrière
- Faculté de médecine, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UMR CNRS 7278, IRD 198, INSERM 1095, 27, Boulevard Jean Moulin-Cedex 5, Marseille, France.
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Bzdrenga J, Hiblot J, Gotthard G, Champion C, Elias M, Chabriere E. SacPox from the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius is a proficient lactonase. BMC Res Notes 2014; 7:333. [PMID: 24894602 PMCID: PMC4068969 DOI: 10.1186/1756-0500-7-333] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 05/27/2014] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND SacPox, an enzyme from the extremophilic crenarchaeal Sulfolobus acidocaldarius (Sac), was isolated by virtue of its phosphotriesterase (or paraoxonase; Pox) activity, i.e. its ability to hydrolyze the neurotoxic organophosphorus insecticides. Later on, SacPox was shown to belong to the Phosphotriesterase-Like Lactonase family that comprises natural lactonases, possibly involved in quorum sensing, and endowed with promiscuous, phosphotriesterase activity. RESULTS Here, we present a comprehensive and broad enzymatic characterization of the natural lactonase and promiscuous organophosphorus hydrolase activities of SacPox, as well as a structural analysis using a model. CONCLUSION Kinetic experiments show that SacPox is a proficient lactonase, including at room temperature. Moreover, we discuss the observed differences in substrate specificity between SacPox and its closest homologues SsoPox and SisLac together with the possible structural causes for these observations.
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Affiliation(s)
- Janek Bzdrenga
- URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
| | - Julien Hiblot
- URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
| | - Guillaume Gotthard
- URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
| | - Charlotte Champion
- URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
| | - Mikael Elias
- Weizmann Institute of Science, Biological Chemistry, Rehovot, Israel
| | - Eric Chabriere
- URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
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Gonzalez D, Hiblot J, Darbinian N, Miller JC, Gotthard G, Amini S, Chabriere E, Elias M. Ancestral mutations as a tool for solubilizing proteins: The case of a hydrophobic phosphate-binding protein. FEBS Open Bio 2014; 4:121-7. [PMID: 24490136 PMCID: PMC3907688 DOI: 10.1016/j.fob.2013.12.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 12/21/2013] [Accepted: 12/23/2013] [Indexed: 12/02/2022] Open
Abstract
Stable and soluble proteins are ideal candidates for functional and structural studies. Unfortunately, some proteins or enzymes can be difficult to isolate, being sometimes poorly expressed in heterologous systems, insoluble and/or unstable. Numerous methods have been developed to address these issues, from the screening of various expression systems to the modification of the target protein itself. Here we use a hydrophobic, aggregation-prone, phosphate-binding protein (HPBP) as a case study. We describe a simple and fast method that selectively uses ancestral mutations to generate a soluble, stable and functional variant of the target protein, here named sHPBP. This variant is highly expressed in Escherichia coli, is easily purified and its structure was solved at much higher resolution than its wild-type progenitor (1.3 versus 1.9 Å, respectively).
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Affiliation(s)
- Daniel Gonzalez
- URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
| | - Julien Hiblot
- URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
| | - Nune Darbinian
- Department of Neuroscience, Temple University School of Medicine, Philadelphia, PA 19140, USA
| | - Jernelle C. Miller
- Department of Neuroscience, Temple University School of Medicine, Philadelphia, PA 19140, USA
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA
| | - Guillaume Gotthard
- URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
| | - Shohreh Amini
- Department of Neuroscience, Temple University School of Medicine, Philadelphia, PA 19140, USA
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA
| | - Eric Chabriere
- URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
| | - Mikael Elias
- Weizmann Institute of Science, Biological Chemistry, Rehovot, Israel
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Gotthard G, Muhammed Ameen S, Drancourt M, Chabriere E. Long-range DHPS mutations unexpectedly increase Mycobacterium chimaera susceptibility to sulfonamides. J Glob Antimicrob Resist 2013; 1:181-188. [DOI: 10.1016/j.jgar.2013.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 05/24/2013] [Indexed: 02/01/2023] Open
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Gotthard G, Hiblot J, Gonzalez D, Elias M, Chabriere E. Structural and enzymatic characterization of the phosphotriesterase OPHC2 from Pseudomonas pseudoalcaligenes. PLoS One 2013; 8:e77995. [PMID: 24223749 PMCID: PMC3817169 DOI: 10.1371/journal.pone.0077995] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Accepted: 09/16/2013] [Indexed: 01/26/2023] Open
Abstract
Background Organophosphates (OPs) are neurotoxic compounds for which current methods of elimination are unsatisfactory; thus bio-remediation is considered as a promising alternative. Here we provide the structural and enzymatic characterization of the recently identified enzyme isolated from Pseudomonas pseudoalcaligenes dubbed OPHC2. OPHC2 belongs to the metallo-β-lactamase superfamily and exhibits an unusual thermal resistance and some OP degrading abilities. Principal findings The X-ray structure of OPHC2 has been solved at 2.1 Å resolution. The enzyme is roughly globular exhibiting a αβ/βα topology typical of the metallo-β-lactamase superfamily. Several structural determinants, such as an extended dimerization surface and an intramolecular disulfide bridge, common features in thermostable enzymes, are consistent with its high Tm (97.8°C). Additionally, we provide the enzymatic characterization of OPHC2 against a wide range of OPs, esters and lactones. Significance OPHC2 possesses a broad substrate activity spectrum, since it hydrolyzes various phosphotriesters, esters, and a lactone. Because of its organophosphorus hydrolase activity, and given its intrinsic thermostability, OPHC2 is an interesting candidate for the development of an OPs bio-decontaminant. Its X-ray structure shed light on its active site, and provides key information for the understanding of the substrate binding mode and catalysis.
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Affiliation(s)
- Guillaume Gotthard
- URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
| | - Julien Hiblot
- URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
| | - Daniel Gonzalez
- URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
| | - Mikael Elias
- Weizmann Institute of Science, Biological Chemistry, Rehovot, Israel
- * E-mail: (ME); (EC)
| | - Eric Chabriere
- URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
- * E-mail: (ME); (EC)
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Hiblot J, Gotthard G, Champion C, Chabriere E, Elias M. Crystallization and preliminary X-ray diffraction analysis of the lactonase VmoLac from Vulcanisaeta moutnovskia. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1235-8. [PMID: 24192357 DOI: 10.1107/s1744309113024846] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 09/05/2013] [Indexed: 02/03/2023]
Abstract
Phosphotriesterase-like lactonases (PLLs) are native lactonases that are capable of hydrolyzing lactones such as aliphatic lactones or acyl-homoserine lactones, which are involved in bacterial quorum sensing. Previously characterized PLLs are moreover endowed with a promiscuous phosphotriesterase activity and are therefore able to detoxify organophosphate insecticides. A novel PLL representative, dubbed VmoLac, has been identified from the hyperthermophilic crenarchaeon Vulcanisaeta moutnovskia. Because of its intrinsic high thermal stability, VmoLac may constitute an appealing candidate for engineering studies with the aim of producing an efficient biodecontaminant for organophosphorus compounds and a bacterial antivirulence agent. In combination with biochemical studies, structural information will allow the identification of the residues involved in substrate specificity and an understanding of the enzymatic catalytic mechanisms. Here, the expression, purification, crystallization and X-ray data collection at 2.4 Å resolution of VmoLac are reported.
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Affiliation(s)
- Julien Hiblot
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergents (URMITE), UMR CNRS-IRD-INSERM, IHU Méditerranée Infection, Aix-Marseille Université, 7 Boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
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Djeghader A, Gotthard G, Suh A, Gonzalez D, Scott K, Chabriere E, Elias M. Crystallization and preliminary X-ray diffraction analysis of a high-affinity phosphate-binding protein endowed with phosphatase activity from Pseudomonas aeruginosa PAO1. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1143-6. [PMID: 24100568 PMCID: PMC3792676 DOI: 10.1107/s1744309113024172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 08/28/2013] [Indexed: 11/10/2022]
Abstract
In prokaryotes, phosphate starvation induces the expression of numerous phosphate-responsive genes, such as the pst operon including the high-affinity phosphate-binding protein (PBP or pstS) and alkaline phosphatases such as PhoA. This response increases the cellular inorganic phosphate import efficiency. Notably, some Pseudomonas species secrete, via a type-2 secretion system, a phosphate-binding protein dubbed LapA endowed with phosphatase activity. Here, the expression, purification, crystallization and X-ray data collection at 0.87 Å resolution of LapA are described. Combined with biochemical and enzymatic characterization, the structure of this intriguing phosphate-binding protein will help to elucidate the molecular origin of its phosphatase activity and to decipher its putative role in phosphate uptake.
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Affiliation(s)
- Ahmed Djeghader
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 27 Boulevard Jean Moulin, 13385 Marseille CEDEX 5, France
| | - Guillaume Gotthard
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 27 Boulevard Jean Moulin, 13385 Marseille CEDEX 5, France
| | - Andrew Suh
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Daniel Gonzalez
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 27 Boulevard Jean Moulin, 13385 Marseille CEDEX 5, France
| | - Ken Scott
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Eric Chabriere
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 27 Boulevard Jean Moulin, 13385 Marseille CEDEX 5, France
| | - Mikael Elias
- Biological Chemistry, Weizman Institute of Science, Rehovot, Israel
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Hiblot J, Gotthard G, Elias M, Chabriere E. Differential active site loop conformations mediate promiscuous activities in the lactonase SsoPox. PLoS One 2013; 8:e75272. [PMID: 24086491 PMCID: PMC3781021 DOI: 10.1371/journal.pone.0075272] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [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: 05/16/2013] [Accepted: 08/14/2013] [Indexed: 11/19/2022] Open
Abstract
Enzymes are proficient catalysts that enable fast rates of Michaelis-complex formation, the chemical step and products release. These different steps may require different conformational states of the active site that have distinct binding properties. Moreover, the conformational flexibility of the active site mediates alternative, promiscuous functions. Here we focused on the lactonase SsoPox from Sulfolobus solfataricus. SsoPox is a native lactonase endowed with promiscuous phosphotriesterase activity. We identified a position in the active site loop (W263) that governs its flexibility, and thereby affects the substrate specificity of the enzyme. We isolated two different sets of substitutions at position 263 that induce two distinct conformational sampling of the active loop and characterized the structural and kinetic effects of these substitutions. These sets of mutations selectively and distinctly mediate the improvement of the promiscuous phosphotriesterase and oxo-lactonase activities of SsoPox by increasing active-site loop flexibility. These observations corroborate the idea that conformational diversity governs enzymatic promiscuity and is a key feature of protein evolvability.
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Affiliation(s)
- Julien Hiblot
- URMITE UMR CNRS-IRD 6236, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
| | - Guillaume Gotthard
- URMITE UMR CNRS-IRD 6236, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
| | - Mikael Elias
- Weizmann Institute of Science, Biological Chemistry, Rehovot, Israel
| | - Eric Chabriere
- URMITE UMR CNRS-IRD 6236, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
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Djeghader A, Gotthard G, Suh A, Gonzalez D, Scott K, Elias M, Chabriere E. Crystallization and preliminary X-ray diffraction analysis of a DING protein from Pseudomonas aeruginosa PA14. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:425-9. [PMID: 23545651 PMCID: PMC3614170 DOI: 10.1107/s1744309113005356] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 02/24/2013] [Indexed: 11/10/2022]
Abstract
DING proteins form an emergent family of proteins consisting of an increasing number of homologues that have been identified in all kingdoms of life. They belong to the superfamily of phosphate-binding proteins and exhibit a high affinity for phosphate. In eukaryotes, DING proteins have been isolated by virtue of their implication in several diseases and biological processes. Some of them are potent inhibitors of HIV-1 replication/transcription, raising the question of their potential involvement in the human defence system. Recently, a protein from Pseudomonas aeruginosa strain PA14, named PA14DING or LapC, belonging to the DING family has been identified. The structure of PA14DING, combined with detailed biochemical characterization and comparative analysis with available DING protein structures, will be helpful in understanding the structural determinants implicated in the inhibition of HIV-1 by DING proteins. Here, the expression, purification and crystallization of PA14DING and the collection of X-ray data to 1.9 Å resolution are reported.
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Affiliation(s)
- Ahmed Djeghader
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 27 Boulevard Jean Moulin, 13385 Marseille CEDEX 5, France
| | - Guillaume Gotthard
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 27 Boulevard Jean Moulin, 13385 Marseille CEDEX 5, France
| | - Andrew Suh
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Daniel Gonzalez
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 27 Boulevard Jean Moulin, 13385 Marseille CEDEX 5, France
| | - Ken Scott
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Mikael Elias
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Eric Chabriere
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 27 Boulevard Jean Moulin, 13385 Marseille CEDEX 5, France
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Gotthard G, Hiblot J, Gonzalez D, Chabrière E, Elias M. Crystallization and preliminary X-ray diffraction analysis of the organophosphorus hydrolase OPHC2 from Pseudomonas pseudoalcaligenes. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:73-6. [PMID: 23295492 PMCID: PMC3539709 DOI: 10.1107/s174430911205049x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 12/11/2012] [Indexed: 02/02/2023]
Abstract
Enzymes that are capable of degrading neurotoxic organophosphorus compounds are of increasing interest because of the lack of efficient and clean methods for their removal. Recently, a novel organophosphorus hydrolase belonging to the metallo-β-lactamase superfamily was identified and isolated from the mesophilic bacterium Pseudomonas pseudoalcaligenes. This enzyme, named OPHC2, is endowed with significant thermal and pH stability, making it an appealing candidate for engineering studies to develop an efficient organophosphorus biodecontaminant. Combined with biochemical studies, structural information will help decipher the catalytic mechanism of organophosphorus hydrolysis by OPHC2 and identify the residues involved in its substrate specificity. Here, the expression, purification, crystallization and X-ray data collection at 2.1 Å resolution of OPHC2 are presented.
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Affiliation(s)
- Guillaume Gotthard
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
| | - Julien Hiblot
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
| | - Daniel Gonzalez
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
| | - Eric Chabrière
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
- Département de Toxicologie, Institut de Recherches Biomédicales des Armées-CRSSA, BP 87, 38702 La Tronche CEDEX, France
| | - Mikael Elias
- Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
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Hiblot J, Gotthard G, Chabriere E, Elias M. Characterisation of the organophosphate hydrolase catalytic activity of SsoPox. Sci Rep 2012; 2:779. [PMID: 23139857 PMCID: PMC3493116 DOI: 10.1038/srep00779] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [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: 06/08/2012] [Accepted: 09/24/2012] [Indexed: 01/26/2023] Open
Abstract
SsoPox is a lactonase endowed with promiscuous phosphotriesterase activity isolated from Sulfolobus solfataricus that belongs to the Phosphotriesterase-Like Lactonase family. Because of its intrinsic thermal stability, SsoPox is seen as an appealing candidate as a bioscavenger for organophosphorus compounds. A comprehensive kinetic characterisation of SsoPox has been performed with various phosphotriesters (insecticides) and phosphodiesters (nerve agent analogues) as substrates. We show that SsoPox is active for a broad range of OPs and remains active under denaturing conditions. In addition, its OP hydrolase activity is highly stimulated by anionic detergent at ambient temperature and exhibits catalytic efficiencies as high as kcat/KM of 105 M−1s−1 against a nerve agent analogue. The structure of SsoPox bound to the phosphotriester fensulfothion reveals an unexpected and non-productive binding mode. This feature suggests that SsoPox's active site is sub-optimal for phosphotriester binding, which depends not only upon shape but also on localised charge of the ligand.
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Affiliation(s)
- Julien Hiblot
- URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
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Hiblot J, Gotthard G, Chabriere E, Elias M. Structural and enzymatic characterization of the lactonase SisLac from Sulfolobus islandicus. PLoS One 2012; 7:e47028. [PMID: 23071703 PMCID: PMC3468530 DOI: 10.1371/journal.pone.0047028] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [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: 05/28/2012] [Accepted: 09/07/2012] [Indexed: 11/19/2022] Open
Abstract
Background A new member of the Phosphotriesterase-Like Lactonases (PLL) family from the hyperthermophilic archeon Sulfolobus islandicus (SisLac) has been characterized. SisLac is a native lactonase that exhibits a high promiscuous phosphotriesterase activity. SisLac thus represents a promising target for engineering studies, exhibiting both detoxification and bacterial quorum quenching abilities, including human pathogens such as Pseudomonas aeruginosa. Methodology/Principal Findings Here, we describe the substrate specificity of SisLac, providing extensive kinetic studies performed with various phosphotriesters, esters, N-acyl-homoserine lactones (AHLs) and other lactones as substrates. Moreover, we solved the X-ray structure of SisLac and structural comparisons with the closely related SsoPox structure highlighted differences in the surface salt bridge network and the dimerization interface. SisLac and SsoPox being close homologues (91% sequence identity), we undertook a mutational study to decipher these structural differences and their putative consequences on the stability and the catalytic properties of these proteins. Conclusions/Significance We show that SisLac is a very proficient lactonase against aroma lactones and AHLs as substrates. Hence, data herein emphasize the potential role of SisLac as quorum quenching agent in Sulfolobus. Moreover, despite the very high sequence homology with SsoPox, we highlight key epistatic substitutions that influence the enzyme stability and activity.
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Affiliation(s)
- Julien Hiblot
- URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
| | - Guillaume Gotthard
- URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
| | - Eric Chabriere
- URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
- * E-mail: (EC); (ME)
| | - Mikael Elias
- Weizmann Institute of Science, Biological Chemistry, Rehovot, Israel
- * E-mail: (EC); (ME)
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Djeghader A, Aragonès G, Darbinian N, Elias M, Gonzalez D, García-Heredia A, Beltrán-Debón R, Kaminski R, Gotthard G, Hiblot J, Rull A, Rohr O, Schwartz C, Alonso-Villaverde C, Joven J, Camps J, Chabriere E. The level of DING proteins is increased in HIV-infected patients: in vitro and in vivo studies. PLoS One 2012; 7:e33062. [PMID: 22427948 PMCID: PMC3302901 DOI: 10.1371/journal.pone.0033062] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Accepted: 02/03/2012] [Indexed: 01/09/2023] Open
Abstract
DING proteins constitute an interesting family, owing to their intriguing and important activities. However, after a decade of research, little is known about these proteins. In humans, at least five different DING proteins have been identified, which were implicated in important biological processes and diseases, including HIV. Indeed, recent data from different research groups have highlighted the anti-HIV activity of some DING representatives. These proteins share the ability to inhibit the transcriptional step of HIV-1, a key step of the viral cycle that is not yet targeted by the current therapies. Since such proteins have been isolated from humans, we undertook a comprehensive study that focuses on the relationship between these proteins and HIV-infection in an infectious context. Hence, we developed a home-made ELISA for the quantification of the concentration of DING proteins in human serum. Using this method, we were able to determine the concentration of DING proteins in healthy and HIV-infected patients. Interestingly, we observed a significant increase of the concentration of DING proteins in non treated and treated HIV-infected patients compared to controls. In addition, cell cultures infected with HIV also show an increased expression of DING proteins, ruling out the possible role of antiretroviral treatment in the increase of the expression of DING proteins. In conclusion, results from this study show that the organism reacts to HIV-infection by an overexpression of DING proteins.
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Affiliation(s)
- Ahmed Djeghader
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Centre National de la Recherche Scientifique, Faculté de Médecine Aix-Marseille University, Marseille, France
| | - Gerard Aragonès
- Centre de Recerca Biomèdica, Hospital Universitari de Sant Joan, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Catalonia, Spain
| | - Nune Darbinian
- Department of Neuroscience, Center for Neurovirology, Temple University School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Mikael Elias
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Daniel Gonzalez
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Centre National de la Recherche Scientifique, Faculté de Médecine Aix-Marseille University, Marseille, France
| | - Anabel García-Heredia
- Centre de Recerca Biomèdica, Hospital Universitari de Sant Joan, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Catalonia, Spain
| | - Raúl Beltrán-Debón
- Centre de Recerca Biomèdica, Hospital Universitari de Sant Joan, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Catalonia, Spain
| | - Rafal Kaminski
- Department of Neuroscience, Center for Neurovirology, Temple University School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Guillaume Gotthard
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Centre National de la Recherche Scientifique, Faculté de Médecine Aix-Marseille University, Marseille, France
| | - Julien Hiblot
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Centre National de la Recherche Scientifique, Faculté de Médecine Aix-Marseille University, Marseille, France
| | - Anna Rull
- Centre de Recerca Biomèdica, Hospital Universitari de Sant Joan, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Catalonia, Spain
| | - Olivier Rohr
- Institut de Parasitologie et Pathologie Tropicale, Université de Strasbourg, Strasbourg, France
| | - Christian Schwartz
- Institut de Parasitologie et Pathologie Tropicale, Université de Strasbourg, Strasbourg, France
| | | | - Jorge Joven
- Centre de Recerca Biomèdica, Hospital Universitari de Sant Joan, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Catalonia, Spain
| | - Jordi Camps
- Centre de Recerca Biomèdica, Hospital Universitari de Sant Joan, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Catalonia, Spain
- * E-mail: (JC); (EC)
| | - Eric Chabriere
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Centre National de la Recherche Scientifique, Faculté de Médecine Aix-Marseille University, Marseille, France
- * E-mail: (JC); (EC)
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Cherrier T, Elias M, Jeudy A, Gotthard G, Le Douce V, Hallay H, Masson P, Janossy A, Candolfi E, Rohr O, Chabrière E, Schwartz C. Human-Phosphate-Binding-Protein inhibits HIV-1 gene transcription and replication. Virol J 2011; 8:352. [PMID: 21762475 PMCID: PMC3157455 DOI: 10.1186/1743-422x-8-352] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [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: 04/19/2011] [Accepted: 07/15/2011] [Indexed: 01/04/2023] Open
Abstract
The Human Phosphate-Binding protein (HPBP) is a serendipitously discovered lipoprotein that binds phosphate with high affinity. HPBP belongs to the DING protein family, involved in various biological processes like cell cycle regulation. We report that HPBP inhibits HIV-1 gene transcription and replication in T cell line, primary peripherical blood lymphocytes and primary macrophages. We show that HPBP is efficient in naïve and HIV-1 AZT-resistant strains. Our results revealed HPBP as a new and potent anti HIV molecule that inhibits transcription of the virus, which has not yet been targeted by HAART and therefore opens new strategies in the treatment of HIV infection.
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Affiliation(s)
- Thomas Cherrier
- Institut de Parasitologie et Pathologie Tropicale, EA 4438, Université de Strasbourg, 3 rue Koeberlé, 67000 Strasbourg, France
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Gotthard G, Hiblot J, Elias M, Chabrière E. Crystallization and preliminary X-ray diffraction analysis of the hyperthermophilic Sulfolobus islandicus lactonase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:354-7. [PMID: 21393842 PMCID: PMC3053162 DOI: 10.1107/s1744309110053819] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Accepted: 12/22/2010] [Indexed: 11/11/2022]
Abstract
Phosphotriesterase-like lactonases (PLLs) constitute an interesting family of enzymes that are of paramount interest in biotechnology with respect to their catalytic functions. As natural lactonases, they may act against pathogens such as Pseudomonas aeruginosa by shutting down their quorum-sensing system (quorum quenching) and thus decreasing pathogen virulence. Owing to their promiscuous phosphotriesterase activity, which can inactivate toxic organophosphorus compounds such as pesticides and nerve agents, they are equally appealing as potent bioscavengers. A new representative of the PLL family has been identified (SisPox) and its gene was cloned from the hyperthermophilic archeon Sulfolobus islandicus. Owing to its hyperthermostable architecture, SisPox appears to be a good candidate for engineering studies. Here, production, purification, crystallization conditions and data collection to 2.34 Å resolution are reported for this lactonase from the hyperthermophilic S. islandicus.
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Affiliation(s)
- Guillaume Gotthard
- Architecture et Fonction des Macromolécules Biologiques, CNRS–Aix Marseille Université, 13288 Marseille, France
| | - Julien Hiblot
- Architecture et Fonction des Macromolécules Biologiques, CNRS–Aix Marseille Université, 13288 Marseille, France
| | - Mikael Elias
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Eric Chabrière
- Architecture et Fonction des Macromolécules Biologiques, CNRS–Aix Marseille Université, 13288 Marseille, France
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Elias M, Liebschner D, Gotthard G, Chabriere E. Structural insights and ab initio sequencing within the DING proteins family. J Synchrotron Radiat 2011; 18:45-49. [PMID: 21169690 PMCID: PMC3004253 DOI: 10.1107/s0909049510036009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Accepted: 09/07/2010] [Indexed: 05/30/2023]
Abstract
DING proteins constitute an intriguing family of phosphate-binding proteins that was identified in a wide range of organisms, from prokaryotes and archae to eukaryotes. Despite their seemingly ubiquitous occurrence in eukaryotes, their encoding genes are missing from sequenced genomes. Such a lack has considerably hampered functional studies. In humans, these proteins have been related to several diseases, like atherosclerosis, kidney stones, inflammation processes and HIV inhibition. The human phosphate binding protein is a human representative of the DING family that was serendipitously discovered from human plasma. An original approach was developed to determine ab initio the complete and exact sequence of this 38 kDa protein by utilizing mass spectrometry and X-ray data in tandem. Taking advantage of this first complete eukaryotic DING sequence, a immunohistochemistry study was undertaken to check the presence of DING proteins in various mice tissues, revealing that these proteins are widely expressed. Finally, the structure of a bacterial representative from Pseudomonas fluorescens was solved at sub-angstrom resolution, allowing the molecular mechanism of the phosphate binding in these high-affinity proteins to be elucidated.
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Collombet JM, Elias M, Gotthard G, Four E, Renault F, Joffre A, Baubichon D, Rochu D, Chabrière E. Eukaryotic DING proteins are endogenous: an immunohistological study in mouse tissues. PLoS One 2010; 5:e9099. [PMID: 20161715 PMCID: PMC2817009 DOI: 10.1371/journal.pone.0009099] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2009] [Accepted: 01/20/2010] [Indexed: 11/19/2022] Open
Abstract
Background DING proteins encompass an intriguing protein family first characterized by their conserved N-terminal sequences. Some of these proteins seem to have key roles in various human diseases, e.g., rheumatoid arthritis, atherosclerosis, HIV suppression. Although this protein family seems to be ubiquitous in eukaryotes, their genes are consistently lacking from genomic databases. Such a lack has considerably hampered functional studies and has fostered therefore the hypothesis that DING proteins isolated from eukaryotes were in fact prokaryotic contaminants. Principal Findings In the framework of our study, we have performed a comprehensive immunological detection of DING proteins in mice. We demonstrate that DING proteins are present in all tissues tested as isoforms of various molecular weights (MWs). Their intracellular localization is tissue-dependant, being exclusively nuclear in neurons, but cytoplasmic and nuclear in other tissues. We also provide evidence that germ-free mouse plasma contains as much DING protein as wild-type. Significance Hence, data herein provide a valuable basis for future investigations aimed at eukaryotic DING proteins, revealing that these proteins seem ubiquitous in mouse tissue. Our results strongly suggest that mouse DING proteins are endogenous. Moreover, the determination in this study of the precise cellular localization of DING proteins constitute a precious evidence to understand their molecular involvements in their related human diseases.
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Affiliation(s)
- Jean-Marc Collombet
- Département de Toxicologie, Institut de Recherche Biomédicale des Armées, Centre de Recherche du Service de Santé des Armées, La Tronche, France
| | - Mikael Elias
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique-Aix Marseille Université, Marseille, France
| | - Guillaume Gotthard
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique-Aix Marseille Université, Marseille, France
| | - Elise Four
- Département de Toxicologie, Institut de Recherche Biomédicale des Armées, Centre de Recherche du Service de Santé des Armées, La Tronche, France
| | - Frédérique Renault
- Département de Toxicologie, Institut de Recherche Biomédicale des Armées, Centre de Recherche du Service de Santé des Armées, La Tronche, France
| | - Aurélie Joffre
- Service de Microscopie et d'Imagerie Médicale, Institut de Recherche Biomédicale des Armées, Centre de Recherche du Service de Santé des Armées, La Tronche, France
| | - Dominique Baubichon
- Département de Toxicologie, Institut de Recherche Biomédicale des Armées, Centre de Recherche du Service de Santé des Armées, La Tronche, France
| | - Daniel Rochu
- Département de Toxicologie, Institut de Recherche Biomédicale des Armées, Centre de Recherche du Service de Santé des Armées, La Tronche, France
| | - Eric Chabrière
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique-Aix Marseille Université, Marseille, France
- * E-mail:
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