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Engilberge S, Caramello N, Bukhdruker S, Byrdin M, Giraud T, Jacquet P, Scortani D, Biv R, Gonzalez H, Broquet A, van der Linden P, Rose SL, Flot D, Balandin T, Gordeliy V, Lahey-Rudolph JM, Roessle M, de Sanctis D, Leonard GA, Mueller-Dieckmann C, Royant A. The TR-icOS setup at the ESRF: time-resolved microsecond UV-Vis absorption spectroscopy on protein crystals. Acta Crystallogr D Struct Biol 2024; 80:16-25. [PMID: 38088897 PMCID: PMC10833346 DOI: 10.1107/s2059798323010483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 12/06/2023] [Indexed: 01/12/2024] Open
Abstract
The technique of time-resolved macromolecular crystallography (TR-MX) has recently been rejuvenated at synchrotrons, resulting in the design of dedicated beamlines. Using pump-probe schemes, this should make the mechanistic study of photoactive proteins and other suitable systems possible with time resolutions down to microseconds. In order to identify relevant time delays, time-resolved spectroscopic experiments directly performed on protein crystals are often desirable. To this end, an instrument has been built at the icOS Lab (in crystallo Optical Spectroscopy Laboratory) at the European Synchrotron Radiation Facility using reflective focusing objectives with a tuneable nanosecond laser as a pump and a microsecond xenon flash lamp as a probe, called the TR-icOS (time-resolved icOS) setup. Using this instrument, pump-probe spectra can rapidly be recorded from single crystals with time delays ranging from a few microseconds to seconds and beyond. This can be repeated at various laser pulse energies to track the potential presence of artefacts arising from two-photon absorption, which amounts to a power titration of a photoreaction. This approach has been applied to monitor the rise and decay of the M state in the photocycle of crystallized bacteriorhodopsin and showed that the photocycle is increasingly altered with laser pulses of peak fluence greater than 100 mJ cm-2, providing experimental laser and delay parameters for a successful TR-MX experiment.
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Affiliation(s)
- Sylvain Engilberge
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38403 Grenoble CEDEX 9, France
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, CS 10090, 38044 Grenoble CEDEX 9, France
| | - Nicolas Caramello
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38403 Grenoble CEDEX 9, France
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Sergei Bukhdruker
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38403 Grenoble CEDEX 9, France
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - Martin Byrdin
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, CS 10090, 38044 Grenoble CEDEX 9, France
| | - Thierry Giraud
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38403 Grenoble CEDEX 9, France
| | - Philippe Jacquet
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, CS 10090, 38044 Grenoble CEDEX 9, France
| | - Damien Scortani
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38403 Grenoble CEDEX 9, France
| | - Rattana Biv
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38403 Grenoble CEDEX 9, France
| | - Hervé Gonzalez
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38403 Grenoble CEDEX 9, France
| | - Antonin Broquet
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38403 Grenoble CEDEX 9, France
| | - Peter van der Linden
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38403 Grenoble CEDEX 9, France
- PSCM (Partnership for Soft Condensed Matter), ESRF, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Samuel L. Rose
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38403 Grenoble CEDEX 9, France
| | - David Flot
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38403 Grenoble CEDEX 9, France
| | - Taras Balandin
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - Valentin Gordeliy
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, CS 10090, 38044 Grenoble CEDEX 9, France
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - J. Mia Lahey-Rudolph
- Technische Hochschule Lübeck – University of Applied Sciences, Mönkhofer Weg 239, 23562 Lübeck, Germany
| | - Manfred Roessle
- Technische Hochschule Lübeck – University of Applied Sciences, Mönkhofer Weg 239, 23562 Lübeck, Germany
| | - Daniele de Sanctis
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38403 Grenoble CEDEX 9, France
| | - Gordon A. Leonard
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38403 Grenoble CEDEX 9, France
| | | | - Antoine Royant
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38403 Grenoble CEDEX 9, France
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, CS 10090, 38044 Grenoble CEDEX 9, France
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Schroer MA, Schewa S, Gruzinov AY, Rönnau C, Lahey-Rudolph JM, Blanchet CE, Zickmantel T, Song YH, Svergun DI, Roessle M. Probing the existence of non-thermal Terahertz radiation induced changes of the protein solution structure. Sci Rep 2021; 11:22311. [PMID: 34785744 PMCID: PMC8595702 DOI: 10.1038/s41598-021-01774-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/26/2021] [Indexed: 01/14/2023] Open
Abstract
During the last decades discussions were taking place on the existence of global, non-thermal structural changes in biological macromolecules induced by Terahertz (THz) radiation. Despite numerous studies, a clear experimental proof of this effect for biological particles in solution is still missing. We developed a setup combining THz-irradiation with small angle X-ray scattering (SAXS), which is a sensitive method for detecting the expected structural changes. We investigated in detail protein systems with different shape morphologies (bovine serum albumin, microtubules), which have been proposed to be susceptible to THz-radiation, under variable parameters (THz wavelength, THz power densities up to 6.8 mW/cm2, protein concentrations). None of the studied systems and conditions revealed structural changes detectable by SAXS suggesting that the expected non-thermal THz-induced effects do not lead to alterations of the overall structures, which are revealed by scattering from dissolved macromolecules. This leaves us with the conclusion that, if such effects are present, these are either local or outside of the spectrum and power range covered by the present study.
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Affiliation(s)
- Martin A. Schroer
- grid.475756.20000 0004 0444 5410European Molecular Biology Laboratory (EMBL), Hamburg Outstation C/O DESY, Notkestr. 85, 22607 Hamburg, Germany ,grid.5718.b0000 0001 2187 5445Present Address: Nanoparticle Process Technology, University of Duisburg-Essen, Lotharstr. 1, 47057 Duisburg, Germany
| | - Siawosch Schewa
- University of Applied Sciences Luebeck, Moenkhofer Weg 239, 23562 Luebeck, Germany
| | - Andrey Yu. Gruzinov
- grid.475756.20000 0004 0444 5410European Molecular Biology Laboratory (EMBL), Hamburg Outstation C/O DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Christian Rönnau
- grid.4562.50000 0001 0057 2672Institute of Physics, University of Luebeck, Ratzeburger Allee 160, 23562 Luebeck, Germany
| | | | - Clement E. Blanchet
- grid.475756.20000 0004 0444 5410European Molecular Biology Laboratory (EMBL), Hamburg Outstation C/O DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Till Zickmantel
- grid.4562.50000 0001 0057 2672Institute of Physics, University of Luebeck, Ratzeburger Allee 160, 23562 Luebeck, Germany
| | - Young-Hwa Song
- grid.4562.50000 0001 0057 2672Institute of Physics, University of Luebeck, Ratzeburger Allee 160, 23562 Luebeck, Germany
| | - Dmitri I. Svergun
- grid.475756.20000 0004 0444 5410European Molecular Biology Laboratory (EMBL), Hamburg Outstation C/O DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Manfred Roessle
- University of Applied Sciences Luebeck, Moenkhofer Weg 239, 23562 Luebeck, Germany
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Schewa S, Schroer MA, Zickmantel T, Song YH, Blanchet CE, Gruzinov AY, Katona G, Svergun DI, Roessle M. A THz transparent 3D printed microfluidic cell for small angle x-ray scattering. Rev Sci Instrum 2020; 91:084101. [PMID: 32872894 DOI: 10.1063/5.0004706] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 07/09/2020] [Indexed: 06/11/2023]
Abstract
Excitation frequencies in the terahertz (THz) range are expected to lead to functionally relevant domain movements within the biological macromolecules such as proteins. The possibility of examining such movements in an aqueous environment is particularly valuable since here proteins are not deprived of any motional degrees of freedom. Small angle x-ray scattering (SAXS) is a powerful method to study the structure and domain movements of proteins in solution. Here, we present a microfluidic cell for SAXS experiments, which is also transparent for THz radiation. Specifically, cell dimensions and material were optimized for both radiation sources. In addition, the polystyrene cell can be 3D printed and easily assembled. We demonstrate the practicality of our design for SAXS measurements on several proteins in solution.
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Affiliation(s)
- S Schewa
- University of Applied Sciences Lübeck, Mönkhofer Weg 239, 23562 Lübeck, Germany
| | - M A Schroer
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - T Zickmantel
- Physics Institute, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Y-H Song
- Physics Institute, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - C E Blanchet
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - A Yu Gruzinov
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - G Katona
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - D I Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - M Roessle
- University of Applied Sciences Lübeck, Mönkhofer Weg 239, 23562 Lübeck, Germany
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4
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Schroer MA, Schewa S, Blanchet CE, Gruzinov AY, Zickmantel T, Fiedler S, Katona G, Roessle M, Svergun DI. Recent developments towards high-flux time-resolved and terahertz SAXS experiments on the EMBL P12 BioSAXS beamline. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s2053273319089174] [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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5
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Gruzinov A, Blanchet CE, Schroer MA, Wieland DCF, Spilotros A, Franke D, Hajizadeh N, Jeffries CM, Fiedler S, Filippov S, Roessle M, Katona G, Svergun DI. High-flux time-resolved experiments and anomalous scattering at EMBL P12 beamline. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s2053273317089616] [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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6
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Beyerlein KR, Dierksmeyer D, Mariani V, Kuhn M, Sarrou I, Ottaviano A, Awel S, Knoska J, Fuglerud S, Jönsson O, Stern S, Wiedorn MO, Yefanov O, Adriano L, Bean R, Burkhardt A, Fischer P, Heymann M, Horke DA, Jungnickel KEJ, Kovaleva E, Lorbeer O, Metz M, Meyer J, Morgan A, Pande K, Panneerselvam S, Seuring C, Tolstikova A, Lieske J, Aplin S, Roessle M, White TA, Chapman HN, Meents A, Oberthuer D. Mix-and-diffuse serial synchrotron crystallography. IUCrJ 2017; 4:769-777. [PMID: 29123679 PMCID: PMC5668862 DOI: 10.1107/s2052252517013124] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 09/13/2017] [Indexed: 05/21/2023]
Abstract
Unravelling the interaction of biological macromolecules with ligands and substrates at high spatial and temporal resolution remains a major challenge in structural biology. The development of serial crystallography methods at X-ray free-electron lasers and subsequently at synchrotron light sources allows new approaches to tackle this challenge. Here, a new polyimide tape drive designed for mix-and-diffuse serial crystallography experiments is reported. The structure of lysozyme bound by the competitive inhibitor chitotriose was determined using this device in combination with microfluidic mixers. The electron densities obtained from mixing times of 2 and 50 s show clear binding of chitotriose to the enzyme at a high level of detail. The success of this approach shows the potential for high-throughput drug screening and even structural enzymology on short timescales at bright synchrotron light sources.
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Affiliation(s)
- Kenneth R. Beyerlein
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Correspondence e-mail: ,
| | | | - Valerio Mariani
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Manuela Kuhn
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Iosifina Sarrou
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Angelica Ottaviano
- Department of Physics, California State University, Northridge, California, USA
| | - Salah Awel
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany
| | - Juraj Knoska
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, 22607 Hamburg, Germany
| | - Silje Fuglerud
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics, Norwegian University of Science and Technology, Trondheim, Norway
| | - Olof Jönsson
- Department of Physics and Astronomy, Uppsala University, Uppsala, Sweden
| | - Stephan Stern
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- European X-ray Free-Electron Laser Facility GmbH (XFEL), Schenefeld, Germany
| | - Max O. Wiedorn
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, 22607 Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Luigi Adriano
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Richard Bean
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Anja Burkhardt
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Pontus Fischer
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Michael Heymann
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Daniel A. Horke
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany
| | | | - Elena Kovaleva
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Olga Lorbeer
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Markus Metz
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Jan Meyer
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Andrew Morgan
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Kanupriya Pande
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Carolin Seuring
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany
| | - Aleksandra Tolstikova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Julia Lieske
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Steve Aplin
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Thomas A. White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Henry N. Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, 22607 Hamburg, Germany
| | - Alke Meents
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Dominik Oberthuer
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Correspondence e-mail: ,
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Cianci M, Bourenkov G, Pompidor G, Karpics I, Kallio J, Bento I, Roessle M, Cipriani F, Fiedler S, Schneider TR. P13, the EMBL macromolecular crystallography beamline at the low-emittance PETRA III ring for high- and low-energy phasing with variable beam focusing. J Synchrotron Radiat 2017; 24:323-332. [PMID: 28009574 PMCID: PMC5182027 DOI: 10.1107/s1600577516016465] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 10/15/2016] [Indexed: 05/26/2023]
Abstract
The macromolecular crystallography P13 beamline is part of the European Molecular Biology Laboratory Integrated Facility for Structural Biology at PETRA III (DESY, Hamburg, Germany) and has been in user operation since mid-2013. P13 is tunable across the energy range from 4 to 17.5 keV to support crystallographic data acquisition exploiting a wide range of elemental absorption edges for experimental phase determination. An adaptive Kirkpatrick-Baez focusing system provides an X-ray beam with a high photon flux and tunable focus size to adapt to diverse experimental situations. Data collections at energies as low as 4 keV (λ = 3.1 Å) are possible due to a beamline design minimizing background and maximizing photon flux particularly at low energy (up to 1011 photons s-1 at 4 keV), a custom calibration of the PILATUS 6M-F detector for use at low energies, and the availability of a helium path. At high energies, the high photon flux (5.4 × 1011 photons s-1 at 17.5 keV) combined with a large area detector mounted on a 2θ arm allows data collection to sub-atomic resolution (0.55 Å). A peak flux of about 8.0 × 1012 photons s-1 is reached at 11 keV. Automated sample mounting is available by means of the robotic sample changer `MARVIN' with a dewar capacity of 160 samples. In close proximity to the beamline, laboratories have been set up for sample preparation and characterization; a laboratory specifically equipped for on-site heavy atom derivatization with a library of more than 150 compounds is available to beamline users.
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Affiliation(s)
- Michele Cianci
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, 22603 Hamburg, Germany
| | - Gleb Bourenkov
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, 22603 Hamburg, Germany
| | - Guillaume Pompidor
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, 22603 Hamburg, Germany
| | - Ivars Karpics
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, 22603 Hamburg, Germany
| | - Johanna Kallio
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, 22603 Hamburg, Germany
| | - Isabel Bento
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, 22603 Hamburg, Germany
| | - Manfred Roessle
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, 22603 Hamburg, Germany
- Fachhochschule Lübeck, Fachbereich Angewandte Naturwissenschaften, Mönkhofer Weg 239, 23562 Lübeck, Germany
| | - Florent Cipriani
- European Molecular Biology Laboratory, Institut Laue-Langevin, BP 181, 6 rue Jules Horowitz, 38042 Grenoble Cedex 9, France
| | - Stefan Fiedler
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, 22603 Hamburg, Germany
| | - Thomas R. Schneider
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, 22603 Hamburg, Germany
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Rajasekar KV, Lovering AL, Dancea F, Scott DJ, Harris SA, Bingle LEH, Roessle M, Thomas CM, Hyde EI, White SA. Flexibility of KorA, a plasmid-encoded, global transcription regulator, in the presence and the absence of its operator. Nucleic Acids Res 2016; 44:4947-56. [PMID: 27016739 PMCID: PMC4889941 DOI: 10.1093/nar/gkw191] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 03/08/2016] [Accepted: 03/11/2016] [Indexed: 12/03/2022] Open
Abstract
The IncP (Incompatibility group P) plasmids are important carriers in the spread of antibiotic resistance across Gram-negative bacteria. Gene expression in the IncP-1 plasmids is stringently controlled by a network of four global repressors, KorA, KorB, TrbA and KorC interacting cooperatively. Intriguingly, KorA and KorB can act as co-repressors at varying distances between their operators, even when they are moved to be on opposite sides of the DNA. KorA is a homodimer with the 101-amino acid subunits, folding into an N-terminal DNA-binding domain and a C-terminal dimerization domain. In this study, we have determined the structures of the free KorA repressor and two complexes each bound to a 20-bp palindromic DNA duplex containing its consensus operator sequence. Using a combination of X-ray crystallography, nuclear magnetic resonance spectroscopy, SAXS and molecular dynamics calculations, we show that the linker between the two domains is very flexible and the protein remains highly mobile in the presence of DNA. This flexibility allows the DNA-binding domains of the dimer to straddle the operator DNA on binding and is likely to be important in cooperative binding to KorB. Unexpectedly, the C-terminal domain of KorA is structurally similar to the dimerization domain of the tumour suppressor p53.
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Affiliation(s)
- Karthik V Rajasekar
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Andrew L Lovering
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Felician Dancea
- School of Cancer Studies, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - David J Scott
- School of Biosciences, Sutton Bonington Campus, University of Nottingham, Nottingham LE12 5RD, UK
| | - Sarah A Harris
- School of Physics and Astronomy and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Lewis E H Bingle
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | | | - Christopher M Thomas
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Eva I Hyde
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Scott A White
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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9
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Bojahr A, Gohlke M, Leitenberger W, Pudell J, Reinhardt M, von Reppert A, Roessle M, Sander M, Gaal P, Bargheer M. Second Harmonic Generation of Nanoscale Phonon Wave Packets. Phys Rev Lett 2015; 115:195502. [PMID: 26588396 DOI: 10.1103/physrevlett.115.195502] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Indexed: 05/06/2023]
Abstract
Phonons are often regarded as delocalized quasiparticles with certain energy and momentum. The anharmonic interaction of phonons determines macroscopic properties of the solid, such as thermal expansion or thermal conductivity, and a detailed understanding becomes increasingly important for functional nanostructures. Although phonon-phonon scattering processes depicted in simple wave-vector diagrams are the basis of theories describing these macroscopic phenomena, experiments directly accessing these coupling channels are scarce. We synthesize monochromatic acoustic phonon wave packets with only a few cycles to introduce nonlinear phononics as the acoustic counterpart to nonlinear optics. Control of the wave vector, bandwidth, and consequently spatial extent of the phonon wave packets allows us to observe nonlinear phonon interaction, in particular, second harmonic generation, in real time by wave-vector-sensitive Brillouin scattering with x-rays and optical photons.
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Affiliation(s)
- A Bojahr
- Institut für Physik and Astronomie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - M Gohlke
- Institut für Physik and Astronomie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - W Leitenberger
- Institut für Physik and Astronomie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - J Pudell
- Institut für Physik and Astronomie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - M Reinhardt
- Helmholtz Zentrum Berlin, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - A von Reppert
- Institut für Physik and Astronomie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - M Roessle
- Institut für Physik and Astronomie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - M Sander
- Institut für Physik and Astronomie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - P Gaal
- Helmholtz Zentrum Berlin, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - M Bargheer
- Institut für Physik and Astronomie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
- Helmholtz Zentrum Berlin, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
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10
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Blanchet CE, Spilotros A, Schwemmer F, Graewert MA, Kikhney A, Jeffries CM, Franke D, Mark D, Zengerle R, Cipriani F, Fiedler S, Roessle M, Svergun DI. Versatile sample environments and automation for biological solution X-ray scattering experiments at the P12 beamline (PETRA III, DESY). J Appl Crystallogr 2015; 48:431-443. [PMID: 25844078 PMCID: PMC4379436 DOI: 10.1107/s160057671500254x] [Citation(s) in RCA: 394] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 02/06/2015] [Indexed: 11/12/2023] Open
Abstract
A high-brilliance synchrotron P12 beamline of the EMBL located at the PETRA III storage ring (DESY, Hamburg) is dedicated to biological small-angle X-ray scattering (SAXS) and has been designed and optimized for scattering experiments on macromolecular solutions. Scatterless slits reduce the parasitic scattering, a custom-designed miniature active beamstop ensures accurate data normalization and the photon-counting PILATUS 2M detector enables the background-free detection of weak scattering signals. The high flux and small beam size allow for rapid experiments with exposure time down to 30-50 ms covering the resolution range from about 300 to 0.5 nm. P12 possesses a versatile and flexible sample environment system that caters for the diverse experimental needs required to study macromolecular solutions. These include an in-vacuum capillary mode for standard batch sample analyses with robotic sample delivery and for continuous-flow in-line sample purification and characterization, as well as an in-air capillary time-resolved stopped-flow setup. A novel microfluidic centrifugal mixing device (SAXS disc) is developed for a high-throughput screening mode using sub-microlitre sample volumes. Automation is a key feature of P12; it is controlled by a beamline meta server, which coordinates and schedules experiments from either standard or nonstandard operational setups. The integrated SASFLOW pipeline automatically checks for consistency, and processes and analyses the data, providing near real-time assessments of overall parameters and the generation of low-resolution models within minutes of data collection. These advances, combined with a remote access option, allow for rapid high-throughput analysis, as well as time-resolved and screening experiments for novice and expert biological SAXS users.
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Affiliation(s)
- Clement E. Blanchet
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, Hamburg, 22603, Germany
| | - Alessandro Spilotros
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, Hamburg, 22603, Germany
| | - Frank Schwemmer
- Laboratory for MEMS Applications, IMTEK – Department of Microsystems Engineering, University of Freiburg, Georges-Koegler-Allee 103, Freiburg, 79110, Germany
| | - Melissa A. Graewert
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, Hamburg, 22603, Germany
| | - Alexey Kikhney
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, Hamburg, 22603, Germany
| | - Cy M. Jeffries
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, Hamburg, 22603, Germany
| | - Daniel Franke
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, Hamburg, 22603, Germany
| | - Daniel Mark
- Laboratory for MEMS Applications, IMTEK – Department of Microsystems Engineering, University of Freiburg, Georges-Koegler-Allee 103, Freiburg, 79110, Germany
| | - Roland Zengerle
- Laboratory for MEMS Applications, IMTEK – Department of Microsystems Engineering, University of Freiburg, Georges-Koegler-Allee 103, Freiburg, 79110, Germany
| | - Florent Cipriani
- European Molecular Biology Laboratory, Grenoble Outstation, 6 rue Jules Horowitz, BP 181, Grenoble, 38042, France
| | - Stefan Fiedler
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, Hamburg, 22603, Germany
| | - Manfred Roessle
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, Hamburg, 22603, Germany
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, Hamburg, 22603, Germany
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11
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Broglie Daeppen M, Roessle M, Kiessling S, Soltermann A, Haile S, Huber G, Stoeckli S. PO-101: Podoplanin expression in oropharyngeal cancer influences staging and prognosis only in p16 negative tumors. Radiother Oncol 2015. [DOI: 10.1016/s0167-8140(15)34861-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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12
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Round A, Felisaz F, Fodinger L, Gobbo A, Huet J, Villard C, Blanchet CE, Pernot P, McSweeney S, Roessle M, Svergun DI, Cipriani F. BioSAXS Sample Changer: a robotic sample changer for rapid and reliable high-throughput X-ray solution scattering experiments. Acta Crystallogr D Biol Crystallogr 2015; 71:67-75. [PMID: 25615861 PMCID: PMC4304687 DOI: 10.1107/s1399004714026959] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 12/08/2014] [Indexed: 11/10/2022]
Abstract
Small-angle X-ray scattering (SAXS) of macromolecules in solution is in increasing demand by an ever more diverse research community, both academic and industrial. To better serve user needs, and to allow automated and high-throughput operation, a sample changer (BioSAXS Sample Changer) that is able to perform unattended measurements of up to several hundred samples per day has been developed. The Sample Changer is able to handle and expose sample volumes of down to 5 µl with a measurement/cleaning cycle of under 1 min. The samples are stored in standard 96-well plates and the data are collected in a vacuum-mounted capillary with automated positioning of the solution in the X-ray beam. Fast and efficient capillary cleaning avoids cross-contamination and ensures reproducibility of the measurements. Independent temperature control for the well storage and for the measurement capillary allows the samples to be kept cool while still collecting data at physiological temperatures. The Sample Changer has been installed at three major third-generation synchrotrons: on the BM29 beamline at the European Synchrotron Radiation Facility (ESRF), the P12 beamline at the PETRA-III synchrotron (EMBL@PETRA-III) and the I22/B21 beamlines at Diamond Light Source, with the latter being the first commercial unit supplied by Bruker ASC.
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Affiliation(s)
- Adam Round
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
- Unit for Virus Host Cell Interactions, Université Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Franck Felisaz
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
- Unit for Virus Host Cell Interactions, Université Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Lukas Fodinger
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Alexandre Gobbo
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Julien Huet
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
- Unit for Virus Host Cell Interactions, Université Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Cyril Villard
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Clement E. Blanchet
- European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
| | - Petra Pernot
- ESRF, 6 Rue Jules Horowitz, 38000 Grenoble, France
| | | | - Manfred Roessle
- European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
| | - Florent Cipriani
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
- Unit for Virus Host Cell Interactions, Université Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
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13
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Jäger J, Keese S, Roessle M, Steinert M, Schromm AB. Fusion of Legionella pneumophila outer membrane vesicles with eukaryotic membrane systems is a mechanism to deliver pathogen factors to host cell membranes. Cell Microbiol 2014; 17:607-20. [PMID: 25363599 DOI: 10.1111/cmi.12392] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 10/22/2014] [Accepted: 10/23/2014] [Indexed: 01/19/2023]
Abstract
The formation and release of outer membrane vesicles (OMVs) is a phenomenon observed in many bacteria, including Legionella pneumophila. During infection, this human pathogen primarily invades alveolar macrophages and replicates within a unique membrane-bound compartment termed Legionella-containing vacuole. In the current study, we analysed the membrane architecture of L. pneumophila OMVs by small-angle X-ray scattering and biophysically characterized OMV membranes. We investigated the interaction of L. pneumophila OMVs with model membranes by Förster resonance energy transfer and Fourier transform infrared spectroscopy. These experiments demonstrated the incorporation of OMV membrane material into liposomes composed of different eukaryotic phospholipids, revealing an endogenous property of OMVs to fuse with eukaryotic membranes. Cellular co-incubation experiments showed a dose- and time-dependent binding of fluorophore-labelled OMVs to macrophages. Trypan blue quenching experiments disclosed a rapid internalization of OMVs into macrophages at 37 and 4 °C. Purified OMVs induced tumour necrosis factor-α production in human macrophages at concentrations starting at 300 ng ml(-1). Experiments on HEK293-TLR2 and TLR4/MD-2 cell lines demonstrated a dominance of TLR2-dependent signalling pathways. In summary, we demonstrate binding, internalization and biological activity of L. pneumophila OMVs on human macrophages. Our data support OMV membrane fusion as a mechanism for the remote delivery of virulence factors to host cells.
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Affiliation(s)
- Jens Jäger
- Department of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
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14
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Keese SP, Brandenburg K, Roessle M, Schromm AB. Pulmonary surfactant protein A-induced changes in the molecular conformation of bacterial deep-rough LPS lead to reduced activity on human macrophages. Innate Immun 2013; 20:787-98. [PMID: 24122298 DOI: 10.1177/1753425913506269] [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] [Indexed: 11/15/2022] Open
Abstract
The lung is constantly exposed to immune stimulation by LPS from inhaled microorganisms. A primary mechanism to maintain immune homeostasis is based on anti-inflammatory regulation by surfactant protein A (SP-A), a secreted component of lung innate immunity. The architecture of LPS aggregates is strongly associated with biological activity. We therefore investigated whether SP-A affects the physico-chemical properties of LPS. Determination of the three-dimensional aggregate structure of LPS by small-angle X-ray scattering demonstrated that SP-A induced the formation of multi-lamellar aggregate structures. Determination of the acyl-chain-fluidity of LPS aggregates by Fourier transform infrared (FTIR) spectroscopy showed that the phase transition temperature of LPS was reduced in the presence of SP-A. The phosphate groups at the diglucosamine backbone of LPS represent important functional groups for the bioactivity of LPS. FTIR analysis revealed changes in the vibrational bands νas PO-(2), indicating an interaction of SP-A with the 1-phosphate, but not with the 4'-phosphate. The physico-chemical changes induced by SP-A were associated with up to 90% reduction in LPS-induced TNF-α-production by human macrophages. In conclusion, our data demonstrate that the SP-A/LPS interaction induces conformational changes in LPS aggregates leading to biologically less active structures, thereby providing a new molecular mechanism of immune modulation by SP-A.
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Affiliation(s)
- Susanne P Keese
- Division of Immunobiophysics, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Borstel, Germany
| | - Klaus Brandenburg
- Division of Biophysics, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Borstel, Germany
| | - Manfred Roessle
- European Molecular Biology Laboratory c/o DESY, Hamburg, Germany
| | - Andra B Schromm
- Division of Immunobiophysics, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Borstel, Germany
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15
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Züllig L, Roessle M, Weber C, Graf N, Haerle SK, Jochum W, Stoeckli SJ, Moch H, Huber GF. High sex determining region Y-box 2 expression is a negative predictor of occult lymph node metastasis in early squamous cell carcinomas of the oral cavity. Eur J Cancer 2013; 49:1915-22. [PMID: 23414798 DOI: 10.1016/j.ejca.2013.01.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Revised: 12/14/2012] [Accepted: 01/08/2013] [Indexed: 12/19/2022]
Abstract
BACKGROUND The transcription factor sex determining region Y (SRY)-box 2 (SOX2) (3q26.3-q27) has been recently identified as a recurrently activated major oncogene in squamous cell carcinoma of various sites. Its prognostic value in head and neck squamous cell carcinoma (HNSCC) is currently unclear. AIM To correlate SOX2 protein expression with the occurrence of occult lymph node metastasis and relapse free survival in early oral SCC. METHODS SOX2 expression in 120 T1/T2 oral SCC patients was evaluated using a tissue microarray technique. Intensity of SOX2 expression was quantified by assessing the Intensity/Reactivity Scores (IRSs). These scores were correlated with the lymph node status of biopsied sentinel lymph nodes and recurrence. Log rank univariate and Cox regression multivariate analysis was used to determine statistical significance. RESULTS Twenty-six of 120 primary tumours (21.7%) showed high SOX2 expression. High expression levels of SOX2 significantly correlated with negative lymph node status in univariate (p=0.001) and multivariate analysis (p=0.003). Sensitivity was found to be 95.6% with a negative predictive value of 92.3%. Specificity was 32% with a positive predictive value of 45.7%. CONCLUSION SOX2 up-regulation is frequent in early SCC of the oral cavity and associated with decreased risk of lymphatic metastasis. SOX2 immunohistochemistry may be used as a predictor for lymph node metastasis in squamous cell carcinoma of the oral cavity.
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Affiliation(s)
- L Züllig
- Otorhinolaryngology, Head and Neck Surgery, University Hospital Zurich, Frauenklinikstrasse 24, 8091 Zürich, Switzerland
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16
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Hofmann J, Heider C, Li W, Krausze J, Roessle M, Wilharm G. Recombinant production of Yersinia enterocolitica pyruvate kinase isoenzymes PykA and PykF. Protein Expr Purif 2013; 88:243-7. [PMID: 23384479 DOI: 10.1016/j.pep.2013.01.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 01/22/2013] [Indexed: 10/27/2022]
Abstract
The glycolytic enzyme pyruvate kinase (PK) generates ATP from ADP through substrate-level phosphorylation powered by the conversion of phosphoenolpyruvate to pyruvate. In contrast to other bacteria, Enterobacteriaceae, such as pathogenic yersiniae, harbour two pyruvate kinases encoded by pykA and pykF. The individual roles of these isoenzymes are poorly understood. In an attempt to make the Yersinia enterocolitica pyruvate kinases PykA and PykF amenable to structural and functional characterisation, we produced them untagged in Escherichia coli and purified them to near homogeneity through a combination of ion exchange and size exclusion chromatography, yielding more than 180 mg per litre of batch culture. The solution structure of PykA and PykF was analysed through small angle X-ray scattering which revealed the formation of PykA and PykF tetramers and confirmed the binding of the allosteric effector fructose-1,6-bisphosphate (FBP) to PykF but not to PykA.
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Affiliation(s)
- Julia Hofmann
- Robert Koch-Institute, Wernigerode Branch, Burgstr. 37, D-38855 Wernigerode, Germany
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17
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Biuković G, Basak S, Manimekalai MSS, Rishikesan S, Roessle M, Dick T, Rao SPS, Hunke C, Grüber G. Variations of subunit {varepsilon} of the Mycobacterium tuberculosis F1Fo ATP synthase and a novel model for mechanism of action of the tuberculosis drug TMC207. Antimicrob Agents Chemother 2013; 57:168-76. [PMID: 23089752 PMCID: PMC3535943 DOI: 10.1128/aac.01039-12] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [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: 05/13/2012] [Accepted: 10/11/2012] [Indexed: 11/20/2022] Open
Abstract
The subunit ε of bacterial F(1)F(O) ATP synthases plays an important regulatory role in coupling and catalysis via conformational transitions of its C-terminal domain. Here we present the first low-resolution solution structure of ε of Mycobacterium tuberculosis (Mtε) F(1)F(O) ATP synthase and the nuclear magnetic resonance (NMR) structure of its C-terminal segment (Mtε(103-120)). Mtε is significantly shorter (61.6 Å) than forms of the subunit in other bacteria, reflecting a shorter C-terminal sequence, proposed to be important in coupling processes via the catalytic β subunit. The C-terminal segment displays an α-helical structure and a highly positive surface charge due to the presence of arginine residues. Using NMR spectroscopy, fluorescence spectroscopy, and mutagenesis, we demonstrate that the new tuberculosis (TB) drug candidate TMC207, proposed to bind to the proton translocating c-ring, also binds to Mtε. A model for the interaction of TMC207 with both ε and the c-ring is presented, suggesting that TMC207 forms a wedge between the two rotating subunits by interacting with the residues W15 and F50 of ε and the c-ring, respectively. T19 and R37 of ε provide the necessary polar interactions with the drug molecule. This new model of the mechanism of TMC207 provides the basis for the design of new drugs targeting the F(1)F(O) ATP synthase in M. tuberculosis.
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Affiliation(s)
- Goran Biuković
- School of Biological Sciences, Nanyang Technological University, Singapore, Republic of Singapore
| | - Sandip Basak
- School of Biological Sciences, Nanyang Technological University, Singapore, Republic of Singapore
| | | | | | - Manfred Roessle
- European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY, Hamburg, Germany
| | - Thomas Dick
- National University of Singapore, Yong Loo Lin School of Medicine, Department of Microbiology, Singapore, Republic of Singapore
| | - Srinivasa P. S. Rao
- Novartis Institute for Tropical Diseases Pte. Ltd., Singapore, Republic of Singapore
| | - Cornelia Hunke
- School of Biological Sciences, Nanyang Technological University, Singapore, Republic of Singapore
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, Singapore, Republic of Singapore
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Sayers Z, Aydin M, Bal E, Yesilirmak F, Konarev PV, Petoukhov MV, Roessle M, Kikhney AG, Shang W, Svergun DI. Comparative Characterization of Apo-, Reconstituted- and In Vivo-Folded forms of a Durum Wheat Metallothionein. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.2209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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19
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Schneider TR, Bourenkov G, Cianci M, Roessle M, Svergun D, Cipriani F, Fiedler S. EMBL beamlines for life-science applications at PETRA III. Acta Crystallogr A 2012. [DOI: 10.1107/s0108767312097164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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20
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Dip PV, Saw WG, Roessle M, Marshansky V, Grüber G. Solution structure of subunit a, a 104-363, of the Saccharomyces cerevisiae V-ATPase and the importance of its C-terminus in structure formation. J Bioenerg Biomembr 2012; 44:341-50. [DOI: 10.1007/s10863-012-9442-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Accepted: 04/19/2012] [Indexed: 11/30/2022]
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21
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Blanchet CE, Zozulya AV, Kikhney AG, Franke D, Konarev PV, Shang W, Klaering R, Robrahn B, Hermes C, Cipriani F, Svergun DI, Roessle M. Instrumental setup for high-throughput small- and wide-angle solution scattering at the X33 beamline of EMBL Hamburg. J Appl Crystallogr 2012. [DOI: 10.1107/s0021889812013490] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
A setup is presented for automated high-throughput measurements of small-angle X-ray scattering (SAXS) from macromolecular solutions on the bending-magnet beamline X33 of EMBL at the storage ring DORIS-III (DESY, Hamburg). A new multi-cell compartment allows for rapid switching between in-vacuum and in-air operation, for digital camera assisted control of cell filling and for colour sample illumination. The beamline is equipped with a Pilatus 1 M-W pixel detector for SAXS and a Pilatus 300 k-W for wide-angle scattering (WAXS), and results from the use of the Pilatus detectors for scattering studies are reported. The setup provides a broad resolution range from 100 to 0.36 nm without the necessity of changing the sample-to-detector distance. A new optimized robotic sample changer is installed, permitting rapid and reliable automated sample loading and cell cleaning with a required sample volume of 40 µl. All the devices are fully integrated into the beamline control software system, ensuring fully automated and user-friendly operation (attended, unattended and remote) with a throughput of up to 15 measurements per hour.
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Yeo GC, Baldock C, Tuukkanen A, Roessle M, Dyksterhuis LB, Wise SG, Matthews J, Mithieux SM, Weiss AS. Tropoelastin bridge region positions the cell-interactive C terminus and contributes to elastic fiber assembly. Proc Natl Acad Sci U S A 2012; 109:2878-83. [PMID: 22328151 PMCID: PMC3286909 DOI: 10.1073/pnas.1111615108] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The tropoelastin monomer undergoes stages of association by coacervation, deposition onto microfibrils, and cross-linking to form elastic fibers. Tropoelastin consists of an elastic N-terminal coil region and a cell-interactive C-terminal foot region linked together by a highly exposed bridge region. The bridge region is conveniently positioned to modulate elastic fiber assembly through association by coacervation and its proximity to dominant cross-linking domains. Tropoelastin constructs that either modify or remove the entire bridge and downstream regions were assessed for elastogenesis. These constructs focused on a single alanine substitution (R515A) and a truncation (M155n) at the highly conserved arginine 515 site that borders the bridge. Each form displayed less efficient coacervation, impaired hydrogel formation, and decreased dermal fibroblast attachment compared to wild-type tropoelastin. The R515A mutant protein additionally showed reduced elastic fiber formation upon addition to human retinal pigmented epithelium cells and dermal fibroblasts. The small-angle X-ray scattering nanostructure of the R515A mutant protein revealed greater conformational flexibility around the bridge and C-terminal regions. This increased flexibility of the R515A mutant suggests that the tropoelastin R515 residue stabilizes the structure of the bridge region, which is critical for elastic fiber assembly.
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Affiliation(s)
- Giselle C Yeo
- School of Molecular Bioscience, University of Sydney, New South Wales 2006, Australia
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23
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Cipriani F, Felisaz F, Fodinger L, Gobbo A, Huet J, Moya R, Villard C, Round A, Roessle M, Svergun D, Pernot P. An automated sample environment for biological solution scattering experiments at third-generation synchrotrons. Acta Crystallogr A 2011. [DOI: 10.1107/s0108767311093147] [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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Rochel N, Ciesielski F, Godet J, Moman E, Roessle M, Peluso-Iltis C, Moulin M, Haertlein M, Callow P, Mély Y, Svergun DI, Moras D. Common architecture of nuclear receptor heterodimers on DNA direct repeat elements with different spacings. Nat Struct Mol Biol 2011; 18:564-70. [DOI: 10.1038/nsmb.2054] [Citation(s) in RCA: 153] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Accepted: 01/27/2011] [Indexed: 11/09/2022]
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Li QA, Mavrodi DV, Thomashow LS, Roessle M, Blankenfeldt W. Ligand binding induces an ammonia channel in 2-amino-2-desoxyisochorismate (ADIC) synthase PhzE. J Biol Chem 2011; 286:18213-21. [PMID: 21454481 DOI: 10.1074/jbc.m110.183418] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
PhzE utilizes chorismate and glutamine to synthesize 2-amino-2-desoxyisochorismate (ADIC) in the first step of phenazine biosynthesis. The PhzE monomer contains both a chorismate-converting menaquinone, siderophore, tryptophan biosynthesis (MST) and a type 1 glutamine amidotransferase (GATase1) domain connected by a 45-residue linker. We present here the crystal structure of PhzE from Burkholderia lata 383 in a ligand-free open and ligand-bound closed conformation at 2.9 and 2.1 Å resolution, respectively. PhzE arranges in an intertwined dimer such that the GATase1 domain of one chain provides NH(3) to the MST domain of the other. This quaternary structure was confirmed by small angle x-ray scattering. Binding of chorismic acid, which was found converted to benzoate and pyruvate in the MST active centers of the closed form, leads to structural rearrangements that establish an ammonia transport channel approximately 25 Å in length within each of the two MST/GATase1 functional units of the dimer. The assignment of PhzE as an ADIC synthase was confirmed by mass spectrometric analysis of the product, which was also visualized at 1.9 Å resolution by trapping in crystals of an inactive mutant of PhzD, an isochorismatase that catalyzes the subsequent step in phenazine biosynthesis. Unlike in some of the related anthranilate synthases, no allosteric inhibition was observed in PhzE. This can be attributed to a tryptophan residue of the protein blocking the potential regulatory site. Additional electron density in the GATase1 active center was identified as zinc, and it was demonstrated that Zn(2+), Mn(2+), and Ni(2+) reduce the activity of PhzE.
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Affiliation(s)
- Qi-Ang Li
- Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
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Toh YK, Kamariah N, Maurer-Stroh S, Roessle M, Eisenhaber F, Adhikari S, Eisenhaber B, Grüber G. Structural insight into the glycosylphosphatidylinositol transamidase subunits PIG-K and PIG-S from yeast. J Struct Biol 2011; 173:271-81. [DOI: 10.1016/j.jsb.2010.11.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Revised: 09/16/2010] [Accepted: 11/30/2010] [Indexed: 10/18/2022]
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Basak S, Gayen S, Thaker YR, Manimekalai MSS, Roessle M, Hunke C, Grüber G. Solution structure of subunit F (Vma7p) of the eukaryotic V(1)V(O) ATPase from Saccharomyces cerevisiae derived from SAXS and NMR spectroscopy. Biochim Biophys Acta 2010; 1808:360-8. [PMID: 20840841 DOI: 10.1016/j.bbamem.2010.09.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Revised: 09/03/2010] [Accepted: 09/07/2010] [Indexed: 11/26/2022]
Abstract
Vacuolar ATPases use the energy derived from ATP hydrolysis, catalyzed in the A(3)B(3) sector of the V(1) ATPase to pump protons via the membrane-embedded V(O) sector. The energy coupling between the two sectors occurs via the so-called central stalk, to which subunit F does belong. Here we present the first low resolution structure of recombinant subunit F (Vma7p) of a eukaryotic V-ATPase from Saccharomyces cerevisiae, analyzed by small angle X-ray scattering (SAXS). The protein is divided into a 5.5nm long egg-like shaped region, connected via a 1.5nm linker to a hook-like segment at one end. Circular dichroism spectroscopy revealed that subunit F comprises of 43% α-helix, 32% β-sheet and a 25% random coil arrangement. To determine the localization of the N- and C-termini in the protein, the C-terminal truncated form of F, F(1-94) was produced and analyzed by SAXS. Comparison of the F(1-94) shape with the one of subunit F showed the missing hook-like region in F(1-94), supported by the decreased D(max) value of F(1-94) (7.0nm), and indicating that the hook-like region consists of the C-terminal residues. The NMR solution structure of the C-terminal peptide, F(90-116), was solved, displaying an α-helical region between residues 103 and 113. The F(90-116) solution structure fitted well in the hook-like region of subunit F. Finally, the arrangement of subunit F within the V(1) ATPase is discussed.
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Affiliation(s)
- Sandip Basak
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
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Li Q, Mavrodi DV, Thomashow LS, Roessle M, Blankenfeldt W. Structural and functional studies of phenazine biosynthesis protein PhzE, a 2-amino-2-desoxyisochorismate synthase. Acta Crystallogr A 2010. [DOI: 10.1107/s0108767310096728] [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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Bourenkov G, Cianci M, Fiedler S, Roessle M, Schneider TR. Microfocus beamline for macromolecular crystallography MX2 @ PETRA III. Acta Crystallogr A 2010. [DOI: 10.1107/s0108767310097448] [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] [Indexed: 11/10/2022] Open
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Richter W, Vogel V, Howe J, Steiniger F, Brauser A, Koch MH, Roessle M, Gutsmann T, Garidel P, Mäntele W, Brandenburg K. Morphology, size distribution, and aggregate structure of lipopolysaccharide and lipid A dispersions from enterobacterial origin. Innate Immun 2010; 17:427-38. [PMID: 20682588 DOI: 10.1177/1753425910372434] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Lipopolysaccharides (LPSs) from Gram-negative bacteria are strong elicitors of the human immune systems. There is strong evidence that aggregates and not monomers of LPS play a decisive role at least in the initial stages of cell activation of immune cells such as mononuclear cells. In previous reports, it was shown that the biologically most active part of enterobacterial LPS, hexa-acyl bisphosphorylated lipid A, adopts a particular supramolecular conformation, a cubic aggregate structure. However, little is known about the size and morphology of these aggregates, regarding the fact that LPS may have strong variations in the length of the saccharide chains (various rough mutant and smooth-form LPS). Thus, in the present paper, several techniques for the determination of details of the aggregate morphology such as freeze-fracture and cryo-electron microscopy, analytical ultracentrifugation, laser backscattering analysis, and small-angle X-ray scattering were applied for various endotoxin (lipid A and different LPS) preparations. The data show a variety of different morphologies not only for different endotoxins but also when comparing different applied techniques. The data are interpreted with respect to the suitability of the single techniques, in particular on the basis of available literature data.
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Affiliation(s)
- Walter Richter
- Elektronenmikroskopisches Zentrum, Friedrich-Schiller-Universität Jena, Germany
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31
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Hunke C, Tadwal VS, Manimekalai MSS, Roessle M, Grüber G. The effect of NBD-Cl in nucleotide-binding of the major subunit alpha and B of the motor proteins F1FO ATP synthase and A1AO ATP synthase. J Bioenerg Biomembr 2010; 42:1-10. [PMID: 20082212 DOI: 10.1007/s10863-009-9266-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Accepted: 12/10/2009] [Indexed: 11/24/2022]
Abstract
Subunit alpha of the Escherichia coli F(1)F(O) ATP synthase has been produced, and its low-resolution structure has been determined. The monodispersity of alpha allowed the studies of nucleotide-binding and inhibitory effect of 4-Chloro-7-nitrobenzofurazan (NBD-Cl) to ATP/ADP-binding. Binding constants (K ( d )) of 1.6 microM of bound MgATP-ATTO-647N and 2.9 microM of MgADP-ATTO-647N have been determined from fluorescence correlation spectroscopy data. A concentration of 51 microM and 55 microM of NBD-Cl dropped the MgATP-ATTO-647N and MgADP-ATTO-647N binding capacity to 50% (IC(50)), respectively. In contrast, no effect was observed in the presence of N,N'-dicyclohexylcarbodiimide. As subunit alpha is the homologue of subunit B of the A(1)A(O) ATP synthase, the interaction of NBD-Cl with B of the A-ATP synthase from Methanosarcina mazei Gö1 has also been shown. The data reveal a reduction of nucleotide-binding of B due to NBD-Cl, resulting in IC(50) values of 41 microM and 42 microM for MgATP-ATTO-647N and MgADP-ATTO-647N, respectively.
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Affiliation(s)
- Cornelia Hunke
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Republic of Singapore
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Brandenburg K, Howe J, Sanchez-Gomez S, Garidel P, Roessle M, Andra J, Jerala R, Zweytick D, Lohner K, Rappolt M, Blondelle S, Moriyon I, de Tejada G. Effective Antimicrobial and Anti-Endotoxin Activity of Cationic Peptides Based on Lactoferricin: A Biophysical and Microbiological Study. ACTA ACUST UNITED AC 2010. [DOI: 10.2174/187152110790886736] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Pires R, Hartlieb B, Signor L, Schoehn G, Lata S, Roessle M, Moriscot C, Popov S, Hinz A, Jamin M, Boyer V, Sadoul R, Forest E, Svergun DI, Göttlinger HG, Weissenhorn W. A crescent-shaped ALIX dimer targets ESCRT-III CHMP4 filaments. Structure 2009; 17:843-56. [PMID: 19523902 DOI: 10.1016/j.str.2009.04.007] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2009] [Revised: 03/27/2009] [Accepted: 04/15/2009] [Indexed: 12/20/2022]
Abstract
ALIX recruits ESCRT-III CHMP4 and is involved in membrane remodeling during endosomal receptor sorting, budding of some enveloped viruses, and cytokinesis. We show that ALIX dimerizes via the middle domain (ALIX(-V)) in solution. Structural modeling based on small angle X-ray scattering (SAXS) data reveals an elongated crescent-shaped conformation for dimeric ALIX lacking the proline-rich domain (ALIX(BRO1-V)). Mutations at the dimerization interface prevent dimerization and induce an open elongated monomeric conformation of ALIX(-V) as determined by SAXS modeling. ALIX dimerizes in vivo and dimeric ALIX colocalizes with CHMP4B upon coexpression. We show further that ALIX dimerization affects HIV-1 budding. C-terminally truncated activated CHMP4B retaining the ALIX binding site forms linear, circular, and helical filaments in vitro, which can be bridged by ALIX. Our data suggest that dimeric ALIX represents the active form that interacts with ESCRT-III CHMP4 polymers and functions as a scaffolding protein during membrane remodeling processes.
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Affiliation(s)
- Ricardo Pires
- Unit of Virus Host Cell Interactions (UVHCI) UMI 3265, Université Joseph Fourier-EMBL-CNRS, 6 rue Jules Horowitz, 38042 Grenoble, Cedex 9, France
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35
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Schromm AB, Reiling N, Howe J, Wiesmüller KH, Roessle M, Brandenburg K. Influence of serum on the immune recognition of a synthetic lipopeptide mimetic of the 19-kDa lipoprotein from Mycobacterium tuberculosis. Innate Immun 2009; 16:213-25. [DOI: 10.1177/1753425909339232] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The innate immune response provides a critical first-line defense against Mycobacterium tuberculosis, an intracellular pathogen that represents a major health threat world-wide. A synthetic lipopeptide (LP) mimicking the lipid moiety of the cell-wall associated 19-kDa lipoprotein from M. tuberculosis has recently been assigned an important role in the induction of an antibacterial immune response in host macrophages. Here, we present experimental data on the biological activities and the biophysical mechanisms underlying cell activation by synthetic 19-kDa M. tuberculosis-derived lipopeptide (Mtb-LP). Investigation of the geometry of the LP (i.e. the molecular conformation and supramolecular aggregate structure) and the preference for membrane intercalation provide an explanation for the biological activities of the mycobacterial LP. Cell activation by low concentrations of Mtb-LP was enhanced by the lipopolysaccharide—binding protein and CD14. However, surprisingly, we found that activation of human macrophages to induce pro- as well as antiinflammatory mediators (tumor necrosis factor(TNF)-α, Interleukin(IL)-6, IL-8, and IL-10) in response to the Mtb-LP is strongly reduced in the presence of serum. This observation could be confirmed for the immune response of murine macrophages which showed a strongly enhanced TNF-α release in the absence of serum, suggesting that the molecular mechanisms of immune recognition of the Mtb-LP are tailored to the ambient conditions of the lung.
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Affiliation(s)
- Andra B. Schromm
- Department of Molecular Infection Biology, Emmy Noether Group of Immunobiophysics, Leibniz-Center for Medicine and Biosciences, Research Center Borstel, Borstel, Germany,
| | - Norbert Reiling
- Division of Molecular Infection Biology, Leibniz-Center for Medicine and Biosciences, Research Center Borstel, Borstel, Germany
| | - Jörg Howe
- Division of Biophysics, Leibniz-Center for Medicine and Biosciences, Research Center Borstel, Borstel, Germany
| | | | - Manfred Roessle
- European Molecular Biology Laboratory c/o DESY, Hamburg, Germany
| | - Klaus Brandenburg
- Division of Biophysics, Leibniz-Center for Medicine and Biosciences, Research Center Borstel, Borstel, Germany
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Berry R, Jowitt TA, Ferrand J, Roessle M, Grossmann JG, Canty-Laird EG, Kammerer RA, Kadler KE, Baldock C. Role of dimerization and substrate exclusion in the regulation of bone morphogenetic protein-1 and mammalian tolloid. Proc Natl Acad Sci U S A 2009; 106:8561-6. [PMID: 19429706 PMCID: PMC2689009 DOI: 10.1073/pnas.0812178106] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [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: 12/02/2008] [Indexed: 11/18/2022] Open
Abstract
The bone morphogenetic protein (BMP)-1/tolloid metalloproteinases are evolutionarily conserved enzymes that are fundamental to dorsal-ventral patterning and tissue morphogenesis. The lack of knowledge regarding how these proteinases recognize and cleave their substrates represents a major hurdle to understanding tissue assembly and embryonic patterning. Although BMP-1 and mammalian tolloid (mTLD) are splice variants, it is puzzling why BMP-1, which lacks 3 of the 7 noncatalytic domains present in all other family members, is the most effective proteinase. Using a combination of single-particle electron microscopy, small-angle X-ray scattering, and other biophysical measurements in solution, we show that mTLD, but not BMP-1, forms a calcium-ion-dependent dimer under physiological conditions. Using a domain deletion approach, we provide evidence that EGF2, which is absent in BMP-1, is critical to the formation of the dimer. Based on a combination of structural and functional data, we propose that mTLD activity is regulated by a substrate exclusion mechanism. These results provide a mechanistic insight into how alternative splicing of the Bmp1 gene produces 2 proteinases with differing biological activities and have broad implications for regulation of BMP-1/mTLD and related proteinases during BMP signaling and tissue assembly.
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Affiliation(s)
- Richard Berry
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Thomas A. Jowitt
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Johanna Ferrand
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Manfred Roessle
- European Molecular Biology Laboratory-Hamburg Outstation, c/o Deutsches Elektronen Synchrotron, 22603 Hamburg, Germany; and
| | - J. Günter Grossmann
- Synchrotron Radiation Department, Council for Central Laboratory of the Research Councils, Daresbury Laboratory, Warrington WA4 4AD, United Kingdom
| | - Elizabeth G. Canty-Laird
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Richard A. Kammerer
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Karl E. Kadler
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Clair Baldock
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
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Gerber S, Wulf M, Milkereit G, Vill V, Howe J, Roessle M, Garidel P, Gutsmann T, Brandenburg K. Phase diagrams of monoacylated amide-linked disaccharide glycolipids. Chem Phys Lipids 2009; 158:118-30. [DOI: 10.1016/j.chemphyslip.2009.01.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Revised: 01/13/2009] [Accepted: 01/13/2009] [Indexed: 11/27/2022]
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Schmid A, Neumayer W, Trülzsch K, Israel L, Imhof A, Roessle M, Sauer G, Richter S, Lauw S, Eylert E, Eisenreich W, Heesemann J, Wilharm G. Cross-talk between type three secretion system and metabolism in Yersinia. J Biol Chem 2009; 284:12165-77. [PMID: 19244229 DOI: 10.1074/jbc.m900773200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Pathogenic yersiniae utilize a type three secretion system (T3SS) to inject Yop proteins into host cells in order to undermine their immune response. YscM1 and YscM2 proteins have been reported to be functionally equivalent regulators of the T3SS in Yersinia enterocolitica. Here, we show by affinity purification, native gel electrophoresis and small angle x-ray scattering that both YscM1 and YscM2 bind to phosphoenolpyruvate carboxylase (PEPC) of Y. enterocolitica. Under in vitro conditions, YscM1, but not YscM2, was found to inhibit PEPC with an apparent IC(50) of 4 mum (K(i) = 1 mum). To analyze the functional roles of PEPC, YscM1, and YscM2 in Yop-producing bacteria, cultures of Y. enterocolitica wild type and mutants defective in the formation of PEPC, YscM1, or YscM2, respectively, were grown under low calcium conditions in the presence of [U-(13)C(6)]glucose. The isotope compositions of secreted Yop proteins and nine amino acids from cellular proteins were analyzed by mass spectrometry. The data indicate that a considerable fraction of oxaloacetate used as precursor for amino acids was derived from [(13)C(3)]phosphoenolpyruvate by the catalytic action of PEPC in the wild-type strain but not in the PEPC(-) mutant. The data imply that PEPC is critically involved in replenishing the oxaloacetate pool in the citrate cycle under virulence conditions. In the YscM1(-) and YscM2(-) mutants, increased rates of pyruvate formation via glycolysis or the Entner-Doudoroff pathway, of oxaloacetate formation via the citrate cycle, and of amino acid biosynthesis suggest that both regulators trigger the central metabolism of Y. enterocolitica. We propose a "load-and-shoot cycle" model to account for the cross-talk between T3SS and metabolism in pathogenic yersiniae.
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Affiliation(s)
- Annika Schmid
- Department of Bacteriology, Max von Pettenkofer-Institute for Hygiene and Medical Microbiology, Pettenkoferstrasse 9a, D-80336 Munich, Germany
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Høiberg-Nielsen R, Tofteng Shelton AP, Sørensen KK, Roessle M, Svergun DI, Thulstrup PW, Jensen KJ, Arleth L. 3- Instead of 4-Helix Formation in a De Novo Designed Protein in Solution Revealed by Small-Angle X-ray Scattering. Chembiochem 2008; 9:2663-72. [DOI: 10.1002/cbic.200800263] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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40
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Groer GJ, Haslbeck M, Roessle M, Gessner A. Structural characterization of soluble E-Syt2. FEBS Lett 2008; 582:3941-7. [DOI: 10.1016/j.febslet.2008.10.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2008] [Revised: 10/17/2008] [Accepted: 10/22/2008] [Indexed: 11/29/2022]
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Round AR, Franke D, Moritz S, Huchler R, Fritsche M, Malthan D, Klaering R, Svergun DI, Roessle M. Automated sample-changing robot for solution scattering experiments at the EMBL Hamburg SAXS station X33. J Appl Crystallogr 2008; 41:913-917. [PMID: 25484841 PMCID: PMC4233401 DOI: 10.1107/s0021889808021018] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2008] [Accepted: 07/07/2008] [Indexed: 11/10/2022] Open
Abstract
An automated sample changer for small-angle X-ray scattering (SAXS) on protein in solution is reported. The technical implementation and integration to a synchrotron-based SAXS beamline is described. There is a rapidly increasing interest in the use of synchrotron small-angle X-ray scattering (SAXS) for large-scale studies of biological macromolecules in solution, and this requires an adequate means of automating the experiment. A prototype has been developed of an automated sample changer for solution SAXS, where the solutions are kept in thermostatically controlled well plates allowing for operation with up to 192 samples. The measuring protocol involves controlled loading of protein solutions and matching buffers, followed by cleaning and drying of the cell between measurements. The system was installed and tested at the X33 beamline of the EMBL, at the storage ring DORIS-III (DESY, Hamburg), where it was used by over 50 external groups during 2007. At X33, a throughput of approximately 12 samples per hour, with a failure rate of sample loading of less than 0.5%, was observed. The feedback from users indicates that the ease of use and reliability of the user operation at the beamline were greatly improved compared with the manual filling mode. The changer is controlled by a client–server-based network protocol, locally and remotely. During the testing phase, the changer was operated in an attended mode to assess its reliability and convenience. Full integration with the beamline control software, allowing for automated data collection of all samples loaded into the machine with remote control from the user, is presently being implemented. The approach reported is not limited to synchrotron-based SAXS but can also be used on laboratory and neutron sources.
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Affiliation(s)
- A R Round
- EMBL Hamburg, Building 25a, Notkestrasse 85, 22603 Hamburg, Germany
| | - D Franke
- EMBL Hamburg, Building 25a, Notkestrasse 85, 22603 Hamburg, Germany
| | - S Moritz
- Fraunhofer Institute for Manufacturing, Engineering and Automation IPA, Department of Production and Process Automation, Nobelstrasse 12, 70659 Stuttgart, Germany
| | - R Huchler
- Fraunhofer Institute for Manufacturing, Engineering and Automation IPA, Department of Production and Process Automation, Nobelstrasse 12, 70659 Stuttgart, Germany
| | - M Fritsche
- Fraunhofer Institute for Manufacturing, Engineering and Automation IPA, Department of Production and Process Automation, Nobelstrasse 12, 70659 Stuttgart, Germany
| | - D Malthan
- Fraunhofer Institute for Manufacturing, Engineering and Automation IPA, Department of Production and Process Automation, Nobelstrasse 12, 70659 Stuttgart, Germany
| | - R Klaering
- EMBL Hamburg, Building 25a, Notkestrasse 85, 22603 Hamburg, Germany
| | - D I Svergun
- EMBL Hamburg, Building 25a, Notkestrasse 85, 22603 Hamburg, Germany ; Institute of Crystallography, Russian Academy of Sciences, Leninsky prospekt 59, 117333 Moscow, Russian Federation
| | - M Roessle
- EMBL Hamburg, Building 25a, Notkestrasse 85, 22603 Hamburg, Germany
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Mashburn-Warren L, Howe J, Garidel P, Richter W, Steiniger F, Roessle M, Brandenburg K, Whiteley M. Interaction of quorum signals with outer membrane lipids: insights into prokaryotic membrane vesicle formation. Mol Microbiol 2008; 69:491-502. [PMID: 18630345 PMCID: PMC2615190 DOI: 10.1111/j.1365-2958.2008.06302.x] [Citation(s) in RCA: 175] [Impact Index Per Article: 10.9] [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] [Indexed: 12/31/2022]
Abstract
Bacteria have evolved elaborate communication strategies to co-ordinate their group activities, a process termed quorum sensing (QS). Pseudomonas aeruginosa is an opportunistic pathogen that utilizes QS for diverse activities, including disease pathogenesis. P. aeruginosa has evolved a novel communication system in which the signal molecule 2-heptyl-3-hydroxy-4-quinolone (Pseudomonas Quinolone Signal, PQS) is trafficked between cells via membrane vesicles (MVs). Not only is PQS packaged into MVs, it is required for MV formation. Although MVs are involved in important biological processes aside from signalling, the molecular mechanism of MV formation is unknown. To provide insight into the molecular mechanism of MV formation, we examined the interaction of PQS with bacterial lipids. Here, we show that PQS interacts strongly with the acyl chains and 4′-phosphate of bacterial lipopolysaccharide (LPS). Using PQS derivatives, we demonstrate that the alkyl side-chain and third position hydroxyl of PQS are critical for these interactions. Finally, we show that PQS stimulated purified LPS to form liposome-like structures. These studies provide molecular insight into P. aeruginosa MV formation and demonstrate that quorum signals serve important non-signalling functions.
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Howe J, Garidel P, Roessle M, Richter W, Alexander C, Fournier K, Mach JP, Waelli T, Gorczynski RM, Ulmer AJ, Zähringer U, Hartmann A, Rietschel ET, Brandenburg K. Structural investigations into the interaction of hemoglobin and part structures with bacterial endotoxins. Innate Immun 2008; 14:39-49. [PMID: 18387918 DOI: 10.1177/1753425907087257] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
An understanding of details of the interaction mechanisms of bacterial endotoxins (lipopolysaccharide, LPS) with the oxygen transport protein hemoglobin is still lacking, despite its high biological relevance. Here, a biophysical investigation into the endotoxin:hemoglobin interaction is presented which comprises the use of various rough mutant LPS as well as free lipid A; in addition to the complete hemoglobin molecule from fetal sheep extract, also the partial structure alpha-chain and the heme-free sample are studied. The investigations comprise the determination of the gel-to-liquid crystalline phase behaviour of the acyl chains of LPS, the ultrastructure (type of aggregate structure and morphology) of the endotoxins, and the incorporation of the hemoglobins into artificial immune cell membranes and into LPS. Our data suggest a model for the interaction between Hb and LPS in which hemoglobins do not react strongly with the hydrophilic or with the hydrophobic moiety of LPS, but with the complete endotoxin aggregate. Hb is able to incorporate into LPS with the longitudinal direction parallel to the lipid A double-layer. Although this does not lead to a strong disturbance of the LPS acyl chain packing, the change of the curvature leads to a slightly conical molecular shape with a change of the three-dimensional arrangement from unilamellar into cubic LPS aggregates. Our previous results show that cubic LPS structures exhibit strong endotoxic activity. The property of Hb on the physical state of LPS described here may explain the observation of an increase in LPS-mediating endotoxicity due to the action of Hb.
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Affiliation(s)
- Jörg Howe
- Forschungszentrum Borstel, Leibniz-Zentrum für Medizin und Biowissenschaften, Borstel, Germany
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Howe J, Garidel P, Wulf M, Gerber S, Milkereit G, Vill V, Roessle M, Brandenburg K. Structural polymorphism of hydrated monoacylated maltose glycolipids. Chem Phys Lipids 2008; 155:31-7. [PMID: 18671955 DOI: 10.1016/j.chemphyslip.2008.07.002] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2008] [Revised: 06/30/2008] [Accepted: 07/01/2008] [Indexed: 11/29/2022]
Abstract
The physico-chemical properties of three fully hydrated monoacyl maltoside glycolipids were investigated with Fourier-transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC) and small-angle X-ray scattering (SAXS). The different synthesized maltoside glycoconjugates vary in the length and saturation of the fatty acid moiety, whereas the constant head group region contains a beta-linked maltose with a OC(2)-NH spacer. The compounds with saturated acyl chains showed a complex pattern of temperature-dependent behaviour, regarding the adopted three-dimensional aggregate structure of the molecules and the main phase transition from the gel to liquid crystalline phase of the acyl chains. A substitution of the saturated acyl chain with an unsaturated acyl chain led to a complete change of the structural preferences, from a high ordered stacking of the bilayers to an unilamellar arrangement of completely disordered and fluid membranes. The presence of the NH group in the spacer, compared to the compounds lacking the NH group allows the formation of a hydrogen bonding network, which influences the observed phase properties. The results of these studies of the hydrated monoacylated maltose glycolipids are discussed in relation to the thermotropic phase properties of the pure compounds in the absence of water.
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Affiliation(s)
- Jörg Howe
- Forschungszentrum Borstel, LG Biophysik, Parkallee 10, D-23845 Borstel, Germany
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Lata S, Roessle M, Solomons J, Jamin M, Gőttlinger HG, Svergun DI, Weissenhorn W. Structural basis for autoinhibition of ESCRT-III CHMP3. J Mol Biol 2008; 378:818-27. [PMID: 18395747 PMCID: PMC2756293 DOI: 10.1016/j.jmb.2008.03.030] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.5] [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: 12/19/2007] [Revised: 03/06/2008] [Accepted: 03/11/2008] [Indexed: 01/26/2023]
Abstract
Endosomal sorting complexes required for transport (ESCRT-0, ESCRT-I, ESCRT-II, and ESCRT-III) are selectively recruited to cellular membranes to exert their function in diverse processes, such as multivesicular body biogenesis, enveloped virus budding, and cytokinesis. ESCRT-III is composed of members of the charged multivesicular body protein (CHMP) family--cytosolic proteins that are targeted to membranes via yet unknown signals. Membrane targeting is thought to result in a membrane-associated protein network that presumably acts at a late budding step. Here we provide structural evidence based on small-angle X-ray scattering data that ESCRT-III CHMP3 can adopt two conformations in solution: a closed globular form that most likely represents the cytosolic conformation and an open extended conformation that might represent the activated form of CHMP3. Both the closed and open conformations of CHMP3 interact with AMSH with high affinity. Although the C-terminal region of CHMP3 is required for AMSH interaction, a peptide thereof reveals only weak binding to AMSH, suggesting that other regions of CHMP3 contribute to the high-affinity interaction. Thus, AMSH, including its MIT (microtubule interacting and transport) domain, interacts with ESCRT-III CHMP3 differently from reported Vps4 MIT domain-CHMP protein interactions.
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Affiliation(s)
- Suman Lata
- Unit for Virus Host Cell Interaction, UMR 5233 UJF-EMBL-CNRS, 6 rue Jules Horowitz 38042 Grenoble cedex 9, France
| | - Manfred Roessle
- European Molecular Biology Laboratory, Notkestrasse 85, 22603 Hamburg, Germany
| | - Julianna Solomons
- Unit for Virus Host Cell Interaction, UMR 5233 UJF-EMBL-CNRS, 6 rue Jules Horowitz 38042 Grenoble cedex 9, France
| | - Marc Jamin
- Unit for Virus Host Cell Interaction, UMR 5233 UJF-EMBL-CNRS, 6 rue Jules Horowitz 38042 Grenoble cedex 9, France
| | - Heinrich G. Gőttlinger
- Program in Gene Function and Expression, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Dimitri I. Svergun
- European Molecular Biology Laboratory, Notkestrasse 85, 22603 Hamburg, Germany
| | - Winfried Weissenhorn
- Unit for Virus Host Cell Interaction, UMR 5233 UJF-EMBL-CNRS, 6 rue Jules Horowitz 38042 Grenoble cedex 9, France
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King-Scott J, Nowak E, Mylonas E, Panjikar S, Roessle M, Svergun DI, Tucker PA. The Structure of a Full-length Response Regulator from Mycobacterium tuberculosis in a Stabilized Three-dimensional Domain-swapped, Activated State. J Biol Chem 2007; 282:37717-29. [DOI: 10.1074/jbc.m705081200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Thaker YR, Roessle M, Grüber G. The boxing glove shape of subunit d of the yeast V-ATPase in solution and the importance of disulfide formation for folding of this protein. J Bioenerg Biomembr 2007; 39:275-89. [PMID: 17896169 DOI: 10.1007/s10863-007-9089-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [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: 04/27/2007] [Accepted: 05/15/2007] [Indexed: 10/22/2022]
Abstract
The low resolution structure of subunit d (Vma6p) of the Saccharomyces cerevisiae V-ATPase was determined from solution X-ray scattering data. The protein is a boxing glove-shaped molecule consisting of two distinct domains, with a width of about 6.5 nm and 3.5 nm, respectively. To understand the importance of the N- and C-termini inside the protein, four truncated forms of subunit d (d (11-345), d (38-345), d (1-328) and d (1-298)) and mutant subunit d, with a substitution of Cys329 against Ser, were expressed, and only d (11-345), containing all six cysteine residues was soluble. The structural properties of d depends strongly on the presence of a disulfide bond. Changes in response to disulfide formation have been studied by fluorescence- and CD spectroscopy, and biochemical approaches. Cysteins, involved in disulfide bridges, were analyzed by MALDI-TOF mass spectrometry. Finally, the solution structure of subunit d will be discussed in terms of the topological arrangement of the V(1)V(O) ATPase.
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MESH Headings
- Amino Acid Sequence
- Base Sequence
- Circular Dichroism
- DNA Primers/genetics
- DNA, Fungal/genetics
- Disulfides/chemistry
- Models, Molecular
- Molecular Sequence Data
- Molecular Weight
- Mutagenesis, Site-Directed
- Nuclear Magnetic Resonance, Biomolecular
- Protein Folding
- Protein Structure, Tertiary
- Protein Subunits
- Saccharomyces cerevisiae/enzymology
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae Proteins/chemistry
- Saccharomyces cerevisiae Proteins/genetics
- Scattering, Small Angle
- Sequence Homology, Amino Acid
- Spectrometry, Fluorescence
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Vacuolar Proton-Translocating ATPases/chemistry
- Vacuolar Proton-Translocating ATPases/genetics
- X-Ray Diffraction
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Affiliation(s)
- Youg R Thaker
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
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King-Scott J, Nowack E, Panjikar S, Mylonas E, Roessle M, Tucker PA. RegX3 – a full-length response regulator that exhibits 3D-domain swapping. Acta Crystallogr A 2007. [DOI: 10.1107/s0108767307097565] [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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49
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Mumtsidu E, Makhov AM, Roessle M, Bathke A, Tucker PA. Structural features of the Bluetongue virus NS2 protein. J Struct Biol 2007; 160:157-67. [PMID: 17888678 DOI: 10.1016/j.jsb.2007.07.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2007] [Revised: 07/27/2007] [Accepted: 07/27/2007] [Indexed: 11/20/2022]
Abstract
Bluetongue virus (BTV) non-structural protein 2 (NS2) belongs to a class of highly conserved proteins found in members of the orbivirus genus of the reoviridae. NS2 forms large multimeric complexes, localizes to cytoplasmic inclusion bodies in the infected cells and binds non-sequence specifically single-stranded RNA (ssRNA). Due to its ability to bind ssRNA, it has been suggested that the protein is involved in the selection and condensation of the BTV ssRNA segments prior to genome encapsidation. We have previously determined the crystal structure of the 177 amino acid N-terminal domain, sufficient for ssRNA binding ability of NS2, to 2.4A resolution. The C-terminal domain, as determined at low resolution using small-angle X-ray scattering, is an elongated dimer. This domain expressed in insect cells is phosphorylated at S249 and S259. Electron microscopy of the full-length protein shows a variety of species with the largest having a ring-like appearance. Based on the electron micrographs, the crystal structure of the N-terminal domain and the structure of the C-terminal domain reported here, we propose a model for a decamer of the full-length protein. This decamer changes conformation upon binding of a non-hydrolysable ATP analogue.
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Affiliation(s)
- Eleni Mumtsidu
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Notkestrasse 85, D22603 Hamburg, Germany
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50
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Vestergaard B, Groenning M, Roessle M, Kastrup JS, van de Weert M, Flink JM, Frokjaer S, Gajhede M, Svergun DI. A helical structural nucleus is the primary elongating unit of insulin amyloid fibrils. PLoS Biol 2007; 5:e134. [PMID: 17472440 PMCID: PMC1858711 DOI: 10.1371/journal.pbio.0050134] [Citation(s) in RCA: 188] [Impact Index Per Article: 11.1] [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: 09/27/2006] [Accepted: 03/09/2007] [Indexed: 12/31/2022] Open
Abstract
Although amyloid fibrillation is generally believed to be a nucleation-dependent process, the nuclei are largely structurally uncharacterized. This is in part due to the inherent experimental challenge associated with structural descriptions of individual components in a dynamic multi-component equilibrium. There are indications that oligomeric aggregated precursors of fibrillation, and not mature fibrils, are the main cause of cytotoxicity in amyloid disease. This further emphasizes the importance of characterizing early fibrillation events. Here we present a kinetic x-ray solution scattering study of insulin fibrillation, revealing three major components: insulin monomers, mature fibrils, and an oligomeric species. Low-resolution three-dimensional structures are determined for the fibril repeating unit and for the oligomer, the latter being a helical unit composed of five to six insulin monomers. This helical oligomer is likely to be a structural nucleus, which accumulates above the supercritical concentration used in our experiments. The growth rate of the fibrils is proportional to the amount of the helical oligomer present in solution, suggesting that these oligomers elongate the fibrils. Hence, the structural nucleus and elongating unit in insulin amyloid fibrillation may be the same structural component above supercritical concentrations. A novel elongation pathway of insulin amyloid fibrils is proposed, based on the shape and size of the fibrillation precursor. The distinct helical oligomer described in this study defines a conceptually new basis of structure-based drug design against amyloid diseases.
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Affiliation(s)
- Bente Vestergaard
- Department of Medicinal Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Minna Groenning
- Department of Pharmaceutics and Analytical Chemistry, University of Copenhagen, Copenhagen, Denmark
- Biophysics, Novo Nordisk A/S, Bagsvaerd, Denmark
| | - Manfred Roessle
- Hamburg Outstation, European Molecular Biology Laboratory, Hamburg, Germany
| | - Jette S Kastrup
- Department of Medicinal Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Marco van de Weert
- Department of Pharmaceutics and Analytical Chemistry, University of Copenhagen, Copenhagen, Denmark
| | | | - Sven Frokjaer
- Department of Pharmaceutics and Analytical Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Michael Gajhede
- Department of Medicinal Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Dmitri I Svergun
- Hamburg Outstation, European Molecular Biology Laboratory, Hamburg, Germany
- Institute of Crystallography, Russian Academy of Sciences, Moscow, Russia
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