Search

Your search keyword '"Thomas Ursby"' showing total 6 results
Start Over Author "Thomas Ursby" Language english
6 results on '"Thomas Ursby"'

1. Kilohertz serial crystallography with the JUNGFRAU detector at a fourth-generation synchrotron source

Author

Filip Leonarski, Jie Nan, Zdenek Matej, Quentin Bertrand, Antonia Furrer, Ishkhan Gorgisyan, Monika Bjelčić, Michal Kepa, Hannah Glover, Viktoria Hinger, Thomas Eriksson, Aleksander Cehovin, Mikel Eguiraun, Piero Gasparotto, Aldo Mozzanica, Tobias Weinert, Ana Gonzalez, Jörg Standfuss, Meitian Wang, Thomas Ursby, and Florian Dworkowski

Subjects
macromolecular crystallography, time-resolved serial crystallography, x-ray detectors, fourth-generation synchrotrons, jungfrau detector, protein structure, data networks, Crystallography, QD901-999
Abstract

Serial and time-resolved macromolecular crystallography are on the rise. However, beam time at X-ray free-electron lasers is limited and most third-generation synchrotron-based macromolecular crystallography beamlines do not offer the necessary infrastructure yet. Here, a new setup is demonstrated, based on the JUNGFRAU detector and Jungfraujoch data-acquisition system, that enables collection of kilohertz serial crystallography data at fourth-generation synchrotrons. More importantly, it is shown that this setup is capable of collecting multiple-time-point time-resolved protein dynamics at kilohertz rates, allowing the probing of microsecond to second dynamics at synchrotrons in a fraction of the time needed previously. A high-quality complete X-ray dataset was obtained within 1 min from lysozyme microcrystals, and the dynamics of the light-driven sodium-pump membrane protein KR2 with a time resolution of 1 ms could be demonstrated. To make the setup more accessible for researchers, downstream data handling and analysis will be automated to allow on-the-fly spot finding and indexing, as well as data processing.

Published
2023
Full Text
View/download PDF

2. Fast, automated, continuous energy scans for experimental phasing at the BioMAX beamline

Author

Ishkhan Gorgisyan, Paul Bell, Michele Cascella, Mikel Eguiraun, Áureo Freitas, Julio Lidon-Simon, Jie Nan, Carla Takahashi, Hamed Tarawneh, Thomas Ursby, and Ana Gonzalez

Subjects
mx beamline, mad sad phasing, continuous energy scan, flying scan, motion synchronization, Nuclear and particle physics. Atomic energy. Radioactivity, QC770-798, Crystallography, QD901-999
Abstract

In X-ray macromolecular crystallography (MX), single-wavelength anomalous dispersion (SAD) and multi-wavelength anomalous dispersion (MAD) techniques are commonly used for obtaining experimental phases. For an MX synchrotron beamline to support SAD and MAD techniques it is a prerequisite to have a reliable, fast and well automated energy scan routine. This work reports on a continuous energy scan procedure newly implemented at the BioMAX MX beamline at MAX IV Laboratory. The continuous energy scan is fully automated, capable of measuring accurate fluorescence counts over the absorption edge of interest while minimizing the sample exposure to X-rays, and is about a factor of five faster compared with a conventional step scan previously operational at BioMAX. The implementation of the continuous energy scan facilitates the prompt access to the anomalous scattering data, required for the SAD and MAD experiments.

Published
2023
Full Text
View/download PDF

3. Vibrational stability of a cryocooled horizontal double-crystal monochromator

Author

Brian Norsk Jensen, Paw Kristiansen, Thomas Ursby, and Ulf Johansson

Subjects
0301 basic medicine, 030103 biophysics, Nuclear and High Energy Physics, 01 natural sciences, horizontal double-crystal monochromator, law.invention, Crystal, 03 medical and health sciences, Optics, vibrational measurements, law, 0103 physical sciences, monochromator cryocooling, Instrumentation, Monochromator, Radiation, 010308 nuclear & particles physics, Chemistry, business.industry, Liquid nitrogen, Research Papers, Volumetric flow rate, Vibration, Active cooling, Atomic physics, vibrational performance, business, Beam (structure), Relative pitch
Abstract

The 25 nrad RMS, 1–2500 Hz, vibrational performance of a horizontal double-crystal monochromator is presented., The vibrational stability of a horizontally deflecting double-crystal monochromator (HDCM) is investigated. Inherently a HDCM will preserve the vertical beam stability better than a ‘normal’ vertical double-crystal monochromator as the vibrations of a HDCM will almost exclusively affect the horizontal stability. Here both the relative pitch vibration between the first and second crystal and the absolute pitch vibration of the second crystal are measured. All reported measurements are obtained under active cooling by means of flowing liquid nitrogen (LN2). It is found that it is favorable to circulate the LN2 at high pressures and low flow rates (up to 5.9 bar and down to 3 l min−1 is tested) to attain low vibrations. An absolute pitch stability of the second crystal of 18 nrad RMS, 2–2500 Hz, and a relative pitch stability between the two crystals of 25 nrad RMS, 1–2500 Hz, is obtained under cryocooling conditions that allow for 1516 W to be adsorbed by the LN2 before it vaporizes.

Published
2016

4. Automation and Experience of Controlled Crystal Dehydration: Results from the European Synchrotron HC1 Collaboration

Author

Marjolein M. G. M. Thunnissen, Sandor Brockhauser, Thomas L-M. Sorensen, Florent Cipriani, Uwe Mueller, Silvia Russi, Manfred S. Weiss, Matthew W. Bowler, Thomas Ursby, Olof Svensson, Juan Sanchez-Weatherby, Michael G. Bowler, Alexandre Gobbo, European Molecular Biology Laboratory [Grenoble] (EMBL), Unit for Virus Host-Cell Interactions [Grenoble] (UVHCI), Centre National de la Recherche Scientifique (CNRS)-European Molecular Biology Laboratory [Grenoble] (EMBL)-Université Joseph Fourier - Grenoble 1 (UJF), Macromolecular Crystallography - Helmholtz Zentrum Berlin (HZB MX), Helmholtz-Zentrum Berlin für Materialien und Energie GmbH (HZB), DIAMOND Light source, Lund Univ, Ctr Mol Prot Sci, Dept Biochem & Struct Biol, SE-22100 Lund, Sweden, Lund Univ, Max Lab 4, SE-22100 Lund, Sweden, Department of Physics [Oxford], University of Oxford [Oxford], and European Synchrotron Radiation Facility (ESRF)

Subjects
0303 health sciences, business.industry, Computer science, 030303 biophysics, Nanotechnology, General Chemistry, Condensed Matter Physics, Automation, Synchrotron, law.invention, Crystal, 03 medical and health sciences, Light source, Beamline, law, [CHIM]Chemical Sciences, General Materials Science, Inhouse research on structure dynamics and function of matter, business, Process engineering, 030304 developmental biology
Abstract

International audience; Controlled dehydration of macromolecular crystals can lead to significant improvements in crystalline order, which often manifests itself in higher diffraction quality. Devices that can accurately control the humidity surrounding crystals on a beamline have led to this technique being increasingly adopted as experiments become easier and more reproducible. However, these experiments are often carried out by trial and error, and in order to facilitate and streamline them four European synchrotrons have established a collaboration around the HC1b dehydration device. The MAX IV Laboratory, Diamond Light Source, BESSY II, and the EMBL Grenoble Outstation/ESRF have pooled information gathered from user experiments, and on the use of the device, to propose a set of guidelines for these experiments. Here, we present the status and automation of the installations, advice on how best to perform experiments using the device, and an analysis of successful experiments that begins to show some trends in the type of protocols required by some systems. The dehydration methods shown are applicable to any device that allows control of the relative humidity of the air surrounding a macromolecular crystal

Published
2015
Full Text
View/download PDF

5. Mycobacterium tuberculosis thymidylate kinase: structural studies of intermediates along the reaction pathway

Author

Marc Delarue, E. Fioravanti, Thomas Ursby, Dominique Bourgeois, Hélène Munier-Lehmann, Ahmed Haouz, Laboratoire de Cristallographie et Cristallogénèse des Protéines (LCCP), Institut de biologie structurale (IBS - UMR 5075 ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), European Synchrotron Radiation Facility (ESRF), Biochimie Structurale, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Chimie Structurale des Macromolécules (CSM), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)

Subjects
Models, Molecular, Conformational change, Stereochemistry, Protein Conformation, [SDV]Life Sciences [q-bio], Crystallography, X-Ray, Thymidylate kinase, Catalysis, Substrate Specificity, 03 medical and health sciences, Structural Biology, Transferase, Moiety, Molecular Biology, Magnesium ion, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, biology, Chemistry, 030302 biochemistry & molecular biology, Active site, Mycobacterium tuberculosis, 3. Good health, Enzyme, biology.protein, Phosphorylation, Nucleoside-Phosphate Kinase
Abstract

International audience; Mycobacterium tuberculosis TMP kinase (TMPK(Mtub)) represents a promising target for developing drugs against tuberculosis because the configuration of its active site is unique in the TMPK family. To help elucidate the phosphorylation mechanism employed by this enzyme, structural changes occurring upon binding of substrates and subsequent catalysis were investigated by protein crystallography. Six new structures of TMPK(Mtub) were solved at a resolution better than 2.3A, including the first structure of an apo-TMPK, obtained by triggering catalysis in a crystal of a TMPK(Mtub)-TMP complex, which resulted in the release of the TDP product. A series of snapshots along the reaction pathway is obtained, revealing the closure of the active site in going from an empty to a fully occupied state, suggestive of an induced-fit mechanism typical of NMPKs. However, in TMPK(Mtub) the LID closure couples to the binding with an unusual location for a magnesium ion coordinating TMP in the active site. Our data suggest strongly that this ion is required for catalysis, acting as a clamp, possibly in concert with Arg95, to neutralise electrostatic repulsion between the anionic substrates, optimise their proper alignment and activate them through direct and water-mediated interactions. The 3'-hydroxyl moiety of TMP, critical to metal stabilisation, appears to be a target of choice for the design of potent inhibitors. On the other hand, the usual NTP-bound magnesium is not seen in our structures and Arg14, a P-loop residue unique to TMPK(Mtub), may take over its role. Therefore, TMPK(Mtub) seems to have swapped the use of a metal ion as compared with e.g. human TMPK. Finally, TTP was observed in crystals of TMPK(Mtub), locked by Arg14, thus providing a structural explanation for the observed inhibitory effect of TTP putatively involved in a mechanism of feedback regulation of the enzymatic activity.

Published
2003
Full Text
View/download PDF

6. Cryophotolysis of caged compounds: a technique for trapping intermediate states in protein crystals

Author

Maurice Goeldner, Thomas Ursby, Marc Delarue, Dominique Bourgeois, Martin Weik, E. Fioravanti, Laboratoire de Cristallographie et Cristallogénèse des Protéines (LCCP), Institut de biologie structurale (IBS - UMR 5075 ), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), European Synchrotron Radiation Facility (ESRF), Utrecht University [Utrecht], Biochimie Structurale, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Laboratoire de chimie bioorganique (LCB), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), This work was supported by the EU Biotechnology program BIO4-CT98-0354. MW was supported by an EMBO long-term fellowship and is grateful to J. Kroon, P. Gros, I. Silman and J. Sussman for many fruitful discussions., We thank Serge van Calenbergh, University of Leuven for synthesis of NPE-TMP, Ahmed Haouz, Pasteur Institute for enzymatic studies of TMPKmt and Hélène Munier-Lehmann, Pasteur Institute for providing the purified TMPKmt enzyme, Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Models, Molecular, Reaction mechanism, reaction intermediates, cryophotolysis, Quantum yield, Reaction intermediate, Crystallography, X-Ray, 010402 general chemistry, Photochemistry, 01 natural sciences, Crystal, 03 medical and health sciences, Adenosine Triphosphate, Photosensitivity, Structural Biology, [CHIM.CRIS]Chemical Sciences/Cristallography, Phosphorylation, 030304 developmental biology, 0303 health sciences, Binding Sites, Photolysis, Chemistry, thymidylate kinase, X-Rays, Mycobacterium tuberculosis, General Medicine, 0104 chemical sciences, Cold Temperature, caged compounds, Radiolysis, X-ray crystallography, Spectrophotometry, Ultraviolet, Nucleoside-Phosphate Kinase, Protein crystallization
Abstract

International audience; Caged compounds in combination with protein crystallography represent a valuable tool in studies of enzyme reaction intermediates. To date, photochemical triggering of reactions has been performed close to room temperature. Synchronous reaction initiation has only been achieved with enzymes of relatively slow turnover (

Published
2002
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results