1
|
Machine Learning Applied for Spectra Classification in X-ray Free Electorn Laser Sciences. DATA SCIENCE JOURNAL 2022. [DOI: 10.5334/dsj-2022-015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
2
|
Helliwell JR. Raw diffraction data are our ground truth from which all subsequent workflows develop. Acta Crystallogr D Struct Biol 2022; 78:683-689. [PMID: 35647915 PMCID: PMC9159283 DOI: 10.1107/s2059798322003795] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 04/06/2022] [Indexed: 11/11/2022] Open
Abstract
Defining best practice in science is challenging. International consensus is facilitated by the International Science Council via its members such as the International Union of Crystallography (IUCr). The crystallographic community has many decades of tradition linking articles with the underpinning data, and is admired across all sciences accordingly. Crystallography has always been at the forefront of harnessing new technology in the service of consensus. Technology has provided new vast data-archiving opportunities, allowing the preservation of raw diffraction data, along with article and database depositions of a model's coordinates and associated structure factors. The raw diffraction data, which can now be preserved, are the ground truth from which all subsequent workflows develop. Journal editorial boards provide a practical forum for setting the criteria to decide if a study's files are truly the version of record. Within that, reality involves a variance of reasonable workflows. But what is a reasonable variance? Workflows must be detailed carefully by authors in explaining what they have done. There is a great, and increasing, diversity of macromolecular crystallography analyses, and yet an increased constraint on how much can be written in an article about the workflow used. Raw data provide the ultimate reproducibility evidence. A part of reproducibility and replicability is using an agreed vocabulary; the meaning of words such as precision and accuracy and, more recently, the confidence of a protein structure prediction should feature in approaching `truth'.
Collapse
|
3
|
Nanao M, Basu S, Zander U, Giraud T, Surr J, Guijarro M, Lentini M, Felisaz F, Sinoir J, Morawe C, Vivo A, Beteva A, Oscarsson M, Caserotto H, Dobias F, Flot D, Nurizzo D, Gigmes J, Foos N, Siebrecht R, Roth T, Theveneau P, Svensson O, Papp G, Lavault B, Cipriani F, Barrett R, Clavel C, Leonard G. ID23-2: an automated and high-performance microfocus beamline for macromolecular crystallography at the ESRF. JOURNAL OF SYNCHROTRON RADIATION 2022; 29:581-590. [PMID: 35254323 PMCID: PMC8900849 DOI: 10.1107/s1600577522000984] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/28/2022] [Indexed: 05/30/2023]
Abstract
ID23-2 is a fixed-energy (14.2 keV) microfocus beamline at the European Synchrotron Radiation Facility (ESRF) dedicated to macromolecular crystallography. The optics and sample environment have recently been redesigned and rebuilt to take full advantage of the upgrade of the ESRF to the fourth generation Extremely Brilliant Source (ESRF-EBS). The upgraded beamline now makes use of two sets of compound refractive lenses and multilayer mirrors to obtain a highly intense (>1013 photons s-1) focused microbeam (minimum size 1.5 µm × 3 µm full width at half-maximum). The sample environment now includes a FLEX-HCD sample changer/storage system, as well as a state-of-the-art MD3Up high-precision multi-axis diffractometer. Automatic data reduction and analysis are also provided for more advanced protocols such as synchrotron serial crystallographic experiments.
Collapse
Affiliation(s)
- Max Nanao
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Shibom Basu
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Ulrich Zander
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Thierry Giraud
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - John Surr
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Matias Guijarro
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Mario Lentini
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Franck Felisaz
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Jeremy Sinoir
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Christian Morawe
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Amparo Vivo
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Antonia Beteva
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Marcus Oscarsson
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Hugo Caserotto
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Fabien Dobias
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - David Flot
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Didier Nurizzo
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Jonathan Gigmes
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Nicolas Foos
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | | | - Thomas Roth
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Pascal Theveneau
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Olof Svensson
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Gergely Papp
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | | | - Florent Cipriani
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Ray Barrett
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Carole Clavel
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Gordon Leonard
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| |
Collapse
|
4
|
Schulz EC, Henderson SR, Illarionov B, Crosskey T, Southall SM, Krichel B, Uetrecht C, Fischer M, Wilmanns M. The crystal structure of mycobacterial epoxide hydrolase A. Sci Rep 2020; 10:16539. [PMID: 33024154 PMCID: PMC7538969 DOI: 10.1038/s41598-020-73452-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 09/16/2020] [Indexed: 01/08/2023] Open
Abstract
The human pathogen Mycobacterium tuberculosis is the causative agent of tuberculosis resulting in over 1 million fatalities every year, despite decades of research into the development of new anti-TB compounds. Unlike most other organisms M. tuberculosis has six putative genes for epoxide hydrolases (EH) of the α/β-hydrolase family with little known about their individual substrates, suggesting functional significance for these genes to the organism. Due to their role in detoxification, M. tuberculosis EH’s have been identified as potential drug targets. Here, we demonstrate epoxide hydrolase activity of M. thermoresistibile epoxide hydrolase A (Mth-EphA) and report its crystal structure in complex with the inhibitor 1,3-diphenylurea at 2.0 Å resolution. Mth-EphA displays high sequence similarity to its orthologue from M. tuberculosis and generally high structural similarity to α/β-hydrolase EHs. The structure of the inhibitor bound complex reveals the geometry of the catalytic residues and the conformation of the inhibitor. Comparison to other EHs from mycobacteria allows insight into the active site plasticity with respect to substrate specificity. We speculate that mycobacterial EHs may have a narrow substrate specificity providing a potential explanation for the genetic repertoire of epoxide hydrolase genes in M. tuberculosis.
Collapse
Affiliation(s)
- Eike C Schulz
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chausee 149, 22761, Hamburg, Germany. .,European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22603, Hamburg, Germany.
| | - Sara R Henderson
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22603, Hamburg, Germany.,Norwich Medical School, Rosalind Franklin Road, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Boris Illarionov
- Hamburg School of Food Science, Institute of Food Chemistry, Universität Hamburg, Grindelallee 117, 20146, Hamburg, Germany
| | - Thomas Crosskey
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22603, Hamburg, Germany
| | - Stacey M Southall
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22603, Hamburg, Germany.,Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, UK
| | - Boris Krichel
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistraße 52, 20251, Hamburg, Germany
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistraße 52, 20251, Hamburg, Germany.,European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Markus Fischer
- Hamburg School of Food Science, Institute of Food Chemistry, Universität Hamburg, Grindelallee 117, 20146, Hamburg, Germany
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22603, Hamburg, Germany.,University of Hamburg Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| |
Collapse
|
5
|
Hauf S, Heisen B, Aplin S, Beg M, Bergemann M, Bondar V, Boukhelef D, Danilevsky C, Ehsan W, Essenov S, Fabbri R, Flucke G, Fulla Marsa D, Göries D, Giovanetti G, Hickin D, Jarosiewicz T, Kamil E, Khakhulin D, Klimovskaia A, Kluyver T, Kirienko Y, Kuhn M, Maia L, Mamchyk D, Mariani V, Mekinda L, Michelat T, Münnich A, Padee A, Parenti A, Santos H, Silenzi A, Teichmann M, Weger K, Wiggins J, Wrona K, Xu C, Youngman C, Zhu J, Fangohr H, Brockhauser S. The Karabo distributed control system. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:1448-1461. [PMID: 31490132 DOI: 10.1107/s1600577519006696] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 05/09/2019] [Indexed: 06/10/2023]
Abstract
The Karabo distributed control system has been developed to address the challenging requirements of the European X-ray Free Electron Laser facility, including complex and custom-made hardware, high data rates and volumes, and close integration of data analysis for distributed processing and rapid feedback. Karabo is a pluggable, distributed application management system forming a supervisory control and data acquisition environment as part of a distributed control system. Karabo provides integrated control of hardware, monitoring, data acquisition and data analysis on distributed hardware, allowing rapid control feedback based on complex algorithms. Services exist for access control, data logging, configuration management and situational awareness through alarm indicators. The flexible framework enables quick response to the changing requirements in control and analysis, and provides an efficient environment for development, and a single interface to make all changes immediately available to operators and experimentalists.
Collapse
Affiliation(s)
- Steffen Hauf
- European X-ray Free Electron Laser Facility GmbH, Holzkoppel 4, Schenefeld, Germany
| | - Burkhard Heisen
- European X-ray Free Electron Laser Facility GmbH, Holzkoppel 4, Schenefeld, Germany
| | - Steve Aplin
- Centre for Free Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Marijan Beg
- European X-ray Free Electron Laser Facility GmbH, Holzkoppel 4, Schenefeld, Germany
| | - Martin Bergemann
- European X-ray Free Electron Laser Facility GmbH, Holzkoppel 4, Schenefeld, Germany
| | - Valerii Bondar
- European X-ray Free Electron Laser Facility GmbH, Holzkoppel 4, Schenefeld, Germany
| | - Djelloul Boukhelef
- European X-ray Free Electron Laser Facility GmbH, Holzkoppel 4, Schenefeld, Germany
| | - Cyril Danilevsky
- European X-ray Free Electron Laser Facility GmbH, Holzkoppel 4, Schenefeld, Germany
| | - Wajid Ehsan
- European X-ray Free Electron Laser Facility GmbH, Holzkoppel 4, Schenefeld, Germany
| | - Sergey Essenov
- European X-ray Free Electron Laser Facility GmbH, Holzkoppel 4, Schenefeld, Germany
| | - Riccardo Fabbri
- European X-ray Free Electron Laser Facility GmbH, Holzkoppel 4, Schenefeld, Germany
| | - Gero Flucke
- European X-ray Free Electron Laser Facility GmbH, Holzkoppel 4, Schenefeld, Germany
| | - Daniel Fulla Marsa
- European X-ray Free Electron Laser Facility GmbH, Holzkoppel 4, Schenefeld, Germany
| | - Dennis Göries
- European X-ray Free Electron Laser Facility GmbH, Holzkoppel 4, Schenefeld, Germany
| | - Gabriele Giovanetti
- European X-ray Free Electron Laser Facility GmbH, Holzkoppel 4, Schenefeld, Germany
| | - David Hickin
- European X-ray Free Electron Laser Facility GmbH, Holzkoppel 4, Schenefeld, Germany
| | - Tobiasz Jarosiewicz
- European X-ray Free Electron Laser Facility GmbH, Holzkoppel 4, Schenefeld, Germany
| | - Ebad Kamil
- European X-ray Free Electron Laser Facility GmbH, Holzkoppel 4, Schenefeld, Germany
| | - Dmitry Khakhulin
- European X-ray Free Electron Laser Facility GmbH, Holzkoppel 4, Schenefeld, Germany
| | - Anna Klimovskaia
- European X-ray Free Electron Laser Facility GmbH, Holzkoppel 4, Schenefeld, Germany
| | - Thomas Kluyver
- European X-ray Free Electron Laser Facility GmbH, Holzkoppel 4, Schenefeld, Germany
| | - Yury Kirienko
- European X-ray Free Electron Laser Facility GmbH, Holzkoppel 4, Schenefeld, Germany
| | - Manuela Kuhn
- Centre for Free Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Luis Maia
- European X-ray Free Electron Laser Facility GmbH, Holzkoppel 4, Schenefeld, Germany
| | - Denys Mamchyk
- European X-ray Free Electron Laser Facility GmbH, Holzkoppel 4, Schenefeld, Germany
| | - Valerio Mariani
- Centre for Free Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Leonce Mekinda
- European X-ray Free Electron Laser Facility GmbH, Holzkoppel 4, Schenefeld, Germany
| | - Thomas Michelat
- European X-ray Free Electron Laser Facility GmbH, Holzkoppel 4, Schenefeld, Germany
| | - Astrid Münnich
- European X-ray Free Electron Laser Facility GmbH, Holzkoppel 4, Schenefeld, Germany
| | - Anna Padee
- European X-ray Free Electron Laser Facility GmbH, Holzkoppel 4, Schenefeld, Germany
| | - Andrea Parenti
- European X-ray Free Electron Laser Facility GmbH, Holzkoppel 4, Schenefeld, Germany
| | - Hugo Santos
- European X-ray Free Electron Laser Facility GmbH, Holzkoppel 4, Schenefeld, Germany
| | - Alessandro Silenzi
- European X-ray Free Electron Laser Facility GmbH, Holzkoppel 4, Schenefeld, Germany
| | - Martin Teichmann
- European X-ray Free Electron Laser Facility GmbH, Holzkoppel 4, Schenefeld, Germany
| | - Kerstin Weger
- European X-ray Free Electron Laser Facility GmbH, Holzkoppel 4, Schenefeld, Germany
| | - John Wiggins
- European X-ray Free Electron Laser Facility GmbH, Holzkoppel 4, Schenefeld, Germany
| | - Krzysztof Wrona
- European X-ray Free Electron Laser Facility GmbH, Holzkoppel 4, Schenefeld, Germany
| | - Chen Xu
- European X-ray Free Electron Laser Facility GmbH, Holzkoppel 4, Schenefeld, Germany
| | - Christopher Youngman
- European X-ray Free Electron Laser Facility GmbH, Holzkoppel 4, Schenefeld, Germany
| | - Jun Zhu
- European X-ray Free Electron Laser Facility GmbH, Holzkoppel 4, Schenefeld, Germany
| | - Hans Fangohr
- European X-ray Free Electron Laser Facility GmbH, Holzkoppel 4, Schenefeld, Germany
| | - Sandor Brockhauser
- European X-ray Free Electron Laser Facility GmbH, Holzkoppel 4, Schenefeld, Germany
| |
Collapse
|
6
|
Svensson O, Gilski M, Nurizzo D, Bowler MW. A comparative anatomy of protein crystals: lessons from the automatic processing of 56 000 samples. IUCRJ 2019; 6:822-831. [PMID: 31576216 PMCID: PMC6760449 DOI: 10.1107/s2052252519008017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 06/04/2019] [Indexed: 05/12/2023]
Abstract
The fully automatic processing of crystals of macromolecules has presented a unique opportunity to gather information on the samples that is not usually recorded. This has proved invaluable in improving sample-location, characterization and data-collection algorithms. After operating for four years, MASSIF-1 has now processed over 56 000 samples, gathering information at each stage, from the volume of the crystal to the unit-cell dimensions, the space group, the quality of the data collected and the reasoning behind the decisions made in data collection. This provides an unprecedented opportunity to analyse these data together, providing a detailed landscape of macromolecular crystals, intimate details of their contents and, importantly, how the two are related. The data show that mosaic spread is unrelated to the size or shape of crystals and demonstrate experimentally that diffraction intensities scale in proportion to crystal volume and molecular weight. It is also shown that crystal volume scales inversely with molecular weight. The results set the scene for the development of X-ray crystallography in a changing environment for structural biology.
Collapse
Affiliation(s)
- Olof Svensson
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, F-38043 Grenoble, France
| | - Maciej Gilski
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, F-38042 Grenoble, France
| | - Didier Nurizzo
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, F-38043 Grenoble, France
| | - Matthew W. Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, F-38042 Grenoble, France
| |
Collapse
|
7
|
Oscarsson M, Beteva A, Flot D, Gordon E, Guijarro M, Leonard G, McSweeney S, Monaco S, Mueller-Dieckmann C, Nanao M, Nurizzo D, Popov AN, von Stetten D, Svensson O, Rey-Bakaikoa V, Chado I, Chavas LMG, Gadea L, Gourhant P, Isabet T, Legrand P, Savko M, Sirigu S, Shepard W, Thompson A, Mueller U, Nan J, Eguiraun M, Bolmsten F, Nardella A, Milàn-Otero A, Thunnissen M, Hellmig M, Kastner A, Schmuckermaier L, Gerlach M, Feiler C, Weiss MS, Bowler MW, Gobbo A, Papp G, Sinoir J, McCarthy AA, Karpics I, Nikolova M, Bourenkov G, Schneider T, Andreu J, Cuní G, Juanhuix J, Boer R, Fogh R, Keller P, Flensburg C, Paciorek W, Vonrhein C, Bricogne G, de Sanctis D. MXCuBE2: the dawn of MXCuBE Collaboration. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:393-405. [PMID: 30855248 PMCID: PMC6412183 DOI: 10.1107/s1600577519001267] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 01/23/2019] [Indexed: 05/22/2023]
Abstract
MXCuBE2 is the second-generation evolution of the MXCuBE beamline control software, initially developed and used at ESRF - the European Synchrotron. MXCuBE2 extends, in an intuitive graphical user interface (GUI), the functionalities and data collection methods available to users while keeping all previously available features and allowing for the straightforward incorporation of ongoing and future developments. MXCuBE2 introduces an extended abstraction layer that allows easy interfacing of any kind of macromolecular crystallography (MX) hardware component, whether this is a diffractometer, sample changer, detector or optical element. MXCuBE2 also works in strong synergy with the ISPyB Laboratory Information Management System, accessing the list of samples available for a particular experimental session and associating, either from instructions contained in ISPyB or from user input via the MXCuBE2 GUI, different data collection types to them. The development of MXCuBE2 forms the core of a fruitful collaboration which brings together several European synchrotrons and a software development factory and, as such, defines a new paradigm for the development of beamline control platforms for the European MX user community.
Collapse
Affiliation(s)
- Marcus Oscarsson
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Antonia Beteva
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - David Flot
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Elspeth Gordon
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Matias Guijarro
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Gordon Leonard
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Sean McSweeney
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Stephanie Monaco
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | | | - Max Nanao
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Didier Nurizzo
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Alexander N. Popov
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - David von Stetten
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Olof Svensson
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | | | | | | | - Laurent Gadea
- Synchrotron SOLEIL, 91192 Gif-sur-Yvette Cedex, France
| | | | | | | | - Martin Savko
- Synchrotron SOLEIL, 91192 Gif-sur-Yvette Cedex, France
| | - Serena Sirigu
- Synchrotron SOLEIL, 91192 Gif-sur-Yvette Cedex, France
| | | | | | - Uwe Mueller
- MAX IV Laboratory, Lund University, SE-221 00 Lund, Sweden
| | - Jie Nan
- MAX IV Laboratory, Lund University, SE-221 00 Lund, Sweden
| | - Mikel Eguiraun
- MAX IV Laboratory, Lund University, SE-221 00 Lund, Sweden
| | | | | | | | | | - Michael Hellmig
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
| | - Alexandra Kastner
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
| | - Lukas Schmuckermaier
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
| | - Martin Gerlach
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
| | - Christian Feiler
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
| | - Manfred S. Weiss
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
| | - Matthew W. Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Alexandre Gobbo
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Gergely Papp
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Jeremy Sinoir
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Andrew A. McCarthy
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Ivars Karpics
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, 22603 Hamburg, Germany
| | - Marina Nikolova
- 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
| | - Thomas Schneider
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, 22603 Hamburg, Germany
| | - Jordi Andreu
- CELLS-ALBA Synchrotron Light Source, 08290 Cerdanyola del Vallès, Spain
| | - Guifré Cuní
- CELLS-ALBA Synchrotron Light Source, 08290 Cerdanyola del Vallès, Spain
| | - Judith Juanhuix
- CELLS-ALBA Synchrotron Light Source, 08290 Cerdanyola del Vallès, Spain
| | - Roeland Boer
- CELLS-ALBA Synchrotron Light Source, 08290 Cerdanyola del Vallès, Spain
| | - Rasmus Fogh
- Global Phasing Ltd, Sheraton House, Castle Park, Cambridge CB3 0AK, UK
| | - Peter Keller
- Global Phasing Ltd, Sheraton House, Castle Park, Cambridge CB3 0AK, UK
| | - Claus Flensburg
- Global Phasing Ltd, Sheraton House, Castle Park, Cambridge CB3 0AK, UK
| | - Wlodek Paciorek
- Global Phasing Ltd, Sheraton House, Castle Park, Cambridge CB3 0AK, UK
| | - Clemens Vonrhein
- Global Phasing Ltd, Sheraton House, Castle Park, Cambridge CB3 0AK, UK
| | - Gerard Bricogne
- Global Phasing Ltd, Sheraton House, Castle Park, Cambridge CB3 0AK, UK
| | - Daniele de Sanctis
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| |
Collapse
|
8
|
White KI, Bugris V, McCarthy AA, Ravelli RBG, Csankó K, Cassetta A, Brockhauser S. Calibration of rotation axes for multi-axis goniometers in macromolecular crystallography. J Appl Crystallogr 2018; 51:1421-1427. [PMID: 30279641 PMCID: PMC6157707 DOI: 10.1107/s1600576718010956] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 07/31/2018] [Indexed: 11/10/2022] Open
Abstract
An easy to perform rotation calibration procedure has been developed for miniKappa and/or other multi-axis goniometers used in macromolecular crystallography to enhance the precision of experiments involving crystal reorientations. The installation of multi-axis goniometers such as the ESRF/EMBL miniKappa goniometer system has allowed the increased use of sample reorientation in macromolecular crystallography. Old and newly appearing data collection methods require precision and accuracy in crystal reorientation. The proper use of such multi-axis systems has necessitated the development of rapid and easy to perform methods for establishing and evaluating device calibration. A new diffraction-based method meeting these criteria has been developed for the calibration of the motors responsible for rotational motion. This method takes advantage of crystal symmetry by comparing the orientations of a sample rotated about a given axis and checking that the magnitude of the real rotation fits the calculated angle between these two orientations. Hence, the accuracy and precision of rotational motion can be assessed. This rotation calibration procedure has been performed on several beamlines at the ESRF and other synchrotrons. Some resulting data are presented here for reference.
Collapse
Affiliation(s)
- K Ian White
- Department of Molecular and Cellular Physiology, Stanford University, Campus Drive, Stanford, CA 94305, USA.,European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble, 38042, France.,Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Valeria Bugris
- Biological Research Centre (BRC), Hungarian Academy of Sciences, Temesvári körút 62, Szeged, Csongrad 6726, Hungary
| | - Andrew A McCarthy
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble, 38042, France
| | - Raimond B G Ravelli
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble, 38042, France.,M4I Division of Nanoscopy, Maastricht University, PO Box 616, MD Maastricht, 6200, The Netherlands
| | - Krisztián Csankó
- Biological Research Centre (BRC), Hungarian Academy of Sciences, Temesvári körút 62, Szeged, Csongrad 6726, Hungary
| | - Alberto Cassetta
- XRD1 Beamline - Elettra, CNR - Istituto di Cristallografia - Unità di Trieste, S.S. 14 Km 163,5, Trieste, Basovizza I-34012, Italy
| | - Sandor Brockhauser
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble, 38042, France.,Biological Research Centre (BRC), Hungarian Academy of Sciences, Temesvári körút 62, Szeged, Csongrad 6726, Hungary.,European X-ray Free-Electron Laser Facility GmbH (XFEL.EU), Holzkoppel 4, Hamburg, Schenefeld 22869, Germany
| |
Collapse
|
9
|
McCarthy AA, Barrett R, Beteva A, Caserotto H, Dobias F, Felisaz F, Giraud T, Guijarro M, Janocha R, Khadrouche A, Lentini M, Leonard GA, Lopez Marrero M, Malbet-Monaco S, McSweeney S, Nurizzo D, Papp G, Rossi C, Sinoir J, Sorez C, Surr J, Svensson O, Zander U, Cipriani F, Theveneau P, Mueller-Dieckmann C. ID30B - a versatile beamline for macromolecular crystallography experiments at the ESRF. JOURNAL OF SYNCHROTRON RADIATION 2018; 25:1249-1260. [PMID: 29979188 PMCID: PMC6038607 DOI: 10.1107/s1600577518007166] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 05/13/2018] [Indexed: 05/05/2023]
Abstract
ID30B is an undulator-based high-intensity, energy-tuneable (6.0-20 keV) and variable-focus (20-200 µm in diameter) macromolecular crystallography (MX) beamline at the ESRF. It was the last of the ESRF Structural Biology Group's beamlines to be constructed and commissioned as part of the ESRF's Phase I Upgrade Program and has been in user operation since June 2015. Both a modified microdiffractometer (MD2S) incorporating an in situ plate screening capability and a new flexible sample changer (the FlexHCD) were specifically developed for ID30B. Here, the authors provide the current beamline characteristics and detail how different types of MX experiments can be performed on ID30B (http://www.esrf.eu/id30b).
Collapse
Affiliation(s)
- Andrew A. McCarthy
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble 38042, France
| | - Ray Barrett
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble 38043, France
| | - Antonia Beteva
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble 38043, France
| | - Hugo Caserotto
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble 38043, France
| | - Fabien Dobias
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble 38043, France
| | - Franck Felisaz
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble 38042, France
| | - Thierry Giraud
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble 38043, France
| | - Matias Guijarro
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble 38043, France
| | - Robert Janocha
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble 38042, France
| | - Akim Khadrouche
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble 38042, France
| | - Mario Lentini
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble 38043, France
| | - Gordon A. Leonard
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble 38043, France
| | - Marcos Lopez Marrero
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble 38042, France
| | | | - Sean McSweeney
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble 38043, France
| | - Didier Nurizzo
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble 38043, France
| | - Gergely Papp
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble 38042, France
| | - Christopher Rossi
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble 38042, France
| | - Jeremy Sinoir
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble 38042, France
| | - Clement Sorez
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble 38042, France
| | - John Surr
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble 38043, France
| | - Olof Svensson
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble 38043, France
| | - Ulrich Zander
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble 38042, France
| | - Florent Cipriani
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble 38042, France
| | - Pascal Theveneau
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble 38043, France
| | | |
Collapse
|
10
|
Yamamoto M, Hirata K, Yamashita K, Hasegawa K, Ueno G, Ago H, Kumasaka T. Protein microcrystallography using synchrotron radiation. IUCRJ 2017; 4:529-539. [PMID: 28989710 PMCID: PMC5619846 DOI: 10.1107/s2052252517008193] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 06/02/2017] [Indexed: 05/21/2023]
Abstract
The progress in X-ray microbeam applications using synchrotron radiation is beneficial to structure determination from macromolecular microcrystals such as small in meso crystals. However, the high intensity of microbeams causes severe radiation damage, which worsens both the statistical quality of diffraction data and their resolution, and in the worst cases results in the failure of structure determination. Even in the event of successful structure determination, site-specific damage can lead to the misinterpretation of structural features. In order to overcome this issue, technological developments in sample handling and delivery, data-collection strategy and data processing have been made. For a few crystals with dimensions of the order of 10 µm, an elegant two-step scanning strategy works well. For smaller samples, the development of a novel method to analyze multiple isomorphous microcrystals was motivated by the success of serial femtosecond crystallography with X-ray free-electron lasers. This method overcame the radiation-dose limit in diffraction data collection by using a sufficient number of crystals. Here, important technologies and the future prospects for microcrystallography are discussed.
Collapse
Affiliation(s)
- Masaki Yamamoto
- Advanced Photon Technology Division, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Kunio Hirata
- Advanced Photon Technology Division, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Keitaro Yamashita
- Advanced Photon Technology Division, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Kazuya Hasegawa
- Advanced Photon Technology Division, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Go Ueno
- Advanced Photon Technology Division, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Hideo Ago
- Advanced Photon Technology Division, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Takashi Kumasaka
- Advanced Photon Technology Division, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| |
Collapse
|
11
|
Filik J, Ashton AW, Chang PCY, Chater PA, Day SJ, Drakopoulos M, Gerring MW, Hart ML, Magdysyuk OV, Michalik S, Smith A, Tang CC, Terrill NJ, Wharmby MT, Wilhelm H. Processing two-dimensional X-ray diffraction and small-angle scattering data in DAWN 2. J Appl Crystallogr 2017; 50:959-966. [PMID: 28656043 PMCID: PMC5458597 DOI: 10.1107/s1600576717004708] [Citation(s) in RCA: 202] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 03/26/2017] [Indexed: 11/10/2022] Open
Abstract
The Powder Calibration and Processing packages implemented in DAWN 2 provide an automated diffraction-geometry calibration and data processing environment for two-dimensional diffraction experiments. The customizable processing chains permit the execution of data processing steps to convert raw two-dimensional data into meaningful data and diffractograms. The provenance of the processed data is maintained, which guarantees reproducibility and transparency of the data treatment. A software package for the calibration and processing of powder X-ray diffraction and small-angle X-ray scattering data is presented. It provides a multitude of data processing and visualization tools as well as a command-line scripting interface for on-the-fly processing and the incorporation of complex data treatment tasks. Customizable processing chains permit the execution of many data processing steps to convert a single image or a batch of raw two-dimensional data into meaningful data and one-dimensional diffractograms. The processed data files contain the full data provenance of each process applied to the data. The calibration routines can run automatically even for high energies and also for large detector tilt angles. Some of the functionalities are highlighted by specific use cases.
Collapse
Affiliation(s)
- J Filik
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - A W Ashton
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - P C Y Chang
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - P A Chater
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - S J Day
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - M Drakopoulos
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - M W Gerring
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - M L Hart
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - O V Magdysyuk
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - S Michalik
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - A Smith
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - C C Tang
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - N J Terrill
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - M T Wharmby
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - H Wilhelm
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| |
Collapse
|
12
|
Pellegrini E, Palencia A, Braun L, Kapp U, Bougdour A, Belrhali H, Bowler MW, Hakimi MA. Structural Basis for the Subversion of MAP Kinase Signaling by an Intrinsically Disordered Parasite Secreted Agonist. Structure 2016; 25:16-26. [PMID: 27889209 PMCID: PMC5222587 DOI: 10.1016/j.str.2016.10.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 09/21/2016] [Accepted: 10/25/2016] [Indexed: 01/07/2023]
Abstract
The causative agent of toxoplasmosis, the intracellular parasite Toxoplasma gondii, delivers a protein, GRA24, into the cells it infects that interacts with the mitogen-activated protein (MAP) kinase p38α (MAPK14), leading to activation and nuclear translocation of the host kinase and a subsequent inflammatory response that controls the progress of the parasite. The purification of a recombinant complex of GRA24 and human p38α has allowed the molecular basis of this activation to be determined. GRA24 is shown to be intrinsically disordered, binding two kinases that act independently, and is the only factor required to bypass the canonical mitogen-activated protein kinase activation pathway. An adapted kinase interaction motif (KIM) forms a highly stable complex that competes with cytoplasmic regulatory partners. In addition, the recombinant complex forms a powerful in vitro tool to evaluate the specificity and effectiveness of p38α inhibitors that have advanced to clinical trials, as it provides a hitherto unavailable stable and highly active form of p38α. Toxoplasmosis controls its host immune response via a protein effector, GRA24 A recombinant complex of GRA24 and MAPK p38α demonstrates how the protein works An adapted KIM domain ensures activation and a sustained inflammatory response The recombinant complex is useful in the evaluation of p38 inhibitors
Collapse
Affiliation(s)
- Erika Pellegrini
- 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
| | - Andrés Palencia
- IAB, Team Host-Pathogen Interactions & Immunity to Infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, 38700 Grenoble, France
| | - Laurence Braun
- IAB, Team Host-Pathogen Interactions & Immunity to Infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, 38700 Grenoble, France
| | - Ulrike Kapp
- Structural Biology Group, European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Alexandre Bougdour
- IAB, Team Host-Pathogen Interactions & Immunity to Infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, 38700 Grenoble, France
| | - Hassan Belrhali
- 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.
| | - Matthew W Bowler
- 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.
| | - Mohamed-Ali Hakimi
- IAB, Team Host-Pathogen Interactions & Immunity to Infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, 38700 Grenoble, France.
| |
Collapse
|
13
|
Sanchez-Weatherby J, Moraes I. Crystal Dehydration in Membrane Protein Crystallography. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 922:73-89. [PMID: 27553236 PMCID: PMC6126552 DOI: 10.1007/978-3-319-35072-1_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Crystal dehydration has been successfully implemented to facilitate the structural solution of a number of soluble and membrane protein structures over the years. This chapter will present the currently available tools to undertake controlled crystal dehydration, focusing on some successful membrane protein cases. Also discussed here will be some practical considerations regarding membrane protein crystals and the relationship between different techniques in order to help researchers to select the most suitable technique for their projects.
Collapse
Affiliation(s)
| | - Isabel Moraes
- Membrane Protein Laboratory, Diamond Light Source/Imperial College London, Harwell Campus, Didcot, Oxfordshire UK
| |
Collapse
|
14
|
Zander U, Hoffmann G, Cornaciu I, Marquette JP, Papp G, Landret C, Seroul G, Sinoir J, Röwer M, Felisaz F, Rodriguez-Puente S, Mariaule V, Murphy P, Mathieu M, Cipriani F, Márquez JA. Automated harvesting and processing of protein crystals through laser photoablation. Acta Crystallogr D Struct Biol 2016; 72:454-66. [PMID: 27050125 PMCID: PMC4822559 DOI: 10.1107/s2059798316000954] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 01/16/2016] [Indexed: 01/10/2023] Open
Abstract
Currently, macromolecular crystallography projects often require the use of highly automated facilities for crystallization and X-ray data collection. However, crystal harvesting and processing largely depend on manual operations. Here, a series of new methods are presented based on the use of a low X-ray-background film as a crystallization support and a photoablation laser that enable the automation of major operations required for the preparation of crystals for X-ray diffraction experiments. In this approach, the controlled removal of the mother liquor before crystal mounting simplifies the cryocooling process, in many cases eliminating the use of cryoprotectant agents, while crystal-soaking experiments are performed through diffusion, precluding the need for repeated sample-recovery and transfer operations. Moreover, the high-precision laser enables new mounting strategies that are not accessible through other methods. This approach bridges an important gap in automation and can contribute to expanding the capabilities of modern macromolecular crystallography facilities.
Collapse
Affiliation(s)
- Ulrich Zander
- Grenoble Outstation, European Molecular Biology Laboratory; Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Guillaume Hoffmann
- Grenoble Outstation, European Molecular Biology Laboratory; Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Irina Cornaciu
- Grenoble Outstation, European Molecular Biology Laboratory; Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Jean-Pierre Marquette
- Structure Design Informatics and Structural Biology, Sanofi, 13 Quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Gergely Papp
- Grenoble Outstation, European Molecular Biology Laboratory; Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Christophe Landret
- Grenoble Outstation, European Molecular Biology Laboratory; Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Gaël Seroul
- Grenoble Outstation, European Molecular Biology Laboratory; Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Jérémy Sinoir
- Grenoble Outstation, European Molecular Biology Laboratory; Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Martin Röwer
- Grenoble Outstation, European Molecular Biology Laboratory; Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Frank Felisaz
- Grenoble Outstation, European Molecular Biology Laboratory; Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Sonia Rodriguez-Puente
- Grenoble Outstation, European Molecular Biology Laboratory; Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Vincent Mariaule
- Grenoble Outstation, European Molecular Biology Laboratory; Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Peter Murphy
- Grenoble Outstation, European Molecular Biology Laboratory; Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Magali Mathieu
- Structure Design Informatics and Structural Biology, Sanofi, 13 Quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Florent Cipriani
- Grenoble Outstation, European Molecular Biology Laboratory; Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - José Antonio Márquez
- Grenoble Outstation, European Molecular Biology Laboratory; Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France
| |
Collapse
|
15
|
Bowler MW, Svensson O, Nurizzo D. Fully automatic macromolecular crystallography: the impact of MASSIF-1 on the optimum acquisition and quality of data. CRYSTALLOGR REV 2016. [DOI: 10.1080/0889311x.2016.1155050] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
|
16
|
de Sanctis D, Oscarsson M, Popov A, Svensson O, Leonard G. Facilitating best practices in collecting anomalous scattering data for de novo structure solution at the ESRF Structural Biology Beamlines. Acta Crystallogr D Struct Biol 2016; 72:413-20. [PMID: 26960128 PMCID: PMC4784672 DOI: 10.1107/s2059798316001042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 01/18/2016] [Indexed: 11/10/2022] Open
Abstract
The constant evolution of synchrotron structural biology beamlines, the viability of screening protein crystals for a wide range of heavy-atom derivatives, the advent of efficient protein labelling and the availability of automatic data-processing and structure-solution pipelines have combined to make de novo structure solution in macromolecular crystallography a less arduous task. Nevertheless, the collection of diffraction data of sufficient quality for experimental phasing is still a difficult and crucial step. Here, some examples of good data-collection practice for projects requiring experimental phasing are presented and recent developments at the ESRF Structural Biology beamlines that have facilitated these are illustrated.
Collapse
Affiliation(s)
- Daniele de Sanctis
- ESRF – The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Marcus Oscarsson
- ESRF – The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Alexander Popov
- ESRF – The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Olof Svensson
- ESRF – The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Gordon Leonard
- ESRF – The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| |
Collapse
|
17
|
Bowler MW, Nurizzo D, Barrett R, Beteva A, Bodin M, Caserotto H, Delagenière S, Dobias F, Flot D, Giraud T, Guichard N, Guijarro M, Lentini M, Leonard GA, McSweeney S, Oskarsson M, Schmidt W, Snigirev A, von Stetten D, Surr J, Svensson O, Theveneau P, Mueller-Dieckmann C. MASSIF-1: a beamline dedicated to the fully automatic characterization and data collection from crystals of biological macromolecules. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:1540-7. [PMID: 26524320 PMCID: PMC4629869 DOI: 10.1107/s1600577515016604] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 09/05/2015] [Indexed: 05/22/2023]
Abstract
MASSIF-1 (ID30A-1) is an ESRF undulator beamline operating at a fixed wavelength of 0.969 Å (12.8 keV) that is dedicated to the completely automatic characterization of and data collection from crystals of biological macromolecules. The first of the ESRF Upgrade MASSIF beamlines to be commissioned, it has been open since September 2014, providing a unique automated data collection service to academic and industrial users. Here, the beamline characteristics and details of the new service are outlined.
Collapse
Affiliation(s)
- Matthew W. Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, F-38042 Grenoble, France
- Unit for Virus Host Cell Interactions, Université Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, F-38042 Grenoble, France
| | - Didier Nurizzo
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble, France
| | - Ray Barrett
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble, France
| | - Antonia Beteva
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble, France
| | - Marjolaine Bodin
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble, France
| | - Hugo Caserotto
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble, France
| | - Solange Delagenière
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble, France
| | - Fabian Dobias
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble, France
| | - David Flot
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble, France
| | - Thierry Giraud
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble, France
| | - Nicolas Guichard
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble, France
| | - Mattias Guijarro
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble, France
| | - Mario Lentini
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble, France
| | - Gordon A. Leonard
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble, France
| | - Sean McSweeney
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble, France
| | - Marcus Oskarsson
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble, France
| | - Werner Schmidt
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble, France
| | - Anatoli Snigirev
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble, France
| | - David von Stetten
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble, France
| | - John Surr
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble, France
| | - Olof Svensson
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble, France
| | - Pascal Theveneau
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble, France
| | | |
Collapse
|
18
|
Zander U, Bourenkov G, Popov AN, de Sanctis D, Svensson O, McCarthy AA, Round E, Gordeliy V, Mueller-Dieckmann C, Leonard GA. MeshAndCollect: an automated multi-crystal data-collection workflow for synchrotron macromolecular crystallography beamlines. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:2328-43. [PMID: 26527148 PMCID: PMC4631482 DOI: 10.1107/s1399004715017927] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 09/24/2015] [Indexed: 01/30/2023]
Abstract
Here, an automated procedure is described to identify the positions of many cryocooled crystals mounted on the same sample holder, to rapidly predict and rank their relative diffraction strengths and to collect partial X-ray diffraction data sets from as many of the crystals as desired. Subsequent hierarchical cluster analysis then allows the best combination of partial data sets, optimizing the quality of the final data set obtained. The results of applying the method developed to various systems and scenarios including the compilation of a complete data set from tiny crystals of the membrane protein bacteriorhodopsin and the collection of data sets for successful structure determination using the single-wavelength anomalous dispersion technique are also presented.
Collapse
Affiliation(s)
- Ulrich Zander
- Structural Biology Group, European Synchrotron Radiation Facility, CS 40220, 38043 Grenoble, France
| | - Gleb Bourenkov
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, 22607 Hamburg, Germany
| | - Alexander N. Popov
- Structural Biology Group, European Synchrotron Radiation Facility, CS 40220, 38043 Grenoble, France
| | - Daniele de Sanctis
- Structural Biology Group, European Synchrotron Radiation Facility, CS 40220, 38043 Grenoble, France
| | - Olof Svensson
- Structural Biology Group, European Synchrotron Radiation Facility, CS 40220, 38043 Grenoble, France
| | - Andrew A. McCarthy
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
- Unit of Virus Host-Cell Interactions, Université Grenoble Alpes–EMBL–CNRS, 38042 Grenoble, France
| | - Ekaterina Round
- Université Grenoble Alpes, IBS, 38044 Grenoble, France
- CNRS, IBS, 38044 Grenoble, France
- CEA, IBS, 38044 Grenoble, France
- ICS-6: Molecular Biophysics, Institute of Complex Systems (ICS), Research Centre Juelich, 52425 Juelich, Germany
- Laboratory for Advanced Studies of Membrane Proteins, Moscow Institute of Physics and Technology, Dolgoprudniy 141700, Russian Federation
| | - Valentin Gordeliy
- Université Grenoble Alpes, IBS, 38044 Grenoble, France
- CNRS, IBS, 38044 Grenoble, France
- CEA, IBS, 38044 Grenoble, France
- ICS-6: Molecular Biophysics, Institute of Complex Systems (ICS), Research Centre Juelich, 52425 Juelich, Germany
- Laboratory for Advanced Studies of Membrane Proteins, Moscow Institute of Physics and Technology, Dolgoprudniy 141700, Russian Federation
| | | | - Gordon A. Leonard
- Structural Biology Group, European Synchrotron Radiation Facility, CS 40220, 38043 Grenoble, France
| |
Collapse
|
19
|
Svensson O, Malbet-Monaco S, Popov A, Nurizzo D, Bowler MW. Fully automatic characterization and data collection from crystals of biological macromolecules. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1757-67. [PMID: 26249356 PMCID: PMC4528805 DOI: 10.1107/s1399004715011918] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 06/22/2015] [Indexed: 11/24/2022]
Abstract
Considerable effort is dedicated to evaluating macromolecular crystals at synchrotron sources, even for well established and robust systems. Much of this work is repetitive, and the time spent could be better invested in the interpretation of the results. In order to decrease the need for manual intervention in the most repetitive steps of structural biology projects, initial screening and data collection, a fully automatic system has been developed to mount, locate, centre to the optimal diffraction volume, characterize and, if possible, collect data from multiple cryocooled crystals. Using the capabilities of pixel-array detectors, the system is as fast as a human operator, taking an average of 6 min per sample depending on the sample size and the level of characterization required. Using a fast X-ray-based routine, samples are located and centred systematically at the position of highest diffraction signal and important parameters for sample characterization, such as flux, beam size and crystal volume, are automatically taken into account, ensuring the calculation of optimal data-collection strategies. The system is now in operation at the new ESRF beamline MASSIF-1 and has been used by both industrial and academic users for many different sample types, including crystals of less than 20 µm in the smallest dimension. To date, over 8000 samples have been evaluated on MASSIF-1 without any human intervention.
Collapse
Affiliation(s)
- Olof Svensson
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38043 Grenoble, France
| | - Stéphanie Malbet-Monaco
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38043 Grenoble, France
| | - Alexander Popov
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38043 Grenoble, France
| | - Didier Nurizzo
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38043 Grenoble, France
| | - Matthew W. Bowler
- 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, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| |
Collapse
|
20
|
Koromyslova AD, Leuthold MM, Bowler MW, Hansman GS. The sweet quartet: Binding of fucose to the norovirus capsid. Virology 2015; 483:203-8. [PMID: 25980740 DOI: 10.1016/j.virol.2015.04.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 03/24/2015] [Accepted: 04/07/2015] [Indexed: 11/16/2022]
Abstract
Human noroviruses bind histo-blood group antigens (HBGAs) and this interaction is thought to be important for an infection. We identified two additional fucose-binding pockets (termed fucose-3/4 sites) on a genogroup II human (GII.10) norovirus-protruding (P) dimer using X-ray crystallography. Fucose-3/4 sites were located between two previously determined HBGA binding pockets (termed fucose-1/2 sites). We found that four fucose molecules were capable of binding altogether at fucose-1/2/3/4 sites on the P dimer, though the fucose molecules bound in a dose-dependent and step-wise manner. We also showed that HBGA B-trisaccharide molecules bound in a similar way at the fucose-1/2 sites. Interestingly, we discovered that the monomers of the P dimer were asymmetrical in an unliganded state and when a single B-trisaccharide molecule bound, but were symmetrical when two B-trisaccharide molecules bound. We postulate that the symmetrical dimers might favor HBGA binding interactions at fucose-1/2 sites.
Collapse
Affiliation(s)
- Anna D Koromyslova
- Schaller Research Group at the University of Heidelberg and the DKFZ, Heidelberg 69120, Germany; Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg 69120, Germany
| | - Mila M Leuthold
- Schaller Research Group at the University of Heidelberg and the DKFZ, Heidelberg 69120, Germany; Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg 69120, Germany
| | - Matthew W Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, Grenoble, F-38042, France; Unit for Virus Host Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 71 Avenue des Martyrs, CS 90181, Grenoble F-38042, France
| | - Grant S Hansman
- Schaller Research Group at the University of Heidelberg and the DKFZ, Heidelberg 69120, Germany; Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg 69120, Germany.
| |
Collapse
|
21
|
Basham M, Filik J, Wharmby MT, Chang PCY, El Kassaby B, Gerring M, Aishima J, Levik K, Pulford BCA, Sikharulidze I, Sneddon D, Webber M, Dhesi SS, Maccherozzi F, Svensson O, Brockhauser S, Náray G, Ashton AW. Data Analysis WorkbeNch (DAWN). JOURNAL OF SYNCHROTRON RADIATION 2015; 22:853-8. [PMID: 25931106 PMCID: PMC4416692 DOI: 10.1107/s1600577515002283] [Citation(s) in RCA: 202] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 02/03/2015] [Indexed: 05/19/2023]
Abstract
Synchrotron light source facilities worldwide generate terabytes of data in numerous incompatible data formats from a wide range of experiment types. The Data Analysis WorkbeNch (DAWN) was developed to address the challenge of providing a single visualization and analysis platform for data from any synchrotron experiment (including single-crystal and powder diffraction, tomography and spectroscopy), whilst also being sufficiently extensible for new specific use case analysis environments to be incorporated (e.g. ARPES, PEEM). In this work, the history and current state of DAWN are presented, with two case studies to demonstrate specific functionality. The first is an example of a data processing and reduction problem using the generic tools, whilst the second shows how these tools can be targeted to a specific scientific area.
Collapse
Affiliation(s)
- Mark Basham
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Jacob Filik
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Michael T. Wharmby
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Peter C. Y. Chang
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Baha El Kassaby
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Matthew Gerring
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Jun Aishima
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Karl Levik
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Bill C. A. Pulford
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Irakli Sikharulidze
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Duncan Sneddon
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Matthew Webber
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Sarnjeet S. Dhesi
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Francesco Maccherozzi
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Olof Svensson
- European Synchrotron Radiation Facility (ESRF), 71 Rue des Martyrs, Grenoble 38000, France
| | - Sandor Brockhauser
- European Molecular Biology Laboratory (EMBL), 6 Rue Jules Horowitz, Grenoble 38042, France
| | - Gabor Náray
- European Molecular Biology Laboratory (EMBL), 6 Rue Jules Horowitz, Grenoble 38042, France
| | - Alun W. Ashton
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
- Correspondence e-mail:
| |
Collapse
|
22
|
Bowler MG, Bowler MW. Measurement of the intrinsic variability within protein crystals: implications for sample-evaluation and data-collection strategies. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2013; 70:127-32. [PMID: 24419635 DOI: 10.1107/s2053230x13032007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 11/22/2013] [Indexed: 11/10/2022]
Abstract
The advent of micro-focused X-ray beams has led to the development of a number of advanced methods of sample evaluation and data collection. In particular, multiple-position data-collection and helical oscillation strategies are now becoming commonplace in order to alleviate the problems associated with radiation damage. However, intra-crystal and inter-crystal variation means that it is not always obvious on which crystals or on which region or regions of a crystal these protocols should be performed. For the automation of this process for large-scale screening, and to provide an indication of the best strategy for data collection, a metric of crystal variability could be useful. Here, measures of the intrinsic variability within protein crystals are presented and their implications for optimal data-collection strategies are discussed.
Collapse
Affiliation(s)
- Michael G Bowler
- Department of Physics, University of Oxford, Keble Road, Oxford OX1 3RH, England
| | - Matthew W Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 6 Rue Jules Horowitz, 38042 Grenoble, France
| |
Collapse
|
23
|
QsIA disrupts LasR dimerization in antiactivation of bacterial quorum sensing. Proc Natl Acad Sci U S A 2013; 110:20765-70. [PMID: 24319092 DOI: 10.1073/pnas.1314415110] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The human pathogen Pseudomonas aeruginosa coordinates the expression of virulence factors by using quorum sensing (QS), a signaling cascade triggered by the QS signal molecule and its receptor, a member of the LuxR family of QS transcriptional factors (LasR). The QS threshold and response in P. aeruginosa is defined by a QS LasR-specific antiactivator (QslA), which binds to LasR and prevents it from binding to its target promoter. However, how QslA binds to LasR and regulates its DNA binding activity in QS remains elusive. Here we report the crystal structure of QslA in complex with the N-terminal ligand binding domain of LasR. QsIA exists as a functional dimer to interact with the LasR ligand binding domain. Further analysis shows that QsIA binding occupies the LasR dimerization interface and consequently disrupts LasR dimerization, thereby preventing LasR from binding to its target DNA and disturbing normal QS. Our findings provide a structural model for understanding the QslA-mediated antiactivation mechanism in QS through protein-protein interaction.
Collapse
|
24
|
Lsm2 and Lsm3 bridge the interaction of the Lsm1-7 complex with Pat1 for decapping activation. Cell Res 2013; 24:233-46. [PMID: 24247251 PMCID: PMC3915908 DOI: 10.1038/cr.2013.152] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 09/16/2013] [Accepted: 09/28/2013] [Indexed: 02/07/2023] Open
Abstract
The evolutionarily conserved Lsm1-7-Pat1 complex is the most critical activator of mRNA decapping in eukaryotic cells and plays many roles in normal decay, AU-rich element-mediated decay, and miRNA silencing, yet how Pat1 interacts with the Lsm1-7 complex is unknown. Here, we show that Lsm2 and Lsm3 bridge the interaction between the C-terminus of Pat1 (Pat1C) and the Lsm1-7 complex. The Lsm2-3-Pat1C complex and the Lsm1-7-Pat1C complex stimulate decapping in vitro to a similar extent and exhibit similar RNA-binding preference. The crystal structure of the Lsm2-3-Pat1C complex shows that Pat1C binds to Lsm2-3 to form an asymmetric complex with three Pat1C molecules surrounding a heptameric ring formed by Lsm2-3. Structure-based mutagenesis revealed the importance of Lsm2-3-Pat1C interactions in decapping activation in vivo. Based on the structure of Lsm2-3-Pat1C, a model of Lsm1-7-Pat1 complex is constructed and how RNA binds to this complex is discussed.
Collapse
|
25
|
Krojer T, Pike ACW, von Delft F. Squeezing the most from every crystal: the fine details of data collection. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1303-13. [PMID: 23793157 PMCID: PMC3689534 DOI: 10.1107/s0907444913013280] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Accepted: 05/14/2013] [Indexed: 11/11/2022]
Abstract
Modern synchrotron beamlines offer instrumentation of unprecedented quality, which in turn encourages increasingly marginal experiments, and for these, as much as ever, the ultimate success of data collection depends on the experience, but especially the care, of the experimenter. A representative set of difficult cases has been encountered at the Structural Genomics Consortium, a worldwide structural genomics initiative of which the Oxford site currently deposits three novel human structures per month. Achieving this target relies heavily on frequent visits to the Diamond Light Source, and the variety of crystal systems still demand customized data collection, diligent checks and careful planning of each experiment. Here, an overview is presented of the techniques and procedures that have been refined over the years and that are considered synchrotron best practice.
Collapse
Affiliation(s)
- Tobias Krojer
- Structural Genomics Consortium, Oxford University, Roosevelt Drive, Oxford OX3 7DQ, England
| | - Ashley C. W. Pike
- Structural Genomics Consortium, Oxford University, Roosevelt Drive, Oxford OX3 7DQ, England
| | - Frank von Delft
- Structural Genomics Consortium, Oxford University, Roosevelt Drive, Oxford OX3 7DQ, England
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| |
Collapse
|
26
|
Brockhauser S, Ravelli RBG, McCarthy AA. The use of a mini-κ goniometer head in macromolecular crystallography diffraction experiments. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1241-51. [PMID: 23793150 PMCID: PMC3689527 DOI: 10.1107/s0907444913003880] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 02/08/2013] [Indexed: 03/22/2024]
Abstract
Most macromolecular crystallography (MX) diffraction experiments at synchrotrons use a single-axis goniometer. This markedly contrasts with small-molecule crystallography, in which the majority of the diffraction data are collected using multi-axis goniometers. A novel miniaturized κ-goniometer head, the MK3, has been developed to allow macromolecular crystals to be aligned. It is available on the majority of the structural biology beamlines at the ESRF, as well as elsewhere. In addition, the Strategy for the Alignment of Crystals (STAC) software package has been developed to facilitate the use of the MK3 and other similar devices. Use of the MK3 and STAC is streamlined by their incorporation into online analysis tools such as EDNA. The current use of STAC and MK3 on the MX beamlines at the ESRF is discussed. It is shown that the alignment of macromolecular crystals can result in improved diffraction data quality compared with data obtained from randomly aligned crystals.
Collapse
Affiliation(s)
- Sandor Brockhauser
- European Molecular Biology Laboratory (EMBL), 6 Rue Jules Horowitz, 38042 Grenoble, France
- Unit of Virus Host-Cell Interactions, UJF–EMBL–CNRS UMI 3265, 6 Rue Jules Horowitz, 38043 Grenoble, France
| | - Raimond B. G. Ravelli
- Leiden University Medical Center (LUMC), PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Andrew A. McCarthy
- European Molecular Biology Laboratory (EMBL), 6 Rue Jules Horowitz, 38042 Grenoble, France
- Unit of Virus Host-Cell Interactions, UJF–EMBL–CNRS UMI 3265, 6 Rue Jules Horowitz, 38043 Grenoble, France
| |
Collapse
|
27
|
Tsai Y, McPhillips SE, González A, McPhillips TM, Zinn D, Cohen AE, Feese MD, Bushnell D, Tiefenbrunn T, Stout CD, Ludaescher B, Hedman B, Hodgson KO, Soltis SM. AutoDrug: fully automated macromolecular crystallography workflows for fragment-based drug discovery. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:796-803. [PMID: 23633588 PMCID: PMC3640469 DOI: 10.1107/s0907444913001984] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 01/20/2013] [Indexed: 11/10/2022]
Abstract
AutoDrug is software based upon the scientific workflow paradigm that integrates the Stanford Synchrotron Radiation Lightsource macromolecular crystallography beamlines and third-party processing software to automate the crystallography steps of the fragment-based drug-discovery process. AutoDrug screens a cassette of fragment-soaked crystals, selects crystals for data collection based on screening results and user-specified criteria and determines optimal data-collection strategies. It then collects and processes diffraction data, performs molecular replacement using provided models and detects electron density that is likely to arise from bound fragments. All processes are fully automated, i.e. are performed without user interaction or supervision. Samples can be screened in groups corresponding to particular proteins, crystal forms and/or soaking conditions. A single AutoDrug run is only limited by the capacity of the sample-storage dewar at the beamline: currently 288 samples. AutoDrug was developed in conjunction with RestFlow, a new scientific workflow-automation framework. RestFlow simplifies the design of AutoDrug by managing the flow of data and the organization of results and by orchestrating the execution of computational pipeline steps. It also simplifies the execution and interaction of third-party programs and the beamline-control system. Modeling AutoDrug as a scientific workflow enables multiple variants that meet the requirements of different user groups to be developed and supported. A workflow tailored to mimic the crystallography stages comprising the drug-discovery pipeline of CoCrystal Discovery Inc. has been deployed and successfully demonstrated. This workflow was run once on the same 96 samples that the group had examined manually and the workflow cycled successfully through all of the samples, collected data from the same samples that were selected manually and located the same peaks of unmodeled density in the resulting difference Fourier maps.
Collapse
Affiliation(s)
- Yingssu Tsai
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Department of Chemistry, Stanford University, 333 Campus Drive, Mudd Building, Stanford, CA 94305-5080, USA
| | - Scott E. McPhillips
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Ana González
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Timothy M. McPhillips
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Daniel Zinn
- LogicBlox Inc., 1349 West Peachtree Street NW, Atlanta, GA 30309, USA
| | - Aina E. Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Michael D. Feese
- Cocrystal Discovery Inc., 19805 North Creek Parkway, Bothell, WA 98011, USA
| | - David Bushnell
- Cocrystal Discovery Inc., 19805 North Creek Parkway, Bothell, WA 98011, USA
| | - Theresa Tiefenbrunn
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - C. David Stout
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Bertram Ludaescher
- Department of Computer Science and Genome Center, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Department of Chemistry, Stanford University, 333 Campus Drive, Mudd Building, Stanford, CA 94305-5080, USA
| | - Keith O. Hodgson
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Department of Chemistry, Stanford University, 333 Campus Drive, Mudd Building, Stanford, CA 94305-5080, USA
| | - S. Michael Soltis
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| |
Collapse
|
28
|
Leal RMF, Bourenkov G, Russi S, Popov AN. A survey of global radiation damage to 15 different protein crystal types at room temperature: a new decay model. JOURNAL OF SYNCHROTRON RADIATION 2013; 20:14-22. [PMID: 23254652 PMCID: PMC3943537 DOI: 10.1107/s0909049512049114] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 11/29/2012] [Indexed: 05/11/2023]
Abstract
The radiation damage rates to crystals of 15 model macromolecular structures were studied using an automated radiation sensitivity characterization procedure. The diffracted intensity variation with dose is described by a two-parameter model. This model includes a strong resolution-independent decay specific to room-temperature measurements along with a linear increase in overall Debye-Waller factors. An equivalent representation of sensitivity via a single parameter, normalized half-dose, is introduced. This parameter varies by an order of magnitude between the different structures studied. The data show a correlation of crystal radiation sensitivity with crystal solvent content but no dose-rate dependency was detected in the range 0.05-300 kGy s(-1). The results of the crystal characterization are suitable for either optimal planning of room-temperature data collection or in situ crystallization plate screening experiments.
Collapse
Affiliation(s)
| | - Gleb Bourenkov
- EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85b, Hamburg 22607, Germany
| | | | | |
Collapse
|