1
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Thompson MC. Combining temperature perturbations with X-ray crystallography to study dynamic macromolecules: A thorough discussion of experimental methods. Methods Enzymol 2023; 688:255-305. [PMID: 37748829 DOI: 10.1016/bs.mie.2023.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Temperature is an important state variable that governs the behavior of microscopic systems, yet crystallographers rarely exploit temperature changes to study the structure and dynamics of biological macromolecules. In fact, approximately 90% of crystal structures in the Protein Data Bank were determined under cryogenic conditions, because sample cryocooling makes crystals robust to X-ray radiation damage and facilitates data collection. On the other hand, cryocooling can introduce artifacts into macromolecular structures, and can suppress conformational dynamics that are critical for function. Fortunately, recent advances in X-ray detector technology, X-ray sources, and computational data processing algorithms make non-cryogenic X-ray crystallography easier and more broadly applicable than ever before. Without the reliance on cryocooling, high-resolution crystallography can be combined with various temperature perturbations to gain deep insight into the conformational landscapes of macromolecules. This Chapter reviews the historical reasons for the prevalence of cryocooling in macromolecular crystallography, and discusses its potential drawbacks. Next, the Chapter summarizes technological developments and methodologies that facilitate non-cryogenic crystallography experiments. Finally, the chapter discusses the theoretical underpinnings and practical aspects of multi-temperature and temperature-jump crystallography experiments, which are powerful tools for understanding the relationship between the structure, dynamics, and function of proteins and other biological macromolecules.
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Affiliation(s)
- Michael C Thompson
- Department of Chemistry and Biochemistry, University of California, Merced, Merced, CA, United States.
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2
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Romero-Romero S, Costas M, Silva Manzano DA, Kordes S, Rojas-Ortega E, Tapia C, Guerra Y, Shanmugaratnam S, Rodríguez-Romero A, Baker D, Höcker B, Fernández-Velasco DA. The Stability Landscape of de novo TIM Barrels Explored by a Modular Design Approach. J Mol Biol 2021; 433:167153. [PMID: 34271011 PMCID: PMC8404036 DOI: 10.1016/j.jmb.2021.167153] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/18/2021] [Accepted: 07/06/2021] [Indexed: 11/25/2022]
Abstract
The TIM barrel is a versatile fold to understand structure-stability relationships. A collection of de novo TIM barrels with improved hydrophobic cores was designed. DeNovoTIMs are reversible in chemical and thermal unfolding, which is uncommon in TIM barrels. Epistatic effects play a central role in DeNovoTIMs stabilization. DeNovoTIMs navigate a previously uncharted region of the stability landscape.
The ability to design stable proteins with custom-made functions is a major goal in biochemistry with practical relevance for our environment and society. Understanding and manipulating protein stability provide crucial information on the molecular determinants that modulate structure and stability, and expand the applications of de novo proteins. Since the (β/⍺)8-barrel or TIM-barrel fold is one of the most common functional scaffolds, in this work we designed a collection of stable de novo TIM barrels (DeNovoTIMs), using a computational fixed-backbone and modular approach based on improved hydrophobic packing of sTIM11, the first validated de novo TIM barrel, and subjected them to a thorough folding analysis. DeNovoTIMs navigate a region of the stability landscape previously uncharted by natural TIM barrels, with variations spanning 60 degrees in melting temperature and 22 kcal per mol in conformational stability throughout the designs. Significant non-additive or epistatic effects were observed when stabilizing mutations from different regions of the barrel were combined. The molecular basis of epistasis in DeNovoTIMs appears to be related to the extension of the hydrophobic cores. This study is an important step towards the fine-tuned modulation of protein stability by design.
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Affiliation(s)
- Sergio Romero-Romero
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico; Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Miguel Costas
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico
| | - Daniel-Adriano Silva Manzano
- Department of Biochemistry, University of Washington, 98195 Seattle, USA; Institute for Protein Design, University of Washington, 98195 Seattle, USA
| | - Sina Kordes
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Erendira Rojas-Ortega
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico
| | - Cinthya Tapia
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico
| | - Yasel Guerra
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico
| | | | - Adela Rodríguez-Romero
- Instituto de Química, Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico
| | - David Baker
- Department of Biochemistry, University of Washington, 98195 Seattle, USA; Institute for Protein Design, University of Washington, 98195 Seattle, USA.
| | - Birte Höcker
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany.
| | - D Alejandro Fernández-Velasco
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico.
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3
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Lučić M, Svistunenko DA, Wilson MT, Chaplin AK, Davy B, Ebrahim A, Axford D, Tosha T, Sugimoto H, Owada S, Dworkowski FSN, Tews I, Owen RL, Hough MA, Worrall JAR. Serial Femtosecond Zero Dose Crystallography Captures a Water-Free Distal Heme Site in a Dye-Decolorising Peroxidase to Reveal a Catalytic Role for an Arginine in Fe IV =O Formation. Angew Chem Int Ed Engl 2020; 59:21656-21662. [PMID: 32780931 PMCID: PMC7756461 DOI: 10.1002/anie.202008622] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Indexed: 01/06/2023]
Abstract
Obtaining structures of intact redox states of metal centers derived from zero dose X-ray crystallography can advance our mechanistic understanding of metalloenzymes. In dye-decolorising heme peroxidases (DyPs), controversy exists regarding the mechanistic role of the distal heme residues aspartate and arginine in the heterolysis of peroxide to form the catalytic intermediate compound I (FeIV =O and a porphyrin cation radical). Using serial femtosecond X-ray crystallography (SFX), we have determined the pristine structures of the FeIII and FeIV =O redox states of a B-type DyP. These structures reveal a water-free distal heme site that, together with the presence of an asparagine, imply the use of the distal arginine as a catalytic base. A combination of mutagenesis and kinetic studies corroborate such a role. Our SFX approach thus provides unique insight into how the distal heme site of DyPs can be tuned to select aspartate or arginine for the rate enhancement of peroxide heterolysis.
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Affiliation(s)
- Marina Lučić
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterEssexCO4 3SQUK
| | | | - Michael T. Wilson
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterEssexCO4 3SQUK
| | - Amanda K. Chaplin
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterEssexCO4 3SQUK
| | - Bradley Davy
- Diamond Light SourceHarwell Science and Innovation CampusDidcotOxfordshireOX11 0DEUK
| | - Ali Ebrahim
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterEssexCO4 3SQUK
- Diamond Light SourceHarwell Science and Innovation CampusDidcotOxfordshireOX11 0DEUK
| | - Danny Axford
- Diamond Light SourceHarwell Science and Innovation CampusDidcotOxfordshireOX11 0DEUK
| | | | | | - Shigeki Owada
- RIKEN Spring-8 Center1-1-1 KoutoSayoHyogo679-5148Japan
- Japan Synchrotron Radiation Research Institute1-1-1 KoutoSayoHyogo679-5198Japan
| | | | - Ivo Tews
- Biological SciencesInstitute for Life SciencesUniversity of SouthamptonUniversity RoadSouthamptonSO17 1BJUK
| | - Robin L. Owen
- Diamond Light SourceHarwell Science and Innovation CampusDidcotOxfordshireOX11 0DEUK
| | - Michael A. Hough
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterEssexCO4 3SQUK
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4
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Lučić M, Svistunenko DA, Wilson MT, Chaplin AK, Davy B, Ebrahim A, Axford D, Tosha T, Sugimoto H, Owada S, Dworkowski FSN, Tews I, Owen RL, Hough MA, Worrall JAR. Serial Femtosecond Zero Dose Crystallography Captures a Water‐Free Distal Heme Site in a Dye‐Decolorising Peroxidase to Reveal a Catalytic Role for an Arginine in Fe
IV
=O Formation. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008622] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Marina Lučić
- School of Life Sciences University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
| | | | - Michael T. Wilson
- School of Life Sciences University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
| | - Amanda K. Chaplin
- School of Life Sciences University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
| | - Bradley Davy
- Diamond Light Source Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE UK
| | - Ali Ebrahim
- School of Life Sciences University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
- Diamond Light Source Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE UK
| | - Danny Axford
- Diamond Light Source Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE UK
| | - Takehiko Tosha
- RIKEN Spring-8 Center 1-1-1 Kouto Sayo Hyogo 679-5148 Japan
| | | | - Shigeki Owada
- RIKEN Spring-8 Center 1-1-1 Kouto Sayo Hyogo 679-5148 Japan
- Japan Synchrotron Radiation Research Institute 1-1-1 Kouto Sayo Hyogo 679-5198 Japan
| | | | - Ivo Tews
- Biological Sciences Institute for Life Sciences University of Southampton University Road Southampton SO17 1BJ UK
| | - Robin L. Owen
- Diamond Light Source Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE UK
| | - Michael A. Hough
- School of Life Sciences University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
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5
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Martiel I, Huang CY, Villanueva-Perez P, Panepucci E, Basu S, Caffrey M, Pedrini B, Bunk O, Stampanoni M, Wang M. Low-dose in situ prelocation of protein microcrystals by 2D X-ray phase-contrast imaging for serial crystallography. IUCRJ 2020; 7:1131-1141. [PMID: 33209324 PMCID: PMC7642777 DOI: 10.1107/s2052252520013238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/01/2020] [Indexed: 06/11/2023]
Abstract
Serial protein crystallography has emerged as a powerful method of data collection on small crystals from challenging targets, such as membrane proteins. Multiple microcrystals need to be located on large and often flat mounts while exposing them to an X-ray dose that is as low as possible. A crystal-prelocation method is demonstrated here using low-dose 2D full-field propagation-based X-ray phase-contrast imaging at the X-ray imaging beamline TOMCAT at the Swiss Light Source (SLS). This imaging step provides microcrystal coordinates for automated serial data collection at a microfocus macromolecular crystallography beamline on samples with an essentially flat geometry. This prelocation method was applied to microcrystals of a soluble protein and a membrane protein, grown in a commonly used double-sandwich in situ crystallization plate. The inner sandwiches of thin plastic film enclosing the microcrystals in lipid cubic phase were flash cooled and imaged at TOMCAT. Based on the obtained crystal coordinates, both still and rotation wedge serial data were collected automatically at the SLS PXI beamline, yielding in both cases a high indexing rate. This workflow can be easily implemented at many synchrotron facilities using existing equipment, or potentially integrated as an online technique in the next-generation macromolecular crystallography beamline, and thus benefit a number of dose-sensitive challenging protein targets.
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Affiliation(s)
- Isabelle Martiel
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen, 5232, Switzerland
| | - Chia-Ying Huang
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen, 5232, Switzerland
| | - Pablo Villanueva-Perez
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen, 5232, Switzerland
- Synchrotron Radiation Research and NanoLund, Lund University, Box 118, Lund, 221 00, Sweden
| | - Ezequiel Panepucci
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen, 5232, Switzerland
| | - Shibom Basu
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen, 5232, Switzerland
- EMBL Grenoble, 71 avenue des Martyrs, Grenoble, 38042, France
| | - Martin Caffrey
- School of Medicine and School of Biochemistry and Immunology, Trinity College, Dublin 2, D02 R590, Ireland
| | - Bill Pedrini
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen, 5232, Switzerland
| | - Oliver Bunk
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen, 5232, Switzerland
| | - Marco Stampanoni
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen, 5232, Switzerland
- Institute of Biomedical Engineering, University and ETH Zurich, Zurich, 8092, Switzerland
| | - Meitian Wang
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen, 5232, Switzerland
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6
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Martiel I, Mozzanica A, Opara NL, Panepucci E, Leonarski F, Redford S, Mohacsi I, Guzenko V, Ozerov D, Padeste C, Schmitt B, Pedrini B, Wang M. X-ray fluorescence detection for serial macromolecular crystallography using a JUNGFRAU pixel detector. JOURNAL OF SYNCHROTRON RADIATION 2020; 27:329-339. [PMID: 32153271 PMCID: PMC7064105 DOI: 10.1107/s1600577519016758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 12/14/2019] [Indexed: 05/06/2023]
Abstract
Detection of heavy elements, such as metals, in macromolecular crystallography (MX) samples by X-ray fluorescence is a function traditionally covered at synchrotron MX beamlines by silicon drift detectors, which cannot be used at X-ray free-electron lasers because of the very short duration of the X-ray pulses. Here it is shown that the hybrid pixel charge-integrating detector JUNGFRAU can fulfill this function when operating in a low-flux regime. The feasibility of precise position determination of micrometre-sized metal marks is also demonstrated, to be used as fiducials for offline prelocation in serial crystallography experiments, based on the specific fluorescence signal measured with JUNGFRAU, both at the synchrotron and at SwissFEL. Finally, the measurement of elemental absorption edges at a synchrotron beamline using JUNGFRAU is also demonstrated.
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Affiliation(s)
- Isabelle Martiel
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
| | - Aldo Mozzanica
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
| | - Nadia L. Opara
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Basel 4058, Switzerland
- SwissNanoscience Institute, University of Basel, Basel 4056, Switzerland
| | - Ezequiel Panepucci
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
| | - Filip Leonarski
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
| | - Sophie Redford
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
| | - Istvan Mohacsi
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
| | - Vitaliy Guzenko
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
| | - Dmitry Ozerov
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
| | - Celestino Padeste
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
| | - Bernd Schmitt
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
| | - Bill Pedrini
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
| | - Meitian Wang
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
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7
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Huang CY, Olieric V, Caffrey M, Wang M. In Meso In Situ Serial X-Ray Crystallography (IMISX): A Protocol for Membrane Protein Structure Determination at the Swiss Light Source. Methods Mol Biol 2020; 2127:293-319. [PMID: 32112330 DOI: 10.1007/978-1-0716-0373-4_20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The lipid cubic phases (LCP) have enabled the determination of many important high-resolution structures of membrane proteins such as G-protein-coupled receptors, photosensitive proteins, enzymes, channels, and transporters. However, harvesting the crystals from the glass or plastic plates in which crystals grow is challenging. The in meso in situ serial X-ray crystallography (IMISX) method uses thin plastic windowed plates that minimize LCP crystal manipulation. The method, which is compatible with high-throughput in situ measurements, allows systematic diffraction screening and rapid data collection from hundreds of microcrystals in in meso crystallization wells without direct crystal harvesting. In this chapter, we describe an IMISX protocol for in situ serial X-ray data collection of LCP-grown crystals at both cryogenic and room temperatures which includes the crystallization setup, sample delivery, automated serial diffraction data collection, and experimental phasing. We also detail how the IMISX method was applied successfully for the structure determination of two novel targets-the undecaprenyl-pyrophosphate phosphatase BacA and the chemokine G-protein-coupled receptor CCR2A.
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Affiliation(s)
- Chia-Ying Huang
- Swiss Light Source, Paul Scherrer Institut, Forschungsstrasse 111, Villigen-PSI, 5232, Switzerland.
| | - Vincent Olieric
- Swiss Light Source, Paul Scherrer Institut, Forschungsstrasse 111, Villigen-PSI, 5232, Switzerland
| | - Martin Caffrey
- Membrane Structural and Functional Biology (MS&FB) Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
| | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institut, Forschungsstrasse 111, Villigen-PSI, 5232, Switzerland
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8
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Lučić M, Chaplin AK, Moreno-Chicano T, Dworkowski FSN, Wilson MT, Svistunenko DA, Hough MA, Worrall JAR. A subtle structural change in the distal haem pocket has a remarkable effect on tuning hydrogen peroxide reactivity in dye decolourising peroxidases fromStreptomyces lividans. Dalton Trans 2020; 49:1620-1636. [DOI: 10.1039/c9dt04583j] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A subtle positional shift of the distal haem pocket aspartate in two dye decolourising peroxidase homologs has a remarkable effect on their reactivity with H2O2.
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Affiliation(s)
- Marina Lučić
- School of Life Sciences
- University of Essex
- Colchester
- UK
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9
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Ciatto G, Aubert N, Lecroard M, Engblom C, Fontaine P, Dubuisson JM, Abiven YM, Janolin PE, Kiat JM, Dumont Y, Berini B, Fouchet A, Keller N. FORTE - a multipurpose high-vacuum diffractometer for tender X-ray diffraction and spectroscopy at the SIRIUS beamline of Synchrotron SOLEIL. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:1374-1387. [PMID: 31274467 DOI: 10.1107/s1600577519003722] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 03/18/2019] [Indexed: 06/09/2023]
Abstract
A new high-vacuum multipurpose diffractometer (called FORTE from the French acronyms of the project) has recently been installed at the tender/hard X-ray SIRIUS beamline of Synchrotron SOLEIL, France. The geometry chosen allows one to work either in the classical Eulerian four-circle geometry for bulk X-ray diffraction (XRD) or in the z-axis geometry for surface XRD. The diffractometer nicely fits the characteristics of the SIRIUS beamline, optimized to work in the 1.1-4.5 keV range, and allows one to perform unprecedented diffraction anomalous fine structure (DAFS) experiments in the tender X-ray region, also around non-specular reflections, covering a large reciprocal-space volume. Installation of an X-ray fluorescence detector on a dedicated flange allows simultaneous DAFS and X-ray absorption (XAS) measurements. The access to the tender X-ray region paves the way to resonant investigations around the L-edges of second-row transition elements which are constituents of functional oxide materials. It also enables access to several edges of interest for semiconductors. Finally, the control architecture based on synchronized Delta Tau units opens up exciting perspectives for improvement of the mechanical sphere of confusion.
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Affiliation(s)
- G Ciatto
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48 F-91192 Gif sur Yvette CEDEX, France
| | - N Aubert
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48 F-91192 Gif sur Yvette CEDEX, France
| | - M Lecroard
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48 F-91192 Gif sur Yvette CEDEX, France
| | - C Engblom
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48 F-91192 Gif sur Yvette CEDEX, France
| | - P Fontaine
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48 F-91192 Gif sur Yvette CEDEX, France
| | - J M Dubuisson
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48 F-91192 Gif sur Yvette CEDEX, France
| | - Y M Abiven
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48 F-91192 Gif sur Yvette CEDEX, France
| | - P E Janolin
- Laboratoire SPMS, UMR CNRS-CentraleSupélec, Bâtiment Gustave Eiffel - MB.105, 8-10 rue Joliot-Curie, 91190 Gif-Sur-Yvette CEDEX, France
| | - J M Kiat
- Laboratoire SPMS, UMR CNRS-CentraleSupélec, Bâtiment Gustave Eiffel - MB.105, 8-10 rue Joliot-Curie, 91190 Gif-Sur-Yvette CEDEX, France
| | - Y Dumont
- Groupe d'Etudes de la Matière Condensée (GEMaC), Université Versailles Saint-Quentin en Yvelines - CNRS, Université Paris-Saclay, Versailles, France
| | - B Berini
- Groupe d'Etudes de la Matière Condensée (GEMaC), Université Versailles Saint-Quentin en Yvelines - CNRS, Université Paris-Saclay, Versailles, France
| | - A Fouchet
- Groupe d'Etudes de la Matière Condensée (GEMaC), Université Versailles Saint-Quentin en Yvelines - CNRS, Université Paris-Saclay, Versailles, France
| | - N Keller
- Groupe d'Etudes de la Matière Condensée (GEMaC), Université Versailles Saint-Quentin en Yvelines - CNRS, Université Paris-Saclay, Versailles, France
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10
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de Wijn R, Hennig O, Roche J, Engilberge S, Rollet K, Fernandez-Millan P, Brillet K, Betat H, Mörl M, Roussel A, Girard E, Mueller-Dieckmann C, Fox GC, Olieric V, Gavira JA, Lorber B, Sauter C. A simple and versatile microfluidic device for efficient biomacromolecule crystallization and structural analysis by serial crystallography. IUCRJ 2019; 6:454-464. [PMID: 31098026 PMCID: PMC6503916 DOI: 10.1107/s2052252519003622] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 03/14/2019] [Indexed: 05/15/2023]
Abstract
Determining optimal conditions for the production of well diffracting crystals is a key step in every biocrystallography project. Here, a microfluidic device is described that enables the production of crystals by counter-diffusion and their direct on-chip analysis by serial crystallography at room temperature. Nine 'non-model' and diverse biomacromolecules, including seven soluble proteins, a membrane protein and an RNA duplex, were crystallized and treated on-chip with a variety of standard techniques including micro-seeding, crystal soaking with ligands and crystal detection by fluorescence. Furthermore, the crystal structures of four proteins and an RNA were determined based on serial data collected on four synchrotron beamlines, demonstrating the general applicability of this multipurpose chip concept.
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Affiliation(s)
- Raphaël de Wijn
- Architecture et Réactivité de l’ARN, UPR 9002, CNRS, Institut de Biologie Moléculaire et Cellulaire (IBMC), Université de Strasbourg, 15 Rue René Descartes, 67084 Strasbourg, France
| | - Oliver Hennig
- Institute for Biochemistry, Leipzig University, Bruederstrasse 34, 04103 Leipzig, Germany
| | - Jennifer Roche
- Architecture et Fonction des Macromolécules Biologiques, UMR 7257 CNRS–Aix Marseille University, 163 Avenue de Luminy, 13288 Marseille, France
| | | | - Kevin Rollet
- Architecture et Réactivité de l’ARN, UPR 9002, CNRS, Institut de Biologie Moléculaire et Cellulaire (IBMC), Université de Strasbourg, 15 Rue René Descartes, 67084 Strasbourg, France
| | - Pablo Fernandez-Millan
- Architecture et Réactivité de l’ARN, UPR 9002, CNRS, Institut de Biologie Moléculaire et Cellulaire (IBMC), Université de Strasbourg, 15 Rue René Descartes, 67084 Strasbourg, France
| | - Karl Brillet
- Architecture et Réactivité de l’ARN, UPR 9002, CNRS, Institut de Biologie Moléculaire et Cellulaire (IBMC), Université de Strasbourg, 15 Rue René Descartes, 67084 Strasbourg, France
| | - Heike Betat
- Institute for Biochemistry, Leipzig University, Bruederstrasse 34, 04103 Leipzig, Germany
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University, Bruederstrasse 34, 04103 Leipzig, Germany
| | - Alain Roussel
- Architecture et Fonction des Macromolécules Biologiques, UMR 7257 CNRS–Aix Marseille University, 163 Avenue de Luminy, 13288 Marseille, France
| | - Eric Girard
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | | | - Gavin C. Fox
- PROXIMA 2A beamline, Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin, 91192 Gif-sur-Yvette, France
| | - Vincent Olieric
- Paul Scherrer Institute, Swiss Light Source, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - José A. Gavira
- Laboratorio de Estudios Cristalográficos, IACT, CSIC–Universidad de Granada, Avenida Las Palmeras 4, 18100 Armilla, Granada, Spain
| | - Bernard Lorber
- Architecture et Réactivité de l’ARN, UPR 9002, CNRS, Institut de Biologie Moléculaire et Cellulaire (IBMC), Université de Strasbourg, 15 Rue René Descartes, 67084 Strasbourg, France
| | - Claude Sauter
- Architecture et Réactivité de l’ARN, UPR 9002, CNRS, Institut de Biologie Moléculaire et Cellulaire (IBMC), Université de Strasbourg, 15 Rue René Descartes, 67084 Strasbourg, France
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11
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Structure of activated transcription complex Pol II-DSIF-PAF-SPT6. Nature 2018; 560:607-612. [PMID: 30135578 DOI: 10.1038/s41586-018-0440-4] [Citation(s) in RCA: 256] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 07/17/2018] [Indexed: 11/09/2022]
Abstract
Gene regulation involves activation of RNA polymerase II (Pol II) that is paused and bound by the protein complexes DRB sensitivity-inducing factor (DSIF) and negative elongation factor (NELF). Here we show that formation of an activated Pol II elongation complex in vitro requires the kinase function of the positive transcription elongation factor b (P-TEFb) and the elongation factors PAF1 complex (PAF) and SPT6. The cryo-EM structure of an activated elongation complex of Sus scrofa Pol II and Homo sapiens DSIF, PAF and SPT6 was determined at 3.1 Å resolution and compared to the structure of the paused elongation complex formed by Pol II, DSIF and NELF. PAF displaces NELF from the Pol II funnel for pause release. P-TEFb phosphorylates the Pol II linker to the C-terminal domain. SPT6 binds to the phosphorylated C-terminal-domain linker and opens the RNA clamp formed by DSIF. These results provide the molecular basis for Pol II pause release and elongation activation.
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12
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Schwemmlein N, Pippel J, Gazdag EM, Blankenfeldt W. Crystal Structures of R-Type Bacteriocin Sheath and Tube Proteins CD1363 and CD1364 From Clostridium difficile in the Pre-assembled State. Front Microbiol 2018; 9:1750. [PMID: 30127773 PMCID: PMC6088184 DOI: 10.3389/fmicb.2018.01750] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 07/13/2018] [Indexed: 12/26/2022] Open
Abstract
Diffocins are high-molecular-weight phage tail-like bacteriocins (PTLBs) that some Clostridium difficile strains produce in response to SOS induction. Similar to the related R-type pyocins from Pseudomonas aeruginosa, R-type diffocins act as molecular puncture devices that specifically penetrate the cell envelope of other C. difficile strains to dissipate the membrane potential and kill the attacked bacterium. Thus, R-type diffocins constitute potential therapeutic agents to counter C. difficile-associated infections. PTLBs consist of rigid and contractile protein complexes. They are composed of a baseplate, receptor-binding tail fibers and an inner needle-like tube surrounded by a contractile sheath. In the mature particle, the sheath and tube structure form a complex network comprising up to 200 copies of a sheath and a tube protein each. Here, we report the crystal structures together with small angle X-ray scattering data of the sheath and tube proteins CD1363 (39 kDa) and CD1364 (16 kDa) from C. difficile strain CD630 in a monomeric pre-assembly form at 1.9 and 1.5 Å resolution, respectively. The tube protein CD1364 displays a compact fold and shares highest structural similarity with a tube protein from Bacillus subtilis but is remarkably different from that of the R-type pyocin from P. aeruginosa. The structure of the R-type diffocin sheath protein, on the other hand, is highly conserved. It contains two domains, whereas related members such as bacteriophage tail sheath proteins comprise up to four, indicating that R-type PTLBs may represent the minimal protein required for formation of a complete sheath structure. Comparison of CD1363 and CD1364 with structures of PTLBs and related assemblies suggests that several conformational changes are required to form complete assemblies. In the sheath, rearrangement of the flexible N- and C-terminus enables extensive interactions between the other subunits, whereas for the tube, such contacts are primarily established by mobile α-helices. Together, our results combined with information from structures of homologous assemblies allow constructing a preliminary model of the sheath and tube assembly from R-type diffocin.
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Affiliation(s)
- Nina Schwemmlein
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Jan Pippel
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Emerich-Mihai Gazdag
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Wulf Blankenfeldt
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
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13
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Locating and Visualizing Crystals for X-Ray Diffraction Experiments. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2017; 1607:143-164. [PMID: 28573572 DOI: 10.1007/978-1-4939-7000-1_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Macromolecular crystallography has advanced from using macroscopic crystals, which might be >1 mm on a side, to crystals that are essentially invisible to the naked eye, or even under a standard laboratory microscope. As crystallography requires recognizing crystals when they are produced, and then placing them in an X-ray, electron, or neutron beam, this provides challenges, particularly in the case of advanced X-ray sources, where beams have very small cross sections and crystals may be vanishingly small. Methods for visualizing crystals are reviewed here, and examples of different types of cases are presented, including: standard crystals, crystals grown in mesophase, in situ crystallography, and crystals grown for X-ray Free Electron Laser or Micro Electron Diffraction experiments. As most techniques have limitations, it is desirable to have a range of complementary techniques available to identify and locate crystals. Ideally, a given technique should not cause sample damage, but sometimes it is necessary to use techniques where damage can only be minimized. For extreme circumstances, the act of probing location may be coincident with collecting X-ray diffraction data. Future challenges and directions are also discussed.
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Abstract
Micro-diffraction tools for macromolecular crystallography, first developed at the end of 1990s and now an integral part of many synchrotron beamlines, enable some of the experiments which were not feasible just a decade or so ago. These include data collection from very small samples, just a few micrometers in size; from larger, but severely inhomogeneous samples; and from samples which are optically invisible. Improved micro-diffraction tools led to improved signal-to-noise ratio, to mitigation of radiation damage in some cases, and to better-designed diffraction experiments. Small, micron-scale beams can be attained in different ways and knowing the details of the implementation is important in order to design the diffraction experiment properly. Similarly, precision, reproducibility and stability of the goniometry, and caveats of detection systems need to be taken into account. Lastly, to make micro-diffraction widely applicable, the sophistication, robustness, and user-friendliness of these tools are just as important as the technical capabilities.
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Affiliation(s)
- Ruslan Sanishvili
- GM/CA@APS, Advanced Photon Source, Argonne National Laboratory, Argonne, IL, USA.
| | - Robert F Fischetti
- GM/CA@APS, Advanced Photon Source, Argonne National Laboratory, Argonne, IL, USA
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15
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Owen RL, Juanhuix J, Fuchs M. Current advances in synchrotron radiation instrumentation for MX experiments. Arch Biochem Biophys 2016; 602:21-31. [PMID: 27046341 PMCID: PMC5505570 DOI: 10.1016/j.abb.2016.03.021] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 03/16/2016] [Accepted: 03/21/2016] [Indexed: 11/15/2022]
Abstract
Following pioneering work 40 years ago, synchrotron beamlines dedicated to macromolecular crystallography (MX) have improved in almost every aspect as instrumentation has evolved. Beam sizes and crystal dimensions are now on the single micron scale while data can be collected from proteins with molecular weights over 10 MDa and from crystals with unit cell dimensions over 1000 Å. Furthermore it is possible to collect a complete data set in seconds, and obtain the resulting structure in minutes. The impact of MX synchrotron beamlines and their evolution is reflected in their scientific output, and MX is now the method of choice for a variety of aims from ligand binding to structure determination of membrane proteins, viruses and ribosomes, resulting in a much deeper understanding of the machinery of life. A main driving force of beamline evolution have been advances in almost every aspect of the instrumentation comprising a synchrotron beamline. In this review we aim to provide an overview of the current status of instrumentation at modern MX experiments. The most critical optical components are discussed, as are aspects of endstation design, sample delivery, visualisation and positioning, the sample environment, beam shaping, detectors and data acquisition and processing.
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Affiliation(s)
- Robin L Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.
| | - Jordi Juanhuix
- Alba Synchrotron, Carrer de la llum 2-26, Cerdanyola, 08192, Spain.
| | - Martin Fuchs
- National Synchrotron Light Source II, Brookhaven National Lab, Upton, NY, 11973, USA.
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16
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Wojdyla JA, Panepucci E, Martiel I, Ebner S, Huang CY, Caffrey M, Bunk O, Wang M. Fast two-dimensional grid and transmission X-ray microscopy scanning methods for visualizing and characterizing protein crystals. J Appl Crystallogr 2016; 49:944-952. [PMID: 27275141 PMCID: PMC4886984 DOI: 10.1107/s1600576716006233] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 04/13/2016] [Indexed: 11/17/2022] Open
Abstract
A fast continuous grid scan protocol has been incorporated into the Swiss Light Source (SLS) data acquisition and analysis software suite on the macromolecular crystallography (MX) beamlines. Its combination with fast readout single-photon counting hybrid pixel array detectors (PILATUS and EIGER) allows for diffraction-based identification of crystal diffraction hotspots and the location and centering of membrane protein microcrystals in the lipid cubic phase (LCP) in in meso in situ serial crystallography plates and silicon nitride supports. Diffraction-based continuous grid scans with both still and oscillation images are supported. Examples that include a grid scan of a large (50 nl) LCP bolus and analysis of the resulting diffraction images are presented. Scanning transmission X-ray microscopy (STXM) complements and benefits from fast grid scanning. STXM has been demonstrated at the SLS beamline X06SA for near-zero-dose detection of protein crystals mounted on different types of sample supports at room and cryogenic temperatures. Flash-cooled crystals in nylon loops were successfully identified in differential and integrated phase images. Crystals of just 10 µm thickness were visible in integrated phase images using data collected with the EIGER detector. STXM offers a truly low-dose method for locating crystals on solid supports prior to diffraction data collection at both synchrotron microfocusing and free-electron laser X-ray facilities.
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Affiliation(s)
| | - Ezequiel Panepucci
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Isabelle Martiel
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Simon Ebner
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Chia-Ying Huang
- Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
| | - Martin Caffrey
- Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
| | - Oliver Bunk
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
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17
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Sakaguchi M, Kimura T, Nishida T, Tosha T, Sugimoto H, Yamaguchi Y, Yanagisawa S, Ueno G, Murakami H, Ago H, Yamamoto M, Ogura T, Shiro Y, Kubo M. A nearly on-axis spectroscopic system for simultaneously measuring UV-visible absorption and X-ray diffraction in the SPring-8 structural genomics beamline. JOURNAL OF SYNCHROTRON RADIATION 2016; 23:334-8. [PMID: 26698082 PMCID: PMC5356500 DOI: 10.1107/s1600577515018275] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 09/29/2015] [Indexed: 05/23/2023]
Abstract
UV-visible absorption spectroscopy is useful for probing the electronic and structural changes of protein active sites, and thus the on-line combination of X-ray diffraction and spectroscopic analysis is increasingly being applied. Herein, a novel absorption spectrometer was developed at SPring-8 BL26B2 with a nearly on-axis geometry between the X-ray and optical axes. A small prism mirror was placed near the X-ray beamstop to pass the light only 2° off the X-ray beam, enabling spectroscopic analysis of the X-ray-exposed volume of a crystal during X-ray diffraction data collection. The spectrometer was applied to NO reductase, a heme enzyme that catalyzes NO reduction to N2O. Radiation damage to the heme was monitored in real time during X-ray irradiation by evaluating the absorption spectral changes. Moreover, NO binding to the heme was probed via caged NO photolysis with UV light, demonstrating the extended capability of the spectrometer for intermediate analysis.
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Affiliation(s)
- Miyuki Sakaguchi
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Akoh, Hyogo 678-1297, Japan
| | | | - Takuma Nishida
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Akoh, Hyogo 678-1297, Japan
| | - Takehiko Tosha
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | | | - Yoshihiro Yamaguchi
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Akoh, Hyogo 678-1297, Japan
| | - Sachiko Yanagisawa
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Akoh, Hyogo 678-1297, Japan
| | - Go Ueno
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | | | - Hideo Ago
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Masaki Yamamoto
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Takashi Ogura
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Akoh, Hyogo 678-1297, Japan
| | - Yoshitsugu Shiro
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Akoh, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Minoru Kubo
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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18
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Waltersperger S, Olieric V, Pradervand C, Glettig W, Salathe M, Fuchs MR, Curtin A, Wang X, Ebner S, Panepucci E, Weinert T, Schulze-Briese C, Wang M. PRIGo: a new multi-axis goniometer for macromolecular crystallography. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:895-900. [PMID: 26134792 PMCID: PMC4489532 DOI: 10.1107/s1600577515005354] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 03/15/2015] [Indexed: 05/29/2023]
Abstract
The Parallel Robotics Inspired Goniometer (PRIGo) is a novel compact and high-precision goniometer providing an alternative to (mini-)kappa, traditional three-circle goniometers and Eulerian cradles used for sample reorientation in macromolecular crystallography. Based on a combination of serial and parallel kinematics, PRIGo emulates an arc. It is mounted on an air-bearing stage for rotation around ω and consists of four linear positioners working synchronously to achieve x, y, z translations and χ rotation (0-90°), followed by a ϕ stage (0-360°) for rotation around the sample holder axis. Owing to the use of piezo linear positioners and active correction, PRIGo features spheres of confusion of <1 µm, <7 µm and <10 µm for ω, χ and ϕ, respectively, and is therefore very well suited for micro-crystallography. PRIGo enables optimal strategies for both native and experimental phasing crystallographic data collection. Herein, PRIGo hardware and software, its calibration, as well as applications in macromolecular crystallography are described.
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Affiliation(s)
| | - Vincent Olieric
- Swiss Light Source, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Claude Pradervand
- Swiss Light Source, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Wayne Glettig
- Centre Suisse d’Electronique et Microtechnique SA, Neuchâtel 2002, Switzerland
| | - Marco Salathe
- Swiss Light Source, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Martin R. Fuchs
- Swiss Light Source, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Adrian Curtin
- Swiss Light Source, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Xiaoqiang Wang
- Swiss Light Source, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Simon Ebner
- Swiss Light Source, Paul Scherrer Institute, Villigen PSI, Switzerland
| | | | - Tobias Weinert
- Swiss Light Source, Paul Scherrer Institute, Villigen PSI, Switzerland
| | | | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institute, Villigen PSI, Switzerland
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19
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Dworkowski FSN, Hough MA, Pompidor G, Fuchs MR. Challenges and solutions for the analysis of in situ, in crystallo micro-spectrophotometric data. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:27-35. [PMID: 25615857 PMCID: PMC4304683 DOI: 10.1107/s1399004714015107] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 06/26/2014] [Indexed: 11/22/2022]
Abstract
Combining macromolecular crystallography with in crystallo micro-spectrophotometry yields valuable complementary information on the sample, including the redox states of metal cofactors, the identification of bound ligands and the onset and strength of undesired photochemistry, also known as radiation damage. However, the analysis and processing of the resulting data differs significantly from the approaches used for solution spectrophotometric data. The varying size and shape of the sample, together with the suboptimal sample environment, the lack of proper reference signals and the general influence of the X-ray beam on the sample have to be considered and carefully corrected for. In the present article, how to characterize and treat these sample-dependent artefacts in a reproducible manner is discussed and the SLS-APE in situ, in crystallo optical spectroscopy data-analysis toolbox is demonstrated.
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Affiliation(s)
| | - Michael A. Hough
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | - Guillaume Pompidor
- European Molecular Biology Laboratory Hamburg, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany
| | - Martin R. Fuchs
- Photon Sciences, Brookhaven National Laboratory, Mail Stop 745, Upton, NY 11973, USA
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20
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Shinoda A, Tanaka Y, Yao M, Tanaka I. Anchoring protein crystals to mounting loops with hydrogel using inkjet technology. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:2794-9. [PMID: 25372671 DOI: 10.1107/s139900471401476x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 06/23/2014] [Indexed: 11/10/2022]
Abstract
X-ray crystallography is an important technique for structure-based drug discovery, mainly because it is the only technique that can reveal whether a ligand binds to the target protein as well as where and how it binds. However, ligand screening by X-ray crystallography involves a crystal-soaking experiment, which is usually performed manually. Thus, the throughput is not satisfactory for screening large numbers of candidate ligands. In this study, a technique to anchor protein crystals to mounting loops by using gel and inkjet technology has been developed; the method allows soaking of the mounted crystals in ligand-containing solution. This new technique may assist in the design of a fully automated drug-screening pipeline.
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Affiliation(s)
- Akira Shinoda
- Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Yoshikazu Tanaka
- Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Min Yao
- Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Isao Tanaka
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
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