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Okumura H, Sakai N, Murakami H, Mizuno N, Nakamura Y, Ueno G, Masunaga T, Kawamura T, Baba S, Hasegawa K, Yamamoto M, Kumasaka T. In situ crystal data-collection and ligand-screening system at SPring-8. Acta Crystallogr F Struct Biol Commun 2022; 78:241-251. [PMID: 35647681 PMCID: PMC9158660 DOI: 10.1107/s2053230x22005283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
An in situ X-ray diffraction measurement system using a crystallization plate has been constructed at the SPring-8 protein crystallography beamline. Utilizing small-wedge measurements and incorporating a liquid dispenser to prepare protein–ligand complex crystals, this system will make ligand screening possible. In situ diffraction data collection using crystallization plates has been utilized for macromolecules to evaluate crystal quality without requiring additional sample treatment such as cryocooling. Although it is difficult to collect complete data sets using this technique due to the mechanical limitation of crystal rotation, recent advances in methods for data collection from multiple crystals have overcome this issue. At SPring-8, an in situ diffraction measurement system was constructed consisting of a goniometer for a plate, an articulated robot and plate storage. Using this system, complete data sets were obtained utilizing the small-wedge measurement method. Combining this system with an acoustic liquid handler to prepare protein–ligand complex crystals by applying fragment compounds to trypsin crystals for in situ soaking, binding was confirmed for seven out of eight compounds. These results show that the system functioned properly to collect complete data for structural analysis and to expand the capability for ligand screening in combination with a liquid dispenser.
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Liang M, Yu L, Wang Z, Zhou H, Zhang Y, Wang Q, He J. Novel combined crystallization plate for high-throughput crystal screening and in situ data collection at a crystallography beamline. Acta Crystallogr F Struct Biol Commun 2021; 77:319-327. [PMID: 34473109 PMCID: PMC8411933 DOI: 10.1107/s2053230x21008104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/06/2021] [Indexed: 11/10/2022] Open
Abstract
In situ microplates are small in size, crystal cultivation and operation are difficult, and the efficiency of crystal screening is relatively low. To solve this problem, a novel combined crystallization plate was designed for high-throughput crystal cultivation and in situ data collection. A frame was used to hold 48 in situ microplates, and the in situ microplates were sealed on one side with an ultralow background-scattering Kapton film. An automatic liquid handler (Mosquito) was used to add a liquid drop to the in situ microplates in the frame, and CrystalClear HD tape was used to seal the frame. A sealed frame holding 48 microplates was developed as a novel combined crystallization plate and was used for crystal cultivation under different conditions and in situ data collection at the synchrotron beamline. Moreover, individual microplates can be separated from the combined crystal plate and then fixed on a magnetic base or loaded onto a UniPuck for in situ data collection. Automatic grid scanning was used to locate crystals. The efficiency of the combined crystallization plate for crystal screening was verified. This method avoids the manual manipulation of crystals during crystal screening and diffraction data collection; therefore, the combined crystallization plate is suitable for large-scale screening of microcrystals.
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Affiliation(s)
- Miao Liang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Li Yu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Zhijun Wang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, People’s Republic of China
| | - Huan Zhou
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, People’s Republic of China
| | - Yi Zhang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, People’s Republic of China
| | - Qisheng Wang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, People’s Republic of China
| | - Jianhua He
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
- The Institute for Advanced Studies, Wuhan University, Wuhan 430072, People’s Republic of China
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Wright ND, Collins P, Koekemoer L, Krojer T, Talon R, Nelson E, Ye M, Nowak R, Newman J, Ng JT, Mitrovich N, Wiggers H, von Delft F. The low-cost Shifter microscope stage transforms the speed and robustness of protein crystal harvesting. Acta Crystallogr D Struct Biol 2021; 77:62-74. [PMID: 33404526 PMCID: PMC7787106 DOI: 10.1107/s2059798320014114] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 10/22/2020] [Indexed: 12/05/2022] Open
Abstract
Despite the tremendous success of X-ray cryo-crystallography in recent decades, the transfer of crystals from the drops in which they are grown to diffractometer sample mounts remains a manual process in almost all laboratories. Here, the Shifter, a motorized, interactive microscope stage that transforms the entire crystal-mounting workflow from a rate-limiting manual activity to a controllable, high-throughput semi-automated process, is described. By combining the visual acuity and fine motor skills of humans with targeted hardware and software automation, it was possible to transform the speed and robustness of crystal mounting. Control software, triggered by the operator, manoeuvres crystallization plates beneath a clear protective cover, allowing the complete removal of film seals and thereby eliminating the tedium of repetitive seal cutting. The software, either upon request or working from an imported list, controls motors to position crystal drops under a hole in the cover for human mounting at a microscope. The software automatically captures experimental annotations for uploading to the user's data repository, removing the need for manual documentation. The Shifter facilitates mounting rates of 100-240 crystals per hour in a more controlled process than manual mounting, which greatly extends the lifetime of the drops and thus allows a dramatic increase in the number of crystals retrievable from any given drop without loss of X-ray diffraction quality. In 2015, the first in a series of three Shifter devices was deployed as part of the XChem fragment-screening facility at Diamond Light Source, where they have since facilitated the mounting of over 120 000 crystals. The Shifter was engineered to have a simple design, providing a device that could be readily commercialized and widely adopted owing to its low cost. The versatile hardware design allows use beyond fragment screening and protein crystallography.
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Affiliation(s)
- Nathan David Wright
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Patrick Collins
- I04-1, Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, United Kingdom
| | - Lizbé Koekemoer
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Tobias Krojer
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Romain Talon
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
- I04-1, Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, United Kingdom
| | - Elliot Nelson
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Mingda Ye
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Radosław Nowak
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Joseph Newman
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Jia Tsing Ng
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Nick Mitrovich
- Oxford Lab Technologies Ltd, Kemp House, 160 City Road, London EC1V 2N, United Kingdom
| | - Helton Wiggers
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Frank von Delft
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
- I04-1, Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, United Kingdom
- Faculty of Science, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa
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Membrane protein crystallography in the era of modern structural biology. Biochem Soc Trans 2020; 48:2505-2524. [DOI: 10.1042/bst20200066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 02/07/2023]
Abstract
The aim of structural biology has been always the study of biological macromolecules structures and their mechanistic behaviour at molecular level. To achieve its goal, multiple biophysical methods and approaches have become part of the structural biology toolbox. Considered as one of the pillars of structural biology, X-ray crystallography has been the most successful method for solving three-dimensional protein structures at atomic level to date. It is however limited by the success in obtaining well-ordered protein crystals that diffract at high resolution. This is especially true for challenging targets such as membrane proteins (MPs). Understanding structure-function relationships of MPs at the biochemical level is vital for medicine and drug discovery as they play critical roles in many cellular processes. Though difficult, structure determination of MPs by X-ray crystallography has significantly improved in the last two decades, mainly due to many relevant technological and methodological developments. Today, numerous MP crystal structures have been solved, revealing many of their mechanisms of action. Yet the field of structural biology has also been through significant technological breakthroughs in recent years, particularly in the fields of single particle electron microscopy (cryo-EM) and X-ray free electron lasers (XFELs). Here we summarise the most important advancements in the field of MP crystallography and the significance of these developments in the present era of modern structural biology.
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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] [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).
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Affiliation(s)
- Andrew A. McCarthy
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble 38042, France
- Correspondence e-mail:
| | - 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
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