1
|
Shelley KL, Garman EF. Identifying and avoiding radiation damage in macromolecular crystallography. Acta Crystallogr D Struct Biol 2024; 80:314-327. [PMID: 38700059 PMCID: PMC11066884 DOI: 10.1107/s2059798324003243] [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] [Received: 02/29/2024] [Accepted: 04/15/2024] [Indexed: 05/05/2024] Open
Abstract
Radiation damage remains one of the major impediments to accurate structure solution in macromolecular crystallography. The artefacts of radiation damage can manifest as structural changes that result in incorrect biological interpretations being drawn from a model, they can reduce the resolution to which data can be collected and they can even prevent structure solution entirely. In this article, we discuss how to identify and mitigate against the effects of radiation damage at each stage in the macromolecular crystal structure-solution pipeline.
Collapse
Affiliation(s)
- Kathryn L. Shelley
- Department of Biochemistry, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, United Kingdom
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Institute for Protein Design, University of Washington, Seattle, Washington, USA
| | - Elspeth F. Garman
- Department of Biochemistry, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, United Kingdom
| |
Collapse
|
2
|
Caramello N, Royant A. From femtoseconds to minutes: time-resolved macromolecular crystallography at XFELs and synchrotrons. Acta Crystallogr D Struct Biol 2024; 80:60-79. [PMID: 38265875 PMCID: PMC10836399 DOI: 10.1107/s2059798323011002] [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] [Received: 10/26/2023] [Accepted: 12/21/2023] [Indexed: 01/26/2024] Open
Abstract
Over the last decade, the development of time-resolved serial crystallography (TR-SX) at X-ray free-electron lasers (XFELs) and synchrotrons has allowed researchers to study phenomena occurring in proteins on the femtosecond-to-minute timescale, taking advantage of many technical and methodological breakthroughs. Protein crystals of various sizes are presented to the X-ray beam in either a static or a moving medium. Photoactive proteins were naturally the initial systems to be studied in TR-SX experiments using pump-probe schemes, where the pump is a pulse of visible light. Other reaction initiations through small-molecule diffusion are gaining momentum. Here, selected examples of XFEL and synchrotron time-resolved crystallography studies will be used to highlight the specificities of the various instruments and methods with respect to time resolution, and are compared with cryo-trapping studies.
Collapse
Affiliation(s)
- Nicolas Caramello
- Structural Biology Group, European Synchrotron Radiation Facility, 1 Avenue des Martyrs, CS 40220, 38043 Grenoble CEDEX 9, France
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Antoine Royant
- Structural Biology Group, European Synchrotron Radiation Facility, 1 Avenue des Martyrs, CS 40220, 38043 Grenoble CEDEX 9, France
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, CS 10090, 38044 Grenoble CEDEX 9, France
| |
Collapse
|
3
|
Garman EF, Weik M. Radiation damage to biological macromolecules∗. Curr Opin Struct Biol 2023; 82:102662. [PMID: 37573816 DOI: 10.1016/j.sbi.2023.102662] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/27/2023] [Accepted: 07/04/2023] [Indexed: 08/15/2023]
Abstract
In this review, we describe recent research developments into radiation damage effects in macromolecular X-ray crystallography observed at synchrotrons and X-ray free electron lasers. Radiation damage in small molecule X-ray crystallography, small angle X-ray scattering experiments, microelectron diffraction, and single particle cryo-electron microscopy is briefly covered.
Collapse
Affiliation(s)
- Elspeth F Garman
- Department of Biochemistry, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford, OX1 3QU, UK.
| | - Martin Weik
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044 Grenoble, France.
| |
Collapse
|
4
|
Pei X, Bhatt N, Wang H, Ando N, Meisburger SP. Introduction to diffuse scattering and data collection. Methods Enzymol 2023; 688:1-42. [PMID: 37748823 DOI: 10.1016/bs.mie.2023.07.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
A long-standing goal in X-ray crystallography has been to extract information about the collective motions of proteins from diffuse scattering: the weak, textured signal that is found in the background of diffraction images. In the past few years, the field of macromolecular diffuse scattering has seen dramatic progress, and many of the past challenges in measurement and interpretation are now considered tractable. However, the concept of diffuse scattering is still new to many researchers, and a general set of procedures needed to collect a high-quality dataset has never been described in detail. Here, we provide the first guidelines for performing diffuse scattering experiments, which can be performed at any macromolecular crystallography beamline that supports room-temperature studies with a direct detector. We begin with a brief introduction to the theory of diffuse scattering and then walk the reader through the decision-making processes involved in preparing for and conducting a successful diffuse scattering experiment. Finally, we define quality metrics and describe ways to assess data quality both at the beamline and at home. Data obtained in this way can be processed independently by crystallographic software and diffuse scattering software to produce both a crystal structure, which represents the average atomic coordinates, and a three-dimensional diffuse scattering map that can then be interpreted in terms of models for protein motions.
Collapse
Affiliation(s)
- Xiaokun Pei
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, United States
| | - Neti Bhatt
- Department of Physics, Cornell University, Ithaca, NY, United States
| | - Haoyue Wang
- Graduate Field of Biophysics, Cornell University, Ithaca, NY, United States
| | - Nozomi Ando
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, United States; Department of Physics, Cornell University, Ithaca, NY, United States; Graduate Field of Biophysics, Cornell University, Ithaca, NY, United States.
| | - Steve P Meisburger
- Cornell High Energy Synchrotron Source, Cornell University, Ithaca, NY, United States.
| |
Collapse
|
5
|
Zhao FZ, Wang ZJ, Xiao QJ, Yu L, Sun B, Hou Q, Chen LL, Liang H, Wu H, Guo WH, He JH, Wang QS, Yin DC. Microfluidic rotating-target device capable of three-degrees-of-freedom motion for efficient in situ serial synchrotron crystallography. JOURNAL OF SYNCHROTRON RADIATION 2023; 30:347-358. [PMID: 36891848 PMCID: PMC10000801 DOI: 10.1107/s1600577523000462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
There is an increasing demand for simple and efficient sample delivery technology to match the rapid development of serial crystallography and its wide application in analyzing the structural dynamics of biological macromolecules. Here, a microfluidic rotating-target device is presented, capable of three-degrees-of-freedom motion, including two rotational degrees of freedom and one translational degree of freedom, for sample delivery. Lysozyme crystals were used as a test model with this device to collect serial synchrotron crystallography data and the device was found to be convenient and useful. This device enables in situ diffraction from crystals in a microfluidic channel without the need for crystal harvesting. The circular motion ensures that the delivery speed can be adjusted over a wide range, showing its good compatibility with different light sources. Moreover, the three-degrees-of-freedom motion guarantees the full utilization of crystals. Hence, sample consumption is greatly reduced, and only 0.1 mg of protein is consumed in collecting a complete dataset.
Collapse
Affiliation(s)
- Feng-Zhu Zhao
- School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, People’s Republic of China
- School of NCO, Army Medical University, Shijiazhuang 050081, People’s Republic of China
| | - Zhi-Jun Wang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
| | - Qing-Jie Xiao
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
| | - Li Yu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
| | - Bo Sun
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
| | - Qian Hou
- School of Materials Science and Engineering, Northwestern Polytechnical University, Xi’an 710072, People’s Republic of China
| | - Liang-Liang Chen
- School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, People’s Republic of China
| | - Huan Liang
- School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, People’s Republic of China
| | - Hai Wu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
| | - Wei-Hong Guo
- School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, People’s Republic of China
| | - Jian-Hua He
- The Institute for Advanced Studies, Wuhan University, Wuhan 430072, People’s Republic of China
| | - Qi-Sheng Wang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
| | - Da-Chuan Yin
- School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, People’s Republic of China
| |
Collapse
|
6
|
Thorne RE. Determining biomolecular structures near room temperature using X-ray crystallography: concepts, methods and future optimization. Acta Crystallogr D Struct Biol 2023; 79:78-94. [PMID: 36601809 PMCID: PMC9815097 DOI: 10.1107/s2059798322011652] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 12/04/2022] [Indexed: 01/05/2023] Open
Abstract
For roughly two decades, cryocrystallography has been the overwhelmingly dominant method for determining high-resolution biomolecular structures. Competition from single-particle cryo-electron microscopy and micro-electron diffraction, increased interest in functionally relevant information that may be missing or corrupted in structures determined at cryogenic temperature, and interest in time-resolved studies of the biomolecular response to chemical and optical stimuli have driven renewed interest in data collection at room temperature and, more generally, at temperatures from the protein-solvent glass transition near 200 K to ∼350 K. Fischer has recently reviewed practical methods for room-temperature data collection and analysis [Fischer (2021), Q. Rev. Biophys. 54, e1]. Here, the key advantages and physical principles of, and methods for, crystallographic data collection at noncryogenic temperatures and some factors relevant to interpreting the resulting data are discussed. For room-temperature data collection to realize its potential within the structural biology toolkit, streamlined and standardized methods for delivering crystals prepared in the home laboratory to the synchrotron and for automated handling and data collection, similar to those for cryocrystallography, should be implemented.
Collapse
Affiliation(s)
- Robert E. Thorne
- Physics Department, Cornell University, Ithaca, NY 14853, USA
- MiTeGen LLC, PO Box 3867, Ithaca, NY 14850, USA
| |
Collapse
|
7
|
Aumonier S, Engilberge S, Caramello N, von Stetten D, Gotthard G, Leonard GA, Mueller-Dieckmann C, Royant A. Slow protein dynamics probed by time-resolved oscillation crystallography at room temperature. IUCRJ 2022; 9:756-767. [PMID: 36381146 PMCID: PMC9634615 DOI: 10.1107/s2052252522009150] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/14/2022] [Indexed: 05/23/2023]
Abstract
The development of serial crystallography over the last decade at XFELs and synchrotrons has produced a renaissance in room-temperature macromolecular crystallography (RT-MX), and fostered many technical and methodological breakthroughs designed to study phenomena occurring in proteins on the picosecond-to-second timescale. However, there are components of protein dynamics that occur in much slower regimes, of which the study could readily benefit from state-of-the-art RT-MX. Here, the room-temperature structural study of the relaxation of a reaction intermediate at a synchrotron, exploiting a handful of single crystals, is described. The intermediate in question is formed in microseconds during the photoreaction of the LOV2 domain of phototropin 2 from Arabidopsis thaliana, which then decays in minutes. This work monitored its relaxation in the dark using a fast-readout EIGER X 4M detector to record several complete oscillation X-ray diffraction datasets, each of 1.2 s total exposure time, at different time points in the relaxation process. Coupled with in crystallo UV-Vis absorption spectroscopy, this RT-MX approach allowed the authors to follow the relaxation of the photoadduct, a thio-ether covalent bond between the chromophore and a cysteine residue. Unexpectedly, the return of the chromophore to its spectroscopic ground state is followed by medium-scale protein rearrangements that trigger a crystal phase transition and hinder the full recovery of the structural ground state of the protein. In addition to suggesting a hitherto unexpected role of a conserved tryptophan residue in the regulation of the photocycle of LOV2, this work provides a basis for performing routine time-resolved protein crystallography experiments at synchrotrons for phenomena occurring on the second-to-hour timescale.
Collapse
Affiliation(s)
- Sylvain Aumonier
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs CS 40220, Grenoble 38043, France
| | - Sylvain Engilberge
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs CS 40220, Grenoble 38043, France
| | - Nicolas Caramello
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs CS 40220, Grenoble 38043, France
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - David von Stetten
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs CS 40220, Grenoble 38043, France
| | - Guillaume Gotthard
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs CS 40220, Grenoble 38043, France
| | - Gordon A. Leonard
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs CS 40220, Grenoble 38043, France
| | - Christoph Mueller-Dieckmann
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs CS 40220, Grenoble 38043, France
| | - Antoine Royant
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs CS 40220, Grenoble 38043, France
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71 avenue des Martyrs, Grenoble 38044, France
| |
Collapse
|
8
|
Zielinski KA, Prester A, Andaleeb H, Bui S, Yefanov O, Catapano L, Henkel A, Wiedorn MO, Lorbeer O, Crosas E, Meyer J, Mariani V, Domaracky M, White TA, Fleckenstein H, Sarrou I, Werner N, Betzel C, Rohde H, Aepfelbacher M, Chapman HN, Perbandt M, Steiner RA, Oberthuer D. Rapid and efficient room-temperature serial synchrotron crystallography using the CFEL TapeDrive. IUCRJ 2022; 9:778-791. [PMID: 36381150 PMCID: PMC9634612 DOI: 10.1107/s2052252522010193] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 10/21/2022] [Indexed: 05/22/2023]
Abstract
Serial crystallography at conventional synchrotron light sources (SSX) offers the possibility to routinely collect data at room temperature using micrometre-sized crystals of biological macromolecules. However, SSX data collection is not yet as routine and currently takes significantly longer than the standard rotation series cryo-crystallography. Thus, its use for high-throughput approaches, such as fragment-based drug screening, where the possibility to measure at physio-logical temperatures would be a great benefit, is impaired. On the way to high-throughput SSX using a conveyor belt based sample delivery system - the CFEL TapeDrive - with three different proteins of biological relevance (Klebsiella pneumoniae CTX-M-14 β-lactamase, Nectria haematococca xylanase GH11 and Aspergillus flavus urate oxidase), it is shown here that complete datasets can be collected in less than a minute and only minimal amounts of sample are required.
Collapse
Affiliation(s)
- Kara A Zielinski
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Andreas Prester
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
| | - Hina Andaleeb
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a, Notkestr. 85, 22603 Hamburg, Germany
| | - Soi Bui
- Randall Centre of Cell and Molecular Biophysics, King’s College London, United Kingdom
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Lucrezia Catapano
- Randall Centre of Cell and Molecular Biophysics, King’s College London, United Kingdom
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Alessandra Henkel
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Max O. Wiedorn
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Olga Lorbeer
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Eva Crosas
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Jan Meyer
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Valerio Mariani
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Martin Domaracky
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Thomas A. White
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Holger Fleckenstein
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Iosifina Sarrou
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Nadine Werner
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a, Notkestr. 85, 22603 Hamburg, Germany
| | - Christian Betzel
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a, Notkestr. 85, 22603 Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Holger Rohde
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
| | - Martin Aepfelbacher
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
| | - Henry N. Chapman
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Markus Perbandt
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a, Notkestr. 85, 22603 Hamburg, Germany
| | - Roberto A. Steiner
- Randall Centre of Cell and Molecular Biophysics, King’s College London, United Kingdom
- Department of Biomedical Sciences, University of Padova, via Ugo Bassi 58/B, Padova 35131, Italy
| | - Dominik Oberthuer
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| |
Collapse
|
9
|
Moreno-Chicano T, Carey LM, Axford D, Beale JH, Doak RB, Duyvesteyn HME, Ebrahim A, Henning RW, Monteiro DCF, Myles DA, Owada S, Sherrell DA, Straw ML, Šrajer V, Sugimoto H, Tono K, Tosha T, Tews I, Trebbin M, Strange RW, Weiss KL, Worrall JAR, Meilleur F, Owen RL, Ghiladi RA, Hough MA. Complementarity of neutron, XFEL and synchrotron crystallography for defining the structures of metalloenzymes at room temperature. IUCRJ 2022; 9:610-624. [PMID: 36071813 PMCID: PMC9438502 DOI: 10.1107/s2052252522006418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
Room-temperature macromolecular crystallography allows protein structures to be determined under close-to-physiological conditions, permits dynamic freedom in protein motions and enables time-resolved studies. In the case of metalloenzymes that are highly sensitive to radiation damage, such room-temperature experiments can present challenges, including increased rates of X-ray reduction of metal centres and site-specific radiation-damage artefacts, as well as in devising appropriate sample-delivery and data-collection methods. It can also be problematic to compare structures measured using different crystal sizes and light sources. In this study, structures of a multifunctional globin, dehaloperoxidase B (DHP-B), obtained using several methods of room-temperature crystallographic structure determination are described and compared. Here, data were measured from large single crystals and multiple microcrystals using neutrons, X-ray free-electron laser pulses, monochromatic synchrotron radiation and polychromatic (Laue) radiation light sources. These approaches span a range of 18 orders of magnitude in measurement time per diffraction pattern and four orders of magnitude in crystal volume. The first room-temperature neutron structures of DHP-B are also presented, allowing the explicit identification of the hydrogen positions. The neutron data proved to be complementary to the serial femtosecond crystallography data, with both methods providing structures free of the effects of X-ray radiation damage when compared with standard cryo-crystallography. Comparison of these room-temperature methods demonstrated the large differences in sample requirements, data-collection time and the potential for radiation damage between them. With regard to the structure and function of DHP-B, despite the results being partly limited by differences in the underlying structures, new information was gained on the protonation states of active-site residues which may guide future studies of DHP-B.
Collapse
Affiliation(s)
- Tadeo Moreno-Chicano
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Leiah M. Carey
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA
| | - Danny Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - John H. Beale
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - R. Bruce Doak
- Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Helen M. E. Duyvesteyn
- Division of Structural Biology (STRUBI), University of Oxford, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Ali Ebrahim
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Robert W. Henning
- BioCARS, University of Chicago, Building 434B, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Diana C. F. Monteiro
- Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203-1102, USA
| | - Dean A. Myles
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Shigeki Owada
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Darren A. Sherrell
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Megan L. Straw
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Vukica Šrajer
- BioCARS, University of Chicago, Building 434B, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | | | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Takehiko Tosha
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Ivo Tews
- Biological Sciences, University of Southampton, University Road, Southampton SO17 1BJ, United Kingdom
| | - Martin Trebbin
- Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203-1102, USA
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260, USA
| | - Richard W. Strange
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Kevin L. Weiss
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Jonathan A. R. Worrall
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Flora Meilleur
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Robin L. Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Reza A. Ghiladi
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA
| | - Michael A. Hough
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| |
Collapse
|
10
|
Holmes S, Kirkwood HJ, Bean R, Giewekemeyer K, Martin AV, Hadian-Jazi M, Wiedorn MO, Oberthür D, Marman H, Adriano L, Al-Qudami N, Bajt S, Barák I, Bari S, Bielecki J, Brockhauser S, Coleman MA, Cruz-Mazo F, Danilevski C, Dörner K, Gañán-Calvo AM, Graceffa R, Fanghor H, Heymann M, Frank M, Kaukher A, Kim Y, Kobe B, Knoška J, Laurus T, Letrun R, Maia L, Messerschmidt M, Metz M, Michelat T, Mills G, Molodtsov S, Monteiro DCF, Morgan AJ, Münnich A, Peña Murillo GE, Previtali G, Round A, Sato T, Schubert R, Schulz J, Shelby M, Seuring C, Sellberg JA, Sikorski M, Silenzi A, Stern S, Sztuk-Dambietz J, Szuba J, Trebbin M, Vagovic P, Ve T, Weinhausen B, Wrona K, Xavier PL, Xu C, Yefanov O, Nugent KA, Chapman HN, Mancuso AP, Barty A, Abbey B, Darmanin C. Megahertz pulse trains enable multi-hit serial femtosecond crystallography experiments at X-ray free electron lasers. Nat Commun 2022; 13:4708. [PMID: 35953469 PMCID: PMC9372077 DOI: 10.1038/s41467-022-32434-6] [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: 05/23/2019] [Accepted: 07/28/2022] [Indexed: 11/12/2022] Open
Abstract
The European X-ray Free Electron Laser (XFEL) and Linac Coherent Light Source (LCLS) II are extremely intense sources of X-rays capable of generating Serial Femtosecond Crystallography (SFX) data at megahertz (MHz) repetition rates. Previous work has shown that it is possible to use consecutive X-ray pulses to collect diffraction patterns from individual crystals. Here, we exploit the MHz pulse structure of the European XFEL to obtain two complete datasets from the same lysozyme crystal, first hit and the second hit, before it exits the beam. The two datasets, separated by <1 µs, yield up to 2.1 Å resolution structures. Comparisons between the two structures reveal no indications of radiation damage or significant changes within the active site, consistent with the calculated dose estimates. This demonstrates MHz SFX can be used as a tool for tracking sub-microsecond structural changes in individual single crystals, a technique we refer to as multi-hit SFX. Free-electron lasers are capable of high repetition rates and it is assumed that protein crystals often do not survive the first X-ray pulse. Here the authors address these issues with a demonstration of multi-hit serial crystallography in which multiple FEL pulses interact with the sample without destroying it.
Collapse
Affiliation(s)
- Susannah Holmes
- Department of Mathematical and Physical Sciences, School of Engineering, Computing and Mathematical Sciences, La Trobe University, Melbourne, VIC, 3086, Australia.,La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | | | - Richard Bean
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Andrew V Martin
- School of Science, RMIT University, Melbourne, VIC, 3000, Australia
| | - Marjan Hadian-Jazi
- Department of Mathematical and Physical Sciences, School of Engineering, Computing and Mathematical Sciences, La Trobe University, Melbourne, VIC, 3086, Australia.,European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.,Australian Nuclear Science and Technology Organisation (ANSTO), Sydney, NSW, 2234, Australia
| | - Max O Wiedorn
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany
| | - Dominik Oberthür
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany
| | - Hugh Marman
- Department of Mathematical and Physical Sciences, School of Engineering, Computing and Mathematical Sciences, La Trobe University, Melbourne, VIC, 3086, Australia.,La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Luigi Adriano
- Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany
| | | | - Saša Bajt
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, Hamburg, 22761, Germany
| | - Imrich Barák
- Institute of Molecular Biology, SAS, Dubravska cesta 21, 845 51, Bratislava, Slovakia
| | - Sadia Bari
- Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany
| | | | | | - Mathew A Coleman
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA, 94550, USA
| | - Francisco Cruz-Mazo
- Dept. de Ingeniería Aeroespacial y Mecánica de Fluidos, ETSI, Universidad de Sevilla, 41092, Sevilla, Spain.,Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ, 08544, USA
| | | | | | - Alfonso M Gañán-Calvo
- Dept. de Ingeniería Aeroespacial y Mecánica de Fluidos, ETSI, Universidad de Sevilla, 41092, Sevilla, Spain
| | - Rita Graceffa
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Hans Fanghor
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.,Max-Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 175, 22761, Hamburg, Germany.,University of Southampton, Southampton, SO17 1BJ, UK
| | - Michael Heymann
- Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Am Pfaffenwaldring 57, 70569, Stuttgart, Germany
| | - Matthias Frank
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA, 94550, USA
| | | | - Yoonhee Kim
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Juraj Knoška
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany.,Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Torsten Laurus
- Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany
| | - Romain Letrun
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Luis Maia
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Marc Messerschmidt
- School of Molecular Science, Arizona State University, Tempe, AZ, 85281, USA
| | - Markus Metz
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany
| | | | - Grant Mills
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Serguei Molodtsov
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.,Institute of Experimental Physics, TU Bergakademie Freiberg, Leipziger, Str. 23, 09599, Freiberg, Germany.,ITMO University, Kronverksky pr. 49, St. Petersburg, 197101, Russia
| | - Diana C F Monteiro
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, Hamburg, 22761, Germany.,Hauptman-Woodward Medical Research Institute, 700 Ellicott St., Buffalo, NY, 14203, USA
| | - Andrew J Morgan
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany.,Department of Physics, University of Melbourne, Parkville, VIC, 3010, Australia
| | | | - Gisel E Peña Murillo
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany
| | | | - Adam Round
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Tokushi Sato
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.,Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany
| | | | | | - Megan Shelby
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA, 94550, USA
| | - Carolin Seuring
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, Hamburg, 22761, Germany
| | - Jonas A Sellberg
- Biomedical and X-ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology, SE-106 91, Stockholm, Sweden
| | | | | | - Stephan Stern
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Janusz Szuba
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Martin Trebbin
- Institute of Experimental Physics, TU Bergakademie Freiberg, Leipziger, Str. 23, 09599, Freiberg, Germany.,Department of Chemistry, State University of New York at Buffalo, 760 Natural Sciences Complex, Buffalo, NY, 14260, USA
| | | | - Thomas Ve
- Institute for Glycomics, Griffith University, Southport, QLD, 4222, Australia
| | | | | | - Paul Lourdu Xavier
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.,Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany.,Max-Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 175, 22761, Hamburg, Germany
| | - Chen Xu
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany
| | - Keith A Nugent
- Department of Quantum Science and Technology, Research School of Physics, Australian National University, Canberra, ACT, 2601, Australia
| | - Henry N Chapman
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, Hamburg, 22761, Germany.,Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Adrian P Mancuso
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.,La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Anton Barty
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany
| | - Brian Abbey
- Department of Mathematical and Physical Sciences, School of Engineering, Computing and Mathematical Sciences, La Trobe University, Melbourne, VIC, 3086, Australia. .,La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia.
| | - Connie Darmanin
- Department of Mathematical and Physical Sciences, School of Engineering, Computing and Mathematical Sciences, La Trobe University, Melbourne, VIC, 3086, Australia. .,La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia.
| |
Collapse
|
11
|
Huang CY, Aumonier S, Engilberge S, Eris D, Smith KML, Leonarski F, Wojdyla JA, Beale JH, Buntschu D, Pauluhn A, Sharpe ME, Metz A, Olieric V, Wang M. Probing ligand binding of endothiapepsin by `temperature-resolved' macromolecular crystallography. Acta Crystallogr D Struct Biol 2022; 78:964-974. [PMID: 35916221 PMCID: PMC9344481 DOI: 10.1107/s205979832200612x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 06/09/2022] [Indexed: 12/03/2022] Open
Abstract
A room-temperature X-ray crystallographic method using temperature as a trigger to record movie-like structural snapshots has been developed and applied to study ligand binding and protein plasticity. Continuous developments in cryogenic X-ray crystallography have provided most of our knowledge of 3D protein structures, which has recently been further augmented by revolutionary advances in cryoEM. However, a single structural conformation identified at cryogenic temperatures may introduce a fictitious structure as a result of cryogenic cooling artefacts, limiting the overview of inherent protein physiological dynamics, which play a critical role in the biological functions of proteins. Here, a room-temperature X-ray crystallographic method using temperature as a trigger to record movie-like structural snapshots has been developed. The method has been used to show how TL00150, a 175.15 Da fragment, undergoes binding-mode changes in endothiapepsin. A surprising fragment-binding discrepancy was observed between the cryo-cooled and physiological temperature structures, and multiple binding poses and their interplay with DMSO were captured. The observations here open up new promising prospects for structure determination and interpretation at physiological temperatures with implications for structure-based drug discovery.
Collapse
|
12
|
Yabukarski F, Doukov T, Mokhtari DA, Du S, Herschlag D. Evaluating the impact of X-ray damage on conformational heterogeneity in room-temperature (277 K) and cryo-cooled protein crystals. Acta Crystallogr D Struct Biol 2022; 78:945-963. [PMID: 35916220 PMCID: PMC9344472 DOI: 10.1107/s2059798322005939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 06/02/2022] [Indexed: 11/10/2022] Open
Abstract
Cryo-cooling has been nearly universally adopted to mitigate X-ray damage and facilitate crystal handling in protein X-ray crystallography. However, cryo X-ray crystallographic data provide an incomplete window into the ensemble of conformations that is at the heart of protein function and energetics. Room-temperature (RT) X-ray crystallography provides accurate ensemble information, and recent developments allow conformational heterogeneity (the experimental manifestation of ensembles) to be extracted from single-crystal data. Nevertheless, high sensitivity to X-ray damage at RT raises concerns about data reliability. To systematically address this critical issue, increasingly X-ray-damaged high-resolution data sets (1.02–1.52 Å resolution) were obtained from single proteinase K, thaumatin and lysozyme crystals at RT (277 K). In each case a modest increase in conformational heterogeneity with X-ray damage was observed. Merging data with different extents of damage (as is typically carried out) had negligible effects on conformational heterogeneity until the overall diffraction intensity decayed to ∼70% of its initial value. These effects were compared with X-ray damage effects in cryo-cooled crystals by carrying out an analogous analysis of increasingly damaged proteinase K cryo data sets (0.9–1.16 Å resolution). X-ray damage-associated heterogeneity changes were found that were not observed at RT. This property renders it difficult to distinguish real from artefactual conformations and to determine the conformational response to changes in temperature. The ability to acquire reliable heterogeneity information from single crystals at RT, together with recent advances in RT data collection at accessible synchrotron beamlines, provides a strong motivation for the widespread adoption of RT X-ray crystallography to obtain conformational ensemble information.
Collapse
|
13
|
Gildea RJ, Beilsten-Edmands J, Axford D, Horrell S, Aller P, Sandy J, Sanchez-Weatherby J, Owen CD, Lukacik P, Strain-Damerell C, Owen RL, Walsh MA, Winter G. xia2. multiplex: a multi-crystal data-analysis pipeline. Acta Crystallogr D Struct Biol 2022; 78:752-769. [PMID: 35647922 PMCID: PMC9159281 DOI: 10.1107/s2059798322004399] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/25/2022] [Indexed: 11/11/2022] Open
Abstract
A new program, xia2.multiplex, has been developed to facilitate symmetry analysis, scaling and merging of multi-crystal data sets. In macromolecular crystallography, radiation damage limits the amount of data that can be collected from a single crystal. It is often necessary to merge data sets from multiple crystals; for example, small-wedge data collections from micro-crystals, in situ room-temperature data collections and data collection from membrane proteins in lipidic mesophases. Whilst the indexing and integration of individual data sets may be relatively straightforward with existing software, merging multiple data sets from small wedges presents new challenges. The identification of a consensus symmetry can be problematic, particularly in the presence of a potential indexing ambiguity. Furthermore, the presence of non-isomorphous or poor-quality data sets may reduce the overall quality of the final merged data set. To facilitate and help to optimize the scaling and merging of multiple data sets, a new program, xia2.multiplex, has been developed which takes data sets individually integrated with DIALS and performs symmetry analysis, scaling and merging of multi-crystal data sets. xia2.multiplex also performs analysis of various pathologies that typically affect multi-crystal data sets, including non-isomorphism, radiation damage and preferential orientation. After the description of a number of use cases, the benefit of xia2.multiplex is demonstrated within a wider autoprocessing framework in facilitating a multi-crystal experiment collected as part of in situ room-temperature fragment-screening experiments on the SARS-CoV-2 main protease.
Collapse
|
14
|
Martin-Garcia JM, Botha S, Hu H, Jernigan R, Castellví A, Lisova S, Gil F, Calisto B, Crespo I, Roy-Chowdhury S, Grieco A, Ketawala G, Weierstall U, Spence J, Fromme P, Zatsepin N, Boer DR, Carpena X. Serial macromolecular crystallography at ALBA Synchrotron Light Source. JOURNAL OF SYNCHROTRON RADIATION 2022; 29:896-907. [PMID: 35511023 PMCID: PMC9070724 DOI: 10.1107/s1600577522002508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
The increase in successful adaptations of serial crystallography at synchrotron radiation sources continues. To date, the number of serial synchrotron crystallography (SSX) experiments has grown exponentially, with over 40 experiments reported so far. In this work, we report the first SSX experiments with viscous jets conducted at ALBA beamline BL13-XALOC. Small crystals (15-30 µm) of five soluble proteins (lysozyme, proteinase K, phycocyanin, insulin and α-spectrin-SH3 domain) were suspended in lipidic cubic phase (LCP) and delivered to the X-ray beam with a high-viscosity injector developed at Arizona State University. Complete data sets were collected from all proteins and their high-resolution structures determined. The high quality of the diffraction data collected from all five samples, and the lack of specific radiation damage in the structures obtained in this study, confirm that the current capabilities at the beamline enables atomic resolution determination of protein structures from microcrystals as small as 15 µm using viscous jets at room temperature. Thus, BL13-XALOC can provide a feasible alternative to X-ray free-electron lasers when determining snapshots of macromolecular structures.
Collapse
Affiliation(s)
- Jose M. Martin-Garcia
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano, Spanish National Research Council (CSIC), Madrid, Spain
| | - Sabine Botha
- Department of Physics, Arizona State University, Tempe, AZ, USA
| | - Hao Hu
- Department of Physics, Arizona State University, Tempe, AZ, USA
| | - Rebecca Jernigan
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Albert Castellví
- Molecular Biology Institute of Barcelona, CSIC, Barcelona, Spain
| | - Stella Lisova
- Department of Physics, Arizona State University, Tempe, AZ, USA
| | - Fernando Gil
- ALBA Synchrotron, Cerdanyola del Vallès, Barcelona, Spain
| | | | - Isidro Crespo
- ALBA Synchrotron, Cerdanyola del Vallès, Barcelona, Spain
| | - Shatabdi Roy-Chowdhury
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Alice Grieco
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano, Spanish National Research Council (CSIC), Madrid, Spain
| | - Gihan Ketawala
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Uwe Weierstall
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
- Department of Physics, Arizona State University, Tempe, AZ, USA
| | - John Spence
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
- Department of Physics, Arizona State University, Tempe, AZ, USA
| | - Petra Fromme
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Nadia Zatsepin
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
- Department of Physics, Arizona State University, Tempe, AZ, USA
- ARC Centre of Excellence in Advance Molecular Physics, La Trobe Institute for Molecular ScienceImaging, Department of Chemistry and Physics, La Trobe University, Melbourne, Australia
| | | | - Xavi Carpena
- ALBA Synchrotron, Cerdanyola del Vallès, Barcelona, Spain
| |
Collapse
|
15
|
Chaussavoine I, Isabet T, Lener R, Montaville P, Vasireddi R, Chavas LMG. Implementation of wedged-serial protein crystallography at PROXIMA-1. JOURNAL OF SYNCHROTRON RADIATION 2022; 29:439-446. [PMID: 35254307 PMCID: PMC8900848 DOI: 10.1107/s1600577521013242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
An approach for serial crystallography experiments based on wedged-data collection is described. This is an alternative method for recording in situ X-ray diffraction data on crystalline samples efficiently loaded in an X-ray compatible microfluidic chip. Proper handling of the microfluidic chip places crystalline samples at geometrically known positions with respect to the focused X-ray interaction area for serial data collection of small wedges. The integration of this strategy takes advantage of the greatly modular sample environment available on the endstation, which allows access to both in situ and more classical cryo-crystallography with minimum time loss. The method represents another optional data collection approach that adds up to the already large set of methods made available to users. Coupled with the advances in processing serial crystallography data, the wedged-data collection strategy proves highly efficient in minimizing the amount of required sample crystals for recording a complete dataset. From the advances in microfluidic technology presented here, high-throughput room-temperature crystallography experiments may become routine and should be easily extended to industrial use.
Collapse
Affiliation(s)
| | | | - Robin Lener
- Synchrotron SOLEIL, 91192 Gif-sur-Yvette, France
| | | | | | | |
Collapse
|
16
|
Prangé T, Carpentier P, Dhaussy AC, van der Linden P, Girard E, Colloc'h N. Comparative study of the effects of high hydrostatic pressure per se and high argon pressure on urate oxidase ligand stabilization. Acta Crystallogr D Struct Biol 2022; 78:162-173. [DOI: 10.1107/s2059798321012134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/15/2021] [Indexed: 11/11/2022] Open
Abstract
The stability of the tetrameric enzyme urate oxidase in complex with excess of 8-azaxanthine was investigated either under high hydrostatic pressure per se or under a high pressure of argon. The active site is located at the interface of two subunits, and the catalytic activity is directly related to the integrity of the tetramer. This study demonstrates that applying pressure to a protein–ligand complex drives the thermodynamic equilibrium towards ligand saturation of the complex, revealing a new binding site. A transient dimeric intermediate that occurs during the pressure-induced dissociation process was characterized under argon pressure and excited substates of the enzyme that occur during the catalytic cycle can be trapped by pressure. Comparison of the different structures under pressure infers an allosteric role of the internal hydrophobic cavity in which argon is bound, since this cavity provides the necessary flexibility for the active site to function.
Collapse
|
17
|
Schulz EC, Yorke BA, Pearson AR, Mehrabi P. Best practices for time-resolved serial synchrotron crystallography. Acta Crystallogr D Struct Biol 2022; 78:14-29. [PMID: 34981758 PMCID: PMC8725164 DOI: 10.1107/s2059798321011621] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 11/03/2021] [Indexed: 11/10/2022] Open
Abstract
With recent developments in X-ray sources, instrumentation and data-analysis tools, time-resolved crystallographic experiments, which were originally the preserve of a few expert groups, are becoming simpler and can be carried out at more radiation sources, and are thus increasingly accessible to a growing user base. However, these experiments are just that: discrete experiments, not just `data collections'. As such, careful planning and consideration of potential pitfalls is required to enable a successful experiment. Here, some of the key factors that should be considered during the planning and execution of a time-resolved structural study are outlined, with a particular focus on synchrotron-based experiments.
Collapse
Affiliation(s)
- Eike C. Schulz
- Institute for Nanostructure and Solid State Physics, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Briony A. Yorke
- School of Chemistry and Bioscience, University of Bradford, Bradford BD7 1DP, United Kingdom
| | - Arwen R. Pearson
- Institute for Nanostructure and Solid State Physics, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Pedram Mehrabi
- Institute for Nanostructure and Solid State Physics, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, Germany
| |
Collapse
|
18
|
Stachowski TR, Snell ME, Snell EH. A SAXS-based approach to rationally evaluate radical scavengers - toward eliminating radiation damage in solution and crystallographic studies. JOURNAL OF SYNCHROTRON RADIATION 2021; 28:1309-1320. [PMID: 34475280 PMCID: PMC8415334 DOI: 10.1107/s1600577521004045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 04/15/2021] [Indexed: 05/30/2023]
Abstract
X-ray-based techniques are a powerful tool in structural biology but the radiation-induced chemistry that results can be detrimental and may mask an accurate structural understanding. In the crystallographic case, cryocooling has been employed as a successful mitigation strategy but also has its limitations including the trapping of non-biological structural states. Crystallographic and solution studies performed at physiological temperatures can reveal otherwise hidden but relevant conformations, but are limited by their increased susceptibility to radiation damage. In this case, chemical additives that scavenge the species generated by radiation can mitigate damage but are not always successful and the mechanisms are often unclear. Using a protein designed to undergo a large-scale structural change from breakage of a disulfide bond, radiation damage can be monitored with small-angle X-ray scattering. Using this, we have quantitatively evaluated how three scavengers commonly used in crystallographic experiments - sodium nitrate, cysteine, and ascorbic acid - perform in solution at 10°C. Sodium nitrate was the most effective scavenger and completely inhibited fragmentation of the disulfide bond at a lower concentration (500 µM) compared with cysteine (∼5 mM) while ascorbic acid performed best at 5 mM but could only reduce fragmentation by ∼75% after a total accumulated dose of 792 Gy. The relative effectiveness of each scavenger matches their reported affinities for solvated electrons. Saturating concentrations of each scavenger shifted fragmentation from first order to a zeroth-order process, perhaps indicating the direct contribution of photoabsorption. The SAXS-based method can detect damage at X-ray doses far lower than those accessible crystallographically, thereby providing a detailed picture of scavenger processes. The solution results are also in close agreement with what is known about scavenger performance and mechanism in a crystallographic setting and suggest that a link can be made between the damage phenomenon in the two scenarios. Therefore, our engineered approach might provide a platform for more systematic and comprehensive screening of radioprotectants that can directly inform mitigation strategies for both solution and crystallographic experiments, while also clarifying fundamental radiation damage mechanisms.
Collapse
Affiliation(s)
- Timothy R. Stachowski
- Hauptman-Woodward Medical Research Institute, 700 Ellicott St, Buffalo, NY 14203, USA
- Cell Stress Biology, Roswell Park Comprehensive Cancer Center, 665 Elm Street, Buffalo, NY 14203, USA
| | - Mary E. Snell
- Hauptman-Woodward Medical Research Institute, 700 Ellicott St, Buffalo, NY 14203, USA
| | - Edward H. Snell
- Hauptman-Woodward Medical Research Institute, 700 Ellicott St, Buffalo, NY 14203, USA
- Materials Design and Innovation, State University at New York at Buffalo, 700 Ellicott St, Buffalo, NY 14203, USA
| |
Collapse
|
19
|
Garman EF, Weik M. Radiation damage to biological samples: still a pertinent issue. JOURNAL OF SYNCHROTRON RADIATION 2021; 28:1278-1283. [PMID: 34475277 PMCID: PMC8415327 DOI: 10.1107/s1600577521008845] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
An understanding of radiation damage effects suffered by biological samples during structural analysis using both X-rays and electrons is pivotal to obtain reliable molecular models of imaged molecules. This special issue on radiation damage contains six papers reporting analyses of damage from a range of biophysical imaging techniques. For X-ray diffraction, an in-depth study of multi-crystal small-wedge data collection single-wavelength anomalous dispersion phasing protocols is presented, concluding that an absorbed dose of 5 MGy per crystal was optimal to allow reliable phasing. For small-angle X-ray scattering, experiments are reported that evaluate the efficacy of three radical scavengers using a protein designed to give a clear signature of damage in the form of a large conformational change upon the breakage of a disulfide bond. The use of X-rays to induce OH radicals from the radiolysis of water for X-ray footprinting are covered in two papers. In the first, new developments and the data collection pipeline at the NSLS-II high-throughput dedicated synchrotron beamline are described, and, in the second, the X-ray induced changes in three different proteins under aerobic and low-oxygen conditions are investigated and correlated with the absorbed dose. Studies in XFEL science are represented by a report on simulations of ultrafast dynamics in protic ionic liquids, and, lastly, a broad coverage of possible methods for dose efficiency improvement in modalities using electrons is presented. These papers, as well as a brief synopsis of some other relevant literature published since the last Journal of Synchrotron Radiation Special Issue on Radiation Damage in 2019, are summarized below.
Collapse
Affiliation(s)
- Elspeth F. Garman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Martin Weik
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044 Grenoble, France
| |
Collapse
|
20
|
Hasegawa K, Baba S, Kawamura T, Yamamoto M, Kumasaka T. Evaluation of the data-collection strategy for room-temperature micro-crystallography studied by serial synchrotron rotation crystallography combined with the humid air and glue-coating method. Acta Crystallogr D Struct Biol 2021; 77:300-312. [PMID: 33645534 PMCID: PMC7919407 DOI: 10.1107/s2059798321001686] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 02/11/2021] [Indexed: 11/11/2023] Open
Abstract
Synchrotron serial crystallography (SSX) is an emerging data-collection method for micro-crystallography on synchrotron macromolecular (MX) crystallography beamlines. At SPring-8, the feasibility of the fixed-target approach was examined by collecting data using a 2D raster scan combined with goniometer rotation. Results at cryogenic temperatures demonstrated that rotation is effective for efficient data collection in SSX and the method was named serial synchrotron rotation crystallography (SS-ROX). To use this method for room-temperature (RT) data collection, a humid air and glue-coating (HAG) method was developed in which data were collected from polyvinyl alcohol-coated microcrystals fixed on a loop under humidity-controlled air. The performance and the RT data-collection strategy for micro-crystallography were evaluated using microcrystals of lysozyme. Although a change in unit-cell dimensions of up to 1% was observed during data collection, the impact on data quality was marginal. A comparison of data obtained at various absorbed doses revealed that absorbed doses of up to 210 kGy were tolerable in both global and local damage. Although this limits the number of photons deposited on each crystal, increasing the number of merged images improved the resolution. On the basis of these results, an equation was proposed that relates the achievable resolution to the total photon flux used to obtain a data set.
Collapse
Affiliation(s)
- Kazuya Hasegawa
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Seiki Baba
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Takashi Kawamura
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Masaki Yamamoto
- Advanced Photon Technology Division, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Takashi Kumasaka
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| |
Collapse
|
21
|
Yudenko A, Smolentseva A, Maslov I, Semenov O, Goncharov IM, Nazarenko VV, Maliar NL, Borshchevskiy V, Gordeliy V, Remeeva A, Gushchin I. Rational Design of a Split Flavin-Based Fluorescent Reporter. ACS Synth Biol 2021; 10:72-83. [PMID: 33325704 DOI: 10.1021/acssynbio.0c00454] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein-fragment complementation assays are used ubiquitously for probing protein-protein interactions. Most commonly, the reporter protein is split in two parts, which are then fused to the proteins of interest and can reassemble and provide a readout if the proteins of interest interact with each other. The currently known split fluorescent proteins either can be used only in aerobic conditions and assemble irreversibly, or require addition of exogenous chromophores, which complicates the design of experiments. In recent years, light-oxygen-voltage (LOV) domains of several photoreceptor proteins have been developed into flavin-based fluorescent proteins (FbFPs) that, under some circumstances, can outperform commonly used fluorescent proteins such as GFP. Here, we show that CagFbFP, a small thermostable FbFP based on a LOV domain-containing protein from Chloroflexus aggregans, can serve as a split fluorescent reporter. We use the available genetic and structural information to identify three loops between the conserved secondary structure elements, Aβ-Bβ, Eα-Fα, and Hβ-Iβ, that tolerate insertion of flexible poly-Gly/Ser segments and eventually splitting. We demonstrate that the designed split pairs, when fused to interacting proteins, are fluorescent in vivo in E. coli and human cells and have low background fluorescence. Our results enable probing protein-protein interactions in anaerobic conditions without using exogenous fluorophores and provide a basis for further development of LOV and PAS (Per-Arnt-Sim) domain-based fluorescent reporters and optogenetic tools.
Collapse
Affiliation(s)
- Anna Yudenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Anastasia Smolentseva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Ivan Maslov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Oleg Semenov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Ivan M. Goncharov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Vera V. Nazarenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Nina L. Maliar
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Valentin Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Valentin Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, 38044 Grenoble, France
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| |
Collapse
|
22
|
Analysis of Multi-Hit Crystals in Serial Synchrotron Crystallography Experiments Using High-Viscosity Injectors. CRYSTALS 2021. [DOI: 10.3390/cryst11010049] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Serial Synchrotron Crystallography (SSX) is rapidly emerging as a promising technique for collecting data for time-resolved structural studies or for performing room temperature micro-crystallography measurements using micro-focused beamlines. SSX is often performed using high frame rate detectors in combination with continuous sample scanning or high-viscosity or liquid jet injectors. When performed using ultra-bright X-ray Free Electron Laser (XFEL) sources serial crystallography typically involves a process known as ’diffract-and-destroy’ where each crystal is measured just once before it is destroyed by the intense XFEL pulse. In SSX, however, particularly when using high-viscosity injectors (HVIs) such as Lipidico, the crystal can be intercepted multiple times by the X-ray beam prior to exiting the interaction region. This has a number of important consequences for SSX including whether these multiple-hits can be incorporated into the data analysis or whether they need to be excluded due to the potential impact of radiation damage. Here, we investigate the occurrence and characteristics of multiple hits on single crystals using SSX with lipidico. SSX data are collected from crystals as they tumble within a high viscous stream of silicone grease flowing through a micro-focused X-ray beam. We confirmed that, using the Eiger 16M, we are able to collect up to 42 frames of data from the same single crystal prior to it leaving the X-ray interaction region. The frequency and occurrence of multiple hits may be controlled by varying the sample flow rate and X-ray beam size. Calculations of the absorbed dose confirm that these crystals are likely to undergo radiation damage but that nonetheless incorporating multiple hits into damage-free data should lead to a significant reduction in the number of crystals required for structural analysis when compared to just looking at a single diffraction pattern from each crystal.
Collapse
|
23
|
Abstract
X-ray crystallography enables detailed structural studies of proteins to understand and modulate their function. Conducting crystallographic experiments at cryogenic temperatures has practical benefits but potentially limits the identification of functionally important alternative protein conformations that can be revealed only at room temperature (RT). This review discusses practical aspects of preparing, acquiring, and analyzing X-ray crystallography data at RT to demystify preconceived impracticalities that freeze progress of routine RT data collection at synchrotron sources. Examples are presented as conceptual and experimental templates to enable the design of RT-inspired studies; they illustrate the diversity and utility of gaining novel insights into protein conformational landscapes. An integrative view of protein conformational dynamics enables opportunities to advance basic and biomedical research.
Collapse
|
24
|
Myšková J, Rybakova O, Brynda J, Khoroshyy P, Bondar A, Lazar J. Directionality of light absorption and emission in representative fluorescent proteins. Proc Natl Acad Sci U S A 2020; 117:32395-32401. [PMID: 33273123 PMCID: PMC7768707 DOI: 10.1073/pnas.2017379117] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 10/30/2020] [Indexed: 12/13/2022] Open
Abstract
Fluorescent molecules are like antennas: The rate at which they absorb light depends on their orientation with respect to the incoming light wave, and the apparent intensity of their emission depends on their orientation with respect to the observer. However, the directions along which the most important fluorescent molecules in biology, fluorescent proteins (FPs), absorb and emit light are generally not known. Our optical and X-ray investigations of FP crystals have now allowed us to determine the molecular orientations of the excitation and emission transition dipole moments in the FPs mTurquoise2, eGFP, and mCherry, and the photoconvertible FP mEos4b. Our results will allow using FP directionality in studies of molecular and biological processes, but also in development of novel bioengineering and bioelectronics applications.
Collapse
Affiliation(s)
- Jitka Myšková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
| | - Olga Rybakova
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
- Institute of Microbiology, Czech Academy of Sciences, 37333 Nové Hrady, Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
- Institute of Molecular Genetics, Czech Academy of Sciences, 14220 Prague 4, Czech Republic
| | - Petro Khoroshyy
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
- Institute of Microbiology, Czech Academy of Sciences, 37333 Nové Hrady, Czech Republic
| | - Alexey Bondar
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
- Institute of Microbiology, Czech Academy of Sciences, 37333 Nové Hrady, Czech Republic
| | - Josef Lazar
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic;
- Institute of Microbiology, Czech Academy of Sciences, 37333 Nové Hrady, Czech Republic
| |
Collapse
|
25
|
Doukov T, Herschlag D, Yabukarski F. Instrumentation and experimental procedures for robust collection of X-ray diffraction data from protein crystals across physiological temperatures. J Appl Crystallogr 2020; 53:1493-1501. [PMID: 33312102 DOI: 10.1107/s1600576720013503] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 10/08/2020] [Indexed: 11/10/2022] Open
Abstract
Traditional X-ray diffraction data collected at cryo-temperatures have delivered invaluable insights into the three-dimensional structures of proteins, providing the backbone of structure-function studies. While cryo-cooling mitigates radiation damage, cryo-temperatures can alter protein conformational ensembles and solvent structure. Furthermore, conformational ensembles underlie protein function and energetics, and recent advances in room-temperature X-ray crystallography have delivered conformational heterogeneity information that can be directly related to biological function. Given this capability, the next challenge is to develop a robust and broadly applicable method to collect single-crystal X-ray diffraction data at and above room temperature. This challenge is addressed herein. The approach described provides complete diffraction data sets with total collection times as short as ∼5 s from single protein crystals, dramatically increasing the quantity of data that can be collected within allocated synchrotron beam time. Its applicability was demonstrated by collecting 1.09-1.54 Å resolution data over a temperature range of 293-363 K for proteinase K, thaumatin and lysozyme crystals at BL14-1 at the Stanford Synchrotron Radiation Lightsource. The analyses presented here indicate that the diffraction data are of high quality and do not suffer from excessive dehydration or radiation damage.
Collapse
Affiliation(s)
- Tzanko Doukov
- SMB, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA.,Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA.,Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Filip Yabukarski
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
26
|
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.
Collapse
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
| | | |
Collapse
|
27
|
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
| | | |
Collapse
|
28
|
Stachowski TR, Snell ME, Snell EH. SAXS studies of X-ray induced disulfide bond damage: Engineering high-resolution insight from a low-resolution technique. PLoS One 2020; 15:e0239702. [PMID: 33201877 PMCID: PMC7671560 DOI: 10.1371/journal.pone.0239702] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 09/12/2020] [Indexed: 12/17/2022] Open
Abstract
A significant problem in biological X-ray crystallography is the radiation chemistry caused by the incident X-ray beam. This produces both global and site-specific damage. Site specific damage can misdirect the biological interpretation of the structural models produced. Cryo-cooling crystals has been successful in mitigating damage but not eliminating it altogether; however, cryo-cooling can be difficult in some cases and has also been shown to limit functionally relevant protein conformations. The doses used for X-ray crystallography are typically in the kilo-gray to mega-gray range. While disulfide bonds are among the most significantly affected species in proteins in the crystalline state at both cryogenic and higher temperatures, there is limited information on their response to low X-ray doses in solution, the details of which might inform biomedical applications of X-rays. In this work we engineered a protein that dimerizes through a susceptible disulfide bond to relate the radiation damage processes seen in cryo-cooled crystals to those closer to physiologic conditions. This approach enables a low-resolution technique, small angle X-ray scattering (SAXS), to detect and monitor a residue specific process. A dose dependent fragmentation of the engineered protein was seen that can be explained by a dimer to monomer transition through disulfide bond cleavage. This supports the crystallographically derived mechanism and demonstrates that results obtained crystallographically can be usefully extrapolated to physiologic conditions. Fragmentation was influenced by pH and the conformation of the dimer, providing information on mechanism and pointing to future routes for investigation and potential mitigation. The novel engineered protein approach to generate a large-scale change through a site-specific interaction represents a promising tool for advancing radiation damage studies under solution conditions.
Collapse
Affiliation(s)
- Timothy R. Stachowski
- Hauptman-Woodward Medical Research Institute, Buffalo, New York, United States of America
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, United States of America
| | - Mary E. Snell
- Hauptman-Woodward Medical Research Institute, Buffalo, New York, United States of America
| | - Edward H. Snell
- Hauptman-Woodward Medical Research Institute, Buffalo, New York, United States of America
- Department of Materials Design and Innovation, State University at New York at Buffalo, Buffalo, New York, United States of America
| |
Collapse
|
29
|
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.
Collapse
|
30
|
Aumonier S, Santoni G, Gotthard G, von Stetten D, Leonard GA, Royant A. Millisecond time-resolved serial oscillation crystallography of a blue-light photoreceptor at a synchrotron. IUCRJ 2020; 7:728-736. [PMID: 32695419 PMCID: PMC7340269 DOI: 10.1107/s2052252520007411] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 06/03/2020] [Indexed: 05/23/2023]
Abstract
The recent development of serial crystallography has popularized time-resolved crystallography as a technique to determine the structure of protein-reaction intermediate states. However, most approaches rely on the availability of thousands to millions of microcrystals. A method is reported here, using monochromatic synchrotron radiation, for the room-temperature collection, processing and merging of X-ray oscillation diffraction data from <100 samples in order to observe the build up of a photoreaction intermediate species. Using this method, we monitored with a time resolution of 63 ms how the population of a blue-light photoreceptor domain in a crystal progressively photoconverts from the dark to the light state. The series of resulting snapshots allows us to visualize in detail the gradual rearrangement of both the protein and chromophore during this process.
Collapse
Affiliation(s)
- Sylvain Aumonier
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble Cedex 9, 38043, France
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, 71 avenue des Martyrs, Grenoble Cedex 9, 38044, France
| | - Gianluca Santoni
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble Cedex 9, 38043, France
| | - Guillaume Gotthard
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble Cedex 9, 38043, France
| | - David von Stetten
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble Cedex 9, 38043, France
| | - Gordon A. Leonard
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble Cedex 9, 38043, France
| | - Antoine Royant
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble Cedex 9, 38043, France
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, 71 avenue des Martyrs, Grenoble Cedex 9, 38044, France
| |
Collapse
|
31
|
von Stetten D, Carpentier P, Flot D, Beteva A, Caserotto H, Dobias F, Guijarro M, Giraud T, Lentini M, McSweeney S, Royant A, Petitdemange S, Sinoir J, Surr J, Svensson O, Theveneau P, Leonard GA, Mueller-Dieckmann C. ID30A-3 (MASSIF-3) - a beamline for macromolecular crystallography at the ESRF with a small intense beam. JOURNAL OF SYNCHROTRON RADIATION 2020; 27:844-851. [PMID: 32381789 PMCID: PMC7206554 DOI: 10.1107/s1600577520004002] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/20/2020] [Indexed: 05/05/2023]
Abstract
ID30A-3 (or MASSIF-3) is a mini-focus (beam size 18 µm × 14 µm) highly intense (2.0 × 1013 photons s-1), fixed-energy (12.81 keV) beamline for macromolecular crystallography (MX) experiments at the European Synchrotron Radiation Facility (ESRF). MASSIF-3 is one of two fixed-energy beamlines sited on the first branch of the canted undulator setup on the ESRF ID30 port and is equipped with a MD2 micro-diffractometer, a Flex HCD sample changer, and an Eiger X 4M fast hybrid photon-counting detector. MASSIF-3 is recommended for collecting diffraction data from single small crystals (≤15 µm in one dimension) or for experiments using serial methods. The end-station has been in full user operation since December 2014, and here its current characteristics and capabilities are described.
Collapse
Affiliation(s)
- David von Stetten
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Philippe Carpentier
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
- Institut de Biosciences et Biotechnologies de Grenoble (BIG) – Laboratoire Chimie et Biologie des Métaux (LCBM), Université Grenoble Alpes, CNRS, CEA, 38000 Grenoble, France
| | - David Flot
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Antonia Beteva
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Hugo Caserotto
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Fabien Dobias
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Matias Guijarro
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Thierry Giraud
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Mario Lentini
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Sean McSweeney
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Antoine Royant
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | | | - Jeremy Sinoir
- EMBL Outstation Grenoble, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - John Surr
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Olof Svensson
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Pascal Theveneau
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Gordon A. Leonard
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | | |
Collapse
|
32
|
Radiation damage and dose limits in serial synchrotron crystallography at cryo- and room temperatures. Proc Natl Acad Sci U S A 2020; 117:4142-4151. [PMID: 32047034 PMCID: PMC7049125 DOI: 10.1073/pnas.1821522117] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Macromolecular X-ray crystallography (MX) is the most prolific structure determination method in structural biology but is limited by radiation damage. To reduce damage progression, MX is usually carried out at cryogenic temperatures, sometimes blocking functionally important conformational heterogeneity. Lacking this shortcoming, room temperature MX has gained momentum with the recent advent of serial crystallography, whereby distribution of the X-ray dose over thousands of crystals mitigates damage. Here, an approach to serial crystallography is presented allowing visualization of specific damage to amino acids at room temperature and determination of a dose limit above which structural information from electron density maps decreases due to radiation damage. This limit provides important guidance for the growing number of synchrotron room temperature MX experiments. Radiation damage limits the accuracy of macromolecular structures in X-ray crystallography. Cryogenic (cryo-) cooling reduces the global radiation damage rate and, therefore, became the method of choice over the past decades. The recent advent of serial crystallography, which spreads the absorbed energy over many crystals, thereby reducing damage, has rendered room temperature (RT) data collection more practical and also extendable to microcrystals, both enabling and requiring the study of specific and global radiation damage at RT. Here, we performed sequential serial raster-scanning crystallography using a microfocused synchrotron beam that allowed for the collection of two series of 40 and 90 full datasets at 2- and 1.9-Å resolution at a dose rate of 40.3 MGy/s on hen egg white lysozyme (HEWL) crystals at RT and cryotemperature, respectively. The diffraction intensity halved its initial value at average doses (D1/2) of 0.57 and 15.3 MGy at RT and 100 K, respectively. Specific radiation damage at RT was observed at disulfide bonds but not at acidic residues, increasing and then apparently reversing, a peculiar behavior that can be modeled by accounting for differential diffraction intensity decay due to the nonuniform illumination by the X-ray beam. Specific damage to disulfide bonds is evident early on at RT and proceeds at a fivefold higher rate than global damage. The decay modeling suggests it is advisable not to exceed a dose of 0.38 MGy per dataset in static and time-resolved synchrotron crystallography experiments at RT. This rough yardstick might change for proteins other than HEWL and at resolutions other than 2 Å.
Collapse
|
33
|
Junius N, Jaho S, Sallaz-Damaz Y, Borel F, Salmon JB, Budayova-Spano M. A microfluidic device for both on-chip dialysis protein crystallization and in situ X-ray diffraction. LAB ON A CHIP 2020; 20:296-310. [PMID: 31804643 DOI: 10.1039/c9lc00651f] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
This paper reports a versatile microfluidic chip developed for on-chip crystallization of proteins through the dialysis method and in situ X-ray diffraction experiments. A microfabrication process enabling the integration of regenerated cellulose dialysis membranes between two layers of the microchip is thoroughly described. We also describe a rational approach for optimizing on-chip protein crystallization via chemical composition and temperature control, allowing the crystal size, number and quality to be tailored. Combining optically transparent microfluidics and dialysis provides both precise control over the experiment and reversible exploration of the crystallization conditions. In addition, the materials composing the microfluidic chip were tested for their transparency to X-rays in order to assess their compatibility for in situ diffraction data collection. Background scattering was evaluated using a synchrotron X-ray source and the background noise generated by our microfluidic device was compared to that produced by commercial crystallization plates used for diffraction experiments at room temperature. Once crystals of 3 model proteins (lysozyme, IspE, and insulin) were grown on-chip, the microchip was mounted onto the beamline and partial diffraction data sets were collected in situ from several isomorphous crystals and were merged to a complete data set for structure determination. We therefore propose a robust and inexpensive way to fabricate microchips that cover the whole pipeline from crystal growth to the beam and does not require any handling of the protein crystals prior to the diffraction experiment, allowing the collection of crystallographic data at room temperature for solving the three-dimensional structure of the proteins under study. The results presented here allow serial crystallography experiments on synchrotrons and X-ray lasers under dynamically controllable sample conditions to be observed using the developed microchips.
Collapse
Affiliation(s)
- Niels Junius
- Université Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Sofia Jaho
- Université Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
| | | | - Franck Borel
- Université Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
| | | | | |
Collapse
|
34
|
Förster A, Schulze-Briese C. A shared vision for macromolecular crystallography over the next five years. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2019; 6:064302. [PMID: 31832486 PMCID: PMC6892709 DOI: 10.1063/1.5131017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 11/19/2019] [Indexed: 05/12/2023]
Abstract
Macromolecular crystallography (MX) is the dominant means of determining the three-dimensional structures of biological macromolecules, but the method has reached a critical juncture. New diffraction-limited storage rings and upgrades to the existing sources will provide beamlines with higher flux and brilliance, and even the largest detectors can collect at rates of several hundred hertz. Electron cryomicroscopy is successfully competing for structural biologists' most exciting projects. As a result, formerly scarce beam time is becoming increasingly abundant, and beamlines must innovate to attract users and ensure continued funding. Here, we will show how data collection has changed over the preceding five years and how alternative methods have emerged. We then explore how MX at synchrotrons might develop over the next five years. We predict that, despite the continued dominance of rotation crystallography, applications previously considered niche or experimental, such as serial crystallography, pink-beam crystallography, and crystallography at energies above 25 keV and below 5 keV, will rise in prominence as beamlines specialize to offer users the best value. Most of these emerging methods will require new hardware and software. With these advances, MX will more efficiently provide the high-resolution structures needed for drug development. MX will also be able to address a broader range of questions than before and contribute to a deeper understanding of biological processes in the context of integrative structural biology.
Collapse
|
35
|
Garman EF, Weik M. X-ray radiation damage to biological samples: recent progress. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:907-911. [PMID: 31274412 DOI: 10.1107/s1600577519009408] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 06/30/2019] [Indexed: 05/20/2023]
Abstract
With the continuing development of beamlines for macromolecular crystallography (MX) over the last few years providing ever higher X-ray flux densities, it has become even more important to be aware of the effects of radiation damage on the resulting structures. Nine papers in this issue cover a range of aspects related to the physics and chemistry of the manifestations of this damage, as observed in both MX and small-angle X-ray scattering (SAXS) on crystals, solutions and tissue samples. The reports include measurements of the heating caused by X-ray irradiation in ruby microcrystals, low-dose experiments examining damage rates as a function of incident X-ray energy up to 30 keV on a metallo-enzyme using a CdTe detector of high quantum efficiency as well as a theoretical analysis of the gains predicted in diffraction efficiency using these detectors, a SAXS examination of low-dose radiation exposure effects on the dissociation of a protein complex related to human health, theoretical calculations describing radiation chemistry pathways which aim to explain the specific structural damage widely observed in proteins, investigation of radiation-induced damage effects in a DNA crystal, a case study on a metallo-enzyme where structural movements thought to be mechanism related might actually be radiation-damage-induced changes, and finally a review describing what X-ray radiation-induced cysteine modifications can teach us about protein dynamics and catalysis. These papers, along with some other relevant literature published since the last Journal of Synchrotron Radiation Radiation Damage special issue in 2017, are briefly summarized below.
Collapse
Affiliation(s)
- Elspeth F Garman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Martin Weik
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044 Grenoble, France
| |
Collapse
|