1
|
Henning RW, Kosheleva I, Šrajer V, Kim IS, Zoellner E, Ranganathan R. BioCARS: Synchrotron facility for probing structural dynamics of biological macromolecules. Struct Dyn 2024; 11:014301. [PMID: 38304444 PMCID: PMC10834067 DOI: 10.1063/4.0000238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 01/10/2024] [Indexed: 02/03/2024]
Abstract
A major goal in biomedical science is to move beyond static images of proteins and other biological macromolecules to the internal dynamics underlying their function. This level of study is necessary to understand how these molecules work and to engineer new functions and modulators of function. Stemming from a visionary commitment to this problem by Keith Moffat decades ago, a community of structural biologists has now enabled a set of x-ray scattering technologies for observing intramolecular dynamics in biological macromolecules at atomic resolution and over the broad range of timescales over which motions are functionally relevant. Many of these techniques are provided by BioCARS, a cutting-edge synchrotron radiation facility built under Moffat leadership and located at the Advanced Photon Source at Argonne National Laboratory. BioCARS enables experimental studies of molecular dynamics with time resolutions spanning from 100 ps to seconds and provides both time-resolved x-ray crystallography and small- and wide-angle x-ray scattering. Structural changes can be initiated by several methods-UV/Vis pumping with tunable picosecond and nanosecond laser pulses, substrate diffusion, and global perturbations, such as electric field and temperature jumps. Studies of dynamics typically involve subtle perturbations to molecular structures, requiring specialized computational techniques for data processing and interpretation. In this review, we present the challenges in experimental macromolecular dynamics and describe the current state of experimental capabilities at this facility. As Moffat imagined years ago, BioCARS is now positioned to catalyze the scientific community to make fundamental advances in understanding proteins and other complex biological macromolecules.
Collapse
Affiliation(s)
- Robert W. Henning
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - Irina Kosheleva
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - Vukica Šrajer
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - In-Sik Kim
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - Eric Zoellner
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - Rama Ranganathan
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| |
Collapse
|
2
|
Birch J, Kwan TOC, Judge PJ, Axford D, Aller P, Butryn A, Reis RI, Bada Juarez JF, Vinals J, Owen RL, Nango E, Tanaka R, Tono K, Joti Y, Tanaka T, Owada S, Sugahara M, Iwata S, Orville AM, Watts A, Moraes I. A versatile approach to high-density microcrystals in lipidic cubic phase for room-temperature serial crystallography. J Appl Crystallogr 2023; 56:1361-1370. [PMID: 37791355 PMCID: PMC10543674 DOI: 10.1107/s1600576723006428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 07/24/2023] [Indexed: 10/05/2023] Open
Abstract
Serial crystallography has emerged as an important tool for structural studies of integral membrane proteins. The ability to collect data from micrometre-sized weakly diffracting crystals at room temperature with minimal radiation damage has opened many new opportunities in time-resolved studies and drug discovery. However, the production of integral membrane protein microcrystals in lipidic cubic phase at the desired crystal density and quantity is challenging. This paper introduces VIALS (versatile approach to high-density microcrystals in lipidic cubic phase for serial crystallography), a simple, fast and efficient method for preparing hundreds of microlitres of high-density microcrystals suitable for serial X-ray diffraction experiments at both synchrotron and free-electron laser sources. The method is also of great benefit for rational structure-based drug design as it facilitates in situ crystal soaking and rapid determination of many co-crystal structures. Using the VIALS approach, room-temperature structures are reported of (i) the archaerhodopsin-3 protein in its dark-adapted state and 110 ns photocycle intermediate, determined to 2.2 and 1.7 Å, respectively, and (ii) the human A2A adenosine receptor in complex with two different ligands determined to a resolution of 3.5 Å.
Collapse
Affiliation(s)
- James Birch
- Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0FA, United Kingdom
| | - Tristan O. C. Kwan
- ChemBio, National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW, United Kingdom
| | - Peter J. Judge
- Biochemistry Department, Oxford University, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Danny Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Pierre Aller
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0FA, United Kingdom
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Agata Butryn
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0FA, United Kingdom
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Rosana I. Reis
- ChemBio, National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW, United Kingdom
| | - Juan F. Bada Juarez
- Biochemistry Department, Oxford University, South Parks Road, Oxford OX1 3QU, United Kingdom
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, Lausanne, CH-1015, Switzerland
| | - Javier Vinals
- Biochemistry Department, Oxford University, South Parks Road, Oxford OX1 3QU, United Kingdom
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Robin L. Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Kensuke Tono
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Yasumasa Joti
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Tomoyuki Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Shigeki Owada
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Michihiro Sugahara
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - So Iwata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Allen M. Orville
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0FA, United Kingdom
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Anthony Watts
- Biochemistry Department, Oxford University, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Isabel Moraes
- ChemBio, National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW, United Kingdom
| |
Collapse
|
3
|
Stagno JR, Knoska J, Chapman HN, Wang YX. Mix-and-Inject Serial Femtosecond Crystallography to Capture RNA Riboswitch Intermediates. Methods Mol Biol 2023; 2568:243-249. [PMID: 36227573 DOI: 10.1007/978-1-0716-2687-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Time-resolved structure determination of macromolecular conformations and ligand-bound intermediates is extremely challenging, particularly for RNA. With rapid technological advances in both microfluidic liquid injection and X-ray free electron lasers (XFEL), a new frontier has emerged in time-resolved crystallography whereby crystals can be mixed with ligand and then probed with X-rays (mix-and-inject) in real time and at room temperature. This chapter outlines the basic setup and procedures for mix-and-inject experiments for recording time-resolved crystallographic data of riboswitch RNA reaction states using serial femtosecond crystallography (SFX) and an XFEL.
Collapse
Affiliation(s)
- Jason R Stagno
- Protein-Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Juraj Knoska
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
- Department of Physics, Universität Hamburg, Hamburg, Germany
| | - Henry N Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
- Department of Physics, Universität Hamburg, Hamburg, Germany
- Centre for Ultrafast Imaging, Universität Hamburg, Hamburg, Germany
| | - Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
| |
Collapse
|
4
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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
|
5
|
Sherrell DA, Lavens A, Wilamowski M, Kim Y, Chard R, Lazarski K, Rosenbaum G, Vescovi R, Johnson JL, Akins C, Chang C, Michalska K, Babnigg G, Foster I, Joachimiak A. Fixed-target serial crystallography at the Structural Biology Center. J Synchrotron Radiat 2022; 29:1141-1151. [PMID: 36073872 PMCID: PMC9455217 DOI: 10.1107/s1600577522007895] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 08/05/2022] [Indexed: 05/30/2023]
Abstract
Serial synchrotron crystallography enables the study of protein structures under physiological temperature and reduced radiation damage by collection of data from thousands of crystals. The Structural Biology Center at Sector 19 of the Advanced Photon Source has implemented a fixed-target approach with a new 3D-printed mesh-holder optimized for sample handling. The holder immobilizes a crystal suspension or droplet emulsion on a nylon mesh, trapping and sealing a near-monolayer of crystals in its mother liquor between two thin Mylar films. Data can be rapidly collected in scan mode and analyzed in near real-time using piezoelectric linear stages assembled in an XYZ arrangement, controlled with a graphical user interface and analyzed using a high-performance computing pipeline. Here, the system was applied to two β-lactamases: a class D serine β-lactamase from Chitinophaga pinensis DSM 2588 and L1 metallo-β-lactamase from Stenotrophomonas maltophilia K279a.
Collapse
Affiliation(s)
- Darren A. Sherrell
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Alex Lavens
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Mateusz Wilamowski
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60667, USA
| | - Youngchang Kim
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60667, USA
| | - Ryan Chard
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Krzysztof Lazarski
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Gerold Rosenbaum
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Rafael Vescovi
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Jessica L. Johnson
- Biosciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Chase Akins
- Biosciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Changsoo Chang
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60667, USA
| | - Karolina Michalska
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60667, USA
| | - Gyorgy Babnigg
- Biosciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Ian Foster
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Andrzej Joachimiak
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60667, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60367, USA
| |
Collapse
|
6
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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
|
7
|
Nass K, Bacellar C, Cirelli C, Dworkowski F, Gevorkov Y, James D, Johnson PJM, Kekilli D, Knopp G, Martiel I, Ozerov D, Tolstikova A, Vera L, Weinert T, Yefanov O, Standfuss J, Reiche S, Milne CJ. Pink-beam serial femtosecond crystallography for accurate structure-factor determination at an X-ray free-electron laser. IUCrJ 2021; 8:905-920. [PMID: 34804544 PMCID: PMC8562661 DOI: 10.1107/s2052252521008046] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/05/2021] [Indexed: 05/25/2023]
Abstract
Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) enables essentially radiation-damage-free macromolecular structure determination using microcrystals that are too small for synchrotron studies. However, SFX experiments often require large amounts of sample in order to collect highly redundant data where some of the many stochastic errors can be averaged out to determine accurate structure-factor amplitudes. In this work, the capability of the Swiss X-ray free-electron laser (SwissFEL) was used to generate large-bandwidth X-ray pulses [Δλ/λ = 2.2% full width at half-maximum (FWHM)], which were applied in SFX with the aim of improving the partiality of Bragg spots and thus decreasing sample consumption while maintaining the data quality. Sensitive data-quality indicators such as anomalous signal from native thaumatin micro-crystals and de novo phasing results were used to quantify the benefits of using pink X-ray pulses to obtain accurate structure-factor amplitudes. Compared with data measured using the same setup but using X-ray pulses with typical quasi-monochromatic XFEL bandwidth (Δλ/λ = 0.17% FWHM), up to fourfold reduction in the number of indexed diffraction patterns required to obtain similar data quality was achieved. This novel approach, pink-beam SFX, facilitates the yet underutilized de novo structure determination of challenging proteins at XFELs, thereby opening the door to more scientific breakthroughs.
Collapse
Affiliation(s)
- Karol Nass
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Camila Bacellar
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Claudio Cirelli
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Florian Dworkowski
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Yaroslav Gevorkov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Daniel James
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | | | - Demet Kekilli
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Gregor Knopp
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Isabelle Martiel
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Dmitry Ozerov
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Alexandra Tolstikova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Laura Vera
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Tobias Weinert
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Jörg Standfuss
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Sven Reiche
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | | |
Collapse
|
8
|
Koch RJ, Roth N, Liu Y, Ivashko O, Dippel AC, Petrovic C, Iversen BB, V Zimmermann M, Bozin ES. On single-crystal total scattering data reduction and correction protocols for analysis in direct space. Acta Crystallogr A Found Adv 2021; 77:611-636. [PMID: 34726636 DOI: 10.1107/s2053273321010159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 09/30/2021] [Indexed: 11/10/2022] Open
Abstract
Data reduction and correction steps and processed data reproducibility in the emerging single-crystal total-scattering-based technique of three-dimensional differential atomic pair distribution function (3D-ΔPDF) analysis are explored. All steps from sample measurement to data processing are outlined using a crystal of CuIr2S4 as an example, studied in a setup equipped with a high-energy X-ray beam and a flat-panel area detector. Computational overhead as pertains to data sampling and the associated data-processing steps is also discussed. Various aspects of the final 3D-ΔPDF reproducibility are explicitly tested by varying the data-processing order and included steps, and by carrying out a crystal-to-crystal data comparison. Situations in which the 3D-ΔPDF is robust are identified, and caution against a few particular cases which can lead to inconsistent 3D-ΔPDFs is noted. Although not all the approaches applied herein will be valid across all systems, and a more in-depth analysis of some of the effects of the data-processing steps may still needed, the methods collected herein represent the start of a more systematic discussion about data processing and corrections in this field.
Collapse
Affiliation(s)
- Robert J Koch
- Condensed Matter Physics and Materials Science Division, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Nikolaj Roth
- Center for Materials Crystallography, Department of Chemistry and iNANO, Aarhus University, DK-8000, Aarhus, Denmark
| | - Yiu Liu
- Condensed Matter Physics and Materials Science Division, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Oleh Ivashko
- Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | | | - Cedomir Petrovic
- Condensed Matter Physics and Materials Science Division, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Bo B Iversen
- Center for Materials Crystallography, Department of Chemistry and iNANO, Aarhus University, DK-8000, Aarhus, Denmark
| | | | - Emil S Bozin
- Condensed Matter Physics and Materials Science Division, Brookhaven National Laboratory, Upton, NY 11973, USA
| |
Collapse
|
9
|
Bücker R, Hogan-Lamarre P, Miller RJD. Serial Electron Diffraction Data Processing With diffractem and CrystFEL. Front Mol Biosci 2021; 8:624264. [PMID: 34095217 PMCID: PMC8171297 DOI: 10.3389/fmolb.2021.624264] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 04/28/2021] [Indexed: 12/03/2022] Open
Abstract
Serial electron diffraction (SerialED) is an emerging technique, which applies the snapshot data-collection mode of serial X-ray crystallography to three-dimensional electron diffraction (3D Electron Diffraction), forgoing the conventional rotation method. Similarly to serial X-ray crystallography, this approach leads to almost complete absence of radiation damage effects even for the most sensitive samples, and allows for a high level of automation. However, SerialED also necessitates new techniques of data processing, which combine existing pipelines for rotation electron diffraction and serial X-ray crystallography with some more particular solutions for challenges arising in SerialED specifically. Here, we introduce our analysis pipeline for SerialED data, and its implementation using the CrystFEL and diffractem program packages. Detailed examples are provided in extensive supplementary code.
Collapse
Affiliation(s)
- Robert Bücker
- Max Planck Institute for the Structure and Dynamics of Matter, Center for Free-Electron Laser Science, Hamburg, Germany.,Centre for Structural Systems Biology, Department of Chemistry, University of Hamburg, Hamburg, Germany
| | - Pascal Hogan-Lamarre
- Max Planck Institute for the Structure and Dynamics of Matter, Center for Free-Electron Laser Science, Hamburg, Germany.,Department of Physics, University of Toronto, Toronto, ON, Canada.,Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - R J Dwayne Miller
- Department of Physics, University of Toronto, Toronto, ON, Canada.,Department of Chemistry, University of Toronto, Toronto, ON, Canada
| |
Collapse
|
10
|
Ramakrishnan S, Stagno JR, Conrad CE, Ding J, Yu P, Bhandari YR, Lee YT, Pauly G, Yefanov O, Wiedorn MO, Knoska J, Oberthür D, White TA, Barty A, Mariani V, Li C, Brehm W, Heinz WF, Magidson V, Lockett S, Hunter MS, Boutet S, Zatsepin NA, Zuo X, Grant TD, Pandey S, Schmidt M, Spence JCH, Chapman HN, Wang YX. Synchronous RNA conformational changes trigger ordered phase transitions in crystals. Nat Commun 2021; 12:1762. [PMID: 33741910 PMCID: PMC7979858 DOI: 10.1038/s41467-021-21838-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 12/02/2020] [Indexed: 11/20/2022] Open
Abstract
Time-resolved studies of biomacromolecular crystals have been limited to systems involving only minute conformational changes within the same lattice. Ligand-induced changes greater than several angstroms, however, are likely to result in solid-solid phase transitions, which require a detailed understanding of the mechanistic interplay between conformational and lattice transitions. Here we report the synchronous behavior of the adenine riboswitch aptamer RNA in crystal during ligand-triggered isothermal phase transitions. Direct visualization using polarized video microscopy and atomic force microscopy shows that the RNA molecules undergo cooperative rearrangements that maintain lattice order, whose cell parameters change distinctly as a function of time. The bulk lattice order throughout the transition is further supported by time-resolved diffraction data from crystals using an X-ray free electron laser. The synchronous molecular rearrangements in crystal provide the physical basis for studying large conformational changes using time-resolved crystallography and micro/nanocrystals. Time-resolved crystallography (TRX) is used for monitoring only small conformational changes of biomacromolecules within the same lattice. Here, the authors report the interplay between synchronous molecular rearrangements and lattice phase transitions in RNA crystals, providing the basis for the investigation of large conformational changes using TRX.
Collapse
Affiliation(s)
| | - Jason R Stagno
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Chelsie E Conrad
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Jienyu Ding
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Ping Yu
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Yuba R Bhandari
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Yun-Tzai Lee
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Gary Pauly
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Max O Wiedorn
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Juraj Knoska
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.,Department of Physics, Universität Hamburg, Hamburg, Germany
| | - Dominik Oberthür
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Thomas A White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Valerio Mariani
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Chufeng Li
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.,Department of Physics, Arizona State University, Tempe, AZ, USA
| | - Wolfgang Brehm
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - William F Heinz
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Valentin Magidson
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Stephen Lockett
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Nadia A Zatsepin
- Department of Physics, Arizona State University, Tempe, AZ, USA.,Department of Chemistry and Physics, ARC Centre of Excellence in Advanced Molecular Imaging, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, 3086, Victoria, Australia
| | - Xiaobing Zuo
- X-ray Science Division, Argonne National Laboratory, Lemont, IL, USA
| | - Thomas D Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, NY, USA
| | - Suraj Pandey
- Kenwood Interdisciplinary Research Complex Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Marius Schmidt
- Kenwood Interdisciplinary Research Complex Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - John C H Spence
- Department of Physics, Arizona State University, Tempe, AZ, USA
| | - Henry N Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.,Department of Physics, Universität Hamburg, Hamburg, Germany.,Centre for Ultrafast Imaging, Universität Hamburg, Hamburg, Germany
| | - Yun-Xing Wang
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA.
| |
Collapse
|
11
|
Abstract
Microcrystal electron diffraction (MicroED) has recently emerged as a promising method for macromolecular structure determination in structural biology. Since the first protein structure was determined in 2013, the method has been evolving rapidly. Several protein structures have been determined and various studies indicate that MicroED is capable of (i) revealing atomic structures with charges, (ii) solving new protein structures by molecular replacement, (iii) visualizing ligand-binding interactions and (iv) determining membrane-protein structures from microcrystals embedded in lipidic mesophases. However, further development and optimization is required to make MicroED experiments more accurate and more accessible to the structural biology community. Here, we provide an overview of the current status of the field, and highlight the ongoing development, to provide an indication of where the field may be going in the coming years. We anticipate that MicroED will become a robust method for macromolecular structure determination, complementing existing methods in structural biology.
Collapse
Affiliation(s)
- Max T. B. Clabbers
- Department of Materials and Environmental Chemistry, Stockholm University, 106 91 Stockholm, Sweden
| | - Hongyi Xu
- Department of Materials and Environmental Chemistry, Stockholm University, 106 91 Stockholm, Sweden
| |
Collapse
|
12
|
Zhu L, Chen X, Abola EE, Jing L, Liu W. Serial Crystallography for Structure-Based Drug Discovery. Trends Pharmacol Sci 2020; 41:830-839. [PMID: 32950259 PMCID: PMC7572805 DOI: 10.1016/j.tips.2020.08.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 07/17/2020] [Accepted: 08/25/2020] [Indexed: 02/07/2023]
Abstract
Rational drug discovery has greatly accelerated the development of safer and more efficacious therapeutics, assisted significantly by insights from experimentally determined 3D structures of ligands in complex with their targets. Serial crystallography (SX) with X-ray free-electron lasers has enabled structural determination using micrometer- or nanometer-size crystals. This technology, applied in the past decade to solve structures of notoriously difficult-to-study drug targets at room temperature, has now been adapted for use in synchrotron radiation facilities. Ultrashort time scales allow time-resolved characterization of dynamic structural changes and pave the road to study the molecular mechanisms by 'molecular movie.' This article summarizes the latest progress in SX technology and deliberates its demanding applications in future structure-based drug discovery.
Collapse
Affiliation(s)
- Lan Zhu
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Xiaoyu Chen
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Enrique E Abola
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Liang Jing
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Wei Liu
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA.
| |
Collapse
|
13
|
Abstract
The advent of the X-ray free electron laser (XFEL) in the last decade created the discipline of serial crystallography but also the challenge of how crystal samples are delivered to X-ray. Early sample delivery methods demonstrated the proof-of-concept for serial crystallography and XFEL but were beset with challenges of high sample consumption, jet clogging and low data collection efficiency. The potential of XFEL and serial crystallography as the next frontier of structural solution by X-ray for small and weakly diffracting crystals and provision of ultra-fast time-resolved structural data spawned a huge amount of scientific interest and innovation. To utilize the full potential of XFEL and broaden its applicability to a larger variety of biological samples, researchers are challenged to develop better sample delivery methods. Thus, sample delivery is one of the key areas of research and development in the serial crystallography scientific community. Sample delivery currently falls into three main systems: jet-based methods, fixed-target chips, and drop-on-demand. Huge strides have since been made in reducing sample consumption and improving data collection efficiency, thus enabling the use of XFEL for many biological systems to provide high-resolution, radiation damage-free structural data as well as time-resolved dynamics studies. This review summarizes the current main strategies in sample delivery and their respective pros and cons, as well as some future direction.
Collapse
|
14
|
Weinert T, Panneels V. Membrane Protein Preparation for Serial Crystallography Using High-Viscosity Injectors: Rhodopsin as an Example. Methods Mol Biol 2020; 2127:321-38. [PMID: 32112331 DOI: 10.1007/978-1-0716-0373-4_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Membrane proteins are highly interesting targets due to their pivotal role in cell function and disease. They are inserted in cell membranes, are often intrinsically flexible, and can adopt several conformational states to carry out their function. Although most overall folds of membrane proteins are known, many questions remain about specific functionally relevant intramolecular rearrangements that require experimental structure determination. Here, using the example of rhodopsin, we describe how to prepare and analyze membrane protein crystals for serial crystallography at room temperature, a new technique allowing to merge diffraction data from thousands of injector-delivered crystals that are too tiny for classical single-crystal analysis even in cryogenic conditions. The application of serial crystallography for studying protein dynamics is mentioned.
Collapse
|
15
|
Gevorkov Y, Barty A, Brehm W, White TA, Tolstikova A, Wiedorn MO, Meents A, Grigat RR, Chapman HN, Yefanov O. pinkIndexer - a universal indexer for pink-beam X-ray and electron diffraction snapshots. Acta Crystallogr A Found Adv 2020; 76:121-131. [PMID: 32124850 PMCID: PMC7053222 DOI: 10.1107/s2053273319015559] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/18/2019] [Indexed: 12/15/2022] Open
Abstract
A crystallographic indexing algorithm, pinkIndexer, is presented for the analysis of snapshot diffraction patterns. It can be used in a variety of contexts including measurements made with a monochromatic radiation source, a polychromatic source or with radiation of very short wavelength. As such, the algorithm is particularly suited to automated data processing for two emerging measurement techniques for macromolecular structure determination: serial pink-beam X-ray crystallography and serial electron crystallography, which until now lacked reliable programs for analyzing many individual diffraction patterns from crystals of uncorrelated orientation. The algorithm requires approximate knowledge of the unit-cell parameters of the crystal, but not the wavelengths associated with each Bragg spot. The use of pinkIndexer is demonstrated by obtaining 1005 lattices from a published pink-beam serial crystallography data set that had previously yielded 140 indexed lattices. Additionally, in tests on experimental serial crystallography diffraction data recorded with quasi-monochromatic X-rays and with electrons the algorithm indexed more patterns than other programs tested.
Collapse
Affiliation(s)
- Yaroslav Gevorkov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
- Vision Systems, Hamburg University of Technology, 21071 Hamburg, Germany
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Wolfgang Brehm
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Thomas A. White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Aleksandra Tolstikova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Max O. Wiedorn
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Alke Meents
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Rolf-Rainer Grigat
- Vision Systems, Hamburg University of Technology, 21071 Hamburg, Germany
| | - Henry N. Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| |
Collapse
|
16
|
Yefanov O, Oberthür D, Bean R, Wiedorn MO, Knoska J, Pena G, Awel S, Gumprecht L, Domaracky M, Sarrou I, Lourdu Xavier P, Metz M, Bajt S, Mariani V, Gevorkov Y, White TA, Tolstikova A, Villanueva-Perez P, Seuring C, Aplin S, Estillore AD, Küpper J, Klyuev A, Kuhn M, Laurus T, Graafsma H, Monteiro DCF, Trebbin M, Maia FRNC, Cruz-Mazo F, Gañán-Calvo AM, Heymann M, Darmanin C, Abbey B, Schmidt M, Fromme P, Giewekemeyer K, Sikorski M, Graceffa R, Vagovic P, Kluyver T, Bergemann M, Fangohr H, Sztuk-Dambietz J, Hauf S, Raab N, Bondar V, Mancuso AP, Chapman H, Barty A. Evaluation of serial crystallographic structure determination within megahertz pulse trains. Struct Dyn 2019; 6:064702. [PMID: 31832488 PMCID: PMC6892710 DOI: 10.1063/1.5124387] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 10/21/2019] [Indexed: 05/30/2023]
Abstract
The new European X-ray Free-Electron Laser (European XFEL) is the first X-ray free-electron laser capable of delivering intense X-ray pulses with a megahertz interpulse spacing in a wavelength range suitable for atomic resolution structure determination. An outstanding but crucial question is whether the use of a pulse repetition rate nearly four orders of magnitude higher than previously possible results in unwanted structural changes due to either radiation damage or systematic effects on data quality. Here, separate structures from the first and subsequent pulses in the European XFEL pulse train were determined, showing that there is essentially no difference between structures determined from different pulses under currently available operating conditions at the European XFEL.
Collapse
Affiliation(s)
- Oleksandr Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Dominik Oberthür
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Richard Bean
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | - Juraj Knoska
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Gisel Pena
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Salah Awel
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Lars Gumprecht
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Martin Domaracky
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Iosifina Sarrou
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - P Lourdu Xavier
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Markus Metz
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Saša Bajt
- Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Valerio Mariani
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Thomas A White
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Aleksandra Tolstikova
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Pablo Villanueva-Perez
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Carolin Seuring
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Steve Aplin
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Armando D Estillore
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Alexander Klyuev
- Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Manuela Kuhn
- Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Torsten Laurus
- Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Heinz Graafsma
- Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | | | | | | | - Francisco Cruz-Mazo
- Dept. de Ingeniería Aeroespacial y Mecánica de Fluidos, ETSI, Universidad de Sevilla, 41092 Sevilla, Spain
| | - Alfonso M Gañán-Calvo
- Dept. de Ingeniería Aeroespacial y Mecánica de Fluidos, ETSI, Universidad de Sevilla, 41092 Sevilla, Spain
| | - Michael Heymann
- Intelligent Biointegrative Systems Group, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, D-70569 Stuttgart, Germany
| | - Connie Darmanin
- ARC Centre of Excellence in Advanced Molecular Imaging, La Trobe Institute for Molecular Sciences, La Trobe University, Victoria 3086, Australia
| | - Brian Abbey
- ARC Centre of Excellence in Advanced Molecular Imaging, La Trobe Institute for Molecular Sciences, La Trobe University, Victoria 3086, Australia
| | - Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave, Milwaukee, Wisconsin 53211, USA
| | - Petra Fromme
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona 85287-1604, USA
| | | | | | - Rita Graceffa
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | | | | | - Hans Fangohr
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | - Steffen Hauf
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Natascha Raab
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | | | | | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| |
Collapse
|
17
|
Shimazu Y, Tono K, Tanaka T, Yamanaka Y, Nakane T, Mori C, Terakado Kimura K, Fujiwara T, Sugahara M, Tanaka R, Doak RB, Shimamura T, Iwata S, Nango E, Yabashi M. High-viscosity sample-injection device for serial femtosecond crystallography at atmospheric pressure. J Appl Crystallogr 2019; 52:1280-1288. [PMID: 31798359 PMCID: PMC6878880 DOI: 10.1107/s1600576719012846] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Accepted: 09/16/2019] [Indexed: 11/21/2022] Open
Abstract
A high-viscosity cartridge-type injector for serial femtosecond crystallography has been developed at SPring-8 Angstrom Compact Free-Electron Laser. A sample-injection device has been developed at SPring-8 Angstrom Compact Free-Electron Laser (SACLA) for serial femtosecond crystallography (SFX) at atmospheric pressure. Microcrystals embedded in a highly viscous carrier are stably delivered from a capillary nozzle with the aid of a coaxial gas flow and a suction device. The cartridge-type sample reservoir is easily replaceable and facilitates sample reloading or exchange. The reservoir is positioned in a cooling jacket with a temperature-regulated water flow, which is useful to prevent drastic changes in the sample temperature during data collection. This work demonstrates that the injector successfully worked in SFX of the human A2A adenosine receptor complexed with an antagonist, ZM241385, in lipidic cubic phase and for hen egg-white lysozyme microcrystals in a grease carrier. The injection device has also been applied to many kinds of proteins, not only for static structural analyses but also for dynamics studies using pump–probe techniques.
Collapse
Affiliation(s)
- Yoshiaki Shimazu
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Kensuke Tono
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.,Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Tomoyuki Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.,Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yasuaki Yamanaka
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Takanori Nakane
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo, Tokyo 113-0032, Japan
| | - Chihiro Mori
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kanako Terakado Kimura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Takaaki Fujiwara
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Michihiro Sugahara
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.,Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - R Bruce Doak
- Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Tatsuro Shimamura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - So Iwata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.,Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.,Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Makina Yabashi
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| |
Collapse
|
18
|
Gevorkov Y, Yefanov O, Barty A, White TA, Mariani V, Brehm W, Tolstikova A, Grigat RR, Chapman HN. XGANDALF - extended gradient descent algorithm for lattice finding. Acta Crystallogr A Found Adv 2019; 75:694-704. [PMID: 31475914 PMCID: PMC6718201 DOI: 10.1107/s2053273319010593] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 07/26/2019] [Indexed: 11/24/2022] Open
Abstract
Serial crystallography records still diffraction patterns from single, randomly oriented crystals, then merges data from hundreds or thousands of them to form a complete data set. To process the data, the diffraction patterns must first be indexed, equivalent to determining the orientation of each crystal. A novel automatic indexing algorithm is presented, which in tests usually gives significantly higher indexing rates than alternative programs currently available for this task. The algorithm does not require prior knowledge of the lattice parameters but can make use of that information if provided, and also allows indexing of diffraction patterns generated by several crystals in the beam. Cases with a small number of Bragg spots per pattern appear to particularly benefit from the new approach. The algorithm has been implemented and optimized for fast execution, making it suitable for real-time feedback during serial crystallography experiments. It is implemented in an open-source C++ library and distributed under the LGPLv3 licence. An interface to it has been added to the CrystFEL software suite.
Collapse
Affiliation(s)
- Yaroslav Gevorkov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
- Institute of Vision Systems, Hamburg University of Technology, Harburger Schloßstraße 20, 21079 Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Thomas A. White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Valerio Mariani
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Wolfgang Brehm
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Aleksandra Tolstikova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Rolf-Rainer Grigat
- Institute of Vision Systems, Hamburg University of Technology, Harburger Schloßstraße 20, 21079 Hamburg, Germany
| | - Henry N. Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| |
Collapse
|
19
|
Tolstikova A, Levantino M, Yefanov O, Hennicke V, Fischer P, Meyer J, Mozzanica A, Redford S, Crosas E, Opara NL, Barthelmess M, Lieske J, Oberthuer D, Wator E, Mohacsi I, Wulff M, Schmitt B, Chapman HN, Meents A. 1 kHz fixed-target serial crystallography using a multilayer monochromator and an integrating pixel detector. IUCrJ 2019; 6:927-937. [PMID: 31576225 PMCID: PMC6760437 DOI: 10.1107/s205225251900914x] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 06/25/2019] [Indexed: 05/18/2023]
Abstract
Reliable sample delivery and efficient use of limited beam time have remained bottlenecks for serial crystallography (SX). Using a high-intensity polychromatic X-ray beam in combination with a newly developed charge-integrating JUNGFRAU detector, we have applied the method of fixed-target SX to collect data at a rate of 1 kHz at a synchrotron-radiation facility. According to our data analysis for the given experimental conditions, only about 3 000 diffraction patterns are required for a high-quality diffraction dataset. With indexing rates of up to 25%, recording of such a dataset takes less than 30 s.
Collapse
Affiliation(s)
- A. Tolstikova
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Correspondence e-mail: ,
| | - M. Levantino
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - O. Yefanov
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - V. Hennicke
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - P. Fischer
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - J. Meyer
- Deutsches Elektronen Synchrotron, Photon Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - A. Mozzanica
- Paul Scherrer Institute, 111 Forschungsstrasse, 5232 Villigen, Switzerland
| | - S. Redford
- Paul Scherrer Institute, 111 Forschungsstrasse, 5232 Villigen, Switzerland
| | - E. Crosas
- Deutsches Elektronen Synchrotron, Photon Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - N. L. Opara
- Paul Scherrer Institute, 111 Forschungsstrasse, 5232 Villigen, Switzerland
- C-CINA, Biozentrum, University of Basel, Mattenstrasse 26, 4002 Basel, Switzerland
| | - M. Barthelmess
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - J. Lieske
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - D. Oberthuer
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - E. Wator
- Malopolska Centre of Biotechnology, Jagiellonian University, Cracow 30-387, Poland
| | - I. Mohacsi
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - M. Wulff
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - B. Schmitt
- Paul Scherrer Institute, 111 Forschungsstrasse, 5232 Villigen, Switzerland
| | - H. N. Chapman
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Centre for Ultrafast Imaging, University of Hamburg, Luruper Chaussee 149, Hamburg 22761, Germany
| | - A. Meents
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Deutsches Elektronen Synchrotron, Photon Science, Notkestrasse 85, 22607 Hamburg, Germany
- Correspondence e-mail: ,
| |
Collapse
|
20
|
Trachman RJ, Stagno JR, Conrad C, Jones CP, Fischer P, Meents A, Wang YX, Ferré-D'Amaré AR. Co-crystal structure of the iMango-III fluorescent RNA aptamer using an X-ray free-electron laser. Acta Crystallogr F Struct Biol Commun 2019; 75:547-551. [PMID: 31397326 DOI: 10.1107/s2053230x19010136] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 07/15/2019] [Indexed: 11/10/2022]
Abstract
Turn-on aptamers are in vitro-selected RNAs that bind to conditionally fluorescent small molecules and enhance their fluorescence. Upon binding TO1-biotin, the iMango-III aptamer achieves the largest fluorescence enhancement reported for turn-on aptamers (over 5000-fold). This aptamer was generated by structure-guided engineering and functional reselection of the parental aptamer Mango-III. Structures of both Mango-III and iMango-III have previously been determined by conventional cryocrystallography using synchrotron X-radiation. Using an X-ray free-electron laser (XFEL), the room-temperature iMango-III-TO1-biotin co-crystal structure has now been determined at 3.0 Å resolution. This structural model, which was refined against a data set of ∼1300 diffraction images (each from a single crystal), is largely consistent with the structures determined from single-crystal data sets collected at 100 K. This constitutes a technical benchmark on the way to XFEL pump-probe experiments on fluorescent RNA-small molecule complexes.
Collapse
Affiliation(s)
- Robert J Trachman
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, Maryland, USA
| | - Jason R Stagno
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Chelsie Conrad
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Christopher P Jones
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, Maryland, USA
| | - Pontus Fischer
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Alke Meents
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Yun Xing Wang
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, Maryland, USA
| |
Collapse
|
21
|
Halsted TP, Yamashita K, Gopalasingam CC, Shenoy RT, Hirata K, Ago H, Ueno G, Blakeley MP, Eady RR, Antonyuk SV, Yamamoto M, Hasnain SS. Catalytically important damage-free structures of a copper nitrite reductase obtained by femtosecond X-ray laser and room-temperature neutron crystallography. IUCrJ 2019; 6:761-772. [PMID: 31316819 PMCID: PMC6608623 DOI: 10.1107/s2052252519008285] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 06/12/2019] [Indexed: 05/31/2023]
Abstract
Copper-containing nitrite reductases (CuNiRs) that convert NO2 - to NO via a CuCAT-His-Cys-CuET proton-coupled redox system are of central importance in nitrogen-based energy metabolism. These metalloenzymes, like all redox enzymes, are very susceptible to radiation damage from the intense synchrotron-radiation X-rays that are used to obtain structures at high resolution. Understanding the chemistry that underpins the enzyme mechanisms in these systems requires resolutions of better than 2 Å. Here, for the first time, the damage-free structure of the resting state of one of the most studied CuNiRs was obtained by combining X-ray free-electron laser (XFEL) and neutron crystallography. This represents the first direct comparison of neutron and XFEL structural data for any protein. In addition, damage-free structures of the reduced and nitrite-bound forms have been obtained to high resolution from cryogenically maintained crystals by XFEL crystallography. It is demonstrated that AspCAT and HisCAT are deprotonated in the resting state of CuNiRs at pH values close to the optimum for activity. A bridging neutral water (D2O) is positioned with one deuteron directed towards AspCAT Oδ1 and one towards HisCAT N∊2. The catalytic T2Cu-ligated water (W1) can clearly be modelled as a neutral D2O molecule as opposed to D3O+ or OD-, which have previously been suggested as possible alternatives. The bridging water restricts the movement of the unprotonated AspCAT and is too distant to form a hydrogen bond to the O atom of the bound nitrite that interacts with AspCAT. Upon the binding of NO2 - a proton is transferred from the bridging water to the Oδ2 atom of AspCAT, prompting electron transfer from T1Cu to T2Cu and reducing the catalytic redox centre. This triggers the transfer of a proton from AspCAT to the bound nitrite, enabling the reaction to proceed.
Collapse
Affiliation(s)
- Thomas P. Halsted
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| | - Keitaro Yamashita
- SR Life Science Instrumentation Unit, RIKEN SPring-8 Centre, Sayo 679-5148, Japan
| | - Chai C. Gopalasingam
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| | - Rajesh T. Shenoy
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| | - Kunio Hirata
- SR Life Science Instrumentation Unit, RIKEN SPring-8 Centre, Sayo 679-5148, Japan
| | - Hideo Ago
- SR Life Science Instrumentation Unit, RIKEN SPring-8 Centre, Sayo 679-5148, Japan
| | - Go Ueno
- SR Life Science Instrumentation Unit, RIKEN SPring-8 Centre, Sayo 679-5148, Japan
| | - Matthew P. Blakeley
- Large-Scale Structures Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Robert R. Eady
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| | - Svetlana V. Antonyuk
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| | - Masaki Yamamoto
- SR Life Science Instrumentation Unit, RIKEN SPring-8 Centre, Sayo 679-5148, Japan
| | - S. Samar Hasnain
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| |
Collapse
|
22
|
Ebrahim A, Moreno-Chicano T, Appleby MV, Chaplin AK, Beale JH, Sherrell DA, Duyvesteyn HME, Owada S, Tono K, Sugimoto H, Strange RW, Worrall JAR, Axford D, Owen RL, Hough MA. Dose-resolved serial synchrotron and XFEL structures of radiation-sensitive metalloproteins. IUCrJ 2019; 6:543-551. [PMID: 31316799 PMCID: PMC6608622 DOI: 10.1107/s2052252519003956] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 03/22/2019] [Indexed: 05/18/2023]
Abstract
An approach is demonstrated to obtain, in a sample- and time-efficient manner, multiple dose-resolved crystal structures from room-temperature protein microcrystals using identical fixed-target supports at both synchrotrons and X-ray free-electron lasers (XFELs). This approach allows direct comparison of dose-resolved serial synchrotron and damage-free XFEL serial femtosecond crystallography structures of radiation-sensitive proteins. Specifically, serial synchrotron structures of a heme peroxidase enzyme reveal that X-ray induced changes occur at far lower doses than those at which diffraction quality is compromised (the Garman limit), consistent with previous studies on the reduction of heme proteins by low X-ray doses. In these structures, a functionally relevant bond length is shown to vary rapidly as a function of absorbed dose, with all room-temperature synchrotron structures exhibiting linear deformation of the active site compared with the XFEL structure. It is demonstrated that extrapolation of dose-dependent synchrotron structures to zero dose can closely approximate the damage-free XFEL structure. This approach is widely applicable to any protein where the crystal structure is altered by the synchrotron X-ray beam and provides a solution to the urgent requirement to determine intact structures of such proteins in a high-throughput and accessible manner.
Collapse
Affiliation(s)
- Ali Ebrahim
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Tadeo Moreno-Chicano
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Martin V. Appleby
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Amanda K. Chaplin
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - John H. Beale
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Darren A. Sherrell
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Helen M. E. Duyvesteyn
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
- Division of Structural Biology (STRUBI), The Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, UK
| | - 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
| | - Kensuke Tono
- 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
| | - Hiroshi Sugimoto
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Richard W. Strange
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Jonathan A. R. Worrall
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Danny Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Robin L. Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Michael A. Hough
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| |
Collapse
|
23
|
Jones C, Tran B, Conrad C, Stagno J, Trachman R, Fischer P, Meents A, Ferré-D'Amaré A. Co-crystal structure of the Fusobacterium ulcerans ZTP riboswitch using an X-ray free-electron laser. Acta Crystallogr F Struct Biol Commun 2019; 75:496-500. [PMID: 31282869 DOI: 10.1107/s2053230x19008549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 06/15/2019] [Indexed: 11/10/2022]
Abstract
Riboswitches are conformationally dynamic RNAs that regulate gene expression by binding specific small molecules. ZTP riboswitches bind the purine-biosynthetic intermediate 5-aminoimidazole-4-carboxamide riboside 5'-monophosphate (ZMP) and its triphosphorylated form (ZTP). Ligand binding to this riboswitch ultimately upregulates genes involved in folate and purine metabolism. Using an X-ray free-electron laser (XFEL), the room-temperature structure of the Fusobacterium ulcerans ZTP riboswitch bound to ZMP has now been determined at 4.1 Å resolution. This model, which was refined against a data set from ∼750 diffraction images (each from a single crystal), was found to be consistent with that previously obtained from data collected at 100 K using conventional synchrotron X-radiation. These experiments demonstrate the feasibility of time-resolved XFEL experiments to understand how the ZTP riboswitch accommodates cognate ligand binding.
Collapse
Affiliation(s)
- Christopher Jones
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, 50 South Drive, MSC 8012, Bethesda, MD 20892, USA
| | - Brandon Tran
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, 50 South Drive, MSC 8012, Bethesda, MD 20892, USA
| | - Chelsie Conrad
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Jason Stagno
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Robert Trachman
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, 50 South Drive, MSC 8012, Bethesda, MD 20892, USA
| | - Pontus Fischer
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Alke Meents
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Adrian Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, 50 South Drive, MSC 8012, Bethesda, MD 20892, USA
| |
Collapse
|
24
|
Abstract
X-ray free-electron lasers provide femtosecond-duration pulses of hard X-rays with a peak brightness approximately one billion times greater than is available at synchrotron radiation facilities. One motivation for the development of such X-ray sources was the proposal to obtain structures of macromolecules, macromolecular complexes, and virus particles, without the need for crystallization, through diffraction measurements of single noncrystalline objects. Initial explorations of this idea and of outrunning radiation damage with femtosecond pulses led to the development of serial crystallography and the ability to obtain high-resolution structures of small crystals without the need for cryogenic cooling. This technique allows the understanding of conformational dynamics and enzymatics and the resolution of intermediate states in reactions over timescales of 100 fs to minutes. The promise of more photons per atom recorded in a diffraction pattern than electrons per atom contributing to an electron micrograph may enable diffraction measurements of single molecules, although challenges remain.
Collapse
Affiliation(s)
- Henry N. Chapman
- Center for Free-Electron Laser Science, DESY, 22607 Hamburg, Germany
- Department of Physics, University of Hamburg, 22761 Hamburg, Germany
- Centre for Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany
| |
Collapse
|
25
|
Martin-Garcia JM, Zhu L, Mendez D, Lee MY, Chun E, Li C, Hu H, Subramanian G, Kissick D, Ogata C, Henning R, Ishchenko A, Dobson Z, Zhang S, Weierstall U, Spence JCH, Fromme P, Zatsepin NA, Fischetti RF, Cherezov V, Liu W. High-viscosity injector-based pink-beam serial crystallography of microcrystals at a synchrotron radiation source. IUCrJ 2019; 6:412-425. [PMID: 31098022 PMCID: PMC6503920 DOI: 10.1107/s205225251900263x] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 02/20/2019] [Indexed: 05/29/2023]
Abstract
Since the first successful serial crystallography (SX) experiment at a synchrotron radiation source, the popularity of this approach has continued to grow showing that third-generation synchrotrons can be viable alternatives to scarce X-ray free-electron laser sources. Synchrotron radiation flux may be increased ∼100 times by a moderate increase in the bandwidth ('pink beam' conditions) at some cost to data analysis complexity. Here, we report the first high-viscosity injector-based pink-beam SX experiments. The structures of proteinase K (PK) and A2A adenosine receptor (A2AAR) were determined to resolutions of 1.8 and 4.2 Å using 4 and 24 consecutive 100 ps X-ray pulse exposures, respectively. Strong PK data were processed using existing Laue approaches, while weaker A2AAR data required an alternative data-processing strategy. This demonstration of the feasibility presents new opportunities for time-resolved experiments with microcrystals to study structural changes in real time at pink-beam synchrotron beamlines worldwide.
Collapse
Affiliation(s)
- Jose M. Martin-Garcia
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Lan Zhu
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Derek Mendez
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, 550 East Tyler Drive, Tempe, AZ 85287, USA
| | - Ming-Yue Lee
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Eugene Chun
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Chufeng Li
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, 550 East Tyler Drive, Tempe, AZ 85287, USA
| | - Hao Hu
- Department of Physics, Arizona State University, 550 East Tyler Drive, Tempe, AZ 85287, USA
| | - Ganesh Subramanian
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, 550 East Tyler Drive, Tempe, AZ 85287, USA
| | - David Kissick
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Ave, Lemont, IL 90439, USA
| | - Craig Ogata
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Ave, Lemont, IL 90439, USA
| | - Robert Henning
- Center for Advanced Radiation Sources, The University of Chicago, Argonne National Laboratory, 9700 South Cass Ave, Lemont, IL 90439, USA
| | - Andrii Ishchenko
- Department of Chemistry, Bridge Institute, University of Southern California, 1002 Childs Way, Los Angeles, CA 90089, USA
| | - Zachary Dobson
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Shangji Zhang
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Uwe Weierstall
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, 550 East Tyler Drive, Tempe, AZ 85287, USA
| | - John C. H. Spence
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, 550 East Tyler Drive, Tempe, AZ 85287, USA
| | - Petra Fromme
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Nadia A. Zatsepin
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, 550 East Tyler Drive, Tempe, AZ 85287, USA
| | - Robert F. Fischetti
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Ave, Lemont, IL 90439, USA
| | - Vadim Cherezov
- Department of Chemistry, Bridge Institute, University of Southern California, 1002 Childs Way, Los Angeles, CA 90089, USA
| | - Wei Liu
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| |
Collapse
|
26
|
I Ciftci H, G Sierra R, Yoon CH, Su Z, Tateishi H, Koga R, Kotaro K, Yumoto F, Senda T, Liang M, Wakatsuki S, Otsuka M, Fujita M, DeMirci H. Serial Femtosecond X-Ray Diffraction of HIV-1 Gag MA-IP6 Microcrystals at Ambient Temperature. Int J Mol Sci 2019; 20:ijms20071675. [PMID: 30987231 PMCID: PMC6479536 DOI: 10.3390/ijms20071675] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 03/22/2019] [Accepted: 04/01/2019] [Indexed: 01/24/2023] Open
Abstract
The Human immunodeficiency virus-1 (HIV-1) matrix (MA) domain is involved in the highly regulated assembly process of the virus particles that occur at the host cell’s plasma membrane. High-resolution structures of the MA domain determined using cryo X-ray crystallography have provided initial insights into the possible steps in the viral assembly process. However, these structural studies have relied on large and frozen crystals in order to reduce radiation damage caused by the intense X-rays. Here, we report the first X-ray free-electron laser (XFEL) study of the HIV-1 MA domain’s interaction with inositol hexaphosphate (IP6), a phospholipid headgroup mimic. We also describe the purification, characterization and microcrystallization of two MA crystal forms obtained in the presence of IP6. In addition, we describe the capabilities of serial femtosecond X-ray crystallography (SFX) using an XFEL to elucidate the diffraction data of MA-IP6 complex microcrystals in liquid suspension at ambient temperature. Two different microcrystal forms of the MA-IP6 complex both diffracted to beyond 3.5 Å resolution, demonstrating the feasibility of using SFX to study the complexes of MA domain of HIV-1 Gag polyprotein with IP6 at near-physiological temperatures. Further optimization of the experimental and data analysis procedures will lead to better understanding of the MA domain of HIV-1 Gag and IP6 interaction at high resolution and will provide basis for optimization of the lead compounds for efficient inhibition of the Gag protein recruitment to the plasma membrane prior to virion formation.
Collapse
Affiliation(s)
- Halil I Ciftci
- Department of Drug Discovery, Science Farm Ltd., Kumamoto 862-0976, Japan.
- Department of Bioorganic Medicinal Chemistry, School of Pharmacy, Kumamoto University, Kumamoto 862-0973, Japan.
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
| | - Raymond G Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
| | - Chun Hong Yoon
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
| | - Zhen Su
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA.
| | - Hiroshi Tateishi
- Department of Bioorganic Medicinal Chemistry, School of Pharmacy, Kumamoto University, Kumamoto 862-0973, Japan.
| | - Ryoko Koga
- Department of Bioorganic Medicinal Chemistry, School of Pharmacy, Kumamoto University, Kumamoto 862-0973, Japan.
| | - Koiwai Kotaro
- Structural Biology Research Center, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, Tsukuba, Ibaraki 305-0034, Japan.
| | - Fumiaki Yumoto
- Structural Biology Research Center, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, Tsukuba, Ibaraki 305-0034, Japan.
| | - Toshiya Senda
- Structural Biology Research Center, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, Tsukuba, Ibaraki 305-0034, Japan.
| | - Mengling Liang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
| | - Soichi Wakatsuki
- Biosciences Division, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
| | - Masami Otsuka
- Department of Bioorganic Medicinal Chemistry, School of Pharmacy, Kumamoto University, Kumamoto 862-0973, Japan.
| | - Mikako Fujita
- Research Institute for Drug Discovery, School of Pharmacy, Kumamoto University, Kumamoto 862-0973, Japan.
| | - Hasan DeMirci
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
- Biosciences Division, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
| |
Collapse
|
27
|
Hirata K, Yamashita K, Ueno G, Kawano Y, Hasegawa K, Kumasaka T, Yamamoto M. ZOO: an automatic data-collection system for high-throughput structure analysis in protein microcrystallography. Acta Crystallogr D Struct Biol 2019; 75:138-150. [PMID: 30821703 PMCID: PMC6400253 DOI: 10.1107/s2059798318017795] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 12/17/2018] [Indexed: 11/10/2022] Open
Abstract
Owing to the development of brilliant microfocus beamlines, rapid-readout detectors and sample changers, protein microcrystallography is rapidly becoming a popular technique for accessing structural information from complex biological samples. However, the method is time-consuming and labor-intensive and requires technical expertise to obtain high-resolution protein crystal structures. At SPring-8, an automated data-collection system named ZOO has been developed. This system enables faster data collection, facilitates advanced data-collection and data-processing techniques, and permits the collection of higher quality data. In this paper, the key features of the functionality put in place on the SPring-8 microbeam beamline BL32XU are described and the major advantages of this system are outlined. The ZOO system will be a major driving force in the evolution of the macromolecular crystallography beamlines at SPring-8.
Collapse
Affiliation(s)
- Kunio Hirata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology (PRESTO), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | | | - Go Ueno
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Yoshiaki Kawano
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Kazuya Hasegawa
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo 679-5198, Hyogo, Japan
| | - Takashi Kumasaka
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo 679-5198, Hyogo, Japan
| | - Masaki Yamamoto
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| |
Collapse
|
28
|
White TA. Processing serial crystallography data with CrystFEL: a step-by-step guide. Acta Crystallogr D Struct Biol 2019; 75:219-233. [PMID: 30821710 PMCID: PMC6400257 DOI: 10.1107/s205979831801238x] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 08/31/2018] [Indexed: 11/11/2022]
Abstract
A step-by-step guide to processing serial crystallography data from X-ray free-electron lasers and synchrotron sources using CrystFEL is provided. This article provides a step-by-step guide to the use of the CrystFEL software for processing serial crystallography data from an X-ray free-electron laser or a synchrotron light source. Whereas previous papers have described the theory and algorithms and their rationale, this paper describes the steps to be performed from a user perspective, including command-line examples.
Collapse
Affiliation(s)
- Thomas A White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg, Germany
| |
Collapse
|
29
|
Wiedorn MO, Oberthür D, Bean R, Schubert R, Werner N, Abbey B, Aepfelbacher M, Adriano L, Allahgholi A, Al-Qudami N, Andreasson J, Aplin S, Awel S, Ayyer K, Bajt S, Barák I, Bari S, Bielecki J, Botha S, Boukhelef D, Brehm W, Brockhauser S, Cheviakov I, Coleman MA, Cruz-Mazo F, Danilevski C, Darmanin C, Doak RB, Domaracky M, Dörner K, Du Y, Fangohr H, Fleckenstein H, Frank M, Fromme P, Gañán-Calvo AM, Gevorkov Y, Giewekemeyer K, Ginn HM, Graafsma H, Graceffa R, Greiffenberg D, Gumprecht L, Göttlicher P, Hajdu J, Hauf S, Heymann M, Holmes S, Horke DA, Hunter MS, Imlau S, Kaukher A, Kim Y, Klyuev A, Knoška J, Kobe B, Kuhn M, Kupitz C, Küpper J, Lahey-Rudolph JM, Laurus T, Le Cong K, Letrun R, Xavier PL, Maia L, Maia FRNC, Mariani V, Messerschmidt M, Metz M, Mezza D, Michelat T, Mills G, Monteiro DCF, Morgan A, Mühlig K, Munke A, Münnich A, Nette J, Nugent KA, Nuguid T, Orville AM, Pandey S, Pena G, Villanueva-Perez P, Poehlsen J, Previtali G, Redecke L, Riekehr WM, Rohde H, Round A, Safenreiter T, Sarrou I, Sato T, Schmidt M, Schmitt B, Schönherr R, Schulz J, Sellberg JA, Seibert MM, Seuring C, Shelby ML, Shoeman RL, Sikorski M, Silenzi A, Stan CA, Shi X, Stern S, Sztuk-Dambietz J, Szuba J, Tolstikova A, Trebbin M, Trunk U, Vagovic P, Ve T, Weinhausen B, White TA, Wrona K, Xu C, Yefanov O, Zatsepin N, Zhang J, Perbandt M, Mancuso AP, Betzel C, Chapman H, Barty A. Megahertz serial crystallography. Nat Commun 2018; 9:4025. [PMID: 30279492 PMCID: PMC6168542 DOI: 10.1038/s41467-018-06156-7] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 08/21/2018] [Indexed: 01/08/2023] Open
Abstract
The new European X-ray Free-Electron Laser is the first X-ray free-electron laser capable of delivering X-ray pulses with a megahertz inter-pulse spacing, more than four orders of magnitude higher than previously possible. However, to date, it has been unclear whether it would indeed be possible to measure high-quality diffraction data at megahertz pulse repetition rates. Here, we show that high-quality structures can indeed be obtained using currently available operating conditions at the European XFEL. We present two complete data sets, one from the well-known model system lysozyme and the other from a so far unknown complex of a β-lactamase from K. pneumoniae involved in antibiotic resistance. This result opens up megahertz serial femtosecond crystallography (SFX) as a tool for reliable structure determination, substrate screening and the efficient measurement of the evolution and dynamics of molecular structures using megahertz repetition rate pulses available at this new class of X-ray laser source.
Collapse
Grants
- Project oriented funds Helmholtz-Gemeinschaft (Helmholtz Gemeinschaft)
- DFG-EXC1074 Deutsche Forschungsgemeinschaft (German Research Foundation)
- R01 GM117342 NIGMS NIH HHS
- R01 GM095583 NIGMS NIH HHS
- 609920 European Research Council
- Wellcome Trust
- : The Helmholtz organisation through program oriented funds; excellence cluster "The Hamburg Center for Ultrafast Imaging – Structure, Dynamics and Control of Matter at the Atomic Scale" of the Deutsche Forschungsgemeinschaft (CUI, DFG-EXC1074); the European Research Council, “Frontiers in Attosecond X-ray Science: Imaging and Spectroscopy (AXSIS)”, ERC-2013-SyG 609920 (2014-2018); the Gottfried Wilhelm Leibniz Program of the DFG; the project “X-probe” funded by the European Union’s 2020 Research and Innovation Program under the Marie Sklodowska-Curie grant agreement 637295; the BMBF German-Russian Cooperation “SyncFELMed” grant 05K14CHA; European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) through the Consolidator Grant COMOTION (ERC-614507-Küpper); the Helmholtz Gemeinschaft through the "Impuls und Vernetzungsfond"; Helmholtz Initiative and Networking Fund through the Young Investigators Program and by the Deutsche Forschungsgemeinschaft SFB755/B03; the Swedish Research Council; the Knut and Alice Wallenberg Foundation; the Röntgen-Angström Cluster; the BMBF via projects 05K13GU7 and 05E13GU1; the from Ministry of Education, Science, Research and Sport of the Slovak Republic; the Joachim Herz Stiftung; the Deutsche Forschungsgemeinschaft (DFG) Cluster of Excellence “Inflammation at interfaces” (EXC 306); the Swedish Research Council; the Swedish Foundation for Strategic Research; the Australian Research Council Centre of Excellence in Advanced Molecular Imaging [CE140100011]; the Australian Nuclear Science and Technology Organisation (ANSTO); the International Synchrotron Access Program (ISAP) managed by the Australian Synchrotron, part of ANSTO, and funded by the Australian Government; The projects Structural dynamics of biomolecular systems (CZ.02.1.01/0.0/0.0/15_003/0000447) (ELIBIO) and Advanced research using high intensity laser produced photons and particles (CZ.02.1.01/0.0/0.0/16_019/0000789) (ADONIS) from European Regional Development Fund, the Ministry of Education, Youth and Sports as part of targeted support from the National Programme of Sustainability II; the Röntgen Ångström Cluster; the Chalmers Area of Advance, Material science; the Project DPI2016-78887-C3-1-R, Ministerio de Economía y Competitividad; the Wellcome Trust (studentship 075491/04); Rutgers University, Newark; the Max Planck Society; the NSF-STC “BioXFEL” through award STC-1231306; the Slovak Research and Development Agency under contract APVV-14-0181; the Wellcome Trust; Helmholtz Strategic Investment funds; Australian Research Council Centre of Excellence in Advanced Molecular Imaging [CE140100011], Australian Nuclear Science and Technology Organisation (ANSTO); The Swedish Research Council, the Knut and Alice Wallenberg Foundation, and the Röntgen-Angström Cluster, BMBF via projects 05K13GU7 and 05E13GU1, Ministry of Education, Science, Research and Sport of the Slovak Republic; BMBF grants 05K16GUA and 05K12GU3; the Joachim Herz Foundation through and Add-on Fellowship; NHMRC project grants 1107804 and 1108859, ARC Discovery Early Career Research Award (DE170100783); National Health and Medical Research Council (NHMRC grants 1107804, 1071659). BK is NHMRC Principal Research Fellow (1110971); National Science Foundation Grant # 1565180, "ABI Innovation: New Algorithms for Biological X-ray Free Electron Laser Data"; Diamond Light Source and from a Strategic Award from the Wellcome Trust and the Biotechnology and Biological Sciences Research Council (grant 102593); use of the XBI biological sample preparation laboratory, enabled by the XBI User Consortium. This work was performed, in part, under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. MLS, MAC and MF were supported by NIH grant 1R01GM117342-01
Collapse
Affiliation(s)
- Max O Wiedorn
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Dominik Oberthür
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Richard Bean
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Robin Schubert
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Notkestrasse 85, 22607, Hamburg, Germany
- Integrated Biology Infrastructure Life-Science Facility at the European XFEL (XBI), Holzkoppel 4, 22869, Schenefeld, Germany
| | - Nadine Werner
- Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Notkestrasse 85, 22607, Hamburg, Germany
| | - Brian Abbey
- Australian Research Council (ARC) Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Sciences, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Martin Aepfelbacher
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246, Hamburg, Germany
| | - Luigi Adriano
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Aschkan Allahgholi
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | | | - Jakob Andreasson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, 751 24, Sweden
- ELI Beamlines, Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 21, Prague, Czech Republic
- Condensed Matter Physics, Department of Physics, Chalmers University of Technology, Gothenburg, 412 96, Sweden
| | - Steve Aplin
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Salah Awel
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Kartik Ayyer
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Saša Bajt
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Imrich Barák
- Institute of Molecular Biology, SAS, Dubravska cesta 21, 845 51, Bratislava, Slovakia
| | - Sadia Bari
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Johan Bielecki
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Sabine Botha
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Notkestrasse 85, 22607, Hamburg, Germany
| | | | - Wolfgang Brehm
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Sandor Brockhauser
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
- Biological Research Centre (BRC), Hungarian Academy of Sciences, Temesvári krt. 62, Szeged, 6726, Hungary
| | - Igor Cheviakov
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246, Hamburg, Germany
| | - Matthew A Coleman
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA, 94550, USA
| | - Francisco Cruz-Mazo
- Depart. Ingeniería Aeroespacial y Mecánica de Fluidos ETSI, Universidad de Sevilla, 41092, Sevilla, Spain
| | | | - Connie Darmanin
- Australian Research Council (ARC) Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Sciences, La Trobe University, Bundoora, VIC, 3086, Australia
| | - R Bruce Doak
- Max Planck Institute for Medical Research, Jahnstr. 29, 69120, Heidelberg, Germany
| | - Martin Domaracky
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Katerina Dörner
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Yang Du
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Hans Fangohr
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
- Engineering and the Environment, University of Southampton, SO17 1BJ, Southampton, UK
| | - Holger Fleckenstein
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Matthias Frank
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA, 94550, USA
| | - Petra Fromme
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-1604, USA
| | - Alfonso M Gañán-Calvo
- Depart. Ingeniería Aeroespacial y Mecánica de Fluidos ETSI, Universidad de Sevilla, 41092, Sevilla, Spain
| | - Yaroslav Gevorkov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Hamburg University of Technology, Vision Systems E-2, Harburger Schloßstr. 20, 21079, Hamburg, Germany
| | | | - Helen Mary Ginn
- Division of Structural Biology, Headington, Oxford, OX3 7BN, UK
- Diamond Light Source, Research Complex at Harwell, and University of Oxford, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - Heinz Graafsma
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Mid Sweden University, Holmgatan 10, 85170, Sundsvall, Sweden
| | - Rita Graceffa
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Lars Gumprecht
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Peter Göttlicher
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, 751 24, Sweden
- ELI Beamlines, Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 21, Prague, Czech Republic
| | - Steffen Hauf
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Michael Heymann
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Susannah Holmes
- Australian Research Council (ARC) Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Sciences, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Daniel A Horke
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, 94025, CA, USA
| | - Siegfried Imlau
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | | | - Yoonhee Kim
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Alexander Klyuev
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Juraj Knoška
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, 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
| | - Manuela Kuhn
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Christopher Kupitz
- Physics Department, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI, 53211, USA
| | - Jochen Küpper
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Department of Chemistry, Universität Hamburg, Martin-Luther-King Platz 6, 20146, Hamburg, Germany
| | - Janine Mia Lahey-Rudolph
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Torsten Laurus
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Karoline Le Cong
- Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Notkestrasse 85, 22607, Hamburg, Germany
| | - Romain Letrun
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - P Lourdu Xavier
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Max-Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Luis Maia
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Filipe R N C Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, 751 24, Sweden
- NERSC, Lawrence Berkeley National Laboratory, Berkeley, 94720, CA, USA
| | - Valerio Mariani
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | | | - Markus Metz
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Davide Mezza
- Paul Scherrer Institut, Forschungsstrasse 111, 5232, Villigen, Switzerland
| | - Thomas Michelat
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Grant Mills
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Diana C F Monteiro
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Andrew Morgan
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Kerstin Mühlig
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, 751 24, Sweden
| | - Anna Munke
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, 751 24, Sweden
| | - Astrid Münnich
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Julia Nette
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Keith A Nugent
- Australian Research Council (ARC) Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Sciences, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Theresa Nuguid
- Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Notkestrasse 85, 22607, Hamburg, Germany
| | - Allen M Orville
- Diamond Light Source, Research Complex at Harwell, and University of Oxford, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - Suraj Pandey
- Physics Department, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI, 53211, USA
| | - Gisel Pena
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Pablo Villanueva-Perez
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Jennifer Poehlsen
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | | | - Lars Redecke
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246, Hamburg, Germany
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Winnie Maria Riekehr
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Holger Rohde
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246, Hamburg, Germany
| | - Adam Round
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Tatiana Safenreiter
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Iosifina Sarrou
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Tokushi Sato
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI, 53211, USA
| | - Bernd Schmitt
- Paul Scherrer Institut, Forschungsstrasse 111, 5232, Villigen, Switzerland
| | - Robert Schönherr
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Joachim Schulz
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Jonas A Sellberg
- Biomedical and X-Ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology, Stockholm, 106 91, Sweden
| | - M Marvin Seibert
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, 751 24, Sweden
| | - Carolin Seuring
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Megan L Shelby
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA, 94550, USA
| | - Robert L Shoeman
- Max Planck Institute for Medical Research, Jahnstr. 29, 69120, Heidelberg, Germany
| | - Marcin Sikorski
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Claudiu A Stan
- Physics Department, Rutgers University Newark, Newark, NJ, 07102, USA
| | - Xintian Shi
- Paul Scherrer Institut, Forschungsstrasse 111, 5232, Villigen, Switzerland
| | - Stephan Stern
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Janusz Szuba
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Aleksandra Tolstikova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Martin Trebbin
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Department of Chemistry, University at Buffalo, 359 Natural Sciences Complex, Buffalo, NY, 14260, USA
- Institute of Nanostructure and Solid State Physics, Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Ulrich Trunk
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Patrik Vagovic
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Thomas Ve
- Institute for Glycomics, Griffith University, Southport, QLD, 4222, Australia
| | | | - Thomas A White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Krzysztof Wrona
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Chen Xu
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Nadia Zatsepin
- Department of Physics, Arizona State University, Tempe, AZ, 85287, USA
| | - Jiaguo Zhang
- Paul Scherrer Institut, Forschungsstrasse 111, 5232, Villigen, Switzerland
| | - Markus Perbandt
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Notkestrasse 85, 22607, Hamburg, Germany
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246, Hamburg, Germany
| | | | - Christian Betzel
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Notkestrasse 85, 22607, Hamburg, Germany
- Integrated Biology Infrastructure Life-Science Facility at the European XFEL (XBI), Holzkoppel 4, 22869, Schenefeld, Germany
| | - Henry Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.
| |
Collapse
|
30
|
Birch J, Axford D, Foadi J, Meyer A, Eckhardt A, Thielmann Y, Moraes I. The fine art of integral membrane protein crystallisation. Methods 2018; 147:150-162. [PMID: 29778646 DOI: 10.1016/j.ymeth.2018.05.014] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 05/13/2018] [Accepted: 05/15/2018] [Indexed: 11/29/2022] Open
Abstract
Integral membrane proteins are among the most fascinating and important biomolecules as they play a vital role in many biological functions. Knowledge of their atomic structures is fundamental to the understanding of their biochemical function and key in many drug discovery programs. However, over the years, structure determination of integral membrane proteins has proven to be far from trivial, hence they are underrepresented in the protein data bank. Low expression levels, insolubility and instability are just a few of the many hurdles one faces when studying these proteins. X-ray crystallography has been the most used method to determine atomic structures of membrane proteins. However, the production of high quality membrane protein crystals is always very challenging, often seen more as art than a rational experiment. Here we review valuable approaches, methods and techniques to successful membrane protein crystallisation.
Collapse
Affiliation(s)
- James Birch
- Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Danny Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE, UK
| | - James Foadi
- Department of Mathematical Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Arne Meyer
- XtalConcepts GmbH, Schnackenburgallee 13, 22525 Hamburg, Germany
| | - Annette Eckhardt
- XtalConcepts GmbH, Schnackenburgallee 13, 22525 Hamburg, Germany
| | - Yvonne Thielmann
- Max Planck Institute of Biophysics, Molecular Membrane Biology, Max-von-Laue-Strasse 3, 60438 Frankfurt, Germany
| | - Isabel Moraes
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK; Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE, UK; National Physical Laboratory, Hampton Road, Teddington TW11 0LW, UK.
| |
Collapse
|
31
|
Affiliation(s)
- Max T. B. Clabbers
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Basel, Switzerland
| | - Jan Pieter Abrahams
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Basel, Switzerland
- Department of Biology and Chemistry, Paul Scherrer Institute (PSI), Villigen PSI, Switzerland
- Institute of Biology Leiden (IBL), Leiden, Netherlands
| |
Collapse
|
32
|
Cheng RKY, Abela R, Hennig M. X-ray free electron laser: opportunities for drug discovery. Essays Biochem 2017; 61:529-42. [PMID: 29118098 DOI: 10.1042/EBC20170031] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/02/2017] [Accepted: 10/03/2017] [Indexed: 01/16/2023]
Abstract
Past decades have shown the impact of structural information derived from complexes of drug candidates with their protein targets to facilitate the discovery of safe and effective medicines. Despite recent developments in single particle cryo-electron microscopy, X-ray crystallography has been the main method to derive structural information. The unique properties of X-ray free electron laser (XFEL) with unmet peak brilliance and beam focus allow X-ray diffraction data recording and successful structure determination from smaller and weaker diffracting crystals shortening timelines in crystal optimization. To further capitalize on the XFEL advantage, innovations in crystal sample delivery for the X-ray experiment, data collection and processing methods are required. This development was a key contributor to serial crystallography allowing structure determination at room temperature yielding physiologically more relevant structures. Adding the time resolution provided by the femtosecond X-ray pulse will enable monitoring and capturing of dynamic processes of ligand binding and associated conformational changes with great impact to the design of candidate drug compounds.
Collapse
|
33
|
Beyerlein KR, Dierksmeyer D, Mariani V, Kuhn M, Sarrou I, Ottaviano A, Awel S, Knoska J, Fuglerud S, Jönsson O, Stern S, Wiedorn MO, Yefanov O, Adriano L, Bean R, Burkhardt A, Fischer P, Heymann M, Horke DA, Jungnickel KEJ, Kovaleva E, Lorbeer O, Metz M, Meyer J, Morgan A, Pande K, Panneerselvam S, Seuring C, Tolstikova A, Lieske J, Aplin S, Roessle M, White TA, Chapman HN, Meents A, Oberthuer D. Mix-and-diffuse serial synchrotron crystallography. IUCrJ 2017; 4:769-777. [PMID: 29123679 PMCID: PMC5668862 DOI: 10.1107/s2052252517013124] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 09/13/2017] [Indexed: 05/21/2023]
Abstract
Unravelling the interaction of biological macromolecules with ligands and substrates at high spatial and temporal resolution remains a major challenge in structural biology. The development of serial crystallography methods at X-ray free-electron lasers and subsequently at synchrotron light sources allows new approaches to tackle this challenge. Here, a new polyimide tape drive designed for mix-and-diffuse serial crystallography experiments is reported. The structure of lysozyme bound by the competitive inhibitor chitotriose was determined using this device in combination with microfluidic mixers. The electron densities obtained from mixing times of 2 and 50 s show clear binding of chitotriose to the enzyme at a high level of detail. The success of this approach shows the potential for high-throughput drug screening and even structural enzymology on short timescales at bright synchrotron light sources.
Collapse
Affiliation(s)
- Kenneth R. Beyerlein
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Correspondence e-mail: ,
| | | | - Valerio Mariani
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Manuela Kuhn
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Iosifina Sarrou
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Angelica Ottaviano
- Department of Physics, California State University, Northridge, California, USA
| | - Salah Awel
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany
| | - Juraj Knoska
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, 22607 Hamburg, Germany
| | - Silje Fuglerud
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics, Norwegian University of Science and Technology, Trondheim, Norway
| | - Olof Jönsson
- Department of Physics and Astronomy, Uppsala University, Uppsala, Sweden
| | - Stephan Stern
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- European X-ray Free-Electron Laser Facility GmbH (XFEL), Schenefeld, Germany
| | - Max O. Wiedorn
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, 22607 Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Luigi Adriano
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Richard Bean
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Anja Burkhardt
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Pontus Fischer
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Michael Heymann
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Daniel A. Horke
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany
| | | | - Elena Kovaleva
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Olga Lorbeer
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Markus Metz
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Jan Meyer
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Andrew Morgan
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Kanupriya Pande
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Carolin Seuring
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany
| | - Aleksandra Tolstikova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Julia Lieske
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Steve Aplin
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Thomas A. White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Henry N. Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, 22607 Hamburg, Germany
| | - Alke Meents
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Dominik Oberthuer
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Correspondence e-mail: ,
| |
Collapse
|
34
|
Abstract
Macromolecular crystallography was immensely successful in the last two decades. To a large degree this success resulted from use of powerful third generation synchrotron X-ray sources. An expansive database of more than 100,000 protein structures, of which many were determined at resolution better than 2 Å, is available today. With this achievement, the spotlight in structural biology is shifting from determination of static structures to elucidating dynamic aspects of protein function. A powerful tool for addressing these aspects is time-resolved crystallography, where a genuine biological function is triggered in the crystal with a goal of capturing molecules in action and determining protein kinetics and structures of intermediates (Schmidt et al., 2005a; Schmidt 2008; Neutze and Moffat, 2012; Šrajer 2014). In this approach, short and intense X-ray pulses are used to probe intermediates in real time and at room temperature, in an ongoing reaction that is initiated synchronously and rapidly in the crystal. Time-resolved macromolecular crystallography with 100 ps time resolution at synchrotron X-ray sources is in its mature phase today, particularly for studies of reversible, light-initiated reactions. The advent of the new free electron lasers for hard X-rays (XFELs; 5-20 keV), which provide exceptionally intense, femtosecond X-ray pulses, marks a new frontier for time-resolved crystallography. The exploration of ultra-fast events becomes possible in high-resolution structural detail, on sub-picosecond time scales (Tenboer et al., 2014; Barends et al., 2015; Pande et al., 2016). We review here state-of-the-art time-resolved crystallographic experiments both at synchrotrons and XFELs. We also outline challenges and further developments necessary to broaden the application of these methods to many important proteins and enzymes of biomedical relevance.
Collapse
Affiliation(s)
- Vukica Šrajer
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, IL, USA
| | - Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, IL, USA
| |
Collapse
|
35
|
Coquelle N, Sliwa M, Woodhouse J, Schirò G, Adam V, Aquila A, Barends TRM, Boutet S, Byrdin M, Carbajo S, De la Mora E, Doak RB, Feliks M, Fieschi F, Foucar L, Guillon V, Hilpert M, Hunter MS, Jakobs S, Koglin JE, Kovacsova G, Lane TJ, Lévy B, Liang M, Nass K, Ridard J, Robinson JS, Roome CM, Ruckebusch C, Seaberg M, Thepaut M, Cammarata M, Demachy I, Field M, Shoeman RL, Bourgeois D, Colletier JP, Schlichting I, Weik M. Chromophore twisting in the excited state of a photoswitchable fluorescent protein captured by time-resolved serial femtosecond crystallography. Nat Chem 2018; 10:31-7. [PMID: 29256511 DOI: 10.1038/nchem.2853] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 07/27/2017] [Indexed: 12/23/2022]
Abstract
Chromophores absorb light in photosensitive proteins and thereby initiate fundamental biological processes such as photosynthesis, vision and biofluorescence. An important goal in their understanding is the provision of detailed structural descriptions of the ultrafast photochemical events that they undergo, in particular of the excited states that connect chemistry to biological function. Here we report on the structures of two excited states in the reversibly photoswitchable fluorescent protein rsEGFP2. We populated the states through femtosecond illumination of rsEGFP2 in its non-fluorescent off state and observed their build-up (within less than one picosecond) and decay (on the several picosecond timescale). Using an X-ray free-electron laser, we performed picosecond time-resolved crystallography and show that the hydroxybenzylidene imidazolinone chromophore in one of the excited states assumes a near-canonical twisted configuration halfway between the trans and cis isomers. This is in line with excited-state quantum mechanics/molecular mechanics and classical molecular dynamics simulations. Our new understanding of the structure around the twisted chromophore enabled the design of a mutant that displays a twofold increase in its off-to-on photoswitching quantum yield.
Collapse
|
36
|
Ryan RA, Williams S, Martin AV, Dilanian RA, Darmanin C, Putkunz CT, Wood D, Streltsov VA, Jones MWM, Gaffney N, Hofmann F, Williams GJ, Boutet S, Messerschmidt M, Seibert MM, Curwood EK, Balaur E, Peele AG, Nugent KA, Quiney HM, Abbey B. Measurements of Long-range Electronic Correlations During Femtosecond Diffraction Experiments Performed on Nanocrystals of Buckminsterfullerene. J Vis Exp 2017. [PMID: 28872125 PMCID: PMC5614354 DOI: 10.3791/56296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The precise details of the interaction of intense X-ray pulses with matter are a topic of intense interest to researchers attempting to interpret the results of femtosecond X-ray free electron laser (XFEL) experiments. An increasing number of experimental observations have shown that although nuclear motion can be negligible, given a short enough incident pulse duration, electronic motion cannot be ignored. The current and widely accepted models assume that although electrons undergo dynamics driven by interaction with the pulse, their motion could largely be considered 'random'. This would then allow the supposedly incoherent contribution from the electronic motion to be treated as a continuous background signal and thus ignored. The original aim of our experiment was to precisely measure the change in intensity of individual Bragg peaks, due to X-ray induced electronic damage in a model system, crystalline C60. Contrary to this expectation, we observed that at the highest X-ray intensities, the electron dynamics in C60 were in fact highly correlated, and over sufficiently long distances that the positions of the Bragg reflections are significantly altered. This paper describes in detail the methods and protocols used for these experiments, which were conducted both at the Linac Coherent Light Source (LCLS) and the Australian Synchrotron (AS) as well as the crystallographic approaches used to analyse the data.
Collapse
Affiliation(s)
- Rebecca A Ryan
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne
| | - Sophie Williams
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne
| | - Andrew V Martin
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne
| | - Ruben A Dilanian
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne
| | - Connie Darmanin
- Australian Research Council (ARC) Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Sciences, La Trobe University
| | - Corey T Putkunz
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne
| | - David Wood
- Department of Physics, Imperial College London
| | | | - Michael W M Jones
- Science and Engineering Faculty, Queensland University of Technology
| | | | - Felix Hofmann
- Department of Engineering Science, University of Oxford
| | | | - Sebastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory
| | | | - M Marvin Seibert
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University
| | - Evan K Curwood
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University
| | - Eugeniu Balaur
- Australian Research Council (ARC) Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Sciences, La Trobe University
| | - Andrew G Peele
- Science and Engineering Faculty, Queensland University of Technology
| | - Keith A Nugent
- Australian Research Council (ARC) Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Sciences, La Trobe University
| | - Harry M Quiney
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne;
| | - Brian Abbey
- Australian Research Council (ARC) Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Sciences, La Trobe University;
| |
Collapse
|
37
|
Mylona A, Carr S, Aller P, Moraes I, Treisman R, Evans G, Foadi J. A Novel Approach to Data Collection for Difficult Structures: Data Management for Large Numbers of Crystals with the BLEND Software. Crystals (Basel) 2017; 7:242. [PMID: 29456874 PMCID: PMC5813789 DOI: 10.3390/cryst7080242] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The present article describes how to use the computer program BLEND to help assemble complete datasets for the solution of macromolecular structures, starting from partial or complete datasets, derived from data collection from multiple crystals. The program is demonstrated on more than two hundred X-ray diffraction datasets obtained from 50 crystals of a complex formed between the SRF transcription factor, its cognate DNA, and a peptide from the SRF cofactor MRTF-A. This structure is currently in the process of being fully solved. While full details of the structure are not yet available, the repeated application of BLEND on data from this structure, as they have become available, has made it possible to produce electron density maps clear enough to visualise the potential location of MRTF sequences.
Collapse
Affiliation(s)
- Anastasia Mylona
- Signalling and Transcription Laboratory, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Stephen Carr
- Research Complex at Harwell, Rutherford Appleton Laboratory, Oxford OX11 0FA, UK
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Pierre Aller
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Isabel Moraes
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Richard Treisman
- Signalling and Transcription Laboratory, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Gwyndaf Evans
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - James Foadi
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| |
Collapse
|
38
|
Dods R, Båth P, Arnlund D, Beyerlein KR, Nelson G, Liang M, Harimoorthy R, Berntsen P, Malmerberg E, Johansson L, Andersson R, Bosman R, Carbajo S, Claesson E, Conrad CE, Dahl P, Hammarin G, Hunter MS, Li C, Lisova S, Milathianaki D, Robinson J, Safari C, Sharma A, Williams G, Wickstrand C, Yefanov O, Davidsson J, DePonte DP, Barty A, Brändén G, Neutze R. From Macrocrystals to Microcrystals: A Strategy for Membrane Protein Serial Crystallography. Structure 2017; 25:1461-1468.e2. [PMID: 28781082 DOI: 10.1016/j.str.2017.07.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 06/19/2017] [Accepted: 07/06/2017] [Indexed: 01/13/2023]
Abstract
Serial protein crystallography was developed at X-ray free-electron lasers (XFELs) and is now also being applied at storage ring facilities. Robust strategies for the growth and optimization of microcrystals are needed to advance the field. Here we illustrate a generic strategy for recovering high-density homogeneous samples of microcrystals starting from conditions known to yield large (macro) crystals of the photosynthetic reaction center of Blastochloris viridis (RCvir). We first crushed these crystals prior to multiple rounds of microseeding. Each cycle of microseeding facilitated improvements in the RCvir serial femtosecond crystallography (SFX) structure from 3.3-Å to 2.4-Å resolution. This approach may allow known crystallization conditions for other proteins to be adapted to exploit novel scientific opportunities created by serial crystallography.
Collapse
Affiliation(s)
- Robert Dods
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Petra Båth
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - David Arnlund
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Kenneth R Beyerlein
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Garrett Nelson
- Department of Physics, Arizona State University, Tempe, AZ, USA
| | - Mengling Liang
- Linac Coherent Light Source, Stanford Linear Accelerator Center (SLAC) National Accelerator Laboratory, Menlo Park, CA, USA
| | - Rajiv Harimoorthy
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Peter Berntsen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3086, Australia
| | - Erik Malmerberg
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA
| | - Linda Johansson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden; The Bridge Institute, Department of Chemistry, University of Southern California, Los Angeles, CA 90089-3303, USA
| | - Rebecka Andersson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Robert Bosman
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Sergio Carbajo
- Linac Coherent Light Source, Stanford Linear Accelerator Center (SLAC) National Accelerator Laboratory, Menlo Park, CA, USA
| | - Elin Claesson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | | | - Peter Dahl
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Greger Hammarin
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Mark S Hunter
- Linac Coherent Light Source, Stanford Linear Accelerator Center (SLAC) National Accelerator Laboratory, Menlo Park, CA, USA
| | - Chufeng Li
- Department of Physics, Arizona State University, Tempe, AZ, USA
| | - Stella Lisova
- Department of Physics, Arizona State University, Tempe, AZ, USA
| | - Despina Milathianaki
- Linac Coherent Light Source, Stanford Linear Accelerator Center (SLAC) National Accelerator Laboratory, Menlo Park, CA, USA
| | - Joseph Robinson
- Linac Coherent Light Source, Stanford Linear Accelerator Center (SLAC) National Accelerator Laboratory, Menlo Park, CA, USA
| | - Cecilia Safari
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Amit Sharma
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Garth Williams
- Linac Coherent Light Source, Stanford Linear Accelerator Center (SLAC) National Accelerator Laboratory, Menlo Park, CA, USA
| | - Cecilia Wickstrand
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Jan Davidsson
- Department of Photochemistry and Molecular Science, Uppsala University, Uppsala, Sweden
| | - Daniel P DePonte
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Gisela Brändén
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.
| |
Collapse
|
39
|
Espinosa S, Zhang L, Li X, Zhao R. Understanding pre-mRNA splicing through crystallography. Methods 2017; 125:55-62. [PMID: 28506657 PMCID: PMC5546983 DOI: 10.1016/j.ymeth.2017.04.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 04/11/2017] [Accepted: 04/26/2017] [Indexed: 01/07/2023] Open
Abstract
Crystallography is a powerful tool to determine the atomic structures of proteins and RNAs. X-ray crystallography has been used to determine the structure of many splicing related proteins and RNAs, making major contributions to our understanding of the molecular mechanism and regulation of pre-mRNA splicing. Compared to other structural methods, crystallography has its own advantage in the high-resolution structural information it can provide and the unique biological questions it can answer. In addition, two new crystallographic methods - the serial femtosecond crystallography and 3D electron crystallography - were developed to overcome some of the limitations of traditional X-ray crystallography and broaden the range of biological problems that crystallography can solve. This review discusses the theoretical basis, instrument requirements, troubleshooting, and exciting potential of these crystallographic methods to further our understanding of pre-mRNA splicing, a critical event in gene expression of all eukaryotes.
Collapse
|
40
|
Abstract
Membrane proteins, including G protein-coupled receptors (GPCRs), constitute the most important drug targets. The increasing number of targets requires new structural information, which has proven tremendously challenging due to the difficulties in growing diffraction-quality crystals. Recent developments of serial femtosecond crystallography at X-ray free electron lasers combined with the use of membrane-mimetic gel-like matrix of lipidic cubic phase (LCP-SFX) for crystal growth and delivery hold significant promise to accelerate structural studies of membrane proteins. This chapter describes the development and current status of the LCP-SFX technology and elaborates its future role in structural biology of membrane proteins.
Collapse
Affiliation(s)
- Lan Zhu
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA.,Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University, Tempe, AZ, 85287-1604, USA
| | - Uwe Weierstall
- Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University, Tempe, AZ, 85287-1604, USA.,Department of Physics, Arizona State University, Tempe, AZ, 85287, USA
| | - Vadim Cherezov
- Bridge Institute, University of Southern California, Los Angeles, CA, 90089, USA.,Department of Chemistry, University of Southern California, Los Angeles, CA, 90089, USA
| | - Wei Liu
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA. .,Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University, Tempe, AZ, 85287-1604, USA.
| |
Collapse
|
41
|
Beyerlein KR, White TA, Yefanov O, Gati C, Kazantsev IG, Nielsen NFG, Larsen PM, Chapman HN, Schmidt S. FELIX: an algorithm for indexing multiple crystallites in X-ray free-electron laser snapshot diffraction images. J Appl Crystallogr 2017; 50:1075-1083. [PMID: 28808433 PMCID: PMC5541352 DOI: 10.1107/s1600576717007506] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 05/21/2017] [Indexed: 01/31/2023] Open
Abstract
The FELIX algorithm for indexing snaphot images containing multiple diffraction patterns is described and its performance is tested. A novel algorithm for indexing multiple crystals in snapshot X-ray diffraction images, especially suited for serial crystallography data, is presented. The algorithm, FELIX, utilizes a generalized parametrization of the Rodrigues–Frank space, in which all crystal systems can be represented without singularities. The new algorithm is shown to be capable of indexing more than ten crystals per image in simulations of cubic, tetragonal and monoclinic crystal diffraction patterns. It is also used to index an experimental serial crystallography dataset from lysozyme microcrystals. The increased number of indexed crystals is shown to result in a better signal-to-noise ratio, and fewer images are needed to achieve the same data quality as when indexing one crystal per image. The relative orientations between the multiple crystals indexed in an image show a slight tendency of the lysozme microcrystals to adhere on (10) facets.
Collapse
Affiliation(s)
- Kenneth R Beyerlein
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Thomas A White
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Cornelius Gati
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Ivan G Kazantsev
- Institute of Computational Mathematics and Mathematical Geophysics, Lavrentieva 6, 630090 Novosibirsk, Russian Federation
| | | | - Peter M Larsen
- Department of Physics, Technical University of Denmark, DK-2800, Denmark
| | - Henry N Chapman
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Søren Schmidt
- Department of Physics, Technical University of Denmark, DK-2800, Denmark
| |
Collapse
|
42
|
Martin-Garcia JM, Conrad CE, Nelson G, Stander N, Zatsepin NA, Zook J, Zhu L, Geiger J, Chun E, Kissick D, Hilgart MC, Ogata C, Ishchenko A, Nagaratnam N, Roy-Chowdhury S, Coe J, Subramanian G, Schaffer A, James D, Ketwala G, Venugopalan N, Xu S, Corcoran S, Ferguson D, Weierstall U, Spence JCH, Cherezov V, Fromme P, Fischetti RF, Liu W. Serial millisecond crystallography of membrane and soluble protein microcrystals using synchrotron radiation. IUCrJ 2017; 4:439-454. [PMID: 28875031 PMCID: PMC5571807 DOI: 10.1107/s205225251700570x] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 04/13/2017] [Indexed: 05/17/2023]
Abstract
Crystal structure determination of biological macromolecules using the novel technique of serial femtosecond crystallography (SFX) is severely limited by the scarcity of X-ray free-electron laser (XFEL) sources. However, recent and future upgrades render microfocus beamlines at synchrotron-radiation sources suitable for room-temperature serial crystallography data collection also. Owing to the longer exposure times that are needed at synchrotrons, serial data collection is termed serial millisecond crystallography (SMX). As a result, the number of SMX experiments is growing rapidly, with a dozen experiments reported so far. Here, the first high-viscosity injector-based SMX experiments carried out at a US synchrotron source, the Advanced Photon Source (APS), are reported. Microcrystals (5-20 µm) of a wide variety of proteins, including lysozyme, thaumatin, phycocyanin, the human A2A adenosine receptor (A2AAR), the soluble fragment of the membrane lipoprotein Flpp3 and proteinase K, were screened. Crystals suspended in lipidic cubic phase (LCP) or a high-molecular-weight poly(ethylene oxide) (PEO; molecular weight 8 000 000) were delivered to the beam using a high-viscosity injector. In-house data-reduction (hit-finding) software developed at APS as well as the SFX data-reduction and analysis software suites Cheetah and CrystFEL enabled efficient on-site SMX data monitoring, reduction and processing. Complete data sets were collected for A2AAR, phycocyanin, Flpp3, proteinase K and lysozyme, and the structures of A2AAR, phycocyanin, proteinase K and lysozyme were determined at 3.2, 3.1, 2.65 and 2.05 Å resolution, respectively. The data demonstrate the feasibility of serial millisecond crystallography from 5-20 µm crystals using a high-viscosity injector at APS. The resolution of the crystal structures obtained in this study was dictated by the current flux density and crystal size, but upcoming developments in beamline optics and the planned APS-U upgrade will increase the intensity by two orders of magnitude. These developments will enable structure determination from smaller and/or weakly diffracting microcrystals.
Collapse
Affiliation(s)
- Jose M. Martin-Garcia
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Chelsie E. Conrad
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Garrett Nelson
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, PO Box 871504, Tempe, AZ 85287, USA
| | - Natasha Stander
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, PO Box 871504, Tempe, AZ 85287, USA
| | - Nadia A. Zatsepin
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, PO Box 871504, Tempe, AZ 85287, USA
| | - James Zook
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Lan Zhu
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - James Geiger
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Eugene Chun
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - David Kissick
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Mark C. Hilgart
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Craig Ogata
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Andrii Ishchenko
- Department of Chemistry, Bridge Institute, University of Southern California, 3430 South Vermont Avenue, MC 3303, Los Angeles, CA 90089, USA
| | - Nirupa Nagaratnam
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Shatabdi Roy-Chowdhury
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Jesse Coe
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Ganesh Subramanian
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, PO Box 871504, Tempe, AZ 85287, USA
| | - Alexander Schaffer
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Daniel James
- Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Gihan Ketwala
- Department of Physics, Arizona State University, PO Box 871504, Tempe, AZ 85287, USA
| | - Nagarajan Venugopalan
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Shenglan Xu
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Stephen Corcoran
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Dale Ferguson
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Uwe Weierstall
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, PO Box 871504, Tempe, AZ 85287, USA
| | - John C. H. Spence
- Department of Physics, Arizona State University, PO Box 871504, Tempe, AZ 85287, USA
| | - Vadim Cherezov
- Department of Chemistry, Bridge Institute, University of Southern California, 3430 South Vermont Avenue, MC 3303, Los Angeles, CA 90089, USA
| | - Petra Fromme
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Robert F. Fischetti
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Wei Liu
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| |
Collapse
|
43
|
Zhang X, Zhao F, Wu Y, Yang J, Han GW, Zhao S, Ishchenko A, Ye L, Lin X, Ding K, Dharmarajan V, Griffin PR, Gati C, Nelson G, Hunter MS, Hanson MA, Cherezov V, Stevens RC, Tan W, Tao H, Xu F. Crystal structure of a multi-domain human smoothened receptor in complex with a super stabilizing ligand. Nat Commun 2017; 8:15383. [PMID: 28513578 PMCID: PMC5442369 DOI: 10.1038/ncomms15383] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 03/24/2017] [Indexed: 02/06/2023] Open
Abstract
The Smoothened receptor (SMO) belongs to the Class Frizzled of the G protein-coupled receptor (GPCR) superfamily, constituting a key component of the Hedgehog signalling pathway. Here we report the crystal structure of the multi-domain human SMO, bound and stabilized by a designed tool ligand TC114, using an X-ray free-electron laser source at 2.9 Å. The structure reveals a precise arrangement of three distinct domains: a seven-transmembrane helices domain (TMD), a hinge domain (HD) and an intact extracellular cysteine-rich domain (CRD). This architecture enables allosteric interactions between the domains that are important for ligand recognition and receptor activation. By combining the structural data, molecular dynamics simulation, and hydrogen-deuterium-exchange analysis, we demonstrate that transmembrane helix VI, extracellular loop 3 and the HD play a central role in transmitting the signal employing a unique GPCR activation mechanism, distinct from other multi-domain GPCRs. Smoothened receptors (SMO) play a key role in the Hedgehog signalling pathway. Here the authors present the structure of a multi-domain human SMO with a rationally designed stabilizing ligand bound in the transmembrane domain of the receptor, and propose a model for SMO activation.
Collapse
Affiliation(s)
- Xianjun Zhang
- iHuman Institute, ShanghaiTech University, 2F Building 6, 99 Haike Road, Pudong New District, Shanghai 201210, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fei Zhao
- iHuman Institute, ShanghaiTech University, 2F Building 6, 99 Haike Road, Pudong New District, Shanghai 201210, China
| | - Yiran Wu
- iHuman Institute, ShanghaiTech University, 2F Building 6, 99 Haike Road, Pudong New District, Shanghai 201210, China
| | - Jun Yang
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Gye Won Han
- Departments of Chemistry, Biological Sciences and Physics &Astronomy, Bridge Institute, University of Southern California, Los Angeles, California 90089, USA
| | - Suwen Zhao
- iHuman Institute, ShanghaiTech University, 2F Building 6, 99 Haike Road, Pudong New District, Shanghai 201210, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Andrii Ishchenko
- Departments of Chemistry, Biological Sciences and Physics &Astronomy, Bridge Institute, University of Southern California, Los Angeles, California 90089, USA
| | - Lintao Ye
- iHuman Institute, ShanghaiTech University, 2F Building 6, 99 Haike Road, Pudong New District, Shanghai 201210, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,Shanghai Institute of Materia Medica, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 555 Zuchongzhi Lu, Building 3, Room 426, Shanghai 201203, China
| | - Xi Lin
- iHuman Institute, ShanghaiTech University, 2F Building 6, 99 Haike Road, Pudong New District, Shanghai 201210, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kang Ding
- iHuman Institute, ShanghaiTech University, 2F Building 6, 99 Haike Road, Pudong New District, Shanghai 201210, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | | | - Patrick R Griffin
- Department of Molecular Therapeutics, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, USA
| | - Cornelius Gati
- Medical Research Council, Laboratory of Molecular Biology, Cambridge, Biomedical Campus, Francis Crick Avenue, Cambridge CB2 OQH, UK
| | - Garrett Nelson
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | | | - Vadim Cherezov
- Departments of Chemistry, Biological Sciences and Physics &Astronomy, Bridge Institute, University of Southern California, Los Angeles, California 90089, USA
| | - Raymond C Stevens
- iHuman Institute, ShanghaiTech University, 2F Building 6, 99 Haike Road, Pudong New District, Shanghai 201210, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Wenfu Tan
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Houchao Tao
- iHuman Institute, ShanghaiTech University, 2F Building 6, 99 Haike Road, Pudong New District, Shanghai 201210, China
| | - Fei Xu
- iHuman Institute, ShanghaiTech University, 2F Building 6, 99 Haike Road, Pudong New District, Shanghai 201210, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| |
Collapse
|
44
|
Zhang H, Qiao A, Yang D, Yang L, Dai A, de Graaf C, Reedtz-Runge S, Dharmarajan V, Zhang H, Han GW, Grant TD, Sierra RG, Weierstall U, Nelson G, Liu W, Wu Y, Ma L, Cai X, Lin G, Wu X, Geng Z, Dong Y, Song G, Griffin PR, Lau J, Cherezov V, Yang H, Hanson MA, Stevens RC, Zhao Q, Jiang H, Wang MW, Wu B. Structure of the full-length glucagon class B G-protein-coupled receptor. Nature 2017; 546:259-64. [PMID: 28514451 DOI: 10.1038/nature22363] [Citation(s) in RCA: 155] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 04/12/2017] [Indexed: 12/19/2022]
Abstract
The human glucagon receptor, GCGR, belongs to the class B G-protein-coupled receptor family and plays a key role in glucose homeostasis and the pathophysiology of type 2 diabetes. Here we report the 3.0 Å crystal structure of full-length GCGR containing both the extracellular domain and transmembrane domain in an inactive conformation. The two domains are connected by a 12-residue segment termed the stalk, which adopts a β-strand conformation, instead of forming an α-helix as observed in the previously solved structure of the GCGR transmembrane domain. The first extracellular loop exhibits a β-hairpin conformation and interacts with the stalk to form a compact β-sheet structure. Hydrogen-deuterium exchange, disulfide crosslinking and molecular dynamics studies suggest that the stalk and the first extracellular loop have critical roles in modulating peptide ligand binding and receptor activation. These insights into the full-length GCGR structure deepen our understanding of the signalling mechanisms of class B G-protein-coupled receptors.
Collapse
|
45
|
Gati C, Oberthuer D, Yefanov O, Bunker RD, Stellato F, Chiu E, Yeh SM, Aquila A, Basu S, Bean R, Beyerlein KR, Botha S, Boutet S, DePonte DP, Doak RB, Fromme R, Galli L, Grotjohann I, James DR, Kupitz C, Lomb L, Messerschmidt M, Nass K, Rendek K, Shoeman RL, Wang D, Weierstall U, White TA, Williams GJ, Zatsepin NA, Fromme P, Spence JC, Goldie KN, Jehle JA, Metcalf P, Barty A, Chapman HN. Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser. Proc Natl Acad Sci U S A 2017; 114:2247-52. [PMID: 28202732 DOI: 10.1073/pnas.1609243114] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To understand how molecules function in biological systems, new methods are required to obtain atomic resolution structures from biological material under physiological conditions. Intense femtosecond-duration pulses from X-ray free-electron lasers (XFELs) can outrun most damage processes, vastly increasing the tolerable dose before the specimen is destroyed. This in turn allows structure determination from crystals much smaller and more radiation sensitive than previously considered possible, allowing data collection from room temperature structures and avoiding structural changes due to cooling. Regardless, high-resolution structures obtained from XFEL data mostly use crystals far larger than 1 μm3 in volume, whereas the X-ray beam is often attenuated to protect the detector from damage caused by intense Bragg spots. Here, we describe the 2 Å resolution structure of native nanocrystalline granulovirus occlusion bodies (OBs) that are less than 0.016 μm3 in volume using the full power of the Linac Coherent Light Source (LCLS) and a dose up to 1.3 GGy per crystal. The crystalline shell of granulovirus OBs consists, on average, of about 9,000 unit cells, representing the smallest protein crystals to yield a high-resolution structure by X-ray crystallography to date. The XFEL structure shows little to no evidence of radiation damage and is more complete than a model determined using synchrotron data from recombinantly produced, much larger, cryocooled granulovirus granulin microcrystals. Our measurements suggest that it should be possible, under ideal experimental conditions, to obtain data from protein crystals with only 100 unit cells in volume using currently available XFELs and suggest that single-molecule imaging of individual biomolecules could almost be within reach.
Collapse
|
46
|
Abstract
The intense X-ray pulses from free-electron lasers, of only femtoseconds duration, outrun most of the processes that lead to structural degradation in X-ray exposures of macromolecules. Using these sources it is therefore possible to increase the dose to macromolecular crystals by several orders of magnitude higher than usually tolerable in conventional measurements, allowing crystal size to be decreased dramatically in diffraction measurements and without the need to cool the sample. Such pulses lead to the eventual vaporization of the sample, which has required a measurement approach, called serial crystallography, of consolidating snapshot diffraction patterns of many individual crystals. This in turn has further separated the connection between dose and obtainable diffraction information, with the only requirement from a single pattern being that to give enough information to place it, in three-dimensional reciprocal space, in relation to other patterns. Millions of extremely weak patterns can be collected and combined in this way, requiring methods to rapidly replenish the sample into the beam while generating the lowest possible background . The method is suited to time-resolved measurements over timescales below 1 ps to several seconds, and opens new opportunities for phasing. Some straightforward considerations of achievable signal levels are discussed and compared with a wide variety of recent experiments carried out at XFEL, synchrotron, and even laboratory sources, to discuss the capabilities of these new approaches and give some perspectives on their further development.
Collapse
Affiliation(s)
- Henry N Chapman
- Center for Free-Electron Laser Science, DESY, Hamburg, 22607, Germany.
- Department of Physics, University of Hamburg, Hamburg, 22607, Germany.
- The Centre for Ultrafast Imaging, University of Hamburg, Hamburg, 22607, Germany.
| |
Collapse
|
47
|
Nango E, Royant A, Kubo M, Nakane T, Wickstrand C, Kimura T, Tanaka T, Tono K, Song C, Tanaka R, Arima T, Yamashita A, Kobayashi J, Hosaka T, Mizohata E, Nogly P, Sugahara M, Nam D, Nomura T, Shimamura T, Im D, Fujiwara T, Yamanaka Y, Jeon B, Nishizawa T, Oda K, Fukuda M, Andersson R, Båth P, Dods R, Davidsson J, Matsuoka S, Kawatake S, Murata M, Nureki O, Owada S, Kameshima T, Hatsui T, Joti Y, Schertler G, Yabashi M, Bondar AN, Standfuss J, Neutze R, Iwata S. A three-dimensional movie of structural changes in bacteriorhodopsin. Science 2016; 354:1552-1557. [DOI: 10.1126/science.aah3497] [Citation(s) in RCA: 294] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 11/21/2016] [Indexed: 01/24/2023]
|
48
|
Stagno JR, Liu Y, Bhandari YR, Conrad CE, Panja S, Swain M, Fan L, Nelson G, Li C, Wendel DR, White TA, Coe JD, Wiedorn MO, Knoska J, Oberthuer D, Tuckey RA, Yu P, Dyba M, Tarasov SG, Weierstall U, Grant TD, Schwieters CD, Zhang J, Ferré-D'Amaré AR, Fromme P, Draper DE, Liang M, Hunter MS, Boutet S, Tan K, Zuo X, Ji X, Barty A, Zatsepin NA, Chapman HN, Spence JC, Woodson SA, Wang YX. Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography. Nature 2017; 541:242-6. [PMID: 27841871 DOI: 10.1038/nature20599] [Citation(s) in RCA: 207] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 11/04/2016] [Indexed: 12/27/2022]
Abstract
Riboswitches are structural RNA elements that are generally located in the 5' untranslated region of messenger RNA. During regulation of gene expression, ligand binding to the aptamer domain of a riboswitch triggers a signal to the downstream expression platform. A complete understanding of the structural basis of this mechanism requires the ability to study structural changes over time. Here we use femtosecond X-ray free electron laser (XFEL) pulses to obtain structural measurements from crystals so small that diffusion of a ligand can be timed to initiate a reaction before diffraction. We demonstrate this approach by determining four structures of the adenine riboswitch aptamer domain during the course of a reaction, involving two unbound apo structures, one ligand-bound intermediate, and the final ligand-bound conformation. These structures support a reaction mechanism model with at least four states and illustrate the structural basis of signal transmission. The three-way junction and the P1 switch helix of the two apo conformers are notably different from those in the ligand-bound conformation. Our time-resolved crystallographic measurements with a 10-second delay captured the structure of an intermediate with changes in the binding pocket that accommodate the ligand. With at least a 10-minute delay, the RNA molecules were fully converted to the ligand-bound state, in which the substantial conformational changes resulted in conversion of the space group. Such notable changes in crystallo highlight the important opportunities that micro- and nanocrystals may offer in these and similar time-resolved diffraction studies. Together, these results demonstrate the potential of 'mix-and-inject' time-resolved serial crystallography to study biochemically important interactions between biomacromolecules and ligands, including those that involve large conformational changes.
Collapse
|
49
|
Nakane T, Hanashima S, Suzuki M, Saiki H, Hayashi T, Kakinouchi K, Sugiyama S, Kawatake S, Matsuoka S, Matsumori N, Nango E, Kobayashi J, Shimamura T, Kimura K, Mori C, Kunishima N, Sugahara M, Takakyu Y, Inoue S, Masuda T, Hosaka T, Tono K, Joti Y, Kameshima T, Hatsui T, Yabashi M, Inoue T, Nureki O, Iwata S, Murata M, Mizohata E. Membrane protein structure determination by SAD, SIR, or SIRAS phasing in serial femtosecond crystallography using an iododetergent. Proc Natl Acad Sci U S A 2016; 113:13039-44. [PMID: 27799539 DOI: 10.1073/pnas.1602531113] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The 3D structure determination of biological macromolecules by X-ray crystallography suffers from a phase problem: to perform Fourier transformation to calculate real space density maps, both intensities and phases of structure factors are necessary; however, measured diffraction patterns give only intensities. Although serial femtosecond crystallography (SFX) using X-ray free electron lasers (XFELs) has been steadily developed since 2009, experimental phasing still remains challenging. Here, using 7.0-keV (1.771 Å) X-ray pulses from the SPring-8 Angstrom Compact Free Electron Laser (SACLA), iodine single-wavelength anomalous diffraction (SAD), single isomorphous replacement (SIR), and single isomorphous replacement with anomalous scattering (SIRAS) phasing were performed in an SFX regime for a model membrane protein bacteriorhodopsin (bR). The crystals grown in bicelles were derivatized with an iodine-labeled detergent heavy-atom additive 13a (HAD13a), which contains the magic triangle, I3C head group with three iodine atoms. The alkyl tail was essential for binding of the detergent to the surface of bR. Strong anomalous and isomorphous difference signals from HAD13a enabled successful phasing using reflections up to 2.1-Å resolution from only 3,000 and 4,000 indexed images from native and derivative crystals, respectively. When more images were merged, structure solution was possible with data truncated at 3.3-Å resolution, which is the lowest resolution among the reported cases of SFX phasing. Moreover, preliminary SFX experiment showed that HAD13a successfully derivatized the G protein-coupled A2a adenosine receptor crystallized in lipidic cubic phases. These results pave the way for de novo structure determination of membrane proteins, which often diffract poorly, even with the brightest XFEL beams.
Collapse
|
50
|
Barty A. Single molecule imaging using X-ray free electron lasers. Curr Opin Struct Biol 2016; 40:186-94. [DOI: 10.1016/j.sbi.2016.11.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 11/21/2016] [Accepted: 11/21/2016] [Indexed: 02/02/2023]
|