51
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Liu S, Hattne J, Reyes FE, Sanchez-Martinez S, Jason de la Cruz M, Shi D, Gonen T. Atomic resolution structure determination by the cryo-EM method MicroED. Protein Sci 2016; 26:8-15. [PMID: 27452773 DOI: 10.1002/pro.2989] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 07/18/2016] [Accepted: 07/19/2016] [Indexed: 12/21/2022]
Abstract
The electron cryo-microscopy (cryoEM) method MicroED has been rapidly developing. In this review we highlight some of the key steps in MicroED from crystal analysis to structure determination. We compare and contrast MicroED and the latest X-ray based diffraction method the X-ray free-electron laser (XFEL). Strengths and shortcomings of both MicroED and XFEL are discussed. Finally, all current MicroED structures are tabulated with a view to the future.
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Affiliation(s)
- Shian Liu
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia, 20148
| | - Johan Hattne
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia, 20148
| | - Francis E Reyes
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia, 20148
| | - Silvia Sanchez-Martinez
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia, 20148
| | - M Jason de la Cruz
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia, 20148
| | - Dan Shi
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia, 20148
| | - Tamir Gonen
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia, 20148
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52
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Ginn HM, Evans G, Sauter NK, Stuart DI. On the release of cppxfel for processing X-ray free-electron laser images. J Appl Crystallogr 2016; 49:1065-1072. [PMID: 27275149 PMCID: PMC4886992 DOI: 10.1107/s1600576716006981] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 04/25/2016] [Indexed: 12/21/2022] Open
Abstract
As serial femtosecond crystallography expands towards a variety of delivery methods, including chip-based methods, and smaller collected data sets, the requirement to optimize the data analysis to produce maximum structure quality is becoming increasingly pressing. Here cppxfel, a software package primarily written in C++, which showcases several data analysis techniques, is released. This software package presently indexes images using DIALS (diffraction integration for advanced light sources) and performs an initial orientation matrix refinement, followed by post-refinement of individual images against a reference data set. Cppxfel is released with the hope that the unique and useful elements of this package can be repurposed for existing software packages. However, as released, it produces high-quality crystal structures and is therefore likely to be also useful to experienced users of X-ray free-electron laser (XFEL) software who wish to maximize the information extracted from a limited number of XFEL images.
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Affiliation(s)
- Helen Mary Ginn
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, UK
| | - Gwyndaf Evans
- Diamond House, Harwell Science and Innovation Campus, Fermi Avenue, Didcot, Oxfordshire OX11 QX, UK
| | - Nicholas K. Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - David Ian Stuart
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, UK
- Diamond House, Harwell Science and Innovation Campus, Fermi Avenue, Didcot, Oxfordshire OX11 QX, UK
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53
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Nakane T, Joti Y, Tono K, Yabashi M, Nango E, Iwata S, Ishitani R, Nureki O. Data processing pipeline for serial femtosecond crystallography at SACLA. J Appl Crystallogr 2016; 49:1035-1041. [PMID: 27275146 PMCID: PMC4886989 DOI: 10.1107/s1600576716005720] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 04/06/2016] [Indexed: 11/10/2022] Open
Abstract
A data processing pipeline for serial femtosecond crystallography at SACLA was developed, based on Cheetah [Barty et al. (2014). J. Appl. Cryst.47, 1118-1131] and CrystFEL [White et al. (2016). J. Appl. Cryst.49, 680-689]. The original programs were adapted for data acquisition through the SACLA API, thread and inter-node parallelization, and efficient image handling. The pipeline consists of two stages: The first, online stage can analyse all images in real time, with a latency of less than a few seconds, to provide feedback on hit rate and detector saturation. The second, offline stage converts hit images into HDF5 files and runs CrystFEL for indexing and integration. The size of the filtered compressed output is comparable to that of a synchrotron data set. The pipeline enables real-time feedback and rapid structure solution during beamtime.
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Affiliation(s)
- Takanori Nakane
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo, Tokyo 113-0032, Japan
| | - Yasumasa Joti
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
| | - Makina Yabashi
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
| | - Eriko Nango
- 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
| | - Ryuichiro Ishitani
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo, Tokyo 113-0032, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo, Tokyo 113-0032, Japan
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54
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Martin-Garcia JM, Conrad CE, Coe J, Roy-Chowdhury S, Fromme P. Serial femtosecond crystallography: A revolution in structural biology. Arch Biochem Biophys 2016; 602:32-47. [PMID: 27143509 DOI: 10.1016/j.abb.2016.03.036] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 03/16/2016] [Accepted: 03/21/2016] [Indexed: 10/21/2022]
Abstract
Macromolecular crystallography at synchrotron sources has proven to be the most influential method within structural biology, producing thousands of structures since its inception. While its utility has been instrumental in progressing our knowledge of structures of molecules, it suffers from limitations such as the need for large, well-diffracting crystals, and radiation damage that can hamper native structural determination. The recent advent of X-ray free electron lasers (XFELs) and their implementation in the emerging field of serial femtosecond crystallography (SFX) has given rise to a remarkable expansion upon existing crystallographic constraints, allowing structural biologists access to previously restricted scientific territory. SFX relies on exceptionally brilliant, micro-focused X-ray pulses, which are femtoseconds in duration, to probe nano/micrometer sized crystals in a serial fashion. This results in data sets comprised of individual snapshots, each capturing Bragg diffraction of single crystals in random orientations prior to their subsequent destruction. Thus structural elucidation while avoiding radiation damage, even at room temperature, can now be achieved. This emerging field has cultivated new methods for nanocrystallogenesis, sample delivery, and data processing. Opportunities and challenges within SFX are reviewed herein.
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Affiliation(s)
- Jose M Martin-Garcia
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Chelsie E Conrad
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Jesse Coe
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Shatabdi Roy-Chowdhury
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Petra Fromme
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA.
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55
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Zhou XE, Gao X, Barty A, Kang Y, He Y, Liu W, Ishchenko A, White TA, Yefanov O, Han GW, Xu Q, de Waal PW, Suino-Powell KM, Boutet S, Williams GJ, Wang M, Li D, Caffrey M, Chapman HN, Spence JCH, Fromme P, Weierstall U, Stevens RC, Cherezov V, Melcher K, Xu HE. X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex. Sci Data 2016; 3:160021. [PMID: 27070998 PMCID: PMC4828943 DOI: 10.1038/sdata.2016.21] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 02/25/2016] [Indexed: 01/01/2023] Open
Abstract
Serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solved with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.
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Affiliation(s)
- X Edward Zhou
- Laboratory of Structural Sciences, Center for Structural Biology and Drug Discovery, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA
| | - Xiang Gao
- Laboratory of Structural Sciences, Center for Structural Biology and Drug Discovery, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA
| | - Anton Barty
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Yanyong Kang
- Laboratory of Structural Sciences, Center for Structural Biology and Drug Discovery, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA
| | - Yuanzheng He
- Laboratory of Structural Sciences, Center for Structural Biology and Drug Discovery, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA
| | - Wei Liu
- School of Molecular Sciences, and Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona 85287-1604, USA
| | - Andrii Ishchenko
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, California 90089, USA
| | - Thomas A White
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Gye Won Han
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, California 90089, USA.,Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, California 90089, USA
| | - Qingping Xu
- Joint Center for Structural Genomics, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Parker W de Waal
- Laboratory of Structural Sciences, Center for Structural Biology and Drug Discovery, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA
| | - Kelly M Suino-Powell
- Laboratory of Structural Sciences, Center for Structural Biology and Drug Discovery, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA
| | - Sébastien Boutet
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Garth J Williams
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Meitian Wang
- Swiss Light Source at Paul Scherrer Institute, CH-5232 Villigen, Switzerland
| | - Dianfan Li
- School of Medicine and School of Biochemistry and Immunology, Trinity College, Dublin D02 R590, Ireland
| | - Martin Caffrey
- School of Medicine and School of Biochemistry and Immunology, Trinity College, Dublin D02 R590, Ireland
| | - Henry N Chapman
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany.,Centre for Ultrafast Imaging, 22761 Hamburg, Germany
| | - John C H Spence
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany.,Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
| | - Petra Fromme
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Uwe Weierstall
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany.,Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
| | - Raymond C Stevens
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, California 90089, USA.,Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, California 90089, USA.,iHuman Institute, Shanghai Tech University, 2F Building 6, 99 Haike Road, Pudong New District, Shanghai 201210, China
| | - Vadim Cherezov
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, California 90089, USA
| | - Karsten Melcher
- Laboratory of Structural Sciences, Center for Structural Biology and Drug Discovery, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA
| | - H Eric Xu
- Laboratory of Structural Sciences, Center for Structural Biology and Drug Discovery, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA.,VARI-SIMM Center, Center for Structure and Function of Drug Targets, CAS-Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
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56
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White TA, Mariani V, Brehm W, Yefanov O, Barty A, Beyerlein KR, Chervinskii F, Galli L, Gati C, Nakane T, Tolstikova A, Yamashita K, Yoon CH, Diederichs K, Chapman HN. Recent developments in CrystFEL. J Appl Crystallogr 2016; 49:680-689. [PMID: 27047311 PMCID: PMC4815879 DOI: 10.1107/s1600576716004751] [Citation(s) in RCA: 179] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 03/21/2016] [Indexed: 12/04/2022] Open
Abstract
CrystFEL is a suite of programs for processing data from 'serial crystallography' experiments, which are usually performed using X-ray free-electron lasers (FELs) but also increasingly with other X-ray sources. The CrystFEL software suite has been under development since 2009, just before the first hard FEL experiments were performed, and has been significantly updated and improved since then. This article describes the most important improvements which have been made to CrystFEL since the first release version. These changes include the addition of new programs to the suite, the ability to resolve 'indexing ambiguities' and several ways to improve the quality of the integrated data by more accurately modelling the underlying diffraction physics.
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Affiliation(s)
- Thomas A. White
- Centre for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Valerio Mariani
- Centre for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Wolfgang Brehm
- Department of Biology, Universität Konstanz, Box 647, 78457 Konstanz, Germany
| | - Oleksandr Yefanov
- Centre for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Anton Barty
- Centre for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Kenneth R. Beyerlein
- Centre for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Fedor Chervinskii
- Moscow Institute of Physics and Technology, 141700 Moscow, Russian Federation
| | - Lorenzo Galli
- Centre for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Cornelius Gati
- Centre for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Takanori Nakane
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Alexandra Tolstikova
- Centre for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | | | - Chun Hong Yoon
- Centre for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Kay Diederichs
- Department of Biology, Universität Konstanz, Box 647, 78457 Konstanz, Germany
| | - Henry N. Chapman
- Centre for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
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57
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Colletier JP, Sliwa M, Gallat FX, Sugahara M, Guillon V, Schirò G, Coquelle N, Woodhouse J, Roux L, Gotthard G, Royant A, Uriarte LM, Ruckebusch C, Joti Y, Byrdin M, Mizohata E, Nango E, Tanaka T, Tono K, Yabashi M, Adam V, Cammarata M, Schlichting I, Bourgeois D, Weik M. Serial Femtosecond Crystallography and Ultrafast Absorption Spectroscopy of the Photoswitchable Fluorescent Protein IrisFP. J Phys Chem Lett 2016; 7:882-887. [PMID: 26866390 DOI: 10.1021/acs.jpclett.5b02789] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Reversibly photoswitchable fluorescent proteins find growing applications in cell biology, yet mechanistic details, in particular on the ultrafast photochemical time scale, remain unknown. We employed time-resolved pump-probe absorption spectroscopy on the reversibly photoswitchable fluorescent protein IrisFP in solution to study photoswitching from the nonfluorescent (off) to the fluorescent (on) state. Evidence is provided for the existence of several intermediate states on the pico- and microsecond time scales that are attributed to chromophore isomerization and proton transfer, respectively. Kinetic modeling favors a sequential mechanism with the existence of two excited state intermediates with lifetimes of 2 and 15 ps, the second of which controls the photoswitching quantum yield. In order to support that IrisFP is suited for time-resolved experiments aiming at a structural characterization of these ps intermediates, we used serial femtosecond crystallography at an X-ray free electron laser and solved the structure of IrisFP in its on state. Sample consumption was minimized by embedding crystals in mineral grease, in which they remain photoswitchable. Our spectroscopic and structural results pave the way for time-resolved serial femtosecond crystallography aiming at characterizing the structure of ultrafast intermediates in reversibly photoswitchable fluorescent proteins.
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Affiliation(s)
| | - Michel Sliwa
- Université de Lille , CNRS, UMR 8516, LASIR, Laboratoire de Spectrochimie Infrarouge et Raman, F59 000 Lille, France
| | - François-Xavier Gallat
- Institut de Biologie Structurale , Université de Grenoble Alpes, CEA, CNRS, F-38044 Grenoble, France
| | - Michihiro Sugahara
- RIKEN SPring-8 Center , 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Virginia Guillon
- Institut de Biologie Structurale , Université de Grenoble Alpes, CEA, CNRS, F-38044 Grenoble, France
| | - Giorgio Schirò
- Institut de Biologie Structurale , Université de Grenoble Alpes, CEA, CNRS, F-38044 Grenoble, France
| | - Nicolas Coquelle
- Institut de Biologie Structurale , Université de Grenoble Alpes, CEA, CNRS, F-38044 Grenoble, France
| | - Joyce Woodhouse
- Institut de Biologie Structurale , Université de Grenoble Alpes, CEA, CNRS, F-38044 Grenoble, France
| | - Laure Roux
- Institut de Biologie Structurale , Université de Grenoble Alpes, CEA, CNRS, F-38044 Grenoble, France
| | - Guillaume Gotthard
- Institut de Biologie Structurale , Université de Grenoble Alpes, CEA, CNRS, F-38044 Grenoble, France
- The European Synchrotron Radiation Facility (ESRF) , 6 rue Jules Horowitz, BP 220, 38043 Grenoble Cedex, France
| | - Antoine Royant
- Institut de Biologie Structurale , Université de Grenoble Alpes, CEA, CNRS, F-38044 Grenoble, France
- The European Synchrotron Radiation Facility (ESRF) , 6 rue Jules Horowitz, BP 220, 38043 Grenoble Cedex, France
| | - Lucas Martinez Uriarte
- Université de Lille , CNRS, UMR 8516, LASIR, Laboratoire de Spectrochimie Infrarouge et Raman, F59 000 Lille, France
| | - Cyril Ruckebusch
- Université de Lille , CNRS, UMR 8516, LASIR, Laboratoire de Spectrochimie Infrarouge et Raman, F59 000 Lille, France
| | - Yasumasa Joti
- Japan Synchrotron Radiation Research Institute , 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Martin Byrdin
- Institut de Biologie Structurale , Université de Grenoble Alpes, CEA, CNRS, F-38044 Grenoble, France
| | - Eiichi Mizohata
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University , Osaka 565-0871, Japan
| | - Eriko Nango
- RIKEN SPring-8 Center , 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
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute , 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Makina Yabashi
- RIKEN SPring-8 Center , 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Virgile Adam
- Institut de Biologie Structurale , Université de Grenoble Alpes, CEA, CNRS, F-38044 Grenoble, France
| | - Marco Cammarata
- Department of Physics, UMR UR1-CNRS 6251, University of Rennes 1 , Rennes, France
| | - Ilme Schlichting
- Max-Planck-Institut für medizinische Forschung , Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Dominique Bourgeois
- Institut de Biologie Structurale , Université de Grenoble Alpes, CEA, CNRS, F-38044 Grenoble, France
| | - Martin Weik
- Institut de Biologie Structurale , Université de Grenoble Alpes, CEA, CNRS, F-38044 Grenoble, France
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58
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Macromolecular diffractive imaging using imperfect crystals. Nature 2016; 530:202-6. [PMID: 26863980 PMCID: PMC4839592 DOI: 10.1038/nature16949] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 12/14/2015] [Indexed: 12/20/2022]
Abstract
The three-dimensional structures of macromolecules and their complexes are predominantly elucidated by X-ray protein crystallography. A major limitation is access to high-quality crystals, to ensure X-ray diffraction extends to sufficiently large scattering angles and hence yields sufficiently high-resolution information that the crystal structure can be solved. The observation that crystals with shrunken unit-cell volumes and tighter macromolecular packing often produce higher-resolution Bragg peaks1,2 hints that crystallographic resolution for some macromolecules may be limited not by their heterogeneity but rather by a deviation of strict positional ordering of the crystalline lattice. Such displacements of molecules from the ideal lattice give rise to a continuous diffraction pattern, equal to the incoherent sum of diffraction from rigid single molecular complexes aligned along several discrete crystallographic orientations and hence with an increased information content3. Although such continuous diffraction patterns have long been observed—and are of interest as a source of information about the dynamics of proteins4 —they have not been used for structure determination. Here we show for crystals of the integral membrane protein complex photosystem II that lattice disorder increases the information content and the resolution of the diffraction pattern well beyond the 4.5 Å limit of measurable Bragg peaks, which allows us to directly phase5 the pattern. With the molecular envelope conventionally determined at 4.5 Å as a constraint, we then obtain a static image of the photosystem II dimer at 3.5 Å resolution. This result shows that continuous diffraction can be used to overcome long-supposed resolution limits of macromolecular crystallography, with a method that puts great value in commonly encountered imperfect crystals and opens up the possibility for model-free phasing6,7.
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59
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Lunin VY, Lunina NL, Petrova TE, Baumstark MW, Urzhumtsev AG. Mask-based approach to phasing of single-particle diffraction data. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:147-57. [DOI: 10.1107/s2059798315022652] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 11/25/2015] [Indexed: 11/10/2022]
Abstract
A Monte Carlo-type approach for low- and medium-resolution phasing of single-particle diffraction data is suggested. Firstly, the single-particle phase problem is substituted with the phase problem for an imaginary crystal. A unit cell of this crystal contains a single isolated particle surrounded by a large volume of bulk solvent. The developed phasing procedure then generates a large number of connected and finite molecular masks, calculates their Fourier coefficients, selects the sets with magnitudes that are highly correlated with the experimental values and finally aligns the selected phase sets and calculates the averaged phase values. A test with the known structure of monomeric photosystem II resulted in phases that have 97% correlation with the exact phases in the full 25 Å resolution shell (1054 structure factors) and correlations of 99, 94, 81 and 79% for the resolution shells ∞–60, 60–40, 40–30 and 30–25 Å, respectively. The same procedure may be used for crystallographicab initiophasing.
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60
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Sierra RG, Gati C, Laksmono H, Dao EH, Gul S, Fuller F, Kern J, Chatterjee R, Ibrahim M, Brewster AS, Young ID, Michels-Clark T, Aquila A, Liang M, Hunter MS, Koglin JE, Boutet S, Junco EA, Hayes B, Bogan MJ, Hampton CY, Puglisi EV, Sauter NK, Stan CA, Zouni A, Yano J, Yachandra VK, Soltis SM, Puglisi JD, DeMirci H. Concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem II. Nat Methods 2016; 13:59-62. [PMID: 26619013 PMCID: PMC4890631 DOI: 10.1038/nmeth.3667] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 10/14/2015] [Indexed: 01/30/2023]
Abstract
We describe a concentric-flow electrokinetic injector for efficiently delivering microcrystals for serial femtosecond X-ray crystallography analysis that enables studies of challenging biological systems in their unadulterated mother liquor. We used the injector to analyze microcrystals of Geobacillus stearothermophilus thermolysin (2.2-Å structure), Thermosynechococcus elongatus photosystem II (<3-Å diffraction) and Thermus thermophilus small ribosomal subunit bound to the antibiotic paromomycin at ambient temperature (3.4-Å structure).
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Affiliation(s)
- Raymond G. Sierra
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Cornelius Gati
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - Hartawan Laksmono
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - E. Han Dao
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Sheraz Gul
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Jan Kern
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | | | - Mohamed Ibrahim
- Institute für Biologie, Humboldt University of Berlin, Berlin, Germany
| | | | - Iris D. Young
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Andrew Aquila
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Mengning Liang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Mark S. Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Jason E. Koglin
- 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
| | - Elia A. Junco
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Brandon Hayes
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Michael J. Bogan
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Christina Y. Hampton
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Elisabetta V. Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Claudiu A. Stan
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Athina Zouni
- Institute für Biologie, Humboldt University of Berlin, Berlin, Germany
| | - Junko Yano
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - S. Michael Soltis
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Joseph D. Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Hasan DeMirci
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
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61
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Gavira JA. Current trends in protein crystallization. Arch Biochem Biophys 2015; 602:3-11. [PMID: 26747744 DOI: 10.1016/j.abb.2015.12.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 12/16/2015] [Accepted: 12/22/2015] [Indexed: 10/24/2022]
Abstract
UNLABELLED Proteins belong to the most complex colloidal system in terms of their physicochemical properties, size and conformational-flexibility. This complexity contributes to their great sensitivity to any external change and dictate the uncertainty of crystallization. The need of 3D models to understand their functionality and interaction mechanisms with other neighbouring (macro)molecules has driven the tremendous effort put into the field of crystallography that has also permeated other fields trying to shed some light into reluctant-to-crystallize proteins. This review is aimed at revising protein crystallization from a regular-laboratory point of view. It is also devoted to highlight the latest developments and achievements to produce, identify and deliver high-quality protein crystals for XFEL, Micro-ED or neutron diffraction. The low likelihood of protein crystallization is rationalized by considering the intrinsic polypeptide nature (folded state, surface charge, etc) followed by a description of the standard crystallization methods (batch, vapour diffusion and counter-diffusion), including high throughput advances. Other methodologies aimed at determining protein features in solution (NMR, SAS, DLS) or to gather structural information from single particles such as Cryo-EM are also discussed. Finally, current approaches showing the convergence of different structural biology techniques and the cross-methodologies adaptation to tackle the most difficult problems, are presented. SYNOPSIS Current advances in biomacromolecules crystallization, from nano crystals for XFEL and Micro-ED to large crystals for neutron diffraction, are covered with special emphasis in methodologies applicable at laboratory scale.
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Affiliation(s)
- José A Gavira
- Laboratorio de Estudios Cristalográficos, IACT (CSIC-UGR), Avda. de las Palmeras, 4. 18100 Armilla, Granada, Spain
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Kang Y, Gao X, Zhou XE, He Y, Melcher K, Xu HE. A structural snapshot of the rhodopsin-arrestin complex. FEBS J 2015; 283:816-21. [PMID: 26467309 DOI: 10.1111/febs.13561] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Revised: 10/08/2015] [Accepted: 10/12/2015] [Indexed: 01/01/2023]
Abstract
The crystal structure of the rhodopsin-arrestin complex provides important insights into how G protein-coupled receptor signaling is terminated by arrestin and a structural basis for understanding the mechanism of arrestin-based signaling.
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Affiliation(s)
- Yanyong Kang
- Laboratory of Structural Sciences and Laboratory of Structural Biology and Biochemistry, Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Xiang Gao
- Laboratory of Structural Sciences and Laboratory of Structural Biology and Biochemistry, Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, MI, USA
| | - X Edward Zhou
- Laboratory of Structural Sciences and Laboratory of Structural Biology and Biochemistry, Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, MI, USA.,VARI-SIMM Center, CAS-Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yuanzheng He
- Laboratory of Structural Sciences and Laboratory of Structural Biology and Biochemistry, Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Karsten Melcher
- Laboratory of Structural Sciences and Laboratory of Structural Biology and Biochemistry, Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, MI, USA.,VARI-SIMM Center, CAS-Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - H Eric Xu
- Laboratory of Structural Sciences and Laboratory of Structural Biology and Biochemistry, Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, MI, USA.,VARI-SIMM Center, CAS-Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
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63
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Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography. Nat Commun 2015; 5:3309. [PMID: 24525480 DOI: 10.1038/ncomms4309] [Citation(s) in RCA: 442] [Impact Index Per Article: 49.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 01/24/2014] [Indexed: 01/23/2023] Open
Abstract
Lipidic cubic phase (LCP) crystallization has proven successful for high-resolution structure determination of challenging membrane proteins. Here we present a technique for extruding gel-like LCP with embedded membrane protein microcrystals, providing a continuously renewed source of material for serial femtosecond crystallography. Data collected from sub-10-μm-sized crystals produced with less than 0.5 mg of purified protein yield structural insights regarding cyclopamine binding to the Smoothened receptor.
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64
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Yefanov O, Mariani V, Gati C, White TA, Chapman HN, Barty A. Accurate determination of segmented X-ray detector geometry. OPTICS EXPRESS 2015; 23:28459-70. [PMID: 26561117 PMCID: PMC4646514 DOI: 10.1364/oe.23.028459] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 09/18/2015] [Accepted: 10/09/2015] [Indexed: 05/21/2023]
Abstract
Recent advances in X-ray detector technology have resulted in the introduction of segmented detectors composed of many small detector modules tiled together to cover a large detection area. Due to mechanical tolerances and the desire to be able to change the module layout to suit the needs of different experiments, the pixels on each module might not align perfectly on a regular grid. Several detectors are designed to permit detector sub-regions (or modules) to be moved relative to each other for different experiments. Accurate determination of the location of detector elements relative to the beam-sample interaction point is critical for many types of experiment, including X-ray crystallography, coherent diffractive imaging (CDI), small angle X-ray scattering (SAXS) and spectroscopy. For detectors with moveable modules, the relative positions of pixels are no longer fixed, necessitating the development of a simple procedure to calibrate detector geometry after reconfiguration. We describe a simple and robust method for determining the geometry of segmented X-ray detectors using measurements obtained by serial crystallography. By comparing the location of observed Bragg peaks to the spot locations predicted from the crystal indexing procedure, the position, rotation and distance of each module relative to the interaction region can be refined. We show that the refined detector geometry greatly improves the results of experiments.
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Affiliation(s)
- Oleksandr Yefanov
- 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
| | - Cornelius Gati
- 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
- Department of Physics, University of Hamburg, Luruper Chaussee 149, 22607 Hamburg, Germany
- Centre for Ultrafast Imaging, Luruper Chaussee 149, 22607 Hamburg, Germany
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
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65
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Galli L, Son SK, Barends TRM, White TA, Barty A, Botha S, Boutet S, Caleman C, Doak RB, Nanao MH, Nass K, Shoeman RL, Timneanu N, Santra R, Schlichting I, Chapman HN. Towards phasing using high X-ray intensity. IUCRJ 2015; 2:627-34. [PMID: 26594370 PMCID: PMC4645107 DOI: 10.1107/s2052252515014049] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 07/24/2015] [Indexed: 05/11/2023]
Abstract
X-ray free-electron lasers (XFELs) show great promise for macromolecular structure determination from sub-micrometre-sized crystals, using the emerging method of serial femtosecond crystallography. The extreme brightness of the XFEL radiation can multiply ionize most, if not all, atoms in a protein, causing their scattering factors to change during the pulse, with a preferential 'bleaching' of heavy atoms. This paper investigates the effects of electronic damage on experimental data collected from a Gd derivative of lysozyme microcrystals at different X-ray intensities, and the degree of ionization of Gd atoms is quantified from phased difference Fourier maps. A pattern sorting scheme is proposed to maximize the ionization contrast and the way in which the local electronic damage can be used for a new experimental phasing method is discussed.
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Affiliation(s)
- Lorenzo Galli
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg, 22607, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, Hamburg, 22761, Germany
| | - Sang-Kil Son
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg, 22607, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, Hamburg, 22761, Germany
| | - Thomas R. M. Barends
- Biomolecular Mechanisms, MPI for Medical Research, Jahnstrasse 29, Heidelberg, 69120, Germany
| | - Thomas A. White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - Sabine Botha
- Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, 69120, Germany
| | - Sébastien Boutet
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, 94025, USA
| | - Carl Caleman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg, 22607, Germany
- Department of Physics and Astronomy, Uppsala University, Box 516, Uppsala, 75120, Sweden
| | - R. Bruce Doak
- Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, 69120, Germany
| | - Max H. Nanao
- EMBL, Grenoble Outstation, Rue Jules Horowitz 6, Grenoble, 38042, France
| | - Karol Nass
- Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, 69120, Germany
| | - Robert L. Shoeman
- Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, 69120, Germany
| | - Nicusor Timneanu
- Department of Physics and Astronomy, Uppsala University, Box 516, Uppsala, 75120, Sweden
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Box 596, Uppsala, 75124, Sweden
| | - Robin Santra
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg, 22607, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, Hamburg, 22761, Germany
- Department of Physics, University of Hamburg, Juniungstrasse 6, Hamburg, 20355, Germany
| | - Ilme Schlichting
- Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, 69120, Germany
| | - Henry N. Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg, 22607, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, Hamburg, 22761, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, Hamburg, 22761, Germany
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66
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Zander U, Bourenkov G, Popov AN, de Sanctis D, Svensson O, McCarthy AA, Round E, Gordeliy V, Mueller-Dieckmann C, Leonard GA. MeshAndCollect: an automated multi-crystal data-collection workflow for synchrotron macromolecular crystallography beamlines. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:2328-43. [PMID: 26527148 PMCID: PMC4631482 DOI: 10.1107/s1399004715017927] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 09/24/2015] [Indexed: 01/30/2023]
Abstract
Here, an automated procedure is described to identify the positions of many cryocooled crystals mounted on the same sample holder, to rapidly predict and rank their relative diffraction strengths and to collect partial X-ray diffraction data sets from as many of the crystals as desired. Subsequent hierarchical cluster analysis then allows the best combination of partial data sets, optimizing the quality of the final data set obtained. The results of applying the method developed to various systems and scenarios including the compilation of a complete data set from tiny crystals of the membrane protein bacteriorhodopsin and the collection of data sets for successful structure determination using the single-wavelength anomalous dispersion technique are also presented.
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Affiliation(s)
- Ulrich Zander
- Structural Biology Group, European Synchrotron Radiation Facility, CS 40220, 38043 Grenoble, France
| | - Gleb Bourenkov
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, 22607 Hamburg, Germany
| | - Alexander N. Popov
- Structural Biology Group, European Synchrotron Radiation Facility, CS 40220, 38043 Grenoble, France
| | - Daniele de Sanctis
- Structural Biology Group, European Synchrotron Radiation Facility, CS 40220, 38043 Grenoble, France
| | - Olof Svensson
- Structural Biology Group, European Synchrotron Radiation Facility, CS 40220, 38043 Grenoble, France
| | - Andrew A. McCarthy
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
- Unit of Virus Host-Cell Interactions, Université Grenoble Alpes–EMBL–CNRS, 38042 Grenoble, France
| | - Ekaterina Round
- Université Grenoble Alpes, IBS, 38044 Grenoble, France
- CNRS, IBS, 38044 Grenoble, France
- CEA, IBS, 38044 Grenoble, France
- ICS-6: Molecular Biophysics, Institute of Complex Systems (ICS), Research Centre Juelich, 52425 Juelich, Germany
- Laboratory for Advanced Studies of Membrane Proteins, Moscow Institute of Physics and Technology, Dolgoprudniy 141700, Russian Federation
| | - Valentin Gordeliy
- Université Grenoble Alpes, IBS, 38044 Grenoble, France
- CNRS, IBS, 38044 Grenoble, France
- CEA, IBS, 38044 Grenoble, France
- ICS-6: Molecular Biophysics, Institute of Complex Systems (ICS), Research Centre Juelich, 52425 Juelich, Germany
- Laboratory for Advanced Studies of Membrane Proteins, Moscow Institute of Physics and Technology, Dolgoprudniy 141700, Russian Federation
| | | | - Gordon A. Leonard
- Structural Biology Group, European Synchrotron Radiation Facility, CS 40220, 38043 Grenoble, France
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67
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Barends TRM, Foucar L, Ardevol A, Nass K, Aquila A, Botha S, Doak RB, Falahati K, Hartmann E, Hilpert M, Heinz M, Hoffmann MC, Köfinger J, Koglin JE, Kovacsova G, Liang M, Milathianaki D, Lemke HT, Reinstein J, Roome CM, Shoeman RL, Williams GJ, Burghardt I, Hummer G, Boutet S, Schlichting I. Direct observation of ultrafast collective motions in CO myoglobin upon ligand dissociation. Science 2015; 350:445-50. [PMID: 26359336 DOI: 10.1126/science.aac5492] [Citation(s) in RCA: 263] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 08/26/2015] [Indexed: 11/02/2022]
Abstract
The hemoprotein myoglobin is a model system for the study of protein dynamics. We used time-resolved serial femtosecond crystallography at an x-ray free-electron laser to resolve the ultrafast structural changes in the carbonmonoxy myoglobin complex upon photolysis of the Fe-CO bond. Structural changes appear throughout the protein within 500 femtoseconds, with the C, F, and H helices moving away from the heme cofactor and the E and A helices moving toward it. These collective movements are predicted by hybrid quantum mechanics/molecular mechanics simulations. Together with the observed oscillations of residues contacting the heme, our calculations support the prediction that an immediate collective response of the protein occurs upon ligand dissociation, as a result of heme vibrational modes coupling to global modes of the protein.
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Affiliation(s)
- Thomas R M Barends
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120 Heidelberg, Germany.
| | - Lutz Foucar
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120 Heidelberg, Germany
| | - Albert Ardevol
- Max-Planck-Institut für Biophysik, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Karol Nass
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120 Heidelberg, Germany
| | - Andrew Aquila
- European XFEL GmbH, Albert-Einstein-Ring 19, 22761 Hamburg, Germany
| | - Sabine Botha
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120 Heidelberg, Germany
| | - R Bruce Doak
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120 Heidelberg, Germany
| | - Konstantin Falahati
- Institut für Physikalische und Theoretische Chemie, Goethe-Universität, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Elisabeth Hartmann
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120 Heidelberg, Germany
| | - Mario Hilpert
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120 Heidelberg, Germany
| | - Marcel Heinz
- Max-Planck-Institut für Biophysik, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany. Institut für Physikalische und Theoretische Chemie, Goethe-Universität, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Matthias C Hoffmann
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Jürgen Köfinger
- Max-Planck-Institut für Biophysik, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Jason E Koglin
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Gabriela Kovacsova
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120 Heidelberg, Germany
| | - Mengning Liang
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Despina Milathianaki
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Henrik T Lemke
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Jochen Reinstein
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120 Heidelberg, Germany
| | - Christopher M Roome
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120 Heidelberg, Germany
| | - Robert L Shoeman
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120 Heidelberg, Germany
| | - Garth J Williams
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Irene Burghardt
- Institut für Physikalische und Theoretische Chemie, Goethe-Universität, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Gerhard Hummer
- Max-Planck-Institut für Biophysik, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Sébastien Boutet
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Ilme Schlichting
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120 Heidelberg, Germany.
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68
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Kern J, Yachandra VK, Yano J. Metalloprotein structures at ambient conditions and in real-time: biological crystallography and spectroscopy using X-ray free electron lasers. Curr Opin Struct Biol 2015; 34:87-98. [PMID: 26342144 DOI: 10.1016/j.sbi.2015.07.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 07/23/2015] [Accepted: 07/24/2015] [Indexed: 10/23/2022]
Abstract
Although the structure of enzymes and the chemistry at the catalytic sites have been studied intensively, an understanding of the atomic-scale chemistry requires a new approach beyond steady state X-ray crystallography and X-ray spectroscopy at cryogenic temperatures. Following the dynamic changes in the geometric and electronic structure of metallo-enzymes at ambient conditions, while overcoming the severe X-ray-induced changes to the redox active catalytic center, is key for deriving reaction mechanisms. Such studies become possible by the intense and ultra-short femtosecond (fs) X-ray pulses from an X-ray free electron laser (XFEL) by acquiring a signal before the sample is destroyed. This review describes the recent and pioneering uses of XFELs to study the protein structure and dynamics of metallo-enzymes using crystallography and scattering, as well as the chemical structure and dynamics of the catalytic complexes (charge, spin, and covalency) using spectroscopy during the reaction to understand the electron-transfer processes and elucidate the mechanism.
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Affiliation(s)
- Jan Kern
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
| | - Vittal K Yachandra
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Junko Yano
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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69
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Kroon-Batenburg LMJ, Schreurs AMM, Ravelli RBG, Gros P. Accounting for partiality in serial crystallography using ray-tracing principles. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1799-811. [PMID: 26327370 PMCID: PMC4556312 DOI: 10.1107/s1399004715011803] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 06/19/2015] [Indexed: 02/04/2023]
Abstract
Serial crystallography generates `still' diffraction data sets that are composed of single diffraction images obtained from a large number of crystals arbitrarily oriented in the X-ray beam. Estimation of the reflection partialities, which accounts for the expected observed fractions of diffraction intensities, has so far been problematic. In this paper, a method is derived for modelling the partialities by making use of the ray-tracing diffraction-integration method EVAL. The method estimates partialities based on crystal mosaicity, beam divergence, wavelength dispersion, crystal size and the interference function, accounting for crystallite size. It is shown that modelling of each reflection by a distribution of interference-function weighted rays yields a `still' Lorentz factor. Still data are compared with a conventional rotation data set collected from a single lysozyme crystal. Overall, the presented still integration method improves the data quality markedly. The R factor of the still data compared with the rotation data decreases from 26% using a Monte Carlo approach to 12% after applying the Lorentz correction, to 5.3% when estimating partialities by EVAL and finally to 4.7% after post-refinement. The merging R(int) factor of the still data improves from 105 to 56% but remains high. This suggests that the accuracy of the model parameters could be further improved. However, with a multiplicity of around 40 and an R(int) of ∼50% the merged still data approximate the quality of the rotation data. The presented integration method suitably accounts for the partiality of the observed intensities in still diffraction data, which is a critical step to improve data quality in serial crystallography.
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Affiliation(s)
- Loes M. J. Kroon-Batenburg
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Antoine M. M. Schreurs
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Raimond B. G. Ravelli
- M4I Division of Nanoscopy, Maastricht University, PO Box 616, 6200 MD Maastricht, The Netherlands
| | - Piet Gros
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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70
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Abstract
G-protein-coupled receptors (GPCRs) signal primarily through G proteins or arrestins. Arrestin binding to GPCRs blocks G protein interaction and redirects signalling to numerous G-protein-independent pathways. Here we report the crystal structure of a constitutively active form of human rhodopsin bound to a pre-activated form of the mouse visual arrestin, determined by serial femtosecond X-ray laser crystallography. Together with extensive biochemical and mutagenesis data, the structure reveals an overall architecture of the rhodopsin-arrestin assembly in which rhodopsin uses distinct structural elements, including transmembrane helix 7 and helix 8, to recruit arrestin. Correspondingly, arrestin adopts the pre-activated conformation, with a ∼20° rotation between the amino and carboxy domains, which opens up a cleft in arrestin to accommodate a short helix formed by the second intracellular loop of rhodopsin. This structure provides a basis for understanding GPCR-mediated arrestin-biased signalling and demonstrates the power of X-ray lasers for advancing the frontiers of structural biology.
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71
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Galli L, Son SK, Klinge M, Bajt S, Barty A, Bean R, Betzel C, Beyerlein KR, Caleman C, Doak RB, Duszenko M, Fleckenstein H, Gati C, Hunt B, Kirian RA, Liang M, Nanao MH, Nass K, Oberthür D, Redecke L, Shoeman R, Stellato F, Yoon CH, White TA, Yefanov O, Spence J, Chapman HN. Electronic damage in S atoms in a native protein crystal induced by an intense X-ray free-electron laser pulse. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2015; 2:041703. [PMID: 26798803 PMCID: PMC4711609 DOI: 10.1063/1.4919398] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 04/17/2015] [Indexed: 05/07/2023]
Abstract
Current hard X-ray free-electron laser (XFEL) sources can deliver doses to biological macromolecules well exceeding 1 GGy, in timescales of a few tens of femtoseconds. During the pulse, photoionization can reach the point of saturation in which certain atomic species in the sample lose most of their electrons. This electronic radiation damage causes the atomic scattering factors to change, affecting, in particular, the heavy atoms, due to their higher photoabsorption cross sections. Here, it is shown that experimental serial femtosecond crystallography data collected with an extremely bright XFEL source exhibit a reduction of the effective scattering power of the sulfur atoms in a native protein. Quantitative methods are developed to retrieve information on the effective ionization of the damaged atomic species from experimental data, and the implications of utilizing new phasing methods which can take advantage of this localized radiation damage are discussed.
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Affiliation(s)
| | | | - M Klinge
- Joint Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, University of Hamburg and Institute of Biochemistry, University of Luebeck at DESY, 22607 Hamburg, Germany
| | - S Bajt
- Photon Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, 22607 Hamburg, Germany
| | - A Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, 22607 Hamburg, Germany
| | - R Bean
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, 22607 Hamburg, Germany
| | - C Betzel
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, University of Hamburg at DESY, 22607 Hamburg, Germany
| | - K R Beyerlein
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, 22607 Hamburg, Germany
| | | | - R B Doak
- Department of Biomolecular Mechanisms, Max Planck-Institute for Medical Research , Jahnstrasse 29, 69120 Heidelberg, Germany
| | - M Duszenko
- Interfaculty Institute of Biochemistry, University of Tübingen , 72076 Tübingen, Germany
| | - H Fleckenstein
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, 22607 Hamburg, Germany
| | - C Gati
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, 22607 Hamburg, Germany
| | - B Hunt
- Department of Physics and Astronomy, Brigham Young University , Provo, Utah 84602, USA
| | - R A Kirian
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, 22607 Hamburg, Germany
| | - M Liang
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, 22607 Hamburg, Germany
| | - M H Nanao
- EMBL , Grenoble Outstation, Rue Jules Horowitz 6, Grenoble 38042, France
| | - K Nass
- Department of Biomolecular Mechanisms, Max Planck-Institute for Medical Research , Jahnstrasse 29, 69120 Heidelberg, Germany
| | - D Oberthür
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, 22607 Hamburg, Germany
| | - L Redecke
- Joint Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, University of Hamburg and Institute of Biochemistry, University of Luebeck at DESY, 22607 Hamburg, Germany
| | - R Shoeman
- Department of Biomolecular Mechanisms, Max Planck-Institute for Medical Research , Jahnstrasse 29, 69120 Heidelberg, Germany
| | - F Stellato
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, 22607 Hamburg, Germany
| | | | - T A White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, 22607 Hamburg, Germany
| | - O Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, 22607 Hamburg, Germany
| | - J Spence
- Department of Physics, Arizona State University , Tempe, Arizona 85287-1504, USA
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72
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Lawrence RM, Conrad CE, Zatsepin NA, Grant TD, Liu H, James D, Nelson G, Subramanian G, Aquila A, Hunter MS, Liang M, Boutet S, Coe J, Spence JCH, Weierstall U, Liu W, Fromme P, Cherezov V, Hogue BG. Serial femtosecond X-ray diffraction of enveloped virus microcrystals. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2015; 2:041720. [PMID: 26798819 PMCID: PMC4711640 DOI: 10.1063/1.4929410] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 08/12/2015] [Indexed: 05/22/2023]
Abstract
Serial femtosecond crystallography (SFX) using X-ray free-electron lasers has produced high-resolution, room temperature, time-resolved protein structures. We report preliminary SFX of Sindbis virus, an enveloped icosahedral RNA virus with ∼700 Å diameter. Microcrystals delivered in viscous agarose medium diffracted to ∼40 Å resolution. Small-angle diffuse X-ray scattering overlaid Bragg peaks and analysis suggests this results from molecular transforms of individual particles. Viral proteins undergo structural changes during entry and infection, which could, in principle, be studied with SFX. This is an important step toward determining room temperature structures from virus microcrystals that may enable time-resolved studies of enveloped viruses.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Andrew Aquila
- Linac Coherent Light Source, SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - Mengning Liang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | | | | | | | | | | | - Vadim Cherezov
- Department of Chemistry, Bridge Institute, University of Southern California , Los Angeles, California 90089, USA
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73
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Chavas LMG, Gumprecht L, Chapman HN. Possibilities for serial femtosecond crystallography sample delivery at future light sources. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2015; 2:041709. [PMID: 26798808 PMCID: PMC4711622 DOI: 10.1063/1.4921220] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 05/06/2015] [Indexed: 05/23/2023]
Abstract
Serial femtosecond crystallography (SFX) uses X-ray pulses from free-electron laser (FEL) sources that can outrun radiation damage and thereby overcome long-standing limits in the structure determination of macromolecular crystals. Intense X-ray FEL pulses of sufficiently short duration allow the collection of damage-free data at room temperature and give the opportunity to study irreversible time-resolved events. SFX may open the way to determine the structure of biological molecules that fail to crystallize readily into large well-diffracting crystals. Taking advantage of FELs with high pulse repetition rates could lead to short measurement times of just minutes. Automated delivery of sample suspensions for SFX experiments could potentially give rise to a much higher rate of obtaining complete measurements than at today's third generation synchrotron radiation facilities, as no crystal alignment or complex robotic motions are required. This capability will also open up extensive time-resolved structural studies. New challenges arise from the resulting high rate of data collection, and in providing reliable sample delivery. Various developments for fully automated high-throughput SFX experiments are being considered for evaluation, including new implementations for a reliable yet flexible sample environment setup. Here, we review the different methods developed so far that best achieve sample delivery for X-ray FEL experiments and present some considerations towards the goal of high-throughput structure determination with X-ray FELs.
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Affiliation(s)
- L M G Chavas
- Center for Free-Electron Laser Science, DESY , Notkestraße 85, 22607 Hamburg, Germany
| | - L Gumprecht
- Center for Free-Electron Laser Science, DESY , Notkestraße 85, 22607 Hamburg, Germany
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74
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Dejoie C, Smeets S, Baerlocher C, Tamura N, Pattison P, Abela R, McCusker LB. Serial snapshot crystallography for materials science with SwissFEL. IUCRJ 2015; 2:361-70. [PMID: 25995845 PMCID: PMC4420546 DOI: 10.1107/s2052252515006740] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 04/03/2015] [Indexed: 06/04/2023]
Abstract
New opportunities for studying (sub)microcrystalline materials with small unit cells, both organic and inorganic, will open up when the X-ray free electron laser (XFEL) presently being constructed in Switzerland (SwissFEL) comes online in 2017. Our synchrotron-based experiments mimicking the 4%-energy-bandpass mode of the SwissFEL beam show that it will be possible to record a diffraction pattern of up to 10 randomly oriented crystals in a single snapshot, to index the resulting reflections, and to extract their intensities reliably. The crystals are destroyed with each XFEL pulse, but by combining snapshots from several sets of crystals, a complete set of data can be assembled, and crystal structures of materials that are difficult to analyze otherwise will become accessible. Even with a single shot, at least a partial analysis of the crystal structure will be possible, and with 10-50 femtosecond pulses, this offers tantalizing possibilities for time-resolved studies.
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Affiliation(s)
- Catherine Dejoie
- Laboratory of Crystallography, ETH Zurich, Vladimir-Prelog-Weg 5, Zurich, 8093, Switzerland
| | - Stef Smeets
- Laboratory of Crystallography, ETH Zurich, Vladimir-Prelog-Weg 5, Zurich, 8093, Switzerland
| | - Christian Baerlocher
- Laboratory of Crystallography, ETH Zurich, Vladimir-Prelog-Weg 5, Zurich, 8093, Switzerland
| | - Nobumichi Tamura
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Philip Pattison
- Swiss-Norwegian Beamlines, European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble, 38042, France
- Laboratory of Crystallography, EPFL, Rte de la Sorge, Lausanne, 1015, Switzerland
| | - Rafael Abela
- SwissFEL, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Lynne B. McCusker
- Laboratory of Crystallography, ETH Zurich, Vladimir-Prelog-Weg 5, Zurich, 8093, Switzerland
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75
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Coquelle N, Brewster AS, Kapp U, Shilova A, Weinhausen B, Burghammer M, Colletier JP. Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1184-96. [PMID: 25945583 PMCID: PMC4427202 DOI: 10.1107/s1399004715004514] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 03/04/2015] [Indexed: 01/30/2023]
Abstract
High-resolution structural information was obtained from lysozyme microcrystals (20 µm in the largest dimension) using raster-scanning serial protein crystallography on micro- and nano-focused beamlines at the ESRF. Data were collected at room temperature (RT) from crystals sandwiched between two silicon nitride wafers, thereby preventing their drying, while limiting background scattering and sample consumption. In order to identify crystal hits, new multi-processing and GUI-driven Python-based pre-analysis software was developed, named NanoPeakCell, that was able to read data from a variety of crystallographic image formats. Further data processing was carried out using CrystFEL, and the resultant structures were refined to 1.7 Å resolution. The data demonstrate the feasibility of RT raster-scanning serial micro- and nano-protein crystallography at synchrotrons and validate it as an alternative approach for the collection of high-resolution structural data from micro-sized crystals. Advantages of the proposed approach are its thriftiness, its handling-free nature, the reduced amount of sample required, the adjustable hit rate, the high indexing rate and the minimization of background scattering.
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Affiliation(s)
- Nicolas Coquelle
- Université Grenoble Alpes, IBS, 38044 Grenoble, France
- CNRS, IBS, 38044 Grenoble, France
- CEA, IBS, 38044 Grenoble, France
| | - Aaron S. Brewster
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ulrike Kapp
- European Synchrotron Radiation Facility, BP 220, 38043 Grenoble, France
| | - Anastasya Shilova
- European Synchrotron Radiation Facility, BP 220, 38043 Grenoble, France
| | - Britta Weinhausen
- European Synchrotron Radiation Facility, BP 220, 38043 Grenoble, France
| | - Manfred Burghammer
- European Synchrotron Radiation Facility, BP 220, 38043 Grenoble, France
- Department of Analytical Chemistry, Ghent University, Ghent B-9000, Belgium
| | - Jacques-Philippe Colletier
- Université Grenoble Alpes, IBS, 38044 Grenoble, France
- CNRS, IBS, 38044 Grenoble, France
- CEA, IBS, 38044 Grenoble, France
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76
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Structure of the Angiotensin receptor revealed by serial femtosecond crystallography. Cell 2015; 161:833-44. [PMID: 25913193 DOI: 10.1016/j.cell.2015.04.011] [Citation(s) in RCA: 262] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 12/30/2014] [Accepted: 03/02/2015] [Indexed: 01/01/2023]
Abstract
Angiotensin II type 1 receptor (AT(1)R) is a G protein-coupled receptor that serves as a primary regulator for blood pressure maintenance. Although several anti-hypertensive drugs have been developed as AT(1)R blockers (ARBs), the structural basis for AT(1)R ligand-binding and regulation has remained elusive, mostly due to the difficulties of growing high-quality crystals for structure determination using synchrotron radiation. By applying the recently developed method of serial femtosecond crystallography at an X-ray free-electron laser, we successfully determined the room-temperature crystal structure of the human AT(1)R in complex with its selective antagonist ZD7155 at 2.9-Å resolution. The AT(1)R-ZD7155 complex structure revealed key structural features of AT(1)R and critical interactions for ZD7155 binding. Docking simulations of the clinically used ARBs into the AT(1)R structure further elucidated both the common and distinct binding modes for these anti-hypertensive drugs. Our results thereby provide fundamental insights into AT(1)R structure-function relationship and structure-based drug design.
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77
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Nogly P, James D, Wang D, White TA, Zatsepin N, Shilova A, Nelson G, Liu H, Johansson L, Heymann M, Jaeger K, Metz M, Wickstrand C, Wu W, Båth P, Berntsen P, Oberthuer D, Panneels V, Cherezov V, Chapman H, Schertler G, Neutze R, Spence J, Moraes I, Burghammer M, Standfuss J, Weierstall U. Lipidic cubic phase serial millisecond crystallography using synchrotron radiation. IUCRJ 2015; 2:168-76. [PMID: 25866654 PMCID: PMC4392771 DOI: 10.1107/s2052252514026487] [Citation(s) in RCA: 153] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 12/01/2014] [Indexed: 05/19/2023]
Abstract
Lipidic cubic phases (LCPs) have emerged as successful matrixes for the crystallization of membrane proteins. Moreover, the viscous LCP also provides a highly effective delivery medium for serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs). Here, the adaptation of this technology to perform serial millisecond crystallography (SMX) at more widely available synchrotron microfocus beamlines is described. Compared with conventional microcrystallography, LCP-SMX eliminates the need for difficult handling of individual crystals and allows for data collection at room temperature. The technology is demonstrated by solving a structure of the light-driven proton-pump bacteriorhodopsin (bR) at a resolution of 2.4 Å. The room-temperature structure of bR is very similar to previous cryogenic structures but shows small yet distinct differences in the retinal ligand and proton-transfer pathway.
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Affiliation(s)
- Przemyslaw Nogly
- Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Daniel James
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Dingjie Wang
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Thomas A. White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg 22607, Germany
| | - Nadia Zatsepin
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Anastasya Shilova
- European Synchrotron Radiation Facility, Grenoble Cedex 9, F-38043, France
| | - Garrett Nelson
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Haiguang Liu
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Linda Johansson
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California USA
| | - Michael Heymann
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg 22607, Germany
| | - Kathrin Jaeger
- Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Markus Metz
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg 22607, Germany
- Centre for Ultrafast Imaging, Hamburg 22607, Germany
| | - Cecilia Wickstrand
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Wenting Wu
- Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Petra Båth
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Peter Berntsen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Dominik Oberthuer
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg 22607, Germany
- Centre for Ultrafast Imaging, Hamburg 22607, Germany
| | - Valerie Panneels
- Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Vadim Cherezov
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California USA
| | - Henry Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg 22607, Germany
- Department of Physics, University of Hamburg, Hamburg 22607, Germany
| | - Gebhard Schertler
- Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen 5232, Switzerland
- Deparment of Biology, ETH Zurich, Zürich 8093, Switzerland
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - John Spence
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Isabel Moraes
- Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Chilton, Oxfordshire OX11 0DE, England
- Department of Life Sciences, Imperial College London, London, England
- Research Complex at Harwell Rutherford, Appleton Laboratory, Harwell, Didcot, Oxfordshire OX11 0FA, England
| | - Manfred Burghammer
- European Synchrotron Radiation Facility, Grenoble Cedex 9, F-38043, France
- Department of Analytical Chemistry, Ghent University, Ghent B-9000, Belgium
| | - Joerg Standfuss
- Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Uwe Weierstall
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
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78
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Schlichting I. Serial femtosecond crystallography: the first five years. IUCRJ 2015; 2:246-55. [PMID: 25866661 PMCID: PMC4392417 DOI: 10.1107/s205225251402702x] [Citation(s) in RCA: 221] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 12/09/2014] [Indexed: 05/18/2023]
Abstract
Protein crystallography using synchrotron radiation sources has had a tremendous impact on biology, having yielded the structures of thousands of proteins and given detailed insight into their mechanisms. However, the technique is limited by the requirement for macroscopic crystals, which can be difficult to obtain, as well as by the often severe radiation damage caused in diffraction experiments, in particular when using tiny crystals. To slow radiation damage, data collection is typically performed at cryogenic temperatures. With the advent of free-electron lasers (FELs) capable of delivering extremely intense femtosecond X-ray pulses, this situation appears to be remedied, allowing the structure determination of undamaged macromolecules using either macroscopic or microscopic crystals. The latter are exposed to the FEL beam in random orientations and their diffraction data are collected at cryogenic or room temperature in a serial fashion, since each crystal is destroyed upon a single exposure. The new approaches required for crystal growth and delivery, and for diffraction data analysis, including de novo phasing, are reviewed. The opportunities and challenges of SFX are described, including applications such as time-resolved measurements and the analysis of radiation damage-prone systems.
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Affiliation(s)
- Ilme Schlichting
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, Heidelberg 69120, Germany
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79
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Galli L, Son SK, White TA, Santra R, Chapman HN, Nanao MH. Towards RIP using free-electron laser SFX data. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:249-55. [PMID: 25723926 DOI: 10.1107/s1600577514027854] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Accepted: 12/21/2014] [Indexed: 05/03/2023]
Abstract
Here, it is shown that simulated native serial femtosecond crystallography (SFX) cathepsin B data can be phased by rapid ionization of sulfur atoms. Utilizing standard software adopted for radiation-damage-induced phasing (RIP), the effects on both substructure determination and phasing of the number of collected patterns and fluences are explored for experimental conditions already available at current free-electron laser facilities.
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Affiliation(s)
- Lorenzo Galli
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Sang Kil Son
- 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
| | - Robin Santra
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Henry N Chapman
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Max H Nanao
- EMBL, Grenoble Outstation, Rue Jules Horowitz 6, 38042 Grenoble, France
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80
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Abstract
Next-generation synchrotron radiation sources, such as X-ray free-electron lasers, energy recovery linacs, and ultra-low-emittance storage rings, are catalyzing novel methods of biomolecular microcrystallography and solution scattering. These methods are described and future trends are predicted. Importantly, there is a growing realization that serial microcrystallography and certain cutting-edge solution scattering experiments can be performed at existing storage ring sources by utilizing new technology. In this sense, next-generation sources are serving two distinct functions, namely, provision of new capabilities that require the newer sources and inspiration of new methods that can be performed at existing sources.
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81
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Spence JCH, Zatsepin NA, Li C. Coherent convergent-beam time-resolved X-ray diffraction. Philos Trans R Soc Lond B Biol Sci 2015; 369:20130325. [PMID: 24914153 DOI: 10.1098/rstb.2013.0325] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The use of coherent X-ray lasers for structural biology allows the use of nanometre diameter X-ray beams with large beam divergence. Their application to the structure analysis of protein nanocrystals and single particles raises new challenges and opportunities. We discuss the form of these coherent convergent-beam (CCB) hard X-ray diffraction patterns and their potential use for time-resolved crystallography, normally achieved by Laue (polychromatic) diffraction, for which the monochromatic laser radiation of a free-electron X-ray laser is unsuitable. We discuss the possibility of obtaining single-shot, angle-integrated rocking curves from CCB patterns, and the dependence of the resulting patterns on the focused beam coordinate when the beam diameter is larger or smaller than a nanocrystal, or smaller than one unit cell. We show how structure factor phase information is provided at overlapping interfering orders and how a common phase origin between different shots may be obtained. Their use in refinement of the phase-sensitive intensity between overlapping orders is suggested.
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Affiliation(s)
- John C H Spence
- Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA
| | - Nadia A Zatsepin
- Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA
| | - Chufeng Li
- Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA
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82
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Abstract
X-ray free-electron lasers have opened up the possibility of structure determination of protein crystals at room temperature, free of radiation damage. The femtosecond-duration pulses of these sources enable diffraction signals to be collected from samples at doses of 1000 MGy or higher. The sample is vaporized by the intense pulse, but not before the scattering that gives rise to the diffraction pattern takes place. Consequently, only a single flash diffraction pattern can be recorded from a crystal, giving rise to the method of serial crystallography where tens of thousands of patterns are collected from individual crystals that flow across the beam and the patterns are indexed and aggregated into a set of structure factors. The high-dose tolerance and the many-crystal averaging approach allow data to be collected from much smaller crystals than have been examined at synchrotron radiation facilities, even from radiation-sensitive samples. Here, we review the interaction of intense femtosecond X-ray pulses with materials and discuss the implications for structure determination. We identify various dose regimes and conclude that the strongest achievable signals for a given sample are attained at the highest possible dose rates, from highest possible pulse intensities.
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Affiliation(s)
- Henry 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, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Carl Caleman
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany Department of Physics and Astronomy, Uppsala University, Box 516, 75120 Uppsala, Sweden
| | - Nicusor Timneanu
- Department of Physics and Astronomy, Uppsala University, Box 516, 75120 Uppsala, Sweden Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
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83
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Abstract
A post-refinement procedure has been devised for 'snapshot' diffraction data consisting entirely of partially recorded reflections, each diffraction pattern from a crystal in an orientation unrelated to the others. Initial estimates of the diffraction geometry are used to calculate initial partialities, which are then used to scale the entire dataset together to produce initial estimates of the fully integrated intensities. The geometrical parameters for each pattern are then refined to maximize the agreement between these estimates and the calculated intensities in each pattern, and the procedure repeated iteratively. The performance of the procedure was investigated using simulated data and found to yield a significant improvement in the data quality.
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Affiliation(s)
- Thomas A White
- Center for Free-Electron Laser Science, Deutches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
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84
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Millane RP, Chen JPJ. Aspects of direct phasing in femtosecond nanocrystallography. Philos Trans R Soc Lond B Biol Sci 2015; 369:20130498. [PMID: 24914165 DOI: 10.1098/rstb.2013.0498] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
X-ray free-electron laser diffraction patterns from protein nanocrystals provide information on the diffracted amplitudes between the Bragg reflections, offering the possibility of direct phase retrieval without the use of ancillary experimental data. Proposals for implementing direct phase retrieval are reviewed. These approaches are limited by the signal-to-noise levels in the data and the presence of different and incomplete unit cells in the nanocrystals. The effects of low signal to noise can be ameliorated by appropriate selection of the intensity data samples that are used. The effects of incomplete unit cells may be small in some cases, and a unique solution is likely if there are four or fewer molecular orientations in the unit cell.
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Affiliation(s)
- Rick P Millane
- Computational Imaging Group, Department of Electrical and Computer Engineering, University of Canterbury, Christchurch, New Zealand
| | - Joe P J Chen
- Computational Imaging Group, Department of Electrical and Computer Engineering, University of Canterbury, Christchurch, New Zealand
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85
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Lunin VY, Grum-Grzhimailo AN, Gryzlova EV, Sinitsyn DO, Petrova TE, Lunina NL, Balabaev NK, Tereshkina KB, Stepanov AS, Krupyanskii YF. Efficient calculation of diffracted intensities in the case of nonstationary scattering by biological macromolecules under XFEL pulses. ACTA ACUST UNITED AC 2015; 71:293-303. [PMID: 25664739 DOI: 10.1107/s1399004714025450] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 11/20/2014] [Indexed: 11/10/2022]
Abstract
The calculation of diffracted intensities from an atomic model is a routine step in the course of structure solution, and its efficiency may be crucial for the feasibility of the study. An intense X-ray free-electron laser (XFEL) pulse can change the electron configurations of atoms during its action. This results in time-dependence of the diffracted intensities and complicates their calculation. An algorithm is suggested that enables this calculation with a computational cost comparable to that for the time-independent case. The intensity is calculated as a sum of the `effective' intensity and a finite series of `correcting' intensities. These intensities are calculated in the conventional way but with modified atomic scattering factors that are specially derived for a particular XFEL experiment. The total number of members of the series does not exceed the number of chemically different elements present in the object under study. This number is small for biological molecules; in addition, the correcting terms are negligible within the parameter range and accuracy acceptable in biological crystallography. The time-dependent atomic scattering factors were estimated for different pulse fluence levels by solving the system of rate equations. The simulation showed that the changes in a diffraction pattern caused by the time-dependence of scattering factors are negligible if the pulse fluence does not exceed the limit that is currently achieved in experiments with biological macromolecular crystals (10(4) photons Å(-2) per pulse) but become significant with an increase in the fluence to 10(6) or 10(8) photons Å(-2) per pulse.
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Affiliation(s)
- Vladimir Y Lunin
- Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russian Federation
| | - Alexei N Grum-Grzhimailo
- Skobeltsyn Institute of Nuclear Physics, Lomonosov Moscow State University, Moscow 119991, Russian Federation
| | - Elena V Gryzlova
- Skobeltsyn Institute of Nuclear Physics, Lomonosov Moscow State University, Moscow 119991, Russian Federation
| | - Dmitry O Sinitsyn
- Semenov Institute of Chemical Physics, Russian Academy of Sciences, 4 Kosygina Street, Moscow 119991, Russian Federation
| | - Tatiana E Petrova
- Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russian Federation
| | - Natalia L Lunina
- Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russian Federation
| | - Nikolai K Balabaev
- Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russian Federation
| | - Ksenia B Tereshkina
- Semenov Institute of Chemical Physics, Russian Academy of Sciences, 4 Kosygina Street, Moscow 119991, Russian Federation
| | - Alexei S Stepanov
- Semenov Institute of Chemical Physics, Russian Academy of Sciences, 4 Kosygina Street, Moscow 119991, Russian Federation
| | - Yurii F Krupyanskii
- Semenov Institute of Chemical Physics, Russian Academy of Sciences, 4 Kosygina Street, Moscow 119991, Russian Federation
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86
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van Thor JJ, Madsen A. A split-beam probe-pump-probe scheme for femtosecond time resolved protein X-ray crystallography. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2015; 2:014102. [PMID: 26798786 PMCID: PMC4711627 DOI: 10.1063/1.4906354] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Accepted: 01/09/2015] [Indexed: 05/14/2023]
Abstract
In order to exploit the femtosecond pulse duration of X-ray Free-Electron Lasers (XFEL) operating in the hard X-ray regime for ultrafast time-resolved protein crystallography experiments, critical parameters that determine the crystallographic signal-to-noise (I/σI) must be addressed. For single-crystal studies under low absorbed dose conditions, it has been shown that the intrinsic pulse intensity stability as well as mode structure and jitter of this structure, significantly affect the crystallographic signal-to-noise. Here, geometrical parameters are theoretically explored for a three-beam scheme: X-ray probe, optical pump, X-ray probe (or "probe-pump-probe") which will allow experimental determination of the photo-induced structure factor amplitude differences, ΔF, in a ratiometric manner, thereby internally referencing the intensity noise of the XFEL source. In addition to a non-collinear split-beam geometry which separates un-pumped and pumped diffraction patterns on an area detector, applying an additional convergence angle to both beams by focusing leads to integration over mosaic blocks in the case of well-ordered stationary protein crystals. Ray-tracing X-ray diffraction simulations are performed for an example using photoactive yellow protein crystals in order to explore the geometrical design parameters which would be needed. The specifications for an X-ray split and delay instrument that implements both an offset angle and focused beams are discussed, for implementation of a probe-pump-probe scheme at the European XFEL. We discuss possible extension of single crystal studies to serial femtosecond crystallography, particularly in view of the expected X-ray damage and ablation due to the first probe pulse.
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Affiliation(s)
- Jasper J van Thor
- Division of Molecular Biosciences, Imperial College London , South Kensington Campus. SW7 2AZ London, United Kingdom
| | - Anders Madsen
- European X-Ray Free-Electron Laser Facility , Albert-Einstein-Ring 19, 22761 Hamburg, Germany
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87
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Liu W, Ishchenko A, Cherezov V. Preparation of microcrystals in lipidic cubic phase for serial femtosecond crystallography. Nat Protoc 2014; 9:2123-34. [PMID: 25122522 DOI: 10.1038/nprot.2014.141] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We have recently established a procedure for serial femtosecond crystallography (SFX) in lipidic cubic phase (LCP) for protein structure determination at X-ray free-electron lasers (XFELs). LCP-SFX uses the gel-like LCP as a matrix for growth and delivery of membrane protein microcrystals for crystallographic data collection. LCP is a liquid-crystalline mesophase composed of lipids and water. It provides a membrane-mimicking environment that stabilizes membrane proteins and supports their crystallization. Here we describe detailed procedures for the preparation and characterization of microcrystals for LCP-SFX applications. The advantages of LCP-SFX over traditional crystallographic methods include the capability of collecting room-temperature high-resolution data with minimal effects of radiation damage from sub-10-μm crystals of membrane and soluble proteins that are difficult to crystallize, while eliminating the need for crystal harvesting and cryo-cooling. Compared with SFX methods for microcrystals in solution using liquid injectors, LCP-SFX reduces protein consumption by 2-3 orders of magnitude for data collection at currently available XFELs. The whole procedure typically takes 3-5 d, including the time required for the crystals to grow.
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Affiliation(s)
- Wei Liu
- 1] Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA. [2] Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening and Marine Drug Research Institute, Huaihai Institute of Technology, Lianyungang, China
| | - Andrii Ishchenko
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Vadim Cherezov
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
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88
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Chen JPJ, Millane RP. Diffraction by nanocrystals II. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2014; 31:1730-1737. [PMID: 25121528 DOI: 10.1364/josaa.31.001730] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Nanocrystals with more than one molecule in the unit cell will generally crystallize with incomplete unit cells on the crystal surface. Previous results show that the ensemble-averaged diffraction by such crystals consists of a usual Bragg component and two other Bragg-like components due to the incomplete unit cells. Using an intrinsic flexibility in the definition of the incomplete-unit-cell part of a crystal, the problem is formulated such that the magnitude of the Bragg-like components is minimized, which leads to a simpler and more useful interpretation of the diffraction. Simulations show the nature of the relative magnitudes of the diffraction components in different regions of reciprocal space and the effect of crystal faceting.
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89
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Kabsch W. Processing of X-ray snapshots from crystals in random orientations. ACTA ACUST UNITED AC 2014; 70:2204-16. [PMID: 25084339 PMCID: PMC4118830 DOI: 10.1107/s1399004714013534] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 06/10/2014] [Indexed: 11/10/2022]
Abstract
A functional expression is introduced that relates scattered X-ray intensities from a still or a rotation snapshot to the corresponding structure-factor amplitudes. The new approach was implemented in the program nXDS for processing monochromatic diffraction images recorded by a multi-segment detector where each exposure could come from a different crystal. For images containing indexable spots, the intensities of the expected reflections and their variances are obtained by profile fitting after mapping the contributing pixel contents to the Ewald sphere. The varying intensity decline owing to the angular distance of the reflection from the surface of the Ewald sphere is estimated using a Gaussian rocking curve. This decline is dubbed `Ewald offset correction', which is well defined even for still images. Together with an image-scaling factor and other corrections, an explicit expression is defined that predicts each recorded intensity from its corresponding structure-factor amplitude. All diffraction parameters, scaling and correction factors are improved by post-refinement. The ambiguous case of a lower point group than the lattice symmetry is resolved by a method reminiscent of the technique of `selective breeding'. It selects the indexing alternative for each image that yields, on average, the highest correlation with intensities from all other images. Processing a test set of rotation images by XDS and treating the same images by nXDS as snapshots of crystals in random orientations yields data of comparable quality, clearly indicating an anomalous signal from Se atoms.
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Affiliation(s)
- Wolfgang Kabsch
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, D-69120 Heidelberg, Germany
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90
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Kern J, Tran R, Alonso-Mori R, Koroidov S, Echols N, Hattne J, Ibrahim M, Gul S, Laksmono H, Sierra RG, Gildea RJ, Han G, Hellmich J, Lassalle-Kaiser B, Chatterjee R, Brewster AS, Stan CA, Glöckner C, Lampe A, DiFiore D, Milathianaki D, Fry AR, Seibert MM, Koglin JE, Gallo E, Uhlig J, Sokaras D, Weng TC, Zwart PH, Skinner DE, Bogan MJ, Messerschmidt M, Glatzel P, Williams GJ, Boutet S, Adams PD, Zouni A, Messinger J, Sauter NK, Bergmann U, Yano J, Yachandra VK. Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy. Nat Commun 2014; 5:4371. [PMID: 25006873 PMCID: PMC4151126 DOI: 10.1038/ncomms5371] [Citation(s) in RCA: 188] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 06/10/2014] [Indexed: 01/07/2023] Open
Abstract
The dioxygen we breathe is formed by light-induced oxidation of water in photosystem II. O2 formation takes place at a catalytic manganese cluster within milliseconds after the photosystem II reaction centre is excited by three single-turnover flashes. Here we present combined X-ray emission spectra and diffraction data of 2-flash (2F) and 3-flash (3F) photosystem II samples, and of a transient 3F' state (250 μs after the third flash), collected under functional conditions using an X-ray free electron laser. The spectra show that the initial O-O bond formation, coupled to Mn reduction, does not yet occur within 250 μs after the third flash. Diffraction data of all states studied exhibit an anomalous scattering signal from Mn but show no significant structural changes at the present resolution of 4.5 Å. This study represents the initial frames in a molecular movie of the structural changes during the catalytic reaction in photosystem II.
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Affiliation(s)
- Jan Kern
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA,LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Rosalie Tran
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Sergey Koroidov
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, Umeå, Sweden
| | - Nathaniel Echols
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Johan Hattne
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Mohamed Ibrahim
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany,Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universität, D-10623 Berlin, Germany
| | - Sheraz Gul
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Hartawan Laksmono
- PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Raymond G. Sierra
- PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Richard J. Gildea
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Guangye Han
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Julia Hellmich
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany,Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universität, D-10623 Berlin, Germany
| | | | - Ruchira Chatterjee
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Aaron S. Brewster
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Claudiu A. Stan
- PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Carina Glöckner
- Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universität, D-10623 Berlin, Germany
| | - Alyssa Lampe
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Dörte DiFiore
- Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universität, D-10623 Berlin, Germany
| | | | - Alan R. Fry
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - M. Marvin Seibert
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Jason E. Koglin
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Erik Gallo
- European Synchrotron Radiation Facility, F-38043 Grenoble Cedex, France
| | - Jens Uhlig
- European Synchrotron Radiation Facility, F-38043 Grenoble Cedex, France
| | | | - Tsu-Chien Weng
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Petrus H. Zwart
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - David E. Skinner
- National Energy Research Scientific Computing Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Michael J. Bogan
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA,PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | - Pieter Glatzel
- European Synchrotron Radiation Facility, F-38043 Grenoble Cedex, France
| | - Garth J. Williams
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Sébastien Boutet
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Paul D. Adams
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Athina Zouni
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany,Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universität, D-10623 Berlin, Germany
| | - Johannes Messinger
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, Umeå, Sweden
| | - Nicholas K. Sauter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Uwe Bergmann
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA,Corresponding authors. (U.B.), , (J.Y.), (V.K.Y)
| | - Junko Yano
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA,Corresponding authors. (U.B.), , (J.Y.), (V.K.Y)
| | - Vittal K. Yachandra
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA,Corresponding authors. (U.B.), , (J.Y.), (V.K.Y)
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91
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Stellato F, Oberthür D, Liang M, Bean R, Gati C, Yefanov O, Barty A, Burkhardt A, Fischer P, Galli L, Kirian RA, Meyer J, Panneerselvam S, Yoon CH, Chervinskii F, Speller E, White TA, Betzel C, Meents A, Chapman HN. Room-temperature macromolecular serial crystallography using synchrotron radiation. IUCRJ 2014; 1:204-12. [PMID: 25075341 PMCID: PMC4107920 DOI: 10.1107/s2052252514010070] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 05/05/2014] [Indexed: 05/18/2023]
Abstract
A new approach for collecting data from many hundreds of thousands of microcrystals using X-ray pulses from a free-electron laser has recently been developed. Referred to as serial crystallography, diffraction patterns are recorded at a constant rate as a suspension of protein crystals flows across the path of an X-ray beam. Events that by chance contain single-crystal diffraction patterns are retained, then indexed and merged to form a three-dimensional set of reflection intensities for structure determination. This approach relies upon several innovations: an intense X-ray beam; a fast detector system; a means to rapidly flow a suspension of crystals across the X-ray beam; and the computational infrastructure to process the large volume of data. Originally conceived for radiation-damage-free measurements with ultrafast X-ray pulses, the same methods can be employed with synchrotron radiation. As in powder diffraction, the averaging of thousands of observations per Bragg peak may improve the ratio of signal to noise of low-dose exposures. Here, it is shown that this paradigm can be implemented for room-temperature data collection using synchrotron radiation and exposure times of less than 3 ms. Using lysozyme microcrystals as a model system, over 40 000 single-crystal diffraction patterns were obtained and merged to produce a structural model that could be refined to 2.1 Å resolution. The resulting electron density is in excellent agreement with that obtained using standard X-ray data collection techniques. With further improvements the method is well suited for even shorter exposures at future and upgraded synchrotron radiation facilities that may deliver beams with 1000 times higher brightness than they currently produce.
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Affiliation(s)
- Francesco Stellato
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Dominik Oberthür
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg 22607, Germany
| | - Mengning Liang
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Richard Bean
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Cornelius Gati
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Oleksandr Yefanov
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Anton Barty
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | | | | | - Lorenzo Galli
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, Hamburg 22607, Germany
| | - Richard A. Kirian
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Jan Meyer
- Photon Science, DESY, Hamburg 22607, Germany
| | | | - Chun Hong Yoon
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
- European XFEL GmbH, Albert Einstein Ring 19, Hamburg 22761, Germany
| | - Fedor Chervinskii
- Moscow Institute of Physics and Technology, 141700 Moscow, Russian Federation
| | - Emily Speller
- Department of Physics, University of York, Heslington, York YO10 5DD, UK
| | - Thomas A. White
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Christian Betzel
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg 22607, Germany
- Center for Ultrafast Imaging, Luruper Chaussee 149, Hamburg 22761, Germany
| | - Alke Meents
- Photon Science, DESY, Hamburg 22607, Germany
| | - Henry N. Chapman
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, Hamburg 22607, Germany
- Center for Ultrafast Imaging, Luruper Chaussee 149, Hamburg 22761, Germany
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92
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Feld GK, Frank M. Enabling membrane protein structure and dynamics with X-ray free electron lasers. Curr Opin Struct Biol 2014; 27:69-78. [PMID: 24930119 DOI: 10.1016/j.sbi.2014.05.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 05/09/2014] [Accepted: 05/12/2014] [Indexed: 10/25/2022]
Abstract
Determining the three-dimensional structures and dynamics of membrane proteins remains one of the great challenges of modern biology. The recent availability of X-ray free electron laser (XFEL) light sources has opened the door to a new and revolutionary approach to performing X-ray analysis of these important biomolecules. Recent advances in sample delivery, data reduction, and phasing have enabled the high-resolution structural probing of membrane proteins at room temperature. While considerable challenges remain, the recent developments described in this review may ultimately provide structural biologists with powerful tools for obtaining unprecedented atomic-scale and dynamic visualization of membrane proteins at near-physiological conditions.
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Affiliation(s)
- Geoffrey K Feld
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Matthias Frank
- Physics Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.
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93
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Hattne J, Echols N, Tran R, Kern J, Gildea RJ, Brewster AS, Alonso-Mori R, Glöckner C, Hellmich J, Laksmono H, Sierra RG, Lassalle-Kaiser B, Lampe A, Han G, Gul S, DiFiore D, Milathianaki D, Fry AR, Miahnahri A, White WE, Schafer DW, Seibert MM, Koglin JE, Sokaras D, Weng TC, Sellberg J, Latimer MJ, Glatzel P, Zwart PH, Grosse-Kunstleve RW, Bogan MJ, Messerschmidt M, Williams GJ, Boutet S, Messinger J, Zouni A, Yano J, Bergmann U, Yachandra VK, Adams PD, Sauter NK. Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers. Nat Methods 2014; 11:545-8. [PMID: 24633409 DOI: 10.1038/nmeth.2887] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2013] [Accepted: 02/04/2014] [Indexed: 01/19/2023]
Abstract
X-ray free-electron laser (XFEL) sources enable the use of crystallography to solve three-dimensional macromolecular structures under native conditions and without radiation damage. Results to date, however, have been limited by the challenge of deriving accurate Bragg intensities from a heterogeneous population of microcrystals, while at the same time modeling the X-ray spectrum and detector geometry. Here we present a computational approach designed to extract meaningful high-resolution signals from fewer diffraction measurements.
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Affiliation(s)
- Johan Hattne
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Nathaniel Echols
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Rosalie Tran
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jan Kern
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Richard J Gildea
- 1] Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA. [2]
| | - Aaron S Brewster
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Roberto Alonso-Mori
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Carina Glöckner
- Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universität, Berlin, Germany
| | - Julia Hellmich
- Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universität, Berlin, Germany
| | - Hartawan Laksmono
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Raymond G Sierra
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | | | - Alyssa Lampe
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Guangye Han
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Sheraz Gul
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Dörte DiFiore
- Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universität, Berlin, Germany
| | - Despina Milathianaki
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Alan R Fry
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Alan Miahnahri
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - William E White
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Donald W Schafer
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - M Marvin Seibert
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Jason E Koglin
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Dimosthenis Sokaras
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Tsu-Chien Weng
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Jonas Sellberg
- 1] Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, USA. [2] Department of Physics, AlbaNova, Stockholm University, Stockholm, Sweden
| | - Matthew J Latimer
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Pieter Glatzel
- European Synchrotron Radiation Facility, Grenoble, France
| | - Petrus H Zwart
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Ralf W Grosse-Kunstleve
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Michael J Bogan
- 1] Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California, USA. [2] Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Marc Messerschmidt
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Garth J Williams
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Sébastien Boutet
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Johannes Messinger
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, Umeå, Sweden
| | - Athina Zouni
- 1] Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universität, Berlin, Germany. [2] Institut für Biologie, Humboldt Universität zu Berlin, Berlin, Germany
| | - Junko Yano
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Uwe Bergmann
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Vittal K Yachandra
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Paul D Adams
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Nicholas K Sauter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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94
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Rossmann MG. Serial crystallography using synchrotron radiation. IUCRJ 2014; 1:84-6. [PMID: 25075323 PMCID: PMC4062086 DOI: 10.1107/s2052252514000499] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Accepted: 12/24/2013] [Indexed: 05/06/2023]
Abstract
A brief history is given of how X-ray diffraction data from crystals have been recorded. Today there are new possibilities, spawned by the availability of free electron lasers that produce powerful femtosecond long X-ray pulses.
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Affiliation(s)
- Michael G. Rossmann
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
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95
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Gati C, Bourenkov G, Klinge M, Rehders D, Stellato F, Oberthür D, Yefanov O, Sommer BP, Mogk S, Duszenko M, Betzel C, Schneider TR, Chapman HN, Redecke L. Serial crystallography on in vivo grown microcrystals using synchrotron radiation. IUCRJ 2014; 1:87-94. [PMID: 25075324 PMCID: PMC4062088 DOI: 10.1107/s2052252513033939] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 12/16/2013] [Indexed: 05/03/2023]
Abstract
Crystal structure determinations of biological macromolecules are limited by the availability of sufficiently sized crystals and by the fact that crystal quality deteriorates during data collection owing to radiation damage. Exploiting a micrometre-sized X-ray beam, high-precision diffractometry and shutterless data acquisition with a pixel-array detector, a strategy for collecting data from many micrometre-sized crystals presented to an X-ray beam in a vitrified suspension is demonstrated. By combining diffraction data from 80 Trypanosoma brucei procathepsin B crystals with an average volume of 9 µm(3), a complete data set to 3.0 Å resolution has been assembled. The data allowed the refinement of a structural model that is consistent with that previously obtained using free-electron laser radiation, providing mutual validation. Further improvements of the serial synchrotron crystallography technique and its combination with serial femtosecond crystallography are discussed that may allow the determination of high-resolution structures of micrometre-sized crystals.
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Affiliation(s)
- Cornelius Gati
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronensynchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Gleb Bourenkov
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607 Hamburg, Germany
| | - Marco Klinge
- Joint Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, University of Hamburg, and Institute of Biochemistry, University of Lübeck, Notkestrasse 85, 22607 Hamburg, Germany
| | - Dirk Rehders
- Joint Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, University of Hamburg, and Institute of Biochemistry, University of Lübeck, Notkestrasse 85, 22607 Hamburg, Germany
| | - Francesco Stellato
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronensynchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Dominik Oberthür
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronensynchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Notkestrasse 85, 22607 Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronensynchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Benjamin P. Sommer
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Notkestrasse 85, 22607 Hamburg, Germany
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Strasse 4, 72076 Tübingen, Germany
| | - Stefan Mogk
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Strasse 4, 72076 Tübingen, Germany
| | - Michael Duszenko
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Strasse 4, 72076 Tübingen, Germany
| | - Christian Betzel
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Notkestrasse 85, 22607 Hamburg, Germany
| | - Thomas R. Schneider
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607 Hamburg, Germany
| | - Henry N. Chapman
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronensynchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
- Institute of Experimental Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Lars Redecke
- Joint Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, University of Hamburg, and Institute of Biochemistry, University of Lübeck, Notkestrasse 85, 22607 Hamburg, Germany
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96
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Abstract
X-ray diffraction patterns from crystals of biological macromolecules contain sufficient information to define atomic structures, but atomic positions are inextricable without having electron-density images. Diffraction measurements provide amplitudes, but the computation of electron density also requires phases for the diffracted waves. The resonance phenomenon known as anomalous scattering offers a powerful solution to this phase problem. Exploiting scattering resonances from diverse elements, the methods of MAD (multiwavelength anomalous diffraction) and SAD (single-wavelength anomalous diffraction) now predominate for de novo determinations of atomic-level biological structures. This review describes the physical underpinnings of anomalous diffraction methods, the evolution of these methods to their current maturity, the elements, procedures and instrumentation used for effective implementation, and the realm of applications.
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Affiliation(s)
- Wayne A. Hendrickson
- Department of Biochemistry and Molecular Biophysics, and Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032 USA. New York Structural Biology Center, 89 Convent Avenue, New York, NY 10027 USA
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97
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Brehm W, Diederichs K. Breaking the indexing ambiguity in serial crystallography. ACTA ACUST UNITED AC 2013; 70:101-9. [PMID: 24419383 DOI: 10.1107/s1399004713025431] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 09/13/2013] [Indexed: 11/10/2022]
Abstract
In serial crystallography, a very incomplete partial data set is obtained from each diffraction experiment (a `snapshot'). In some space groups, an indexing ambiguity exists which requires that the indexing mode of each snapshot needs to be established with respect to a reference data set. In the absence of such re-indexing information, crystallographers have thus far resorted to a straight merging of all snapshots, yielding a perfectly twinned data set of higher symmetry which is poorly suited for structure solution and refinement. Here, two algorithms have been designed for assembling complete data sets by clustering those snapshots that are indexed in the same way, and they have been tested using 15,445 snapshots from photosystem I [Chapman et al. (2011), Nature (London), 470, 73-77] and with noisy model data. The results of the clustering are unambiguous and enabled the construction of complete data sets in the correct space group P63 instead of (twinned) P6322 that researchers have been forced to use previously in such cases of indexing ambiguity. The algorithms thus extend the applicability and reach of serial crystallography.
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Affiliation(s)
- Wolfgang Brehm
- Department of Biology, Universität Konstanz, Box 647, 78457 Konstanz, Germany
| | - Kay Diederichs
- Department of Biology, Universität Konstanz, Box 647, 78457 Konstanz, Germany
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98
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Liu W, Wacker D, Gati C, Han GW, James D, Wang D, Nelson G, Weierstall U, Katritch V, Barty A, Zatsepin NA, Li D, Messerschmidt M, Boutet S, Williams GJ, Koglin JE, Seibert MM, Wang C, Shah ST, Basu S, Fromme R, Kupitz C, Rendek KN, Grotjohann I, Fromme P, Kirian RA, Beyerlein KR, White TA, Chapman HN, Caffrey M, Spence JC, Stevens RC, Cherezov V. Serial femtosecond crystallography of G protein-coupled receptors. Science 2013; 342:1521-4. [PMID: 24357322 PMCID: PMC3902108 DOI: 10.1126/science.1244142] [Citation(s) in RCA: 331] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
X-ray crystallography of G protein-coupled receptors and other membrane proteins is hampered by difficulties associated with growing sufficiently large crystals that withstand radiation damage and yield high-resolution data at synchrotron sources. We used an x-ray free-electron laser (XFEL) with individual 50-femtosecond-duration x-ray pulses to minimize radiation damage and obtained a high-resolution room-temperature structure of a human serotonin receptor using sub-10-micrometer microcrystals grown in a membrane mimetic matrix known as lipidic cubic phase. Compared with the structure solved by using traditional microcrystallography from cryo-cooled crystals of about two orders of magnitude larger volume, the room-temperature XFEL structure displays a distinct distribution of thermal motions and conformations of residues that likely more accurately represent the receptor structure and dynamics in a cellular environment.
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Affiliation(s)
- Wei Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel Wacker
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Cornelius Gati
- Center for Free Electron Laser Science, DESY, 22607 Hamburg, Germany
| | - Gye Won Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel James
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Dingjie Wang
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Garrett Nelson
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Uwe Weierstall
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Vsevolod Katritch
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Anton Barty
- Center for Free Electron Laser Science, DESY, 22607 Hamburg, Germany
| | - Nadia A. Zatsepin
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Dianfan Li
- School of Medicine and School of Biochemistry and Immunology, Trinity College, Dublin, Dublin 2, Ireland
| | - Marc Messerschmidt
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Sébastien Boutet
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Garth J. Williams
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Jason E. Koglin
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - M. Marvin Seibert
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Chong Wang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Syed T.A. Shah
- School of Medicine and School of Biochemistry and Immunology, Trinity College, Dublin, Dublin 2, Ireland
| | - Shibom Basu
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Raimund Fromme
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Christopher Kupitz
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Kimberley N. Rendek
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Ingo Grotjohann
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Petra Fromme
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Richard A. Kirian
- Center for Free Electron Laser Science, DESY, 22607 Hamburg, Germany
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | | | - Thomas A. White
- Center for Free Electron Laser Science, DESY, 22607 Hamburg, Germany
| | - Henry N. Chapman
- Center for Free Electron Laser Science, DESY, 22607 Hamburg, Germany
- Institute for Experimental Physics, University of Hamburg, 22761 Hamburg, Germany
- Center for Ultrafast Imaging, 22607 Hamburg, Germany
| | - Martin Caffrey
- School of Medicine and School of Biochemistry and Immunology, Trinity College, Dublin, Dublin 2, Ireland
| | - John C.H. Spence
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Raymond C. Stevens
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Vadim Cherezov
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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99
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Chen JPJ, Millane RP. Diffraction by nanocrystals. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2013; 30:2627-2634. [PMID: 24323025 DOI: 10.1364/josaa.30.002627] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
X-ray femtosecond nanocrystallography is a new, potentially powerful technique for imaging biological macromolecules that uses ensemble-averaged measurements of diffraction of x-ray free-electron laser pulses from nanocrytalline specimens. Nanocrystals have some diffraction characteristics that are distinct from those of macroscopic crystals, due to the presence of different kinds of unit cell in the crystal and of truncated unit cells on the crystal surface. Expressions are derived for diffraction by nanocrystals with variable and incomplete unit cells, averaged over a distribution of crystal sizes and shapes. The diffraction contains differently modulated Bragg components that are due to interference effects within and between the full and incomplete unit cells. Estimates are obtained for the relative magnitudes of the components. The nature of the diffraction is illustrated by two-dimensional simulations. Implications for molecular imaging are discussed.
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100
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Demirci H, Sierra RG, Laksmono H, Shoeman RL, Botha S, Barends TRM, Nass K, Schlichting I, Doak RB, Gati C, Williams GJ, Boutet S, Messerschmidt M, Jogl G, Dahlberg AE, Gregory ST, Bogan MJ. Serial femtosecond X-ray diffraction of 30S ribosomal subunit microcrystals in liquid suspension at ambient temperature using an X-ray free-electron laser. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1066-9. [PMID: 23989164 PMCID: PMC3758164 DOI: 10.1107/s174430911302099x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 07/27/2013] [Indexed: 12/03/2022]
Abstract
High-resolution ribosome structures determined by X-ray crystallography have provided important insights into the mechanism of translation. Such studies have thus far relied on large ribosome crystals kept at cryogenic temperatures to reduce radiation damage. Here, the application of serial femtosecond X-ray crystallography (SFX) using an X-ray free-electron laser (XFEL) to obtain diffraction data from ribosome microcrystals in liquid suspension at ambient temperature is described. 30S ribosomal subunit microcrystals diffracted to beyond 6 Å resolution, demonstrating the feasibility of using SFX for ribosome structural studies. The ability to collect diffraction data at near-physiological temperatures promises to provide fundamental insights into the structural dynamics of the ribosome and its functional complexes.
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Affiliation(s)
- Hasan Demirci
- Molecular Biology, Cell Biology and Biochemistry, Brown University, 185 Meeting Street, Providence, RI 02912, USA.
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