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Ginzel JD, Chapman H, Sills JE, Allen EJ, Barak LS, Cardiff RD, Borowsky AD, Lyerly HK, Rogers BW, Snyder JC. Nonlinear progression across the occult transition establishes cancer lethality. bioRxiv 2024:2024.04.23.590826. [PMID: 38712192 PMCID: PMC11071403 DOI: 10.1101/2024.04.23.590826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Cancer screening is based upon a linear model of growth and invasion. Yet, early dissemination during the lengthy pre-diagnostic phase suggests that nonlinearity in growth can also occur. Therefore, we quantitatively traced the invisible and visible phases of tumorigenesis in the mammary gland for more than two-thousand tumors. Dynamic mathematical models of the invisible phase revealed an occult checkpoint resulting in nonlinear progression of transformed field cells. We found that expansile fields have increased dwell time at the occult checkpoint resulting in a large reservoir of image detectable precursors prior to invasion. In contrast, slowly proliferating lesions disseminate early and then transition rapidly through an occult checkpoint in a process we term nascent lethality. Our data illustrate how nonlinear growth across an occult checkpoint can account for a paradoxical increase in early-stage cancer detection without a dramatic reduction in metastatic burden. Highlights Growth during the invisible phase of tumorigenesis is a nonlinear processField size and field growth rate are uncoupled from metastatic potentialOccult transition rates vary by genotypeNascent lethal lesions are currently undetectable.
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Schmidt M, Malla TN, Zielinski K, Aldama L, Bajt S, Feliz D, Hayes B, Hunter M, Kupitz C, Lisova S, Knoska J, Martin-Garcia J, Mariani V, Pandey S, Poudyal I, Sierra R, Tolstikova A, Yefanov O, Yoon CH, Ourmazd A, Fromme P, Schwander P, Barty A, Chapman H, Stojković E, Batyuk A, Boutet S, Phillips G, Pollack L. Heterogeneity in the M. tuberculosis β-Lactamase Inhibition by Sulbactam. Res Sq 2023:rs.3.rs-2334665. [PMID: 36712138 PMCID: PMC9882615 DOI: 10.21203/rs.3.rs-2334665/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
For decades, researchers have been determined to elucidate essential enzymatic functions on the atomic lengths scale by tracing atomic positions in real time. Our work builds on new possibilities unleashed by mix-and-inject serial crystallography (MISC) 1-5 at X-ray free electron laser facilities. In this approach, enzymatic reactions are triggered by mixing substrate or ligand solutions with enzyme microcrystals 6 . Here, we report in atomic detail and with millisecond time-resolution how the Mycobacterium tuberculosis enzyme BlaC is inhibited by sulbactam (SUB). Our results reveal ligand binding heterogeneity, ligand gating 7-9 , cooperativity, induced fit 10,11 and conformational selection 11-13 all from the same set of MISC data, detailing how SUB approaches the catalytic clefts and binds to the enzyme non-covalently before reacting to a trans- enamine. This was made possible in part by the application of the singular value decomposition 14 to the MISC data using a newly developed program that remains functional even if unit cell parameters change during the reaction.
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Galchenkova M, Tolstikova A, Yefanov O, Chapman H. Data reduction in protein crystallography. Acta Cryst Sect A 2022. [DOI: 10.1107/s2053273322094517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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McKee DC, Chapman H, Yi J, Magtibay PM. Robotic Excision of Transobturator Midurethral Sling. J Minim Invasive Gynecol 2021. [DOI: 10.1016/j.jmig.2021.09.470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Stagno J, Lee YT, Chen J, Ding J, Yu P, Yefanov O, White T, Barty A, Sierra R, Spence J, Chapman H, Wang YX. Microgravity crystallization for improving uniformity and homogeneity of crystals for time-resolved diffusive mixing XFEL experiments. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321097531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Sarrou I, Feiler CG, Falke S, Peard N, Yefanov O, Chapman H. C-phycocyanin as a highly attractive model system in protein crystallography: unique crystallization properties and packing-diversity screening. Acta Crystallogr D Struct Biol 2021; 77:224-236. [PMID: 33559611 PMCID: PMC7869899 DOI: 10.1107/s2059798320016071] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/09/2020] [Indexed: 01/08/2023] Open
Abstract
The unique crystallization properties of the antenna protein C-phycocyanin (C-PC) from the thermophilic cyanobacterium Thermosynechococcus elongatus are reported and discussed. C-PC crystallizes in hundreds of significantly different conditions within a broad pH range and in the presence of a wide variety of precipitants and additives. Remarkably, the crystal dimensions vary from a few micrometres, as used in serial crystallography, to several hundred micrometres, with a very diverse crystal morphology. More than 100 unique single-crystal X-ray diffraction data sets were collected from randomly selected crystals and analysed. The addition of small-molecule additives revealed three new crystal packings of C-PC, which are discussed in detail. The high propensity of this protein to crystallize, combined with its natural blue colour and its fluorescence characteristics, make it an excellent candidate as a superior and highly adaptable model system in crystallography. C-PC can be used in technical and methods development approaches for X-ray and neutron diffraction techniques, and as a system for comprehending the fundamental principles of protein crystallography.
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Affiliation(s)
- Iosifina Sarrou
- Centre for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Christian G. Feiler
- Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - Sven Falke
- Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Notkestrasse 85, 22607 Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22607 Hamburg, Germany
| | - Nolan Peard
- Centre for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Oleksandr Yefanov
- Centre for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Henry Chapman
- Centre for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22607 Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22607 Hamburg, Germany
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Falke S, Feiler C, Chapman H, Sarrou I. Crystal structures of native cytochrome c 6 from Thermosynechococcus elongatus in two different space groups and implications for its oligomerization. Acta Crystallogr F Struct Biol Commun 2020; 76:444-452. [PMID: 32880593 PMCID: PMC7470040 DOI: 10.1107/s2053230x20010249] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 07/23/2020] [Indexed: 11/10/2022] Open
Abstract
Native cytochrome c6 was purified from an extract of strain BP-1 of the thermophilic cyanobacterium Thermosynechococcus elongatus. The protein was crystallized, and with only slight modifications of the buffer and vapour-diffusion conditions two different space groups were observed, namely H3 and C2. Both crystal structures were solved; they contained three and six molecules per asymmetric unit and were refined to 1.7 and 2.25 Å resolution, respectively. To date, the structure of native cytochrome c6 from T. elongatus has only been reported as a monomer using NMR spectroscopy, i.e. without addressing putative oligomerization, and related structures have only previously been solved using X-ray crystallography after recombinant gene overexpression in Escherichia coli. The reported space groups of related cyanobacterial cytochrome c6 structures differ from those reported here. Interestingly, the protein-protein interfaces that were observed utilizing X-ray crystallography could also explain homo-oligomerization in solution; specifically, trimerization is indicated by infra-red dynamic light scattering and blue native gel electrophoresis in solution. Trimers were also detected by mass spectrometry. Furthermore, there is an indication of post-translational methylation in the crystal structure. Additionally, the possibility of modifying the crystal size and the redox activity in the context of photosynthesis is shaping the investigated cytochrome as a highly suitable model protein for advanced serial crystallography at highly brilliant X-ray free-electron laser sources.
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Affiliation(s)
- Sven Falke
- Institute for Biochemistry and Molecular Biology, University of Hamburg, c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
| | - Christian Feiler
- Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - Henry Chapman
- Center for Free-Electron Laser Science, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Iosifina Sarrou
- Center for Free-Electron Laser Science, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
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Chapman H, McHenry A, Hibner M, de Souza K. 77: Tips and tricks: Presacral neurectomy. Am J Obstet Gynecol 2020. [DOI: 10.1016/j.ajog.2019.12.226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Yefanov O, Oberthür D, Bean R, Wiedorn MO, Knoska J, Pena G, Awel S, Gumprecht L, Domaracky M, Sarrou I, Lourdu Xavier P, Metz M, Bajt S, Mariani V, Gevorkov Y, White TA, Tolstikova A, Villanueva-Perez P, Seuring C, Aplin S, Estillore AD, Küpper J, Klyuev A, Kuhn M, Laurus T, Graafsma H, Monteiro DCF, Trebbin M, Maia FRNC, Cruz-Mazo F, Gañán-Calvo AM, Heymann M, Darmanin C, Abbey B, Schmidt M, Fromme P, Giewekemeyer K, Sikorski M, Graceffa R, Vagovic P, Kluyver T, Bergemann M, Fangohr H, Sztuk-Dambietz J, Hauf S, Raab N, Bondar V, Mancuso AP, Chapman H, Barty A. Evaluation of serial crystallographic structure determination within megahertz pulse trains. Struct Dyn 2019; 6:064702. [PMID: 31832488 PMCID: PMC6892710 DOI: 10.1063/1.5124387] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 10/21/2019] [Indexed: 05/30/2023]
Abstract
The new European X-ray Free-Electron Laser (European XFEL) is the first X-ray free-electron laser capable of delivering intense X-ray pulses with a megahertz interpulse spacing in a wavelength range suitable for atomic resolution structure determination. An outstanding but crucial question is whether the use of a pulse repetition rate nearly four orders of magnitude higher than previously possible results in unwanted structural changes due to either radiation damage or systematic effects on data quality. Here, separate structures from the first and subsequent pulses in the European XFEL pulse train were determined, showing that there is essentially no difference between structures determined from different pulses under currently available operating conditions at the European XFEL.
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Affiliation(s)
- Oleksandr Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Dominik Oberthür
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Richard Bean
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | - Juraj Knoska
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Gisel Pena
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Salah Awel
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Lars Gumprecht
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Martin Domaracky
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Iosifina Sarrou
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - P Lourdu Xavier
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Markus Metz
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Saša Bajt
- Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Valerio Mariani
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Thomas A White
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Aleksandra Tolstikova
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Pablo Villanueva-Perez
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Carolin Seuring
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Steve Aplin
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Armando D Estillore
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Alexander Klyuev
- Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Manuela Kuhn
- Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Torsten Laurus
- Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Heinz Graafsma
- Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | | | | | | | - Francisco Cruz-Mazo
- Dept. de Ingeniería Aeroespacial y Mecánica de Fluidos, ETSI, Universidad de Sevilla, 41092 Sevilla, Spain
| | - Alfonso M Gañán-Calvo
- Dept. de Ingeniería Aeroespacial y Mecánica de Fluidos, ETSI, Universidad de Sevilla, 41092 Sevilla, Spain
| | - Michael Heymann
- Intelligent Biointegrative Systems Group, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, D-70569 Stuttgart, Germany
| | - Connie Darmanin
- ARC Centre of Excellence in Advanced Molecular Imaging, La Trobe Institute for Molecular Sciences, La Trobe University, Victoria 3086, Australia
| | - Brian Abbey
- ARC Centre of Excellence in Advanced Molecular Imaging, La Trobe Institute for Molecular Sciences, La Trobe University, Victoria 3086, Australia
| | - Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave, Milwaukee, Wisconsin 53211, USA
| | - Petra Fromme
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona 85287-1604, USA
| | | | | | - Rita Graceffa
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | | | | | - Hans Fangohr
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | - Steffen Hauf
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Natascha Raab
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | | | | | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
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Sarrou I, Falke S, Komadina D, Tritschler F, Yefanov O, Chapman H. One step co-purification and crystallization of three soluble proteins from cyanobacteria, the unique crystallization properties of C-phycocyanin. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s2053273319094907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Chapman H, Moghaddam N. Published research on stress. Br Dent J 2019; 227:72. [PMID: 31350475 DOI: 10.1038/s41415-019-0577-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Jensen SC, Sullivan B, Hartzler D, Aguilar JM, Awel S, Bajt S, Basu S, Bean R, Chapman H, Conrad C, Frank M, Fromme R, Martin-Garcia JM, Grant TD, Heymann M, Hunter MS, Ketawala G, Kirian RA, Knoska J, Kupitz C, Li X, Liang M, Lisova S, Mariani V, Mazalova V, Messerschmidt M, Moran M, Nelson G, Oberthür D, Schaffer A, Sierra RG, Vaughn N, Weierstall U, Wiedorn MO, Xavier L, Yang JH, Yefanov O, Zatsepin NA, Aquila A, Fromme P, Boutet S, Seidler GT, Pushkar Y. X-ray Emission Spectroscopy at X-ray Free Electron Lasers: Limits to Observation of the Classical Spectroscopic Response for Electronic Structure Analysis. J Phys Chem Lett 2019; 10:441-446. [PMID: 30566358 PMCID: PMC7047744 DOI: 10.1021/acs.jpclett.8b03595] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
X-ray free electron lasers (XFELs) provide ultrashort intense X-ray pulses suitable to probe electron dynamics but can also induce a multitude of nonlinear excitation processes. These affect spectroscopic measurements and interpretation, particularly for upcoming brighter XFELs. Here we identify and discuss the limits to observing classical spectroscopy, where only one photon is absorbed per atom for a Mn2+ in a light element (O, C, H) environment. X-ray emission spectroscopy (XES) with different incident photon energies, pulse intensities, and pulse durations is presented. A rate equation model based on sequential ionization and relaxation events is used to calculate populations of multiply ionized states during a single pulse and to explain the observed X-ray induced spectral lines shifts. This model provides easy estimation of spectral shifts, which is essential for experimental designs at XFELs and illustrates that shorter X-ray pulses will not overcome sequential ionization but can reduce electron cascade effects.
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Affiliation(s)
- Scott C Jensen
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Brendan Sullivan
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Daniel Hartzler
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Jose Meza Aguilar
- Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Salah Awel
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, D-22607 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, 22761 Hamburg, Germany
| | - Saša Bajt
- Photon Science, Deutsches Elektronen-Synchrotron, D-22607 Hamburg, Germany
| | - Shibom Basu
- Paul Sherrer Institut, 5232 Villigen PSI, Switzerland
| | | | - Henry Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, D-22607 Hamburg, Germany
| | - Chelsie Conrad
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Matthias Frank
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Raimund Fromme
- Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
| | | | - Thomas D Grant
- Hauptman-Woodward Institute, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, NY 14203
- BioXFEL Science and Technology Center, Buffalo, NY 14203, USA
| | - Michael Heymann
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, D-22607 Hamburg, Germany
- Max Planck Institute of Biochemistry, 82152 Planegg, Germany
| | - Mark S. Hunter
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Gihan Ketawala
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Richard A Kirian
- Department of Physics, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Juraj Knoska
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, D-22607 Hamburg, Germany
| | - Christopher Kupitz
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53201, USA
| | - Xuanxuan Li
- Beijing Computational Science Research Center, Beijing 100193, China
| | - Mengning Liang
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Stella Lisova
- Department of Physics, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Valerio Mariani
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, D-22607 Hamburg, Germany
| | - Victoria Mazalova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, D-22607 Hamburg, Germany
| | | | - Michael Moran
- Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Garrett Nelson
- Department of Physics, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Dominik Oberthür
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, D-22607 Hamburg, Germany
| | - Alex Schaffer
- Department of Biochemistry, University of California Davis, Davis, CA 95616, USA
| | - Raymond G Sierra
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Natalie Vaughn
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Uwe Weierstall
- Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
- Department of Physics, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Max O. Wiedorn
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, D-22607 Hamburg, Germany
| | - Lourdu Xavier
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, D-22607 Hamburg, Germany
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Jay-How Yang
- Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, D-22607 Hamburg, Germany
| | - Nadia A Zatsepin
- Department of Physics, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Andrew Aquila
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Petra Fromme
- Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ85287-1604
| | - Sébastien Boutet
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Gerald T Seidler
- Department of Physics, University of Washington, Seattle, Washington 98195-1560, USA
| | - Yulia Pushkar
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
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Wiedorn MO, Oberthür D, Bean R, Schubert R, Werner N, Abbey B, Aepfelbacher M, Adriano L, Allahgholi A, Al-Qudami N, Andreasson J, Aplin S, Awel S, Ayyer K, Bajt S, Barák I, Bari S, Bielecki J, Botha S, Boukhelef D, Brehm W, Brockhauser S, Cheviakov I, Coleman MA, Cruz-Mazo F, Danilevski C, Darmanin C, Doak RB, Domaracky M, Dörner K, Du Y, Fangohr H, Fleckenstein H, Frank M, Fromme P, Gañán-Calvo AM, Gevorkov Y, Giewekemeyer K, Ginn HM, Graafsma H, Graceffa R, Greiffenberg D, Gumprecht L, Göttlicher P, Hajdu J, Hauf S, Heymann M, Holmes S, Horke DA, Hunter MS, Imlau S, Kaukher A, Kim Y, Klyuev A, Knoška J, Kobe B, Kuhn M, Kupitz C, Küpper J, Lahey-Rudolph JM, Laurus T, Le Cong K, Letrun R, Xavier PL, Maia L, Maia FRNC, Mariani V, Messerschmidt M, Metz M, Mezza D, Michelat T, Mills G, Monteiro DCF, Morgan A, Mühlig K, Munke A, Münnich A, Nette J, Nugent KA, Nuguid T, Orville AM, Pandey S, Pena G, Villanueva-Perez P, Poehlsen J, Previtali G, Redecke L, Riekehr WM, Rohde H, Round A, Safenreiter T, Sarrou I, Sato T, Schmidt M, Schmitt B, Schönherr R, Schulz J, Sellberg JA, Seibert MM, Seuring C, Shelby ML, Shoeman RL, Sikorski M, Silenzi A, Stan CA, Shi X, Stern S, Sztuk-Dambietz J, Szuba J, Tolstikova A, Trebbin M, Trunk U, Vagovic P, Ve T, Weinhausen B, White TA, Wrona K, Xu C, Yefanov O, Zatsepin N, Zhang J, Perbandt M, Mancuso AP, Betzel C, Chapman H, Barty A. Megahertz serial crystallography. Nat Commun 2018; 9:4025. [PMID: 30279492 PMCID: PMC6168542 DOI: 10.1038/s41467-018-06156-7] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 08/21/2018] [Indexed: 01/08/2023] Open
Abstract
The new European X-ray Free-Electron Laser is the first X-ray free-electron laser capable of delivering X-ray pulses with a megahertz inter-pulse spacing, more than four orders of magnitude higher than previously possible. However, to date, it has been unclear whether it would indeed be possible to measure high-quality diffraction data at megahertz pulse repetition rates. Here, we show that high-quality structures can indeed be obtained using currently available operating conditions at the European XFEL. We present two complete data sets, one from the well-known model system lysozyme and the other from a so far unknown complex of a β-lactamase from K. pneumoniae involved in antibiotic resistance. This result opens up megahertz serial femtosecond crystallography (SFX) as a tool for reliable structure determination, substrate screening and the efficient measurement of the evolution and dynamics of molecular structures using megahertz repetition rate pulses available at this new class of X-ray laser source.
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Grants
- Project oriented funds Helmholtz-Gemeinschaft (Helmholtz Gemeinschaft)
- DFG-EXC1074 Deutsche Forschungsgemeinschaft (German Research Foundation)
- R01 GM117342 NIGMS NIH HHS
- R01 GM095583 NIGMS NIH HHS
- 609920 European Research Council
- Wellcome Trust
- : The Helmholtz organisation through program oriented funds; excellence cluster "The Hamburg Center for Ultrafast Imaging – Structure, Dynamics and Control of Matter at the Atomic Scale" of the Deutsche Forschungsgemeinschaft (CUI, DFG-EXC1074); the European Research Council, “Frontiers in Attosecond X-ray Science: Imaging and Spectroscopy (AXSIS)”, ERC-2013-SyG 609920 (2014-2018); the Gottfried Wilhelm Leibniz Program of the DFG; the project “X-probe” funded by the European Union’s 2020 Research and Innovation Program under the Marie Sklodowska-Curie grant agreement 637295; the BMBF German-Russian Cooperation “SyncFELMed” grant 05K14CHA; European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) through the Consolidator Grant COMOTION (ERC-614507-Küpper); the Helmholtz Gemeinschaft through the "Impuls und Vernetzungsfond"; Helmholtz Initiative and Networking Fund through the Young Investigators Program and by the Deutsche Forschungsgemeinschaft SFB755/B03; the Swedish Research Council; the Knut and Alice Wallenberg Foundation; the Röntgen-Angström Cluster; the BMBF via projects 05K13GU7 and 05E13GU1; the from Ministry of Education, Science, Research and Sport of the Slovak Republic; the Joachim Herz Stiftung; the Deutsche Forschungsgemeinschaft (DFG) Cluster of Excellence “Inflammation at interfaces” (EXC 306); the Swedish Research Council; the Swedish Foundation for Strategic Research; the Australian Research Council Centre of Excellence in Advanced Molecular Imaging [CE140100011]; the Australian Nuclear Science and Technology Organisation (ANSTO); the International Synchrotron Access Program (ISAP) managed by the Australian Synchrotron, part of ANSTO, and funded by the Australian Government; The projects Structural dynamics of biomolecular systems (CZ.02.1.01/0.0/0.0/15_003/0000447) (ELIBIO) and Advanced research using high intensity laser produced photons and particles (CZ.02.1.01/0.0/0.0/16_019/0000789) (ADONIS) from European Regional Development Fund, the Ministry of Education, Youth and Sports as part of targeted support from the National Programme of Sustainability II; the Röntgen Ångström Cluster; the Chalmers Area of Advance, Material science; the Project DPI2016-78887-C3-1-R, Ministerio de Economía y Competitividad; the Wellcome Trust (studentship 075491/04); Rutgers University, Newark; the Max Planck Society; the NSF-STC “BioXFEL” through award STC-1231306; the Slovak Research and Development Agency under contract APVV-14-0181; the Wellcome Trust; Helmholtz Strategic Investment funds; Australian Research Council Centre of Excellence in Advanced Molecular Imaging [CE140100011], Australian Nuclear Science and Technology Organisation (ANSTO); The Swedish Research Council, the Knut and Alice Wallenberg Foundation, and the Röntgen-Angström Cluster, BMBF via projects 05K13GU7 and 05E13GU1, Ministry of Education, Science, Research and Sport of the Slovak Republic; BMBF grants 05K16GUA and 05K12GU3; the Joachim Herz Foundation through and Add-on Fellowship; NHMRC project grants 1107804 and 1108859, ARC Discovery Early Career Research Award (DE170100783); National Health and Medical Research Council (NHMRC grants 1107804, 1071659). BK is NHMRC Principal Research Fellow (1110971); National Science Foundation Grant # 1565180, "ABI Innovation: New Algorithms for Biological X-ray Free Electron Laser Data"; Diamond Light Source and from a Strategic Award from the Wellcome Trust and the Biotechnology and Biological Sciences Research Council (grant 102593); use of the XBI biological sample preparation laboratory, enabled by the XBI User Consortium. This work was performed, in part, under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. MLS, MAC and MF were supported by NIH grant 1R01GM117342-01
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Affiliation(s)
- Max O Wiedorn
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Dominik Oberthür
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Richard Bean
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Robin Schubert
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Notkestrasse 85, 22607, Hamburg, Germany
- Integrated Biology Infrastructure Life-Science Facility at the European XFEL (XBI), Holzkoppel 4, 22869, Schenefeld, Germany
| | - Nadine Werner
- Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Notkestrasse 85, 22607, Hamburg, Germany
| | - Brian Abbey
- Australian Research Council (ARC) Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Sciences, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Martin Aepfelbacher
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246, Hamburg, Germany
| | - Luigi Adriano
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Aschkan Allahgholi
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | | | - Jakob Andreasson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, 751 24, Sweden
- ELI Beamlines, Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 21, Prague, Czech Republic
- Condensed Matter Physics, Department of Physics, Chalmers University of Technology, Gothenburg, 412 96, Sweden
| | - Steve Aplin
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Salah Awel
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Kartik Ayyer
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Saša Bajt
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Imrich Barák
- Institute of Molecular Biology, SAS, Dubravska cesta 21, 845 51, Bratislava, Slovakia
| | - Sadia Bari
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Johan Bielecki
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Sabine Botha
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Notkestrasse 85, 22607, Hamburg, Germany
| | | | - Wolfgang Brehm
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Sandor Brockhauser
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
- Biological Research Centre (BRC), Hungarian Academy of Sciences, Temesvári krt. 62, Szeged, 6726, Hungary
| | - Igor Cheviakov
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246, Hamburg, Germany
| | - Matthew A Coleman
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA, 94550, USA
| | - Francisco Cruz-Mazo
- Depart. Ingeniería Aeroespacial y Mecánica de Fluidos ETSI, Universidad de Sevilla, 41092, Sevilla, Spain
| | | | - Connie Darmanin
- Australian Research Council (ARC) Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Sciences, La Trobe University, Bundoora, VIC, 3086, Australia
| | - R Bruce Doak
- Max Planck Institute for Medical Research, Jahnstr. 29, 69120, Heidelberg, Germany
| | - Martin Domaracky
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Katerina Dörner
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Yang Du
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Hans Fangohr
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
- Engineering and the Environment, University of Southampton, SO17 1BJ, Southampton, UK
| | - Holger Fleckenstein
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Matthias Frank
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA, 94550, USA
| | - Petra Fromme
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-1604, USA
| | - Alfonso M Gañán-Calvo
- Depart. Ingeniería Aeroespacial y Mecánica de Fluidos ETSI, Universidad de Sevilla, 41092, Sevilla, Spain
| | - Yaroslav Gevorkov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Hamburg University of Technology, Vision Systems E-2, Harburger Schloßstr. 20, 21079, Hamburg, Germany
| | | | - Helen Mary Ginn
- Division of Structural Biology, Headington, Oxford, OX3 7BN, UK
- Diamond Light Source, Research Complex at Harwell, and University of Oxford, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - Heinz Graafsma
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Mid Sweden University, Holmgatan 10, 85170, Sundsvall, Sweden
| | - Rita Graceffa
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Lars Gumprecht
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Peter Göttlicher
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, 751 24, Sweden
- ELI Beamlines, Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 21, Prague, Czech Republic
| | - Steffen Hauf
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Michael Heymann
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Susannah Holmes
- Australian Research Council (ARC) Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Sciences, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Daniel A Horke
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, 94025, CA, USA
| | - Siegfried Imlau
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | | | - Yoonhee Kim
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Alexander Klyuev
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Juraj Knoška
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Manuela Kuhn
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Christopher Kupitz
- Physics Department, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI, 53211, USA
| | - Jochen Küpper
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Department of Chemistry, Universität Hamburg, Martin-Luther-King Platz 6, 20146, Hamburg, Germany
| | - Janine Mia Lahey-Rudolph
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Torsten Laurus
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Karoline Le Cong
- Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Notkestrasse 85, 22607, Hamburg, Germany
| | - Romain Letrun
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - P Lourdu Xavier
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Max-Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Luis Maia
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Filipe R N C Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, 751 24, Sweden
- NERSC, Lawrence Berkeley National Laboratory, Berkeley, 94720, CA, USA
| | - Valerio Mariani
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | | | - Markus Metz
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Davide Mezza
- Paul Scherrer Institut, Forschungsstrasse 111, 5232, Villigen, Switzerland
| | - Thomas Michelat
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Grant Mills
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Diana C F Monteiro
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Andrew Morgan
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Kerstin Mühlig
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, 751 24, Sweden
| | - Anna Munke
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, 751 24, Sweden
| | - Astrid Münnich
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Julia Nette
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Keith A Nugent
- Australian Research Council (ARC) Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Sciences, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Theresa Nuguid
- Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Notkestrasse 85, 22607, Hamburg, Germany
| | - Allen M Orville
- Diamond Light Source, Research Complex at Harwell, and University of Oxford, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - Suraj Pandey
- Physics Department, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI, 53211, USA
| | - Gisel Pena
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Pablo Villanueva-Perez
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Jennifer Poehlsen
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | | | - Lars Redecke
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246, Hamburg, Germany
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Winnie Maria Riekehr
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Holger Rohde
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246, Hamburg, Germany
| | - Adam Round
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Tatiana Safenreiter
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Iosifina Sarrou
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Tokushi Sato
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI, 53211, USA
| | - Bernd Schmitt
- Paul Scherrer Institut, Forschungsstrasse 111, 5232, Villigen, Switzerland
| | - Robert Schönherr
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Joachim Schulz
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Jonas A Sellberg
- Biomedical and X-Ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology, Stockholm, 106 91, Sweden
| | - M Marvin Seibert
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, 751 24, Sweden
| | - Carolin Seuring
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Megan L Shelby
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA, 94550, USA
| | - Robert L Shoeman
- Max Planck Institute for Medical Research, Jahnstr. 29, 69120, Heidelberg, Germany
| | - Marcin Sikorski
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Claudiu A Stan
- Physics Department, Rutgers University Newark, Newark, NJ, 07102, USA
| | - Xintian Shi
- Paul Scherrer Institut, Forschungsstrasse 111, 5232, Villigen, Switzerland
| | - Stephan Stern
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Janusz Szuba
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Aleksandra Tolstikova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Martin Trebbin
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Department of Chemistry, University at Buffalo, 359 Natural Sciences Complex, Buffalo, NY, 14260, USA
- Institute of Nanostructure and Solid State Physics, Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Ulrich Trunk
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Patrik Vagovic
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Thomas Ve
- Institute for Glycomics, Griffith University, Southport, QLD, 4222, Australia
| | | | - Thomas A White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Krzysztof Wrona
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Chen Xu
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Nadia Zatsepin
- Department of Physics, Arizona State University, Tempe, AZ, 85287, USA
| | - Jiaguo Zhang
- Paul Scherrer Institut, Forschungsstrasse 111, 5232, Villigen, Switzerland
| | - Markus Perbandt
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Notkestrasse 85, 22607, Hamburg, Germany
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246, Hamburg, Germany
| | | | - Christian Betzel
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Notkestrasse 85, 22607, Hamburg, Germany
- Integrated Biology Infrastructure Life-Science Facility at the European XFEL (XBI), Holzkoppel 4, 22869, Schenefeld, Germany
| | - Henry Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.
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Lee DB, Kim JM, Seok JH, Lee JH, Jo JD, Mun JY, Conrad C, Coe J, Nelson G, Hogue B, White TA, Zatsepin N, Weierstall U, Barty A, Chapman H, Fromme P, Spence J, Chung MS, Oh CH, Kim KH. Supersaturation-controlled microcrystallization and visualization analysis for serial femtosecond crystallography. Sci Rep 2018; 8:2541. [PMID: 29416086 PMCID: PMC5803221 DOI: 10.1038/s41598-018-20899-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 01/23/2018] [Indexed: 11/09/2022] Open
Abstract
Time-resolved serial femtosecond crystallography with X-ray free electron laser (XFEL) holds the potential to view fast reactions occurring at near-physiological temperature. However, production and characterization of homogeneous micron-sized protein crystals at high density remain a bottleneck, due to the lack of the necessary equipments in ordinary laboratories. We describe here supersaturation-controlled microcrystallization and visualization and analysis tools that can be easily used in any laboratory. The microcrystallization conditions of the influenza virus hemagglutinin were initially obtained with low reproducibility, which was improved by employing a rapid evaporation of hanging drops. Supersaturation-controlled microcrystallization was then developed in a vapor diffusion mode, where supersaturation was induced by evaporation in hanging drops sequentially for durations ranging from 30 sec to 3 min, depending on the protein. It was applied successfully to the microcrystal formation of lysozyme, ferritin and hemagglutinin with high density. Moreover, visualization and analysis tools were developed to characterize the microcrystals observed by light microscopy. The size and density distributions of microcrystals analyzed by the tools were found to be consistent with the results of manual analysis, further validated by high-resolution microscopic analyses. Our supersaturation-controlled microcrystallization and visualization and analysis tools will provide universal access to successful XFEL studies.
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Affiliation(s)
- Dan Bi Lee
- Department of Biotechnology & Bioinformatics, Korea University, Sejong, Korea
| | - Jong-Min Kim
- Department of Electronics & Information Engineering, Korea University, Sejong, Korea
| | - Jong Hyeon Seok
- Department of Biotechnology & Bioinformatics, Korea University, Sejong, Korea
| | - Ji-Hye Lee
- Department of Biotechnology & Bioinformatics, Korea University, Sejong, Korea
| | - Jae Deok Jo
- Department of Biotechnology & Bioinformatics, Korea University, Sejong, Korea
| | - Ji Young Mun
- Department of Structure and Function of Neural Network, Korea Brain Research Institute, Daegu, Korea
| | - Chelsie Conrad
- Department of Chemistry, Arizona State University, Tempe, Arizona, USA
| | - Jesse Coe
- Department of Chemistry, Arizona State University, Tempe, Arizona, USA
| | - Garrett Nelson
- Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Brenda Hogue
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona, USA
| | - Thomas A White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Nadia Zatsepin
- Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Uwe Weierstall
- Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Henry Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Petra Fromme
- Department of Chemistry, Arizona State University, Tempe, Arizona, USA
| | - John Spence
- Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Mi Sook Chung
- Department of Food and Nutrition, Duksung Women's University, Seoul, Korea
| | - Chang-Hyun Oh
- Department of Electronics & Information Engineering, Korea University, Sejong, Korea.
| | - Kyung Hyun Kim
- Department of Biotechnology & Bioinformatics, Korea University, Sejong, Korea.
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15
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Chapman H. Macromolecular structure determination using X-ray FELs. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s2053273317095262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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16
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Li X, Chiu CY, Wang HJ, Kassemeyer S, Botha S, Shoeman RL, Lawrence RM, Kupitz C, Kirian R, James D, Wang D, Nelson G, Messerschmidt M, Boutet S, Williams GJ, Hartmann E, Jafarpour A, Foucar LM, Barty A, Chapman H, Liang M, Menzel A, Wang F, Basu S, Fromme R, Doak RB, Fromme P, Weierstall U, Huang MH, Spence JCH, Schlichting I, Hogue BG, Liu H. Corrigendum: Diffraction data of core-shell nanoparticles from an X-ray free electron laser. Sci Data 2017; 4:170154. [PMID: 29064473 PMCID: PMC5654363 DOI: 10.1038/sdata.2017.154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
This corrects the article DOI: 10.1038/sdata.2017.48.
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17
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Popp D, Loh ND, Zorgati H, Ghoshdastider U, Liow LT, Ivanova MI, Larsson M, DePonte DP, Bean R, Beyerlein KR, Gati C, Oberthuer D, Arnlund D, Brändén G, Berntsen P, Cascio D, Chavas LMG, Chen JPJ, Ding K, Fleckenstein H, Gumprecht L, Harimoorthy R, Mossou E, Sawaya MR, Brewster AS, Hattne J, Sauter NK, Seibert M, Seuring C, Stellato F, Tilp T, Eisenberg DS, Messerschmidt M, Williams GJ, Koglin JE, Makowski L, Millane RP, Forsyth T, Boutet S, White TA, Barty A, Chapman H, Chen SL, Liang M, Neutze R, Robinson RC. Flow-aligned, single-shot fiber diffraction using a femtosecond X-ray free-electron laser. Cytoskeleton (Hoboken) 2017; 74:472-481. [PMID: 28574190 DOI: 10.1002/cm.21378] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 05/25/2017] [Accepted: 05/29/2017] [Indexed: 01/26/2023]
Abstract
A major goal for X-ray free-electron laser (XFEL) based science is to elucidate structures of biological molecules without the need for crystals. Filament systems may provide some of the first single macromolecular structures elucidated by XFEL radiation, since they contain one-dimensional translational symmetry and thereby occupy the diffraction intensity region between the extremes of crystals and single molecules. Here, we demonstrate flow alignment of as few as 100 filaments (Escherichia coli pili, F-actin, and amyloid fibrils), which when intersected by femtosecond X-ray pulses result in diffraction patterns similar to those obtained from classical fiber diffraction studies. We also determine that F-actin can be flow-aligned to a disorientation of approximately 5 degrees. Using this XFEL-based technique, we determine that gelsolin amyloids are comprised of stacked β-strands running perpendicular to the filament axis, and that a range of order from fibrillar to crystalline is discernable for individual α-synuclein amyloids.
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Affiliation(s)
- David Popp
- Institute of Molecular and Cell Biology, Biopolis, A*STAR (Agency for Science, Technology and Research), 138673, Singapore
| | - N Duane Loh
- Department of Physics, National University of Singapore, 117557, Singapore.,Centre for BioImaging Sciences, National University of Singapore, 117546, Singapore
| | - Habiba Zorgati
- Institute of Molecular and Cell Biology, Biopolis, A*STAR (Agency for Science, Technology and Research), 138673, Singapore.,Department of Biochemistry, National University of Singapore, 117597, Singapore
| | - Umesh Ghoshdastider
- Institute of Molecular and Cell Biology, Biopolis, A*STAR (Agency for Science, Technology and Research), 138673, Singapore
| | - Lu Ting Liow
- Department of Medicine, National University of Singapore, 119074, Singapore
| | - Magdalena I Ivanova
- Department of Neurology, University of Michigan, 109 Zina Pitcher Pl, Ann Arbor, Michigan, 48109
| | - Mårten Larsson
- Institute of Molecular and Cell Biology, Biopolis, A*STAR (Agency for Science, Technology and Research), 138673, Singapore
| | - Daniel P DePonte
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025
| | - Richard Bean
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - Kenneth R Beyerlein
- 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
| | - Dominik Oberthuer
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607, Germany.,Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, 22607, Germany
| | - David Arnlund
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Gisela Brändén
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Peter Berntsen
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Duilio Cascio
- Howard Hughes Medical Institute, University of California, Los Angeles, California, 90095
| | - Leonard M G Chavas
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - Joe P J Chen
- Department of Electrical and Computer Engineering, Computational Imaging Group, University of Canterbury, Christchurch, New Zealand
| | - Ke Ding
- Institute of Molecular and Cell Biology, Biopolis, A*STAR (Agency for Science, Technology and Research), 138673, Singapore
| | - Holger Fleckenstein
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - Lars Gumprecht
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - Rajiv Harimoorthy
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Estelle Mossou
- Institut Laue-Langevin, Grenoble, 38000, France.,EPSAM/ISTM, Keele University, Staffordshire, ST5 5BG, United Kingdom
| | - Michael R Sawaya
- Howard Hughes Medical Institute, University of California, Los Angeles, California, 90095
| | - Aaron S Brewster
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Johan Hattne
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Nicholas K Sauter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Marvin Seibert
- Department of Cell and Molecular Biology, Molecular Biophysics, Uppsala University, Uppsala, 751 24, Sweden
| | - Carolin Seuring
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - Francesco Stellato
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - Thomas Tilp
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - David S Eisenberg
- Howard Hughes Medical Institute, University of California, Los Angeles, California, 90095
| | - Marc Messerschmidt
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025
| | - Garth J Williams
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025
| | - Jason E Koglin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025
| | - Lee Makowski
- Department of Bioengineering, Northeastern University, 360 Huntington Ave, Boston, Massachusetts, 02115
| | - Rick P Millane
- Department of Electrical and Computer Engineering, Computational Imaging Group, University of Canterbury, Christchurch, New Zealand
| | - Trevor Forsyth
- Institut Laue-Langevin, Grenoble, 38000, France.,EPSAM/ISTM, Keele University, Staffordshire, ST5 5BG, United Kingdom
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025
| | - Thomas A White
- 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
| | - Henry 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
| | - Swaine L Chen
- Department of Medicine, National University of Singapore, 119074, Singapore.,Genome Institute of Singapore, Biopolis, A*STAR (Agency for Science, Technology and Research), 138672, Singapore
| | - Mengning Liang
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Robert C Robinson
- Institute of Molecular and Cell Biology, Biopolis, A*STAR (Agency for Science, Technology and Research), 138673, Singapore.,Department of Biochemistry, National University of Singapore, 117597, Singapore.,Research Institute for Interdisciplinary Science, Okayama University, Okayama, 700-8530, Japan
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18
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Fischetti RF, Martin-Garcia J, Zatsepin N, Stander N, Zhu L, Subramanian G, Nelson G, Coe J, Nagaratnam N, Roy-Chowdury S, Kissick D, Ishchenko A, Conrad C, Ketawala G, James D, Zook J, Ogata C, Venugopalan N, Xu S, Meents A, Srajer V, Henning R, Chapman H, Spence J, Weierstall U, Cherezov V, Fromme P, Liu W. Monochromatic and polychromatic serial crystallography at the Advanced Photon Source. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s0108767317096404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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19
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Li X, Chiu CY, Wang HJ, Kassemeyer S, Botha S, Shoeman RL, Lawrence RM, Kupitz C, Kirian R, James D, Wang D, Nelson G, Messerschmidt M, Boutet S, Williams GJ, Hartmann E, Jafarpour A, Foucar LM, Barty A, Chapman H, Liang M, Menzel A, Wang F, Basu S, Fromme R, Doak RB, Fromme P, Weierstall U, Huang MH, Spence JCH, Schlichting I, Hogue BG, Liu H. Diffraction data of core-shell nanoparticles from an X-ray free electron laser. Sci Data 2017; 4:170048. [PMID: 28398334 PMCID: PMC5387922 DOI: 10.1038/sdata.2017.48] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 03/13/2017] [Indexed: 11/09/2022] Open
Abstract
X-ray free-electron lasers provide novel opportunities to conduct single particle analysis on nanoscale particles. Coherent diffractive imaging experiments were performed at the Linac Coherent Light Source (LCLS), SLAC National Laboratory, exposing single inorganic core-shell nanoparticles to femtosecond hard-X-ray pulses. Each facetted nanoparticle consisted of a crystalline gold core and a differently shaped palladium shell. Scattered intensities were observed up to about 7 nm resolution. Analysis of the scattering patterns revealed the size distribution of the samples, which is consistent with that obtained from direct real-space imaging by electron microscopy. Scattering patterns resulting from single particles were selected and compiled into a dataset which can be valuable for algorithm developments in single particle scattering research.
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Affiliation(s)
- Xuanxuan Li
- Complex Systems Division, Beijing Computational Science Research Center, ZPark II, Haidian, Beijing 100193, China.,Department of Engineering Physics, Tsinghua University, Beijing 100086, China
| | - Chun-Ya Chiu
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Hsiang-Ju Wang
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Stephan Kassemeyer
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120 Heidelberg, Germany
| | - Sabine Botha
- 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
| | - Robert M Lawrence
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, Arizona 85287, USA.,Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona 85287, USA
| | - Christopher Kupitz
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Richard Kirian
- Department of Physics, Arizona State University, Tempe, Arizona 85297, USA
| | - Daniel James
- Department of Physics, Arizona State University, Tempe, Arizona 85297, USA
| | - Dingjie Wang
- Department of Physics, Arizona State University, Tempe, Arizona 85297, USA
| | - Garrett Nelson
- Department of Physics, Arizona State University, Tempe, Arizona 85297, USA
| | - Marc Messerschmidt
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California 94025, 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
| | - Elisabeth Hartmann
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120 Heidelberg, Germany
| | - Aliakbar Jafarpour
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120 Heidelberg, Germany
| | - Lutz M Foucar
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120 Heidelberg, Germany
| | - Anton Barty
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Henry Chapman
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Mengning Liang
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Andreas Menzel
- Swiss Light Source, Paul Scherrer Institute, CH-5232 Villigen, Switzerland
| | - Fenglin Wang
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Shibom Basu
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona 85287, USA.,School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Raimund Fromme
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona 85287, USA.,School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - R Bruce Doak
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120 Heidelberg, Germany
| | - Petra Fromme
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona 85287, USA.,School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Uwe Weierstall
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona 85287, USA.,Department of Physics, Arizona State University, Tempe, Arizona 85297, USA
| | - Michael H Huang
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - John C H Spence
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona 85287, USA.,Department of Physics, Arizona State University, Tempe, Arizona 85297, USA
| | - Ilme Schlichting
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120 Heidelberg, Germany
| | - Brenda G Hogue
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, Arizona 85287, USA.,Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona 85287, USA.,School of Life Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Haiguang Liu
- Complex Systems Division, Beijing Computational Science Research Center, ZPark II, Haidian, Beijing 100193, China
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20
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Nogly P, Panneels V, Nelson G, Gati C, Kimura T, Milne C, Milathianaki D, Kubo M, Wu W, Conrad C, Coe J, Bean R, Zhao Y, Bath P, Dods R, Harimoorthy R, Beyerlein K, Rheinberger J, James D, DePonte D, Li C, Sala L, Williams G, Hunter M, Koglin JE, Berntsen P, Nango E, Iwata S, Chapman H, Fromme P, Frank M, Abela R, Boutet S, Barty A, White TA, Weierstall U, Spence J, Neutze R, Schertler G, Standfuss J. Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography. Acta Crystallogr A Found Adv 2016. [DOI: 10.1107/s2053273316099368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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21
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Viisanen H, Chapman H, Wei H, Lasierra Losada M, Koivisto A, Akerman KE, Pertovaara A. Pronociceptive effects induced by cutaneous application of a transient receptor potential ankyrin 1 (TRPA1) channel agonist methylglyoxal in diabetic animals: comparison with tunicamycin-induced endoplastic reticulum stress. J Physiol Pharmacol 2016; 67:587-594. [PMID: 27779479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 08/16/2016] [Indexed: 06/06/2023]
Abstract
Methylglyoxal (MG) is a reactive carbonyl compound generated in diabetes mellitus. MG is an established transient receptor potential ankyrin 1 (TRPA1) channel agonist that contributes to TRPA1-mediated diabetic pain hypersensitivity. Here we studied whether exposure to diabetes and thereby to elevated endogenous MG modulates hypersensitivity induced by intradermal MG. Moreover, since diabetes induces endoplasmic reticulum (ER) stress, we compared the role of TRPA1 in diabetes and ER stress by assessing whether tunicamycin-induced ER stress, without diabetes, produces TRPA1-mediated pain hypersensitivity and by assessing whether ER stress and diabetes have similar modulatory effects on MG-induced hypersensitivity. In vitro patch clamp recording was performed to assess whether tunicamycin is a TRPA1 agonist. Behavioral tests showed that mechanical hypersensitivity induced by MG is reduced in diabetes and ER stress. In healthy controls, hypersensitivity induced by MG was reduced when MG was administered for the second time in the same but not adjacent plantar sites. Hypersensitivity induced by ER stress was reversed by pharmacological blocking of TRPA1. In vitro patch clamp recording indicated that tunicamycin itself (30 μM) is not a TRPA1 agonist. The results indicate that pain hypersensitivity induced by non-diabetic ER stress as well as that induced by diabetes is mediated TRPA1. Reduction of MG-induced hypersensitivity in diabetes or ER stress may, at least partly, be explained by peripheral mechanisms.
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Affiliation(s)
- H Viisanen
- Department of Physiology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - H Chapman
- Orion Corporation, OrionPharma, Turku, Finland
| | - H Wei
- Department of Physiology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - M Lasierra Losada
- Department of Physiology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - A Koivisto
- Orion Corporation, OrionPharma, Turku, Finland
| | - K E Akerman
- Department of Physiology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - A Pertovaara
- Department of Physiology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
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22
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Chapman H, Bloomfield D, Cameron D, Bliss J, Barrett-Lee P, Canney P, Morden J, Velikova G, Hall P. 1231 Cost-effectiveness analysis of the use of pegfilgrastim to enable accelerated adjuvant chemotherapy in the TACT2 trial (CRUK/05/019). Eur J Cancer 2015. [DOI: 10.1016/s0959-8049(16)30535-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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23
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24
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Barends T, White TA, Barty A, Foucar L, Messerschmidt M, Alonso-Mori R, Botha S, Chapman H, Doak RB, Galli L, Gati C, Gutmann M, Koglin J, Markvardsen A, Nass K, Oberthur D, Shoeman RL, Schlichting I, Boutet S. Effects of self-seeding and crystal post-selection on the quality of Monte Carlo-integrated SFX data. J Synchrotron Radiat 2015; 22:644-52. [PMID: 25931080 DOI: 10.1107/s1600577515005184] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 03/13/2015] [Indexed: 05/17/2023]
Abstract
Serial femtosecond crystallography (SFX) is an emerging method for data collection at free-electron lasers (FELs) in which single diffraction snapshots are taken from a large number of crystals. The partial intensities collected in this way are then combined in a scheme called Monte Carlo integration, which provides the full diffraction intensities. However, apart from having to perform this merging, the Monte Carlo integration must also average out all variations in crystal quality, crystal size, X-ray beam properties and other factors, necessitating data collection from thousands of crystals. Because the pulses provided by FELs running in the typical self-amplified spontaneous emission (SASE) mode of operation have very irregular, spiky spectra that vary strongly from pulse to pulse, it has been suggested that this is an important source of variation contributing to inaccuracies in the intensities, and that, by using monochromatic pulses produced through a process called self-seeding, fewer images might be needed for Monte Carlo integration to converge, resulting in more accurate data. This paper reports the results of two experiments performed at the Linac Coherent Light Source in which data collected in both SASE and self-seeded mode were compared. Importantly, no improvement attributable to the use of self-seeding was detected. In addition, other possible sources of variation that affect SFX data quality were investigated, such as crystal-to-crystal variations reflected in the unit-cell parameters; however, these factors were found to have no influence on data quality either. Possibly, there is another source of variation as yet undetected that affects SFX data quality much more than any of the factors investigated here.
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Affiliation(s)
- Thomas Barends
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
| | - Thomas A White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Lutz Foucar
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
| | - Marc Messerschmidt
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Roberto Alonso-Mori
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Sabine Botha
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
| | - Henry Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - R Bruce Doak
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
| | - Lorenzo Galli
- 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
| | - Matthias Gutmann
- Rutherford Appleton Laboratory, Harwell, Oxford OX11 0QX, England
| | - Jason Koglin
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | | | - Karol Nass
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
| | - Dominik Oberthur
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Robert L Shoeman
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
| | - Ilme Schlichting
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
| | - Sébastien Boutet
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
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25
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Ekeberg T, Svenda M, Abergel C, Maia FRNC, Seltzer V, Claverie JM, Hantke M, Jönsson O, Nettelblad C, van der Schot G, Liang M, DePonte DP, Barty A, Seibert MM, Iwan B, Andersson I, Loh ND, Martin AV, Chapman H, Bostedt C, Bozek JD, Ferguson KR, Krzywinski J, Epp SW, Rolles D, Rudenko A, Hartmann R, Kimmel N, Hajdu J. Three-dimensional reconstruction of the giant mimivirus particle with an x-ray free-electron laser. Phys Rev Lett 2015; 114:098102. [PMID: 25793853 DOI: 10.1103/physrevlett.114.098102] [Citation(s) in RCA: 183] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Indexed: 05/19/2023]
Abstract
We present a proof-of-concept three-dimensional reconstruction of the giant mimivirus particle from experimentally measured diffraction patterns from an x-ray free-electron laser. Three-dimensional imaging requires the assembly of many two-dimensional patterns into an internally consistent Fourier volume. Since each particle is randomly oriented when exposed to the x-ray pulse, relative orientations have to be retrieved from the diffraction data alone. We achieve this with a modified version of the expand, maximize and compress algorithm and validate our result using new methods.
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Affiliation(s)
- Tomas Ekeberg
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Martin Svenda
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Chantal Abergel
- Génomique & Structurale - IGS - UMR 7256, CNRS, Aix-Marseille Université, Institut de Microbiologie de la Méditerranée, Parc Scientifique de Luminy, Case 934, 13288 Marseille Cedex 9, France
| | - Filipe R N C Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- NERSC, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Virginie Seltzer
- Génomique & Structurale - IGS - UMR 7256, CNRS, Aix-Marseille Université, Institut de Microbiologie de la Méditerranée, Parc Scientifique de Luminy, Case 934, 13288 Marseille Cedex 9, France
| | - Jean-Michel Claverie
- Génomique & Structurale - IGS - UMR 7256, CNRS, Aix-Marseille Université, Institut de Microbiologie de la Méditerranée, Parc Scientifique de Luminy, Case 934, 13288 Marseille Cedex 9, France
| | - Max Hantke
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Olof Jönsson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Carl Nettelblad
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Gijs van der Schot
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Mengning Liang
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Daniel P DePonte
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Anton Barty
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - M Marvin Seibert
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Bianca Iwan
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- Attophysics Group, CEA-Saclay, 91191 Gif sur Yvette Cedex, France
| | - Inger Andersson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - N Duane Loh
- Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4 Blk S1 A, Singapore 117546, Singapore
| | - Andrew V Martin
- The University of Melbourne, Parkville, 3010 Victoria, Australia
| | - Henry Chapman
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- University of Hamburg, Notkestrasse 85, 22607 Hamburg, Germany
| | - Christoph Bostedt
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - John D Bozek
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Ken R Ferguson
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Jacek Krzywinski
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Sascha W Epp
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - Daniel Rolles
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
- J. R. Macdonald Laboratory, Department of Physics, Kansas State University, 116 Cardwell Hall, Manhattan, Kansas 66506, USA
| | - Artem Rudenko
- J. R. Macdonald Laboratory, Department of Physics, Kansas State University, 116 Cardwell Hall, Manhattan, Kansas 66506, USA
| | | | - Nils Kimmel
- Max-Planck-Institut Halbleiterlabor, Otto-Hahn-Ring 6, 81739 München, Germany
- Max-Planck-Institut für extraterrestrische Physik, Giessenbachstrasse, 85741 Garching, Germany
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- European XFEL, Albert-Einstein-Ring 19, 22761 Hamburg, Germany
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26
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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27
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Vendrell O, Küpper J, Wolf M, Chapman H, Chergui M, Reid K, von Haeften K, Moshammer R, Williams G, Tehlar A, Dixit G, Wörner HJ, Underwood J, Marangos J, Woerner M, Bressler C, Minitti M, Kirrander A, Vozzi C, Rolles D. Chemical reaction dynamics I and electron dynamics in molecules: general discussion. Faraday Discuss 2014; 171:145-68. [PMID: 25285433 DOI: 10.1039/c4fd90014f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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28
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Küpper J, Williams G, Chapman H, Reid K, Christensen J, Wörner HJ, Seddon E, Dixit G, Campbell E, Underwood J, Woerner M, Spence J, van Thor J, Wolf M, Vendrell O, Giovanni DN, Bressler C, Berrah N. Instrumentation and methods: general discussion. Faraday Discuss 2014; 171:505-23. [PMID: 25285779 DOI: 10.1039/c4fd90017k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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Chapman H, Chergui M, Küpper J, Wolf M, Reid K, Flavell W, Williams G, Gierz I, Seddon E, Wörner HJ, Rossnagel K, Underwood J, Woerner M, Weinstein J, Bressler C, Smolentsev G, von Haeften K, Spencer B, Neppl S, Berrah N. Chemical reaction dynamics II and Correlated systems, surfaces and catalysis: general discussion. Faraday Discuss 2014; 171:323-56. [DOI: 10.1039/c4fd90015d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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30
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Chapman H, Chergui M, McCoustra M, van Thor J, Underwood J, Woerner M, Bressler C, Smolentsev G, Küpper J, Jacobsen C. Nanoscale and bio imaging: general discussion. Faraday Discuss 2014; 171:419-27. [DOI: 10.1039/c4fd90016b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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31
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Saarnilehto M, Chapman H, Savinko T, Lindstedt K, Lauerma AI, Koivisto A. Contact sensitizer 2,4-dinitrochlorobenzene is a highly potent human TRPA1 agonist. Allergy 2014; 69:1424-7. [PMID: 25041656 DOI: 10.1111/all.12488] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2014] [Indexed: 11/27/2022]
Abstract
2,4-Dinitrochlorobenzene (DNCB) is widely used in human clinical studies and in experimental animal studies to evoke allergic contact dermatitis. 2,4-Dinitrochlorobenzene is a potent immunogen capable of inducing contact sensitization in all humans exposed. However, the mechanism by which DNCB evokes such symptoms is presently unknown. TRPA1 is a nonselective cation channel that is expressed in peptidergic sensory neurons and fibroblasts. TRPA1 activation was recently implicated in the pathophysiology of atopic dermatitis especially in transducing cutaneous itch signals. Here, we test the hypothesis that DNCB acts as a TRPA1 agonist and thereby evokes allergic symptoms. We found that DNCB activates human TRPA1 dose dependently in FLIPR experiments with an EC50 of 167 nM, an effect that was fully blocked by selective TRPA1 antagonists Chembridge-5861528 and A-967079. Similarly, DNCB activated nonselective TRPA1 current in patch clamp studies. Neutralization of 3 critical cysteines in TRPA1 resulted in a loss of DNCB agonism.
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Affiliation(s)
| | - H. Chapman
- In Vitro Biology; R&D; Orion Pharma; Turku Finland
| | - T. Savinko
- Institute of Biotechnology; University of Helsinki; Helsinki Finland
| | | | - A. I. Lauerma
- Department of Dermatology; University of Helsinki and Helsinki University Central Hospital; Helsinki Finland
| | - A. Koivisto
- In Vitro Biology; R&D; Orion Pharma; Turku Finland
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32
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Messerschmidt M, Chavas L, Ananthaneni S, Dadgostar H, Graafsma H, Liang M, Mancuso A, Raabe S, Stern S, Vagovic P, Chapman H. Serial Femtosecond Crystallography user's consortium apparatus at European XFEL. Acta Crystallogr A Found Adv 2014. [DOI: 10.1107/s2053273314082515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The Serial Femtosecond Crystallography (SFX) user's consortium apparatus is to be installed within the Single Particles, Clusters and Biomolecules (SPB) instrument of the European X-ray Free-Electron Laser facility (XFEL.EU) [1, 2]. The XFEL.EU will provide ultra-short, highly intense, coherent X-ray pulses at an unprecedented repetition rate. The experimental setup and methodological approaches of many scientific areas will be transformed, including structural biology that could potentially overcome common problems and bottlenecks encountered in crystallography, such as creating large crystals, dealing with radiation damage, or understanding sub-picosecond time-resolved phenomena. The key concept of the SFX method is based on the kinetic insertion of protein crystal samples in solution via a gas dynamic virtual nozzle jet and recording diffraction signals of individual, randomly oriented crystals passing through the XFEL beam, as first demonstrated by Chapman et al. [3]. The SFX-apparatus will refocus the beam spent by the SPB instrument into a second interaction region, in some cases enabling two parallel experiments. The planned photon energy range at the SPB instrument is from 3 to 16 keV. The Adaptive Gain Integrating Pixel Detector (AGIPD) is to be implemented in the SPB instrument, including a 4 Megapixel version for the SFX-apparatus. The AGIPD is designed to store over 350 data frames from successive pulses, and aims to collect more than 3,000 images per second. Together with the implementation of automated procedures for sample exchange and injection, high-throughput nanocrystallography experiments can be integrated at the SFX-apparatus. In this work, we review the overall design of the SFX-apparatus and discuss the main parameters and challenges
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33
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Passon D, Jakobi A, Stellato F, Liang M, Knoops K, Komadina D, Williams C, White T, Bourenkov G, Messerschmidt M, van der Klei I, Chapman H, Wilmanns M. Serial femtosecond X-ray diffraction of in vivo crystals in intact yeast cells. Acta Crystallogr A Found Adv 2014. [DOI: 10.1107/s2053273314094297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Peroxisomes are membrane-enclosed organelles in eukaryotic cells with important roles in lipid metabolism and the scavenging of reactive oxygen species. Peroxisomes are capable of carrying an unusually high load of proteins, which under appropriate nutrient conditions results in the in situ crystallization of peroxisomal proteins in several yeast species and vertebrate hepatocytes [1,2]. In the methylotrophic yeast H.polymorpha, the predominant peroxisomal protein alcohol/methanol oxidase (AO) oligomerizes into octameric assemblies with a molecular mass of 600 kDa that spontaneously form 200-500 nm crystallites within peroxisomes [1]. We exposed H.polymorpha cell suspensions containing peroxisome-confined AO crystallites to femtosecond X-ray pulses at the Coherent X-ray Imaging (CXI) experimental endstation at the Linac Coherent Light Source. Peak detection routines mining the resulting scattering profiles identified >5000 Bragg-sampled diffraction patterns, providing the proof of concept that background scattering from the cells does not deteriorate the signal-to-noise ratio to an extent precluding observation of diffraction from individual AO crystallites. Summation patterns assembled from the individual frames match low-resolution powder diffraction patterns from concentrated suspensions of purified peroxisomes collected at the P14 beamline at the PETRAIII synchrotron, confirming that the observed diffraction mainly results from Bragg scattering of peroxisomal crystallites. To the best of our knowledge our data are the first to report room temperature X-ray diffraction from functional protein crystals in their native cellular environment. Currently the maximum resolution achieved in the diffraction patterns is limited to 20-15 Å. Future work will need to address improved sample preparation protocols in order to assess whether diffraction to a resolution sufficient to permit structure solution can be obtained. Protein crystal formation in vivo has been observed under physiological or pathological conditions in a number of other systems [3]. We hope that our results will help to establish serial femtosecond X-ray diffraction (SFX) as a method for structural characterization of cellular structures with crystalline content and provide a proof of concept for using in situ crystallization of proteins as a means to generate nanocrystalline samples for SFX.
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34
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Gati C, Bourenkov G, Klinge M, Rehders D, Stellato F, Oberthuer D, Betzel C, Schneider T, Chapman H, Redecke L. Serial crystallography using synchrotron radiation - novel strategies for microcrystallography. Acta Crystallogr A Found Adv 2014. [DOI: 10.1107/s2053273314096831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Protein crystallography continues to be one of the most frequently used techniques to obtain structural information of biomacromolecules to atomic resolution. Since protein crystals of delicate target systems are often limited in size, one of the main goals in the design of modern beamlines is the construction of highly intense X-ray beams with small focal size to obtain high resolution diffraction images of microcrystals. However, this development has led to the situation, that the full intensity of the beam can destroy a protein crystal within fractions of a second. Therefore often only a small number of diffraction patterns can be obtained from one single crystal. Here we describe the adaptation of the serial crystallography approach, which has first been developed at X-ray Free-Electron Lasers (Chapman et al. 2011) to the usage of a microfocus synchrotron beamline, using a standard cryogenic loop for sample delivery. We proved this concept with in vivo grown cathepsinB microcrystals (TbCatB, Koopmann et al. 2012, Redecke et al. 2013) (average of 9 μm3), a medically and pharmaceutically relevant protein, involved in the life cycle of T. brucei. In these experiments it was possible to show that serial crystallography enables the utilization and outcome of the above described bottlenecks and features of modern 3rd generation synchrotron microfocus beamlines. Our strategy exploits the combination of a micron-sized X-ray beam, high precision diffractometry and shutterless data acquisition with a pixel-array detector. By combining the data of 80 TbCatB crystals, it was possible to assemble a dataset to 3.0 Å resolution. The data allow the refinement of a structural model that is consistent with that previously obtained using FEL radiation, providing mutual validation.
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35
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Stern S, Chavas L, Chapman H, Mancuso A, Aquila A, Giewekemeyer K, Becker J, Graafsma H, Schmitt B. AGIPD detector for Serial Femtosecond Crystallography Apparatus at European XFEL. Acta Crystallogr A Found Adv 2014. [DOI: 10.1107/s205327331409305x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The European X-ray Free-Electron Laser (XFEL.EU) [1] will provide ultra-short, highly-intense, coherent x-ray pulses at an unprecedented repetition rate, transforming experiments in many scientific areas, including serial femtosecond crystallography (SFX). For the purpose of SFX experiments at the XFEL.EU, a dedicated endstation is being developed to be installed within the Single Particles, Clusters and Biomolecules (SPB) instrument [2]. The setup will refocus the beam spent by SPB into a second interaction region, thereby enabling two parallel experiments. In order to overcome various challenges in XFEL crystallography, and to optimize the output for SFX experiments at XFEL.EU, the Adaptive Gain Integrating Pixel Detector (AGIPD) [3] is currently under development and is to be implemented in the SPB instrument, including a 4 Megapixel version for the SFX apparatus. The AGIPD is a hybrid-pixel detector with pixels of 200 x 200 micron^2 each. The gain of each single pixel dynamically and independently adapts to the incoming signal. Thus, diffraction patterns of high dynamic range can be recorded, with the measured signal within a single data frame ranging from single photons and up to 1e+4 photons at 12 keV. Moreover, the AGIPD is designed to store over 350 data frames from successive pulses prior to digitization and read-out, thereby enabling operation at the European XFEL with its challenging repetition rate with 10 Hz pulse trains and a 4.5 MHz intra-train repetition rate. Furthermore, the incorporation of a veto system in AGIPD will allow one to potentially store only the frames that contain diffraction data from actual crystal hits, which ultimately increases the efficiency of the detector and DAQ systems dramatically. In the present work, we will review the design of the 4Mpix AGIPD for the SFX apparatus and discuss simulations and tests of its expected performance under the conditions foreseen for SFX experiments at the XFEL.EU.
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36
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Barty A, Kirian RA, Maia FRNC, Hantke M, Yoon CH, White TA, Chapman H. Cheetah: software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction data. J Appl Crystallogr 2014; 47:1118-1131. [PMID: 24904246 PMCID: PMC4038800 DOI: 10.1107/s1600576714007626] [Citation(s) in RCA: 262] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 04/04/2014] [Indexed: 11/10/2022] Open
Abstract
The emerging technique of serial X-ray diffraction, in which diffraction data are collected from samples flowing across a pulsed X-ray source at repetition rates of 100 Hz or higher, has necessitated the development of new software in order to handle the large data volumes produced. Sorting of data according to different criteria and rapid filtering of events to retain only diffraction patterns of interest results in significant reductions in data volume, thereby simplifying subsequent data analysis and management tasks. Meanwhile the generation of reduced data in the form of virtual powder patterns, radial stacks, histograms and other meta data creates data set summaries for analysis and overall experiment evaluation. Rapid data reduction early in the analysis pipeline is proving to be an essential first step in serial imaging experiments, prompting the authors to make the tool described in this article available to the general community. Originally developed for experiments at X-ray free-electron lasers, the software is based on a modular facility-independent library to promote portability between different experiments and is available under version 3 or later of the GNU General Public License.
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Affiliation(s)
- Anton Barty
- Centre for Free Electron Laser Science, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Richard A. Kirian
- Centre for Free Electron Laser Science, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Filipe R. N. C. Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
- NERSC, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Max Hantke
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Chun Hong Yoon
- Centre for Free Electron Laser Science, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, Hamburg 22607, Germany
- European XFEL GmbH, Albert Einstein Ring 19, Hamburg 22761, Germany
| | - Thomas A. White
- Centre for Free Electron Laser Science, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Henry Chapman
- Centre for Free Electron Laser Science, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, Hamburg 22607, Germany
- University of Hamburg, Luruper Chaussee 14, Hamburg 22761, Germany
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Redecke L, Betzel C, Rehders D, Nass K, DePonte DP, White T, Duszenko M, Spence J, Fromme P, Schlichting I, Chapman H. Free electron laser radiation and in vivogrown nano-crystals open new routes in structural biology and options for time-resolved experiments. Acta Crystallogr A 2013. [DOI: 10.1107/s0108767313099789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Arnlund D, Johansson L, Katona G, Malmerberg E, Davidsson J, Barty A, Schlichting I, Boutet S, Fromme P, Spence J, Chapman H, Neutze R. Visualising rapid structural changes in photosynthetic reaction centres with XFEL radiation. Acta Crystallogr A 2012. [DOI: 10.1107/s010876731209976x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Fromme P, Chapman H, Kupitz C, Hunter MS, Kirian RA, Barty A, White TA, Aquilla A, Stellato F, Beyerlein K, DePonte DP, Frank M, Schlichting I, Shoeman R, Lomb L, Steinbrenner J, Nass K, Boutet S, Bogan MJ, Williams G, Zatsepin N, Basu S, Wang D, James D, Fromme R, Grotjohann I, Bottin H, Cherezov V, Stevens R, Cobbe D, Cramer W, Stroud R, Doak RB, Weierstall U, Schmidt K, Spence JCH. Femtosecond nanocrystallography of membrane proteins opens a new era for structural biology. Acta Crystallogr A 2012. [DOI: 10.1107/s0108767312099461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Betzel C, Meyer A, Dierks K, Einspahr H, Hilgenfeld R, Redecke L, Duszensko M, Chapman H. Latest methods to grow and prepare micro- and nano-crystals for future free-electron laser and synchrotron radiation sources. Acta Crystallogr A 2012. [DOI: 10.1107/s0108767312099795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Huston R, Chan YC, Chapman H, Gardner T, Shaw G. Source apportionment of heavy metals and ionic contaminants in rainwater tanks in a subtropical urban area in Australia. Water Res 2012; 46:1121-1132. [PMID: 22196953 DOI: 10.1016/j.watres.2011.12.008] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Revised: 11/09/2011] [Accepted: 12/05/2011] [Indexed: 05/31/2023]
Abstract
Due to prolonged droughts in recent years, the use of rainwater tanks in urban areas has increased in Australia. In order to apportion sources of contribution to heavy metal and ionic contaminants in rainwater tanks in Brisbane, a subtropical urban area in Australia, monthly tank water samples (24 sites, 31 tanks) and concurrent bulk deposition samples (18 sites) were collected during mainly April 2007-March 2008. The samples were analysed for acid-soluble metals, soluble anions, total inorganic carbon and total organic carbon, and characteristics such as total solid and pH. The Positive Matrix Factorisation model, EPA PMF 3.0, was used to apportion sources of contribution to the contaminants. Four source factors were identified for the bulk deposition samples, including 'crustal matter/sea salt', 'car exhausts/road side dust', 'industrial dust' and 'aged sea salt/secondary aerosols'. For the tank water samples, apart from these atmospheric deposition related factors which contributed in total to 65% of the total contaminant concentration on average, another six rainwater collection system related factors were identified, including 'plumbing', 'building material', 'galvanizing', 'roofing', 'steel' and 'lead flashing/paint' (contributing in total to 35% of the total concentration on average). The Australian Drinking Water Guideline for lead was exceeded in 15% of the tank water samples. The collection system related factors, in particular the 'lead flashing/paint' factor, contributed to 79% of the lead in the tank water samples on average. The concentration of lead in tank water was found to vary with various environmental and collection system factors, in particular the presence of lead flashing on the roof. The results also indicated the important role of sludge dynamics inside the tank on the quality of tank water.
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Affiliation(s)
- R Huston
- School of Environment, Griffith University, Nathan Campus, Queensland, Australia
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Koch CT, Zuo JM, Chapman H. Introduction to the special issue in honor of Regents' Prof. John C.H. Spence in occasion of his 65th birthday. Ultramicroscopy 2011; 111:745-6. [PMID: 21664547 DOI: 10.1016/j.ultramic.2011.03.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Brock J, Jones C, Wells E, Chapman H, Corsini L, Burke K, Brada M. 2064 POSTER Comparing Volumetric Intensity Modulated Arc Therapy With Multiple Static Field Radiosurgery for Brain Metastases. Eur J Cancer 2011. [DOI: 10.1016/s0959-8049(11)71022-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Neutze R, Johansson L, Wöhri A, Katona G, Malmerberg E, Arnlund D, Davidsson J, Wulff M, Groenhof G, Chapman H, Spence J, Fromme P. Potential impact of an X-FEL on time-resolved studies of protein dynamics. Acta Crystallogr A 2011. [DOI: 10.1107/s0108767311097777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Koch C, Zuo JM, Chapman H. J. Spence's 65th birthday. Ultramicroscopy 2011. [DOI: 10.1016/s0304-3991(11)00131-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Padilla MB, Reyes AM, Connolly M, Natsui S, Puello A, Chapman H. Examining the policy climate for HIV prevention in the Caribbean tourism sector: a qualitative study of policy makers in the Dominican Republic. Health Policy Plan 2011; 27:245-55. [DOI: 10.1093/heapol/czr021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Chapman H. Fermtosecond Coherent X-Ray Nanocrystallography at LCLS. Biophys J 2011. [DOI: 10.1016/j.bpj.2010.12.402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Sokolowski-Tinten K, Barty A, Boutet S, Shymanovich U, Chapman H, Bogan M, Marchesini S, Hau-Riege S, Stojanovic N, Bonse J, Rosandi Y, Urbassek HM, Tobey R, Ehrke H, Cavalleri A, Düsterer S, Redlin H, Frank M, Bajt S, Schulz J, Seibert M, Hajdu J, Treusch R, Bostedt C, Hoener M, Möeller T. Short-pulse Laser Induced Transient Structure Formation and Ablation Studied with Time-resolved Coherent XUV-scattering. ACTA ACUST UNITED AC 2011. [DOI: 10.1557/proc-1230-mm05-03] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AbstractThe structural dynamics of short-pulse laser irradiated surfaces and nano-structures has been studied with nm spatial and ultrafast temporal resolution by means of single-shot coherent XUV-scattering techniques. The experiments allowed us to time-resolve the formation of laser-induced periodic surface structures, and to follow the expansion and disintegration of nano-objects during laser ablation.
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Nelson AJ, Toleikis S, Chapman H, Bajt S, Krzywinski J, Chalupsky J, Juha L, Cihelka J, Hajkova V, Vysin L, Burian T, Kozlova M, Fäustlin RR, Nagler B, Vinko SM, Whitcher T, Dzelzainis T, Renner O, Saksl K, Khorsand AR, Heimann PA, Sobierajski R, Klinger D, Jurek M, Pelka J, Iwan B, Andreasson J, Timneanu N, Fajardo M, Wark JS, Riley D, Tschentscher T, Hajdu J, Lee RW. Soft x-ray free electron laser microfocus for exploring matter under extreme conditions. Opt Express 2009; 17:18271-8. [PMID: 19907618 DOI: 10.1364/oe.17.018271] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We have focused a beam (BL3) of FLASH (Free-electron LASer in Hamburg: lambda = 13.5 nm, pulse length 15 fs, pulse energy 10-40 microJ, 5 Hz) using a fine polished off-axis parabola having a focal length of 270 mm and coated with a Mo/Si multilayer with an initial reflectivity of 67% at 13.5 nm. The OAP was mounted and aligned with a picomotor controlled six-axis gimbal. Beam imprints on poly(methyl methacrylate) - PMMA were used to measure focus and the focused beam was used to create isochoric heating of various slab targets. Results show the focal spot has a diameter of < or =1 microm. Observations were correlated with simulations of best focus to provide further relevant information.
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Affiliation(s)
- A J Nelson
- LawrenceLivermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA.
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