1
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Sonker M, Doppler D, Egatz-Gomez A, Zaare S, Rabbani MT, Manna A, Cruz Villarreal J, Nelson G, Ketawala GK, Karpos K, Alvarez RC, Nazari R, Thifault D, Jernigan R, Oberthür D, Han H, Sierra R, Hunter MS, Batyuk A, Kupitz CJ, Sublett RE, Poitevin F, Lisova S, Mariani V, Tolstikova A, Boutet S, Messerschmidt M, Meza-Aguilar JD, Fromme R, Martin-Garcia JM, Botha S, Fromme P, Grant TD, Kirian RA, Ros A. Electrically stimulated droplet injector for reduced sample consumption in serial crystallography. Biophys Rep (N Y) 2022; 2:100081. [PMID: 36425668 PMCID: PMC9680787 DOI: 10.1016/j.bpr.2022.100081] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
With advances in X-ray free-electron lasers (XFELs), serial femtosecond crystallography (SFX) has enabled the static and dynamic structure determination for challenging proteins such as membrane protein complexes. In SFX with XFELs, the crystals are typically destroyed after interacting with a single XFEL pulse. Therefore, thousands of new crystals must be sequentially introduced into the X-ray beam to collect full data sets. Because of the serial nature of any SFX experiment, up to 99% of the sample delivered to the X-ray beam during its "off-time" between X-ray pulses is wasted due to the intrinsic pulsed nature of all current XFELs. To solve this major problem of large and often limiting sample consumption, we report on improvements of a revolutionary sample-saving method that is compatible with all current XFELs. We previously reported 3D-printed injection devices coupled with gas dynamic virtual nozzles (GDVNs) capable of generating samples containing droplets segmented by an immiscible oil phase for jetting crystal-laden droplets into the path of an XFEL. Here, we have further improved the device design by including metal electrodes inducing electrowetting effects for improved control over droplet generation frequency to stimulate the droplet release to matching the XFEL repetition rate by employing an electrical feedback mechanism. We report the improvements in this electrically triggered segmented flow approach for sample conservation in comparison with a continuous GDVN injection using the microcrystals of lysozyme and 3-deoxy-D-manno-octulosonate 8-phosphate synthase and report the segmented flow approach for sample injection applied at the Macromolecular Femtosecond Crystallography instrument at the Linear Coherent Light Source for the first time.
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Affiliation(s)
- Mukul Sonker
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Diandra Doppler
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Ana Egatz-Gomez
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Sahba Zaare
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
- Department of Physics, Arizona State University, Tempe, Arizona
| | - Mohammad T. Rabbani
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Abhik Manna
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Jorvani Cruz Villarreal
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Garrett Nelson
- Department of Physics, Arizona State University, Tempe, Arizona
| | - Gihan K. Ketawala
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Konstantinos Karpos
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
- Department of Physics, Arizona State University, Tempe, Arizona
| | - Roberto C. Alvarez
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
- Department of Physics, Arizona State University, Tempe, Arizona
| | - Reza Nazari
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
- Department of Physics, Arizona State University, Tempe, Arizona
| | - Darren Thifault
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Rebecca Jernigan
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Dominik Oberthür
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | | | - Raymond Sierra
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Mark S. Hunter
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Alexander Batyuk
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Christopher J. Kupitz
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Robert E. Sublett
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Frederic Poitevin
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Stella Lisova
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Valerio Mariani
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Alexandra Tolstikova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - Sebastien Boutet
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Marc Messerschmidt
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - J. Domingo Meza-Aguilar
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Raimund Fromme
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Jose M. Martin-Garcia
- Institute Physical-Chemistry Rocasolano, Spanish National Research Council, Madrid, Spain
| | - Sabine Botha
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
- Department of Physics, Arizona State University, Tempe, Arizona
| | - Petra Fromme
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Thomas D. Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, New York
| | - Richard A. Kirian
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
- Department of Physics, Arizona State University, Tempe, Arizona
| | - Alexandra Ros
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
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2
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Holmes S, Kirkwood HJ, Bean R, Giewekemeyer K, Martin AV, Hadian-Jazi M, Wiedorn MO, Oberthür D, Marman H, Adriano L, Al-Qudami N, Bajt S, Barák I, Bari S, Bielecki J, Brockhauser S, Coleman MA, Cruz-Mazo F, Danilevski C, Dörner K, Gañán-Calvo AM, Graceffa R, Fanghor H, Heymann M, Frank M, Kaukher A, Kim Y, Kobe B, Knoška J, Laurus T, Letrun R, Maia L, Messerschmidt M, Metz M, Michelat T, Mills G, Molodtsov S, Monteiro DCF, Morgan AJ, Münnich A, Peña Murillo GE, Previtali G, Round A, Sato T, Schubert R, Schulz J, Shelby M, Seuring C, Sellberg JA, Sikorski M, Silenzi A, Stern S, Sztuk-Dambietz J, Szuba J, Trebbin M, Vagovic P, Ve T, Weinhausen B, Wrona K, Xavier PL, Xu C, Yefanov O, Nugent KA, Chapman HN, Mancuso AP, Barty A, Abbey B, Darmanin C. Megahertz pulse trains enable multi-hit serial femtosecond crystallography experiments at X-ray free electron lasers. Nat Commun 2022; 13:4708. [PMID: 35953469 PMCID: PMC9372077 DOI: 10.1038/s41467-022-32434-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 07/28/2022] [Indexed: 11/12/2022] Open
Abstract
The European X-ray Free Electron Laser (XFEL) and Linac Coherent Light Source (LCLS) II are extremely intense sources of X-rays capable of generating Serial Femtosecond Crystallography (SFX) data at megahertz (MHz) repetition rates. Previous work has shown that it is possible to use consecutive X-ray pulses to collect diffraction patterns from individual crystals. Here, we exploit the MHz pulse structure of the European XFEL to obtain two complete datasets from the same lysozyme crystal, first hit and the second hit, before it exits the beam. The two datasets, separated by <1 µs, yield up to 2.1 Å resolution structures. Comparisons between the two structures reveal no indications of radiation damage or significant changes within the active site, consistent with the calculated dose estimates. This demonstrates MHz SFX can be used as a tool for tracking sub-microsecond structural changes in individual single crystals, a technique we refer to as multi-hit SFX. Free-electron lasers are capable of high repetition rates and it is assumed that protein crystals often do not survive the first X-ray pulse. Here the authors address these issues with a demonstration of multi-hit serial crystallography in which multiple FEL pulses interact with the sample without destroying it.
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Affiliation(s)
- Susannah Holmes
- Department of Mathematical and Physical Sciences, School of Engineering, Computing and Mathematical Sciences, La Trobe University, Melbourne, VIC, 3086, Australia.,La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | | | - Richard Bean
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Andrew V Martin
- School of Science, RMIT University, Melbourne, VIC, 3000, Australia
| | - Marjan Hadian-Jazi
- Department of Mathematical and Physical Sciences, School of Engineering, Computing and Mathematical Sciences, La Trobe University, Melbourne, VIC, 3086, Australia.,European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.,Australian Nuclear Science and Technology Organisation (ANSTO), Sydney, NSW, 2234, Australia
| | - Max O Wiedorn
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany
| | - Dominik Oberthür
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany
| | - Hugh Marman
- Department of Mathematical and Physical Sciences, School of Engineering, Computing and Mathematical Sciences, La Trobe University, Melbourne, VIC, 3086, Australia.,La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Luigi Adriano
- Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany
| | | | - Saša Bajt
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, Hamburg, 22761, Germany
| | - Imrich Barák
- Institute of Molecular Biology, SAS, Dubravska cesta 21, 845 51, Bratislava, Slovakia
| | - Sadia Bari
- Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany
| | | | | | - Mathew A Coleman
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA, 94550, USA
| | - Francisco Cruz-Mazo
- Dept. de Ingeniería Aeroespacial y Mecánica de Fluidos, ETSI, Universidad de Sevilla, 41092, Sevilla, Spain.,Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ, 08544, USA
| | | | | | - Alfonso M Gañán-Calvo
- Dept. de Ingeniería Aeroespacial y Mecánica de Fluidos, ETSI, Universidad de Sevilla, 41092, Sevilla, Spain
| | - Rita Graceffa
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Hans Fanghor
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.,Max-Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 175, 22761, Hamburg, Germany.,University of Southampton, Southampton, SO17 1BJ, UK
| | - Michael Heymann
- Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Am Pfaffenwaldring 57, 70569, Stuttgart, Germany
| | - Matthias Frank
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA, 94550, USA
| | | | - Yoonhee Kim
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Juraj Knoška
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany.,Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Torsten Laurus
- Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany
| | - Romain Letrun
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Luis Maia
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Marc Messerschmidt
- School of Molecular Science, Arizona State University, Tempe, AZ, 85281, USA
| | - Markus Metz
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany
| | | | - Grant Mills
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Serguei Molodtsov
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.,Institute of Experimental Physics, TU Bergakademie Freiberg, Leipziger, Str. 23, 09599, Freiberg, Germany.,ITMO University, Kronverksky pr. 49, St. Petersburg, 197101, Russia
| | - Diana C F Monteiro
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, Hamburg, 22761, Germany.,Hauptman-Woodward Medical Research Institute, 700 Ellicott St., Buffalo, NY, 14203, USA
| | - Andrew J Morgan
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany.,Department of Physics, University of Melbourne, Parkville, VIC, 3010, Australia
| | | | - Gisel E Peña Murillo
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany
| | | | - Adam Round
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Tokushi Sato
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.,Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany
| | | | | | - Megan Shelby
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA, 94550, USA
| | - Carolin Seuring
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, Hamburg, 22761, Germany
| | - Jonas A Sellberg
- Biomedical and X-ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology, SE-106 91, Stockholm, Sweden
| | | | | | - Stephan Stern
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Janusz Szuba
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Martin Trebbin
- Institute of Experimental Physics, TU Bergakademie Freiberg, Leipziger, Str. 23, 09599, Freiberg, Germany.,Department of Chemistry, State University of New York at Buffalo, 760 Natural Sciences Complex, Buffalo, NY, 14260, USA
| | | | - Thomas Ve
- Institute for Glycomics, Griffith University, Southport, QLD, 4222, Australia
| | | | | | - Paul Lourdu Xavier
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.,Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany.,Max-Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 175, 22761, Hamburg, Germany
| | - Chen Xu
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany
| | - Keith A Nugent
- Department of Quantum Science and Technology, Research School of Physics, Australian National University, Canberra, ACT, 2601, Australia
| | - Henry N Chapman
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, Hamburg, 22761, Germany.,Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Adrian P Mancuso
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.,La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Anton Barty
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany
| | - Brian Abbey
- Department of Mathematical and Physical Sciences, School of Engineering, Computing and Mathematical Sciences, La Trobe University, Melbourne, VIC, 3086, Australia. .,La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia.
| | - Connie Darmanin
- Department of Mathematical and Physical Sciences, School of Engineering, Computing and Mathematical Sciences, La Trobe University, Melbourne, VIC, 3086, Australia. .,La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia.
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3
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Doppler D, Rabbani MT, Letrun R, Cruz Villarreal J, Kim DH, Gandhi S, Egatz-Gomez A, Sonker M, Chen J, Koua FHM, Yang J, Youssef M, Mazalova V, Bajt S, Shelby ML, Coleman MA, Wiedorn MO, Knoska J, Schön S, Sato T, Hunter MS, Hosseinizadeh A, Kuptiz C, Nazari R, Alvarez RC, Karpos K, Zaare S, Dobson Z, Discianno E, Zhang S, Zook JD, Bielecki J, de Wijn R, Round AR, Vagovic P, Kloos M, Vakili M, Ketawala GK, Stander NE, Olson TL, Morin K, Mondal J, Nguyen J, Meza-Aguilar JD, Kodis G, Vaiana S, Martin-Garcia JM, Mariani V, Schwander P, Schmidt M, Messerschmidt M, Ourmazd A, Zatsepin N, Weierstall U, Bruce BD, Mancuso AP, Grant T, Barty A, Chapman HN, Frank M, Fromme R, Spence JCH, Botha S, Fromme P, Kirian RA, Ros A. Co-flow injection for serial crystallography at X-ray free-electron lasers. J Appl Crystallogr 2022; 55:1-13. [PMID: 35153640 PMCID: PMC8805165 DOI: 10.1107/s1600576721011079] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/22/2021] [Indexed: 02/03/2023] Open
Abstract
Serial femtosecond crystallography (SFX) is a powerful technique that exploits X-ray free-electron lasers to determine the structure of macro-molecules at room temperature. Despite the impressive exposition of structural details with this novel crystallographic approach, the methods currently available to introduce crystals into the path of the X-ray beam sometimes exhibit serious drawbacks. Samples requiring liquid injection of crystal slurries consume large quantities of crystals (at times up to a gram of protein per data set), may not be compatible with vacuum configurations on beamlines or provide a high background due to additional sheathing liquids present during the injection. Proposed and characterized here is the use of an immiscible inert oil phase to supplement the flow of sample in a hybrid microfluidic 3D-printed co-flow device. Co-flow generation is reported with sample and oil phases flowing in parallel, resulting in stable injection conditions for two different resin materials experimentally. A numerical model is presented that adequately predicts these flow-rate conditions. The co-flow generating devices reduce crystal clogging effects, have the potential to conserve protein crystal samples up to 95% and will allow degradation-free light-induced time-resolved SFX.
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Affiliation(s)
- Diandra Doppler
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Mohammad T. Rabbani
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | | | - Jorvani Cruz Villarreal
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Dai Hyun Kim
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Sahir Gandhi
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Ana Egatz-Gomez
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Mukul Sonker
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Joe Chen
- Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Faisal H. M. Koua
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Jayhow Yang
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Mohamed Youssef
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Victoria Mazalova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Saša Bajt
- Hamburg Center for Ultrafast Imaging, Hamburg, Germany,Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Megan L. Shelby
- Lawrence Livermore National Laboratory (LLNL), Livermore, California, USA
| | - Matt A. Coleman
- Lawrence Livermore National Laboratory (LLNL), Livermore, California, USA
| | - Max O. Wiedorn
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany,Hamburg Center for Ultrafast Imaging, Hamburg, Germany,Department of Physics, Universität Hamburg, Hamburg, Germany
| | - Juraj Knoska
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Silvan Schön
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | | | - Mark S. Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Ahmad Hosseinizadeh
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Christopher Kuptiz
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Reza Nazari
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Roberto C. Alvarez
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Konstantinos Karpos
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Sahba Zaare
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Zachary Dobson
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Erin Discianno
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Shangji Zhang
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - James D. Zook
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | | | | | - Adam R. Round
- European XFEL, Schenefeld, Germany,School of Chemical and Physical Sciences, Keele University, Staffordshire, UK
| | - Patrik Vagovic
- European XFEL, Schenefeld, Germany,Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | | | | | - Gihan K. Ketawala
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Natasha E. Stander
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Tien L. Olson
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Katherine Morin
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Jyotirmory Mondal
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, USA
| | - Jonathan Nguyen
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - José Domingo Meza-Aguilar
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,European XFEL, Schenefeld, Germany
| | - Gerdenis Kodis
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Sara Vaiana
- Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Jose M. Martin-Garcia
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Crystallography and Structural Biology, Institute of Physical Chemistry ‘Rocasolano’, CSIC, Madrid, Spain
| | - Valerio Mariani
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Peter Schwander
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Marius Schmidt
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Marc Messerschmidt
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Abbas Ourmazd
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Nadia Zatsepin
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA,Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Uwe Weierstall
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Barry D. Bruce
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, USA
| | - Adrian P. Mancuso
- European XFEL, Schenefeld, Germany,Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Thomas Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, New York, USA
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany,Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany,Center for Data and Computing in Natural Science CDCS, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Henry N. Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany,Hamburg Center for Ultrafast Imaging, Hamburg, Germany,Department of Physics, Universität Hamburg, Hamburg, Germany
| | - Matthias Frank
- Lawrence Livermore National Laboratory (LLNL), Livermore, California, USA
| | - Raimund Fromme
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - John C. H. Spence
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Sabine Botha
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Petra Fromme
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Richard A. Kirian
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Alexandra Ros
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Correspondence e-mail:
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4
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Echelmeier A, Cruz Villarreal J, Messerschmidt M, Kim D, Coe JD, Thifault D, Botha S, Egatz-Gomez A, Gandhi S, Brehm G, Conrad CE, Hansen DT, Madsen C, Bajt S, Meza-Aguilar JD, Oberthür D, Wiedorn MO, Fleckenstein H, Mendez D, Knoška J, Martin-Garcia JM, Hu H, Lisova S, Allahgholi A, Gevorkov Y, Ayyer K, Aplin S, Ginn HM, Graafsma H, Morgan AJ, Greiffenberg D, Klujev A, Laurus T, Poehlsen J, Trunk U, Mezza D, Schmidt B, Kuhn M, Fromme R, Sztuk-Dambietz J, Raab N, Hauf S, Silenzi A, Michelat T, Xu C, Danilevski C, Parenti A, Mekinda L, Weinhausen B, Mills G, Vagovic P, Kim Y, Kirkwood H, Bean R, Bielecki J, Stern S, Giewekemeyer K, Round AR, Schulz J, Dörner K, Grant TD, Mariani V, Barty A, Mancuso AP, Weierstall U, Spence JCH, Chapman HN, Zatsepin N, Fromme P, Kirian RA, Ros A. Segmented flow generator for serial crystallography at the European X-ray free electron laser. Nat Commun 2020; 11:4511. [PMID: 32908128 PMCID: PMC7481229 DOI: 10.1038/s41467-020-18156-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [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: 12/23/2019] [Accepted: 07/23/2020] [Indexed: 12/14/2022] Open
Abstract
Serial femtosecond crystallography (SFX) with X-ray free electron lasers (XFELs) allows structure determination of membrane proteins and time-resolved crystallography. Common liquid sample delivery continuously jets the protein crystal suspension into the path of the XFEL, wasting a vast amount of sample due to the pulsed nature of all current XFEL sources. The European XFEL (EuXFEL) delivers femtosecond (fs) X-ray pulses in trains spaced 100 ms apart whereas pulses within trains are currently separated by 889 ns. Therefore, continuous sample delivery via fast jets wastes >99% of sample. Here, we introduce a microfluidic device delivering crystal laden droplets segmented with an immiscible oil reducing sample waste and demonstrate droplet injection at the EuXFEL compatible with high pressure liquid delivery of an SFX experiment. While achieving ~60% reduction in sample waste, we determine the structure of the enzyme 3-deoxy-D-manno-octulosonate-8-phosphate synthase from microcrystals delivered in droplets revealing distinct structural features not previously reported.
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Affiliation(s)
- Austin Echelmeier
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Jorvani Cruz Villarreal
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Marc Messerschmidt
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA.,European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Daihyun Kim
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Jesse D Coe
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Darren Thifault
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Sabine Botha
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA.,Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Ana Egatz-Gomez
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Sahir Gandhi
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Gerrit Brehm
- Institute for X-Ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077, Göttingen, Germany
| | - Chelsie E Conrad
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Debra T Hansen
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Caleb Madsen
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA.,Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Saša Bajt
- Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany.,Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | | | - Dominik Oberthür
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Max O Wiedorn
- Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.,Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Holger Fleckenstein
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Derek Mendez
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA.,Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Juraj Knoška
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany.,Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Jose M Martin-Garcia
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Hao Hu
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA.,Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Stella Lisova
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA.,Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Aschkan Allahgholi
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Yaroslav Gevorkov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany.,Hamburg University of Technology, Vision Systems E-2, Harburger Schloßstraße 20, 21079, Hamburg, Germany
| | - Kartik Ayyer
- 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
| | - Helen Mary Ginn
- Division of Structural Biology, University of Oxford, Oxford, OX1 2JD, United Kingdom.,Diamond Light Source Ltd, Didcot, Oxfordshire, OX11 0DE, United Kingdom
| | - Heinz Graafsma
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Andrew J Morgan
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | | | - Alexander Klujev
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Torsten Laurus
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Jennifer Poehlsen
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Ulrich Trunk
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Davide Mezza
- Paul Scherrer Institute, Forschungsstrasse 111, 5232, Villigen, Switzerland
| | - Bernd Schmidt
- Paul Scherrer Institute, Forschungsstrasse 111, 5232, Villigen, Switzerland
| | - Manuela Kuhn
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Raimund Fromme
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | | | - Natascha Raab
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Steffen Hauf
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | | | - Chen Xu
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | | | | | | | - Grant Mills
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Yoonhee Kim
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Richard Bean
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Stephan Stern
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.,Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | | | - Adam R Round
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.,School of Chemical and Physical Sciences, Keele University, Staffordshire, ST5 5AZ, United Kingdom
| | | | | | - Thomas D Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, 955 Main St, Buffalo, NY, 14203, USA
| | - Valerio Mariani
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Adrian P Mancuso
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.,Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Uwe Weierstall
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA.,Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - John C H Spence
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA.,Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Henry N Chapman
- Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.,Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany.,Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Nadia Zatsepin
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA.,Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA.,ARC Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Petra Fromme
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Richard A Kirian
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA.,Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Alexandra Ros
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA. .,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA.
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5
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Haslinger MJ, Mitteramskogler T, Kopp S, Leichtfried H, Messerschmidt M, Thesen MW, Mühlberger M. Development of a soft UV-NIL step&repeat and lift-off process chain for high speed metal nanomesh fabrication. Nanotechnology 2020; 31:345301. [PMID: 32380487 DOI: 10.1088/1361-6528/ab9130] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In this work, we present a fabrication procedure of metal nanomesh arrays with the newly developed nanoimprint resist mr-NIL212FC used in a bi-layer resist system for a lift-off process. We comparatively analyzed and evaluated nanomeshes fabricated with a freshly prepared h-PDMS/PDMS stamp and a stamp used 501 times. Therefore, we first performed a step&repeat imprint test run in a self-built low cost step&repeat UV-NIL setup. We inspected the imprint behavior of the stamp, the UV-transmission through the stamp as well as stamp lifetime and stamp degradation with regard to the possible changes of its surface roughness. The nanomesh fabrication process is characterized by a good lift-off performance, leading to a low defect density of <1.26 defects 100 µm-2. Even after 501 imprints, only a negligible stamp degradation occurred without effecting the imprint performance. Likewise, the same holds true for the nanomeshes, which showed comparable low defect densities and feature sheet resistances of 3.54 ± 0.14 Ω/□ for the first and 3.48 ± 0.23 Ω/□ for the 501st nanomesh, respectively. AFM analyses further revealed that the maximum height of the roughness Rt changed over the course of the 501 imprints from 6.3 nm to 13.3 nm, representing <5% of the overall imprint height. In general, the mr-NIL212FC resist shows a good wettability and compatibility with standard h-PDMS/PDMS stamps, a fast curing behavior, a high replication fidelity, easy separation characteristics, and a very low diffusion of resist components into the stamp. The mr-NIL212FC resist allows exposure times as short as 2 s in the applied tool setup, enabling high throughput production. Moreover, all performed measurements indicate that a much higher number of imprints with one stamp seem possible.
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Affiliation(s)
- M J Haslinger
- Functional Surfaces and Nanostructures, PROFACTOR GmbH, Steyr-Gleink 4407, Austria. Institute of Applied Physics, Johannes Kepler University, Linz 4040, Austria
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6
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Morgan AJ, Murray KT, Prasciolu M, Fleckenstein H, Yefanov O, Villanueva-Perez P, Mariani V, Domaracky M, Kuhn M, Aplin S, Mohacsi I, Messerschmidt M, Stachnik K, Du Y, Burkhart A, Meents A, Nazaretski E, Yan H, Huang X, Chu YS, Chapman HN, Bajt S. Ptychographic X-ray speckle tracking with multi-layer Laue lens systems. J Appl Crystallogr 2020; 53:927-936. [PMID: 32788900 PMCID: PMC7401788 DOI: 10.1107/s1600576720006925] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 05/22/2020] [Indexed: 11/17/2022] Open
Abstract
The ever-increasing brightness of synchrotron radiation sources demands improved X-ray optics to utilize their capability for imaging and probing biological cells, nano-devices and functional matter on the nanometre scale with chemical sensitivity. Hard X-rays are ideal for high-resolution imaging and spectroscopic applications owing to their short wavelength, high penetrating power and chemical sensitivity. The penetrating power that makes X-rays useful for imaging also makes focusing them technologically challenging. Recent developments in layer deposition techniques have enabled the fabrication of a series of highly focusing X-ray lenses, known as wedged multi-layer Laue lenses. Improvements to the lens design and fabrication technique demand an accurate, robust, in situ and at-wavelength characterization method. To this end, a modified form of the speckle tracking wavefront metrology method has been developed. The ptychographic X-ray speckle tracking method is capable of operating with highly divergent wavefields. A useful by-product of this method is that it also provides high-resolution and aberration-free projection images of extended specimens. Three separate experiments using this method are reported, where the ray path angles have been resolved to within 4 nrad with an imaging resolution of 45 nm (full period). This method does not require a high degree of coherence, making it suitable for laboratory-based X-ray sources. Likewise, it is robust to errors in the registered sample positions, making it suitable for X-ray free-electron laser facilities, where beam-pointing fluctuations can be problematic for wavefront metrology.
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Affiliation(s)
- Andrew J. Morgan
- CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | | | | | - Holger Fleckenstein
- CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Oleksandr Yefanov
- CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Valerio Mariani
- CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Martin Domaracky
- CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Steve Aplin
- CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Marc Messerschmidt
- National Science Foundation BioXFEL Science and Technology Center, 700 Ellicott Street, Buffalo, NY 14203, USA
| | | | - Yang Du
- CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Alke Meents
- DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Evgeny Nazaretski
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Hanfei Yan
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Xiaojing Huang
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Yong S. Chu
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Henry N. Chapman
- CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Saša Bajt
- DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
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7
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Nass K, Redecke L, Perbandt M, Yefanov O, Klinge M, Koopmann R, Stellato F, Gabdulkhakov A, Schönherr R, Rehders D, Lahey-Rudolph JM, Aquila A, Barty A, Basu S, Doak RB, Duden R, Frank M, Fromme R, Kassemeyer S, Katona G, Kirian R, Liu H, Majoul I, Martin-Garcia JM, Messerschmidt M, Shoeman RL, Weierstall U, Westenhoff S, White TA, Williams GJ, Yoon CH, Zatsepin N, Fromme P, Duszenko M, Chapman HN, Betzel C. In cellulo crystallization of Trypanosoma brucei IMP dehydrogenase enables the identification of genuine co-factors. Nat Commun 2020; 11:620. [PMID: 32001697 PMCID: PMC6992785 DOI: 10.1038/s41467-020-14484-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 01/06/2020] [Indexed: 02/07/2023] Open
Abstract
Sleeping sickness is a fatal disease caused by the protozoan parasite Trypanosoma brucei (Tb). Inosine-5’-monophosphate dehydrogenase (IMPDH) has been proposed as a potential drug target, since it maintains the balance between guanylate deoxynucleotide and ribonucleotide levels that is pivotal for the parasite. Here we report the structure of TbIMPDH at room temperature utilizing free-electron laser radiation on crystals grown in living insect cells. The 2.80 Å resolution structure reveals the presence of ATP and GMP at the canonical sites of the Bateman domains, the latter in a so far unknown coordination mode. Consistent with previously reported IMPDH complexes harboring guanosine nucleotides at the second canonical site, TbIMPDH forms a compact oligomer structure, supporting a nucleotide-controlled conformational switch that allosterically modulates the catalytic activity. The oligomeric TbIMPDH structure we present here reveals the potential of in cellulo crystallization to identify genuine allosteric co-factors from a natural reservoir of specific compounds. Trypanosoma brucei inosine-5′-monophosphate dehydrogenase (IMPDH) is an enzyme in the guanine nucleotide biosynthesis pathway and of interest as a drug target. Here the authors present the 2.8 Å room temperature structure of TbIMPDH determined by utilizing X-ray free-electron laser radiation and crystals that were grown in insect cells and find that ATP and GMP are bound at the canonical sites of the Bateman domains.
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Affiliation(s)
- Karol Nass
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.,Paul Scherrer Institute (PSI), Forschungstrasse 111, 5232, Villigen, PSI, Switzerland
| | - Lars Redecke
- Joint Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, University of Hamburg, and Institute of Biochemistry, University of Lübeck, at Deutsches Elektronen-Synchrotron (DESY), Notkestr. 85, 22607, Hamburg, Germany.,German Centre for Infection Research, University of Lübeck, 23562, Lübeck, Germany.,Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany.,Deutsches Elektronen Synchrotron (DESY), Photon Science, Notkestr. 85, 22607, Hamburg, Germany
| | - M Perbandt
- Institute of Biochemistry and Molecular Biology, University of Hamburg, at Deutsches Elektronen-Synchrotron (DESY), Notkestr. 85, 22607, Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging (CUI), Luruper Chaussee 149, 22761, Hamburg, Germany
| | - O Yefanov
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - M Klinge
- Joint Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, University of Hamburg, and Institute of Biochemistry, University of Lübeck, at Deutsches Elektronen-Synchrotron (DESY), Notkestr. 85, 22607, Hamburg, Germany.,BioAgilytix Europe GmbH, Lademannbogen 10, 22339, Hamburg, Germany
| | - R Koopmann
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str.4, 72076, Tübingen, Germany
| | - F Stellato
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.,Dipartimento di Fisica, Università di Roma Tor Vergata and INFN, Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - A Gabdulkhakov
- Institute of Protein Research, Russian Academy of Sciences, 4 Institutskaya Str., Pushchino, Moscow Region, Russia, 142290
| | - R Schönherr
- Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany.,Deutsches Elektronen Synchrotron (DESY), Photon Science, Notkestr. 85, 22607, Hamburg, Germany
| | - D Rehders
- Joint Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, University of Hamburg, and Institute of Biochemistry, University of Lübeck, at Deutsches Elektronen-Synchrotron (DESY), Notkestr. 85, 22607, Hamburg, Germany.,BODE Chemie GmbH, Melanchthonstraße 27, 22525, Hamburg, Germany
| | - J M Lahey-Rudolph
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.,Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - A Aquila
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.,LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - A Barty
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - S Basu
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ, 85287-160, USA.,European Molecular Biology Laboratory (EMBL), Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, Grenoble, France
| | - R B Doak
- Department of Physics, Arizona State University, Tempe, AZ, 85411, USA.,Max Planck Institute for Medical Research, Jahnstr. 29, 69120, Heidelberg, Germany
| | - R Duden
- Institute of Biology, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - M Frank
- Biology and Biotechnology Division, Physical & Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA, 94550, USA
| | - R Fromme
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ, 85287-160, USA
| | - S Kassemeyer
- Max-Planck-Institute for Medical Research, Jahnstr. 29, 69120, Heidelberg, Germany
| | - G Katona
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530, Gothenburg, Sweden
| | - R Kirian
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ, 85287-160, USA
| | - H Liu
- Department of Physics, Arizona State University, Tempe, AZ, 85411, USA.,Complex Systems Division, Beijing Computational Science Research Center, 100193, Beijing, China
| | - I Majoul
- Institute of Biology, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - J M Martin-Garcia
- Center for Applied Structural Discovery (CASD), Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ, 85287, USA
| | - M Messerschmidt
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA.,Center for Applied Structural Discovery (CASD), Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ, 85287, USA
| | - R L Shoeman
- Max-Planck-Institute for Medical Research, Jahnstr. 29, 69120, Heidelberg, Germany
| | - U Weierstall
- Department of Physics, Arizona State University, Tempe, AZ, 85411, USA
| | - S Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530, Gothenburg, Sweden
| | - T A White
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - G J Williams
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA.,Brookhaven National Laboratory (BNL), PO Box 5000, Upton, NY, 11973-5000, USA
| | - C H Yoon
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.,LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - N Zatsepin
- Department of Physics, Arizona State University, Tempe, AZ, 85411, USA.,ARC Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Victoria, 3086, Australia
| | - P Fromme
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ, 85287-160, USA
| | - M Duszenko
- Institute of Neurophysiology, University of Tübingen, Keplerstr. 15, 72074, Tübingen, Germany
| | - H N Chapman
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging (CUI), Luruper Chaussee 149, 22761, Hamburg, Germany.,Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - C Betzel
- Institute of Biochemistry and Molecular Biology, University of Hamburg, at Deutsches Elektronen-Synchrotron (DESY), Notkestr. 85, 22607, Hamburg, Germany. .,The Hamburg Centre for Ultrafast Imaging (CUI), Luruper Chaussee 149, 22761, Hamburg, Germany.
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8
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Gisriel C, Coe J, Letrun R, Yefanov OM, Luna-Chavez C, Stander NE, Lisova S, Mariani V, Kuhn M, Aplin S, Grant TD, Dörner K, Sato T, Echelmeier A, Cruz Villarreal J, Hunter MS, Wiedorn MO, Knoska J, Mazalova V, Roy-Chowdhury S, Yang JH, Jones A, Bean R, Bielecki J, Kim Y, Mills G, Weinhausen B, Meza JD, Al-Qudami N, Bajt S, Brehm G, Botha S, Boukhelef D, Brockhauser S, Bruce BD, Coleman MA, Danilevski C, Discianno E, Dobson Z, Fangohr H, Martin-Garcia JM, Gevorkov Y, Hauf S, Hosseinizadeh A, Januschek F, Ketawala GK, Kupitz C, Maia L, Manetti M, Messerschmidt M, Michelat T, Mondal J, Ourmazd A, Previtali G, Sarrou I, Schön S, Schwander P, Shelby ML, Silenzi A, Sztuk-Dambietz J, Szuba J, Turcato M, White TA, Wrona K, Xu C, Abdellatif MH, Zook JD, Spence JCH, Chapman HN, Barty A, Kirian RA, Frank M, Ros A, Schmidt M, Fromme R, Mancuso AP, Fromme P, Zatsepin NA. Membrane protein megahertz crystallography at the European XFEL. Nat Commun 2019; 10:5021. [PMID: 31685819 PMCID: PMC6828683 DOI: 10.1038/s41467-019-12955-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [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: 01/29/2019] [Accepted: 10/07/2019] [Indexed: 12/02/2022] Open
Abstract
The world’s first superconducting megahertz repetition rate hard X-ray free-electron laser (XFEL), the European XFEL, began operation in 2017, featuring a unique pulse train structure with 886 ns between pulses. With its rapid pulse rate, the European XFEL may alleviate some of the increasing demand for XFEL beamtime, particularly for membrane protein serial femtosecond crystallography (SFX), leveraging orders-of-magnitude faster data collection. Here, we report the first membrane protein megahertz SFX experiment, where we determined a 2.9 Å-resolution SFX structure of the large membrane protein complex, Photosystem I, a > 1 MDa complex containing 36 protein subunits and 381 cofactors. We address challenges to megahertz SFX for membrane protein complexes, including growth of large quantities of crystals and the large molecular and unit cell size that influence data collection and analysis. The results imply that megahertz crystallography could have an important impact on structure determination of large protein complexes with XFELs. The European X-ray free-electron laser (EuXFEL) in Hamburg is the first XFEL with a megahertz repetition rate. Here the authors present the 2.9 Å structure of the large membrane protein complex Photosystem I from T. elongatus that was determined at the EuXFEL.
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Affiliation(s)
- Chris Gisriel
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.,Department of Chemistry, Yale University, New Haven, CT, 06520, USA
| | - Jesse Coe
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA
| | - Romain Letrun
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Oleksandr M Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Cesar Luna-Chavez
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA
| | - Natasha E Stander
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA
| | - Stella Lisova
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA.,Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Valerio Mariani
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Manuela Kuhn
- 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
| | - Thomas D Grant
- Hauptman-Woodward Institute, 700 Ellicott St, Buffalo, NY, 14203-1102, USA.,Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, 700 Ellicott St, Buffalo, NY, 14203-1102, USA
| | - Katerina Dörner
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Tokushi Sato
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany.,Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Austin Echelmeier
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA
| | - Jorvani Cruz Villarreal
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, 94025, CA, USA
| | - Max O Wiedorn
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany.,Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Juraj Knoska
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Victoria Mazalova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Shatabdi Roy-Chowdhury
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA
| | - Jay-How Yang
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA
| | - Alex Jones
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA
| | - Richard Bean
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Johan Bielecki
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Yoonhee Kim
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Grant Mills
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Jose D Meza
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Saša Bajt
- Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Gerrit Brehm
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.,Institute for X-Ray Physics, University of Göttingen, 37077, Göttingen, Germany.,Center Nanoscale Microscopy and Molecular Physiology of the Brain, Göttingen, Germany
| | - Sabine Botha
- Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | | | - Sandor Brockhauser
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany.,Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, Szeged, 6726, Hungary
| | - Barry D Bruce
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee at Knoxville, Knoxville, TN, USA, 37996.,Program in Energy Science and Engineering, University of Tennessee at Knoxville, Knoxville, TN, USA, 37996.,Department of Microbiology, University of Tennessee at Knoxville, Knoxville, TN, USA, 37996
| | - Matthew A Coleman
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA, 94550, USA
| | | | - Erin Discianno
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA
| | - Zachary Dobson
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA
| | - Hans Fangohr
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany.,University of Southampton, University Rd, Southampton, SO17 1BJ, UK
| | - Jose M Martin-Garcia
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA
| | - Yaroslav Gevorkov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany.,Hamburg University of Technology, Vision Systems E-2, Harburger Schloßstraße 20, 21079, Hamburg, Germany
| | - Steffen Hauf
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Ahmad Hosseinizadeh
- Department of Physics, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI, 53211, USA
| | - Friederike Januschek
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany.,Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Gihan K Ketawala
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA
| | - Christopher Kupitz
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, 94025, CA, USA.,Department of Physics, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI, 53211, USA
| | - Luis Maia
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Marc Messerschmidt
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.,European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Thomas Michelat
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Jyotirmoy Mondal
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee at Knoxville, Knoxville, TN, USA, 37996
| | - Abbas Ourmazd
- Department of Physics, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI, 53211, USA
| | | | - Iosifina Sarrou
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Silvan Schön
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Peter Schwander
- Department of Physics, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI, 53211, USA
| | - Megan L Shelby
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA, 94550, USA
| | | | | | - Janusz Szuba
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Monica Turcato
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Thomas A White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, 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
| | - Mohamed H Abdellatif
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - James D Zook
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA
| | - John C H Spence
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA.,Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Henry N Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany.,Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Richard A Kirian
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA.,Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Matthias Frank
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA, 94550, USA
| | - Alexandra Ros
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA
| | - Marius Schmidt
- Department of Physics, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI, 53211, USA
| | - Raimund Fromme
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA
| | - Adrian P Mancuso
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany.,Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, 3086, Victoria, Australia
| | - Petra Fromme
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA. .,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
| | - Nadia A Zatsepin
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA. .,Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA. .,ARC Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, 3086, Victoria, Australia.
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9
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Brändén G, Hammarin G, Harimoorthy R, Johansson A, Arnlund D, Malmerberg E, Barty A, Tångefjord S, Berntsen P, DePonte DP, Seuring C, White TA, Stellato F, Bean R, Beyerlein KR, Chavas LMG, Fleckenstein H, Gati C, Ghoshdastider U, Gumprecht L, Oberthür D, Popp D, Seibert M, Tilp T, Messerschmidt M, Williams GJ, Loh ND, Chapman HN, Zwart P, Liang M, Boutet S, Robinson RC, Neutze R. Coherent diffractive imaging of microtubules using an X-ray laser. Nat Commun 2019; 10:2589. [PMID: 31197138 PMCID: PMC6565740 DOI: 10.1038/s41467-019-10448-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [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: 06/20/2018] [Accepted: 05/02/2019] [Indexed: 01/09/2023] Open
Abstract
X-ray free electron lasers (XFELs) create new possibilities for structural studies of biological objects that extend beyond what is possible with synchrotron radiation. Serial femtosecond crystallography has allowed high-resolution structures to be determined from micro-meter sized crystals, whereas single particle coherent X-ray imaging requires development to extend the resolution beyond a few tens of nanometers. Here we describe an intermediate approach: the XFEL imaging of biological assemblies with helical symmetry. We collected X-ray scattering images from samples of microtubules injected across an XFEL beam using a liquid microjet, sorted these images into class averages, merged these data into a diffraction pattern extending to 2 nm resolution, and reconstructed these data into a projection image of the microtubule. Details such as the 4 nm tubulin monomer became visible in this reconstruction. These results illustrate the potential of single-molecule X-ray imaging of biological assembles with helical symmetry at room temperature.
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Affiliation(s)
- Gisela Brändén
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530, Gothenburg, Sweden.
| | - Greger Hammarin
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530, Gothenburg, Sweden
| | - Rajiv Harimoorthy
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530, Gothenburg, Sweden
| | - Alexander Johansson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530, Gothenburg, Sweden
| | - David Arnlund
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530, Gothenburg, Sweden
| | - Erik Malmerberg
- Molecular Biophysics and Integrated Bio-Imaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, 94720, Berkeley, CA, USA
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - Stefan Tångefjord
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530, Gothenburg, Sweden
| | - Peter Berntsen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530, Gothenburg, Sweden
| | - Daniel P DePonte
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Carolin Seuring
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany.,The Hamburg Center for Ultrafast Imaging, 22761, Hamburg, Germany
| | - Thomas A White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - Francesco Stellato
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - Richard Bean
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - Kenneth R Beyerlein
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - Leonard M G Chavas
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - Holger Fleckenstein
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - Cornelius Gati
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - Umesh Ghoshdastider
- Institute of Molecular and Cell Biology, Biopolis, A*STAR (Agency for Science, Technology and Research), 138673, Singapore, Singapore
| | - Lars Gumprecht
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - Dominik Oberthür
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - David Popp
- Institute of Molecular and Cell Biology, Biopolis, A*STAR (Agency for Science, Technology and Research), 138673, Singapore, Singapore
| | - Marvin Seibert
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Thomas Tilp
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - Marc Messerschmidt
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Garth J Williams
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - N Duane Loh
- Department of Physics, National University of Singapore, 117551, Singapore, Singapore
| | - Henry N Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany.,The Hamburg Center for Ultrafast Imaging, 22761, Hamburg, Germany.,Department of Physics, University of Hamburg, 22761, Hamburg, Germany
| | - Peter Zwart
- Molecular Biophysics and Integrated Bio-Imaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, 94720, Berkeley, CA, USA
| | - Mengning Liang
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany.,Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Robert C Robinson
- Institute of Molecular and Cell Biology, Biopolis, A*STAR (Agency for Science, Technology and Research), 138673, Singapore, Singapore.,Department of Biochemistry, National University of Singapore, 117597, Singapore, Singapore.,Research Institute for Interdisciplinary Science, Okayama University, Okayama, 700-8530, Japan
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530, Gothenburg, Sweden.
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10
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Mancuso AP, Aquila A, Batchelor L, Bean RJ, Bielecki J, Borchers G, Doerner K, Giewekemeyer K, Graceffa R, Kelsey OD, Kim Y, Kirkwood HJ, Legrand A, Letrun R, Manning B, Lopez Morillo L, Messerschmidt M, Mills G, Raabe S, Reimers N, Round A, Sato T, Schulz J, Signe Takem C, Sikorski M, Stern S, Thute P, Vagovič P, Weinhausen B, Tschentscher T. The Single Particles, Clusters and Biomolecules and Serial Femtosecond Crystallography instrument of the European XFEL: initial installation. J Synchrotron Radiat 2019; 26:660-676. [PMID: 31074429 PMCID: PMC6510195 DOI: 10.1107/s1600577519003308] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 03/07/2019] [Indexed: 05/22/2023]
Abstract
The European X-ray Free-Electron Laser (FEL) became the first operational high-repetition-rate hard X-ray FEL with first lasing in May 2017. Biological structure determination has already benefitted from the unique properties and capabilities of X-ray FELs, predominantly through the development and application of serial crystallography. The possibility of now performing such experiments at data rates more than an order of magnitude greater than previous X-ray FELs enables not only a higher rate of discovery but also new classes of experiments previously not feasible at lower data rates. One example is time-resolved experiments requiring a higher number of time steps for interpretation, or structure determination from samples with low hit rates in conventional X-ray FEL serial crystallography. Following first lasing at the European XFEL, initial commissioning and operation occurred at two scientific instruments, one of which is the Single Particles, Clusters and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument. This instrument provides a photon energy range, focal spot sizes and diagnostic tools necessary for structure determination of biological specimens. The instrumentation explicitly addresses serial crystallography and the developing single particle imaging method as well as other forward-scattering and diffraction techniques. This paper describes the major science cases of SPB/SFX and its initial instrumentation - in particular its optical systems, available sample delivery methods, 2D detectors, supporting optical laser systems and key diagnostic components. The present capabilities of the instrument will be reviewed and a brief outlook of its future capabilities is also described.
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Affiliation(s)
- Adrian P. Mancuso
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
- Correspondence e-mail:
| | - Andrew Aquila
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | | | | | | | | | | | - Rita Graceffa
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | - Yoonhee Kim
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | | | - Romain Letrun
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | | | | | - Grant Mills
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Steffen Raabe
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestraße 85, 22607 Hamburg, Germany
| | - Nadja Reimers
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Adam Round
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Tokushi Sato
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestraße 85, 22607 Hamburg, Germany
| | | | | | | | - Stephan Stern
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Prasad Thute
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Patrik Vagovič
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestraße 85, 22607 Hamburg, Germany
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11
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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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12
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Casadei CM, Nass K, Barty A, Hunter MS, Padeste C, Tsai CJ, Boutet S, Messerschmidt M, Sala L, Williams GJ, Ozerov D, Coleman M, Li XD, Frank M, Pedrini B. Structure-factor amplitude reconstruction from serial femtosecond crystallography of two-dimensional membrane-protein crystals. IUCrJ 2019; 6:34-45. [PMID: 30713701 PMCID: PMC6327180 DOI: 10.1107/s2052252518014641] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 10/16/2018] [Indexed: 06/09/2023]
Abstract
Serial femtosecond crystallography of two-dimensional membrane-protein crystals at X-ray free-electron lasers has the potential to address the dynamics of functionally relevant large-scale motions, which can be sterically hindered in three-dimensional crystals and suppressed in cryocooled samples. In previous work, diffraction data limited to a two-dimensional reciprocal-space slice were evaluated and it was demonstrated that the low intensity of the diffraction signal can be overcome by collecting highly redundant data, thus enhancing the achievable resolution. Here, the application of a newly developed method to analyze diffraction data covering three reciprocal-space dimensions, extracting the reciprocal-space map of the structure-factor amplitudes, is presented. Despite the low resolution and completeness of the data set, it is shown by molecular replacement that the reconstructed amplitudes carry meaningful structural information. Therefore, it appears that these intrinsic limitations in resolution and completeness from two-dimensional crystal diffraction may be overcome by collecting highly redundant data along the three reciprocal-space axes, thus allowing the measurement of large-scale dynamics in pump-probe experiments.
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Affiliation(s)
| | - Karol Nass
- Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Anton Barty
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Mark S. Hunter
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | | | - Ching-Ju Tsai
- Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Sébastien Boutet
- Linac Coherent Light Source, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Marc Messerschmidt
- Linac Coherent Light Source, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- National Science Foundation BioXFEL Science and Technology Center, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Leonardo Sala
- Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Garth J. Williams
- Linac Coherent Light Source, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- NSLS-II, Brookhaven National Laboratory, PO Box 5000, Upton, NY 11973, USA
| | - Dmitry Ozerov
- Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Matthew Coleman
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Xiao-Dan Li
- Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Matthias Frank
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Bill Pedrini
- Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
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13
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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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14
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Messerschmidt M. First crystallography experiments at the European XFEL. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s0108767318096095] [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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15
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Bajt S, Prasciolu M, Fleckenstein H, Domaracký M, Chapman HN, Morgan AJ, Yefanov O, Messerschmidt M, Du Y, Murray KT, Mariani V, Kuhn M, Aplin S, Pande K, Villanueva-Perez P, Stachnik K, Chen JPJ, Andrejczuk A, Meents A, Burkhardt A, Pennicard D, Huang X, Yan H, Nazaretski E, Chu YS, Hamm CE. X-ray focusing with efficient high-NA multilayer Laue lenses. Light Sci Appl 2018; 7:17162. [PMID: 30839543 PMCID: PMC6060042 DOI: 10.1038/lsa.2017.162] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 11/19/2017] [Accepted: 11/20/2017] [Indexed: 05/22/2023]
Abstract
Multilayer Laue lenses are volume diffraction elements for the efficient focusing of X-rays. With a new manufacturing technique that we introduced, it is possible to fabricate lenses of sufficiently high numerical aperture (NA) to achieve focal spot sizes below 10 nm. The alternating layers of the materials that form the lens must span a broad range of thicknesses on the nanometer scale to achieve the necessary range of X-ray deflection angles required to achieve a high NA. This poses a challenge to both the accuracy of the deposition process and the control of the materials properties, which often vary with layer thickness. We introduced a new pair of materials-tungsten carbide and silicon carbide-to prepare layered structures with smooth and sharp interfaces and with no material phase transitions that hampered the manufacture of previous lenses. Using a pair of multilayer Laue lenses (MLLs) fabricated from this system, we achieved a two-dimensional focus of 8.4 × 6.8 nm2 at a photon energy of 16.3 keV with high diffraction efficiency and demonstrated scanning-based imaging of samples with a resolution well below 10 nm. The high NA also allowed projection holographic imaging with strong phase contrast over a large range of magnifications. An error analysis indicates the possibility of achieving 1 nm focusing.
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Affiliation(s)
- Saša Bajt
- Photon Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Mauro Prasciolu
- Photon Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Holger Fleckenstein
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Martin Domaracký
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Henry N Chapman
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, Hamburg 22607, Germany
- Centre for Ultrafast Imaging, Luruper Chaussee 149, Hamburg 22607, Germany
| | - Andrew J Morgan
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Marc Messerschmidt
- National Science Foundation BioXFEL Science and Technology Center, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Yang Du
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Kevin T Murray
- Photon Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Valerio Mariani
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Manuela Kuhn
- Photon Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Steven Aplin
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Kanupriya Pande
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | | | | | - Joe PJ Chen
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Andrzej Andrejczuk
- Faculty of Physics, University of Bialystok, Ciolkowskiego 1L Str., Bialystok 15-245, Poland
| | - Alke Meents
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Anja Burkhardt
- Photon Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - David Pennicard
- Photon Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Xiaojing Huang
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Hanfei Yan
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Evgeny Nazaretski
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Yong S Chu
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Christian E Hamm
- Alfred-Wegener Institute, Helmholtz Center for Polar and Marine Research, Bussestr. 27, Bremerhaven 27570, Germany
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16
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Casadei CM, Tsai CJ, Barty A, Hunter MS, Zatsepin NA, Padeste C, Capitani G, Benner WH, Boutet S, Hau-Riege SP, Kupitz C, Messerschmidt M, Ogren JI, Pardini T, Rothschild KJ, Sala L, Segelke B, Williams GJ, Evans JE, Li XD, Coleman M, Pedrini B, Frank M. Resolution extension by image summing in serial femtosecond crystallography of two-dimensional membrane-protein crystals. IUCrJ 2018; 5:103-117. [PMID: 29354276 PMCID: PMC5755582 DOI: 10.1107/s2052252517017043] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 11/27/2017] [Indexed: 05/08/2023]
Abstract
Previous proof-of-concept measurements on single-layer two-dimensional membrane-protein crystals performed at X-ray free-electron lasers (FELs) have demonstrated that the collection of meaningful diffraction patterns, which is not possible at synchrotrons because of radiation-damage issues, is feasible. Here, the results obtained from the analysis of a thousand single-shot, room-temperature X-ray FEL diffraction images from two-dimensional crystals of a bacteriorhodopsin mutant are reported in detail. The high redundancy in the measurements boosts the intensity signal-to-noise ratio, so that the values of the diffracted intensities can be reliably determined down to the detector-edge resolution of 4 Å. The results show that two-dimensional serial crystallography at X-ray FELs is a suitable method to study membrane proteins to near-atomic length scales at ambient temperature. The method presented here can be extended to pump-probe studies of optically triggered structural changes on submillisecond timescales in two-dimensional crystals, which allow functionally relevant large-scale motions that may be quenched in three-dimensional crystals.
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Affiliation(s)
| | - Ching-Ju Tsai
- Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Anton Barty
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Mark S. Hunter
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Nadia A. Zatsepin
- Arizona State University, 300 East University Drive, Tempe, AZ 85287, USA
| | | | | | - W. Henry Benner
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Stefan P. Hau-Riege
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Christopher Kupitz
- Arizona State University, 300 East University Drive, Tempe, AZ 85287, USA
| | - Marc Messerschmidt
- Linac Coherent Light Source, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- National Science Foundation BioXFEL Science and Technology Center, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - John I. Ogren
- Physics Departement, Boston University, 590 Commonwealth Avenue, Boston, MA 02215, USA
| | - Tom Pardini
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Kenneth J. Rothschild
- Physics Departement, Boston University, 590 Commonwealth Avenue, Boston, MA 02215, USA
| | - Leonardo Sala
- Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Brent Segelke
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Garth J. Williams
- Linac Coherent Light Source, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - James E. Evans
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Boulevard, Richland, WA 99354, USA
| | - Xiao-Dan Li
- Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Matthew Coleman
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Bill Pedrini
- Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
- Correspondence e-mail:
| | - Matthias Frank
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
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17
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Meents A, Wiedorn MO, Srajer V, Henning R, Sarrou I, Bergtholdt J, Barthelmess M, Reinke PYA, Dierksmeyer D, Tolstikova A, Schaible S, Messerschmidt M, Ogata CM, Kissick DJ, Taft MH, Manstein DJ, Lieske J, Oberthuer D, Fischetti RF, Chapman HN. Pink-beam serial crystallography. Nat Commun 2017; 8:1281. [PMID: 29097720 PMCID: PMC5668288 DOI: 10.1038/s41467-017-01417-3] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 09/14/2017] [Indexed: 02/02/2023] Open
Abstract
Serial X-ray crystallography allows macromolecular structure determination at both X-ray free electron lasers (XFELs) and, more recently, synchrotron sources. The time resolution for serial synchrotron crystallography experiments has been limited to millisecond timescales with monochromatic beams. The polychromatic, "pink", beam provides a more than two orders of magnitude increased photon flux and hence allows accessing much shorter timescales in diffraction experiments at synchrotron sources. Here we report the structure determination of two different protein samples by merging pink-beam diffraction patterns from many crystals, each collected with a single 100 ps X-ray pulse exposure per crystal using a setup optimized for very low scattering background. In contrast to experiments with monochromatic radiation, data from only 50 crystals were required to obtain complete datasets. The high quality of the diffraction data highlights the potential of this method for studying irreversible reactions at sub-microsecond timescales using high-brightness X-ray facilities.
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Affiliation(s)
- A Meents
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany. .,Deutsches Elektronen Synchrotron (DESY), Photon Science, Notkestrasse 85, 22607, Hamburg, Germany.
| | - M O Wiedorn
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany.,Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - V Srajer
- Center for Advanced Radiation Sources, The University of Chicago, 9700 South Cass Avenue, Argonne, IL, 60439, USA
| | - R Henning
- Center for Advanced Radiation Sources, The University of Chicago, 9700 South Cass Avenue, Argonne, IL, 60439, USA
| | - I Sarrou
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - J Bergtholdt
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - M Barthelmess
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - P Y A Reinke
- Medizinische Hochschule Hannover (MHH), Institut für Biophysikalische Chemie, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - D Dierksmeyer
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - A Tolstikova
- Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - S Schaible
- Deutsches Elektronen Synchrotron (DESY), Photon Science, Notkestrasse 85, 22607, Hamburg, Germany
| | - M Messerschmidt
- National Science Foundation BioXFEL Science and Technology Center, 700 Ellicott Street, Buffalo, NY, 14203, USA
| | - C M Ogata
- Advanced Photon Source, Argonne National Laboratory, 9700 S. Cass Ave, Lemont, IL, 60439, USA
| | - D J Kissick
- Advanced Photon Source, Argonne National Laboratory, 9700 S. Cass Ave, Lemont, IL, 60439, USA
| | - M H Taft
- Medizinische Hochschule Hannover (MHH), Institut für Biophysikalische Chemie, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - D J Manstein
- Medizinische Hochschule Hannover (MHH), Institut für Biophysikalische Chemie, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - J Lieske
- Deutsches Elektronen Synchrotron (DESY), Photon Science, Notkestrasse 85, 22607, Hamburg, Germany
| | - D Oberthuer
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - R F Fischetti
- Advanced Photon Source, Argonne National Laboratory, 9700 S. Cass Ave, Lemont, IL, 60439, USA
| | - H N Chapman
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany.,Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.,Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany
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18
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Hadian-Jazi M, Messerschmidt M, Darmanin C, Giewekemeyer K, Mancuso AP, Abbey B. A peak-finding algorithm based on robust statistical analysis in serial crystallography. J Appl Crystallogr 2017. [DOI: 10.1107/s1600576717014340] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [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 recent development of serial crystallography at synchrotron and X-ray free-electron laser (XFEL) sources is producing crystallographic datasets of ever increasing volume. The size of these datasets is such that fast and efficient analysis presents a range of challenges that have to be overcome to enable real-time data analysis, which is essential for the effective management of XFEL experiments. Among the blocks which constitute the analysis pipeline, one major bottleneck is `peak finding', whose goal is to identify the Bragg peaks within (often) noisy diffraction patterns. Development of faster and more reliable peak-finding algorithms will allow for efficient processing and storage of the incoming data, as well as the optimal use of diffraction data for structure determination. This paper addresses the problem of peak finding and, by extension, `hit finding' in crystallographic XFEL datasets, by exploiting recent developments in robust statistical analysis. The approach described here involves two basic steps: (1) the identification of pixels which contain potential peaks and (2) modeling of the local background in the vicinity of these potential peaks. The presented framework can be generalized to include both complex background models and alternative models for the Bragg peaks.
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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. 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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20
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Dilanian RA, Streltsov V, Coughlan HD, Quiney HM, Martin AV, Klonis N, Dogovski C, Boutet S, Messerschmidt M, Williams GJ, Williams S, Phillips NW, Nugent KA, Tilley L, Abbey B. Nanocrystallography measurements of early stage synthetic malaria pigment. J Appl Crystallogr 2017; 50:1533-1540. [PMID: 29021736 PMCID: PMC5627683 DOI: 10.1107/s1600576717012663] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 09/04/2017] [Indexed: 11/10/2022] Open
Abstract
The recent availability of extremely intense, femtosecond X-ray free-electron laser (XFEL) sources has spurred the development of serial femtosecond nanocrystallography (SFX). Here, SFX is used to analyze nanoscale crystals of β-hematin, the synthetic form of hemozoin which is a waste by-product of the malaria parasite. This analysis reveals significant differences in β-hematin data collected during SFX and synchrotron crystallography experiments. To interpret these differences two possibilities are considered: structural differences between the nanocrystal and larger crystalline forms of β-hematin, and radiation damage. Simulation studies show that structural inhomogeneity appears at present to provide a better fit to the experimental data. If confirmed, these observations will have implications for designing compounds that inhibit hemozoin formation and suggest that, for some systems at least, additional information may be gained by comparing structures obtained from nanocrystals and macroscopic crystals of the same molecule.
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Affiliation(s)
- Ruben A. Dilanian
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | | | - Hannah D. Coughlan
- ARC Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- CSIRO Manufacturing Flagship, Parkville, Victoria, Australia
| | - Harry M. Quiney
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Andrew V. Martin
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Nectarios Klonis
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Con Dogovski
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Sébastien Boutet
- LiNAC Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | - Garth J. Williams
- Brookhaven National Laboratory, PO Box 5000, Upton, NY 11973-5000, USA
| | - Sophie Williams
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Nicholas W. Phillips
- CSIRO, Parkville, Victoria 3052, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Keith A. Nugent
- ARC Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Leann Tilley
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Brian Abbey
- ARC Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
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21
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Ryan RA, Williams S, Martin AV, Dilanian RA, Darmanin C, Putkunz CT, Wood D, Streltsov VA, Jones MWM, Gaffney N, Hofmann F, Williams GJ, Boutet S, Messerschmidt M, Seibert MM, Curwood EK, Balaur E, Peele AG, Nugent KA, Quiney HM, Abbey B. Measurements of Long-range Electronic Correlations During Femtosecond Diffraction Experiments Performed on Nanocrystals of Buckminsterfullerene. J Vis Exp 2017. [PMID: 28872125 PMCID: PMC5614354 DOI: 10.3791/56296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The precise details of the interaction of intense X-ray pulses with matter are a topic of intense interest to researchers attempting to interpret the results of femtosecond X-ray free electron laser (XFEL) experiments. An increasing number of experimental observations have shown that although nuclear motion can be negligible, given a short enough incident pulse duration, electronic motion cannot be ignored. The current and widely accepted models assume that although electrons undergo dynamics driven by interaction with the pulse, their motion could largely be considered 'random'. This would then allow the supposedly incoherent contribution from the electronic motion to be treated as a continuous background signal and thus ignored. The original aim of our experiment was to precisely measure the change in intensity of individual Bragg peaks, due to X-ray induced electronic damage in a model system, crystalline C60. Contrary to this expectation, we observed that at the highest X-ray intensities, the electron dynamics in C60 were in fact highly correlated, and over sufficiently long distances that the positions of the Bragg reflections are significantly altered. This paper describes in detail the methods and protocols used for these experiments, which were conducted both at the Linac Coherent Light Source (LCLS) and the Australian Synchrotron (AS) as well as the crystallographic approaches used to analyse the data.
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Affiliation(s)
- Rebecca A Ryan
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne
| | - Sophie Williams
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne
| | - Andrew V Martin
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne
| | - Ruben A Dilanian
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne
| | - Connie Darmanin
- Australian Research Council (ARC) Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Sciences, La Trobe University
| | - Corey T Putkunz
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne
| | - David Wood
- Department of Physics, Imperial College London
| | | | - Michael W M Jones
- Science and Engineering Faculty, Queensland University of Technology
| | | | - Felix Hofmann
- Department of Engineering Science, University of Oxford
| | | | - Sebastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory
| | | | - M Marvin Seibert
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University
| | - Evan K Curwood
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University
| | - Eugeniu Balaur
- Australian Research Council (ARC) Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Sciences, La Trobe University
| | - Andrew G Peele
- Science and Engineering Faculty, Queensland University of Technology
| | - Keith A Nugent
- Australian Research Council (ARC) Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Sciences, La Trobe University
| | - Harry M Quiney
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne;
| | - Brian Abbey
- Australian Research Council (ARC) Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Sciences, La Trobe University;
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22
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Mehrjoo M, Giewekemeyer K, Vagovič P, Stern S, Bean R, Messerschmidt M, Keitel B, Plönjes E, Kuhlmann M, Mey T, Schneidmiller EA, Yurkov MV, Limberg T, Mancuso AP. Single-shot determination of focused FEL wave fields using iterative phase retrieval. Opt Express 2017; 25:17892-17903. [PMID: 28789279 DOI: 10.1364/oe.25.017892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 06/18/2017] [Indexed: 06/07/2023]
Abstract
Determining fluctuations in focus properties is essential for many experiments at Self-Amplified-Spontaneous-Emission (SASE) based Free-Electron-Lasers (FELs), in particular for imaging single non-crystalline biological particles. We report on a diffractive imaging technique to fully characterize highly focused, single-shot pulses using an iterative phase retrieval algorithm, and benchmark it against an existing Hartmann wavefront sensor. The results, both theoretical and experimental, demonstrate the effectiveness of this technique to provide a comprehensive and convenient shot-to-shot measurement of focused-pulse wave fields and source-point positional variations without the need for manipulative optics between the focus and the detector.
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23
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Amaya AJ, Pathak H, Modak VP, Laksmono H, Loh ND, Sellberg JA, Sierra RG, McQueen TA, Hayes MJ, Williams GJ, Messerschmidt M, Boutet S, Bogan MJ, Nilsson A, Stan CA, Wyslouzil BE. How Cubic Can Ice Be? J Phys Chem Lett 2017; 8:3216-3222. [PMID: 28657757 DOI: 10.1021/acs.jpclett.7b01142] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Using an X-ray laser, we investigated the crystal structure of ice formed by homogeneous ice nucleation in deeply supercooled water nanodrops (r ≈ 10 nm) at ∼225 K. The nanodrops were formed by condensation of vapor in a supersonic nozzle, and the ice was probed within 100 μs of freezing using femtosecond wide-angle X-ray scattering at the Linac Coherent Light Source free-electron X-ray laser. The X-ray diffraction spectra indicate that this ice has a metastable, predominantly cubic structure; the shape of the first ice diffraction peak suggests stacking-disordered ice with a cubicity value, χ, in the range of 0.78 ± 0.05. The cubicity value determined here is higher than those determined in experiments with micron-sized drops but comparable to those found in molecular dynamics simulations. The high cubicity is most likely caused by the extremely low freezing temperatures and by the rapid freezing, which occurs on a ∼1 μs time scale in single nanodroplets.
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Affiliation(s)
- Andrew J Amaya
- William G. Lowrie Department of Chemical and Biomolecular Engineering, Ohio State University , Columbus, Ohio 43210, United States
| | - Harshad Pathak
- William G. Lowrie Department of Chemical and Biomolecular Engineering, Ohio State University , Columbus, Ohio 43210, United States
| | - Viraj P Modak
- William G. Lowrie Department of Chemical and Biomolecular Engineering, Ohio State University , Columbus, Ohio 43210, United States
| | - Hartawan Laksmono
- Stanford PULSE Institute, SLAC National Acceleratory Laboratory , Menlo Park, California 94025, United States
| | - N Duane Loh
- Stanford PULSE Institute, SLAC National Acceleratory Laboratory , Menlo Park, California 94025, United States
- Department of Physics, National University of Singapore , Singapore 117557
| | - Jonas A Sellberg
- Stanford PULSE Institute, SLAC National Acceleratory Laboratory , Menlo Park, California 94025, United States
- Department of Physics, AlbaNova University Center, Stockholm University , S-106 91 Stockholm, Sweden
- Biomedical and X-ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology , S-106 91 Stockholm, Sweden
- SUNCAT Center for Interface Science & Catalysis, SLAC National Laboratory , Menlo Park, California 94025, United States
| | - Raymond G Sierra
- Stanford PULSE Institute, SLAC National Acceleratory Laboratory , Menlo Park, California 94025, United States
| | - Trevor A McQueen
- SUNCAT Center for Interface Science & Catalysis, SLAC National Laboratory , Menlo Park, California 94025, United States
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Matt J Hayes
- Linac Coherent Light Source, SLAC National Accelerator Laboratory , Menlo Park, California 94025, United States
| | - Garth J Williams
- Linac Coherent Light Source, SLAC National Accelerator Laboratory , Menlo Park, California 94025, United States
- Brookhaven National Laboratory , Upton, New York 11973, United States
| | - Marc Messerschmidt
- Linac Coherent Light Source, SLAC National Accelerator Laboratory , Menlo Park, California 94025, United States
- National Science Foundation BioXFEL Science and Technology Center , Buffalo, New York 14203, United States
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory , Menlo Park, California 94025, United States
| | - Michael J Bogan
- Stanford PULSE Institute, SLAC National Acceleratory Laboratory , Menlo Park, California 94025, United States
| | - Anders Nilsson
- Stanford PULSE Institute, SLAC National Acceleratory Laboratory , Menlo Park, California 94025, United States
- Department of Physics, AlbaNova University Center, Stockholm University , S-106 91 Stockholm, Sweden
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory , Menlo Park, California 94025, United States
| | - Claudiu A Stan
- Stanford PULSE Institute, SLAC National Acceleratory Laboratory , Menlo Park, California 94025, United States
| | - Barbara E Wyslouzil
- William G. Lowrie Department of Chemical and Biomolecular Engineering, Ohio State University , Columbus, Ohio 43210, United States
- Department of Chemistry and Biochemistry, Ohio State University , Columbus, Ohio 43210, United States
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24
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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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25
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Meents A, Wiedorn MO, Srajer V, Henning R, Sarrou I, Bergtholdt J, Barthelmess M, Reinke P, Dierksmeyer D, Tolstikova A, Schaible S, Messerschmidt M, Ogata CM, Kissick DJ, Taft M, Manstein D, Lieske J, Oberthuer D, Fischetti RF, Chapman HN. Low-background pink-beam serial crystallography. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s0108767317096052] [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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26
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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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27
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Colletier JP, Sawaya MR, Gingery M, Rodriguez JA, Cascio D, Brewster AS, Michels-Clark T, Hice RH, Coquelle N, Boutet S, Williams GJ, Messerschmidt M, DePonte DP, Sierra RG, Laksmono H, Koglin JE, Hunter MS, Park HW, Uervirojnangkoorn M, Bideshi DK, Brunger AT, Federici BA, Sauter NK, Eisenberg DS. De novo phasing with X-ray laser reveals mosquito larvicide BinAB structure. Nature 2016; 539:43-47. [PMID: 27680699 PMCID: PMC5161637 DOI: 10.1038/nature19825] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [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: 01/07/2016] [Accepted: 09/07/2016] [Indexed: 11/30/2022]
Abstract
BinAB is a naturally occurring paracrystalline larvicide distributed worldwide to combat the devastating diseases borne by mosquitoes. These crystals are composed of homologous molecules, BinA and BinB, which play distinct roles in the multi-step intoxication process, transforming from harmless, robust crystals, to soluble protoxin heterodimers, to internalized mature toxin, and finally toxic oligomeric pores. The small size of the crystals, 50 unit cells per edge, on average, has impeded structural characterization by conventional means. Here, we report the structure of BinAB solved de novo by serial-femtosecond crystallography at an X-ray free-electron laser (XFEL). The structure reveals tyrosine and carboxylate-mediated contacts acting as pH switches to release soluble protoxin in the alkaline larval midgut. An enormous heterodimeric interface appears responsible for anchoring BinA to receptor-bound BinB for co-internalization. Remarkably, this interface is largely composed of propeptides, suggesting that proteolytic maturation would trigger dissociation of the heterodimer and progression to pore formation.
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Affiliation(s)
| | - Michael R Sawaya
- UCLA-DOE Institute for Genomics and Proteomics, Department of Biological Chemistry, University of California, Los Angeles, California 90095-1570, USA.,Howard Hughes Medical Institute, University of California, Los Angeles, California 90095-1570, USA
| | - Mari Gingery
- UCLA-DOE Institute for Genomics and Proteomics, Department of Biological Chemistry, University of California, Los Angeles, California 90095-1570, USA
| | - Jose A Rodriguez
- UCLA-DOE Institute for Genomics and Proteomics, Department of Biological Chemistry, University of California, Los Angeles, California 90095-1570, USA
| | - Duilio Cascio
- UCLA-DOE Institute for Genomics and Proteomics, Department of Biological Chemistry, University of California, Los Angeles, California 90095-1570, USA
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Tara Michels-Clark
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Robert H Hice
- Department of Entomology and Graduate Program in Cell, Molecular and Developmental Biology, University of California, Riverside, California 92521, USA
| | - Nicolas Coquelle
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Garth J Williams
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Marc Messerschmidt
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Daniel P DePonte
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Raymond G Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Hartawan Laksmono
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Jason E Koglin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Hyun-Woo Park
- Department of Entomology and Graduate Program in Cell, Molecular and Developmental Biology, University of California, Riverside, California 92521, USA.,Department of Biological Sciences, California Baptist University, Riverside, California 92504, USA
| | - Monarin Uervirojnangkoorn
- Molecular and Cellular Physiology, and Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
| | - Dennis K Bideshi
- Department of Entomology and Graduate Program in Cell, Molecular and Developmental Biology, University of California, Riverside, California 92521, USA.,Department of Biological Sciences, California Baptist University, Riverside, California 92504, USA
| | - Axel T Brunger
- Molecular and Cellular Physiology, and Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
| | - Brian A Federici
- Department of Entomology and Graduate Program in Cell, Molecular and Developmental Biology, University of California, Riverside, California 92521, USA
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - David S Eisenberg
- UCLA-DOE Institute for Genomics and Proteomics, Department of Biological Chemistry, University of California, Los Angeles, California 90095-1570, USA.,Howard Hughes Medical Institute, University of California, Los Angeles, California 90095-1570, USA
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28
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Abbey B, Dilanian RA, Darmanin C, Ryan RA, Putkunz CT, Martin AV, Wood D, Streltsov V, Jones MWM, Gaffney N, Hofmann F, Williams GJ, Boutet S, Messerschmidt M, Seibert MM, Williams S, Curwood E, Balaur E, Peele AG, Nugent KA, Quiney HM. X-ray laser-induced electron dynamics observed by femtosecond diffraction from nanocrystals of Buckminsterfullerene. Sci Adv 2016; 2:e1601186. [PMID: 27626076 PMCID: PMC5017826 DOI: 10.1126/sciadv.1601186] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 08/09/2016] [Indexed: 06/06/2023]
Abstract
X-ray free-electron lasers (XFELs) deliver x-ray pulses with a coherent flux that is approximately eight orders of magnitude greater than that available from a modern third-generation synchrotron source. The power density of an XFEL pulse may be so high that it can modify the electronic properties of a sample on a femtosecond time scale. Exploration of the interaction of intense coherent x-ray pulses and matter is both of intrinsic scientific interest and of critical importance to the interpretation of experiments that probe the structures of materials using high-brightness femtosecond XFEL pulses. We report observations of the diffraction of extremely intense 32-fs nanofocused x-ray pulses by a powder sample of crystalline C60. We find that the diffraction pattern at the highest available incident power significantly differs from the one obtained using either third-generation synchrotron sources or XFEL sources operating at low output power and does not correspond to the diffraction pattern expected from any known phase of crystalline C60. We interpret these data as evidence of a long-range, coherent dynamic electronic distortion that is driven by the interaction of the periodic array of C60 molecular targets with intense x-ray pulses of femtosecond duration.
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Affiliation(s)
- 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, Victoria 3086, Australia
| | - Ruben A. Dilanian
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne, Parkville, Victoria 3010, Australia
| | - 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, Victoria 3086, Australia
| | - Rebecca A. Ryan
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Corey T. Putkunz
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Andrew V. Martin
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne, Parkville, Victoria 3010, Australia
| | - David Wood
- Department of Physics, Imperial College London, London SW7 2AZ, UK
| | - Victor Streltsov
- Florey Institute of Neuroscience and Mental Health, 30 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Michael W. M. Jones
- Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Naylyn Gaffney
- Swinburne University of Technology, Melbourne, Victoria 3122, Australia
| | - Felix Hofmann
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK
| | - Garth J. Williams
- Brookhaven National Laboratory, PO Box 5000, Upton, NY 11973–5000, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Marc Messerschmidt
- BioXFEL Science and Technology Center, 700 Ellicott Street, Buffalo, NY 1420, USA
| | - M. Marvin Seibert
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Sophie Williams
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Evan Curwood
- Florey Institute of Neuroscience and Mental Health, Heidelberg, Victoria 3084, Australia
| | - Eugeniu Balaur
- Australian Research Council (ARC) Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Sciences, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Andrew G. Peele
- Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - 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, Victoria 3086, Australia
| | - Harry M. Quiney
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne, Parkville, Victoria 3010, Australia
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29
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von Arnim U, Wex T, Link A, Messerschmidt M, Venerito M, Miehlke S, Malfertheiner P. Helicobacter pylori infection is associated with a reduced risk of developing eosinophilic oesophagitis. Aliment Pharmacol Ther 2016; 43:825-30. [PMID: 26898731 DOI: 10.1111/apt.13560] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 01/11/2016] [Accepted: 01/26/2016] [Indexed: 12/19/2022]
Abstract
BACKGROUND Eosinophilic oesophagitis (EoE) represents a chronic immune-antigen-mediated allergic disease of the oesophagus of still unknown aetiology. Environmental exposure has been postulated to play a pathogenetic role. Helicobacter pylori (H. pylori) infection has been inversely associated with allergic diseases including atopic dermatitis, asthma and allergic rhinitis and H. pylori may play a protective role in these conditions. Little is known about the relationship between EoE and H. pylori. AIM To investigate in a case-control study whether H. pylori infection is associated with a reduced risk of developing EoE. METHODS H. pylori infection was evaluated by serology in 58 [11(19%) female, 47 (81%) male, median age: 36.5 years, range 20-72 years] patients with a clinical and histologically proven diagnosis of EoE and 116 age and sex-matched controls (1 case: 2 controls). Antibodies against H. pylori were identified by enzyme-linked immunosorbent assay. Patients with H. pylori-specific IgG ≥ 30 enzyme immunounits were classified as H. pylori-positive. RESULTS 3/58 (5.2%) patients with EoE had serological evidence of H. pylori infection (EoE - H. pylori current infection) and 5/58 (8.6%) reported prior eradication therapy for H. pylori infection (EoE - H. pylori former infection). The control group demonstrated significantly higher seroprevalence of H. pylori (37.9%, P < 0.0001) when compared to patients with EoE. EoE was inversely associated with H. pylori infection [odds ratio (OR) 0.24, 95% confidence interval (CI) 0.11-0.50]. CONCLUSION Helicobacter pylori infection is inversely associated with EoE. Our results may contribute to further understanding the pathogenesis and evolving aetiology of EoE.
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Affiliation(s)
- U von Arnim
- Department of Gastroenterology, Hepatology and Infectious diseases, Otto-von-Guericke University of Magdeburg, Magdeburg, Germany
| | - T Wex
- Department of Gastroenterology, Hepatology and Infectious diseases, Otto-von-Guericke University of Magdeburg, Magdeburg, Germany
| | - A Link
- Department of Gastroenterology, Hepatology and Infectious diseases, Otto-von-Guericke University of Magdeburg, Magdeburg, Germany
| | - M Messerschmidt
- Department of Gastroenterology, Hepatology and Infectious diseases, Otto-von-Guericke University of Magdeburg, Magdeburg, Germany
| | - M Venerito
- Department of Gastroenterology, Hepatology and Infectious diseases, Otto-von-Guericke University of Magdeburg, Magdeburg, Germany
| | - S Miehlke
- Cooperation of Internal Medicine, Center for Digestive Diseases, Hamburg, Germany
| | - P Malfertheiner
- Department of Gastroenterology, Hepatology and Infectious diseases, Otto-von-Guericke University of Magdeburg, Magdeburg, Germany
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30
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Jakobi AJ, Passon DM, Knoops K, Stellato F, Liang M, White TA, Seine T, Messerschmidt M, Chapman HN, Wilmanns M. In cellulo serial crystallography of alcohol oxidase crystals inside yeast cells. IUCrJ 2016; 3:88-95. [PMID: 27006771 PMCID: PMC4775156 DOI: 10.1107/s2052252515022927] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/30/2015] [Indexed: 06/05/2023]
Abstract
The possibility of using femtosecond pulses from an X-ray free-electron laser to collect diffraction data from protein crystals formed in their native cellular organelle has been explored. X-ray diffraction of submicrometre-sized alcohol oxidase crystals formed in peroxisomes within cells of genetically modified variants of the methylotrophic yeast Hansenula polymorpha is reported and characterized. The observations are supported by synchrotron radiation-based powder diffraction data and electron microscopy. Based on these findings, the concept of in cellulo serial crystallography on protein targets imported into yeast peroxisomes without the need for protein purification as a requirement for subsequent crystallization is outlined.
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Affiliation(s)
- Arjen J. Jakobi
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, 22607 Hamburg, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Daniel M. Passon
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, 22607 Hamburg, Germany
| | - Kèvin Knoops
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Francesco Stellato
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Mengning Liang
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Thomas A. White
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Thomas Seine
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, 22607 Hamburg, Germany
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Marc Messerschmidt
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Henry N. Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, 22607 Hamburg, Germany
- Center for Ultrafast Imaging, Luruper Chaussee 149, 22607 Hamburg, Germany
| | - Matthias Wilmanns
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, 22607 Hamburg, Germany
- University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
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31
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Ferguson KR, Bucher M, Gorkhover T, Boutet S, Fukuzawa H, Koglin JE, Kumagai Y, Lutman A, Marinelli A, Messerschmidt M, Nagaya K, Turner J, Ueda K, Williams GJ, Bucksbaum PH, Bostedt C. Transient lattice contraction in the solid-to-plasma transition. Sci Adv 2016; 2:e1500837. [PMID: 27152323 PMCID: PMC4846449 DOI: 10.1126/sciadv.1500837] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 11/29/2015] [Indexed: 05/12/2023]
Abstract
In condensed matter systems, strong optical excitations can induce phonon-driven processes that alter their mechanical properties. We report on a new phenomenon where a massive electronic excitation induces a collective change in the bond character that leads to transient lattice contraction. Single large van der Waals clusters were isochorically heated to a nanoplasma state with an intense 10-fs x-ray (pump) pulse. The structural evolution of the nanoplasma was probed with a second intense x-ray (probe) pulse, showing systematic contraction stemming from electron delocalization during the solid-to-plasma transition. These findings are relevant for any material in extreme conditions ranging from the time evolution of warm or hot dense matter to ultrafast imaging with intense x-ray pulses or, more generally, any situation that involves a condensed matter-to-plasma transition.
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Affiliation(s)
- Ken R. Ferguson
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
| | - Maximilian Bucher
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Tais Gorkhover
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
- Institut für Optik und Atomare Physik, Technische Universität Berlin, 10623 Berlin, Germany
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Hironobu Fukuzawa
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - Jason E. Koglin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Yoshiaki Kumagai
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - Alberto Lutman
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Agostino Marinelli
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Marc Messerschmidt
- National Science Foundation BioXFEL Science and Technology Center, Buffalo, NY 14203, USA
| | - Kiyonobu Nagaya
- Division of Physics and Astronomy, Kyoto University, Kyoto 606-8501, Japan
| | - Jim Turner
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Kiyoshi Ueda
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - Garth J. Williams
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Philip H. Bucksbaum
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
- Pulse Institute, Stanford University and SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Christoph Bostedt
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
- Pulse Institute, Stanford University and SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
- Argonne National Laboratory, Lemont, IL 60439, USA
- Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA
- Corresponding author. E-mail:
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32
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Dominiak PM, Volkov A, Li X, Messerschmidt M, Coppens P. A Theoretical Databank of Transferable Aspherical Atoms and Its Application to Electrostatic Interaction Energy Calculations of Macromolecules. J Chem Theory Comput 2015; 3:232-47. [PMID: 26627168 DOI: 10.1021/ct6001994] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A comprehensive version of the theoretical databank of transferable aspherical pseudoatoms is described, and its first application to protein-ligand interaction energies is discussed. The databank contains all atom types present in natural amino acid residues and other biologically relevant molecules. Each atom type results from averaging over a family of chemically unique pseudoatoms, taking into account both first and second neighbors. The spawning procedure is used to ensure that close transferability is obeyed. The databank is applied to the syntenin PDZ2 domain complexed with four-residue peptides and to the PDZ2 dimer. Analysis of the electrostatic interactions energies calculated by the exact-potential/multipole-moment-databank method stresses the importance of the P0 and P-2 residues of the peptide in establishing the interaction, whereas the P-1 residue is shown to play a much smaller role. Unexpectedly, the charged P-3 residue contributes significantly to the interaction. The class I and II peptides are bound with the same strength by the syntenin PDZ2 domain, though the electrostatic interaction energy of the P-2 residue is smaller for class I peptides. There is no difference between the interaction energies of the peptides with PDZ2 domains from single-domain protein fragments and those from PDZ1-PDZ2 tandems.
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Affiliation(s)
- Paulina M Dominiak
- Department of Chemistry, State University of New York at Buffalo, New York 14260
| | - Anatoliy Volkov
- Department of Chemistry, State University of New York at Buffalo, New York 14260
| | - Xue Li
- Department of Chemistry, State University of New York at Buffalo, New York 14260
| | - Marc Messerschmidt
- Department of Chemistry, State University of New York at Buffalo, New York 14260
| | - Philip Coppens
- Department of Chemistry, State University of New York at Buffalo, New York 14260
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33
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Rodriguez JA, Ivanova MI, Sawaya MR, Cascio D, Reyes FE, Shi D, Sangwan S, Guenther EL, Johnson LM, Zhang M, Jiang L, Arbing MA, Nannenga BL, Hattne J, Whitelegge J, Brewster AS, Messerschmidt M, Boutet S, Sauter NK, Gonen T, Eisenberg DS. Structure of the toxic core of α-synuclein from invisible crystals. Nature 2015; 525:486-90. [PMID: 26352473 DOI: 10.1038/nature15368] [Citation(s) in RCA: 444] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 08/13/2015] [Indexed: 12/18/2022]
Abstract
The protein α-synuclein is the main component of Lewy bodies, the neuron-associated aggregates seen in Parkinson disease and other neurodegenerative pathologies. An 11-residue segment, which we term NACore, appears to be responsible for amyloid formation and cytotoxicity of human α-synuclein. Here we describe crystals of NACore that have dimensions smaller than the wavelength of visible light and thus are invisible by optical microscopy. As the crystals are thousands of times too small for structure determination by synchrotron X-ray diffraction, we use micro-electron diffraction to determine the structure at atomic resolution. The 1.4 Å resolution structure demonstrates that this method can determine previously unknown protein structures and here yields, to our knowledge, the highest resolution achieved by any cryo-electron microscopy method to date. The structure exhibits protofibrils built of pairs of face-to-face β-sheets. X-ray fibre diffraction patterns show the similarity of NACore to toxic fibrils of full-length α-synuclein. The NACore structure, together with that of a second segment, inspires a model for most of the ordered portion of the toxic, full-length α-synuclein fibril, presenting opportunities for the design of inhibitors of α-synuclein fibrils.
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Affiliation(s)
- Jose A Rodriguez
- Howard Hughes Medical Institute, UCLA-DOE Institute, Departments of Biological Chemistry and Chemistry and Biochemistry, Box 951570, UCLA, Los Angeles, California 90095-1570, USA
| | - Magdalena I Ivanova
- Howard Hughes Medical Institute, UCLA-DOE Institute, Departments of Biological Chemistry and Chemistry and Biochemistry, Box 951570, UCLA, Los Angeles, California 90095-1570, USA
| | - Michael R Sawaya
- Howard Hughes Medical Institute, UCLA-DOE Institute, Departments of Biological Chemistry and Chemistry and Biochemistry, Box 951570, UCLA, Los Angeles, California 90095-1570, USA
| | - Duilio Cascio
- Howard Hughes Medical Institute, UCLA-DOE Institute, Departments of Biological Chemistry and Chemistry and Biochemistry, Box 951570, UCLA, Los Angeles, California 90095-1570, USA
| | - Francis E Reyes
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, Virginia 20147, USA
| | - Dan Shi
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, Virginia 20147, USA
| | - Smriti Sangwan
- Howard Hughes Medical Institute, UCLA-DOE Institute, Departments of Biological Chemistry and Chemistry and Biochemistry, Box 951570, UCLA, Los Angeles, California 90095-1570, USA
| | - Elizabeth L Guenther
- Howard Hughes Medical Institute, UCLA-DOE Institute, Departments of Biological Chemistry and Chemistry and Biochemistry, Box 951570, UCLA, Los Angeles, California 90095-1570, USA
| | - Lisa M Johnson
- Howard Hughes Medical Institute, UCLA-DOE Institute, Departments of Biological Chemistry and Chemistry and Biochemistry, Box 951570, UCLA, Los Angeles, California 90095-1570, USA
| | - Meng Zhang
- Howard Hughes Medical Institute, UCLA-DOE Institute, Departments of Biological Chemistry and Chemistry and Biochemistry, Box 951570, UCLA, Los Angeles, California 90095-1570, USA
| | - Lin Jiang
- Howard Hughes Medical Institute, UCLA-DOE Institute, Departments of Biological Chemistry and Chemistry and Biochemistry, Box 951570, UCLA, Los Angeles, California 90095-1570, USA
| | - Mark A Arbing
- Howard Hughes Medical Institute, UCLA-DOE Institute, Departments of Biological Chemistry and Chemistry and Biochemistry, Box 951570, UCLA, Los Angeles, California 90095-1570, USA
| | - Brent L Nannenga
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, Virginia 20147, USA
| | - Johan Hattne
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, Virginia 20147, USA
| | - Julian Whitelegge
- Box 42, NPI-Semel Institute, 760 Westwood Plaza, UCLA, Los Angeles, California 90024, USA
| | - Aaron S Brewster
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Marc Messerschmidt
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Nicholas K Sauter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Tamir Gonen
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, Virginia 20147, USA
| | - David S Eisenberg
- Howard Hughes Medical Institute, UCLA-DOE Institute, Departments of Biological Chemistry and Chemistry and Biochemistry, Box 951570, UCLA, Los Angeles, California 90095-1570, USA
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34
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Laksmono H, McQueen T, Sellberg JA, Loh ND, Huang C, Schlesinger D, Sierra RG, Hampton CY, Nordlund D, Beye M, Martin A, Barty A, Seibert MM, Messerschmidt M, Williams G, Boutet S, Amann-Winkel K, Loerting T, Pettersson LM, Bogan MJ, Nilsson A. Anomalous Behavior of the Homogeneous Ice Nucleation Rate in "No-Man's Land". J Phys Chem Lett 2015; 6:2826-2832. [PMID: 26207172 PMCID: PMC4507474 DOI: 10.1021/acs.jpclett.5b01164] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 07/02/2015] [Indexed: 05/30/2023]
Abstract
We present an analysis of ice nucleation kinetics from near-ambient pressure water as temperature decreases below the homogeneous limit TH by cooling micrometer-sized droplets (microdroplets) evaporatively at 103-104 K/s and probing the structure ultrafast using femtosecond pulses from the Linac Coherent Light Source (LCLS) free-electron X-ray laser. Below 232 K, we observed a slower nucleation rate increase with decreasing temperature than anticipated from previous measurements, which we suggest is due to the rapid decrease in water's diffusivity. This is consistent with earlier findings that microdroplets do not crystallize at <227 K, but vitrify at cooling rates of 106-107 K/s. We also hypothesize that the slower increase in the nucleation rate is connected with the proposed "fragile-to-strong" transition anomaly in water.
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Affiliation(s)
- Hartawan Laksmono
- PULSE
Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo
Park, California 94025, United States
| | - Trevor
A. McQueen
- SUNCAT
Ctr Interface Sci & Catalysis, SLAC
National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Jonas A. Sellberg
- SUNCAT
Ctr Interface Sci & Catalysis, SLAC
National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
- Department
of Physics, AlbaNova University Center, Stockholm University, S-106
91 Stockholm, Sweden
| | - N. Duane Loh
- PULSE
Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo
Park, California 94025, United States
- Center
for Bio-Imaging Sciences, National University
of Singapore, Singapore 117543
| | - Congcong Huang
- Stanford
Synchrotron Radiation Lightsource, SLAC
National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Daniel Schlesinger
- Department
of Physics, AlbaNova University Center, Stockholm University, S-106
91 Stockholm, Sweden
| | - Raymond G. Sierra
- PULSE
Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo
Park, California 94025, United States
| | - Christina Y. Hampton
- PULSE
Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo
Park, California 94025, United States
| | - Dennis Nordlund
- Stanford
Synchrotron Radiation Lightsource, SLAC
National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Martin Beye
- SUNCAT
Ctr Interface Sci & Catalysis, SLAC
National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
- Institute
for Methods and Instrumentation in Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und
Energie GmbH, Wilhelm-Conrad-Röntgen
Campus, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - Andrew
V. Martin
- 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
- Linac
Coherent Light Source, SLAC National Accelerator
Laboratory, 2575 Sand
Hill Road, Menlo Park, California 94025, United States
| | - Marc Messerschmidt
- Linac
Coherent Light Source, SLAC National Accelerator
Laboratory, 2575 Sand
Hill Road, Menlo Park, California 94025, United States
- National
Science
Foundation BioXFEL Science and Technology Center, 700 Ellicott Street, Buffalo, New York 14203, United
States
| | - Garth
J. Williams
- Linac
Coherent Light Source, SLAC National Accelerator
Laboratory, 2575 Sand
Hill Road, Menlo Park, California 94025, United States
| | - Sébastien Boutet
- Linac
Coherent Light Source, SLAC National Accelerator
Laboratory, 2575 Sand
Hill Road, Menlo Park, California 94025, United States
| | - Katrin Amann-Winkel
- Department
of Physics, AlbaNova University Center, Stockholm University, S-106
91 Stockholm, Sweden
- Institute of Physical Chemistry, University
of Innsbruck, Innrain
80-82, A-6020 Innsbruck, Austria
| | - Thomas Loerting
- Institute of Physical Chemistry, University
of Innsbruck, Innrain
80-82, A-6020 Innsbruck, Austria
| | - Lars
G. M. Pettersson
- Department
of Physics, AlbaNova University Center, Stockholm University, S-106
91 Stockholm, Sweden
| | - Michael J. Bogan
- PULSE
Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo
Park, California 94025, United States
| | - Anders Nilsson
- SUNCAT
Ctr Interface Sci & Catalysis, SLAC
National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
- Department
of Physics, AlbaNova University Center, Stockholm University, S-106
91 Stockholm, Sweden
- Stanford
Synchrotron Radiation Lightsource, SLAC
National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
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35
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Hattne J, Echols N, Tran R, Kern J, Gildea RJ, Brewster AS, Alonso-Mori R, Glöckner C, Hellmich J, Laksmono H, Sierra RG, Lassalle-Kaiser B, Lampe A, Han G, Gul S, DiFiore D, Milathianaki D, Fry AR, Miahnahri A, White WE, Schafer DW, Seibert MM, Koglin JE, Sokaras D, Weng TC, Sellberg J, Latimer MJ, Glatzel P, Zwart PH, Grosse-Kunstleve RW, Bogan MJ, Messerschmidt M, Williams GJ, Boutet S, Messinger J, Zouni A, Yano J, Bergmann U, Yachandra VK, Adams PD, Sauter NK. Erratum: Corrigendum: Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers. Nat Methods 2015. [DOI: 10.1038/nmeth0715-692d] [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: 11/09/2022]
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36
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Bublitz M, Nass K, Drachmann ND, Markvardsen AJ, Gutmann MJ, Barends TRM, Mattle D, Shoeman RL, Doak RB, Boutet S, Messerschmidt M, Seibert MM, Williams GJ, Foucar L, Reinhard L, Sitsel O, Gregersen JL, Clausen JD, Boesen T, Gotfryd K, Wang KT, Olesen C, Møller JV, Nissen P, Schlichting I. Structural studies of P-type ATPase-ligand complexes using an X-ray free-electron laser. IUCrJ 2015; 2:409-20. [PMID: 26175901 PMCID: PMC4491313 DOI: 10.1107/s2052252515008969] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 05/08/2015] [Indexed: 05/24/2023]
Abstract
Membrane proteins are key players in biological systems, mediating signalling events and the specific transport of e.g. ions and metabolites. Consequently, membrane proteins are targeted by a large number of currently approved drugs. Understanding their functions and molecular mechanisms is greatly dependent on structural information, not least on complexes with functionally or medically important ligands. Structure determination, however, is hampered by the difficulty of obtaining well diffracting, macroscopic crystals. Here, the feasibility of X-ray free-electron-laser-based serial femtosecond crystallography (SFX) for the structure determination of membrane protein-ligand complexes using microcrystals of various native-source and recombinant P-type ATPase complexes is demonstrated. The data reveal the binding sites of a variety of ligands, including lipids and inhibitors such as the hallmark P-type ATPase inhibitor orthovanadate. By analyzing the resolution dependence of ligand densities and overall model qualities, SFX data quality metrics as well as suitable refinement procedures are discussed. Even at relatively low resolution and multiplicity, the identification of ligands can be demonstrated. This makes SFX a useful tool for ligand screening and thus for unravelling the molecular mechanisms of biologically active proteins.
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Affiliation(s)
- Maike Bublitz
- Department of Molecular Biology and Genetics, Centre for Membrane Pumps in Cells and Disease – PUMPkin, Danish National Research Foundation, Aarhus University, Gustav Wieds Vej 10c, 8000 Aarhus C, Denmark
| | - Karol Nass
- Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Nikolaj D. Drachmann
- Department of Molecular Biology and Genetics, Centre for Membrane Pumps in Cells and Disease – PUMPkin, Danish National Research Foundation, Aarhus University, Gustav Wieds Vej 10c, 8000 Aarhus C, Denmark
| | | | - Matthias J. Gutmann
- Rutherford Appleton Laboratory, ISIS Facility, Chilton, Didcot OX11 0QX, England
| | - Thomas R. M. Barends
- Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Daniel Mattle
- Department of Molecular Biology and Genetics, Centre for Membrane Pumps in Cells and Disease – PUMPkin, Danish National Research Foundation, Aarhus University, Gustav Wieds Vej 10c, 8000 Aarhus C, Denmark
| | - Robert L. Shoeman
- Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - R. Bruce Doak
- Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Marc Messerschmidt
- Linac Coherent Light Source, LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Marvin M. Seibert
- Linac Coherent Light Source, LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Garth J. Williams
- Linac Coherent Light Source, LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Lutz Foucar
- Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Linda Reinhard
- Department of Molecular Biology and Genetics, Centre for Membrane Pumps in Cells and Disease – PUMPkin, Danish National Research Foundation, Aarhus University, Gustav Wieds Vej 10c, 8000 Aarhus C, Denmark
| | - Oleg Sitsel
- Department of Molecular Biology and Genetics, Centre for Membrane Pumps in Cells and Disease – PUMPkin, Danish National Research Foundation, Aarhus University, Gustav Wieds Vej 10c, 8000 Aarhus C, Denmark
| | - Jonas L. Gregersen
- Department of Molecular Biology and Genetics, Centre for Membrane Pumps in Cells and Disease – PUMPkin, Danish National Research Foundation, Aarhus University, Gustav Wieds Vej 10c, 8000 Aarhus C, Denmark
| | - Johannes D. Clausen
- Department of Molecular Biology and Genetics, Centre for Membrane Pumps in Cells and Disease – PUMPkin, Danish National Research Foundation, Aarhus University, Gustav Wieds Vej 10c, 8000 Aarhus C, Denmark
- Department of Biomedicine, Aarhus University, Ole Worms Allé 3, 8000 Aarhus C, Denmark
| | - Thomas Boesen
- Department of Molecular Biology and Genetics, Centre for Membrane Pumps in Cells and Disease – PUMPkin, Danish National Research Foundation, Aarhus University, Gustav Wieds Vej 10c, 8000 Aarhus C, Denmark
| | - Kamil Gotfryd
- Department of Neuroscience and Pharmacology, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Kai-Tuo Wang
- Department of Molecular Biology and Genetics, Centre for Membrane Pumps in Cells and Disease – PUMPkin, Danish National Research Foundation, Aarhus University, Gustav Wieds Vej 10c, 8000 Aarhus C, Denmark
| | - Claus Olesen
- Department of Molecular Biology and Genetics, Centre for Membrane Pumps in Cells and Disease – PUMPkin, Danish National Research Foundation, Aarhus University, Gustav Wieds Vej 10c, 8000 Aarhus C, Denmark
- Department of Biomedicine, Aarhus University, Ole Worms Allé 3, 8000 Aarhus C, Denmark
| | - Jesper V. Møller
- Department of Molecular Biology and Genetics, Centre for Membrane Pumps in Cells and Disease – PUMPkin, Danish National Research Foundation, Aarhus University, Gustav Wieds Vej 10c, 8000 Aarhus C, Denmark
- Department of Biomedicine, Aarhus University, Ole Worms Allé 3, 8000 Aarhus C, Denmark
| | - Poul Nissen
- Department of Molecular Biology and Genetics, Centre for Membrane Pumps in Cells and Disease – PUMPkin, Danish National Research Foundation, Aarhus University, Gustav Wieds Vej 10c, 8000 Aarhus C, Denmark
- DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark
| | - Ilme Schlichting
- Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
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37
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Feld GK, Heymann M, Benner WH, Pardini T, Tsai CJ, Boutet S, Coleman MA, Hunter MS, Li X, Messerschmidt M, Opathalage A, Pedrini B, Williams GJ, Krantz BA, Fraden S, Hau-Riege S, Evans JE, Segelke BW, Frank M. Low-Zpolymer sample supports for fixed-target serial femtosecond X-ray crystallography. J Appl Crystallogr 2015. [DOI: 10.1107/s1600576715010493] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [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
X-ray free-electron lasers (XFELs) offer a new avenue to the structural probing of complex materials, including biomolecules. Delivery of precious sample to the XFEL beam is a key consideration, as the sample of interest must be serially replaced after each destructive pulse. The fixed-target approach to sample delivery involves depositing samples on a thin-film support and subsequent serial introductionviaa translating stage. Some classes of biological materials, including two-dimensional protein crystals, must be introduced on fixed-target supports, as they require a flat surface to prevent sample wrinkling. A series of wafer and transmission electron microscopy (TEM)-style grid supports constructed of low-Zplastic have been custom-designed and produced. Aluminium TEM grid holders were engineered, capable of delivering up to 20 different conventional or plastic TEM grids using fixed-target stages available at the Linac Coherent Light Source (LCLS). As proof-of-principle, X-ray diffraction has been demonstrated from two-dimensional crystals of bacteriorhodopsin and three-dimensional crystals of anthrax toxin protective antigen mounted on these supports at the LCLS. The benefits and limitations of these low-Zfixed-target supports are discussed; it is the authors' belief that they represent a viable and efficient alternative to previously reported fixed-target supports for conducting diffraction studies with XFELs.
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38
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Stern S, Holmegaard L, Filsinger F, Rouzée A, Rudenko A, Johnsson P, Martin AV, Barty A, Bostedt C, Bozek J, Coffee R, Epp S, Erk B, Foucar L, Hartmann R, Kimmel N, Kühnel KU, Maurer J, Messerschmidt M, Rudek B, Starodub D, Thøgersen J, Weidenspointner G, White TA, Stapelfeldt H, Rolles D, Chapman HN, Küpper J. Toward atomic resolution diffractive imaging of isolated molecules with X-ray free-electron lasers. Faraday Discuss 2015; 171:393-418. [PMID: 25415561 DOI: 10.1039/c4fd00028e] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We give a detailed account of the theoretical analysis and the experimental results of an X-ray-diffraction experiment on quantum-state selected and strongly laser-aligned gas-phase ensembles of the prototypical large asymmetric rotor molecule 2,5-diiodobenzonitrile, performed at the Linac Coherent Light Source [Phys. Rev. Lett.112, 083002 (2014)]. This experiment is the first step toward coherent diffractive imaging of structures and structural dynamics of isolated molecules at atomic resolution, i.e., picometers and femtoseconds, using X-ray free-electron lasers.
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Affiliation(s)
- S Stern
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany.
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39
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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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40
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Ferguson KR, Bucher M, Bozek JD, Carron S, Castagna JC, Coffee R, Curiel GI, Holmes M, Krzywinski J, Messerschmidt M, Minitti M, Mitra A, Moeller S, Noonan P, Osipov T, Schorb S, Swiggers M, Wallace A, Yin J, Bostedt C. The Atomic, Molecular and Optical Science instrument at the Linac Coherent Light Source. J Synchrotron Radiat 2015; 22:492-7. [PMID: 25931058 PMCID: PMC4416665 DOI: 10.1107/s1600577515004646] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 03/06/2015] [Indexed: 05/13/2023]
Abstract
The Atomic, Molecular and Optical Science (AMO) instrument at the Linac Coherent Light Source (LCLS) provides a tight soft X-ray focus into one of three experimental endstations. The flexible instrument design is optimized for studying a wide variety of phenomena requiring peak intensity. There is a suite of spectrometers and two photon area detectors available. An optional mirror-based split-and-delay unit can be used for X-ray pump-probe experiments. Recent scientific highlights illustrate the imaging, time-resolved spectroscopy and high-power density capabilities of the AMO instrument.
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Affiliation(s)
- Ken R. Ferguson
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Department of Applied Physics, Stanford University, 348 Via Pueblo, Stanford, CA 94305, USA
| | - Maximilian Bucher
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - John D. Bozek
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Sebastian Carron
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Jean-Charles Castagna
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Ryan Coffee
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Pulse Institute, Stanford University and SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - G. Ivan Curiel
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Michael Holmes
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Jacek Krzywinski
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Marc Messerschmidt
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Michael Minitti
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Ankush Mitra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Stefan Moeller
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Peter Noonan
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Timur Osipov
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Sebastian Schorb
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Michele Swiggers
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Alexander Wallace
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Jing Yin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Christoph Bostedt
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Pulse Institute, Stanford University and SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
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41
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Liang M, Williams GJ, Messerschmidt M, Seibert MM, Montanez PA, Hayes M, Milathianaki D, Aquila A, Hunter MS, Koglin JE, Schafer DW, Guillet S, Busse A, Bergan R, Olson W, Fox K, Stewart N, Curtis R, Miahnahri AA, Boutet S. The Coherent X-ray Imaging instrument at the Linac Coherent Light Source. J Synchrotron Radiat 2015; 22:514-9. [PMID: 25931062 PMCID: PMC4416669 DOI: 10.1107/s160057751500449x] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 03/04/2015] [Indexed: 05/19/2023]
Abstract
The Coherent X-ray Imaging (CXI) instrument specializes in hard X-ray, in-vacuum, high power density experiments in all areas of science. Two main sample chambers, one containing a 100 nm focus and one a 1 µm focus, are available, each with multiple diagnostics, sample injection, pump-probe and detector capabilities. The flexibility of CXI has enabled it to host a diverse range of experiments, from biological to extreme matter.
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Affiliation(s)
- Mengning Liang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Garth J. Williams
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Marc Messerschmidt
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - M. Marvin Seibert
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Paul A. Montanez
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Matt Hayes
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Despina Milathianaki
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Andrew Aquila
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Mark S. Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Jason E. Koglin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Donald W. Schafer
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Serge Guillet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Armin Busse
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Robert Bergan
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - William Olson
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Kay Fox
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Nathaniel Stewart
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Robin Curtis
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Alireza Alan Miahnahri
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
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42
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Feng Y, Alonso-Mori R, Barends TRM, Blank VD, Botha S, Chollet M, Damiani DS, Doak RB, Glownia JM, Koglin JM, Lemke HT, Messerschmidt M, Nass K, Nelson S, Schlichting I, Shoeman RL, Shvyd’ko YV, Sikorski M, Song S, Stoupin S, Terentyev S, Williams GJ, Zhu D, Robert A, Boutet S. Demonstration of simultaneous experiments using thin crystal multiplexing at the Linac Coherent Light Source. J Synchrotron Radiat 2015; 22:626-33. [PMID: 25931078 PMCID: PMC4416679 DOI: 10.1107/s1600577515003999] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 02/26/2015] [Indexed: 05/06/2023]
Abstract
Multiplexing of the Linac Coherent Light Source beam was demonstrated for hard X-rays by spectral division using a near-perfect diamond thin-crystal monochromator operating in the Bragg geometry. The wavefront and coherence properties of both the reflected and transmitted beams were well preserved, thus allowing simultaneous measurements at two separate instruments. In this report, the structure determination of a prototypical protein was performed using serial femtosecond crystallography simultaneously with a femtosecond time-resolved XANES studies of photoexcited spin transition dynamics in an iron spin-crossover system. The results of both experiments using the multiplexed beams are similar to those obtained separately, using a dedicated beam, with no significant differences in quality.
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Affiliation(s)
- Y. Feng
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - R. Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | | | - V. D. Blank
- Technological Institute for Superhard and Novel Carbon Materials, Troitsk, Russia
| | - S. Botha
- Max-Planck Institute for Medical Research, Heidelberg, Germany
| | - M. Chollet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - D. S. Damiani
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - R. B. Doak
- Max-Planck Institute for Medical Research, Heidelberg, Germany
| | - J. M. Glownia
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - J. M. Koglin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - H. T. Lemke
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - M. Messerschmidt
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - K. Nass
- Max-Planck Institute for Medical Research, Heidelberg, Germany
| | - S. Nelson
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - I. Schlichting
- Max-Planck Institute for Medical Research, Heidelberg, Germany
| | - R. L. Shoeman
- Max-Planck Institute for Medical Research, Heidelberg, Germany
| | - Yu. V. Shvyd’ko
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - M. Sikorski
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - S. Song
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - S. Stoupin
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - S. Terentyev
- Technological Institute for Superhard and Novel Carbon Materials, Troitsk, Russia
| | - G. J. Williams
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - D. Zhu
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - A. Robert
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - S. Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
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43
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Boutet S, Foucar L, Barends TRM, Botha S, Doak RB, Koglin JE, Messerschmidt M, Nass K, Schlichting I, Seibert MM, Shoeman RL, Williams GJ. Characterization and use of the spent beam for serial operation of LCLS. J Synchrotron Radiat 2015; 22:634-43. [PMID: 25931079 PMCID: PMC4416680 DOI: 10.1107/s1600577515004002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 02/26/2015] [Indexed: 05/30/2023]
Abstract
X-ray free-electron laser sources such as the Linac Coherent Light Source offer very exciting possibilities for unique research. However, beam time at such facilities is very limited and in high demand. This has led to significant efforts towards beam multiplexing of various forms. One such effort involves re-using the so-called spent beam that passes through the hole in an area detector after a weak interaction with a primary sample. This beam can be refocused into a secondary interaction region and used for a second, independent experiment operating in series. The beam profile of this refocused beam was characterized for a particular experimental geometry at the Coherent X-ray Imaging instrument at LCLS. A demonstration of this multiplexing capability was performed with two simultaneous serial femtosecond crystallography experiments, both yielding interpretable data of sufficient quality to produce electron density maps.
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Affiliation(s)
- Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Lutz Foucar
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Thomas R. M. Barends
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Sabine Botha
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - R. Bruce Doak
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Jason E. Koglin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Marc Messerschmidt
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Karol Nass
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Ilme Schlichting
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - M. Marvin Seibert
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Robert L. Shoeman
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Garth J. Williams
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
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44
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Ginn HM, Messerschmidt M, Ji X, Zhang H, Axford D, Gildea RJ, Winter G, Brewster AS, Hattne J, Wagner A, Grimes JM, Evans G, Sauter NK, Sutton G, Stuart DI. Structure of CPV17 polyhedrin determined by the improved analysis of serial femtosecond crystallographic data. Nat Commun 2015; 6:6435. [PMID: 25751308 PMCID: PMC4403592 DOI: 10.1038/ncomms7435] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [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: 11/05/2014] [Accepted: 01/28/2015] [Indexed: 11/09/2022] Open
Abstract
The X-ray free-electron laser (XFEL) allows the analysis of small weakly diffracting protein crystals, but has required very many crystals to obtain good data. Here we use an XFEL to determine the room temperature atomic structure for the smallest cytoplasmic polyhedrosis virus polyhedra yet characterized, which we failed to solve at a synchrotron. These protein microcrystals, roughly a micron across, accrue within infected cells. We use a new physical model for XFEL diffraction, which better estimates the experimental signal, delivering a high-resolution XFEL structure (1.75 Å), using fewer crystals than previously required for this resolution. The crystal lattice and protein core are conserved compared with a polyhedrin with less than 10% sequence identity. We explain how the conserved biological phenotype, the crystal lattice, is maintained in the face of extreme environmental challenge and massive evolutionary divergence. Our improved methods should open up more challenging biological samples to XFEL analysis. Serial femtosecond crystallography and the use of X-ray free-electron lasers (XFEL) promise to revolutionize structural biology. Here, the authors describe refinements that reduce the redundancy required to obtain quality XFEL data and report a 1.75-Å structure—not obtainable by synchrotron radiation—using less than 6,000 crystals.
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Affiliation(s)
- Helen M Ginn
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, UK
| | - Marc Messerschmidt
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Xiaoyun Ji
- 1] Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, UK [2] Molecular Biophysics and Biochemistry, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
| | - Hanwen Zhang
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, UK
| | - Danny Axford
- Diamond House, Diamond Light Source, Harwell Science &Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Richard J Gildea
- Diamond House, Diamond Light Source, Harwell Science &Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Graeme Winter
- Diamond House, Diamond Light Source, Harwell Science &Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Aaron S Brewster
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Johan Hattne
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Armin Wagner
- Diamond House, Diamond Light Source, Harwell Science &Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Jonathan M Grimes
- 1] Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, UK [2] Diamond House, Diamond Light Source, Harwell Science &Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Gwyndaf Evans
- Diamond House, Diamond Light Source, Harwell Science &Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Nicholas K Sauter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Geoff Sutton
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, UK
| | - David I Stuart
- 1] Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, UK [2] Diamond House, Diamond Light Source, Harwell Science &Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
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45
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Vinko SM, Ciricosta O, Preston TR, Rackstraw DS, Brown CRD, Burian T, Chalupský J, Cho BI, Chung HK, Engelhorn K, Falcone RW, Fiokovinini R, Hájková V, Heimann PA, Juha L, Lee HJ, Lee RW, Messerschmidt M, Nagler B, Schlotter W, Turner JJ, Vysin L, Zastrau U, Wark JS. Investigation of femtosecond collisional ionization rates in a solid-density aluminium plasma. Nat Commun 2015; 6:6397. [PMID: 25731816 DOI: 10.1038/ncomms7397] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 01/26/2015] [Indexed: 11/09/2022] Open
Abstract
The rate at which atoms and ions within a plasma are further ionized by collisions with the free electrons is a fundamental parameter that dictates the dynamics of plasma systems at intermediate and high densities. While collision rates are well known experimentally in a few dilute systems, similar measurements for nonideal plasmas at densities approaching or exceeding those of solids remain elusive. Here we describe a spectroscopic method to study collision rates in solid-density aluminium plasmas created and diagnosed using the Linac Coherent light Source free-electron X-ray laser, tuned to specific interaction pathways around the absorption edges of ionic charge states. We estimate the rate of collisional ionization in solid-density aluminium plasmas at temperatures ~30 eV to be several times higher than that predicted by standard semiempirical models.
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Affiliation(s)
- S M Vinko
- Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, UK
| | - O Ciricosta
- Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, UK
| | - T R Preston
- Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, UK
| | - D S Rackstraw
- Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, UK
| | - C R D Brown
- Department of Plasma Physics, AWE Aldermaston, Reading RG7 4PR, UK
| | - T Burian
- Institute of Physics ASCR, Na Slovance 2, Prague 8 18221, Czech Republic
| | - J Chalupský
- Institute of Physics ASCR, Na Slovance 2, Prague 8 18221, Czech Republic
| | - B I Cho
- 1] Center for Relativistic Laser Science, Institute for Basic Science (IBS), Gwangju 500-712, Korea [2] Department of Physics and Photon Science, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea
| | - H-K Chung
- Atomic and Molecular Data Unit, Nuclear Data Section, IAEA, PO Box 100, Vienna A-1400, Austria
| | - K Engelhorn
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, California 94720, USA
| | - R W Falcone
- 1] Lawrence Berkeley National Laboratory, 1 Cyclotron Road, California 94720, USA [2] Department of Physics, University of California, Berkeley, California 94720, USA
| | - R Fiokovinini
- Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, UK
| | - V Hájková
- Institute of Physics ASCR, Na Slovance 2, Prague 8 18221, Czech Republic
| | - P A Heimann
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - L Juha
- Institute of Physics ASCR, Na Slovance 2, Prague 8 18221, Czech Republic
| | - H J Lee
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - R W Lee
- Department of Physics, University of California, Berkeley, California 94720, USA
| | - M Messerschmidt
- National Science Foundation BioXFEL Science and Technology Center, 700 Ellicott Street, Buffalo, New York 14203, USA
| | - B Nagler
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - W Schlotter
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - J J Turner
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - L Vysin
- Institute of Physics ASCR, Na Slovance 2, Prague 8 18221, Czech Republic
| | - U Zastrau
- IOQ, Friedrich-Schiller-Universität Jena, Max-Wien-Platz 1, Jena 07743, Germany
| | - J S Wark
- Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, UK
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46
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Nass K, Foucar L, Barends TRM, Hartmann E, Botha S, Shoeman RL, Doak RB, Alonso-Mori R, Aquila A, Bajt S, Barty A, Bean R, Beyerlein KR, Bublitz M, Drachmann N, Gregersen J, Jönsson HO, Kabsch W, Kassemeyer S, Koglin JE, Krumrey M, Mattle D, Messerschmidt M, Nissen P, Reinhard L, Sitsel O, Sokaras D, Williams GJ, Hau-Riege S, Timneanu N, Caleman C, Chapman HN, Boutet S, Schlichting I. Indications of radiation damage in ferredoxin microcrystals using high-intensity X-FEL beams. J Synchrotron Radiat 2015; 22:225-38. [PMID: 25723924 DOI: 10.1107/s1600577515002349] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 02/03/2015] [Indexed: 05/23/2023]
Abstract
Proteins that contain metal cofactors are expected to be highly radiation sensitive since the degree of X-ray absorption correlates with the presence of high-atomic-number elements and X-ray energy. To explore the effects of local damage in serial femtosecond crystallography (SFX), Clostridium ferredoxin was used as a model system. The protein contains two [4Fe-4S] clusters that serve as sensitive probes for radiation-induced electronic and structural changes. High-dose room-temperature SFX datasets were collected at the Linac Coherent Light Source of ferredoxin microcrystals. Difference electron density maps calculated from high-dose SFX and synchrotron data show peaks at the iron positions of the clusters, indicative of decrease of atomic scattering factors due to ionization. The electron density of the two [4Fe-4S] clusters differs in the FEL data, but not in the synchrotron data. Since the clusters differ in their detailed architecture, this observation is suggestive of an influence of the molecular bonding and geometry on the atomic displacement dynamics following initial photoionization. The experiments are complemented by plasma code calculations.
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Affiliation(s)
- Karol Nass
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
| | - Lutz Foucar
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
| | - Thomas R M Barends
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
| | - Elisabeth Hartmann
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
| | - Sabine Botha
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
| | - Robert L Shoeman
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
| | - R Bruce Doak
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
| | - Roberto Alonso-Mori
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Andrew Aquila
- European XFEL GmbH, Albert-Einstein-Ring 19, 22761 Hamburg, Germany
| | - Saša Bajt
- Photon Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Anton Barty
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Richard Bean
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Kenneth R Beyerlein
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Maike Bublitz
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, Aarhus 8000, Denmark
| | - Nikolaj Drachmann
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, Aarhus 8000, Denmark
| | - Jonas Gregersen
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, Aarhus 8000, Denmark
| | - H Olof Jönsson
- Department of Physics and Astronomy, Uppsala University, Box 516, Uppsala 75120, Sweden
| | - Wolfgang Kabsch
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
| | - Stephan Kassemeyer
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
| | - Jason E Koglin
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Michael Krumrey
- Physikalisch-Technische Bundesanstalt (PTB), Abbestrasse 2-12, 10587 Berlin, Germany
| | - Daniel Mattle
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, Aarhus 8000, Denmark
| | - Marc Messerschmidt
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Poul Nissen
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, Aarhus 8000, Denmark
| | - Linda Reinhard
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, Aarhus 8000, Denmark
| | - Oleg Sitsel
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, Aarhus 8000, Denmark
| | - Dimosthenis Sokaras
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Garth J Williams
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Stefan Hau-Riege
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Nicusor Timneanu
- Department of Physics and Astronomy, Uppsala University, Box 516, Uppsala 75120, Sweden
| | - Carl Caleman
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Henry N Chapman
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Sébastien Boutet
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Ilme Schlichting
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
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47
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Fenalti G, Zatsepin NA, Betti C, Giguere P, Han GW, Ishchenko A, Liu W, Guillemyn K, Zhang H, James D, Wang D, Weierstall U, Spence JCH, Boutet S, Messerschmidt M, Williams GJ, Gati C, Yefanov OM, White TA, Oberthuer D, Metz M, Yoon CH, Barty A, Chapman HN, Basu S, Coe J, Conrad CE, Fromme R, Fromme P, Tourwé D, Schiller PW, Roth BL, Ballet S, Katritch V, Stevens RC, Cherezov V. Structural basis for bifunctional peptide recognition at human δ-opioid receptor. Nat Struct Mol Biol 2015; 22:265-8. [PMID: 25686086 PMCID: PMC4351130 DOI: 10.1038/nsmb.2965] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 01/05/2015] [Indexed: 02/07/2023]
Abstract
Bi-functional μ- and δ- opioid receptor (OR) ligands are potential therapeutic alternatives to alkaloid opiate analgesics with diminished side effects. We solved the structure of human δ-OR bound to the bi-functional δ-OR antagonist and μ-OR agonist tetrapeptide H-Dmt(1)-Tic(2)-Phe(3)-Phe(4)-NH2 (DIPP-NH2) by serial femtosecond crystallography, revealing a cis-peptide bond between H-Dmt(1) and Tic(2). The observed receptor-peptide interactions are critical to understand the pharmacological profiles of opioid peptides, and to develop improved analgesics.
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Affiliation(s)
- Gustavo Fenalti
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Nadia A Zatsepin
- Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Cecilia Betti
- 1] Department of Chemistry, Vrije Universiteit Brussel, Brussels, Belgium. [2] Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Patrick Giguere
- 1] National Institute of Mental Health Psychoactive Drug Screening Program, University of North Carolina Chapel Hill Medical School, Chapel Hill, North Carolina, USA. [2] Department of Pharmacology, University of North Carolina Chapel Hill Medical School, Chapel Hill, North Carolina, USA. [3] Division of Chemical Biology and Medicinal Chemistry, University of North Carolina Chapel Hill Medical School, Chapel Hill, North Carolina, USA
| | - Gye Won Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Andrii Ishchenko
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Wei Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Karel Guillemyn
- 1] Department of Chemistry, Vrije Universiteit Brussel, Brussels, Belgium. [2] Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Haitao Zhang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Daniel James
- Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Dingjie Wang
- Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Uwe Weierstall
- Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - John C H Spence
- Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Marc Messerschmidt
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Garth J Williams
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Cornelius Gati
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Oleksandr M Yefanov
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Thomas A White
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Dominik Oberthuer
- 1] Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany. [2] Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Markus Metz
- 1] Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany. [2] Department of Physics, University of Hamburg, Hamburg, Germany
| | - Chun Hong Yoon
- 1] Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany. [2] European X-ray Free-Electron Laser Facility (XFEL GmbH), Hamburg, Germany
| | - Anton Barty
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Henry N Chapman
- 1] Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany. [2] Department of Physics, University of Hamburg, Hamburg, Germany
| | - Shibom Basu
- 1] Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona, USA. [2] Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Jesse Coe
- 1] Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona, USA. [2] Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Chelsie E Conrad
- 1] Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona, USA. [2] Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Raimund Fromme
- 1] Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona, USA. [2] Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Petra Fromme
- 1] Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona, USA. [2] Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Dirk Tourwé
- 1] Department of Chemistry, Vrije Universiteit Brussel, Brussels, Belgium. [2] Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Peter W Schiller
- Laboratory of Chemical Biology and Peptide Research, Clinical Research Institute of Montreal, Montreal, Quebec, Canada
| | - Bryan L Roth
- 1] National Institute of Mental Health Psychoactive Drug Screening Program, University of North Carolina Chapel Hill Medical School, Chapel Hill, North Carolina, USA. [2] Department of Pharmacology, University of North Carolina Chapel Hill Medical School, Chapel Hill, North Carolina, USA. [3] Division of Chemical Biology and Medicinal Chemistry, University of North Carolina Chapel Hill Medical School, Chapel Hill, North Carolina, USA
| | - Steven Ballet
- 1] Department of Chemistry, Vrije Universiteit Brussel, Brussels, Belgium. [2] Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Vsevolod Katritch
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Raymond C Stevens
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Vadim Cherezov
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
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48
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Tiedtke K, Sorokin AA, Jastrow U, Juranić P, Kreis S, Gerken N, Richter M, Arp U, Feng Y, Nordlund D, Soufli R, Fernández-Perea M, Juha L, Heimann P, Nagler B, Lee HJ, Mack S, Cammarata M, Krupin O, Messerschmidt M, Holmes M, Rowen M, Schlotter W, Moeller S, Turner JJ. Absolute pulse energy measurements of soft x-rays at the Linac Coherent Light Source. Opt Express 2014; 22:21214-26. [PMID: 25321502 DOI: 10.1364/oe.22.021214] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
This paper reports novel measurements of x-ray optical radiation on an absolute scale from the intense and ultra-short radiation generated in the soft x-ray regime of a free electron laser. We give a brief description of the detection principle for radiation measurements which was specifically adapted for this photon energy range. We present data characterizing the soft x-ray instrument at the Linac Coherent Light Source (LCLS) with respect to the radiant power output and transmission by using an absolute detector temporarily placed at the downstream end of the instrument. This provides an estimation of the reflectivity of all x-ray optical elements in the beamline and provides the absolute photon number per bandwidth per pulse. This parameter is important for many experiments that need to understand the trade-offs between high energy resolution and high flux, such as experiments focused on studying materials via resonant processes. Furthermore, the results are compared with the LCLS diagnostic gas detectors to test the limits of linearity, and observations are reported on radiation contamination from spontaneous undulator radiation and higher harmonic content.
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49
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Boll R, Rouzée A, Adolph M, Anielski D, Aquila A, Bari S, Bomme C, Bostedt C, Bozek JD, Chapman HN, Christensen L, Coffee R, Coppola N, De S, Decleva P, Epp SW, Erk B, Filsinger F, Foucar L, Gorkhover T, Gumprecht L, Hömke A, Holmegaard L, Johnsson P, Kienitz JS, Kierspel T, Krasniqi F, Kühnel KU, Maurer J, Messerschmidt M, Moshammer R, Müller NLM, Rudek B, Savelyev E, Schlichting I, Schmidt C, Scholz F, Schorb S, Schulz J, Seltmann J, Stener M, Stern S, Techert S, Thøgersen J, Trippel S, Viefhaus J, Vrakking M, Stapelfeldt H, Küpper J, Ullrich J, Rudenko A, Rolles D. Imaging molecular structure through femtosecond photoelectron diffraction on aligned and oriented gas-phase molecules. Faraday Discuss 2014; 171:57-80. [PMID: 25290160 DOI: 10.1039/c4fd00037d] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This paper gives an account of our progress towards performing femtosecond time-resolved photoelectron diffraction on gas-phase molecules in a pump-probe setup combining optical lasers and an X-ray free-electron laser. We present results of two experiments aimed at measuring photoelectron angular distributions of laser-aligned 1-ethynyl-4-fluorobenzene (C(8)H(5)F) and dissociating, laser-aligned 1,4-dibromobenzene (C(6)H(4)Br(2)) molecules and discuss them in the larger context of photoelectron diffraction on gas-phase molecules. We also show how the strong nanosecond laser pulse used for adiabatically laser-aligning the molecules influences the measured electron and ion spectra and angular distributions, and discuss how this may affect the outcome of future time-resolved photoelectron diffraction experiments.
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Affiliation(s)
- Rebecca Boll
- Deutsches Elektronen-Synchrotron (DESY), 22607 Hamburg, Germany.
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50
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Hunter MS, Segelke B, Messerschmidt M, Williams GJ, Zatsepin NA, Barty A, Benner WH, Carlson DB, Coleman M, Graf A, Hau-Riege SP, Pardini T, Seibert MM, Evans J, Boutet S, Frank M. Fixed-target protein serial microcrystallography with an x-ray free electron laser. Sci Rep 2014; 4:6026. [PMID: 25113598 PMCID: PMC4129423 DOI: 10.1038/srep06026] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 07/04/2014] [Indexed: 01/25/2023] Open
Abstract
We present results from experiments at the Linac Coherent Light Source (LCLS) demonstrating that serial femtosecond crystallography (SFX) can be performed to high resolution (~2.5 Å) using protein microcrystals deposited on an ultra-thin silicon nitride membrane and embedded in a preservation medium at room temperature. Data can be acquired at a high acquisition rate using x-ray free electron laser sources to overcome radiation damage, while sample consumption is dramatically reduced compared to flowing jet methods. We achieved a peak data acquisition rate of 10 Hz with a hit rate of ~38%, indicating that a complete data set could be acquired in about one 12-hour LCLS shift using the setup described here, or in even less time using hardware optimized for fixed target SFX. This demonstration opens the door to ultra low sample consumption SFX using the technique of diffraction-before-destruction on proteins that exist in only small quantities and/or do not produce the copious quantities of microcrystals required for flowing jet methods.
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Affiliation(s)
- Mark S. Hunter
- Physics Division, Lawrence Livermore National Laboratory, 7000 East Avenue, Mail Stop L-211, Livermore, CA 94550, USA
| | - Brent Segelke
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, 7000 East Avenue, Mail Stop L-452, Livermore, CA 94550, USA
| | - Marc Messerschmidt
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Garth J. Williams
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Nadia A. Zatsepin
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Anton Barty
- Centre for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - W. Henry Benner
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, 7000 East Avenue, Mail Stop L-452, Livermore, CA 94550, USA
| | - David B. Carlson
- Dept. of Molecular and Cellular Biology, University of California, Davis, 1 Shields Ave, Davis, CA, 95616, USA
| | - Matthew Coleman
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, 7000 East Avenue, Mail Stop L-452, Livermore, CA 94550, USA
- Department of Radiation Oncology, University of California at Davis Medical Center, Sacramento, CA 95817
| | - Alexander Graf
- Physics Division, Lawrence Livermore National Laboratory, 7000 East Avenue, Mail Stop L-211, Livermore, CA 94550, USA
| | - Stefan P. Hau-Riege
- Physics Division, Lawrence Livermore National Laboratory, 7000 East Avenue, Mail Stop L-211, Livermore, CA 94550, USA
| | - Tommaso Pardini
- Physics Division, Lawrence Livermore National Laboratory, 7000 East Avenue, Mail Stop L-211, Livermore, CA 94550, USA
| | - M. Marvin Seibert
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - James Evans
- Dept. of Molecular and Cellular Biology, University of California, Davis, 1 Shields Ave, Davis, CA, 95616, USA
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Blvd., Richland, WA, 99354, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Matthias Frank
- Physics Division, Lawrence Livermore National Laboratory, 7000 East Avenue, Mail Stop L-211, Livermore, CA 94550, USA
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