1
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Patra KK, Eliah Dawod I, Martin AV, Greaves TL, Persson D, Caleman C, Timneanu N. Ultrafast dynamics and scattering of protic ionic liquids induced by XFEL pulses. JOURNAL OF SYNCHROTRON RADIATION 2021; 28:1296-1308. [PMID: 34475279 PMCID: PMC8415341 DOI: 10.1107/s1600577521007657] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 07/26/2021] [Indexed: 05/30/2023]
Abstract
X-rays are routinely used for structural studies through scattering, and femtosecond X-ray lasers can probe ultrafast dynamics. We aim to capture the femtosecond dynamics of liquid samples using simulations and deconstruct the interplay of ionization and atomic motion within the X-ray laser pulse. This deconstruction is resolution dependent, as ionization influences the low momentum transfers through changes in scattering form factors, while atomic motion has a greater effect at high momentum transfers through loss of coherence. Our methodology uses a combination of classical molecular dynamics and plasma simulation on a protic ionic liquid to quantify the contributions to the scattering signal and how these evolve with time during the X-ray laser pulse. Our method is relevant for studies of organic liquids, biomolecules in solution or any low-Z materials at liquid densities that quickly turn into a plasma while probed with X-rays.
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Affiliation(s)
- Kajwal Kumar Patra
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Ibrahim Eliah Dawod
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
- European XFEL, Holzkoppel 4, DE-22869 Schenefeld, Germany
| | - Andrew V. Martin
- School of Science, RMIT University, 124 La Trobe Street, Melbourne, VIC 3000, Australia
| | - Tamar L. Greaves
- School of Science, RMIT University, 124 La Trobe Street, Melbourne, VIC 3000, Australia
| | - Daniel Persson
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Carl Caleman
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, DE-22607 Hamburg, Germany
| | - Nicusor Timneanu
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
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2
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Czyzewski A, Krawiec F, Brzezinski D, Porebski PJ, Minor W. Detecting anomalies in X-ray diffraction images using convolutional neural networks. EXPERT SYSTEMS WITH APPLICATIONS 2021; 174:114740. [PMID: 34366575 PMCID: PMC8341115 DOI: 10.1016/j.eswa.2021.114740] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Our understanding of life is based upon the interpretation of macromolecular structures and their dynamics. Almost 90% of currently known macromolecular models originated from electron density maps constructed using X-ray diffraction images. Even though diffraction images are critical for structure determination, due to their vast amounts and noisy, non-intuitive nature, their quality is rarely inspected. In this paper, we use recent advances in machine learning to automatically detect seven types of anomalies in X-ray diffraction images. For this purpose, we utilize a novel X-ray beam center detection algorithm, propose three different image representations, and compare the predictive performance of general-purpose classifiers and deep convolutional neural networks (CNNs). In benchmark tests on a set of 6,311 X-ray diffraction images, the proposed CNN achieved between 87% and 99% accuracy depending on the type of anomaly. Experimental results show that the proposed anomaly detection system can be considered suitable for early detection of sub-optimal data collection conditions and malfunctions at X-ray experimental stations.
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Affiliation(s)
- Adam Czyzewski
- Institute of Computing Science, Poznan University of
Technology, ul. Piotrowo 2, 60-965 Poznan, Poland
| | - Faustyna Krawiec
- Institute of Computing Science, Poznan University of
Technology, ul. Piotrowo 2, 60-965 Poznan, Poland
| | - Dariusz Brzezinski
- Institute of Computing Science, Poznan University of
Technology, ul. Piotrowo 2, 60-965 Poznan, Poland
- Center for Biocrystallographic Research, Institute of
Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61-714, Poland
- Center for Artificial Intelligence and Machine Learning,
Poznan University of Technology, ul. Piotrowo 2, 60-965 Poznan, Poland
- Department of Molecular Physiology and Biological Physics,
University of Virginia, Charlottesville, VA 22901, USA
| | - Przemyslaw Jerzy Porebski
- Department of Molecular Physiology and Biological Physics,
University of Virginia, Charlottesville, VA 22901, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics,
University of Virginia, Charlottesville, VA 22901, USA
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3
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Kozlov A, Gureyev TE, Paganin DM, Martin AV, Caleman C, Quiney HM. Recovery of undamaged electron-density maps in the presence of damage-induced partial coherence in single-particle imaging. IUCRJ 2020; 7:1114-1123. [PMID: 33209322 PMCID: PMC7642773 DOI: 10.1107/s2052252520013019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 09/25/2020] [Indexed: 06/11/2023]
Abstract
Resolving the electronic structure of single biological molecules in their native state was among the primary motivations behind X-ray free-electron lasers. The ultra-short pulses they produce can outrun the atomic motion induced by radiation damage, but the electronic structure of the sample is still significantly modified from its original state. This paper explores the decoherence of the scattered signal induced by temporal evolution of the electronic structure in the sample molecule. It is shown that the undamaged electron density of a single-molecule sample can often be retrieved using only the two most occupied modes from the coherent mode decomposition of the partially coherent diffraction fluence.
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Affiliation(s)
- Alexander Kozlov
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Timur E. Gureyev
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne, Parkville, Victoria 3010, Australia
- Faculty of Health Sciences, University of Sydney, Sydney, NSW 2006, Australia
- School of Science and Technology, University of New England, Armidale, NSW 2351, Australia
- School of Physics and Astronomy, Monash University, Clayton, Victoria 3800, Australia
| | - David M. Paganin
- School of Physics and Astronomy, Monash University, Clayton, Victoria 3800, Australia
| | - Andrew V. Martin
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne, Parkville, Victoria 3010, Australia
- School of Physics, RMIT University, Melbourne, Victoria 3000, Australia
| | - Carl Caleman
- Department of Physics and Astronomy, Uppsala University, PO Box 516, SE-751 20 Uppsala, Sweden
- Center for Free-Electron Laser Science, DESY, Notkestraße 85, DE-22607 Hamburg, Germany
| | - 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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4
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A Perspective on Molecular Structure and Bond-Breaking in Radiation Damage in Serial Femtosecond Crystallography. CRYSTALS 2020. [DOI: 10.3390/cryst10070585] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
X-ray free-electron lasers (XFELs) have a unique capability for time-resolved studies of protein dynamics and conformational changes on femto- and pico-second time scales. The extreme intensity of X-ray pulses can potentially cause significant modifications to the sample structure during exposure. Successful time-resolved XFEL crystallography depends on the unambiguous interpretation of the protein dynamics of interest from the effects of radiation damage. Proteins containing relatively heavy elements, such as sulfur or metals, have a higher risk for radiation damage. In metaloenzymes, for example, the dynamics of interest usually occur at the metal centers, which are also hotspots for damage due to the higher atomic number of the elements they contain. An ongoing challenge with such local damage is to understand the residual bonding in these locally ionized systems and bond-breaking dynamics. Here, we present a perspective on radiation damage in XFEL experiments with a particular focus on the impacts for time-resolved protein crystallography. We discuss recent experimental and modelling results of bond-breaking and ion motion at disulfide bonding sites in protein crystals.
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5
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Hybrid Plasma/Molecular-Dynamics Approach for Efficient XFEL Radiation Damage Simulations. CRYSTALS 2020. [DOI: 10.3390/cryst10060478] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
X-ray free-electron laser pulses initiate a complex series of changes to the electronic and nuclear structure of matter on femtosecond timescales. These damage processes include widespread ionization, the formation of a quasi-plasma state and the ultimate explosion of the sample due to Coulomb forces. The accurate simulation of these dynamical effects is critical in designing feasible XFEL experiments and interpreting the results. Current molecular dynamics simulations are, however, computationally intensive, particularly when they treat unbound electrons as classical point particles. On the other hand, plasma simulations are computationally efficient but do not model atomic motion. Here we present a hybrid approach to XFEL damage simulation that combines molecular dynamics for the nuclear motion and plasma models to describe the evolution of the low-energy electron continuum. The plasma properties of the unbound electron gas are used to define modified inter-ionic potentials for the molecular dynamics, including Debye screening and drag forces. The hybrid approach is significantly faster than damage simulations that treat unbound electrons as classical particles, enabling simulations to be performed on large sample volumes.
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6
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Östlin C, Timneanu N, Caleman C, Martin AV. Is radiation damage the limiting factor in high-resolution single particle imaging with X-ray free-electron lasers? STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2019; 6:044103. [PMID: 31463335 PMCID: PMC6701976 DOI: 10.1063/1.5098309] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 07/31/2019] [Indexed: 05/24/2023]
Abstract
The prospect of single particle imaging with atomic resolution is one of the scientific drivers for the development of X-ray free-electron lasers. The assumption since the beginning has been that damage to the sample caused by intense X-ray pulses is one of the limiting factors for achieving subnanometer X-ray imaging of single particles and that X-ray pulses need to be as short as possible. Based on the molecular dynamics simulations of proteins in X-ray fields of various durations (5 fs, 25 fs, and 50 fs), we show that the noise in the diffracted signal caused by radiation damage is less than what can be expected from other sources, such as sample inhomogeneity and X-ray shot-to-shot variations. These findings show a different aspect of the feasibility of high-resolution single particle imaging using free-electron lasers, where employing X-ray pulses of longer durations could still provide a useful diffraction signal above the noise due to the Coulomb explosion.
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Affiliation(s)
- C Östlin
- Molecular and Condensed Matter Physics, Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - N Timneanu
- Molecular and Condensed Matter Physics, Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - C Caleman
- Molecular and Condensed Matter Physics, Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - A V Martin
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia
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7
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Nass K. Radiation damage in protein crystallography at X-ray free-electron lasers. Acta Crystallogr D Struct Biol 2019; 75:211-218. [PMID: 30821709 PMCID: PMC6400258 DOI: 10.1107/s2059798319000317] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 01/07/2019] [Indexed: 01/17/2023] Open
Abstract
Radiation damage is still the most limiting factor in obtaining high-resolution structures of macromolecules in crystallographic experiments at synchrotrons. With the advent of X-ray free-electron lasers (XFELs) that produce ultrashort and highly intense X-ray pulses, it became possible to outrun most of the radiation-damage processes occurring in the sample during exposure to XFEL radiation. Although this is generally the case, several experimental and theoretical studies have indicated that structures from XFELs may not always be radiation-damage free. This is especially true when higher intensity pulses are used and protein molecules that contain heavy elements in their structures are studied. Here, the radiation-damage mechanisms that occur in samples exposed to XFEL pulses are summarized, results that show indications of radiation damage are reviewed and methods that can partially overcome it are discussed.
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Affiliation(s)
- Karol Nass
- Swiss Light Source, Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen, Switzerland
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8
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Opara NL, Mohacsi I, Makita M, Castano-Diez D, Diaz A, Juranić P, Marsh M, Meents A, Milne CJ, Mozzanica A, Padeste C, Panneels V, Sikorski M, Song S, Stahlberg H, Vartiainen I, Vera L, Wang M, Willmott PR, David C. Demonstration of femtosecond X-ray pump X-ray probe diffraction on protein crystals. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2018; 5:054303. [PMID: 30364211 PMCID: PMC6192410 DOI: 10.1063/1.5050618] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 09/12/2018] [Indexed: 05/24/2023]
Abstract
The development of X-ray free-electron lasers (XFELs) has opened the possibility to investigate the ultrafast dynamics of biomacromolecules using X-ray diffraction. Whereas an increasing number of structures solved by means of serial femtosecond crystallography at XFELs is available, the effect of radiation damage on protein crystals during ultrafast exposures has remained an open question. We used a split-and-delay line based on diffractive X-ray optics at the Linac Coherent Light Source XFEL to investigate the time dependence of X-ray radiation damage to lysozyme crystals. For these tests, crystals were delivered to the X-ray beam using a fixed-target approach. The presented experiments provide probe signals at eight different delay times between 19 and 213 femtoseconds after a single pump event, thereby covering the time-scales relevant for femtosecond serial crystallography. Even though significant impact on the crystals was observed at long time scales after exposure with a single X-ray pulse, the collected diffraction data did not show significant signal reduction that could be assigned to beam damage on the crystals in the sampled time window and resolution range. This observation is in agreement with estimations of the applied radiation dose, which in our experiment was clearly below the values expected to cause damage on the femtosecond time scale. The experiments presented here demonstrate the feasibility of time-resolved pump-multiprobe X-ray diffraction experiments on protein crystals.
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Affiliation(s)
| | | | | | | | - Ana Diaz
- Paul Scherrer Institut, CH-5232 Villigen-PSI, Switzerland
| | - Pavle Juranić
- Paul Scherrer Institut, CH-5232 Villigen-PSI, Switzerland
| | - May Marsh
- Paul Scherrer Institut, CH-5232 Villigen-PSI, Switzerland
| | - Alke Meents
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, D-22607 Hamburg, Germany
| | | | - Aldo Mozzanica
- Paul Scherrer Institut, CH-5232 Villigen-PSI, Switzerland
| | | | | | - Marcin Sikorski
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Sanghoon Song
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | | | | | - Laura Vera
- Paul Scherrer Institut, CH-5232 Villigen-PSI, Switzerland
| | - Meitian Wang
- Paul Scherrer Institut, CH-5232 Villigen-PSI, Switzerland
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9
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Ultrafast nonthermal heating of water initiated by an X-ray Free-Electron Laser. Proc Natl Acad Sci U S A 2018; 115:5652-5657. [PMID: 29760050 DOI: 10.1073/pnas.1711220115] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The bright ultrafast pulses of X-ray Free-Electron Lasers allow investigation into the structure of matter under extreme conditions. We have used single pulses to ionize and probe water as it undergoes a phase transition from liquid to plasma. We report changes in the structure of liquid water on a femtosecond time scale when irradiated by single 6.86 keV X-ray pulses of more than 106 J/cm2 These observations are supported by simulations based on molecular dynamics and plasma dynamics of a water system that is rapidly ionized and driven out of equilibrium. This exotic ionic and disordered state with the density of a liquid is suggested to be structurally different from a neutral thermally disordered state.
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10
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Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser. Proc Natl Acad Sci U S A 2017; 114:2247-2252. [PMID: 28202732 DOI: 10.1073/pnas.1609243114] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To understand how molecules function in biological systems, new methods are required to obtain atomic resolution structures from biological material under physiological conditions. Intense femtosecond-duration pulses from X-ray free-electron lasers (XFELs) can outrun most damage processes, vastly increasing the tolerable dose before the specimen is destroyed. This in turn allows structure determination from crystals much smaller and more radiation sensitive than previously considered possible, allowing data collection from room temperature structures and avoiding structural changes due to cooling. Regardless, high-resolution structures obtained from XFEL data mostly use crystals far larger than 1 μm3 in volume, whereas the X-ray beam is often attenuated to protect the detector from damage caused by intense Bragg spots. Here, we describe the 2 Å resolution structure of native nanocrystalline granulovirus occlusion bodies (OBs) that are less than 0.016 μm3 in volume using the full power of the Linac Coherent Light Source (LCLS) and a dose up to 1.3 GGy per crystal. The crystalline shell of granulovirus OBs consists, on average, of about 9,000 unit cells, representing the smallest protein crystals to yield a high-resolution structure by X-ray crystallography to date. The XFEL structure shows little to no evidence of radiation damage and is more complete than a model determined using synchrotron data from recombinantly produced, much larger, cryocooled granulovirus granulin microcrystals. Our measurements suggest that it should be possible, under ideal experimental conditions, to obtain data from protein crystals with only 100 unit cells in volume using currently available XFELs and suggest that single-molecule imaging of individual biomolecules could almost be within reach.
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11
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Galli L, Son SK, Barends TRM, White TA, Barty A, Botha S, Boutet S, Caleman C, Doak RB, Nanao MH, Nass K, Shoeman RL, Timneanu N, Santra R, Schlichting I, Chapman HN. Towards phasing using high X-ray intensity. IUCRJ 2015; 2:627-34. [PMID: 26594370 PMCID: PMC4645107 DOI: 10.1107/s2052252515014049] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 07/24/2015] [Indexed: 05/11/2023]
Abstract
X-ray free-electron lasers (XFELs) show great promise for macromolecular structure determination from sub-micrometre-sized crystals, using the emerging method of serial femtosecond crystallography. The extreme brightness of the XFEL radiation can multiply ionize most, if not all, atoms in a protein, causing their scattering factors to change during the pulse, with a preferential 'bleaching' of heavy atoms. This paper investigates the effects of electronic damage on experimental data collected from a Gd derivative of lysozyme microcrystals at different X-ray intensities, and the degree of ionization of Gd atoms is quantified from phased difference Fourier maps. A pattern sorting scheme is proposed to maximize the ionization contrast and the way in which the local electronic damage can be used for a new experimental phasing method is discussed.
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Affiliation(s)
- Lorenzo Galli
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg, 22607, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, Hamburg, 22761, Germany
| | - Sang-Kil Son
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg, 22607, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, Hamburg, 22761, Germany
| | - Thomas R. M. Barends
- Biomolecular Mechanisms, MPI for Medical Research, Jahnstrasse 29, Heidelberg, 69120, Germany
| | - Thomas A. White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - Sabine Botha
- Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, 69120, Germany
| | - Sébastien Boutet
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, 94025, USA
| | - Carl Caleman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg, 22607, Germany
- Department of Physics and Astronomy, Uppsala University, Box 516, Uppsala, 75120, Sweden
| | - R. Bruce Doak
- Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, 69120, Germany
| | - Max H. Nanao
- EMBL, Grenoble Outstation, Rue Jules Horowitz 6, Grenoble, 38042, France
| | - Karol Nass
- Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, 69120, Germany
| | - Robert L. Shoeman
- Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, 69120, Germany
| | - Nicusor Timneanu
- Department of Physics and Astronomy, Uppsala University, Box 516, Uppsala, 75120, Sweden
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Box 596, Uppsala, 75124, Sweden
| | - Robin Santra
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg, 22607, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, Hamburg, 22761, Germany
- Department of Physics, University of Hamburg, Juniungstrasse 6, Hamburg, 20355, Germany
| | - Ilme Schlichting
- Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, 69120, Germany
| | - Henry N. Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg, 22607, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, Hamburg, 22761, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, Hamburg, 22761, Germany
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12
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Martin AV, Corso JK, Caleman C, Timneanu N, Quiney HM. Single-molecule imaging with longer X-ray laser pulses. IUCRJ 2015; 2:661-74. [PMID: 26594374 PMCID: PMC4645111 DOI: 10.1107/s2052252515016887] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 09/09/2015] [Indexed: 05/24/2023]
Abstract
During the last five years, serial femtosecond crystallography using X-ray laser pulses has been developed into a powerful technique for determining the atomic structures of protein molecules from micrometre- and sub-micrometre-sized crystals. One of the key reasons for this success is the 'self-gating' pulse effect, whereby the X-ray laser pulses do not need to outrun all radiation damage processes. Instead, X-ray-induced damage terminates the Bragg diffraction prior to the pulse completing its passage through the sample, as if the Bragg diffraction were generated by a shorter pulse of equal intensity. As a result, serial femtosecond crystallography does not need to be performed with pulses as short as 5-10 fs, but can succeed for pulses 50-100 fs in duration. It is shown here that a similar gating effect applies to single-molecule diffraction with respect to spatially uncorrelated damage processes like ionization and ion diffusion. The effect is clearly seen in calculations of the diffraction contrast, by calculating the diffraction of the average structure separately to the diffraction from statistical fluctuations of the structure due to damage ('damage noise'). The results suggest that sub-nanometre single-molecule imaging with 30-50 fs pulses, like those produced at currently operating facilities, should not yet be ruled out. The theory presented opens up new experimental avenues to measure the impact of damage on single-particle diffraction, which is needed to test damage models and to identify optimal imaging conditions.
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Affiliation(s)
- Andrew V. Martin
- ARC Centre of Excellence for Advanced Molecular Imaging, School of Physics, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Justine K. Corso
- ARC Centre of Excellence for Advanced Molecular Imaging, School of Physics, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Carl Caleman
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, DE-22607 Hamburg, Germany
| | - Nicusor Timneanu
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Harry M. Quiney
- ARC Centre of Excellence for Advanced Molecular Imaging, School of Physics, University of Melbourne, Parkville, Victoria 3010, Australia
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13
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Galli L, Son SK, Klinge M, Bajt S, Barty A, Bean R, Betzel C, Beyerlein KR, Caleman C, Doak RB, Duszenko M, Fleckenstein H, Gati C, Hunt B, Kirian RA, Liang M, Nanao MH, Nass K, Oberthür D, Redecke L, Shoeman R, Stellato F, Yoon CH, White TA, Yefanov O, Spence J, Chapman HN. Electronic damage in S atoms in a native protein crystal induced by an intense X-ray free-electron laser pulse. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2015; 2:041703. [PMID: 26798803 PMCID: PMC4711609 DOI: 10.1063/1.4919398] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 04/17/2015] [Indexed: 05/07/2023]
Abstract
Current hard X-ray free-electron laser (XFEL) sources can deliver doses to biological macromolecules well exceeding 1 GGy, in timescales of a few tens of femtoseconds. During the pulse, photoionization can reach the point of saturation in which certain atomic species in the sample lose most of their electrons. This electronic radiation damage causes the atomic scattering factors to change, affecting, in particular, the heavy atoms, due to their higher photoabsorption cross sections. Here, it is shown that experimental serial femtosecond crystallography data collected with an extremely bright XFEL source exhibit a reduction of the effective scattering power of the sulfur atoms in a native protein. Quantitative methods are developed to retrieve information on the effective ionization of the damaged atomic species from experimental data, and the implications of utilizing new phasing methods which can take advantage of this localized radiation damage are discussed.
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Affiliation(s)
| | | | - M Klinge
- Joint Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, University of Hamburg and Institute of Biochemistry, University of Luebeck at DESY, 22607 Hamburg, Germany
| | - S Bajt
- Photon Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, 22607 Hamburg, Germany
| | - A Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, 22607 Hamburg, Germany
| | - R Bean
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, 22607 Hamburg, Germany
| | - C Betzel
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, University of Hamburg at DESY, 22607 Hamburg, Germany
| | - K R Beyerlein
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, 22607 Hamburg, Germany
| | | | - R B Doak
- Department of Biomolecular Mechanisms, Max Planck-Institute for Medical Research , Jahnstrasse 29, 69120 Heidelberg, Germany
| | - M Duszenko
- Interfaculty Institute of Biochemistry, University of Tübingen , 72076 Tübingen, Germany
| | - H Fleckenstein
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, 22607 Hamburg, Germany
| | - C Gati
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, 22607 Hamburg, Germany
| | - B Hunt
- Department of Physics and Astronomy, Brigham Young University , Provo, Utah 84602, USA
| | - R A Kirian
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, 22607 Hamburg, Germany
| | - M Liang
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, 22607 Hamburg, Germany
| | - M H Nanao
- EMBL , Grenoble Outstation, Rue Jules Horowitz 6, Grenoble 38042, France
| | - K Nass
- Department of Biomolecular Mechanisms, Max Planck-Institute for Medical Research , Jahnstrasse 29, 69120 Heidelberg, Germany
| | - D Oberthür
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, 22607 Hamburg, Germany
| | - L Redecke
- Joint Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, University of Hamburg and Institute of Biochemistry, University of Luebeck at DESY, 22607 Hamburg, Germany
| | - R Shoeman
- Department of Biomolecular Mechanisms, Max Planck-Institute for Medical Research , Jahnstrasse 29, 69120 Heidelberg, Germany
| | - F Stellato
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, 22607 Hamburg, Germany
| | | | - T A White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, 22607 Hamburg, Germany
| | - O Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, 22607 Hamburg, Germany
| | - J Spence
- Department of Physics, Arizona State University , Tempe, Arizona 85287-1504, USA
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14
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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. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:225-38. [PMID: 25723924 DOI: 10.1107/s1600577515002349] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [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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15
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Jönsson HO, Tîmneanu N, Östlin C, Scott HA, Caleman C. Simulations of radiation damage as a function of the temporal pulse profile in femtosecond X-ray protein crystallography. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:256-66. [PMID: 25723927 DOI: 10.1107/s1600577515002878] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 02/10/2015] [Indexed: 05/07/2023]
Abstract
Serial femtosecond X-ray crystallography of protein nanocrystals using ultrashort and intense pulses from an X-ray free-electron laser has proved to be a successful method for structural determination. However, due to significant variations in diffraction pattern quality from pulse to pulse only a fraction of the collected frames can be used. Experimentally, the X-ray temporal pulse profile is not known and can vary with every shot. This simulation study describes how the pulse shape affects the damage dynamics, which ultimately affects the biological interpretation of electron density. The instantaneously detected signal varies during the pulse exposure due to the pulse properties, as well as the structural and electronic changes in the sample. Here ionization and atomic motion are simulated using a radiation transfer plasma code. Pulses with parameters typical for X-ray free-electron lasers are considered: pulse energies ranging from 10(4) to 10(7) J cm(-2) with photon energies from 2 to 12 keV, up to 100 fs long. Radiation damage in the form of sample heating that will lead to a loss of crystalline periodicity and changes in scattering factor due to electronic reconfigurations of ionized atoms are considered here. The simulations show differences in the dynamics of the radiation damage processes for different temporal pulse profiles and intensities, where ionization or atomic motion could be predominant. The different dynamics influence the recorded diffracted signal in any given resolution and will affect the subsequent structure determination.
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Affiliation(s)
- H Olof Jönsson
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Nicuşor Tîmneanu
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Christofer Östlin
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Howard A Scott
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Carl Caleman
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
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16
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Abstract
X-ray free-electron lasers have opened up the possibility of structure determination of protein crystals at room temperature, free of radiation damage. The femtosecond-duration pulses of these sources enable diffraction signals to be collected from samples at doses of 1000 MGy or higher. The sample is vaporized by the intense pulse, but not before the scattering that gives rise to the diffraction pattern takes place. Consequently, only a single flash diffraction pattern can be recorded from a crystal, giving rise to the method of serial crystallography where tens of thousands of patterns are collected from individual crystals that flow across the beam and the patterns are indexed and aggregated into a set of structure factors. The high-dose tolerance and the many-crystal averaging approach allow data to be collected from much smaller crystals than have been examined at synchrotron radiation facilities, even from radiation-sensitive samples. Here, we review the interaction of intense femtosecond X-ray pulses with materials and discuss the implications for structure determination. We identify various dose regimes and conclude that the strongest achievable signals for a given sample are attained at the highest possible dose rates, from highest possible pulse intensities.
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Affiliation(s)
- Henry N Chapman
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Carl Caleman
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany Department of Physics and Astronomy, Uppsala University, Box 516, 75120 Uppsala, Sweden
| | - Nicusor Timneanu
- Department of Physics and Astronomy, Uppsala University, Box 516, 75120 Uppsala, Sweden Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
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