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Time-Resolved Crystallography. CRYSTALS 2022. [DOI: 10.3390/cryst12040561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
This Special Issue on ‘Time-Resolved Crystallography’ is a collection of eight original articles providing interesting results that give insight into the processes involved in generating and analysing time-resolved data [...]
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Eliah Dawod I, Tîmneanu N, Mancuso AP, Caleman C, Grånäs O. Imaging of femtosecond bond breaking and charge dynamics in ultracharged peptides. Phys Chem Chem Phys 2021; 24:1532-1543. [PMID: 34939631 DOI: 10.1039/d1cp03419g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
X-ray free-electrons lasers have revolutionized the method of imaging biological macromolecules such as proteins, viruses and cells by opening the door to structural determination of both single particles and crystals at room temperature. By utilizing high intensity X-ray pulses on femtosecond timescales, the effects of radiation damage can be reduced. Achieving high resolution structures will likely require knowledge of how radiation damage affects the structure on an atomic scale, since the experimentally obtained electron densities will be reconstructed in the presence of radiation damage. Detailed understanding of the expected damage scenarios provides further information, in addition to guiding possible corrections that may need to be made to obtain a damage free reconstruction. In this work, we have quantified the effects of ionizing photon-matter interactions using first principles molecular dynamics. We utilize density functional theory to calculate bond breaking and charge dynamics in three ultracharged molecules and two different structural conformations that are important to the structural integrity of biological macromolecules, comparing to our previous studies on amino acids. The effects of the ultracharged states and subsequent bond breaking in real space are studied in reciprocal space using coherent diffractive imaging of an ensemble of aligned biomolecules in the gas phase.
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Affiliation(s)
- Ibrahim Eliah Dawod
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-75120 Uppsala, Sweden. .,European XFEL, Holzkoppel 4, DE-22869 Schenefeld, Germany
| | - Nicusor Tîmneanu
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-75120 Uppsala, Sweden.
| | - Adrian P Mancuso
- European XFEL, Holzkoppel 4, DE-22869 Schenefeld, Germany.,Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Carl Caleman
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-75120 Uppsala, Sweden. .,Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestraße 85, DE-22607 Hamburg, Germany
| | - Oscar Grånäs
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-75120 Uppsala, Sweden.
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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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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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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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