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Reproducibility of Single Protein Explosions Induced by X-ray Lasers
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.ORCID iD: 0000-0002-0021-4354
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.ORCID iD: 0000-0001-7328-0400
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.ORCID iD: 0000-0002-2076-0918
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
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2018 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 20, no 18, p. 12381-12389Article in journal (Refereed) Published
Abstract [en]

Single particle imaging (SPI) using X-ray pulses has become increasingly attainable with the advent of high-intensity free electron lasers. Eliminating the need for crystallized samples enables structural studies of molecules previously inaccessible by conventional crystallography. While this emerging technique already demonstrates substantial promise, some obstacles need to be overcome before SPI can reach its full potential. One such problem is determining the spatial orientation of the sample at the time of X-ray interaction. Existing solutions rely on diffraction data and are computationally demanding and sensitive to noise. In this in silico study, we explore the possibility of aiding these methods by mapping the ion distribution as the sample undergoes a Coulomb explosion following the intense ionization. By detecting the ions ejected from the fragmented sample, the orientation of the original sample should be possible to determine. Knowledge of the orientation has been shown earlier to be of substantial advantage in the reconstruction of the original structure. 150 explosions of each of twelve separate systems – four polypeptides with different amounts of surface bound water – were simulated with molecular dynamics (MD) and the average angular distribution of carbon and sulfur ions was investigated independently. The results show that the explosion maps are reproducible in both cases, supporting the idea that orientation information is preserved. Additional water seems to restrict the carbon ion trajectories further through a shielding mechanism, making the maps more distinct. For sulfurs, water has no significant impact on the trajectories, likely due to their higher mass and greater ionization cross section, indicating that they could be of particular interest. Based on these findings, we conclude that explosion data can aid spatial orientation in SPI experiments and could substantially improve the capabilities of the novel technique.

Place, publisher, year, edition, pages
2018. Vol. 20, no 18, p. 12381-12389
Keywords [en]
XFEL, Single-particle imaging, Coulomb explosion, ultrafast, GROMACS, simulation.
National Category
Atom and Molecular Physics and Optics
Identifiers
URN: urn:nbn:se:uu:diva-329340DOI: 10.1039/C7CP07267HISI: 000431825300006OAI: oai:DiVA.org:uu-329340DiVA, id: diva2:1140804
Funder
Swedish Research Council, 2013-3940Swedish Foundation for Strategic Research Carl Tryggers foundation Available from: 2017-09-13 Created: 2017-09-13 Last updated: 2019-04-28Bibliographically approved
In thesis
1. Advances in Biomolecular Imaging with X-ray Free-Electron Lasers
Open this publication in new window or tab >>Advances in Biomolecular Imaging with X-ray Free-Electron Lasers
2017 (English)Licentiate thesis, comprehensive summary (Other academic)
Abstract [en]

Utilizing X-rays to solve molecular structures has proven to be an immensely powerful and im- portant scientific technique. The invention of X-ray crystallography has allowed for countless breakthroughs in chemistry, biology and material science and remains the number one method used for structural determination today. Of particular interest is the structures of biomolecules, such as proteins, due to their medical relevance. Unfortunately, the need for crystals of sufficient size constitutes the biggest drawback to this approach. This is troubling since many of the im- portant biomolecules, in particular membrane proteins, have proven to be difficult or sometimes even impossible to crystalize. When limited to a small nanocrystal or even a single particle, con- ventional crystallography is no longer adequate to probe the structure at high enough resolution. Recent developments, most notably the introduction of X-ray free-electron lasers (XFELs), have opened up new possibilities for circumventing these limitations. The high intensities and ultra- short pulse lengths provided by XFELs allows for diffractive imaging of smaller crystals through Serial Femtosecond Crystallography (SFX) and can even be extended to single molecules, Single Particle Imaging (SPI). These methods are still in their infancies, and much research and refine- ment is needed before they can be properly established.

The current work covers fundamental studies of X-ray interaction with biomatter carried out to aid and improve upon SFX and SPI. Three papers based on computer simulation studies are presented, related to mainly two central aspects faced when imaging molecules with XFELs. Pa- per I explores a novel approach using explosion mapping to facilitate spatial orientation of single particles, which is necessary to reconstruct the three dimensional structure from two dimensional diffraction patterns. Paper II concerns radiation damage of the sample in SFX experiments using a plasma model and studies the impact of different pulse profiles on these processes. Lastly, pa- per III outlines the details of an online database available to researchers worldwide that contains simulated data on damage development in samples exposed to an XFEL pulse.

In the first study, molecular dynamics was adopted to map the XFEL-induced Coulomb explo- sions in SPI for biomolecules. Four proteins were investigated, each with three different levels of hydration, and it was found that explosion patterns for both carbon and sulfur ions are re- producible for all twelve systems. However, water bound to the protein surface seems to have a shielding effect on carbons, causing their trajectories to be favored toward the exposed parts of the sample. This complicates the adoption for orientation determination as the water content would have to be known. Sulfurs, on the other hand, showed no signs of water dependence and consistently produced similar explosion patterns regardless of hydration level. We speculate that this is because of their higher mass and ionization cross section and conclude that mapping of heavier ions could provide valuable information for spatial orientation.

In the second study, radiation damage in terms of ionization and atomic displacement within a nanometer-sized crystal illuminated by an XFEL pulse was explored with a non-local thermody- namic equilibrium plasma code. Different temporal distributions of the same number of photons was employed to assess its impact of damage dynamics. The results show that the pulse profile is substantially important. A front-loaded pulse is more beneficial for imaging purposes since the bulk of the photons encounters an undamaged sample. If the majority of photons instead arrive late, early photons will already have initiated the crystal decay causing further contribution to the diffraction pattern to be degraded.

In the third study, the free-electron laser damage simulation database (FreeDam) was estab- lished. It presents simulated time-resolved data for average ionization, ion and electron temper- atures and atomic displacement for various materials and XFEL parameters. Simulations were carried out using the same code as in paper II, and the data is freely available online.

This thesis is aimed to provide one of the stepping stones toward atomic resolution imaging of nanocrystals and single particles with free-electron lasers. If realized, these techniques could well turn out to be one of the greatest scientific achievements of the 21th century.

Place, publisher, year, edition, pages
Uppsala University, 2017
Keywords
XFEL, serial femtosecond x-ray crystallography, single particle imaging, radiation damage, GROMACS, Cretin, computer simulation
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-329500 (URN)
Presentation
2017-10-13, Å2001, Ångströmlaboratoriet, Lägerhyddsvägen 1, Uppsala, Sweden, 10:15 (Swedish)
Supervisors
Available from: 2017-09-18 Created: 2017-09-17 Last updated: 2017-09-18Bibliographically approved
2. Simulations of Biomolecular Fragmentation and Diffraction with Ultrafast X-ray Lasers
Open this publication in new window or tab >>Simulations of Biomolecular Fragmentation and Diffraction with Ultrafast X-ray Lasers
2019 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Studies of biomolecules have recently seen substantial developments. New X-ray lasers allow for high-resolution imaging of protein crystals too small for conventional X-ray crystallography. Even structures of single particles have been determined at lower resolutions with these new sources. The secret lies in the ultrashort high-intensity pulses, which allow for diffraction and retrieval of structural information before the sample gets fragmented. However, the attainable resolution is still limited, in particular when imaging non-crystalline samples, making further advancements highly desired. In this thesis, some of the resolution-limiting obstacles facing single particle imaging (SPI) of proteins are studied in silico.

As the X-ray pulse interacts with injected single molecules, their spatial orientation is generally unknown. Recovering the orientation is essential to the structure determination process, and currently nontrivial. Molecular dynamics simulations show that the Coulomb explosion due to intense X-ray ionization could provide information pertaining to the original orientation. Used in conjunction with current methods, this would lead to an enhanced three-dimensional reconstruction of the protein.

Radiation damage and sample heterogeneity constitute considerable sources of noise in SPI. Pulse durations are presently not brief enough to circumvent damage, causing the sample to deteriorate during imaging, and the accuracy of the averaged diffraction pattern is impaired by structural variations. The extent of these effects were studied by molecular dynamics. Our findings suggest that radiation damage in terms of ionization and atomic displacement promotes a gating mechanism, benefiting imaging with longer pulses. Because of this, sample heterogeneity poses a greater challenge and efforts should be made to minimize its impact.

X-ray lasers generate pulses with a stochastic temporal distribution of photons, affecting the achievable resolution on a  pulse-to-pulse basis. Plasma simulations were performed to investigate how these fluctuations influence the damage dynamics and the diffraction signal. The results reveal that structural information is particularly well-preserved if the temporal distribution is skewed such that most photons are concentrated at the beginning.

While many obstacles remain, the prospect of atomic-resolution SPI is drawing ever closer. This thesis is but one of the stepping stones necessary to get us there. Once we do, the possibilities are limitless.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2019. p. 84
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1815
Keywords
X-ray free-electron laser, X-ray imaging, Single particle imaging, Computer simulation, Radiation damage, Molecular dynamics, Diffraction theory, Coulomb explosion, Sample heterogeneity, Diffractive noise, XFEL, SPI
National Category
Biophysics
Research subject
Physics with specialization in Biophysics
Identifiers
urn:nbn:se:uu:diva-382441 (URN)978-91-513-0669-8 (ISBN)
Public defence
2019-06-14, Häggsalen, Ångströmlaboratoriet, Lägerhyddsvägen 1, Uppsala, 10:15 (English)
Opponent
Supervisors
Funder
Swedish Research Council
Available from: 2019-05-23 Created: 2019-04-28 Last updated: 2019-06-18

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Östlin, ChristoferTimneanu, NicusorJönsson, H. OlofEkeberg, TomasCaleman, Carl

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