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Heavy-element damage seeding in proteins under XFEL illumination

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Bibliographic Details
Title: Heavy-element damage seeding in proteins under XFEL illumination
Authors: Passmore, Spencer K, Sanders, Alaric L, Martin, Andrew V, Quiney, Harry M
Contributors: Apollo - University of Cambridge Repository
Source: Journal of Synchrotron Radiation. 32:1124-1142
Publication Status: Preprint
Publisher Information: International Union of Crystallography (IUCr), 2025.
Publication Year: 2025
Subject Terms: heavy-element damage seeding, XFEL, Lasers, X-Rays, femtosecond studies, Proteins, FOS: Physical sciences, Electrons, Computational Physics (physics.comp-ph), Crystallography, X-Ray, Physics - Plasma Physics, diffract-then-destroy, Plasma Physics (physics.plasm-ph), pump–probe, Biological Physics (physics.bio-ph), radiation damage, single particles, SFX, serial crystallography, Physics - Biological Physics, protein structure, Physics - Computational Physics
Description: Serial femtosecond X-ray crystallography (SFX) captures the structure and dynamics of biological macromolecules at high spatial and temporal resolutions. The ultrashort pulse produced by an X-ray free-electron laser (XFEL) `outruns' much of the radiation damage that impairs conventional crystallography. However, the rapid onset of `electronic damage' due to ionization limits this benefit. Here, we distinguish the influence of different atomic species on the ionization of protein crystals by employing a plasma code that tracks the unbound electrons as a continuous energy distribution. The simulations show that trace quantities of heavy atoms (Z > 10) contribute a substantial proportion of global radiation damage by rapidly seeding electron ionization cascades. In a typical protein crystal, sulfur atoms and solvated salts induce a substantial fraction of light-atom ionization. In further modeling of various targets, global ionization peaks at photon energies roughly 2 keV above inner-shell absorption edges, where sub-2 keV photoelectrons ejected from these shells initiate ionization cascades that are briefer than the XFEL pulse. These results indicate that relatively small quantities of heavy elements can substantially affect global radiation damage in XFEL experiments.
Document Type: Article
File Description: text/xml; application/pdf
ISSN: 1600-5775
DOI: 10.1107/s1600577525005934
DOI: 10.48550/arxiv.2405.10298
Access URL: http://arxiv.org/abs/2405.10298
https://www.repository.cam.ac.uk/handle/1810/388763
https://doi.org/10.1107/s1600577525005934
Rights: CC BY
arXiv Non-Exclusive Distribution
Accession Number: edsair.doi.dedup.....68e230856a2fea60e4f484ef5ac48820
Database: OpenAIRE
Description
Abstract:Serial femtosecond X-ray crystallography (SFX) captures the structure and dynamics of biological macromolecules at high spatial and temporal resolutions. The ultrashort pulse produced by an X-ray free-electron laser (XFEL) `outruns' much of the radiation damage that impairs conventional crystallography. However, the rapid onset of `electronic damage' due to ionization limits this benefit. Here, we distinguish the influence of different atomic species on the ionization of protein crystals by employing a plasma code that tracks the unbound electrons as a continuous energy distribution. The simulations show that trace quantities of heavy atoms (Z > 10) contribute a substantial proportion of global radiation damage by rapidly seeding electron ionization cascades. In a typical protein crystal, sulfur atoms and solvated salts induce a substantial fraction of light-atom ionization. In further modeling of various targets, global ionization peaks at photon energies roughly 2 keV above inner-shell absorption edges, where sub-2 keV photoelectrons ejected from these shells initiate ionization cascades that are briefer than the XFEL pulse. These results indicate that relatively small quantities of heavy elements can substantially affect global radiation damage in XFEL experiments.
ISSN:16005775
DOI:10.1107/s1600577525005934