Indications of radiation damage in ferredoxin microcrystals using high-intensity X-FEL beams
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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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This heavy-atom effect is observable in x-ray diffraction patterns from biological objects containing sulfur, selenium, iodine atoms or heavy metal centers, and can be exploited for phasing of diffraction data.
“This is observable in the x-ray diffraction patterns from biological objects containing, e.g., sulfur, selenium, and iodine atoms [84], or heavy metal centers, and can be exploited for phasing of the acquired diffraction data [85].”
From Roadmap of ultrafast x-ray atomic and molecular physics (2018) · cites this paper as [84]
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- Authors
- Nass, K., Foucar, L., Barends, T. R. M., Hartmann, E., Botha, S., Shoeman, R. L., Doak, R. B., Alonso-Mori, R., Aquila, A., Bajt, S., Barty, A., Bean, R., Beyerlein, K. R., Bublitz, M., Drachmann, N., Gregersen, J., Jönsson, H. O., Kabsch, W., Kassemeyer, S., Koglin, J. E., Krumrey, M., Mattle, D., Messerschmidt, M., Nissen, P., Reinhard, L., Sitsel, O., Sokaras, D., Williams, G. J., Hau-Riege, S., Timneanu, N., Caleman, C., Chapman, H. N., Boutet, S., & Schlichting, I.
- Affiliations
- Max Planck Institute for Medical Research (DE)
- European X-Ray Free-Electron Laser (DE)
- Deutsches Elektronen-Synchrotron DESY (DE)
- Aarhus University (DK)
- Uppsala University (SE)
- SLAC National Accelerator Laboratory (US)
- Physikalisch-Technische Bundesanstalt (DE)
- Universität Hamburg (DE)
- ORCID
- Nass, Karol
- Barends, Thomas R. M.
- Botha, Sabine
- Shoeman, Robert L.
- Aquila, Andrew
- Bajt, Saša
- Barty, Anton
- Bean, Richard
- Beyerlein, Kenneth R.
- Bublitz, Maike
- Jönsson, H. Olof
- Koglin, Jason E.
- Krumrey, Michael
- Messerschmidt, Marc
- Nissen, Poul
- Reinhard, Linda
- Sitsel, Oleg
- Sokaras, Dimosthenis
- Williams, Garth J.
- Caleman, Carl
- Chapman, Henry N.
- Boutet, Sébastien
- Schlichting, Ilme
- Venue
- Journal of Synchrotron Radiation
- Published
- 2015-02-17
- Volume
- 22
- Issue
- 2
- Pages
- 225-238
- ISSN
- 0909-0495 (ISSN-L)
- 1600-5775
- OpenAlex
- W2100699108
- Cited by
- 131
- References
- 64
- Citations by year
- 2026: 4 · 2025: 6 · 2024: 8 · 2023: 4 · 2022: 7 · 2021: 10 · 2020: 18 · 2019: 15 · 2018: 14 · 2017: 20 · 2016: 16 · 2015: 9
- FWCI
- 7.97
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Journal of Synchrotron Radiation (publishedVersion)
- PubMed (publishedVersion)
- DESY Publication Database (PUBDB) (Deutsches Elektronen-Synchrotron) (submittedVersion, other-oa)
- DORA PSI (Paul Scherrer Institute) (submittedVersion)
- HZB Repository (Helmholtz-Zentrum Berlin für Materialien und Energie GmbH (HZB)) (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- European XFEL (submittedVersion)
- Funders
- U.S. Department of Energy
- Max-Planck-Gesellschaft
- Vetenskapsrådet
- Novo Nordisk Fonden (NNF12OC0002082)
- Deutsches Elektronen-Synchrotron
- Uppsala Multidisciplinary Center for Advanced Computational Science
- Basic Energy Sciences
- Topics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Physical Sciences › Physics and Astronomy › Radiation › Advanced X-ray Imaging Techniques
- Physical Sciences › Physics and Astronomy › Radiation › X-ray Spectroscopy and Fluorescence Analysis
- Keywords
- radiation damage, ferredoxin, [4Fe-4S] cluster, serial femtosecond crystallography, X-ray free-electron laser, photoionization, atomic scattering factors, electron density maps
- MeSH terms
- Clostridium, Dose-Response Relationship, Radiation, Ferredoxins, Humans, Metalloproteins, Models, Molecular, Radiation Injuries, Sensitivity and Specificity, Synchrotrons, Crystallography, X-Ray
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