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  Water layer and radiation damage effects on the orientation recovery of proteins in single-particle imaging at an X-ray free-electron laser

E, J., Stransky, M., Shen, Z., Jurek, Z., Fortmann‑Grote, C., Bean, R., et al. (2023). Water layer and radiation damage effects on the orientation recovery of proteins in single-particle imaging at an X-ray free-electron laser. Scientific Reports, 13(1): 16359. doi:10.1038/s41598-023-43298-1.

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Item Permalink: https://hdl.handle.net/21.11116/0000-000D-C2BF-1 Version Permalink: https://hdl.handle.net/21.11116/0000-000D-C2C0-E
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 Creators:
E, J.1, Author
Stransky, M.1, 2, Author
Shen, Z.3, 4, Author           
Jurek, Z.4, Author
Fortmann‑Grote, C.1, Author
Bean, R.1, Author
Santra, R.4, 5, 6, Author
Ziaja, B.2, 4, Author
Mancus, A. P.1, 7, 8, Author
Affiliations:
1European XFEL, ou_persistent22              
2Institute of Nuclear Physics, Polish Academy of Sciences, ou_persistent22              
3Computational Nanoscale Imaging, Condensed Matter Dynamics Department, Max Planck Institute for the Structure and Dynamics of Matter, Max Planck Society, ou_3012829              
4Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, ou_persistent22              
5The Hamburg Centre for Ultrafast Imaging, ou_persistent22              
6Department of Physics, Universität Hamburg, ou_persistent22              
7Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire, ou_persistent22              
8Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, ou_persistent22              

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 Abstract: The noise caused by sample heterogeneity (including sample solvent) has been identified as one of the determinant factors for a successful X-ray single-particle imaging experiment. It influences both the radiation damage process that occurs during illumination as well as the scattering patterns captured by the detector. Here, we investigate the impact of water layer thickness and radiation damage on orientation recovery from diffraction patterns of the nitrogenase iron protein. Orientation recovery is a critical step for single-particle imaging. It enables to sort a set of diffraction patterns scattered by identical particles placed at unknown orientations and assemble them into a 3D reciprocal space volume. The recovery quality is characterized by a “disconcurrence” metric. Our results show that while a water layer mitigates protein damage, the noise generated by the scattering from it can introduce challenges for orientation recovery and is anticipated to cause problems in the phase retrieval process to extract the desired protein structure. Compared to these disadvantageous effects due to the thick water layer, the effects of radiation damage on the orientation recovery are relatively small. Therefore, minimizing the amount of residual sample solvent should be considered a crucial step in improving the fidelity and resolution of X-ray single-particle imaging experiments.

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Language(s): eng - English
 Dates: 2023-05-232023-09-212023-09-29
 Publication Status: Published online
 Pages: -
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 Table of Contents: -
 Rev. Type: Peer
 Identifiers: DOI: 10.1038/s41598-023-43298-1
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Project name : -
Grant ID : 823852
Funding program : Horizon 2020 (H2020)
Funding organization : European Commission (EC)
Project name : This work is funded by the European Union’s Horizon 2020 research and innovation programme under the grant agreement No. 823852 and an R & D grant of the European XFEL. A.P.M. and B.Z. gratefully acknowledge the funding received from the R & D grant provided by the European XFEL, with the contribution of IFJ PAN in Krakow. A.P.M and J. E thank Dr. Kartik Ayyer for insightful discussions on orientation recovery and Dr. Susanne Fangohr for proofreading the manuscript. M.S. is on leave from the Institute of Physics, Czech Academy of Sciences, Na Slovance 2, 182 21 Prague 8, Czech Republic.
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Title: Scientific Reports
  Abbreviation : Sci. Rep.
Source Genre: Journal
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Publ. Info: London, UK : Nature Publishing Group
Pages: - Volume / Issue: 13 (1) Sequence Number: 16359 Start / End Page: - Identifier: ISSN: 2045-2322
CoNE: https://pure.mpg.de/cone/journals/resource/2045-2322