Water layer and radiation damage effects on the orientation recovery of proteins in single-particle imaging at an X-ray free-electron laser
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 patt...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-09-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-43298-1 |
| _version_ | 1797576684276285440 |
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| author | Juncheng E Michal Stransky Zhou Shen Zoltan Jurek Carsten Fortmann-Grote Richard Bean Robin Santra Beata Ziaja Adrian P. Mancuso |
| author_facet | Juncheng E Michal Stransky Zhou Shen Zoltan Jurek Carsten Fortmann-Grote Richard Bean Robin Santra Beata Ziaja Adrian P. Mancuso |
| author_sort | Juncheng E |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-10T21:57:17Z |
| format | Article |
| id | doaj.art-3cfffbeb138d41f296f31c020873d3c7 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-10T21:57:17Z |
| publishDate | 2023-09-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-3cfffbeb138d41f296f31c020873d3c72023-11-19T13:04:47ZengNature PortfolioScientific Reports2045-23222023-09-0113111110.1038/s41598-023-43298-1Water layer and radiation damage effects on the orientation recovery of proteins in single-particle imaging at an X-ray free-electron laserJuncheng E0Michal Stransky1Zhou Shen2Zoltan Jurek3Carsten Fortmann-Grote4Richard Bean5Robin Santra6Beata Ziaja7Adrian P. Mancuso8European XFELEuropean XFELMax Planck Institute for the Structure and Dynamics of MatterCenter for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESYEuropean XFELEuropean XFELCenter for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESYInstitute of Nuclear Physics, Polish Academy of SciencesEuropean XFELAbstract 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.https://doi.org/10.1038/s41598-023-43298-1 |
| spellingShingle | Juncheng E Michal Stransky Zhou Shen Zoltan Jurek Carsten Fortmann-Grote Richard Bean Robin Santra Beata Ziaja Adrian P. Mancuso 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 |
| title | Water layer and radiation damage effects on the orientation recovery of proteins in single-particle imaging at an X-ray free-electron laser |
| title_full | Water layer and radiation damage effects on the orientation recovery of proteins in single-particle imaging at an X-ray free-electron laser |
| title_fullStr | Water layer and radiation damage effects on the orientation recovery of proteins in single-particle imaging at an X-ray free-electron laser |
| title_full_unstemmed | Water layer and radiation damage effects on the orientation recovery of proteins in single-particle imaging at an X-ray free-electron laser |
| title_short | Water layer and radiation damage effects on the orientation recovery of proteins in single-particle imaging at an X-ray free-electron laser |
| title_sort | water layer and radiation damage effects on the orientation recovery of proteins in single particle imaging at an x ray free electron laser |
| url | https://doi.org/10.1038/s41598-023-43298-1 |
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