Partial Orientation Retrieval of Proteins From Coulomb Explosions
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arXiv
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| Main Authors: | , , , |
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| Format: | Preprint |
| Published: |
2024
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| _version_ | 1866911228576661504 |
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| author | André, Tomas De Santis, Emiliano Timneanu, Nicusor Caleman, Carl |
| author_facet | André, Tomas De Santis, Emiliano Timneanu, Nicusor Caleman, Carl |
| contents | Single Particle Imaging techniques at X-ray lasers have made significant strides, yet the challenge of determining the orientation of freely rotating molecules during delivery remains. In this study, we propose a novel method to partially retrieve the relative orientation of proteins exposed to ultrafast X-ray pulses by analyzing the fragmentation patterns resulting from Coulomb explosions. We simulate these explosions for 45 proteins in the size range 100 -- 4000 atoms using a hybrid Monte Carlo/Molecular Dynamics approach and capture the resulting ion ejection patterns with virtual detectors. Our goal is to exploit information from the explosion to infer orientations of proteins at the time of X-ray exposure. Our results demonstrate that partial orientation information can be extracted, particularly for larger proteins. Our findings can be integrated into existing reconstruction algorithms such as Expand-Maximize-Compress, to improve their efficiency and reduce the need for high-quality diffraction patterns. This method offers a promising avenue for enhancing Single Particle Imaging by leveraging measurable data from the Coulomb explosion to provide valuable insights about orientation. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2410_15965 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Partial Orientation Retrieval of Proteins From Coulomb Explosions André, Tomas De Santis, Emiliano Timneanu, Nicusor Caleman, Carl Chemical Physics Biological Physics Computational Physics Single Particle Imaging techniques at X-ray lasers have made significant strides, yet the challenge of determining the orientation of freely rotating molecules during delivery remains. In this study, we propose a novel method to partially retrieve the relative orientation of proteins exposed to ultrafast X-ray pulses by analyzing the fragmentation patterns resulting from Coulomb explosions. We simulate these explosions for 45 proteins in the size range 100 -- 4000 atoms using a hybrid Monte Carlo/Molecular Dynamics approach and capture the resulting ion ejection patterns with virtual detectors. Our goal is to exploit information from the explosion to infer orientations of proteins at the time of X-ray exposure. Our results demonstrate that partial orientation information can be extracted, particularly for larger proteins. Our findings can be integrated into existing reconstruction algorithms such as Expand-Maximize-Compress, to improve their efficiency and reduce the need for high-quality diffraction patterns. This method offers a promising avenue for enhancing Single Particle Imaging by leveraging measurable data from the Coulomb explosion to provide valuable insights about orientation. |
| title | Partial Orientation Retrieval of Proteins From Coulomb Explosions |
| topic | Chemical Physics Biological Physics Computational Physics |
| url | https://arxiv.org/abs/2410.15965 |