Protein structure classification based on X-ray laser induced Coulomb explosion
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arXiv
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| Main Authors: | , , , , , |
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| Format: | Preprint |
| Published: |
2024
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| _version_ | 1866917975436558336 |
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| author | André, Tomas Dawod, Ibrahim Cardoch, Sebastian De Santis, Emiliano Timneanu, Nicusor Caleman, Carl |
| author_facet | André, Tomas Dawod, Ibrahim Cardoch, Sebastian De Santis, Emiliano Timneanu, Nicusor Caleman, Carl |
| contents | We simulated the Coulomb explosion dynamics due to the fast ionization induced by high-intensity X-rays in six proteins that share similar atomic content and shape. We followed and projected the trajectory of the fragments onto a virtual detector, providing a unique explosion footprint. After collecting 500 explosion footprints for each protein, we utilized principal component analysis and t-distributed stochastic neighbor embedding to classify these. The results show that the classification algorithms were able to separate proteins on the basis of explosion footprints from structurally similar proteins into distinct groups. The explosion footprints, therefore, provide a unique identifier for each of the proteins. We envision that method could be used concurrently with single particle coherent imaging experiments to provide additional information on shape, mass, or conformation. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2410_15934 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Protein structure classification based on X-ray laser induced Coulomb explosion André, Tomas Dawod, Ibrahim Cardoch, Sebastian De Santis, Emiliano Timneanu, Nicusor Caleman, Carl Chemical Physics Biological Physics Computational Physics We simulated the Coulomb explosion dynamics due to the fast ionization induced by high-intensity X-rays in six proteins that share similar atomic content and shape. We followed and projected the trajectory of the fragments onto a virtual detector, providing a unique explosion footprint. After collecting 500 explosion footprints for each protein, we utilized principal component analysis and t-distributed stochastic neighbor embedding to classify these. The results show that the classification algorithms were able to separate proteins on the basis of explosion footprints from structurally similar proteins into distinct groups. The explosion footprints, therefore, provide a unique identifier for each of the proteins. We envision that method could be used concurrently with single particle coherent imaging experiments to provide additional information on shape, mass, or conformation. |
| title | Protein structure classification based on X-ray laser induced Coulomb explosion |
| topic | Chemical Physics Biological Physics Computational Physics |
| url | https://arxiv.org/abs/2410.15934 |