High throughput interactome determination via sulfur anomalous scattering
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arXiv
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| Auteurs principaux: | , , , , |
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| Format: | Preprint |
| Publié: |
2023
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| _version_ | 1866917751636885504 |
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| author | Miotto, Mattia Milanetti, Edoardo Mincigrucci, Riccardo Masciovecchio, Claudio Ruocco, Giancarlo |
| author_facet | Miotto, Mattia Milanetti, Edoardo Mincigrucci, Riccardo Masciovecchio, Claudio Ruocco, Giancarlo |
| contents | We propose a novel approach to detect the binding between proteins making use of the anomalous diffraction of natively present heavy elements inside the molecule 3D structure. In particular, we suggest considering sulfur atoms contained in protein structures at lower percentages than the other atomic species. Here, we run an extensive preliminary investigation to probe both the feasibility and the range of usage of the proposed protocol. In particular, we (i) analytically and numerically show that the diffraction patterns produced by the anomalous scattering of the sulfur atoms in a given direction depend additively on the relative distances between all couples of sulfur atoms. Thus the differences in the patterns produced by bound proteins with respect to their non-bonded states can be exploited to rapidly assess protein complex formation. Next, we (ii) carried out analyses on the abundances of sulfurs in the different proteomes and molecular dynamics simulations on a representative set of protein structures to probe the typical motion of sulfur atoms. Finally, we (iii) suggest a possible experimental procedure to detect protein-protein binding. Overall, the completely label-free and rapid method we propose may be readily extended to probe interactions on a large scale even between other biological molecules, thus paving the way to the development of a novel field of research based on a synchrotron light source. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2311_15802 |
| institution | arXiv |
| publishDate | 2023 |
| record_format | arxiv |
| spellingShingle | High throughput interactome determination via sulfur anomalous scattering Miotto, Mattia Milanetti, Edoardo Mincigrucci, Riccardo Masciovecchio, Claudio Ruocco, Giancarlo Biological Physics Biomolecules We propose a novel approach to detect the binding between proteins making use of the anomalous diffraction of natively present heavy elements inside the molecule 3D structure. In particular, we suggest considering sulfur atoms contained in protein structures at lower percentages than the other atomic species. Here, we run an extensive preliminary investigation to probe both the feasibility and the range of usage of the proposed protocol. In particular, we (i) analytically and numerically show that the diffraction patterns produced by the anomalous scattering of the sulfur atoms in a given direction depend additively on the relative distances between all couples of sulfur atoms. Thus the differences in the patterns produced by bound proteins with respect to their non-bonded states can be exploited to rapidly assess protein complex formation. Next, we (ii) carried out analyses on the abundances of sulfurs in the different proteomes and molecular dynamics simulations on a representative set of protein structures to probe the typical motion of sulfur atoms. Finally, we (iii) suggest a possible experimental procedure to detect protein-protein binding. Overall, the completely label-free and rapid method we propose may be readily extended to probe interactions on a large scale even between other biological molecules, thus paving the way to the development of a novel field of research based on a synchrotron light source. |
| title | High throughput interactome determination via sulfur anomalous scattering |
| topic | Biological Physics Biomolecules |
| url | https://arxiv.org/abs/2311.15802 |