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| Main Authors: | , , , |
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| Format: | Preprint |
| Published: |
2024
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| Subjects: | |
| Online Access: | https://arxiv.org/abs/2404.04431 |
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| _version_ | 1866914742309748736 |
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| author | Mioduszewski, Łukasz Bednarz, Jakub Chwastyk, Mateusz Cieplak, Marek |
| author_facet | Mioduszewski, Łukasz Bednarz, Jakub Chwastyk, Mateusz Cieplak, Marek |
| contents | We present a coarse-grained C$α$-based protein model that can be used to simulate structured, intrinsically disordered and partially disordered proteins. We use a Go-like potential for the structured parts and two different variants of a transferable potential for the disordered parts. The first variant uses dynamic structure-based (DSB) contacts that form and disappear quasi-adiabatically during the simulation. By using specific structural criteria we distinguish sidechain-sidechain, sidechain-backbone and backbone-backbone contacts. The second variant is a non-radial multi-body pseudo-improper-dihedral (PID) potential that does not include time-dependent terms but requires more computational resources. Our model can simulate in reasonable time thousands of residues on millisecond time scales. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2404_04431 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Contact-based molecular dynamics of structured and disordered proteins in a coarse-grained model: fixed contacts, switchable contacts and those described by pseudo-improper-dihedral angles Mioduszewski, Łukasz Bednarz, Jakub Chwastyk, Mateusz Cieplak, Marek Soft Condensed Matter We present a coarse-grained C$α$-based protein model that can be used to simulate structured, intrinsically disordered and partially disordered proteins. We use a Go-like potential for the structured parts and two different variants of a transferable potential for the disordered parts. The first variant uses dynamic structure-based (DSB) contacts that form and disappear quasi-adiabatically during the simulation. By using specific structural criteria we distinguish sidechain-sidechain, sidechain-backbone and backbone-backbone contacts. The second variant is a non-radial multi-body pseudo-improper-dihedral (PID) potential that does not include time-dependent terms but requires more computational resources. Our model can simulate in reasonable time thousands of residues on millisecond time scales. |
| title | Contact-based molecular dynamics of structured and disordered proteins in a coarse-grained model: fixed contacts, switchable contacts and those described by pseudo-improper-dihedral angles |
| topic | Soft Condensed Matter |
| url | https://arxiv.org/abs/2404.04431 |