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| Natura: | Preprint |
| Pubblicazione: |
2023
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| Accesso online: | https://arxiv.org/abs/2304.06884 |
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| _version_ | 1866911759968763904 |
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| author | Hirata, Fumio |
| author_facet | Hirata, Fumio |
| contents | Structural transition induced by a local conformational change in biomolecules is formulated based on the generalized Langevin theory for the structural fluctuation of a molecule in solution, and the linear response theory, derived by Kim and Hirata in 2012. A chemical/mechanical change introduced at a moiety of biomolecules, such as an amino acid substitution or a structural change of a chromophore by the photo-excitation, is considered as a perturbation, and the rest of the protein as the reference system. The linear-response equation consists of two parts: a mechanical/chemical perturbation introduced at the moiety, and the variance-covariance matrix of the reference system that works as a response function. The physical meaning of the equation is transparent: the force exerted by atoms in the moiety induces the displacement in an atom of protein, which propagates through the variance-covariance matrix to cause a global conformational change in the molecule. A few examples of possible application of the theory, including those in industry, are suggested. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2304_06884 |
| institution | arXiv |
| publishDate | 2023 |
| record_format | arxiv |
| spellingShingle | Structural transition induced by a local chemical/mechanical perturbation in biomolecules Hirata, Fumio Statistical Mechanics Structural transition induced by a local conformational change in biomolecules is formulated based on the generalized Langevin theory for the structural fluctuation of a molecule in solution, and the linear response theory, derived by Kim and Hirata in 2012. A chemical/mechanical change introduced at a moiety of biomolecules, such as an amino acid substitution or a structural change of a chromophore by the photo-excitation, is considered as a perturbation, and the rest of the protein as the reference system. The linear-response equation consists of two parts: a mechanical/chemical perturbation introduced at the moiety, and the variance-covariance matrix of the reference system that works as a response function. The physical meaning of the equation is transparent: the force exerted by atoms in the moiety induces the displacement in an atom of protein, which propagates through the variance-covariance matrix to cause a global conformational change in the molecule. A few examples of possible application of the theory, including those in industry, are suggested. |
| title | Structural transition induced by a local chemical/mechanical perturbation in biomolecules |
| topic | Statistical Mechanics |
| url | https://arxiv.org/abs/2304.06884 |