Structural transition induced by a local chemical/mechanical perturbation in biomolecules
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 a...
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| Format: | Article |
| Language: | English |
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Institute for Condensed Matter Physics
2023-12-01
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| Series: | Condensed Matter Physics |
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| Online Access: | https://doi.org/10.5488/CMP.26.43803 |
| _version_ | 1797371738921631744 |
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| author | F. Hirata |
| author_facet | F. Hirata |
| author_sort | F. Hirata |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-08T18:25:15Z |
| format | Article |
| id | doaj.art-f76779d247014befaefca1a24a752222 |
| institution | Directory Open Access Journal |
| issn | 1607-324X 2224-9079 |
| language | English |
| last_indexed | 2024-03-08T18:25:15Z |
| publishDate | 2023-12-01 |
| publisher | Institute for Condensed Matter Physics |
| record_format | Article |
| series | Condensed Matter Physics |
| spelling | doaj.art-f76779d247014befaefca1a24a7522222023-12-30T15:04:27ZengInstitute for Condensed Matter PhysicsCondensed Matter Physics1607-324X2224-90792023-12-012644380310.5488/CMP.26.43803Structural transition induced by a local chemical/mechanical perturbation in biomoleculesF. HirataStructural 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.https://doi.org/10.5488/CMP.26.43803structural phase transitionlangevin equationlinear response theorybiomolecules |
| spellingShingle | F. Hirata Structural transition induced by a local chemical/mechanical perturbation in biomolecules Condensed Matter Physics structural phase transition langevin equation linear response theory biomolecules |
| title | Structural transition induced by a local chemical/mechanical perturbation in biomolecules |
| title_full | Structural transition induced by a local chemical/mechanical perturbation in biomolecules |
| title_fullStr | Structural transition induced by a local chemical/mechanical perturbation in biomolecules |
| title_full_unstemmed | Structural transition induced by a local chemical/mechanical perturbation in biomolecules |
| title_short | Structural transition induced by a local chemical/mechanical perturbation in biomolecules |
| title_sort | structural transition induced by a local chemical mechanical perturbation in biomolecules |
| topic | structural phase transition langevin equation linear response theory biomolecules |
| url | https://doi.org/10.5488/CMP.26.43803 |
| work_keys_str_mv | AT fhirata structuraltransitioninducedbyalocalchemicalmechanicalperturbationinbiomolecules |