A QM/MM study of the nature of the entatic state in plastocyanin
Plastocyanin is a copper containing protein that is involved in the electron transfer process in photosynthetic organisms. The active site of plastocyanin is described as an entatic state whereby its structure represents a compromise between the structures favored by the oxidized and reduced forms....
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| Format: | Article |
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Wiley
2016
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| Online Access: | https://eprints.nottingham.ac.uk/38564/ |
| _version_ | 1848795641697796096 |
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| author | Hurd, Catherine A. Besley, Nicholas A. Robinson, David |
| author_facet | Hurd, Catherine A. Besley, Nicholas A. Robinson, David |
| author_sort | Hurd, Catherine A. |
| building | Nottingham Research Data Repository |
| collection | Online Access |
| description | Plastocyanin is a copper containing protein that is involved in the electron transfer process in photosynthetic organisms. The active site of plastocyanin is described as an entatic state whereby its structure represents a compromise between the structures favored by the oxidized and reduced forms. In this study the nature of the entatic state is investigated through density functional theory based hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations. The strain energy is computed to be 12.8 kcal/mol and 14.5 kcal/mol for the oxidized and reduced forms of the protein, indicating that the active site has an intermediate structure. It is shown that the energy gap between the oxidized and reduced forms varies significantly with the fluctuations in the structure of the active site at room temperature. An accurate determination of the reorganization energy requires averaging over conformation and a large region of the protein around the active site to be treated at the quantum mechanical level. |
| first_indexed | 2025-11-14T19:35:19Z |
| format | Article |
| id | nottingham-38564 |
| institution | University of Nottingham Malaysia Campus |
| institution_category | Local University |
| last_indexed | 2025-11-14T19:35:19Z |
| publishDate | 2016 |
| publisher | Wiley |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | nottingham-385642020-05-04T18:21:13Z https://eprints.nottingham.ac.uk/38564/ A QM/MM study of the nature of the entatic state in plastocyanin Hurd, Catherine A. Besley, Nicholas A. Robinson, David Plastocyanin is a copper containing protein that is involved in the electron transfer process in photosynthetic organisms. The active site of plastocyanin is described as an entatic state whereby its structure represents a compromise between the structures favored by the oxidized and reduced forms. In this study the nature of the entatic state is investigated through density functional theory based hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations. The strain energy is computed to be 12.8 kcal/mol and 14.5 kcal/mol for the oxidized and reduced forms of the protein, indicating that the active site has an intermediate structure. It is shown that the energy gap between the oxidized and reduced forms varies significantly with the fluctuations in the structure of the active site at room temperature. An accurate determination of the reorganization energy requires averaging over conformation and a large region of the protein around the active site to be treated at the quantum mechanical level. Wiley 2016-11-14 Article PeerReviewed Hurd, Catherine A., Besley, Nicholas A. and Robinson, David (2016) A QM/MM study of the nature of the entatic state in plastocyanin. Journal of Computational Chemistry . ISSN 1096-987X QM/MM Electron transfer Plastocyanin http://onlinelibrary.wiley.com/doi/10.1002/jcc.24666/full doi:10.1002/jcc.24666 doi:10.1002/jcc.24666 |
| spellingShingle | QM/MM Electron transfer Plastocyanin Hurd, Catherine A. Besley, Nicholas A. Robinson, David A QM/MM study of the nature of the entatic state in plastocyanin |
| title | A QM/MM study of the nature of the entatic state in plastocyanin |
| title_full | A QM/MM study of the nature of the entatic state in plastocyanin |
| title_fullStr | A QM/MM study of the nature of the entatic state in plastocyanin |
| title_full_unstemmed | A QM/MM study of the nature of the entatic state in plastocyanin |
| title_short | A QM/MM study of the nature of the entatic state in plastocyanin |
| title_sort | qm/mm study of the nature of the entatic state in plastocyanin |
| topic | QM/MM Electron transfer Plastocyanin |
| url | https://eprints.nottingham.ac.uk/38564/ https://eprints.nottingham.ac.uk/38564/ https://eprints.nottingham.ac.uk/38564/ |