DichroCalc: improvements in computing protein circular dichroism spectroscopy in the near-ultraviolet
A fully quantitative theory connecting protein conformation and optical spectroscopy would facilitate deeper insights into biophysical and simulation studies of protein dynamics and folding. The web-server DichroCalc (http://comp.chem.nottingham.ac.uk/dichrocalc) allows one to compute from first pri...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Published: |
Elsevier
2017
|
| Subjects: | |
| Online Access: | https://eprints.nottingham.ac.uk/48783/ |
| _version_ | 1848797845856976896 |
|---|---|
| author | Jasim, Sarah B. Li, Zhou Guest, Ellen E. Hirst, Jonathan D. |
| author_facet | Jasim, Sarah B. Li, Zhou Guest, Ellen E. Hirst, Jonathan D. |
| author_sort | Jasim, Sarah B. |
| building | Nottingham Research Data Repository |
| collection | Online Access |
| description | A fully quantitative theory connecting protein conformation and optical spectroscopy would facilitate deeper insights into biophysical and simulation studies of protein dynamics and folding. The web-server DichroCalc (http://comp.chem.nottingham.ac.uk/dichrocalc) allows one to compute from first principles the electronic circular dichroism spectrum of a (modelled or experimental) protein structure or ensemble of structures. The regular, repeating, chiral nature of secondary structure elements leads to intense bands in the far-ultraviolet. The near-UV bands are much weaker and have been challenging to compute theoretically. We report some advances in the accuracy of calculations in the near-UV, realised through the consideration of the vibrational structure of the electronic transitions of aromatic side chains. The improvements have been assessed over a set of diverse proteins. We illustrate them using bovine pancreatic trypsin inhibitor and present a new, detailed analysis of the interactions which are most important in determining the near-UV CD spectrum. |
| first_indexed | 2025-11-14T20:10:21Z |
| format | Article |
| id | nottingham-48783 |
| institution | University of Nottingham Malaysia Campus |
| institution_category | Local University |
| last_indexed | 2025-11-14T20:10:21Z |
| publishDate | 2017 |
| publisher | Elsevier |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | nottingham-487832020-05-04T19:22:38Z https://eprints.nottingham.ac.uk/48783/ DichroCalc: improvements in computing protein circular dichroism spectroscopy in the near-ultraviolet Jasim, Sarah B. Li, Zhou Guest, Ellen E. Hirst, Jonathan D. A fully quantitative theory connecting protein conformation and optical spectroscopy would facilitate deeper insights into biophysical and simulation studies of protein dynamics and folding. The web-server DichroCalc (http://comp.chem.nottingham.ac.uk/dichrocalc) allows one to compute from first principles the electronic circular dichroism spectrum of a (modelled or experimental) protein structure or ensemble of structures. The regular, repeating, chiral nature of secondary structure elements leads to intense bands in the far-ultraviolet. The near-UV bands are much weaker and have been challenging to compute theoretically. We report some advances in the accuracy of calculations in the near-UV, realised through the consideration of the vibrational structure of the electronic transitions of aromatic side chains. The improvements have been assessed over a set of diverse proteins. We illustrate them using bovine pancreatic trypsin inhibitor and present a new, detailed analysis of the interactions which are most important in determining the near-UV CD spectrum. Elsevier 2017-12-16 Article PeerReviewed Jasim, Sarah B., Li, Zhou, Guest, Ellen E. and Hirst, Jonathan D. (2017) DichroCalc: improvements in computing protein circular dichroism spectroscopy in the near-ultraviolet. Journal of Molecular Biology . ISSN 1089-8638 aromatic; vibronic; ab initio; electronic excited states; quantum http://www.sciencedirect.com/science/article/pii/S0022283617305892 doi:10.1016/j.jmb.2017.12.009 doi:10.1016/j.jmb.2017.12.009 |
| spellingShingle | aromatic; vibronic; ab initio; electronic excited states; quantum Jasim, Sarah B. Li, Zhou Guest, Ellen E. Hirst, Jonathan D. DichroCalc: improvements in computing protein circular dichroism spectroscopy in the near-ultraviolet |
| title | DichroCalc: improvements in computing protein circular dichroism spectroscopy in the near-ultraviolet |
| title_full | DichroCalc: improvements in computing protein circular dichroism spectroscopy in the near-ultraviolet |
| title_fullStr | DichroCalc: improvements in computing protein circular dichroism spectroscopy in the near-ultraviolet |
| title_full_unstemmed | DichroCalc: improvements in computing protein circular dichroism spectroscopy in the near-ultraviolet |
| title_short | DichroCalc: improvements in computing protein circular dichroism spectroscopy in the near-ultraviolet |
| title_sort | dichrocalc: improvements in computing protein circular dichroism spectroscopy in the near-ultraviolet |
| topic | aromatic; vibronic; ab initio; electronic excited states; quantum |
| url | https://eprints.nottingham.ac.uk/48783/ https://eprints.nottingham.ac.uk/48783/ https://eprints.nottingham.ac.uk/48783/ |