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DichroCalc: improvements in computing protein circular dichroism spectroscopy in the near-ultraviolet

Jasim, Sarah B.; Li, Zhou; Guest, Ellen E.; Hirst, Jonathan D.

DichroCalc: improvements in computing protein circular dichroism spectroscopy in the near-ultraviolet Thumbnail


Authors

Sarah B. Jasim

Zhou Li

Ellen E. Guest



Abstract

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.

Citation

Jasim, S. B., Li, Z., Guest, E. E., & Hirst, J. D. (in press). DichroCalc: improvements in computing protein circular dichroism spectroscopy in the near-ultraviolet. Journal of Molecular Biology, https://doi.org/10.1016/j.jmb.2017.12.009

Journal Article Type Article
Acceptance Date Dec 10, 2017
Online Publication Date Dec 16, 2017
Deposit Date Dec 18, 2017
Publicly Available Date Mar 29, 2024
Journal Journal of Molecular Biology
Print ISSN 0022-2836
Electronic ISSN 1089-8638
Publisher Elsevier
Peer Reviewed Peer Reviewed
DOI https://doi.org/10.1016/j.jmb.2017.12.009
Keywords aromatic; vibronic; ab initio; electronic excited states; quantum
Public URL https://nottingham-repository.worktribe.com/output/900091
Publisher URL http://www.sciencedirect.com/science/article/pii/S0022283617305892

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