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

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

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: Dec 18, 2017
• 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