Circular dichroism (CD) spectroscopy is an important technique in studying protein structure, especially for protein secondary structures and conformational changes during biological processes. A fully quantitative theory of the relationship between protein conformation and optical spectroscopy would facilitate deeper interpretation and insight into biophysical and simulation studies of protein dynamics and folding. Vibrational structure in the electronic CD spectra of proteins is an important source of information on protein conformation and can be exploited to study structure and folding. We employ the state-averaged complete active space (CAS) method to calculate the ab initio electronic ground and excited states of N-methylacetamide (NMA), toluene, p-cresol and 3-methylindole (3-MI), which represent chromophores that are significant in the CD spectroscopy of proteins in the far- and near-ultraviolet (UV) regions. The results of these calculations are used to incorporate vibronic levels of the excited states into first principles calculations of CD using an exciton approach. The far-UV CD spectra of a set of 49 proteins, comprising a range of structural types, are calculated to assess the influence of the vibrational structure. The calculated spectra of -helical proteins are better resolved using the vibronic parameters and correlation between the experimental and the calculated intensity of less regular structure proteins improves over most wavelengths in the far-UV. No obvious improvement is observed in the calculated spectra of regular -sheet proteins. The near-UV CD spectra of 40 proteins are calculated with the new parameter set and the correlation between the computed and the experimental intensity from 270 to 290 nm is much improved. The contribution of individual chromophores to the CD spectra has been calculated for several mutants and in many cases helps rationalize changes in their experimental spectra. Considering conformational flexibility by using families of NMR structures leads to further improvements for some proteins and illustrates an informative level of sensitivity to side chain conformation. In several cases, the near-UV CD calculations can distinguish the native protein structure from a set of computer-generated misfolded decoy structures. CD spectra of proteins are better reproduced in both far- and near-UV by considering vibrational structures in electronic transitions of chromophores. This improvement can provide more details in connecting the spectroscopic data to the conformations of proteins and will encourage a broader use of CD in protein studies. Besides shedding light on the importance of vibronic transition, results in this thesis also show other aspects that may further improve CD calculations, such as developing parameters of disulfide bond, calculating CD using molecular dynamics (MD) trajectories and taking into account the influence of surroundings of chromophores.
| Identifer | oai:union.ndltd.org:bl.uk/oai:ethos.bl.uk:748257 |
| Date | January 2018 |
| Creators | Li, Zhuo |
| Publisher | University of Nottingham |
| Source Sets | Ethos UK |
| Detected Language | English |
| Type | Electronic Thesis or Dissertation |
| Source | http://eprints.nottingham.ac.uk/49128/ |
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