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Computational study of the structure and electronic circular dichroism spectroscopy of blue copper proteins

Do, Hainam; Deeth, Robert J.; Besley, Nicholas A.

Authors

Hainam Do

Robert J. Deeth

Nicholas A. Besley



Abstract

The calculation of the electronic circular dichroism (CD) spectra of the oxidised form of the blue copper proteins plastocyanin and cucumber basic protein and the relationship between the observed spectral features and the structure of the active site of the protein is investigated. Excitation energies and transition strengths are computed using multi reference configuration interaction, and it is shown that computed spectra based on coordinates from the crystal structure or a single structure optimised in quantum mechanics/molecular mechanics (QM/MM) or ligand field molecular mechanics (LFMM) are qualitatively incorrect. In particular, the rotational strength of the ligand to metal charge transfer band is predicted to be too small or have the incorrect sign. By considering calculations on active site models with modified structures it is shown that the intensity of this band is sensitive to the non-planarity of the histidine and cysteine ligands coordinated to copper. Calculation of the ultraviolet absorption and CD spectra based upon averaging over many structures drawn from a LFMM molecular dynamics simulation are in good agreement with experiment, and superior to analogous calculations based upon structures from a classical molecular dynamics simulation. This provides evidence that the LFMM force field provides an accurate description of the molecular dynamics of these proteins.

Journal Article Type Article
Publication Date Jun 17, 2013
Journal Journal of Physical Chemistry B
Print ISSN 1520-6106
Electronic ISSN 1520-52707
Publisher American Chemical Society
Peer Reviewed Peer Reviewed
Volume 117
Issue 27
Institution Citation Do, H., Deeth, R. J., & Besley, N. A. (2013). Computational study of the structure and electronic circular dichroism spectroscopy of blue copper proteins. Journal of Physical Chemistry B, 117(27), doi:10.1021/jp404107j
DOI https://doi.org/10.1021/jp404107j
Keywords plastocyanin, cucumber basic protein, ligand-field molecular mechanics, molecular dynamics
Publisher URL http://pubs.acs.org/doi/abs/10.1021/jp404107j
Copyright Statement Copyright information regarding this work can be found at the following address: http://eprints.nottingh.../end_user_agreement.pdf

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Copyright Statement
Copyright information regarding this work can be found at the following address: http://eprints.nottingham.ac.uk/end_user_agreement.pdf





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