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A QM/MM study of the nature of the entatic state in plastocyanin

Hurd, Catherine A.; Besley, Nicholas A.; Robinson, David

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Authors

Catherine A. Hurd

Nicholas A. Besley

David Robinson



Abstract

Plastocyanin is a copper containing protein that is involved in the electron transfer process in photosynthetic organisms. The active site of plastocyanin is described as an entatic state whereby its structure represents a compromise between the structures favored by the oxidized and reduced forms. In this study the nature of the entatic state is investigated through density functional theory based hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations. The strain energy is computed to be 12.8 kcal/mol and 14.5 kcal/mol for the oxidized and reduced forms of the protein, indicating that the active site has an intermediate structure. It is shown that the energy gap between the oxidized and reduced forms varies significantly with the fluctuations in the structure of the active site at room temperature. An accurate determination of the reorganization energy requires averaging over conformation and a large region of the protein around the active site to be treated at the quantum mechanical level.

Citation

Hurd, C. A., Besley, N. A., & Robinson, D. (in press). A QM/MM study of the nature of the entatic state in plastocyanin. Journal of Computational Chemistry, https://doi.org/10.1002/jcc.24666

Journal Article Type Article
Acceptance Date Oct 27, 2016
Online Publication Date Nov 14, 2016
Deposit Date Nov 30, 2016
Publicly Available Date Nov 30, 2016
Journal Journal of Computational Chemistry
Print ISSN 0192-8651
Electronic ISSN 1096-987X
Publisher Wiley
Peer Reviewed Peer Reviewed
DOI https://doi.org/10.1002/jcc.24666
Keywords QM/MM, Electron transfer, Plastocyanin
Public URL https://nottingham-repository.worktribe.com/output/828723
Publisher URL http://onlinelibrary.wiley.com/doi/10.1002/jcc.24666/full

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