A QM/MM study of the nature of the entatic state in plastocyanin. Issue 16 (14th November 2016)

• Record Type: Journal Article
• Authors: Hurd, Catherine A.; Besley, Nicholas A.; Robinson, David
• Other Names: Hirst Jonathan guestEditor.; Im Wonpil guestEditor.; Shea Joan‐Emma guestEditor.
• Is Part Of: Journal of computational chemistry. Volume 38:Issue 16(2017)
• Page Start: 1431
• Page End: 1437
• Publication Date: 2016-11-14
• Subjects: QM/MM -- electron transfer -- plastocyanin; Chemistry -- Data processing -- Periodicals; 542.85
• DOI: 10.1002/jcc.24666
• Languages: English
• ISSNs: 0192-8651

Abstract

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. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. Abstract : The nature of the entatic state in plastocyanin is studied through density functional theory‐based QM/MM calculations. 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. Accurate calculation of the reorganization energy for the electron transfer protein requires conformation averaging and large region around the active site to be treated at the quantum mechanical level.