Molecular dynamics in cytochrome c oxidase Mössbauer spectra deconvolution

• Published in: Biochemical and biophysical research communications 2011-01, Vol.404 (1), p.438-442
• Main Authors: Bossis, Fabrizio, Palese, Luigi L.
• Format: Article
• Language: English
• Subjects: Cytochrome c oxidase; Cytochromes c - chemistry; Heme iron; Molecular dynamics; Molecular Dynamics Simulation; Mössbauer spectra; Paracoccus denitrificans - enzymology; Protein Conformation; Spectral deconvolution; Spectroscopy, Mossbauer
• ISSN: 0006-291X; 1090-2104
• DOI: 10.1016/j.bbrc.2010.11.140

► Cytochrome c oxidase molecular dynamics serve to predict Mössbauer lineshape widths. ► Half height widths are used in modeling of Lorentzian doublets. ► Such spectral deconvolutions are useful in detecting the enzyme intermediates. In this work low temperature molecular dynamics simulations of cytochrome c oxidase are used to predict an experimentally observable, namely Mössbauer spectra width. Predicted lineshapes are used to model Lorentzian doublets, with which published cytochrome c oxidase Mössbauer spectra were simulated. Molecular dynamics imposed constraints to spectral lineshapes permit to obtain useful information, like the presence of multiple chemical species in the binuclear center of cytochrome c oxidase. Moreover, a benchmark of quality for molecular dynamic simulations can be obtained. Despite the overwhelming importance of dynamics in electron–proton transfer systems, limited work has been devoted to unravel how much realistic are molecular dynamics simulations results. In this work, molecular dynamics based predictions are found to be in good agreement with published experimental spectra, showing that we can confidently rely on actual simulations. Molecular dynamics based deconvolution of Mössbauer spectra will lead to a renewed interest for application of this approach in bioenergetics.