Paper Citing NAMD - Abstract
Bossis, Fabrizio; Palese, Luigi L.
Molecular dynamics in cytochrome c oxidase Mossbauer spectra deconvolution
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 404:438-442, JAN 7 2011
In this work low temperature molecular dynamics simulations of cytochrome c oxidase are used to predict an experimentally observable, namely Mossbauer spectra width. Predicted lineshapes are used to model Lorentzian doublets, with which published cytochrome c oxidase Mossbauer 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 Mossbauer spectra will lead to a renewed interest for application of this approach in bioenergetics. (C) 2010 Elsevier Inc. All rights reserved.
