Comparative studies for evaluation of CO2 fixation in the cavity of the Rubisco enzyme using QM, QM/MM and linear-scaling DFT methods

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Title: Comparative studies for evaluation of CO2 fixation in the cavity of the Rubisco enzyme using QM, QM/MM and linear-scaling DFT methods
Authors: El-Hendawy, Morad M.
English, Niall J.
Mooney, Damian A.
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Date: Jun-2013
Online since: 2014-02-28T04:00:08Z
Abstract: We evaluate the minimum energy configuration (MM) and binding free energy (QM/MM and QM) of CO2 to Rubisco, of fundamental importance to the carboxylation step of the reaction. Two structural motifs have been used to achieve this goal, one of which starts from the initial X-ray Protein Data Bank structure of Rubisco's active centre (671 atoms), and the other is a simplified, smaller model (77 atoms) which has been used most successfully, thus far, for study. The small model is subjected to quantum chemical density functional theory (DFT) studies, both in vacuo and using implicit solvation. The effects of the protein environment are also included by means of a hybrid quantum mechanical/molecular mechanical (QM/MM) approach, using PM6/AMBER and B3LYP/AMBER schemes. Finally, linear-scaling DFT methods have also been applied to evaluate energetic features of the large motif, and the result obtained for the binding free energy of the CO2 underlines the importance of the accurate modelling of the surrounding protein milieu using a full DFT description.
Type of material: Journal Article
Publisher: Springer-Verlag
Journal: Journal of Molecular Modeling
Volume: 19
Issue: 6
Start page: 2329
End page: 2334
Copyright (published version): 2013, Springer-Verlag
Keywords: Carboxylation stepLinear-scaling DFTPM6QM/MMRubisco
DOI: 10.1007/s00894-013-1773-4
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Language: en
Status of Item: Not peer reviewed
Appears in Collections:Chemical and Bioprocess Engineering Research Collection

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