Journal of Molecular Modeling

, Volume 19, Issue 6, pp 2329–2334

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

Original Paper

DOI: 10.1007/s00894-013-1773-4

Cite this article as:
El-Hendawy, M.M., English, N.J. & Mooney, D.A. J Mol Model (2013) 19: 2329. doi:10.1007/s00894-013-1773-4


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.


77 atom representation of the Rubisco active site used in QM calculations


Carboxylation step Linear-scaling DFT PM6 QM/MM Rubisco 

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  1. 1.The SFI Strategic Research Cluster in Solar Energy ConversionUniversity College DublinDublin 4Ireland
  2. 2.The Centre for Synthesis and Chemical Biology, School of Chemical and Bioprocess EngineeringUniversity College DublinDublin 4Ireland

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