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

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.

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

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Acknowledgments

The authors acknowledge useful conversations with Jacek Dziedzic, Chris-Kriton Skylaris, Peter Haynes, Daniel Cole and Nicholas Hine. The research was funded primarily by the Science Foundation Ireland (SFI)-funded Solar Energy Conversion (SEC) research cluster [Grant No. 07/SRC/B1160], with input from SFI Research Frontiers Programme 10/RFP/MTR2868. We thank SFI for the provision of funds for high-performance computing facilities and the Irish Centre for High-End Computing (ICHEC) for computational resources. The authors acknowledge the support of industry partners to the SEC cluster: SolarPrint, Celtic Catalysts, Glantreo, Mainstream Renewable Power, Kingspan and SSE Renewables.

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Correspondence to Niall J. English or Damian A. Mooney.

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El-Hendawy, M.M., English, N.J. & Mooney, D.A. Comparative studies for evaluation of CO2 fixation in the cavity of the Rubisco enzyme using QM, QM/MM and linear-scaling DFT methods. J Mol Model 19, 2329–2334 (2013). https://doi.org/10.1007/s00894-013-1773-4

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  • DOI: https://doi.org/10.1007/s00894-013-1773-4

Keywords

  • Carboxylation step
  • Linear-scaling DFT
  • PM6
  • QM/MM
  • Rubisco