title: 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.
authors: The SFI Strategic Research Cluster in Solar Energy Conversion, University College Dublin, Belfield, Dublin 4, Ireland.
authors: Morad M
authors: MM
authors: El-Hendawy
authors: Niall J
authors: NJ
authors: English
authors: Damian A
authors: DA
authors: Mooney
mesh_terms: D057486:Carbon Cycle; D002245:Carbon Dioxide / Q000737:chemistry*; D020134:Catalytic Domain; D008956:Models, Chemical; D008958:Models, Molecular; D008968:Molecular Conformation; D011789:Quantum Theory; D012273:Ribulose-Bisphosphate Carboxylase / Q000737:chemistry*
chemical_list: D002245:Carbon Dioxide; D012273:Ribulose-Bisphosphate Carboxylase
references: J Chem Theory Comput. 2011 Apr 12;7(4):1102-8
references: 26606358
references: Biochemistry. 1998 Nov 3;37(44):15414-22
references: 9799503
references: Nature. 2006 Jun 22;441(7096):940-1
references: 16791182
references: J Exp Bot. 2009;60(8):2235-48
references: 19395390
references: Phys Rev B Condens Matter. 1988 Jan 15;37(2):785-789
references: 9944570
references: J Exp Bot. 2003 May;54(386):1321-33
references: 12709478
references: Photosynth Res. 2007 Oct;94(1):121-43
references: 17665149
references: J Exp Bot. 2008;59(7):1581-95
references: 18436544
references: Science. 2006 Jan 27;311(5760):484-9
references: 16439654
references: J Comput Chem. 2003 Apr 30;24(6):760-9
references: 12666168
references: J Mol Model. 2007 Dec;13(12):1173-213
references: 17828561
references: Phys Rev B Condens Matter. 1992 Jun 15;45(23):13244-13249
references: 10001404
references: Annu Rev Plant Biol. 2002;53:449-75
references: 12221984
references: Chem Rev. 2005 Aug;105(8):2999-3093
references: 16092826
references: Proteins. 2001 Nov 15;45(3):183-9
references: 11599021
references: J Exp Bot. 2000 Feb;51 Spec No:399-406
references: 10938848
references: Annu Rev Biophys Biomol Struct. 2000;29:291-325
references: 10940251
references: J Am Chem Soc. 2008 Nov 12;130(45):15063-80
references: 18855361
references: J Phys Chem B. 2009 Jan 22;113(3):809-17
references: 19117385
references: Plant Cell Environ. 2007 Sep;30(9):1086-106
references: 17661749
references: PLoS Comput Biol. 2011 Jul;7(7):e1002096
references: 21789034
references: Eur J Biochem. 1977 Nov 1;80(2):319-24
references: 923582
references: J Mol Biol. 1996 May 31;259(1):160-74
references: 8648644
references: Phys Rev Lett. 1996 Oct 28;77(18):3865-3868
references: 10062328
references: Biochemistry. 2007 Dec 25;46(51):14838-44
references: 18044969
references: Chem Rev. 2012 Jan 11;112(1):632-72
references: 21866983
references: J Chem Phys. 2005 Feb 22;122(8):84119
references: 15836032