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 CO 2 to Rubisco, of fundamental importance to the carboxylation step of the reaction catalysed by Rubisco. 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 CO 2 underlines the importance of the accurate modelling of the surrounding protein milieu using a full DFT description.

Implicit and explicit solvent models for modeling a bifunctional arene ruthenium hydrogen‐storage catalyst: A classical and ab initio molecular simulation study

“…However, its ability to allow for full‐PBC treatment and size‐convergence of the energetic (van der Waals) interactions is sine qua non for a more accurate energetic estimate (again, quite independent of underlying structural considerations); the use of Born or Poisson–Boltzmann electrostatics on explicitly solvated configurations is (arguably) optimal and to be encouraged; naturally, the use of implicit solvation to generate the configurations in the first place is (arguably grossly) incorrect, whether by MD or other methods. The use of PBC implementations of linear‐scaling, dispersion‐corrected DFT to generate realistic configurations, for example, via AIMD, with sufficient numbers of atoms to achieve essentially size‐independent structures and converged interaction energies is an important goal for future progress in this area.…”

“…Theoretically, one may study these solute–solvent interactions using quantum mechanical (QM) methods, for example, DFT, or classical molecular simulation, for example, molecular dynamics (MD); also possible are mixed quantum‐classical methods (QM/MM), but linear‐scaling DFT methods are becoming comparatively more attractive in this latter respect . In the traditional QM approach, it is computationally and operationally prohibitive to model more than a very limited number of solvent molecules interacting with the solute; this approach means that second or successive coordination “layers” of solvent molecules cannot be realistically models (under the perhaps heroic assumption that a primary layer can even be represented explicitly); even so, DFT functionals have their own drawbacks per se and are often sui generis for accurate representation of specific classes of compounds.…”

Magnesium-based systems for carbon dioxide capture, storage and recycling: from leaves to synthetic nanostructured materials

“…86 The carboxylation and cleavage of RuBP then take places through a six step reaction Recent calculations indicate that the coordination and activation of CO 2 would happens through an acid base mechanism given by a concerted action of the RuBP and the water molecule 30 coordinated to Mg 2+ . 86,102 The Gibbs free energy of CO 2 coordination (solvated system) in the (i) step has been calculated to be of 21 kJ mol -1 by means of quantum mechanics calculations (PBE-D). 102 The structure around Mg 2+ in the transition state that precedes the RuBP cleavage (step v) is reported in Figure 5d, e 35 and f. This transition state is estimated to be about 100 kJ mol -1 higher in energy with respect to step (i).…”

“…86,102 The Gibbs free energy of CO 2 coordination (solvated system) in the (i) step has been calculated to be of 21 kJ mol -1 by means of quantum mechanics calculations (PBE-D). 102 The structure around Mg 2+ in the transition state that precedes the RuBP cleavage (step v) is reported in Figure 5d, e 35 and f. This transition state is estimated to be about 100 kJ mol -1 higher in energy with respect to step (i). In these figures, It is evident that Mg 2+ is in a distorted octahedral coordination.…”

Applications of large-scale density functional theory in biology

“…Furthermore, by decomposing the total protein contribution to binding into intermolecular and intramolecular contributions, we demonstrated that ligand discrimination is dominated by interactions between the charged O 2 molecule and the protein and that steric effects are negligible. Similar methods were used in a study of the CO 2 fixation energy in the ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) magnesium-based enzyme where it was shown that long-ranged interactions between CO 2 and the protein are important determinants of binding [233].…”