Reduction Potentials and Acidity Constants of Mn Superoxide Dismutase Calculated by QM/MM Free‐Energy Methods

Abstract

We used two theoretical methods to estimate reduction potentials and acidity constants in Mn superoxide dismutase (MnSOD), namely combined quantum mechanical and molecular mechanics (QM/MM) thermodynamic cycle perturbation (QTCP) and the QM/MM-PBSA approach. In the latter, QM/MM energies are combined with continuum solvation energies calculated by solving the Poisson-Boltzmann equation (PB) or by the generalised Born approach (GB) and non-polar solvation energies calculated from the solvent-exposed surface area. We show that using the QTCP method, we can obtain accurate and precise estimates of the proton-coupled reduction potential for MnSOD, 0.30±0.01 V, which compares favourably with experimental estimates of 0.26-0.40 V. However, the calculated potentials depend strongly on the DFT functional used: The B3LYP functional gives 0.6 V more positive potentials than the PBE functional. The QM/MM-PBSA approach leads to somewhat too high reduction potentials for the coupled reaction and the results depend on the solvation model used. For reactions involving a change in the net charge of the metal site, the corresponding results differ by up to 1.3 V or 24 pK(a) units, rendering the QM/MM-PBSA method useless to determine absolute potentials. However, it may still be useful to estimate relative shifts, although the QTCP method is expected to be more accurate.

O2 Activation in Salicylate 1,2-Dioxygenase: A QM/MM Study Reveals the Role of His162

“…The QTCP calculations were performed as has been described before: [72][73][74] First, each state of interest was optimised by QM/MM, keeping system 2 fixed at the crystal structure. Then, the protein was further solvated in an octahedral box of TIP3P water molecules, 75 extending at least 9 Å from the QM/MM system.…”

Large Density-Functional and Basis-Set Effects for the DMSO Reductase Catalyzed Oxo-Transfer Reaction

“…This reflects that the oxidation state of the Mo ion has changed in SP and also partly in TS2, something that is frequently problematic to describe with the DFT functionals, giving a strong dependence on the amount of exact exchange of the functionals. 66,67 To get an indication of which DFT functional gives the more reliable results, we estimated the electronic energies for the stationary structures with the LCCSD(T0) method (correcting for basis set incompleteness and domain errors with an MP2 correction as described in the Methods section). In the LCCSD(T0) calculations, the number of pairs included in the CCSD iterations (and the groups included in the triples list) are controlled by distance criteria.…”

Reorganization Energy for Internal Electron Transfer in Multicopper Oxidases

“…Test calculations at the semiempirical level have shown that this is does not affect the final free energies significantly. 70 The QTCP calculations were performed as previously described, 68,69,71,72 with simple extensions to the QM/MM-2QM case: First, each redox state was optimised by QM/MM-2QM, using a solvated spherical system with a radius of 38 Å. 37 Second, the total system was moved into a periodic octahedral box and was further solvated with water molecules extending at least 9 Å from the original system, giving a total of 12270 water molecules (a set of QTCP calculations in which the solvent shell was increased to 15 Å or 19803 water molecules was also performed).…”

“…77 Finally, T is the temperature and S QM/MM is the entropy, calculated from the frequencies, using a normal-mode harmonicoscillator and ideal-gas approximation. 75 In this investigation, we assume that the contribution from the surrounding protein cancels between the reactant and the product, as has been done before, 72,75 so only the entropy of the isolated QM systems in vacuum was considered. Several variants of QM/MM-PBSA are available.…”