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

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    0370744 - ÚOCHB 2012 RIV DE eng J - Článek v odborném periodiku
    Heimdal, J. - Kaukonen, M. - Srnec, Martin - Rulíšek, Lubomír - Ryde, U.
    Reduction Potentials and Acidity Constants of Mn Superoxide Dismutase Calculated by QM/MM Free-Energy Methods.
    ChemPhysChem. Roč. 12, č. 17 (2011), s. 3337-3347. ISSN 1439-4235. E-ISSN 1439-7641
    Grant CEP: GA MŠMT LC512
    Výzkumný záměr: CEZ:AV0Z40550506
    Klíčová slova: acidity constants * enzymes * free-energy * perturbation * molecular modelling * reduction potentials
    Kód oboru RIV: CF - Fyzikální chemie a teoretická chemie
    Impakt faktor: 3.412, rok: 2011

    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 PoissonBoltzmann 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 0.260.40 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 pKa 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.
    Trvalý link: http://hdl.handle.net/11104/0204450

     
     
Počet záznamů: 1  

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