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Issue 11, 2011
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EPR parameters of amino acid radicals in P. eryngiiversatile peroxidase and its W164Y variant computed at the QM/MM level

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Abstract

Quantum mechanics/molecular mechanics (QM/MM) methods, employing density functional theory (DFT), have been used to compute the electron paramagnetic resonance (EPR) parameters of tryptophan and tyrosyl radical intermediates involved in the catalytic cycle of Pleurotus eryngiiversatile peroxidase (VP) and its W164Y variant, respectively. These radicals have been previously experimentally detected and characterized both in the two-electron and one-electron activated forms of the enzymes. In this work, the well-studied W164 radical in VP has been chosen for calibration purposes because its spectroscopic properties have been extensively studied by multifrequency EPR and ENDOR spectroscopies. Using a B3LYP/CHARMM procedure, appropriately accounting for electrostatic, such as hydrogen bonding, and steric environmental interactions, a good agreement between the calculated and measured EPR parameters for both radicals has been achieved; g-tensors, hyperfine coupling constants (hfcc) and Mulliken spin densities have been correlated to changes in geometries, hydrogen bond networks and electrostatic environment, with the aim of understanding the influence of the protein surroundings on EPR properties. In addition, the present calculations demonstrate, for VP, the formation of a neutral tryptophan radical, hydrogen bonded to the nearby E243, via a stepwise electron and proton transfer with earlier involvement of a short-lived tryptophan cationic species. Instead, for W164Y, the QM/MM dynamics simulation shows that the tyrosine oxidation proceeds via a concerted electron and proton transfer and is accompanied by a significant reorganization of residues and water molecules surrounding the tyrosyl radical.

Graphical abstract: EPR parameters of amino acid radicals in P. eryngiiversatile peroxidase and its W164Y variant computed at the QM/MM level

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Publication details

The article was received on 13 Oct 2010, accepted on 22 Nov 2010 and first published on 07 Feb 2011


Article type: Paper
DOI: 10.1039/C0CP02151B
Citation: Phys. Chem. Chem. Phys., 2011,13, 5078-5098
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    EPR parameters of amino acid radicals in P. eryngiiversatile peroxidase and its W164Y variant computed at the QM/MM level

    C. Bernini, R. Pogni, F. J. Ruiz-Dueñas, A. T. Martínez, R. Basosi and A. Sinicropi, Phys. Chem. Chem. Phys., 2011, 13, 5078
    DOI: 10.1039/C0CP02151B

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