Paper Citing NAMD - Abstract
Bernini, Caterina; Pogni, Rebecca; Basosi, Riccardo; Sinicropi, Adalgisa
Prediction of hydrogen-bonding networks around tyrosyl radical in P. eryngii versatile peroxidase W164Y variants: a QM/MMMD study
MOLECULAR SIMULATION, 40:485-490, MAY 3 2014
Quantum mechanics/molecular mechanics molecular dynamics simulations have been used to predict the hydrogen-bonding networks in the active site of three double variants of Pleurotus eryngii versatile peroxidase containing a redox-active tyrosine in place of a tryptophan residue in position 164. The adopted computational strategy has proved to be adequate to correctly reproduce the hydrogen-bonding environment of tyrosyl radical (Tyr) in the single W164Y variant of the enzyme that has been directly identified by electron paramagnetic resonance spectroscopy. In this study, we have investigated the effect of the mutation of a specific amino acid in the local environment of tyrosine 164. We show that the substitution of arginine 257 with a glutamic acid, a leucine or an alanine residue is able to induce the stabilisation of different hydrogen-bonding networks involving Tyr that can potentially affect its physico-chemical properties.
