Paper Citing NAMD - Abstract
Pietra, Francesco
On Dioxygen Permeation through a Dehydrogenase-Pyrroloquinoline Quinone Complex. A Molecular-Dynamics Investigation
CHEMISTRY & BIODIVERSITY, 11:209-216, FEB 2014
In this work, an all atom model of the quinoprotein dehydrogenase PqqC in complex with the PQQ (=4,5-dihydro-4,5-dioxo-1H-pyrrolo[2,3-f]quinoline-2,7,9-tricarboxylic acid) cofactor and dioxygen (O-2), solvated with TIP3 water in periodic boxes, was subjected to random-acceleration molecular dynamics (RAMD). It was found that O-2 leaves the active binding pocket, in front of PQQ, to get to the solvent, as easily as with a variety of other O-2-activating enzymes, O-2 carriers, and gas-sensing proteins. The shortest pathway, orthogonal to the center of the mean plane of PQQ, was largely preferred by O-2 over pathways slightly deviating from this line. These observations challenge the interpretation of an impermeable active binding pocket of PqqC-PQQ, as drawn from both X-ray diffraction data of the crystal at low temperature and physiological experimentation.
