Paper Citing NAMD - Abstract
Pietra, Francesco
On the Permeation by Dioxygen of the Cofactor-Independent Unusual Oxygenase RhCC, in Complex with Substrate 4-Hydroxyphenylenolpyruvate. A Molecular Dynamics Investigation
CHEMISTRY & BIODIVERSITY, 13:331-335, MAR 2016
This work deals with a trimeric bacterial protein, RhCC, which, although belonging to the tautomerase superfamily, shows oxygenase activity. A model of the complex from RhCC and substrate 4-hydroxyphenylenolpyruvate (4HPP), fitting the observation of extra electron densities from X-ray diffraction of the crystal, could be built by autodocking. When subjected to molecular dynamics (MD) aided by an external random force applied to a O-2 molecule placed above 4HPP, this model evolved with O-2 egressing toward the bulk solvent from two nearly opposite gates. These were located between the nearly parallel helices 75-91 and 15-33 of either chain C (gate SE) or chain B (gate FL). Alternatively, with four O-2 molecules in the bulk solvent, unbiased MD led to O-2 entering the protein from gate SE and getting to 4HPP, while forming a stabilizing salt bridge between the 4HPP carboxylate and P1.C +NH2, thus providing scientific ground for a refined model of the complex.
