title: On the Permeation by Dioxygen of the Cofactor-Independent Unusual Oxygenase RhCC, in Complex with Substrate 4-Hydroxyphenylenolpyruvate. A Molecular Dynamics Investigation.
abstract: 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 O2 molecule placed above 4HPP, this model evolved with O2 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 O2 molecules in the bulk solvent, unbiased MD led to O2 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.
authors.affiliation: Accademia Lucchese di Scienze, Lettere e Arti, Classe di Scienze, Palazzo Ducale, IT-55100, Lucca, Italy.
authors.forename: Francesco
authors.initials: F
authors.lastname: Pietra
mesh_terms: D056004:Molecular Dynamics Simulation; D010100:Oxygen / Q000737:chemistry / Q000378:metabolism*; D010105:Oxygenases / Q000737:chemistry / Q000378:metabolism*; D010667:Phenylpyruvic Acids / Q000737:chemistry / Q000378:metabolism*; D012984:Software
chemical_list: D010667:Phenylpyruvic Acids; D010105:Oxygenases; D010100:Oxygen
keywords: Gas permeation of proteins; Molecular dynamics; Oxygenases; Random-acceleration molecular dynamics; Tautomerases