title: On dioxygen permeation through a dehydrogenase-pyrroloquinoline quinone complex. A molecular-dynamics investigation.
abstract: 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 (O2 ), solvated with TIP3 water in periodic boxes, was subjected to random-acceleration molecular dynamics (RAMD). It was found that O2 leaves the active binding pocket, in front of PQQ, to get to the solvent, as easily as with a variety of other O2 -activating enzymes, O2 carriers, and gas-sensing proteins. The shortest pathway, orthogonal to the center of the mean plane of PQQ, was largely preferred by O2 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.
authors.affiliation: Accademia Lucchese di Scienze, Lettere e Arti, Classe di Scienze, Palazzo Ducale, Lucca I-55100 (phone/fax: +39-0583-417336). francesco.pietra@accademialucchese.it.
authors.forename: Francesco
authors.initials: F
authors.lastname: Pietra
mesh_terms: D056004:Molecular Dynamics Simulation; D010088:Oxidoreductases / Q000737:chemistry* / Q000378:metabolism; D010100:Oxygen / Q000737:chemistry* / Q000378:metabolism; D045542:PQQ Cofactor / Q000737:chemistry* / Q000378:metabolism
chemical_list: D045542:PQQ Cofactor; D010088:Oxidoreductases; D010100:Oxygen
keywords: Dioxygen permeation; Klebsiella pneumoniae enzymes; Molecular-dynamics calculations; PQQ Cofactor; PqqC Quinoprotein dehydrogenase; Proteins; Random-acceleration molecular dynamics (RAMD)