title: On the Permeation by Dioxygen of Urate Oxidase from Aspergillus flavus in Complex with Xanthine Anion: Dioxygen Pathways and a Portrait of the Enzyme Cavities from Molecular Dynamics Simulations in Water Solution.
abstract: This work describes molecular dynamics (MD) simulations in aqueous media for the complex of the homotetrameric urate oxidase (UOX) from Aspergillus flavus with xanthine anion (5) in the presence of dioxygen (O2 ). After 196.6 ns of trajectory from unrestrained MD, a O2 molecule was observed leaving the bulk solvent to penetrate the enzyme between two subunits, A/C. From here, the same O2 molecule was observed migrating, across subunit C, to the hydrophobic cavity that shares residue V227 with the active site. The latter was finally attained, after 378.3 ns of trajectory, with O2 at a bonding distance from 5. The reverse same O2 pathway, from 5 to the bulk solvent, was observed as preferred pathway under random acceleration MD (RAMD), where an external, randomly oriented force was acting on O2 . Both MD and RAMD simulations revealed several cavities populated by O2 during its migration from the bulk solvent to the active site or backwards. Paying attention to the last hydrophobic cavity that apparently serves as O2 reservoir for the active site, it was noticed that its volume undergoes ample fluctuations during the MD simulation, as expected from the thermal motion of a flexible protein, independently from the particular subunit and no matter whether the cavity is filled or not by O2 .
authors.affiliation: Accademia Lucchese di Scienze, Lettere e Arti, Classe di Scienze, Palazzo Ducale, Lucca, I-55100.
authors.forename: Francesco
authors.initials: F
authors.lastname: Pietra
mesh_terms: D000838:Anions / Q000737:chemistry / Q000378:metabolism; D001231:Aspergillus flavus / Q000201:enzymology* / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D015394:Molecular Structure; D010100:Oxygen / Q000737:chemistry / Q000378:metabolism*; D012996:Solutions; D014503:Urate Oxidase / Q000737:chemistry / Q000378:metabolism*; D014867:Water / Q000737:chemistry / Q000378:metabolism; D019820:Xanthine / Q000737:chemistry / Q000378:metabolism*
chemical_list: D000838:Anions; D012996:Solutions; D014867:Water; D019820:Xanthine; D014503:Urate Oxidase; D010100:Oxygen
keywords: Gas permeation of proteins; Molecular dynamics; Protein cavities; Urate oxidase