title: Molecular Dynamics Simulation of Nitrobenzene Dioxygenase Using AMBER Force Field.
abstract: Molecular dynamics simulation of the oxygenase component of nitrobenzene dioxygenase (NBDO) system, a member of the naphthalene family of Rieske nonheme iron dioxygenases, has been carried out using the AMBER force field combined with a new set of parameters for the description of the mononuclear nonheme iron center and iron-sulfur Rieske cluster. Simulation results provide information on the structure and dynamics of nitrobenzene dioxygenase in an aqueous environment and shed light on specific interactions that occur in its catalytic center. The results suggest that the architecture of the active site is stabilized by key hydrogen bonds, and Asn258 positions the substrate for oxidation. Analysis of protein-water interactions reveal the presence of a network of solvent molecules at the entrance to the active site, which could be of potential catalytic importance.
authors: Institute of Applied Radiation Chemistry, Lodz University of Technology , Zeromskiego 116, 90-924 Lodz, Poland ; Department of Chemistry and Chemical Biology, Center for Integrative Proteomics Research and BioMaPS Institute for Quantitative Biology, Rutgers, The State University of New Jersey , 174 Frelinghuysen Road, Piscataway, New Jersey 08854, United States.
authors: Anna
authors: A
authors: Pabis
authors: Institute of Applied Radiation Chemistry, Lodz University of Technology , Zeromskiego 116, 90-924 Lodz, Poland.
authors: Inacrist
authors: I
authors: Geronimo
authors: Department of Chemistry and Chemical Biology, Center for Integrative Proteomics Research and BioMaPS Institute for Quantitative Biology, Rutgers, The State University of New Jersey , 174 Frelinghuysen Road, Piscataway, New Jersey 08854, United States.
authors: Darrin M
authors: DM
authors: York
authors: Institute of Applied Radiation Chemistry, Lodz University of Technology , Zeromskiego 116, 90-924 Lodz, Poland.
authors: Piotr
authors: P
authors: Paneth