Molecular Dynamics Simulation of Nitrobenzene Dioxygenase Using AMBER Force Field

Journal of Chemical Theory and Computation vol. 10  p. 2246-2254  DOI: 10.1021/ct500205z
PMID/PMCID: PMC4059247 Published: 2014-06-10 

Anna Pabis, Inacrist Geronimo, Darrin M. York [ ] , Piotr Paneth

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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.