ArticleJournal of chemical theory and computation2014
Molecular Dynamics Simulation of Nitrobenzene Dioxygenase Using AMBER Force Field.
Article in Journal of chemical theory and computation, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Regioselective Sesquiterpene Hydroxylation Directed by Tunnel Remodeling in Rieske Oxygenases.JACS Au · 2026Article
- Design, Synthesis and Herbicidal Activity of 1,2,4-Oxadiazole Compounds as Novel Light-Dependent Protochlorophyllide Oxidoreductase Inhibitors.Molecules (Basel, Switzerland) · 2025Article
- Origins of Catalysis in Non-Heme Fe(II)/2-Oxoglutarate-Dependent Histone Lysine Demethylase KDM4A with Differently Methylated Histone H3 Peptides.Chemistry (Weinheim an der Bergstrasse, Germany) · 2025Article
- Elucidating the Role of OACS environmental Au · 2024Article
- Structural and molecular dynamics simulation studies of CBL-interacting protein kinase CIPK and its complexes related to plant salinity stress.Journal of molecular modeling · 2024Article
- Semi-rational design of nitroarene dioxygenase for catalytic ability toward 2,4-dichloronitrobenzene.Applied and environmental microbiology · 2024Article
- Unusual catalytic strategy by non-heme Fe(ii)/2-oxoglutarate-dependent aspartyl hydroxylase AspH.Chemical science · 2024Article
- Effects of Active-Center Reduction of Plant-Type Ferredoxin on Its Structure and Dynamics: Computational Analysis Using Molecular Dynamics Simulations.International journal of molecular sciences · 2022Article
- Elucidating the Role of OACS environmental Au · 2022Article
- Substrate-Specific Coupling of OACS catalysis · 2022Article
- Role of Structural Dynamics in Selectivity and Mechanism of Non-heme Fe(II) and 2-Oxoglutarate-Dependent Oxygenases Involved in DNA Repair.ACS central science · 2020Article
- VR-SCOSMO: A smooth conductor-like screening model with charge-dependent radii for modeling chemical reactions.The Journal of chemical physics · 2016Article
Corrections and comments
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Authors and funding
4 authors.
Funding
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.
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