title: Mechanisms of Enhanced Catalysis in Enzyme-DNA Nanostructures Revealed through Molecular Simulations and Experimental Analysis.
abstract: Understanding and controlling the molecular interactions between enzyme substrates and DNA nanostructures has important implications in the advancement of enzyme-DNA technologies as solutions in biocatalysis. Such hybrid nanostructures can be used to create enzyme systems with enhanced catalysis by controlling the local chemical and physical environments and the spatial organization of enzymes. Here we have used molecular simulations with corresponding experiments to describe a mechanism of enhanced catalysis due to locally increased substrate concentrations. With a series of DNA nanostructures conjugated to horseradish peroxidase, we show that binding interactions between substrates and the DNA structures can increase local substrate concentrations. Increased local substrate concentrations in HRP(DNA) nanostructures resulted in 2.9- and 2.4-fold decreases in the apparent Michaelis constants of tetramethylbenzidine and 4-aminophenol, substrates of HRP with tunable binding interactions to DNA nanostructures with dissociation constants in the micromolar range. Molecular simulations and kinetic analysis also revealed that increased local substrate concentrations enhanced the rates of substrate association. Identification of the mechanism of increased local concentration of substrates in close proximity to enzymes and their active sites adds to our understanding of nanostructured biocatalysis from which we can develop guidelines for enhancing catalysis in rationally designed systems.
authors.affiliation: The Department of Chemical and Environmental Engineering, University of California-Riverside, 900 University Avenue, Riverside, CA, 92521, USA.
authors.forename: Yingning
authors.initials: Y
authors.lastname: Gao
authors.affiliation: The Department of Chemistry, University of Californi-Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA.
authors.forename: Christopher C
authors.initials: CC
authors.lastname: Roberts
authors.affiliation: The Department of Chemical and Environmental Engineering, University of California-Riverside, 900 University Avenue, Riverside, CA, 92521, USA.
authors.forename: Aaron
authors.initials: A
authors.lastname: Toop
authors.affiliation: The Department of Chemistry, University of Californi-Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA.
authors.forename: Chia-En A
authors.initials: CE
authors.lastname: Chang
authors.affiliation: The Department of Chemical and Environmental Engineering, University of California-Riverside, 900 University Avenue, Riverside, CA, 92521, USA. iwheeldon@engr.ucr.edu.
authors.forename: Ian
authors.initials: I
authors.lastname: Wheeldon
mesh_terms: D001560:Benzidines / Q000378:metabolism; D055162:Biocatalysis; D001709:Biotechnology / Q000379:methods*; D020134:Catalytic Domain; D004247:DNA / Q000378:metabolism*; D004798:Enzymes / Q000378:metabolism*; D006735:Horseradish Peroxidase / Q000378:metabolism; D007700:Kinetics; D008956:Models, Chemical; D049329:Nanostructures / Q000737:chemistry*
chemical_list: D001560:Benzidines; D004798:Enzymes; C021758:3,3',5,5'-tetramethylbenzidine; D004247:DNA; D006735:Horseradish Peroxidase
keywords: Brownian dynamics; DNA nanostructures; bimolecular association; biocatalysis; enzymes