Mechanisms of Enhanced Catalysis in Enzyme-DNA Nanostructures Revealed through Molecular Simulations and Experimental Analysis
Mechanisms of Enhanced Catalysis in Enzyme-DNA Nanostructures Revealed through Molecular Simulations and Experimental Analysis
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DOI：
10.1002/cbic.201600224
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发表时间：
2016-08-03
期刊：
影响因子：
3.2
通讯作者：
Wheeldon, Ian
中科院分区：
文献类型：
--
作者：
Gao, Yingning;Roberts, Christopher C.;Wheeldon, Ian
理解和控制酶底物和DNA纳米结构之间的分子相互作用对酶-DNA技术作为生物催化解决方案的进步具有重要意义。这种混合纳米结构可用于通过控制局部化学和物理环境以及酶的空间组织来产生具有增强的催化作用的酶系统。在这里，我们已经使用了相应的实验分子模拟来描述一种机制，由于局部增加底物浓度的催化增强。与一系列的DNA纳米结构共轭辣根过氧化物酶，我们表明，基板和DNA结构之间的结合相互作用，可以增加本地基板浓度。在HRP（DNA）的纳米结构中的局部底物浓度的增加导致在2.9-和2.4-倍减少的表观米氏常数的四甲基联苯胺和4-氨基苯酚，底物的HRP与可调的结合相互作用的DNA纳米结构的解离常数在微摩尔范围内。分子模拟和动力学分析也表明，增加当地的底物浓度提高底物协会的速度。确定机制的增加本地浓度的底物在接近酶和它们的活性位点增加了我们的理解纳米结构的生物催化，从我们可以制定准则，以提高催化在合理设计的系统。
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.