Diffusive transport phenomena in artificial enzyme cascades on scaffolds

Idan, Ofer; Hess, Henry

doi:10.1038/nnano.2012.222

Cited by 31 publications

(43 citation statements)

References 7 publications

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“…16). Idan and Hess1827 suggested that the aggregation of multiple enzyme pairs on a large scaffold can lead to throughput enhancement. The colocalization of enzymes does ensure the fast consumption of intermediate and prevent it escaping28, but the work presented by Fu et al 11.…”

Section: Resultsmentioning

confidence: 99%

Proximity does not contribute to activity enhancement in the glucose oxidase–horseradish peroxidase cascade

2016

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A proximity effect has been invoked to explain the enhanced activity of enzyme cascades on DNA scaffolds. Using the cascade reaction carried out by glucose oxidase and horseradish peroxidase as a model system, here we study the kinetics of the cascade reaction when the enzymes are free in solution, when they are conjugated to each other and when a competing enzyme is present. No proximity effect is found, which is in agreement with models predicting that the rapidly diffusing hydrogen peroxide intermediate is well mixed. We suggest that the reason for the activity enhancement of enzymes localized by DNA scaffolds is that the pH near the surface of the negatively charged DNA nanostructures is lower than that in the bulk solution, creating a more optimal pH environment for the anchored enzymes. Our findings challenge the notion of a proximity effect and provide new insights into the role of DNA scaffolds.

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Section: Resultsmentioning

confidence: 99%

Proximity does not contribute to activity enhancement in the glucose oxidase–horseradish peroxidase cascade

2016

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“…Our simulations also show that placing the two enzymes a few nanometers apart makes a negligible contribution to product formation on a time scale of seconds. 22 One of the explanations for the increase in throughput of scaffold systems observed in recent experiments is that engineered scaffolds often aggregate a large number of enzyme pairs due to their "ribbon" structure Initially, the reaction rate (black solid line) increases linearly and the product concentration (red dashed line) quadratically with time. On a time scale of hours, the system reaches a steady state and the reaction rate reaches the maximum reaction rate (here limited by the constant production rate of enzyme 1).…”

Section: Resultsmentioning

confidence: 99%

Origins of Activity Enhancement in Enzyme Cascades on Scaffolds

2013

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The concept of "metabolic channeling" as a result of rapid transfer of freely diffusing intermediate substrates between two enzymes on nanoscale scaffolds is examined using simulations and mathematical models. The increase in direct substrate transfer due to the proximity of the two enzymes provides an initial but temporary boost to the throughput of the cascade and loses importance as product molecules of enzyme 1 (substrate molecules of enzyme 2) accumulate in the surrounding container. The characteristic time scale at which this boost is significant is given by the ratio of container volume to the product of substrate diffusion constant and interenzyme distance and is on the order of milliseconds to seconds in some experimental systems. However, the attachment of a large number of enzyme pairs to a scaffold provides an increased number of local "targets", extending the characteristic time. If substrate molecules for enzyme 2 are sequestered by an alternative reaction in the container, a scaffold can result in a permanent boost to cascade throughput with a magnitude given by the ratio of the above-defined time scale to the lifetime of the substrate molecule in the container. Finally, a weak attractive interaction between substrate molecules and the scaffold creates a "virtual compartment" and substantially accelerates initial throughput. If intermediate substrates can diffuse freely, placing individual enzyme pairs on scaffolds is only beneficial in large cells, unconfined extracellular spaces or in systems with sequestering reactions.

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“…However, the chemical attachment of nucleotides to the proteins of interest is not feasible for cellular experiments, therefore, encodable methods must be utilized such as RNA aptamer- protein [49] or zinc finger-DNA [50] interactions. Aldaye and coworkers were able to colocalize proteins involved in hydrogen production in an organelle-like area inside the cell by engineering aptamer domains into the scaffold and fusing aptamer-binding proteins to the proteins of interest.…”

Section: Dna/rna Templated Reactionsmentioning

confidence: 99%

Effective Molarity Redux: Proximity as a Guiding Force in Chemistry and Biology

Hobert

Doerner

Walker

et al. 2013

Israel Journal of Chemistry

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The cell interior is a complex and demanding environment. An incredible variety of molecules jockey to identify the correct position–the specific interactions that promote biology that are hidden among countless unproductive options. Ensuring that the business of the cell is successful requires sophisticated mechanisms to impose temporal and spatial specificity–both on transient interactions and their eventual outcomes. Two strategies employed to regulate macromolecular interactions in a cellular context are co-localization and compartmentalization. Macromolecular interactions can be promoted and specified by localizing the partners within the same subcellular compartment, or by holding them in proximity through covalent or non-covalent interactions with proteins, lipids, or DNA– themes that are familiar to any biologist. The net result of these strategies is an increase in effective molarity: the local concentration of a reactive molecule near its reaction partners. We will focus on this general mechanism, employed by Nature and adapted in the lab, which allows delicate control in complex environments: the power of proximity to accelerate, guide, or otherwise influence the reactivity of signaling proteins and the information that they encode.

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Diffusive transport phenomena in artificial enzyme cascades on scaffolds

Cited by 31 publications

References 7 publications

Proximity does not contribute to activity enhancement in the glucose oxidase–horseradish peroxidase cascade

Proximity does not contribute to activity enhancement in the glucose oxidase–horseradish peroxidase cascade

Origins of Activity Enhancement in Enzyme Cascades on Scaffolds

Effective Molarity Redux: Proximity as a Guiding Force in Chemistry and Biology

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