Kinetic Proofreading using Substrate Gradients and Enzyme Diffusion

Abstract

Low error rates in many of the enzymatic processes in biology, such as translation or DNA replication, are attained by employing the nonequilibrium error correction mechanism called kinetic proofreading. Kinetic proofreading operates by delaying product formation through the introduction of additional biochemical intermediates, giving the enzyme more than one chance to discard the non-cognate substrate before reaching its catalytically active state. The requirements of having multiple biochemically distinct intermediates and direct coupling to NTP hydrolysis, however, limit the flexibility and performance scope of traditional proofreading schemes. In our work, we propose an alternative conceptual mechanism of enzymatic error correction where the necessary delay between initial substrate binding and product formation events is achieved by having them occur at distinct physical locations. Specifically, if the substrates are localized primarily at one end of the physical compartment and enzyme activation takes place only at the other end, then the time that it takes for the enzyme to diffuse the distance between these ends can be leveraged to perform efficient proofreading. Importantly, this mechanism requires neither multiple biochemical intermediates nor the presence of an ATP binding site on the enzyme, making its performance easily adaptable through the tuning of the system's characteristic length scales. We discuss how the tuning of these length scales changes the fidelity, speed and energy dissipation of the mechanism, and propose biological examples of its possible implementation in the cell.

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