Key enzymatic processes use the nonequilibrium error correction mechanism called kinetic proofreading to enhance their specificity. The applicability of traditional proofreading schemes, however, is limited since they typically require dedicated structural features in the enzyme, such as a nucleotide hydrolysis site or multiple intermediate conformations. Here, we explore an alternative conceptual mechanism that achieves error correction by having substrate binding and subsequent product formation occur at distinct physical locations. The time taken by the enzyme-substrate complex to diffuse from one location to another is leveraged to discard wrong substrates. This mechanism does not have the typical structural requirements, making it easier to overlook in experiments. We discuss how the length scales of molecular gradients dictate proofreading performance, and quantify the limitations imposed by realistic diffusion and reaction rates. Our work broadens the applicability of kinetic proofreading and sets the stage for studying spatial gradients as a possible route to specificity.
- Kabir Husain
- Arvind Murugan
- Rob Phillips
- Rob Phillips
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
- Ahmet Yildiz, University of California, Berkeley, United States
- Received: June 26, 2020
- Accepted: December 24, 2020
- Accepted Manuscript published: December 24, 2020 (version 1)
© 2020, Galstyan et al.
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