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Kinetic Proofreading using Substrate Gradients and Enzyme Diffusion

Galstyan, Vahe and Husain, Kabir and Xiao, Fangzhou and Murugan, Arvind and Phillips, Rob (2020) Kinetic Proofreading using Substrate Gradients and Enzyme Diffusion. Biophysical Journal, 118 (3). 573a-574a. ISSN 0006-3495. https://resolver.caltech.edu/CaltechAUTHORS:20200210-085326975

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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.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1016/j.bpj.2019.11.3118DOIArticle
ORCID:
AuthorORCID
Galstyan, Vahe0000-0001-7073-9175
Xiao, Fangzhou0000-0002-5001-5644
Phillips, Rob0000-0003-3082-2809
Additional Information:© 2020 Biophysical Society. Available online 7 February 2020.
Issue or Number:3
Record Number:CaltechAUTHORS:20200210-085326975
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20200210-085326975
Official Citation:Vahe Galstyan, Kabir Husain, Fangzhou Xiao, Arvind Murugan, Rob Phillips, Kinetic Proofreading using Substrate Gradients and Enzyme Diffusion, Biophysical Journal, Volume 118, Issue 3, Supplement 1, 2020, Pages 573a-574a, ISSN 0006-3495, https://doi.org/10.1016/j.bpj.2019.11.3118. (http://www.sciencedirect.com/science/article/pii/S0006349519340512)
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:101190
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:10 Feb 2020 17:02
Last Modified:10 Feb 2020 17:02

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