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Size limits the sensitivity of kinetic schemes

Living things benefit from exquisite molecular sensitivity in many of their key processes, including DNA replication, transcription and translation, chemical sensing, and morphogenesis. At thermodynamic equilibrium, the basic biophysical mechanism for sensitivity is cooperative binding, for which it...

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Autores principales: Owen, Jeremy A., Horowitz, Jordan M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9995461/
https://www.ncbi.nlm.nih.gov/pubmed/36890153
http://dx.doi.org/10.1038/s41467-023-36705-8
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author Owen, Jeremy A.
Horowitz, Jordan M.
author_facet Owen, Jeremy A.
Horowitz, Jordan M.
author_sort Owen, Jeremy A.
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description Living things benefit from exquisite molecular sensitivity in many of their key processes, including DNA replication, transcription and translation, chemical sensing, and morphogenesis. At thermodynamic equilibrium, the basic biophysical mechanism for sensitivity is cooperative binding, for which it can be shown that the Hill coefficient, a sensitivity measure, cannot exceed the number of binding sites. Generalizing this fact, we find that for any kinetic scheme, at or away from thermodynamic equilibrium, a very simple structural quantity, the size of the support of a perturbation, always limits the effective Hill coefficient. We show how this bound sheds light on and unifies diverse sensitivity mechanisms, including kinetic proofreading and a nonequilibrium Monod-Wyman-Changeux (MWC) model proposed for the E. coli flagellar motor switch, representing in each case a simple, precise bridge between experimental observations and the models we write down. In pursuit of mechanisms that saturate the support bound, we find a nonequilibrium binding mechanism, nested hysteresis, with sensitivity exponential in the number of binding sites, with implications for our understanding of models of gene regulation and the function of biomolecular condensates.
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spelling pubmed-99954612023-03-10 Size limits the sensitivity of kinetic schemes Owen, Jeremy A. Horowitz, Jordan M. Nat Commun Article Living things benefit from exquisite molecular sensitivity in many of their key processes, including DNA replication, transcription and translation, chemical sensing, and morphogenesis. At thermodynamic equilibrium, the basic biophysical mechanism for sensitivity is cooperative binding, for which it can be shown that the Hill coefficient, a sensitivity measure, cannot exceed the number of binding sites. Generalizing this fact, we find that for any kinetic scheme, at or away from thermodynamic equilibrium, a very simple structural quantity, the size of the support of a perturbation, always limits the effective Hill coefficient. We show how this bound sheds light on and unifies diverse sensitivity mechanisms, including kinetic proofreading and a nonequilibrium Monod-Wyman-Changeux (MWC) model proposed for the E. coli flagellar motor switch, representing in each case a simple, precise bridge between experimental observations and the models we write down. In pursuit of mechanisms that saturate the support bound, we find a nonequilibrium binding mechanism, nested hysteresis, with sensitivity exponential in the number of binding sites, with implications for our understanding of models of gene regulation and the function of biomolecular condensates. Nature Publishing Group UK 2023-03-08 /pmc/articles/PMC9995461/ /pubmed/36890153 http://dx.doi.org/10.1038/s41467-023-36705-8 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Owen, Jeremy A.
Horowitz, Jordan M.
Size limits the sensitivity of kinetic schemes
title Size limits the sensitivity of kinetic schemes
title_full Size limits the sensitivity of kinetic schemes
title_fullStr Size limits the sensitivity of kinetic schemes
title_full_unstemmed Size limits the sensitivity of kinetic schemes
title_short Size limits the sensitivity of kinetic schemes
title_sort size limits the sensitivity of kinetic schemes
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9995461/
https://www.ncbi.nlm.nih.gov/pubmed/36890153
http://dx.doi.org/10.1038/s41467-023-36705-8
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