The energy cost and optimal design of networks for biological discrimination

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dc.citation.articleNumber20210883en_US
dc.citation.issueNumber188en_US
dc.citation.journalTitleJournal of the Royal Society Interfaceen_US
dc.citation.volumeNumber19en_US
dc.contributor.authorYu, Qiweien_US
dc.contributor.authorKolomeisky, Anatoly B.en_US
dc.contributor.authorIgoshin, Oleg A.en_US
dc.contributor.orgBioengineeringen_US
dc.contributor.orgBiosciencesen_US
dc.contributor.orgChemical and Biomolecular Engineeringen_US
dc.contributor.orgChemistryen_US
dc.contributor.orgPhysics and Astronomyen_US
dc.contributor.orgCenter for Theoretical Biological Physicsen_US
dc.date.accessioned2022-04-18T17:17:28Zen_US
dc.date.available2022-04-18T17:17:28Zen_US
dc.date.issued2022en_US
dc.description.abstractMany biological processes discriminate between correct and incorrect substrates through the kinetic proofreading mechanism that enables lower error at the cost of higher energy dissipation. Elucidating physico-chemical constraints for global minimization of dissipation and error is important for understanding enzyme evolution. Here, we identify theoretically a fundamental error–cost bound that tightly constrains the performance of proofreading networks under any parameter variations preserving the rate discrimination between substrates. The bound is kinetically controlled, i.e. completely determined by the difference between the transition state energies on the underlying free energy landscape. The importance of the bound is analysed for three biological processes. DNA replication by T7 DNA polymerase is shown to be nearly optimized, i.e. its kinetic parameters place it in the immediate proximity of the error–cost bound. The isoleucyl-tRNA synthetase (IleRS) of E. coli also operates close to the bound, but further optimization is prevented by the need for reaction speed. In contrast, E. coli ribosome operates in a high-dissipation regime, potentially in order to speed up protein production. Together, these findings establish a fundamental error–dissipation relation in biological proofreading networks and provide a theoretical framework for studying error–dissipation trade-off in other systems with biological discrimination.en_US
dc.identifier.citationYu, Qiwei, Kolomeisky, Anatoly B. and Igoshin, Oleg A.. "The energy cost and optimal design of networks for biological discrimination." <i>Journal of the Royal Society Interface,</i> 19, no. 188 (2022) The Royal Society: https://doi.org/10.1098/rsif.2021.0883.en_US
dc.identifier.doihttps://doi.org/10.1098/rsif.2021.0883en_US
dc.identifier.urihttps://hdl.handle.net/1911/112104en_US
dc.language.isoengen_US
dc.publisherThe Royal Societyen_US
dc.rightsThis is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by the authors.en_US
dc.titleThe energy cost and optimal design of networks for biological discriminationen_US
dc.typeJournal articleen_US
dc.type.dcmiTexten_US
dc.type.publicationpost-printen_US
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