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Quantifying fluctuations in reversible enzymatic cycles and clocks

Biochemical reactions are fundamentally noisy at a molecular scale. This limits the precision of reaction networks, but it also allows fluctuation measurements that may reveal the structure and dynamics of the underlying biochemical network. Here, we study nonequilibrium reaction cycles, such as the...

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Hauptverfasser: Wierenga, Harmen (VerfasserIn) , Wolde, Pieter Rein ten (VerfasserIn) , Becker, Nils B. (VerfasserIn)
Dokumenttyp: Article (Journal)
Sprache:Englisch
Veröffentlicht: 4 April 2018
In: Physical review
Year: 2018, Jahrgang: 97, Heft: 4
ISSN:2470-0053
DOI:10.1103/PhysRevE.97.042404
Online-Zugang:Verlag, lizenzpflichtig, Volltext: https://doi.org/10.1103/PhysRevE.97.042404
Verlag, lizenzpflichtig, Volltext: https://link.aps.org/doi/10.1103/PhysRevE.97.042404
Volltext
Verfasserangaben:Harmen Wierenga, Pieter Rein ten Wolde, and Nils B. Becker

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520 |a Biochemical reactions are fundamentally noisy at a molecular scale. This limits the precision of reaction networks, but it also allows fluctuation measurements that may reveal the structure and dynamics of the underlying biochemical network. Here, we study nonequilibrium reaction cycles, such as the mechanochemical cycle of molecular motors, the phosphorylation cycle of circadian clock proteins, or the transition state cycle of enzymes. Fluctuations in such cycles may be measured using either of two classical definitions of the randomness parameter, which we show to be equivalent in general microscopically reversible cycles. We define a stochastic period for reversible cycles and present analytical solutions for its moments. Furthermore, we associate the two forms of the randomness parameter with the thermodynamic uncertainty relation, which sets limits on the timing precision of the cycle in terms of thermodynamic quantities. Our results should prove useful also for the study of temporal fluctuations in more general networks. 
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