Trade-offs and thermodynamics of energy-relay proofreading

Abstract

Biological processes that are able to discriminate between different molecules consume energy and dissipate heat. They operate at different levels of fidelity and speed, and as a consequence there exist fundamental trade-offs between these quantities and the entropy production rate. Usually, the energy source required to operate in a high-fidelity regime comes from the consumption of external energetic molecules, e.g., GTP hydrolysis in protein translation . In this work, we study trade-offs between several kinetic and thermodynamic observables for Hopfield's energy-relay mechanism, which does not consume external molecules and is able to operate in depleted regions, at the cost of a higher error rate. The trade-offs are obtained both analytically and numerically via Pareto optimal fronts. We find that the scheme is able to operate in three distinct regimes: an energy relay regime, a mixed relay-Michaelis-Menten regime, and a Michaelis-Menten regime, depending on the kinetic and energetic parameters that tune transitions between states. The mixed regime features a dynamical phase transition in the error-entropy production Pareto trade-off, while the pure energy relay regime contains a region where this type of proofreading energetically outperforms standard kinetic proofreading.

13 pages, 10 figures

References in corpus (8)

• Thermodynamic uncertainty relation for biomolecular processes
• Nonequilibrium sensing and its analogy to kinetic proofreading
• Thermodynamics of accuracy in kinetic proofreading: Dissipation and efficiency trade-offs
• The energy cost and optimal design of networks for biological discrimination
• Emergence of Dynamic Cooperativity in the Stochastic Kinetics of Fluctuating Enzymes
• Pareto optimal fronts of kinetic proofreading
• Universal thermodynamic bounds on the Fano factor of discriminatory networks with unidirectional transitions
• Trade-offs and thermodynamics of energy-relay proofreading

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