Thermodynamics of accuracy in kinetic proofreading: dissipation and efficiency trade-offs

Rao, Riccardo; Peliti, Luca

doi:10.1088/1742-5468/2015/06/p06001

Cited by 40 publications

(48 citation statements)

References 39 publications

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“…According to these assumptions, the model only needs the four rate constants k p ±c and k p ±i for polymerization and depolymerization, together with the two Michaelis-Menten constants K c and K i for correct and incorrect pairings. The simplification that consists in reducing the description to correct and incorrect pairings is also often used to study DNA replication [5,[32][33][34][35][36][37][38].…”

Section: Bernoulli-chain Modelmentioning

confidence: 99%

Kinetics and thermodynamics of exonuclease-deficient DNA polymerases

Gaspard

2016

Phys. Rev. E

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A kinetic theory is developed for exonuclease-deficient DNA polymerases, based on the experimental observation that the rates depend not only on the newly incorporated nucleotide, but also on the previous one, leading to the growth of Markovian DNA sequences from a Bernoullian template. The dependences on nucleotide concentrations and template sequence are explicitly taken into account. In this framework, the kinetic and thermodynamic properties of DNA replication, in particular, the mean growth velocity, the error probability, and the entropy production in terms of the rate constants and the concentrations are calculated analytically. Theory is compared with numerical simulations for the DNA polymerases of T7 viruses and human mitochondria.

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Section: Bernoulli-chain Modelmentioning

confidence: 99%

Kinetics and thermodynamics of exonuclease-deficient DNA polymerases

Gaspard

2016

Phys. Rev. E

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“…with internal discrimination (unequal forward rates) to optimize speed, efficiency, and accuracy [36]. Despite this, simulating the classic HN model of proofreading is still a valuable exercise for students.…”

Section: More Realistic Modelmentioning

confidence: 99%

Stochastic Simulation to Visualize Gene Expression and Error Correction in Living Cells

Chen

Zuckerman

2018

Preprint

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Stochastic simulation can make the molecular processes of cellular control more vivid than the traditional differential-equation approach by generating typical system histories instead of just statistical measures such as the mean and variance of a population. Simple simulations are now easy for students to construct from scratch, that is, without recourse to black-box packages.In some cases, their results can also be compared directly to single-molecule 1 experimental data. After introducing the stochastic simulation algorithm, this article gives two case studies, involving gene expression and error correction, respectively. Code samples and resulting animations showing results are given in the online supplement.

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“…This trade-off is common in NESS kinetic proofreading; see, e.g., Refs. [41,42]. Increasing the discrimination ratio between two possible outcomes beyond its equilibrium value might have other applications, for example, in self-assembly.…”

Section: Constructing a Ness Kinetic Proofreading With Arbitrary Steamentioning

confidence: 99%

Mimicking Nonequilibrium Steady States with Time-Periodic Driving

2016

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Under static conditions, a system satisfying detailed balance generically relaxes to an equilibrium state in which there are no currents. To generate persistent currents, either detailed balance must be broken or the system must be driven in a time-dependent manner. A stationary system that violates detailed balance evolves to a nonequilibrium steady state (NESS) characterized by fixed currents. Conversely, a system that satisfies instantaneous detailed balance but is driven by the time-periodic variation of external parametersalso known as a stochastic pump (SP)-reaches a periodic state with nonvanishing currents. In both cases, these currents are maintained at the cost of entropy production. Are these two paradigmatic scenarios effectively equivalent? For discrete-state systems, we establish a mapping between nonequilibrium stationary states and stochastic pumps. Given a NESS characterized by a particular set of stationary probabilities, currents, and entropy production rates, we show how to construct a SP with exactly the same (time-averaged) values. The mapping works in the opposite direction as well. These results establish a proof of principle: They show that stochastic pumps are able to mimic the behavior of nonequilibrium steady states, and vice versa, within the theoretical framework of discrete-state stochastic thermodynamics. Nonequilibrium steady states and stochastic pumps are often used to model, respectively, biomolecular motors driven by chemical reactions and artificial molecular machines steered by the variation of external, macroscopic parameters. Our results loosely suggest that anything a biomolecular machine can do, an artificial molecular machine can do equally well. We illustrate this principle by showing that kinetic proofreading, a NESS mechanism that explains the low error rates in biochemical reactions, can be effectively mimicked by a constrained periodic driving.

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Thermodynamics of accuracy in kinetic proofreading: dissipation and efficiency trade-offs

Cited by 40 publications

References 39 publications

Kinetics and thermodynamics of exonuclease-deficient DNA polymerases

Kinetics and thermodynamics of exonuclease-deficient DNA polymerases

Stochastic Simulation to Visualize Gene Expression and Error Correction in Living Cells

Mimicking Nonequilibrium Steady States with Time-Periodic Driving

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