Pareto optimal fronts of kinetic proofreading

TL;DR

This paper analyzes the fundamental trade-offs between speed, accuracy, and energy dissipation in biological error correction processes using optimization theory, characterizing Pareto optimal fronts for key models like kinetic proofreading.

Contribution

It introduces a quantitative framework for understanding the trade-offs in biological proofreading, identifying scaling relations and Pareto fronts for key models.

Findings

More proofreading steps improve trade-offs between speed, error, and dissipation.

Scaling relations exist between speed, accuracy, and energy dissipation.

Pareto optimal fronts are characterized for kinetic proofreading and ribosome models.

Abstract

Biological processes such as DNA replication, RNA transcription, and protein translation show remarkable speed and accuracy in selecting the right substrate from pools of chemically identical molecules. This result is obtained by nonequilibrium reactions that dissipate chemical energy. It is widely recognized that there must be a trade-off between speed, error, and dissipation characterizing these systems. In this paper, we quantify the trade-off between speed, error, and dissipation using tools from mathematical optimization theory. We characterize the Pareto optimal front for two paradigmatic models of biological error correction: Hopfield's kinetic proofreading model and a ribosome model. We find that error correction processes with more proofreading steps are characterized by better trade-offs. Furthermore, we identify scaling relations between speed, accuracy, and dissipation on the Pareto front.