Optimality in biological proofreading

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 a nonequilibrium error-reduction mechanism called kinetic proofreading (KPR). The KPR mechanism enhances the accuracy of the biological process at the cost of higher energy dissipation and reduced speed. Hence, there is a trade-off between speed, error, and dissipation. The second law of thermodynamics sets fundamental bounds on speed, error, and dissipation of replicating enzymes. Despite their theoretical interest, these bounds are usually far from the operating regimes of replicating enzymes. This motivates us to formulate the optimality principles for speed, error, and dissipation using concepts from mathematical optimization theory.