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

The high accuracy exhibited by biological information transcription
processes is due to kinetic proofreading, i.e. by a mechanism which reduces the
error rate of the information-handling process by driving it out of equilibrium.
We provide a consistent thermodynamic description of enzyme-assisted assembly
processes involving competing substrates, in a master equation framework. We
introduce and evaluate a measure of the efficiency based on rigorous non-
equilibrium inequalities. The performance of several proofreading models are thus
analyzed and the related time, dissipation and efficiency versus error trade-offs
exhibited for different discrimination regimes. We finally introduce and analyse
in the same framework a simple model which takes into account correlations
between consecutive enzyme-assisted assembly steps. This work highlights the
relevance of the distinction between energetic and kinetic discrimination regimes
in enzyme-substrate interactions.