1. Reaction-path statistical mechanics of enzymatic kinetics.
- Author
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Lim, Hyuntae and Jung, YounJoon
- Subjects
- *
LARGE deviation theory , *STATISTICAL mechanics , *MICHAELIS-Menten mechanism , *PARTITION functions , *LARGE deviations (Mathematics) , *CHEMICAL reactions - Abstract
We introduce a reaction-path statistical mechanics formalism based on the principle of large deviations to quantify the kinetics of single-molecule enzymatic reaction processes under the Michaelis–Menten mechanism, which exemplifies an out-of-equilibrium process in the living system. Our theoretical approach begins with the principle of equal a priori probabilities and defines the reaction path entropy to construct a new nonequilibrium ensemble as a collection of possible chemical reaction paths. As a result, we evaluate a variety of path-based partition functions and free energies by using the formalism of statistical mechanics. They allow us to calculate the timescales of a given enzymatic reaction, even in the absence of an explicit boundary condition that is necessary for the equilibrium ensemble. We also consider the large deviation theory under a closed-boundary condition of the fixed observation time to quantify the enzyme–substrate unbinding rates. The result demonstrates the presence of a phase-separation-like, bimodal behavior in unbinding events at a finite timescale, and the behavior vanishes as its rate function converges to a single phase in the long-time limit. [ABSTRACT FROM AUTHOR]
- Published
- 2022
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