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Reaction-path statistical mechanics of enzymatic kinetics.
- Source :
-
Journal of Chemical Physics . 4/7/2022, Vol. 156 Issue 13, p1-13. 13p. - Publication Year :
- 2022
-
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]
Details
- Language :
- English
- ISSN :
- 00219606
- Volume :
- 156
- Issue :
- 13
- Database :
- Academic Search Index
- Journal :
- Journal of Chemical Physics
- Publication Type :
- Academic Journal
- Accession number :
- 156224832
- Full Text :
- https://doi.org/10.1063/5.0075831