Universally valid reduction of multiscale stochastic biochemical systems using simple non-elementary propensities

Yun Min Song, Hyukpyo Hong and Jae Kyoung Kim

PLOS Computational Biology, 2021, vol. 17, issue 10, 1-21

Abstract: Biochemical systems consist of numerous elementary reactions governed by the law of mass action. However, experimentally characterizing all the elementary reactions is nearly impossible. Thus, over a century, their deterministic models that typically contain rapid reversible bindings have been simplified with non-elementary reaction functions (e.g., Michaelis-Menten and Morrison equations). Although the non-elementary reaction functions are derived by applying the quasi-steady-state approximation (QSSA) to deterministic systems, they have also been widely used to derive propensities for stochastic simulations due to computational efficiency and simplicity. However, the validity condition for this heuristic approach has not been identified even for the reversible binding between molecules, such as protein-DNA, enzyme-substrate, and receptor-ligand, which is the basis for living cells. Here, we find that the non-elementary propensities based on the deterministic total QSSA can accurately capture the stochastic dynamics of the reversible binding in general. However, serious errors occur when reactant molecules with similar levels tightly bind, unlike deterministic systems. In that case, the non-elementary propensities distort the stochastic dynamics of a bistable switch in the cell cycle and an oscillator in the circadian clock. Accordingly, we derive alternative non-elementary propensities with the stochastic low-state QSSA, developed in this study. This provides a universally valid framework for simplifying multiscale stochastic biochemical systems with rapid reversible bindings, critical for efficient stochastic simulations of cell signaling and gene regulation. To facilitate the framework, we provide a user-friendly open-source computational package, ASSISTER, that automatically performs the present framework.Author summary: As experimentally characterizing all underlying processes of reactions in biochemical systems is almost impossible, their combined effects have frequently been described by simplified non-elementary reaction functions (e.g., Hill and Morrison functions). Recently, the deterministically driven non-elementary reaction functions have been heuristically used for stochastic simulations with the Gillespie algorithm. While this approach has been one of the most popular methods for efficient stochastic simulations, its accuracy has been controversial. Here, we finally solve this enigmatic open question. Specifically, we derive a complete condition under which this approach can accurately capture the stochastic dynamics of reversible binding, the critical reaction to describe nearly all biochemical systems such as gene regulation and enzyme catalysis. We illustrate that the use of this approach outside the identified range of validity seriously distorts the stochastic dynamics of a bistable switch in the cell cycle and an oscillator in the circadian clock. Importantly, to overcome this inaccuracy, we propose alternative simplified reaction functions for stochastic reversible binding. Combining the existing and proposed reaction functions, we have developed a computational package, ASSISTER, that performs universally valid stochastic model reduction. This enables accurate and efficient stochastic simulations of multiscale biochemical systems with rapid reversible bindings under any conditions.

Date: 2021
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pcbi00:1008952

DOI: 10.1371/journal.pcbi.1008952

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