Vol. 8, No. 4, 2020

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On a stochastic approach to model the double phosphorylation/dephosphorylation cycle

Alberto Maria Bersani, Alessandro Borri, Francesco Carravetta, Gabriella Mavelli and Pasquale Palumbo

Vol. 8 (2020), No. 4, 261–285
DOI: 10.2140/memocs.2020.8.261
Abstract

Because of the unavoidable intrinsic noise affecting biochemical processes, a stochastic approach is usually preferred whenever a deterministic model gives too rough information or, worse, may lead to erroneous qualitative behaviors and/or quantitatively wrong results. In this work we focus on the chemical master equation (CME)-based method which provides an accurate stochastic description of complex biochemical reaction networks in terms of the probability distribution of the underlying chemical populations. Indeed, deterministic models can be dealt with as first-order approximations of the average-value dynamics coming from the stochastic CME approach. Here we investigate the double phosphorylation/dephosphorylation cycle, a well-studied enzymatic reaction network where the inherent double time scale requires one to exploit quasisteady state approximation (QSSA) approaches to infer qualitative and quantitative information. Within the deterministic realm, several researchers have deeply investigated the use of the proper QSSA, agreeing to highlight that only one type of QSSA (the total QSSA) is able to faithfully replicate the qualitative behavior of bistability occurrences, as well as the correct assessment of the equilibrium points, accordingly to the not approximated (full) model. Based on recent results providing CME solutions that do not resort to Monte Carlo simulations, the proposed stochastic approach shows some counterintuitive facts arising when trying to straightforwardly transfer bistability deterministic results into the stochastic realm, and suggests how to handle such cases according to both theoretical and numerical results.

Keywords
Michaelis–Menten kinetics, quasisteady state approximation, deterministic and stochastic processes, phosphorylation, chemical master equation, Markov processes
Mathematical Subject Classification 2010
Primary: 34F05, 37L55, 60H10, 60H35
Secondary: 92C42, 92C45
Milestones
Received: 10 November 2019
Revised: 24 June 2020
Accepted: 28 July 2020
Published: 9 November 2020

Communicated by Victor A. Eremeyev
Authors
Alberto Maria Bersani
Dipartimento di Ingegneria Meccanica e Aerospaziale
Università degli Studi di Roma “La Sapienza”
Rome
Italy
Alessandro Borri
Istituto di Analisi dei Sistemi et Informatica “Antonio Ruberti”
Consiglio Nazionale delle Ricerche
Rome
Italy
Francesco Carravetta
Istituto di Analisi dei Sistemi et Informatica “Antonio Ruberti”
Consiglio Nazionale delle Ricerche
Rome
Italy
Gabriella Mavelli
Istituto di Analisi dei Sistemi et Informatica “Antonio Ruberti”
Consiglio Nazionale delle Ricerche
Rome
Italy
Pasquale Palumbo
Dipartimento di Biotecnologie e Bioscienze
Università degli Studi Milano-Bicocca
Milano
Italy