Stochastic approach to molecular interactions and computational theory of metabolic and genetic regulations

DOI10.1016/J.JTBI.2007.06.017MaRDI QIDQ2211640zbMATH OpenOpenAlexWikidataFDO

Authors Yanyan Li

Publication date 11 November 2020

Published in Journal of Theoretical Biology (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/q-bio/0612011

zbMATH Keywords

biological regulationMarkov processmolecular interactionprobability flowstationary probability distribution

Mathematics Subject Classification ID

Markov chains (discrete-time Markov processes on discrete state spaces) (60J10) Biochemistry, molecular biology (92C40) Kinetics in biochemical problems (pharmacokinetics, enzyme kinetics, etc.) (92C45)

Abstract: Binding and unbinding of ligands to specific sites of a macromolecule are one of the most elementary molecular interactions inside the cell that embody the computational processes of biological regulations. The interaction between transcription factors and the operators of genes and that between ligands and binding sites of allosteric enzymes are typical examples of such molecular interactions. In order to obtain the general mathematical framework of biological regulations, we formulate these interactions as finite Markov processes and establish a computational theory of regulatory activities of macromolecules based mainly on graphical analysis of their state transition diagrams. The contribution is summarized as follows: (1) Stochastic interpretation of Michaelis-Menten equation is given. (2) Notion of extit{probability flow} is introduced in relation to detailed balance. (3) A stochastic analogy of extit{Wegscheider condition} is given in relation to loops in the state transition diagram. (4) A simple graphical method of computing the regulatory activity in terms of ligands' concentrations is obtained for Wegscheider cases.

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Cites work

• An analytical study of the number of steady states in gene regulatory networks
• scientific article; zbMATH DE number 1090658 (Why is no real title available?)
• Markov Chains

Cited in

(5)

• Mathematical classification of regulatory logics for compound environmental changes
• A statistical mechanics description of environmental variability in metabolic networks
• A new type of neural computation
• Theoretical description of metabolism using queueing theory
• Two coarse-graining studies of stochastic models in molecular biology

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