Basic, simple and extendable kinetic model of protein synthesis

DOI10.3934/MBE.2019329zbMATH Open1468.92034arXiv1204.5941OpenAlexW2958157668WikidataQ91167832 ScholiaQ91167832MaRDI QIDQ2045463FDOQ2045463

Authors: Alexander N. Gorban, A. Harel-Bellan, N. Morozova, A. Zinovyev 

Publication date: 13 August 2021

Published in: Mathematical Biosciences and Engineering (Search for Journal in Brave)

Abstract: Protein synthesis is one of the most fundamental biological processes, which consumes a significant amount of cellular resources. Despite existence of multiple mathematical models of translation, varying in the level of mechanistical details, surprisingly, there is no basic and simple chemical kinetic model of this process, derived directly from the detailed kinetic model. One of the reasons for this is that the translation process is characterized by indefinite number of states, thanks to existence of polysomes. We bypass this difficulty by applying a trick consisting in lumping multiple states of translated mRNA into few dynamical variables and by introducing a variable describing the pool of translating ribosomes. The simplest model can be solved analytically under some assumptions. The basic and simple model can be extended, if necessary, to take into account various phenomena such as the interaction between translating ribosomes, limited amount of ribosomal units or regulation of translation by microRNA. The model can be used as a building block (translation module) for more complex models of cellular processes. We demonstrate the utility of the model in two examples. First, we determine the critical parameters of the single protein synthesis for the case when the ribosomal units are abundant. Second, we demonstrate intrinsic bi-stability in the dynamics of the ribosomal protein turnover and predict that a minimal number of ribosomes should pre-exists in a living cell to sustain its protein synthesis machinery, even in the absence of proliferation.

Full work available at URL: https://arxiv.org/abs/1204.5941

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zbMATH Keywords

model reductiontranslationlumpingkinetic modelingproteinribosomes

Mathematics Subject Classification ID

Qualitative investigation and simulation of ordinary differential equation models (34C60) Systems biology, networks (92C42) Kinetics in biochemical problems (pharmacokinetics, enzyme kinetics, etc.) (92C45)

Cites Work

• A MAX-plus model of ribosome dynamics during mRNA translation
• Dynamic model of the process of protein synthesis in eukaryotic cells

Cited In (12)

• Protein synthesis driven by dynamical stochastic transcription
• Modelling co-transcriptional cleavage in the synthesis of yeast pre-rRNA
• A mathematical model for prokaryotic protein synthesis
• Toxin effect on protein biosynthesis in eukaryotic cells: a simple kinetic model
• A mechanistic model of nutritional control of protein synthesis in animal tissues
• Bifurcations in the interplay of messenger RNA, protein and nonprotein coding RNA
• Formulation of the protein synthesis rate with sequence information
• A simple protein synthesis model for the PURE system operation
• Analysis of protein synthesis dynamic model in eukaryotic cells: input control
• Modeling translation in protein synthesis with TASEP: a tutorial and recent developments
• Protein synthesis as an object of physical and mathematical research and modeling
• Dynamic model of the process of protein synthesis in eukaryotic cells

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