Research Progress and Application of Metabolic Network Model Constrained by Thermodynamic Principles

doi:10.13523/j.cb.2108068

China Biotechnology

2022, Vol. 42

Issue (1/2): 128-138 DOI: 10.13523/j.cb.2108068

Orginal Article

Research Progress and Application of Metabolic Network Model Constrained by Thermodynamic Principles

YU Si-qian¹,XIA Jian-ye^1,^**(

),ZHUANG Ying-ping^1,²

1 State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
2 Qingdao Innovation Research Institute, East China University of Science and Technology, Qingdao 266102, China

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Abstract

High-throughput omics technology provided detailed data for studying life system components. Through the interaction of components among the genome, transcriptome, proteome, and metabolome, it promoted the construction of the genome scale of metabolic network model (GSMM). GSMM, as a commonly used tool in systems biology, allows the complex life process of cells to be studied as a whole system, so it shows more holistic thinking contrary to traditional reductionism. Flux balance analysis (FBA), as the mainstream method of GSMM, is usually difficult to obtain the unique optimal solution due to enough constraints. Thermodynamics is closely related to biological metabolism, so in addition to introducing multiple omics data into the GSMM as additional constraints, adding thermodynamic constraints has also become an effective way to reduce the solution space further. This paper first reviews the method of introducing thermodynamic constraints into the GSMM and the advantages and disadvantages of the methods themselves, and then summarizes the methods and tools for obtaining relevant thermodynamic parameters. Finally, this review introduces the metabolic network model integrating multi-omics and thermodynamic constraints and discusses the practical application of the model based on thermodynamic principle constraints, and puts forward a prospect on how to apply thermodynamic constraints to improve the accuracy of the GSMM.

Key words： Genome-scale metabolic network model(GSMM) Thermodynamics Constraint analysis Gibbs free-energy

Received: 29 August 2021 Published: 03 March 2022

ZTFLH:

Q819

Corresponding Authors: Jian-ye XIA E-mail: jyxia@ecust.edu.cn

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Cite this article:

YU Si-qian,XIA Jian-ye,ZHUANG Ying-ping. Research Progress and Application of Metabolic Network Model Constrained by Thermodynamic Principles. China Biotechnology, 2022, 42(1/2): 128-138.

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https://manu60.magtech.com.cn/biotech/10.13523/j.cb.2108068 OR https://manu60.magtech.com.cn/biotech/Y2022/V42/I1/2/128

Table 1 Comparison of constraint analysis methods NET and TFA based on thermodynamic parameters

Fig.1 Databases and tools for obtaining thermodynamic parameters (a) Methods of estimating thermodynamic parameters (b) Database and tools for obtaining thermodynamic parameters

Fig.2 The development of thermodynamic parameters and analytical methods Purple represents the method of estimating △G⁰, yellow represents the analysis method based on thermodynamic principles, and green represents the comprehensive analysis method with integrated thermodynamic constraints


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