文献类型：期刊文献

中文题名：基于热力学原理约束的代谢网络模型研究进展及其应用

英文题名：Research Progress and Application of Metabolic Network Model Constrained by Thermodynamic Principles

作者：虞思倩[1];夏建业[1];庄英萍[1,2]

机构：[1]华东理工大学生物反应器工程国家重点实验室,上海200237;[2]华东理工大学青岛创新研究院,青岛266102

年份：2022

卷号：42

期号：1

起止页码：128

中文期刊名：中国生物工程杂志

外文期刊名：China Biotechnology

收录：CSTPCD;;北大核心:【北大核心2020】；CSCD:【CSCD2021_2022】；

基金：国家重点研发计划(2020YFA0908300);国家自然科学基金面上项目(21776082);青岛市生物制造行业科学研究智库联合基金(QDSWZK202004)资助项目

语种：中文

中文关键词：基因组规模代谢网络模型;热力学;约束分析;吉布斯自由能

外文关键词：Genome-scale metabolic network model(GSMM);Thermodynamics;Constraint analysis;Gibbs free-energy

摘要：高通量组学技术为人们研究生命系统组件提供了细节数据,通过对基因组、转录组、蛋白质组及代谢组等不同生命层级间相互作用的研究,推动了生化反应网络的重建——基因组规模代谢网络模型(genome scale of metabolic network model,GSMM)。GSMM作为系统生物学领域中研究生命系统的基本手段,表现出与传统还原论相反的整体化思想,它允许将细胞复杂的生命过程作为一个完整的系统来研究。通量平衡分析(flux balance analysis,FBA)作为GSMM的主流方法,因其自身依赖的约束有限,通常难以得到唯一的最优解。而热力学与生物代谢密不可分,目前除将多组学数据作为附加约束引入GSMM模型外,添加热力学约束也已成为有效减小解空间的手段。首先对热力学约束引入GSMM模型的方法及各种方法的优势与不足进行了综述,然后对获得相关热力学参数的方法和工具进行了梳理汇总。最后,介绍了整合多组学及热力学综合约束的GSMM模型以及基于热力学原理约束的模型在实际中的应用,并对如何应用热力学约束提高GSMM模型模拟准确性进行了展望。
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.