基于约束的建模方法在代谢网络中的应用研究

Researching on the application of constrain-based modeling methods in metabolic networks

代谢网络在各种细胞功能和生命过程中发挥着至关重要的作用。随着细胞网络重建工程的迅速发展,可用的基因组水平代谢网络越来越多,因而计算方法在这些网络的结构功能分析中越来越重要。基于约束的建模方法不像图论方法那样仅考虑代谢模型的纯拓扑结构,也不像各种动力学建模方法那样需求详尽的热力学参数,因而极具优势。采用基于约束的建模方法对一个含619个基因,655个代谢物和743个代谢反应的金黄色葡萄球菌(Staphylococcusaureus)代谢网络进行了分析,主要研究了该模型的网络结构特征,以及其最优生长率、动态生长情况和基因删除学习等。本研究提供了一个对金黄色葡萄球菌代谢网络进行约束建模分析的初步框架。

Metabolic network plays an important role in cellular function and process. As the rapid development of cellular networks reconstruction, there are more and more available genome - scale metabolic networks, and thus computational modeling methods are increasingly important in investigation of the structure and function of these networks. Constrain -based modeling methods don＇t like the graph theory methods which study the pure topological structure of metabolic model, neither like dynamics methods which need detailed kinetic parameters, thus with more advantages in metabolic network modeling. The article studied Staphylococcus aureus metabolic network which contains 619 genes, 655 metabolites and 743 metabolic reactions with constrain -based modeling methods, we mainly studied the topological features, optimal growth rates, dynamic growth and gene deletion of the model. The study provided a primary framework of Staphylococcus aureus with constrain - based modeling.