Baart Gino J E, Martens Dirk E
VIB Department of Plant Systems Biology/Department of Biology, Protistology and Aquatic Ecology, Ghent University, Ghent, Belgium.
Methods Mol Biol. 2012;799:107-26. doi: 10.1007/978-1-61779-346-2_7.
Metabolism can be defined as the complete set of chemical reactions that occur in living organisms in order to maintain life. Enzymes are the main players in this process as they are responsible for catalyzing the chemical reactions. The enzyme-reaction relationships can be used for the reconstruction of a network of reactions, which leads to a metabolic model of metabolism. A genome-scale metabolic network of chemical reactions that take place inside a living organism is primarily reconstructed from the information that is present in its genome and the literature and involves steps such as functional annotation of the genome, identification of the associated reactions and determination of their stoichiometry, assignment of localization, determination of the biomass composition, estimation of energy requirements, and definition of model constraints. This information can be integrated into a stoichiometric model of metabolism that can be used for detailed analysis of the metabolic potential of the organism using constraint-based modeling approaches and hence is valuable in understanding its metabolic capabilities.
新陈代谢可定义为生物体中为维持生命而发生的一整套化学反应。酶是这一过程的主要参与者，因为它们负责催化化学反应。酶与反应的关系可用于重建反应网络，从而形成新陈代谢的代谢模型。生物体内部发生的化学反应的基因组规模代谢网络主要是根据其基因组中存在的信息和文献重建的，涉及基因组功能注释、相关反应的识别及其化学计量的确定、定位分配、生物量组成的确定、能量需求的估计以及模型约束的定义等步骤。这些信息可以整合到新陈代谢的化学计量模型中，该模型可用于使用基于约束的建模方法详细分析生物体的代谢潜力，因此对于理解其代谢能力很有价值。
