Reaction routes in biochemical reaction systems: Algebraic properties, validated calculation procedure and example from nucleotide metabolism
Reaction routes in biochemical reaction systems: Algebraic properties, validated calculation procedure and example from nucleotide metabolism
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DOI：
10.1007/s002850200143
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发表时间：
2002-08-01
影响因子：
1.9
通讯作者：
Fell, DA
中科院分区：
文献类型：
--
作者：
Schuster, S;Hilgetag, C;Fell, DA
基本通量模式（直接反应路线）是能够在稳定状态下运行的酶的最小集合，所有不可逆反应都在适当的方向上进行。它们可以被解释为（生物）化学反应网络的组成部分和途径。本文给出了初等模态的两种不同定义，并证明了它们的等价性。然后给出并证明了初等模态的几个代数性质。除其他特征外，这涉及网络中不用于基本模式的酶的最小数量以及不可逆反应被可逆反应所取代的情况。在此基础上，提出了一种改进算法，并形式化地证明了该算法可以独占地生成包含可逆反应或不可逆反应的任意网络的所有基本通量模式。该算法通过一个与核苷酸代谢相关的生化例子来说明。讨论了两种不同编程语言的计算机实现。
Elementary flux modes (direct reaction routes) are minimal sets of enzymes that can operate at steady state, with all irreversible reactions used in the appropriate direction. They can be interpreted as component,pathways of a (bio)chemical reaction network. Here, two different definitions of elementary modes are given and their equivalence is proved. Several algebraic properties of elementary modes are then presented and proved. This concerns, amongst other features, the minimal number of enzymes of the network not used in an elementary mode and the situations where irreversible reactions are replaced by reversible ones. Based on these properties, a refined algorithm is presented, and it is formally proved that this algorithm will exclusively generate all the elementary flux modes of an arbitrary network containing reversible or irreversible reactions or both. The algorithm is illustrated by a biochemical example relevant in nucleotide metabolism. The computer implementation in two different programming languages is discussed.