Analysis of metabolic network based on conservation of molecular structure
Analysis of metabolic network based on conservation of molecular structure
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DOI：
10.1016/j.biosystems.2008.09.002
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发表时间：
2009-03-01
期刊：
影响因子：
1.6
通讯作者：
Shimizu, Hiroshi
中科院分区：
文献类型：
--
作者：
Hogiri, Tomoharu;Furusawa, Chikara;Shimizu, Hiroshi
最近的工作揭示了数百种生物体内的化学反应以及代谢网络的普遍特征，这些特征揭示了网络的进化。然而，个别代谢产物的特征被忽略了。例如，一些碳水化合物具有通过代谢反应分解成小分子的结构，但辅酶如ATP大部分被保留下来。代谢物特征的这种差异对于理解代谢网络的普遍特征是重要的。为了量化代谢物的结构保守性，我们将每种代谢物的“结构保守性指数”（SCI）定义为通过代谢反应恢复到其原始位置的代谢物原子的分数。正如预期的那样，在网络中具有反应回路的辅酶和辅酶样代谢物显示出更高的SCI。利用该指标，我们发现代谢通量的总和与代谢产物的结构保持呈负相关。此外，我们发现，高SCI代谢物周围的每个反应路径独立变化，而低SCI代谢物的反应路径的变化通过进化过程相一致。这些相关性可能为代谢网络的普遍性质提供线索。(C)2008爱思唯尔爱尔兰有限公司保留所有权利。
Recent work has revealed much about chemical reactions inside hundreds of organisms as well as universal characteristics of metabolic networks, which shed light on the evolution of the networks. However, characteristics of individual metabolites have been neglected. For example, some carbohydrates have structures that are decomposed into small molecules by metabolic reactions, but coenzymes such as ATP are mostly preserved. Such differences in metabolite characteristics are important for understanding the universal characteristics of metabolic networks. To quantify the structure conservation of metabolites, we defined the "structure conservation index" (SCI) for each metabolite as the fraction of metabolite atoms restored to their original positions through metabolic reactions. As expected, coenzymes and coenzyme-like metabolites that have reaction loops in the network show a higher SCI. Using the index, we found that the sum of metabolic fluxes is negatively correlated with the structure preservation of metabolite. Also, we found that each reaction path around high SCI metabolites changes independently, while changes in reaction paths involving low SCI metabolites coincide through evolution processes. These correlations may provide a clue to universal properties of metabolic networks. (C) 2008 Elsevier Ireland Ltd. All rights reserved.