Analysis of metabolic network based on conservation of molecular structure.
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.
Hogiri
Tomoharu
T
Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan.
Furusawa
Chikara
C
Shinfuku
Yohei
Y
Ono
Naoaki
N
Shimizu
Hiroshi
H
D016208:Databases, Factual; D053858:Metabolic Networks and Pathways; D015394:Molecular Structure