Computer simulation of Escherichia coli metabolic pathways based on matabolome data

基于代谢组数据的大肠杆菌代谢途径的计算机模拟

• 批准号: 15013252
• 负责人: TOMITA Masaru
• 金额: $ 20.48万
• 依托单位: Keio University
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Scientific Research on Priority Areas
• 财政年份: 2003
• 资助国家: 日本
• 起止时间: 2003 至 2004
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/en/grant/KAKENHI-PROJECT-15013252/
• 关键词: Computer Simulation; E-CELL; Metabolome; Bacteria; E. coli; Metabolites; CE-MS; Bioinformatics; バクテリア; CE; MS; 反応速度式; モデリング; バイオインフォマティクス

1. We constructed a computer model of the Escherichia coli metabolic pathways using E-CELL simulation system. The model contained 190 enzymatic reactions that are responsible for central metabolic pathways such as glycolysis, the TCA cycle, the pentose phosphate pathway and the nucleotide biosynthesis pathways.2. For constructing this model, we initially developed a detection method for whole metabolites in E. coli by using capillary electrophoresis mass spectrometry (CE-MS) system. This method was applied to the comprehensive analysis of metabolic intermediates extracted from E. coli, hundreds of metabolites could be detected for collecting parameters in computer simulation.3. We developed a computational technique to assist in the large-scale identification of charged metabolites. The electrophoretic mobility of metabolites in CE-MS was predicted from their structure, using an ensemble of artificial neural networks (ANNs).4. We also developed a synthetic in vitro glycolysis system using ten purified E. coli enzymes to obtain kinetics for the computer simulation.

1. 我们利用E-CELL模拟系统构建了大肠杆菌代谢途径的计算机模型。该模型包含190个酶促反应，这些酶促反应负责糖酵解、TCA循环、戊糖磷酸途径和核苷酸生物合成途径等中心代谢途径。为了构建该模型，我们初步建立了大肠杆菌全代谢产物的毛细管电泳质谱（CE-MS）检测方法。该方法适用于大肠杆菌代谢中间体的综合分析，可检测出数百种代谢物，为计算机模拟收集参数提供依据。我们开发了一种计算技术来协助大规模鉴定带电代谢物。利用人工神经网络（ann）集合，从结构上预测了CE-MS中代谢物的电泳迁移率。我们还开发了一种体外合成糖酵解系统，使用十种纯化的大肠杆菌酶来获得计算机模拟的动力学。

项目成果

KEGG-based pathway visualization tool for complex omics data

基于 KEGG 的复杂组学数据通路可视化工具

• 发表时间: 2005
• 期刊: In Silico Biology 5・(4)
• 作者: Arakawa;Kazuharu
• 通讯作者: Kazuharu

Qualitative and quantitative analysis of amino acids by capillary electrophresis Electrospray ionization tandem mass spectrometry

毛细管电泳电喷雾电离串联质谱法对氨基酸进行定性和定量分析

• 发表时间: 2004
• 期刊: Electrophoresis 25
• 作者: Soga;T.
• 通讯作者: T.

曽我朋義, 佐藤 滋, 西岡孝明, 冨田 勝: "[総説]ダイナミックな生命現象のメタボローム解析技術"細胞工学. 22. 1337-1341 (2003)

Tomoyoshi Soga、Shigeru Sato、Takaaki Nishioka、Masaru Tomita：“[综述]动态生物现象的代谢组分析技术”Cell Engineering 22. 1337-1341 (2003)。

曽我朋義: "[総説]CE-MSによるメタボローム解析"炎症と免疫(先端医学社). 11(6). 690-699 (2003)

Tomoyoshi Soga：“[综述]CE-MS 代谢组学分析”炎症与免疫（Shinsen Igakusha）11(6) 690-699 (2003)。

Hybrid dynamic/static method for large-scale simulation of metabolism

用于大规模代谢模拟的混合动态/静态方法

• 发表时间: 2005
• 期刊: Theoretical Biology and Medical Modeling 2
• 作者: Tomoya Kitayama;Ayako Kinoshita (Equal contribution);Katsuyuki Yugi
• 通讯作者: Katsuyuki Yugi