Nobeli Irene, Ponstingl Hannes, Krissinel Eugene B, Thornton Janet M
EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
J Mol Biol. 2003 Dec 5;334(4):697-719. doi: 10.1016/j.jmb.2003.10.008.
The Escherichia coli metabolome has been characterised using the two-dimensional structures of 745 metabolites, obtained from the EcoCyc and KEGG databases. Physicochemical properties of the metabolome have been calculated to provide an overview of this set of cognate ligands. A library of fragments commonly found among these molecules has been employed to reveal the main constituents of metabolites, and to assist a broad classification of the metabolome into biochemically relevant classes. Fragment-based fingerprints reveal the metabolome as a continuum in the two-dimensional structural space, where clusters of molecules sharing similar scaffolds can be identified, but are generally overlapping. Nucleotide, carbohydrate and amino acid-like molecules are the most prominent, but at high levels of similarity, a more detailed classification is possible. Classification schemes for the metabolome are a promising tool for understanding the chemical diversity of the metabolome. When used in conjunction with existing classifications of the proteome, they can help to elucidate the binding preferences and promiscuity of proteins and their cognate substrates.
利用从EcoCyc和KEGG数据库获得的745种代谢物的二维结构，对大肠杆菌代谢组进行了表征。计算了代谢组的物理化学性质，以概述这组同源配体。已采用这些分子中常见的片段库来揭示代谢物的主要成分，并协助将代谢组广泛分类为具有生化相关性的类别。基于片段的指纹图谱揭示了代谢组在二维结构空间中是一个连续体，在该空间中可以识别出具有相似支架的分子簇，但这些分子簇通常相互重叠。核苷酸、碳水化合物和氨基酸类分子最为突出，但在高度相似的情况下，可以进行更详细的分类。代谢组的分类方案是理解代谢组化学多样性的一个有前途的工具。当与蛋白质组的现有分类结合使用时，它们有助于阐明蛋白质及其同源底物的结合偏好和混杂性。
