Group contribution method for thermodynamic analysis of complex metabolic networks
Group contribution method for thermodynamic analysis of complex metabolic networks
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DOI：
10.1529/biophysj.107.124784
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发表时间：
2008-08-01
影响因子：
3.4
通讯作者：
Hatzimanikatis, Vassily
中科院分区：
文献类型：
--
作者：
Jankowski, Matthew D.;Henry, Christopher S.;Hatzimanikatis, Vassily
据我们所知，在Mavrovouniotis基贡献法的基础上，引入了基贡献法来估计生化系统中标准的吉布斯生成自由能(δ （f)G′（度））和反应自由能(δ （r)G′（度））。利用多元线性回归对645个反应和224个化合物的训练集估计了74个不同分子亚结构和11个相互作用因子的吉布斯自由能贡献值。拟合值的标准误差为1.90千卡/摩尔。交叉验证分析确定了该方法对未包含在训练集中的反应和化合物估计δ (r)G′（度）和δ (f)G′（度）的准确性，根据交叉验证结果，这些估计涉及的标准误差为2.22 kcal/mol。这种群体贡献方法被证明能够估计大肠杆菌iJR904和iAF1260基因组尺度代谢模型中发现的大多数生化化合物和反应的Delta(r)G‘（度）和Delta(f)G’（度），以及京都基因和基因组百科全书和明尼苏达大学生物催化和生物降解数据库。这种新的小组贡献方法的基于web的实现可以在http:// sparta.chem-eng.northwestern.edu/cgi-bin/GCM/WebGCM.cgi免费获得。
Anew, to our knowledge, group contribution method based on the group contribution method of Mavrovouniotis is introduced for estimating the standard Gibbs free energy of formation (Delta(f)G'(degrees)) and reaction (Delta(r)G'(degrees)) in biochemical systems. Gibbs free energy contribution values were estimated for 74 distinct molecular substructures and 11 interaction factors using multiple linear regression against a training set of 645 reactions and 224 compounds. The standard error for the fitted values was 1.90 kcal/mol. Cross-validation analysis was utilized to determine the accuracy of the methodology in estimating Delta(r)G'(degrees) and Delta(f)G'(degrees) for reactions and compounds not included in the training set, and based on the results of the cross-validation, the standard error involved in these estimations is 2.22 kcal/mol. This group contribution method is demonstrated to be capable of estimating Delta(r)G'(degrees) and Delta(f)G'(degrees) for the majority of the biochemical compounds and reactions found in the iJR904 and iAF1260 genome-scale metabolic models of Escherichia coli and in the Kyoto Encyclopedia of Genes and Genomes and University of Minnesota Biocatalysis and Biodegradation Database. A web-based implementation of this new group contribution method is available free at http:// sparta.chem-eng.northwestern.edu/cgi-bin/GCM/WebGCM.cgi.