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Biophysical Journal 95:1487-1499 (2008)
© 2008 The Biophysical Society

Group Contribution Method for Thermodynamic Analysis of Complex Metabolic Networks

Matthew D. Jankowski *, Christopher S. Henry {dagger}, Linda J. Broadbelt {ddagger} and Vassily Hatzimanikatis §

* Mayo Clinic, Rochester, Minnesota 55905; {dagger} Mathematics and Computer Science, Argonne National Laboratory, Argonne, Illinois 60439; {ddagger} Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, Evanston, Illinois 60208; and § Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland

Correspondence: Address reprint requests to Professor Vassily Hatzimanikatis, EPFL, SB ISIC, LCSB, BCH 3110 (Bât. BCH), CH-1015 Lausanne, Switzerland. Tel.: 41-21-6939870; E-mail: vassily.hatzimanikatis{at}epfl.ch.

A new, 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}fG'°) and reaction ({Delta}rG'°) 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}rG'° and {Delta}fG'° 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}rG'° and {Delta}fG'° 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.






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Copyright © 2008 by the Biophysical Society.