Extraction of a Thermodynamic Property for Biochemical Reactions in the Metabolic Pathway

Abstract

When metabolic reconstruction is performed to elucidate the biological function of a complete genome, the path computation between two compounds is sometimes necessary. For example, if a missing enzyme is found in a biosynthesis pathway for a compound that is supposed to be synthesized, we need to search an alternative enzyme or a path for the enzyme reaction. Typically, the input of the path computation is a set of two compounds that correspond to a substrate and a product, and the output is a set of all possible paths that connect the two compounds. However, this set includes many paths that are not working in actual biological pathways. Previously we have considered the standard Gibbs free energy changes in enzyme reactions and discussed about their applicability to the path computation [1]. In this work, we computed the standard Gibbs free energies of the compounds and the standard Gibbs free energy changes of the reactions registered in the LIGAND database [2]. We covered as many entries as possible with the advent of the automatic compound structure comparison method [3]. We also developed a new function to sort the result of path computation in consideration of the standard Gibbs free energy changes of the pathway. We report here a new addition to the pathway computation tool in the KEGG system and discuss about the distribution of the standard Gibbs free energy changes in the metabolic pathways for further evaluation.