For example, recent work engineering Escherichia coli for 1,4-butanediol production leveraged thermodynamic analysis to highlight the most promising candidate pathways and to eliminate those unlikely to flow to 1,4-butanediol ( 7). Therefore, a metabolic reaction or pathway can be subjected to thermodynamic analysis to determine whether it is feasible under physiological conditions and which conditions enable it to produce the desired outputs ( 6, 10). The cellular conditions-temperature, pH, ionic strength, concentrations of metabolites and ions, etc.-can significantly affect the thermodynamic feasibility of a particular reaction direction. That is, the change in Gibbs energy due to a reaction (Δ r G) must be negative.īiochemical reactions have context: they take place inside cells. In these metabolic research and engineering efforts it is essential to account for thermodynamic constraints: chemical reactions can sustain flux in a given direction only if they lead to a reduction in the Gibbs energy ( G). More recently, metabolic models have succeeded in accurately predicting bacterial growth modes and biologists have succeeded in designing and implementing novel biosynthetic pathways for the production of fuels and other valuable chemicals ( 5–9). The metabolic networks of numerous organisms have been studied in detail as well as their responses to changes in internal and external conditions ( 1–4). The structure and function of cellular metabolism has been a central area of biological inquiry for over a century.
Here we describe the database characteristics and implementation and demonstrate its use.
Chemical reaction thermodynamics calculator code#
The eQuilibrator code is open-source and all thermodynamic source data are freely downloadable in standard formats. The web interface to eQuilibrator ( ) enables easy calculation of Gibbs energies of compounds and reactions given arbitrary pH, ionic strength and metabolite concentrations. To address this problem, eQuilibrator couples a comprehensive and accurate database of thermodynamic properties of biochemical compounds and reactions with a simple and powerful online search and calculation interface. Even simple thermodynamic questions like ‘how much Gibbs energy is released by ATP hydrolysis at pH 5?’ are complicated excessively by the search for accurate data. However, thermodynamic data on biochemical compounds can be difficult to find and is cumbersome to perform calculations with manually. The laws of thermodynamics constrain the action of biochemical systems.
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