Standard Gibbs energy was estimated with the component contribution method [1] and adjusted to in vivo conditions [2] with von Bertalany (version 2) [3, 1]. Standard transformed Gibbs energy was computed at a temperature of 310.15 K, ionic strength of 0.15 mol/L and compartment specic pH and electrical potential (see table below). Bounds on transformed Gibbs energy include a 95% condence interval for estimated standard transformed Gibbs energy and a default range of metabolite concentrations from 10-7 to 10-2 mol/L.

Compartment pH Electrical potential* (mV)
Cytosol 7.2 0
Extracellular 7.4 30
Golgi 6.35 0
Lysosomes 5.5 19
Mitochondria 8 -155
Nucleus 7.2 0
ER 7.2 0
Peroxisomes 7. 12**
*Relative to cytosol
**Dependent on the variable peroxisomal pH [2]

References

  1. Noor E et al. Consistent Estimation of Gibbs Energy Using Component Contributions. PLOS Computational Biology, 2013
  2. Haraldsdottir HS et al. Quantitative assignment of reaction directionality in a multicompartmental human metabolic reconstruction. Biophysical Journal, 2012.
  3. Fleming RMT and Thiele I von Bertalan y 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models. Bioinformatics, 2011

When using thermodynamic information collected in VMH, please cite:

Noor E et al. Consistent Estimation of Gibbs Energy Using Component Contributions. PLoS Comput Biol 9(7):e1003098. doi:10.1371/journal.pcbi.1003098