4.5 Article

Thermodynamic Calculations for Biochemical Transport and Reaction Processes in Metabolic Networks

Journal

BIOPHYSICAL JOURNAL
Volume 99, Issue 10, Pages 3139-3144

Publisher

CELL PRESS
DOI: 10.1016/j.bpj.2010.09.043

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Funding

  1. Swiss Initiative in Systems Biology
  2. Ecole Polytechnique Federale de Lausanne
  3. Swiss National Science Foundation
  4. National Institutes of Health [HL072011]

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Thermodynamic analysis of metabolic networks has recently generated increasing interest for its ability to add constraints on metabolic network operation, and to combine metabolic fluxes and metabolite measurements in a mechanistic manner. Concepts for the calculation of the change in Gibbs energy of biochemical reactions have long been established. However, a concept for incorporation of cross-membrane transport in these calculations is still missing, although the theory for calculating thermodynamic properties of transport processes is long known. Here, we have developed two equivalent equations to calculate the change in Gibbs energy of combined transport and reaction processes based on two different ways of treating biochemical thermodynamics. We illustrate the need for these equations by showing that in some cases there is a significant difference between the proposed correct calculation and using an approximative method. With the developed equations, thermodynamic analysis of metabolic networks spanning over multiple physical compartments can now be correctly described.

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