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Thermodynamic Calculations for Biochemical Transport and Reaction Processes in Metabolic Networks


Jol, Stefan J; Kümmel, Anne; Hatzimanikatis, Vassily; Beard, Daniel A; Heinemann, Matthias (2010). Thermodynamic Calculations for Biochemical Transport and Reaction Processes in Metabolic Networks. Biophysical Journal, 99(10):3139-3144.

Abstract

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.Weillustrate 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.

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.Weillustrate 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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9 citations in Web of Science®
11 citations in Scopus®
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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:Special Collections > SystemsX.ch
Special Collections > SystemsX.ch > Research, Technology and Development Projects > YeastX
Dewey Decimal Classification:570 Life sciences; biology
Language:English
Date:2010
Deposited On:04 Jul 2013 14:45
Last Modified:05 Apr 2016 16:51
Publisher:Biophysical Society
ISSN:0006-3495
Free access at:Publisher DOI. An embargo period may apply.
Publisher DOI:https://doi.org/10.1016/j.bpj.2010.09.043
Permanent URL: https://doi.org/10.5167/uzh-79181

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