Thermodynamic Calculations for Biochemical Transport and Reaction Processes in Metabolic Networks
| Autor: | Vassily Hatzimanikatis, Anne Kümmel, Daniel A. Beard, Stefan J. Jol, Matthias Heinemann |
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| Přispěvatelé: | University of Zurich, Heinemann, Matthias, Molecular Systems Biology |
| Rok vydání: | 2010 |
| Předmět: |
Energy balance
Biophysics Thermodynamics Metabolic network symbols.namesake SX00 SystemsX.ch Biochemical reactions Statistical physics Phosphorylation Pathways Adenosine Triphosphatases Flux Extramural Chemistry Quantitative Biology::Molecular Networks Significant difference Systems Feasibility Biological Transport Succinates Hydrogen-Ion Concentration Energy-Balance Biological Systems and Multicellular Dynamics Cell Compartmentation Gibbs free energy Kinetics Constraints symbols Muscle 570 Life sciences biology SX16 YeastX Protons Law Metabolic Networks and Pathways 1304 Biophysics |
| Zdroj: | Biophysical Journal, 99(10), 3139-3144. CELL PRESS |
| ISSN: | 0006-3495 |
| DOI: | 10.1016/j.bpj.2010.09.043 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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