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Thermodynamics of biological reactions

Abstract:
The purpose of applying Thermodynamics to systems biology is a better understanding of biological reaction networks and an improvement of metabolic network models. These applications focus on the calculation of the Free Energy of individual reactions (ΔRg) with the aim to determine reaction feasibility or flux direction. Several inconsistent results concerning the reaction feasibility due to neglect of important factors certainly influencing ΔRg emphasize the importance of reliable thermodynamic data.

 

Description:

Genomically possible reactions or pathways in a metabolic network are constrained by the Second Law of Thermodynamics. Here the change in Free Energy of reaction (ΔRg) is the most valuable measure to assess the feasibility of reactions. Constraint-based network models, derived from the application of Metabolic Network Analysis to the cellular metabolism, can thus be supplemented with additional or tighter constraints and model assumptions can be supported or disproved [1].

Results of feasibility studies strongly depend on the kind, amount and quality of thermodynamic data. However, the application of thermodynamics as currently carried out obviously neglects several important factors which certainly influence the Free Energy and thus yields questionable results concerning the reaction feasibility [2]. Any kind of intermolecular interaction resulting in non-ideal behavior of the participating components seems to be crucial among these factors.

It is the aim of this work to identify and investigate the most relevant factors for the calculation of ΔRg based on suitable model reactions. This includes the determination of equilibrium constants and activity coefficients under different conditions to calculate a Standard Free Energy of reaction. Furthermore, the PC-SAFT equation of state is used as a model to predict equilibrium and activity data of multi-component systems solely based on binary data like solution densities and osmotic coefficients [3]. This allows for a thermodynamic recalculation of published equilibrium data and for a reduction of experimental effort.

 

References:

[1] C.S. Henry, L.J. Broadbelt, and V. Hatzimanikatis:
"Thermodynamics-Based Metabolic Flux Analysis"
Biophysical Journal, vol. 92, pp. 1792-1805, 2007
[2] T. Maskow, and U. von Stockar:
"How reliable are thermodynamic feasibility statements of biochemical pathways?"
Biotechnology and Bioengineering, vol. 92, pp. 223-230, 2005


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Foto von PD Dr.-Ing. Christoph Held

PD Dr.-Ing. Christoph Held

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TU Dortmund
Fakultät Bio- und Chemieingenieurwesen
Emil-Figge-Str. 70
44227 Dortmund

Raum G2-513