Thermodynamics and Kinetics of Glycolytic Reactions. Part I: Kinetic Modeling Based on Irreversible Thermodynamics and Validation by Calorimetry
In systems biology, material balances, kinetic models, and thermodynamic boundary conditions are increasingly used for metabolic network analysis. It is remarkable that the reversibility of enzyme-catalyzed reactions and the influence of cytosolic conditions are often neglected in kinetic models. In...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2020-11-01
|
| Series: | International Journal of Molecular Sciences |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1422-0067/21/21/8341 |
| _version_ | 1797548630123479040 |
|---|---|
| author | Kristina Vogel Thorsten Greinert Monique Reichard Christoph Held Hauke Harms Thomas Maskow |
| author_facet | Kristina Vogel Thorsten Greinert Monique Reichard Christoph Held Hauke Harms Thomas Maskow |
| author_sort | Kristina Vogel |
| collection | DOAJ |
| description | In systems biology, material balances, kinetic models, and thermodynamic boundary conditions are increasingly used for metabolic network analysis. It is remarkable that the reversibility of enzyme-catalyzed reactions and the influence of cytosolic conditions are often neglected in kinetic models. In fact, enzyme-catalyzed reactions in numerous metabolic pathways such as in glycolysis are often reversible, i.e., they only proceed until an equilibrium state is reached and not until the substrate is completely consumed. Here, we propose the use of irreversible thermodynamics to describe the kinetic approximation to the equilibrium state in a consistent way with very few adjustable parameters. Using a flux-force approach allowed describing the influence of cytosolic conditions on the kinetics by only one single parameter. The approach was applied to reaction steps 2 and 9 of glycolysis (i.e., the phosphoglucose isomerase reaction from glucose 6-phosphate to fructose 6-phosphate and the enolase-catalyzed reaction from 2-phosphoglycerate to phosphoenolpyruvate and water). The temperature dependence of the kinetic parameter fulfills the Arrhenius relation and the derived activation energies are plausible. All the data obtained in this work were measured efficiently and accurately by means of isothermal titration calorimetry (ITC). The combination of calorimetric monitoring with simple flux-force relations has the potential for adequate consideration of cytosolic conditions in a simple manner. |
| first_indexed | 2024-03-10T15:02:22Z |
| format | Article |
| id | doaj.art-acb1de075a4d454d881c12667e2080eb |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T15:02:22Z |
| publishDate | 2020-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-acb1de075a4d454d881c12667e2080eb2023-11-20T20:04:51ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672020-11-012121834110.3390/ijms21218341Thermodynamics and Kinetics of Glycolytic Reactions. Part I: Kinetic Modeling Based on Irreversible Thermodynamics and Validation by CalorimetryKristina Vogel0Thorsten Greinert1Monique Reichard2Christoph Held3Hauke Harms4Thomas Maskow5UFZ–Helmholtz Centre for Environmental Research, Department of Environmental Microbiology, Leipzig, Permoserstr. 15, D-04318 Leipzig, GermanyLaboratory of Thermodynamics, Department of Biochemical and Chemical Engineering, Technische Universitaet Dortmund, Emil-Figge-Str. 70, 44227 Dortmund, GermanyUFZ–Helmholtz Centre for Environmental Research, Department of Environmental Microbiology, Leipzig, Permoserstr. 15, D-04318 Leipzig, GermanyLaboratory of Thermodynamics, Department of Biochemical and Chemical Engineering, Technische Universitaet Dortmund, Emil-Figge-Str. 70, 44227 Dortmund, GermanyUFZ–Helmholtz Centre for Environmental Research, Department of Environmental Microbiology, Leipzig, Permoserstr. 15, D-04318 Leipzig, GermanyUFZ–Helmholtz Centre for Environmental Research, Department of Environmental Microbiology, Leipzig, Permoserstr. 15, D-04318 Leipzig, GermanyIn systems biology, material balances, kinetic models, and thermodynamic boundary conditions are increasingly used for metabolic network analysis. It is remarkable that the reversibility of enzyme-catalyzed reactions and the influence of cytosolic conditions are often neglected in kinetic models. In fact, enzyme-catalyzed reactions in numerous metabolic pathways such as in glycolysis are often reversible, i.e., they only proceed until an equilibrium state is reached and not until the substrate is completely consumed. Here, we propose the use of irreversible thermodynamics to describe the kinetic approximation to the equilibrium state in a consistent way with very few adjustable parameters. Using a flux-force approach allowed describing the influence of cytosolic conditions on the kinetics by only one single parameter. The approach was applied to reaction steps 2 and 9 of glycolysis (i.e., the phosphoglucose isomerase reaction from glucose 6-phosphate to fructose 6-phosphate and the enolase-catalyzed reaction from 2-phosphoglycerate to phosphoenolpyruvate and water). The temperature dependence of the kinetic parameter fulfills the Arrhenius relation and the derived activation energies are plausible. All the data obtained in this work were measured efficiently and accurately by means of isothermal titration calorimetry (ITC). The combination of calorimetric monitoring with simple flux-force relations has the potential for adequate consideration of cytosolic conditions in a simple manner.https://www.mdpi.com/1422-0067/21/21/8341biothermodynamicsglycolysisisothermal titration calorimetrysystems biology |
| spellingShingle | Kristina Vogel Thorsten Greinert Monique Reichard Christoph Held Hauke Harms Thomas Maskow Thermodynamics and Kinetics of Glycolytic Reactions. Part I: Kinetic Modeling Based on Irreversible Thermodynamics and Validation by Calorimetry International Journal of Molecular Sciences biothermodynamics glycolysis isothermal titration calorimetry systems biology |
| title | Thermodynamics and Kinetics of Glycolytic Reactions. Part I: Kinetic Modeling Based on Irreversible Thermodynamics and Validation by Calorimetry |
| title_full | Thermodynamics and Kinetics of Glycolytic Reactions. Part I: Kinetic Modeling Based on Irreversible Thermodynamics and Validation by Calorimetry |
| title_fullStr | Thermodynamics and Kinetics of Glycolytic Reactions. Part I: Kinetic Modeling Based on Irreversible Thermodynamics and Validation by Calorimetry |
| title_full_unstemmed | Thermodynamics and Kinetics of Glycolytic Reactions. Part I: Kinetic Modeling Based on Irreversible Thermodynamics and Validation by Calorimetry |
| title_short | Thermodynamics and Kinetics of Glycolytic Reactions. Part I: Kinetic Modeling Based on Irreversible Thermodynamics and Validation by Calorimetry |
| title_sort | thermodynamics and kinetics of glycolytic reactions part i kinetic modeling based on irreversible thermodynamics and validation by calorimetry |
| topic | biothermodynamics glycolysis isothermal titration calorimetry systems biology |
| url | https://www.mdpi.com/1422-0067/21/21/8341 |
| work_keys_str_mv | AT kristinavogel thermodynamicsandkineticsofglycolyticreactionspartikineticmodelingbasedonirreversiblethermodynamicsandvalidationbycalorimetry AT thorstengreinert thermodynamicsandkineticsofglycolyticreactionspartikineticmodelingbasedonirreversiblethermodynamicsandvalidationbycalorimetry AT moniquereichard thermodynamicsandkineticsofglycolyticreactionspartikineticmodelingbasedonirreversiblethermodynamicsandvalidationbycalorimetry AT christophheld thermodynamicsandkineticsofglycolyticreactionspartikineticmodelingbasedonirreversiblethermodynamicsandvalidationbycalorimetry AT haukeharms thermodynamicsandkineticsofglycolyticreactionspartikineticmodelingbasedonirreversiblethermodynamicsandvalidationbycalorimetry AT thomasmaskow thermodynamicsandkineticsofglycolyticreactionspartikineticmodelingbasedonirreversiblethermodynamicsandvalidationbycalorimetry |