Difference between revisions of "Kinetic model of Central Metabolism"
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==Global parameters== | ==Global parameters== | ||
| − | Some of the Vmax value in the paper "Modeling cancer glycolysis" is given in <math> U \times \text{(mg total cellular protein)}^{-1} </math> unit <ref name="Hernandez2011"></ref>. To homogenize the units it is then converted back to <math>\frac{mM}{min}</math> by multiplying <math> U \times \text{(mg total cellular protein)}^{-1} </math> with 65 as the HeLa cell was incubated in <math> 65 \frac{\text{mg protein}}{\text{mL cell volume}}</math>. | + | Some of the Vmax value in the paper "Modeling cancer glycolysis" is given in <math> U \times \text{(mg total cellular protein)}^{-1} </math> unit <ref name="Hernandez2011"></ref>. To homogenize the units it is then converted back to <math>\frac{mM}{min}</math> by first converting <math>\mu</math>M to <math>mM</math> and then multiplying <math> U \times \text{(mg total cellular protein)}^{-1} </math> with 65 as the HeLa cell was incubated in <math> 65 \frac{\text{mg protein}}{\text{mL cell volume}}</math>. |
==References== | ==References== | ||
<references/> | <references/> | ||
Revision as of 12:31, 22 September 2014
A kinetic model of glycolysis with serine activation is constructed from the literature data [1][2][3][4][5].
Contents
Description of the model
Schematic diagram of the model is given here. The dotted line represents activation(+) or inhibition(-) and the dashed arrow indicate Pentose Phosphate Pathway reactions not included in the model. Click on a reaction to have more information
Reactions
Details of the abbreviations for this model is listed here. Reactions of the model are listed below.
Initial concentration of the metabolites can be found here
Model File
The SBML file of the model can be found here
Notes
Necessary observation during model building and simulation is noted here.
Global parameters
Some of the Vmax value in the paper "Modeling cancer glycolysis" is given in 
unit [1]. To homogenize the units it is then converted back to 
by first converting 
M to Failed to parse (Cannot store math image on filesystem.): mM
and then multiplying with 65 as the HeLa cell was incubated in 
.
References
- ↑ 1.0 1.1 Marín-Hernández A, Gallardo-Pérez JC, Rodríguez-Enríquez S et al (2011). Modeling cancer glycolysis. Biochim Biophys Acta, 1807:755–767 (doi)
- ↑ Turnaev II, Ibragimova SS, Usuda Y et al (2006). Mathematical modeling of serine and glycine synthesis regulation in Escherichia coli. Proceedings of the fifth international conference on bioinformatics of genome regulation and structure 2:78–83
- ↑ Smallbone K, Stanford NJ (2013). Kinetic modeling of metabolic pathways: Application to serine biosynthesis. In: Systems Metabolic Engineering, Humana Press. pp. 113–121
- ↑ Palm, D.C. (2013). The regulatory design of glycogen metabolism in mammalian skeletal muscle (Ph.D.). University of Stellenbosch
- ↑ Ettore Murabito (2010). Application of differential metabolic control analysis to identify new targets in cancer treatment (Ph.D.). University of Manchester
