Difference between revisions of "Mitocondrial pyruvate metabolism"
(→In this model) |
|||
Line 34: | Line 34: | ||
*The steady state concentrations for substrates and products are <math>ATP=8.7 \pm 3 (5)</math>, <math>ADP = 2.7 \pm 1.3</math>, <math>Pyruvate = 8.5 \pm 3.6</math> and <math>Pi = 7.5</math>. | *The steady state concentrations for substrates and products are <math>ATP=8.7 \pm 3 (5)</math>, <math>ADP = 2.7 \pm 1.3</math>, <math>Pyruvate = 8.5 \pm 3.6</math> and <math>Pi = 7.5</math>. | ||
*The <math>K_1</math> value calculated from the above mentioned values are <math>2.20E-018</math> | *The <math>K_1</math> value calculated from the above mentioned values are <math>2.20E-018</math> | ||
− | *To calculate the uncertainty of <math>K_1</math> we first looked at the uncertainty on the substrate and product concentration. The maximum uncertainty reported for these values are <math>\approx 50%</math>. In our model we considered this <math>50%</math> uncertainty in its mean value giving value of <math>1.099E-018</math> | + | *To calculate the uncertainty of <math>K_1</math> we first looked at the uncertainty on the substrate and product concentration. The maximum uncertainty reported for these values are <math>\approx 50%</math>. In our model we considered this <math>50%</math> uncertainty in its mean value giving value of <math>2.20E^{-018} \pm 1.099E^{-018}</math> |
==Parameter values== | ==Parameter values== | ||
Line 48: | Line 48: | ||
| | | | ||
|} | |} | ||
+ | |||
+ | ==Parameters with uncertainty== | ||
+ | {|class="wikitable" | ||
+ | ! Parameter | ||
+ | ! Value | ||
+ | ! Organism | ||
+ | ! Remarks | ||
+ | |- | ||
+ | |<math>K_1</math> | ||
+ | |<math>2.20E^{-018} \pm 1.099E^{-018}</math> | ||
+ | | | ||
+ | | | ||
+ | |} | ||
+ | |||
==References== | ==References== | ||
<references/> | <references/> |
Revision as of 14:38, 12 May 2014
Mitocondrial pyruvate metabolism(MPM) is an enzyme that generates ATP form pyruvate.
Contents
Chemical reaction
Rate equation
- Chemical reactions proceed to equilibrium within closed systems. For a simple reaction it is defined as where forward and reverse rates are equal.
- Equilibrium is not reached in open system due to influx and outflux. Mass action ratio[1] for reaction is defined as where subscript ob represents observable at a given point.
- Deviation from equilibrium is measured with Disequilibrium constant as
- Given the simple uni molecular reaction the mass action equation can be modified as
Considering and we have,
- The generalized arbitrary mass action ratio gives us
For eg. for the reaction , the rate law would be
- This equation demonstrates how a rate expression can be divided into parts that include both kinetics and thermodynamic properties [2].
- Given the net rate of reaction , we have
In this model
- The rate law is defined as
- The overall standard free-energy change for Pyruvate metabolism is Failed to parse (Cannot store math image on filesystem.): \Delta G^o{'}= -30.5 Kj/Mol [3].
- Calculating value from these free energy gives Failed to parse (Cannot store math image on filesystem.): \Delta G' = - 30.5\ kJ.mol^{-1} , Failed to parse (Cannot store math image on filesystem.): Keq = exp(-\frac{\Delta G'}{RT}) = exp(\frac{30500}{8.31*298.15}) \approx 221941.39
- The Flux of pyruvate consumed by mitochondria measured for AS_30D is [4].
- The steady state concentrations for substrates and products are , , and .
- The value calculated from the above mentioned values are Failed to parse (Cannot store math image on filesystem.): 2.20E-018
- To calculate the uncertainty of we first looked at the uncertainty on the substrate and product concentration. The maximum uncertainty reported for these values are . In our model we considered this uncertainty in its mean value giving value of Failed to parse (Cannot store math image on filesystem.): 2.20E^{-018} \pm 1.099E^{-018}
Parameter values
Parameter | Value | Organism | Remarks |
---|---|---|---|
Failed to parse (Cannot store math image on filesystem.): 2.20E^{-018} |
Parameters with uncertainty
Parameter | Value | Organism | Remarks |
---|---|---|---|
Failed to parse (Cannot store math image on filesystem.): 2.20E^{-018} \pm 1.099E^{-018} |
References
- ↑ Hess B. and Brand K. (1965), Enzymes and metabolite profiles. In Control of energy metabolism. III. Ed. B. Chance, R. K. Estabrook and J. R. Williamson. New York: Academic Press
- ↑ Sauro H M, Enzyme Kinetics for Systems Biology, Second Edition, Ambrosius Publishing (2013), ISBN-10: 0-9824773-3-3
- ↑ Nelson D. and Cox M. (2008), Lehninger Principles of Biochemistry, Fight Edition, W.H. Freeman and Company, ISBN-10: 071677108X
- ↑ Marín-Hernández A, Gallardo-Pérez JC, Rodríguez-Enríquez S et al (2011) Modeling cancer glycolysis. Biochim Biophys Acta 1807:755–767 (doi)