Difference between revisions of "Dehydrogenase"

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(Parameters with uncertainty)
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==Parameters with uncertainty==
 
==Parameters with uncertainty==
* This is a pseudo-reaction, modelled using mass action kinetics (i.e., as non-saturable, non-enzymatic reactions) to maintain maximal compatibility with Pyridine Nucleotides balances. The parameter values were adjusted through model simulations and the values chosen were those that best predicted NAD+ concentration (determined experimentally) in Hernandez ''et. al.'' <ref name="Hernandez2011"></ref>. No information is available about the uncertainty of these parameters. As these parameters are strictly positive, they are sampled using a log-normal distribution as are and values. The means are set to the value using fitted by Hernandez et al. <ref name="Hernandez2011"></ref> for the fixed-parameter model. The sampling of the parameters are made to fall within <math>[0.01\times mean \quad 1000 \times mean  ]</math> to allow a large exploration of the parameter space.
+
* This is a pseudo-reaction, modelled using mass action kinetics (i.e., as non-saturable, non-enzymatic reactions) to maintain maximal compatibility with Pyridine Nucleotides balances. The parameter values were adjusted through model simulations and the values chosen were those that best predicted NAD+ concentration (determined experimentally) in Hernandez ''et. al.'' <ref name="Hernandez2011"></ref>. No information is available about the uncertainty of these parameters. As these parameters are strictly positive, they are sampled using a log-normal distribution as are and values. The means are set to the value using fitted by Hernandez et al. <ref name="Hernandez2011"></ref> for the fixed-parameter model. The sampling of the parameters are made to fall within <math>[0.001\times mean \quad 1000 \times mean  ]</math> to allow a large exploration of the parameter space.
  
  
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|-
 
|<math>K_{1}</math>
 
|<math>K_{1}</math>
|<math>250 \pm 130078.125</math>
+
|Sampled between 0.25 and 250000
 
|rowspan="2"|HeLa cell line
 
|rowspan="2"|HeLa cell line
 
|rowspan="2"|
 
|rowspan="2"|
 
|-
 
|-
 
|<math>K_{2}</math>
 
|<math>K_{2}</math>
|1<ref name="Hernandez2011"></ref>
+
|Sampled between 0.001 and 1000
 
|}
 
|}
  
 
==References==
 
==References==
 
<references/>
 
<references/>

Revision as of 11:07, 15 May 2014


A dehydrogenase is an enzyme that oxidizes a substrate by a reduction reaction that transfers one or more hydrides (H) to an electron acceptor, usually Nicotinamide adenine dinucleotide NAD+/NADP.

Chemical reaction

 NADH \rightleftharpoons NAD

Rate equation

Reversible mass action rate law is used

K_{1}[NADH] - K_{2}[NAD]

Parameters

Parameter Value Organism Remarks
K_{1} 250 [1] HeLa cell line
K_{2} 1[1]


Parameters with uncertainty

  • This is a pseudo-reaction, modelled using mass action kinetics (i.e., as non-saturable, non-enzymatic reactions) to maintain maximal compatibility with Pyridine Nucleotides balances. The parameter values were adjusted through model simulations and the values chosen were those that best predicted NAD+ concentration (determined experimentally) in Hernandez et. al. [1]. No information is available about the uncertainty of these parameters. As these parameters are strictly positive, they are sampled using a log-normal distribution as are and values. The means are set to the value using fitted by Hernandez et al. [1] for the fixed-parameter model. The sampling of the parameters are made to fall within [0.001\times mean \quad 1000 \times mean  ] to allow a large exploration of the parameter space.


Parameter Value Organism Remarks
K_{1} Sampled between 0.25 and 250000 HeLa cell line
K_{2} Sampled between 0.001 and 1000

References

  1. 1.0 1.1 1.2 1.3 Marín-Hernández A, Gallardo-Pérez JC, Rodríguez-Enríquez S et al (2011) Modeling cancer glycolysis. Biochim Biophys Acta 1807:755–767 (doi)