Difference between revisions of "MEK-Activation(Raf1)"

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<!--First the measured values are divided by the enzyme amount used. In the paper it says: "The assay mixture contains either 0.82 nM COT30-397, [...] in the presence of 5 mM MnCl<sub>2</sub>; or 1.7 nM COT30-397,[...] in the presence of 10 mM MgCl<sub>2</sub>."<ref> Yong Jia et al. (2005) "Purification and kinetic characterization of recombinant human mitogen-activated protein kinase kinase kinase COT and the complexes with its cellular partner NF-kappa B1 p105." ''Arch Biochem Biophys'' 441.1, pp. 64-74. ([http://www.ncbi.nlm.nih.gov/pubmed/16087150 pmid:16087150]) </ref>
 
<!--First the measured values are divided by the enzyme amount used. In the paper it says: "The assay mixture contains either 0.82 nM COT30-397, [...] in the presence of 5 mM MnCl<sub>2</sub>; or 1.7 nM COT30-397,[...] in the presence of 10 mM MgCl<sub>2</sub>."<ref> Yong Jia et al. (2005) "Purification and kinetic characterization of recombinant human mitogen-activated protein kinase kinase kinase COT and the complexes with its cellular partner NF-kappa B1 p105." ''Arch Biochem Biophys'' 441.1, pp. 64-74. ([http://www.ncbi.nlm.nih.gov/pubmed/16087150 pmid:16087150]) </ref>
 
<math>\frac{15.4\; \frac{1}{min}}{8.2 \cdot 10^{-4}\; \mu M}\; \pm\; \frac{0.7\; \frac{1}{min}}{8.2 \cdot 10^{-4}\; \mu M} = 1.8780 \cdot 10^{4}\; \pm\; 8.5366 \cdot 10^{2}\; \frac{1}{\mu M \cdot min}</math>
 
<math>\frac{15.4\; \frac{1}{min}}{8.2 \cdot 10^{-4}\; \mu M}\; \pm\; \frac{0.7\; \frac{1}{min}}{8.2 \cdot 10^{-4}\; \mu M} = 1.8780 \cdot 10^{4}\; \pm\; 8.5366 \cdot 10^{2}\; \frac{1}{\mu M \cdot min}</math>
 
 
 
<math>\frac{14.7\ \frac{1}{min}}{1.7 \cdot 10^{-3}\; \mu M}\; \pm\; \frac{1.2\ \frac{1}{min}}{1.7 \cdot 10^{-3}\; \mu M} = 8.6471 \cdot 10^{3}\; \pm\; 7.0588 \cdot 10^{2}\; \frac{1}{\mu M \cdot min}</math>-->
 
<math>\frac{14.7\ \frac{1}{min}}{1.7 \cdot 10^{-3}\; \mu M}\; \pm\; \frac{1.2\ \frac{1}{min}}{1.7 \cdot 10^{-3}\; \mu M} = 8.6471 \cdot 10^{3}\; \pm\; 7.0588 \cdot 10^{2}\; \frac{1}{\mu M \cdot min}</math>-->
 
  
 
The values are averaged and then divided by 60 s to change the unit.  
 
The values are averaged and then divided by 60 s to change the unit.  
  
  
<math> k_{cat} = \frac{\frac{15.4 + 14.7}{2}}{60\; s \cdot \mu M}\; \pm\; = 0.25083\; \frac{1}{s}</math>
+
<math> k_{cat} = \frac{\frac{15.4 + 14.7}{2}}{60\; s} = 0.25083\; \frac{1}{s}</math>
  
 
<math>\sigma_{k_{cat}} = \frac{1}{2} \cdot (\frac{0.7}{15.4} + \frac{1.2}{14.7})\cdot 0.25083\; \frac{1}{s} = 0.0159386\; \frac{1}{s}</math>
 
<math>\sigma_{k_{cat}} = \frac{1}{2} \cdot (\frac{0.7}{15.4} + \frac{1.2}{14.7})\cdot 0.25083\; \frac{1}{s} = 0.0159386\; \frac{1}{s}</math>

Latest revision as of 10:28, 12 June 2014

Binding Reaction

\text{Mek} + \text{Raf1PP}  \rightleftharpoons \text{MekPP} + \text{Raf1PP}


Kinetic Equation

v_{\text{Mek-Activation}} = \frac{k_{cat} \cdot [\text{Raf1PP}] \cdot [\text{Mek}] \cdot (1-\frac{[\text{MekPP}]}{[\text{Mek}] \cdot K_{eq}})}{Km_{\text{Mek}} \cdot (1 + \frac{[\text{Mek}]}{Km_{\text{Mek}}} + \frac{[\text{MekPP}]}{Km_{\text{MekPP}}})}

final Parameter

 k_{\text{cat}} = 0.25083\; \pm\; 0.0159386 \cdot 1.5\; \frac{1}{s} = 0.25083\; \pm\; 0.0239079\; \frac{1}{s}

 K_{m} = 0.8\; \mu M \pm 0.5348 \cdot 0.8\; \mu M = 0.8\; \mu M \pm 0.428\; \mu M

Parameter Reference

Parameter Calculation Reference

kcat:

The values are averaged and then divided by 60 s to change the unit.


 k_{cat} = \frac{\frac{15.4 + 14.7}{2}}{60\; s} = 0.25083\; \frac{1}{s}

\sigma_{k_{cat}} = \frac{1}{2} \cdot (\frac{0.7}{15.4} + \frac{1.2}{14.7})\cdot 0.25083\; \frac{1}{s} = 0.0159386\; \frac{1}{s}


The so calculated error is increased by 1.5, because only a similar reaction is measured and so the uncertainty about the parameter is larger.


Km:


Force et al. measured a Km for c-Raf1:
Km = 0.8 μM [1]

For the uncertainty estimation the averaged relative error is used.

L Mek-Activation.png

Yong Jia et al. (2005) [2] table 3


KmP value and equilibrium constant

The Km value for the product is assumed to be similar but slightly higher than the the Km value of the substrate because of the similarity of the both species. Therefore the Km value of the substrate is multiplied by 1.05 to gain the one of the product and the uncertainty is increased by increasing the error on Kmsubstrate by 50%.

For information about the equilibrium constant please see here.

References

  1. Force T. et al (1994) "Enzymatic characteristics of the c-Raf1 protein kinase." Proc Natl Acad Sci USA 91.4:1270-1274
  2. Yong Jia et al. (2005) "Purification and kinetic characterization of recombinant human mitogen-activated protein kinase kinase kinase COT and the complexes with its cellular partner NF-kappa B1 p105." Arch Biochem Biophys 441.1, pp. 64-74. (pmid:16087150)