Difference between revisions of "Team:Aalto-Helsinki/Kinetics"

m (added some equations)
m (added some equations)
Line 102: Line 102:
 
<p>Acetoacetyl-CoA + NADPH + H\(^+\) \(\rightarrow\) 3-Hydroxybutyryl-CoA + NADP\(^+\)</p>
 
<p>Acetoacetyl-CoA + NADPH + H\(^+\) \(\rightarrow\) 3-Hydroxybutyryl-CoA + NADP\(^+\)</p>
  
−
<p>\[ \frac{K_{cat}^{FadB2}\cdot [FadB2] \cdot [Acetoacetyl\text{-}CoA]\cdot [NADPH]}{[Acetoacetyl\text{-}CoA]\cdot [NADPH] + K_{M}^{FadB2:NADPH}\cdot [Acetoacetyl\text{-}CoA]+K_{M}^{FadB2:Acetoacetyl\text{-}CoA}\cdot [NADPH]} \]</p>
 
  
 
<table class="table table-bordered">
 
<table class="table table-bordered">
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<p>3-hydroxybutyryl-CoA \(\rightarrow\) Crotonyl-CoA + H\( _2\)O</p>
 
<p>3-hydroxybutyryl-CoA \(\rightarrow\) Crotonyl-CoA + H\( _2\)O</p>
 +
 +
<p>\[ \frac{K_{cat}^{Crt}\cdot [Crt]\cdot [3\text{-}hydroxybutyryl\text{-}CoA]}{K_{M}^{Crt:3\text{-}Hydroxybutyryl\text{-}CoA} +[3\text{-}hydroxybutyryl\text{-}CoA]} \]</p>
  
 
<table class="table table-bordered">
 
<table class="table table-bordered">
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<p>Crotonyl-CoA + NADH + H\( ^+\) \(\rightarrow\) Butyryl-CoA + NAD\( ^+\)</p>
 
<p>Crotonyl-CoA + NADH + H\( ^+\) \(\rightarrow\) Butyryl-CoA + NAD\( ^+\)</p>
 +
 +
<p>\[ \frac{K_{cat}^{Ter}\cdot [Ter] \cdot [Crotonyl\text{-}CoA]\cdot [NADH]}{[Crotonyl\text{-}CoA]\cdot [NADH] + K_{M}^{Ter:NADH}\cdot [Crotonyl\text{-}CoA]+K_{M}^{Ter:Crotonyl\text{-}CoA}\cdot [NADH]} \]</p>
  
 
<table class="table table-bordered">
 
<table class="table table-bordered">
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<p>Butyryl-CoA + H\( _2\)O \(\rightarrow\) Butyrate + CoA</p>
 
<p>Butyryl-CoA + H\( _2\)O \(\rightarrow\) Butyrate + CoA</p>
 +
 +
<p>\[ \frac{K_{cat}^{YciA}\cdot [YciA]\cdot [Butyryl\text{-}CoA]}{K_{M}^{YciA:Butyryl\text{-}CoA} +[Butyryl\text{-}CoA]} \]</p>
  
 
<table class="table table-bordered">
 
<table class="table table-bordered">
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<h2 id="sfp">Sfp</h2>
 
<h2 id="sfp">Sfp</h2>
 
<h2 id="ado">Ado</h2>
 
<h2 id="ado">Ado</h2>
 +
 +
 +
 +
<p>\[ \frac{K_{cat}^{Ado}\cdot [Ado]\cdot [Butyrate]}{K_{M}^{Ado:Butyrate} +[Butyrate]} \]</p>
  
 
<table class="table table-bordered">
 
<table class="table table-bordered">

Revision as of 12:22, 6 August 2015

Kinetics

AtoB

2\(\cdot\)Actyl-CoA \(\rightarrow\) Acetoacetyl-CoA + CoA

\[ \frac{K_{cat}^{AtoB} \cdot [AtoB] \cdot [Acetyl\text{-}CoA]^2}{[Acetyl\text{-}CoA]^2+2\cdot K_{M}^{AtoB:Acetyl\text{-}CoA}\cdot [Acetyl\text{-}CoA]} \]

Constant

Value

Source

To note

\( K_{cat}^{AtoB} \)

10653 1/min

link

Forward reaction

\( K_{M}^{AtoB:Acetyl\text{-}CoA} \)

0.00047 mol/l

link

Is there something special about this?

FadB2

Acetoacetyl-CoA + NADPH + H\(^+\) \(\rightarrow\) 3-Hydroxybutyryl-CoA + NADP\(^+\)

Constant

Value

Source

To note

\( K_{cat}^{FadB2} \)

0.677 1/min

link

Forward reaction

\( K_{cat}^{FadB2} \)

0.723 1/min

link

Reverse reaction

\( K_{M}^{FadB2:Acetoacetyl\text{-}CoA} \)

65.6 mol/l

link

Forward reaction

\( K_{M}^{FadB2:NADPH} \)

50 mol/l

link

Forward reaction

\( K_{M}^{FadB2:3\text{-}Hydroxybutyryl\text{-}CoA} \)

43.5 mol/l

link

Reverse reaction

\( K_{M}^{FadB2:NADP^+} \)

29.5 mol/l

link

Reverse reaction

Hdb

Acetoacetyl-CoA + NADPH + H\(^+\) \(\rightarrow\) 3-Hydroxybutyryl-CoA + NADP\(^+\)

\[ \frac{K_{cat}^{Hdb}\cdot [Hbd] \cdot [Acetoacetyl\text{-}CoA]\cdot [NADPH]}{[Acetoacetyl\text{-}CoA]\cdot [NADPH] + K_{M}^{Hdb:NADPH}\cdot [Acetoacetyl\text{-}CoA]+K_{M}^{Hdb:Acetoacetyl\text{-}CoA}\cdot [NADPH]} \]

Constant

Value

Source

To note

\( K_{cat}^{Hdb} \)

336.4 1/min

link

Forward reaction

\( K_{M}^{Hdb:Acetoacetyl\text{-}CoA} \)

5e-5 mol/l

link

Is there something special about this?

\( K_{M}^{Hdb:NADPH} \)

7e-5 mol/l

link

Is there something special about this?

Crt

3-hydroxybutyryl-CoA \(\rightarrow\) Crotonyl-CoA + H\( _2\)O

\[ \frac{K_{cat}^{Crt}\cdot [Crt]\cdot [3\text{-}hydroxybutyryl\text{-}CoA]}{K_{M}^{Crt:3\text{-}Hydroxybutyryl\text{-}CoA} +[3\text{-}hydroxybutyryl\text{-}CoA]} \]

Constant

Value

Source

To note

\( K_{cat}^{Crt} \)

1310.8 1/min

link

Forward reaction

\( K_{M}^{Crt:3\text{-}Hydroxybutyryl\text{-}CoA} \)

3e-5 mol/l

link

Is there something special about this?

Ter

Crotonyl-CoA + NADH + H\( ^+\) \(\rightarrow\) Butyryl-CoA + NAD\( ^+\)

\[ \frac{K_{cat}^{Ter}\cdot [Ter] \cdot [Crotonyl\text{-}CoA]\cdot [NADH]}{[Crotonyl\text{-}CoA]\cdot [NADH] + K_{M}^{Ter:NADH}\cdot [Crotonyl\text{-}CoA]+K_{M}^{Ter:Crotonyl\text{-}CoA}\cdot [NADH]} \]

Constant

Value

Source

To note

\( K_{cat}^{Ter} \)

1881.6 1/min

link

Forward reaction

\( K_{M}^{Ter:Crotonyl\text{-}CoA} \)

2.7e-06 mol/l

link

Is there something special about this?

\( K_{M}^{Ter:NADH} \)

5.2e-06 mol/l

link

Is there something special about this?

\( K_{I}^{Ter:Butyryl\text{-}CoA} \)

1.98e-07 mol/l

link

Is there something special about this?

YciA

Butyryl-CoA + H\( _2\)O \(\rightarrow\) Butyrate + CoA

\[ \frac{K_{cat}^{YciA}\cdot [YciA]\cdot [Butyryl\text{-}CoA]}{K_{M}^{YciA:Butyryl\text{-}CoA} +[Butyryl\text{-}CoA]} \]

Constant

Value

Source

To note

\( K_{cat}^{YciA} \)

1320 1/min

link

Forward reaction

\( K_{M}^{YciA:Butyryl\text{-}CoA} \)

3.5e-06 mol/l

link

Is there something special about this?

Car

Butyrate + NADPH + ATP \(\rightarrow\) Butyraldehyde + NADP\(^+\) + AMP + 2P\(_i\)

Constant

Value

Source

To note

\( K_{cat}^{Car} \)

150 1/min

link

Forward reaction

\( K_{M}^{Car:Butyrate} \)

0.013 mol/l

link

Is there something special about this?

\( K_{M}^{Car:NADPH} \)

4.8e-05 mol/l

link

Is there something special about this?

\( K_{I}^{Car:ATP} \)

0.000115 mol/l

link

Is there something special about this?

Sfp

Ado

\[ \frac{K_{cat}^{Ado}\cdot [Ado]\cdot [Butyrate]}{K_{M}^{Ado:Butyrate} +[Butyrate]} \]

Constant

Value

Source

To note

\( K_{cat}^{Ado} \)

0.215 1/min

link

Forward reaction

\( K_{M}^{Ado:Butyraldehyde} \)

0.0101 mol/l

link

Is there something special about this?

Other Constants

This is a table of already known typical concentrations in a cell that we use in our model.

Constant

Value

Source

To note

[Acetyl-CoA]

0.00061 mol/l

link

Is there something special about this?

[Acetoacetyl-CoA]

2.2e-05 mol/l

link

Is there something special about this?

[CoA]

0.00014 mol/l

link

Is there something special about this?

[NADPH]

00012 mol/l

link

Is there something special about this?

[NADP\( ^+\)]

2.1e-06 mol/l

link

Is there something special about this?

[NADH]

8.3e-05 mol/l

link

Is there something special about this?

[NAD\( ^+\)]

0.0026 mol/l

link

Is there something special about this?

[ATP]

0.0096 mol/l

link

Is there something special about this?

[AMP]

0.00028 mol/l

link

Is there something special about this?

[H\( _2\)O]

38.85 mol/l

link

Is there something special about this?