Difference between revisions of "Team:Aalto-Helsinki/Kinetics"
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<p>2\(\cdot\)Acetyl-CoA \(\rightarrow\) Acetoacetyl-CoA + CoA</p> | <p>2\(\cdot\)Acetyl-CoA \(\rightarrow\) Acetoacetyl-CoA + CoA</p> | ||
− | <p>Vf/Vr: 22 | + | <p>AtoB is found from <span style="font-style:italic">Escherichia Coli</span>. The reaction shown above is reversible, but since the ratio of forward and reversible reaction favores strongly the forward one <span style="font-size:13px">(Vf/Vr: 22.3, Source: Molecular and catalytic properties of the acetoacetyl-coenzyme A thiolase of Escherichia coli; Archives of Biochemistry and Biophysics Volume 176, Issue 1, September 1976, Pages 159–170)</span> we can approximate is as irreversible.</p> |
− | </p> | + | <p>Based on <a href="http://www.sciencedirect.com/science/article/pii/S0022283605000409">this</a> article, we know that the reaction follows Ping Pong Bi Bi -model and so get the following rate equation.</p> |
<p>\[ \frac{K_{cat}^{AtoB} \cdot [AtoB] \cdot [Acetyl\text{-}CoA]^2}{[Acetyl\text{-}CoA]^2+2\cdot K_{M}^{AtoB:Acetyl\text{-}CoA}\cdot [Acetyl\text{-}CoA]} \]</p> | <p>\[ \frac{K_{cat}^{AtoB} \cdot [AtoB] \cdot [Acetyl\text{-}CoA]^2}{[Acetyl\text{-}CoA]^2+2\cdot K_{M}^{AtoB:Acetyl\text{-}CoA}\cdot [Acetyl\text{-}CoA]} \]</p> | ||
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<p>Acetoacetyl-CoA + NADPH + H\(^+\) \(\rightarrow\) 3-Hydroxybutyryl-CoA + NADP\(^+\)</p> | <p>Acetoacetyl-CoA + NADPH + H\(^+\) \(\rightarrow\) 3-Hydroxybutyryl-CoA + NADP\(^+\)</p> | ||
− | <p> | + | <p>The enzyme is from Clostridium acetobutylicum, but only values to be found were for Clostridium Kluyveri. This is not a problem however since the species are very close relatives and so the values ought to be close enough for comparison.</p> |
− | <p>The specific activity of the 3-hydroxybutyryl-CoA dehydrogenase (forward) as measured in the direction of acetoacetyl-CoA reduction | + | <p>The reaction is reversible, but according to Purification and Properties of NADP-Dependent L( +)-3-Hydroxybutyryl-CoA Dehydrogenase from Clostridiurn kluyveri; Eur. J. Biochem. 32,51-56 (1973), the specific activity of the 3-hydroxybutyryl-CoA dehydrogenase (forward) as measured in the direction of acetoacetyl-CoA reduction is 478.6 U/mg protein and the rate of the oxidation reaction (reverse) proceeded with 36.6 U / mg protein so we can again approximate the reaction as irreversible.</p> |
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− | </p> | + | <p>We don’t consider how H^+ affects the reaction which is justified by knowing that its concentration in the cell should always be quite constant; otherwise the cell will die. This is why we can assume that the reaction is either random or ordered Bi Bi -reaction and so the rate equation is as follows.</p> |
<p>\[ \frac{K_{cat}^{Hdb}\cdot [Hbd] \cdot [Acetoacetyl\text{-}CoA]\cdot [NADPH]}{[Acetoacetyl\text{-}CoA]\cdot [NADPH] + K_{M}^{Hdb:NADPH}\cdot [Acetoacetyl\text{-}CoA]+K_{M}^{Hdb:Acetoacetyl\text{-}CoA}\cdot [NADPH]} \]</p> | <p>\[ \frac{K_{cat}^{Hdb}\cdot [Hbd] \cdot [Acetoacetyl\text{-}CoA]\cdot [NADPH]}{[Acetoacetyl\text{-}CoA]\cdot [NADPH] + K_{M}^{Hdb:NADPH}\cdot [Acetoacetyl\text{-}CoA]+K_{M}^{Hdb:Acetoacetyl\text{-}CoA}\cdot [NADPH]} \]</p> | ||
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<td><p>336.4 1/min</p></td> | <td><p>336.4 1/min</p></td> | ||
<td><p>Purification and Properties of NADP-Dependent <br/>L( +)-3-Hydroxybutyryl-CoA Dehydrogenase from Clostridiurn kluyveri; Eur. J. Biochem. 32,51-56 (1973)</p></td> | <td><p>Purification and Properties of NADP-Dependent <br/>L( +)-3-Hydroxybutyryl-CoA Dehydrogenase from Clostridiurn kluyveri; Eur. J. Biochem. 32,51-56 (1973)</p></td> | ||
− | <td><p>Forward reaction</p></td> | + | <td><p>Forward reaction, Clostridium Kluyveri</p></td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
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<td><p>5e-5 mol/l</p></td> | <td><p>5e-5 mol/l</p></td> | ||
<td><p>Purification and Properties of NADP-Dependent <br/>L( +)-3-Hydroxybutyryl-CoA Dehydrogenase from Clostridiurn kluyveri; Eur. J. Biochem. 32,51-56 (1973)</p></td> | <td><p>Purification and Properties of NADP-Dependent <br/>L( +)-3-Hydroxybutyryl-CoA Dehydrogenase from Clostridiurn kluyveri; Eur. J. Biochem. 32,51-56 (1973)</p></td> | ||
− | <td><p> | + | <td><p>Clostridium Kluyveri</p></td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
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<td><p>7e-5 mol/l</p></td> | <td><p>7e-5 mol/l</p></td> | ||
<td><p>Purification and Properties of NADP-Dependent <br/>L( +)-3-Hydroxybutyryl-CoA Dehydrogenase from Clostridiurn kluyveri; Eur. J. Biochem. 32,51-56 (1973)</p></td> | <td><p>Purification and Properties of NADP-Dependent <br/>L( +)-3-Hydroxybutyryl-CoA Dehydrogenase from Clostridiurn kluyveri; Eur. J. Biochem. 32,51-56 (1973)</p></td> | ||
− | <td><p> | + | <td><p>Clostridium Kluyveri</p></td> |
</tr> | </tr> | ||
</tbody> | </tbody> |
Revision as of 07:03, 11 August 2015