Difference between revisions of "Team:Manchester/Model/HorseRadishPeroxidaseReaction"
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</table> | </table> | ||
</br> | </br> | ||
| − | + | ||
</br> | </br> | ||
<p id="ParameterSourcing" style="border-bottom: 1px black solid ;font-size:25px;text-weight:bold;display:inline-block">Parameter Sourcing</p> | <p id="ParameterSourcing" style="border-bottom: 1px black solid ;font-size:25px;text-weight:bold;display:inline-block">Parameter Sourcing</p> | ||
<p> | <p> | ||
| − | + | K<sub>cat</sub> and K<sub>m</sub> parameters were collected from | |
<a href="http://www.brenda-enzymes.org/enzyme.php?ecno=1.11.1.7" target="_blank">BRENDA</a> | <a href="http://www.brenda-enzymes.org/enzyme.php?ecno=1.11.1.7" target="_blank">BRENDA</a> | ||
</p> | </p> | ||
<p> | <p> | ||
| − | + | K<sub>eq</sub> was calculated using the Van’t Hoff equation using the Gibbs free energy sourced from | |
<a href="http://metacyc.org/META/NEW-IMAGE?type=REACTION&object=PEROXID-RXN" target="_blank">MetaCyc</a> | <a href="http://metacyc.org/META/NEW-IMAGE?type=REACTION&object=PEROXID-RXN" target="_blank">MetaCyc</a> | ||
</p> | </p> | ||
$$ K_{eq} = e^{\frac{-\Delta G} {RT}}$$ | $$ K_{eq} = e^{\frac{-\Delta G} {RT}}$$ | ||
</br> | </br> | ||
| − | |||
</br> | </br> | ||
<p id="UncertainParameters" style="border-bottom: 1px black solid ;font-size:25px;text-weight:bold;display:inline-block">Parameters with uncertainty</p> | <p id="UncertainParameters" style="border-bottom: 1px black solid ;font-size:25px;text-weight:bold;display:inline-block">Parameters with uncertainty</p> | ||
<p> | <p> | ||
| − | + | <b>K<sub>m</sub><b> | |
</p> | </p> | ||
<img class="full" src="https://static.igem.org/mediawiki/2016/e/e1/T--Manchester--HRPKmPDF.jpg" alt="Probability density function for the Km of Horseradish Peroxidase" /> | <img class="full" src="https://static.igem.org/mediawiki/2016/e/e1/T--Manchester--HRPKmPDF.jpg" alt="Probability density function for the Km of Horseradish Peroxidase" /> | ||
<p> | <p> | ||
| − | Uncertainty in | + | Uncertainty in K<sub>m</sub> is introduced through the range of experimental parameters sourced. Properties of the raw data can be seen in the table below: </p> |
<table> | <table> | ||
<th>Property</th> | <th>Property</th> | ||
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</br> | </br> | ||
<p> | <p> | ||
| − | + | <b>K<sub>cat</sub></b> | |
</p> | </p> | ||
<img class="full" src="https://static.igem.org/mediawiki/2016/5/51/T--Manchester--HRPKcatPDF.jpg" alt="Probability density function for the Kcat of Horseradish Peroxidase" /> | <img class="full" src="https://static.igem.org/mediawiki/2016/5/51/T--Manchester--HRPKcatPDF.jpg" alt="Probability density function for the Kcat of Horseradish Peroxidase" /> | ||
<p> | <p> | ||
| − | Uncertainty in | + | Uncertainty in K<sub>cat</sub> is introduced through the range of experimental parameters sourced. Properties of the raw data can be seen in the table below: |
</p> | </p> | ||
<table> | <table> | ||
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</br> | </br> | ||
<p> | <p> | ||
| − | + | <b>K<sub>eq</sub></b> | |
</p> | </p> | ||
<img class="full" src="https://static.igem.org/mediawiki/2016/6/66/T--Manchester--HRPKeqPDF.jpg" alt="Probability density function for the Keq of Horseradish Peroxidase" /> | <img class="full" src="https://static.igem.org/mediawiki/2016/6/66/T--Manchester--HRPKeqPDF.jpg" alt="Probability density function for the Keq of Horseradish Peroxidase" /> | ||
<p> | <p> | ||
| − | Uncertainty in | + | Uncertainty in K<sub>eq</sub> is introduced using a uniform range of temperature variations (298 K ± 5 K). Properties of this can be seen in the table below: |
</p> | </p> | ||
<table> | <table> | ||
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</br> | </br> | ||
| − | |||
| − | |||
</br> | </br> | ||
<a href="https://2016.igem.org/Team:Manchester/Model">Return to overview</a> | <a href="https://2016.igem.org/Team:Manchester/Model">Return to overview</a> | ||
Revision as of 17:35, 19 October 2016
Horseradish Peroxidase Reaction
Oxidation of ABTS using Horseradish Peroxidase (EC 1.11.1.7)
Chemical Equation
$${Hydrogen}\ {Peroxide} + {ABTS} \rightleftharpoons {ABTS}_{Oxidised} + {Water}$$Rate Equation
$$\nu = \frac{K_{cat}[HRP] \frac{[H_2 O_2]}{K_{m,H_2 O_2}}\left({ 1- \frac{[H_2 O_2][ABTS]}{[ABTS_{Oxidised}]} \frac{1}{K_{eq}}} \right)}{1+\frac{[H_2 O_2]}{K_{m,H_2 O_2}}+\frac{[ABTS]}{K_{m,ABTS}}+\frac{[H_2 O_2][ABTS]}{K_{m,ABTS}K_{m,H_2 O_2}}+\frac{[ABTS_{Oxidised}]}{K_{m,ABTS_{Oxidised}}}} $$where:
| Symbol | Meaning |
|---|---|
| $$K_{m,A}$$ | Michaelis constant of species A |
| $$K_{cat}$$ | Turnover number |
| $$[A]$$ | Concentration of A |
| $$ \nu$$ | Reaction Rate |
Parameter Sourcing
Kcat and Km parameters were collected from BRENDA
Keq was calculated using the Van’t Hoff equation using the Gibbs free energy sourced from MetaCyc
$$ K_{eq} = e^{\frac{-\Delta G} {RT}}$$Parameters with uncertainty
Km
Uncertainty in Km is introduced through the range of experimental parameters sourced. Properties of the raw data can be seen in the table below:
| Property | Value |
|---|---|
| Minimum | 0.005 mM |
| Maximum | 23.3 mM |
| Mean | 1.78 mM |
| Parameters Sourced | 50 |
Kcat
Uncertainty in Kcat is introduced through the range of experimental parameters sourced. Properties of the raw data can be seen in the table below:
| Property | Value |
|---|---|
| Minimum | 0.3 s-1 |
| Maximum | 201.8 s-1 |
| Mean | 59.4 s-1 |
| Parameters Sourced | 5 |
Keq
Uncertainty in Keq is introduced using a uniform range of temperature variations (298 K ± 5 K). Properties of this can be seen in the table below:
| Property | Value |
|---|---|
| $$-\Delta G$$ | 254.520071288 kJ |
| Minimum Temperature | 293 K |
| Maximum Temperature | 303 K |
