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Team:UFMG Brazil/Modeling
From 2013.igem.org
(Difference between revisions)
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<body> | <body> | ||
| - | This is the sketch of our modeling. | + | This is the sketch of our modeling.<br> |
We are going to use TMAO as a biomarker. | We are going to use TMAO as a biomarker. | ||
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<p> $R^{ *}$ is TorR Phosophorilated. </p> | <p> $R^{ *}$ is TorR Phosophorilated. </p> | ||
</div> | </div> | ||
| - | <p> Reactions: </p> | + | |
| + | <p><h1> Reactions:</h1></p> | ||
\[ | \[ | ||
\begin{aligned} | \begin{aligned} | ||
\\ | \\ | ||
| - | + | M+T{{k_{1} \atop\displaystyle\longrightarrow} \atop {\displaystyle\longleftarrow \atop k_{-1}}}TM | |
\\ | \\ | ||
| - | + | 2TM+S{{k_{2} \atop\displaystyle\longrightarrow} \atop {\displaystyle\longleftarrow \atop k_{-2}}}STM | |
\\ | \\ | ||
| - | + | STM+R{{k_{3} \atop\displaystyle\longrightarrow} \atop {\displaystyle\longleftarrow \atop k_{-3}}} X {{k_{cat}\atop\longrightarrow} \atop {\quad \atop \quad }}R^{ *} + STM | |
\\ | \\ | ||
| - | + | R^{ *} + P {{\displaystyle\longrightarrow} \atop {\displaystyle\longleftarrow}} PR^{ *} | |
\\ | \\ | ||
\begin{eqnarray} | \begin{eqnarray} | ||
Revision as of 19:15, 23 June 2013
This is the sketch of our modeling.
We are going to use TMAO as a biomarker.
$M$ is TMAO.
$T$ is TorT.
$TM$ is the complex of T and M.
$S$ is TorS.
$STM$ is the complex of S and TM.
$R$ is TorR.
$R^{ *}$ is TorR Phosophorilated.
Reactions:
\[ \begin{aligned} \\ M+T{{k_{1} \atop\displaystyle\longrightarrow} \atop {\displaystyle\longleftarrow \atop k_{-1}}}TM \\ 2TM+S{{k_{2} \atop\displaystyle\longrightarrow} \atop {\displaystyle\longleftarrow \atop k_{-2}}}STM \\ STM+R{{k_{3} \atop\displaystyle\longrightarrow} \atop {\displaystyle\longleftarrow \atop k_{-3}}} X {{k_{cat}\atop\longrightarrow} \atop {\quad \atop \quad }}R^{ *} + STM \\ R^{ *} + P {{\displaystyle\longrightarrow} \atop {\displaystyle\longleftarrow}} PR^{ *} \\ \begin{eqnarray} \begin{cases} {d M(t)\over d t}&=& -k_1 \cdot M\cdot T + k_{-1}\cdot TM\\\\ \\\\ {d T(t)\over d t}&=& -k_1 \cdot M\cdot T + k_{-1}\cdot TM\\\\ \\\\ {d TM(t)\over d t}&=& k_1 \cdot M\cdot T - k_{-1}\cdot TM - k_2\cdot TM^{2} \cdot S + k_{-2} \cdot STM\\\\ \\\\ {d S(t)\over d t}&=& -k_2 \cdot S\cdot TM^{2} - k_{-1}\cdot TM - k_2\cdot TM^{2} \cdot S + k_{-2} \cdot STM\\\\ \\\\ {d STM(t)\over d t}&=& k_2 \cdot TM^{2} \cdot S - k_{-2}\cdot STM \\\\ \\\\ {d R^{ *}(t)\over d t}&=& k_{cat}\cdot STM \over{k_m + STM}\\\\ \\\\ {d mRNA(t)\over d t}&=& {\alpha \cdot R^{ *^{\gamma}} \over{\beta + R^{ *^{\gamma}}}} - \mu \cdot mRNA\\\\ \\ \end{cases} \end{eqnarray} \\ \end{aligned} \]
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