Difference between revisions of "Team:Aalto-Helsinki/Modeling propane"
m (copasi link working) |
m |
||
(3 intermediate revisions by 2 users not shown) | |||
Line 79: | Line 79: | ||
<h2>Materials and methods: Building the model</h2> | <h2>Materials and methods: Building the model</h2> | ||
− | <p>We built a model of our propane pathway based on Michaelis-Menten enzyme kinetics. It is a way to model enzyme reactions | + | <p>We built a model of our propane pathway based on Michaelis-Menten enzyme kinetics. It is a way to model enzyme reactions which assumes that the change the enzyme causes is faster than the binding or release of the substrate by the enzyme.</p> |
<figure id="fig1" style="margin-bottom:3%;"> | <figure id="fig1" style="margin-bottom:3%;"> | ||
− | <div style="width:100%;margin-left:auto;margin-right:auto;"><img src="https://static.igem.org/mediawiki/2015/3/37/Aalto-Helsinki_pathway_horizontal_hbd.gif" style="max-width:800px;" /></div> | + | <div style="width:100%;margin-left:auto;margin-right:auto;"><a href="https://static.igem.org/mediawiki/2015/3/37/Aalto-Helsinki_pathway_horizontal_hbd.gif"><img src="https://static.igem.org/mediawiki/2015/3/37/Aalto-Helsinki_pathway_horizontal_hbd.gif" style="max-width:800px;" /></a></div> |
<figcaption><b>Figure 1:</b> Propane pathway.</figcaption> | <figcaption><b>Figure 1:</b> Propane pathway.</figcaption> | ||
</figure> | </figure> | ||
Line 104: | Line 104: | ||
<h3 id="caractiv">CAR-activation</h3> | <h3 id="caractiv">CAR-activation</h3> | ||
− | <p>One of the enzymes in our pathway, CAR, needs activation before it can function. To further understand how this affects the function of this enzyme we <a href="https://2015.igem.org/Team:Aalto-Helsinki/ | + | <p>One of the enzymes in our pathway, CAR, needs activation before it can function. To further understand how this affects the function of this enzyme we <a href="https://2015.igem.org/Team:Aalto-Helsinki/Car-activation">modeled the reactions governing the activation</a>. To summarize the results: in most scenarios CAR is mostly in its active form. This is why we have assumed that it is all activated in the following calculations.</p> |
Line 145: | Line 145: | ||
<p>Relative sensitivities are defined as \[\frac{p}{[S]}\frac{d[S]}{dp},\] where \([S]\) is substrate concentration and \(p\) is the parameter by which we wish to calculate the sensitivities. A small sensitivity coefficient with respect to a parameter tells us that the behaviour is robust to the perturbations. If the parameter is large, we have gained knowledge of a control point. There interventions will have significant effects.</p> | <p>Relative sensitivities are defined as \[\frac{p}{[S]}\frac{d[S]}{dp},\] where \([S]\) is substrate concentration and \(p\) is the parameter by which we wish to calculate the sensitivities. A small sensitivity coefficient with respect to a parameter tells us that the behaviour is robust to the perturbations. If the parameter is large, we have gained knowledge of a control point. There interventions will have significant effects.</p> | ||
− | <p>When we calculated the scaled sensitivities in regarding to initial concentrations, | + | <p>When we calculated the scaled sensitivities in regarding to initial concentrations, butyryl-CoA was the most sensitive species of our reaction pathway. Hbd and NADPH influenced it positively (5.14 and 1.89) and YciA had a big negative influence (5.1). This doesn't really matter for us, since this doesn't have any effect on propane production. From the results we could see that propane was positively sensitive to ADO, CAR, Hbd and NADPH. This confirms the main bottlenecks and also suggests that NADPH affects our propane production. To improve the pathway in the future one could add mechanisms to create higher amounts of it in the cell.</p> |
<p style="font-size:13px;">Here you can download the <a href="https://static.igem.org/mediawiki/2015/b/b3/Aalto-Helsinki_sensitivity_initConcentrations.txt" download>sensitivity results for initial concentrations</a> or our whole <a href="https://static.igem.org/mediawiki/2015/8/85/Aalto-Helsinki_propane_pathway_Hbd.zip">copasi file with Hbd</a>.</p> | <p style="font-size:13px;">Here you can download the <a href="https://static.igem.org/mediawiki/2015/b/b3/Aalto-Helsinki_sensitivity_initConcentrations.txt" download>sensitivity results for initial concentrations</a> or our whole <a href="https://static.igem.org/mediawiki/2015/8/85/Aalto-Helsinki_propane_pathway_Hbd.zip">copasi file with Hbd</a>.</p> | ||
Line 157: | Line 157: | ||
<h3 id="timecourse">Time course</h3> | <h3 id="timecourse">Time course</h3> | ||
− | <p>From time course analysis we can have some kind of idea of how much propane our system is able to produce. We performed this analysis with Copasi. Since we knew from the bottleneck calculations that FadB2 should be changed to | + | <p>From time course analysis we can have some kind of idea of how much propane our system is able to produce. We performed this analysis with Copasi. Since we knew from the bottleneck calculations that FadB2 should be changed to Hbd, we considered only the latter. Also we had different amounts of enzymes based on which backbone they were.</p> |
− | <p>In our <a href="https://static.igem.org/mediawiki/2015/8/85/Aalto-Helsinki_propane_pathway_Hbd.zip">copasi file</a> we don't have the competing enzymes that also eat | + | <p>In our <a href="https://static.igem.org/mediawiki/2015/8/85/Aalto-Helsinki_propane_pathway_Hbd.zip">copasi file</a> we don't have the competing enzymes that also eat butyraldehyde, the last substrate before propane. This means that the values obtained here might be higher than in reality.</p> |
<p>With step length of 0.1 minutes and total time 100 min, we got for propane concentration 6.8e-07 mol/l.</p> | <p>With step length of 0.1 minutes and total time 100 min, we got for propane concentration 6.8e-07 mol/l.</p> | ||
Line 180: | Line 180: | ||
<p>We have made some simplifying assumptions that might have some minor effects on the results, mainly assuming some reversible reactions irreversible. This shouldn't however be too much of a problem since those reactions are strongly forward-favored according to their kinetic properties. </p> | <p>We have made some simplifying assumptions that might have some minor effects on the results, mainly assuming some reversible reactions irreversible. This shouldn't however be too much of a problem since those reactions are strongly forward-favored according to their kinetic properties. </p> | ||
− | <p style="padding-bottom:8%;margin-bottom:0;">In the future, our model could be improved by taking other reactions that happen in the cell into account. In our model we concentrated only on properties of our pathway, but for example NADPH and | + | <p style="padding-bottom:8%;margin-bottom:0;">In the future, our model could be improved by taking other reactions that happen in the cell into account. In our model we concentrated only on properties of our pathway, but for example NADPH and acetyl-CoA production are something that happen outside of the pathway and has a strong influence on the propane production.</p> |
</section> | </section> | ||
Latest revision as of 05:56, 17 September 2015