Difference between revisions of "Team:Aalto-Helsinki/Modeling propane"
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<h2> Introduction </h2> | <h2> Introduction </h2> | ||
− | <p>Propane is a commonly used, convenient and clean-burning fuel, currently produced from non-renewable sources. Our project is about producing propane in bacteria, paving way for its sustainable production from renewable biomass. Ultimately, the pathway could be transferred to cyanobacteria, producing propane from | + | <p>Propane is a commonly used, convenient and clean-burning fuel, currently produced from non-renewable sources. Our project is about producing propane in bacteria, paving way for its sustainable production from renewable biomass. Ultimately, the pathway could be transferred to cyanobacteria, producing propane from CO\(_2\) and solar energy. </p> |
− | <p> | + | <p>The pathway is complicated and we had only educated guesses as to what might be the rate-limiting steps that should be improved to increase propane output. To find the bottlenecks and focus our engineering efforts on them, we built a mathematical model of the pathway using the kinetic data available for the enzymes.</p> |
</section> | </section> | ||
<!-- Introduction above --> | <!-- Introduction above --> | ||
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<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 that assumes that the change that the enzyme causes is faster than the binding of the enzyme | + | <p>We built a model of our propane pathway based on Michaelis-Menten enzyme kinetics. It is a way to model enzyme reactions that assumes that the change that 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%;"> | ||
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<h2>Results and implications</h2> | <h2>Results and implications</h2> | ||
− | <p>Our files for | + | <p>Our files for download: <a href="https://static.igem.org/mediawiki/2015/8/85/Aalto-Helsinki_propane_pathway_Hbd.zip">Copasi file with Hbd</a>, <a href="https://static.igem.org/mediawiki/2015/c/ca/Aalto-Helsinki_propane_pathway_fadB2.zip">copasi file with FadB2</a> and our <a href="https://static.igem.org/mediawiki/2015/e/ed/Aalto-Helsinki_bottleneck_plots.m" download>Matlab file</a>.</p> |
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<p>We performed sensitivity analysis of our pathway model to see the robustness of different parameters. We performed this analysis with the aid of Copasi, which has a ready task for it. Further, we performed this analysis based on both parameters and initial concentrations. We did the analysis with different enzyme concentrations based on the backbone copy numbers.</p> | <p>We performed sensitivity analysis of our pathway model to see the robustness of different parameters. We performed this analysis with the aid of Copasi, which has a ready task for it. Further, we performed this analysis based on both parameters and initial concentrations. We did the analysis with different enzyme concentrations based on the backbone copy numbers.</p> | ||
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+ | <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, 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>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> |
Revision as of 07:10, 11 September 2015