Difference between revisions of "Team:Aalto-Helsinki/Modeling propane"
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<p>FadB2 reaction is reversible in our model but for this we approximated it as irreversible. This yields better results for it than in reality.</p> | <p>FadB2 reaction is reversible in our model but for this we approximated it as irreversible. This yields better results for it than in reality.</p> | ||
− | <figure id="fig2"> | + | <figure id="fig2" style="margin-bottom:3%;"> |
<div style="width:80%;margin-left:auto;margin-right:auto;"><img src="https://static.igem.org/mediawiki/2015/d/dd/Aalto-Helsinki_Michaelis_plots.png" style="max-width:100%;" /></div> | <div style="width:80%;margin-left:auto;margin-right:auto;"><img src="https://static.igem.org/mediawiki/2015/d/dd/Aalto-Helsinki_Michaelis_plots.png" style="max-width:100%;" /></div> | ||
<figcaption><b>Figure 2:</b> Michaelis-Menten reaction rate plots for our enzymes.</figcaption> | <figcaption><b>Figure 2:</b> Michaelis-Menten reaction rate plots for our enzymes.</figcaption> | ||
</figure> | </figure> | ||
− | < | + | <figure id="fig3" style="margin-bottom:3%;"> |
+ | <div style="width:80%;margin-left:auto;margin-right:auto;"><img src="https://static.igem.org/mediawiki/2015/a/aa/Aalto-Helsinki_bottleneck_both.png" style="max-width:100%;" /></div> | ||
+ | <figcaption><b>Figure 3:</b> Illustrative figure of the bottleneck results of our pathway.</figcaption> | ||
+ | </figure> | ||
<p>The results shown in <a href="#fig2">figure 2</a> tell us that FadB2 is a really inefficient enzyme and one of the largest bottlenecks in our pathway. This caused us to change it to Hdb; an enzyme with same function and reportedly better performance.</p> | <p>The results shown in <a href="#fig2">figure 2</a> tell us that FadB2 is a really inefficient enzyme and one of the largest bottlenecks in our pathway. This caused us to change it to Hdb; an enzyme with same function and reportedly better performance.</p> | ||
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<p style="padding-top:1%;">After getting these results we performed the bottleneck analysis again out of curiosity with relative enzyme amounts. When before we had all the enzyme concentrations to be 1e-6 mol/l, now we scaled them to correspond to the different copy numbers of different backbones. We had put Car-construct into pSB6A1 (ORI: pMB1, copynumber: 15-20) and Ado-construct into pCDFDuet-1 (ORI: CloDF13, copynumber: 20-40). Based on this we approximated that there is about 1.5 times more of those enzymes that are in Ado construct; see <a href="#fig4">figure 4</a> for results. It is good to remember that we don’t have accurate information on how much there are enzymes in the cell so the actual values might not be right. Despite that this approach gives us a good idea of how one could improve the pathway in the future.</p> | <p style="padding-top:1%;">After getting these results we performed the bottleneck analysis again out of curiosity with relative enzyme amounts. When before we had all the enzyme concentrations to be 1e-6 mol/l, now we scaled them to correspond to the different copy numbers of different backbones. We had put Car-construct into pSB6A1 (ORI: pMB1, copynumber: 15-20) and Ado-construct into pCDFDuet-1 (ORI: CloDF13, copynumber: 20-40). Based on this we approximated that there is about 1.5 times more of those enzymes that are in Ado construct; see <a href="#fig4">figure 4</a> for results. It is good to remember that we don’t have accurate information on how much there are enzymes in the cell so the actual values might not be right. Despite that this approach gives us a good idea of how one could improve the pathway in the future.</p> | ||
− | <figure id="fig4"> | + | <figure id="fig4" style="margin-bottom:3%;"> |
<div style="width:80%;margin-left:auto;margin-right:auto;"><img src="https://static.igem.org/mediawiki/2015/b/ba/Aalto-Helsinki_Michaelis_plots_varying_enzymes.png" style="max-width:100%;" /></div> | <div style="width:80%;margin-left:auto;margin-right:auto;"><img src="https://static.igem.org/mediawiki/2015/b/ba/Aalto-Helsinki_Michaelis_plots_varying_enzymes.png" style="max-width:100%;" /></div> | ||
<figcaption><b>Figure 4:</b> Michaelis-Menten reaction rate plots with different enzyme concentrations based on the backbone copy numbers</figcaption> | <figcaption><b>Figure 4:</b> Michaelis-Menten reaction rate plots with different enzyme concentrations based on the backbone copy numbers</figcaption> |
Revision as of 07:32, 4 September 2015