Difference between revisions of "Team:Aalto-Helsinki/Modeling propane"
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<p>The plot also shows us that Ado isn't a good one either. To ease Ado-bottleneck, we put the construct containing it to the backbone that had higher copy number.</p> | <p>The plot also shows us that Ado isn't a good one either. To ease Ado-bottleneck, we put the construct containing it to the backbone that had higher copy number.</p> | ||
− | <p>Car isn’t the best enzyme in our pathway, and unfortunately we couldn’t do anything to make it’s performance better because it was in different construct than Ado. We had ordered our constructs before we knew the bottleneck results | + | <p>Car isn’t the best enzyme in our pathway, and unfortunately we couldn’t do anything to make it’s performance better because it was in different construct than Ado. We had ordered our constructs before we knew the bottleneck results and because of time restrictions we had to cope with what we had, but based on the obtained results we can deduce a better ordering of constructs than we now have. To the higher copy number backbone we should put as many of the slowest enzymes as possible.</p> |
<p>We could also confirm these results by checking the fluxes through reactions and running parameter scan for different enzymes with Copasi (<span style="color:blue">download link for the file here</span>). After identifying one bottleneck this way we removed that enzyme from our model of the reaction pathway and repeated the calculations.</p> | <p>We could also confirm these results by checking the fluxes through reactions and running parameter scan for different enzymes with Copasi (<span style="color:blue">download link for the file here</span>). After identifying one bottleneck this way we removed that enzyme from our model of the reaction pathway and repeated the calculations.</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 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. It is good to remember that we don’t have real information 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. It is good to remember that we don’t have real information 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> |
<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> |
Revision as of 10:36, 17 August 2015