Difference between revisions of "Team:Aalto-Helsinki/Modeling propane"
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<p style="color:gray">--pic of results here--</p> | <p style="color:gray">--pic of results here--</p> | ||
− | <p>The results shown above tell us that FadB2 is really bad enzyme and quite a large bottleneck in our reaction. This find caused us to change it to Hdb; an enzyme with same function and reportedly better performance.</p> | + | <p>The results shown above tell us that FadB2 is a really bad enzyme and quite a large bottleneck in our reaction. This find caused us to change it to Hdb; an enzyme with same function and reportedly better performance.</p> |
− | <p>The plot also shows us that Ado is really bad enzyme, even though we use the mutated version with better performance than the original one (link to this?). 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 is a really bad enzyme, even though we use the mutated version with better performance than the original one (link to this?). To ease Ado-bottleneck, we put the construct containing it to the backbone that had higher copy number.</p> |
<p>Car isn’t very good enzyme either, 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.</p> | <p>Car isn’t very good enzyme either, 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.</p> | ||
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<p>Based on the results we can further deduce 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>Based on the results we can further deduce 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>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. It is good to remember that we don’t have real information how much there are enzymes in the cell so the actual values of these might not be right. Despite that this approach gives us good idea how one could improve the pathway in the future.</p> | + | <p>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. It is good to remember that we don’t have real information how much there are enzymes in the cell so the actual values of these 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="color:gray">--pic here--</p> | <p style="color:gray">--pic here--</p> | ||
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<h2 id="timecourse">Time course</h2> | <h2 id="timecourse">Time course</h2> | ||
− | <p>From time course analysis we can have some kind of idea how much propane our system is able to produce. We performed this analysis with | + | <p>From time course analysis we can have some kind of idea how much propane our system is able to produce. We performed this analysis with Copasi. Since we knew from the bottleneck analysis that FadB2 should be changed to Hdb, we considered only the latter in our Copasi file. Also we had different amounts of enzymes based on which backbone they were. For Car we knew from our previous analysis that the reaction reaches equilibrium quite fast and then 90-100% of it was active, so we could just put it’s value as constant, as for all other enzymes too.</p> |
<p>With step length of 1 minute and total time 100 min, we got that XX of propane was produced, see the picture below.</p> | <p>With step length of 1 minute and total time 100 min, we got that XX of propane was produced, see the picture below.</p> | ||
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<h2 id="sensitivity">Sensitivity analysis</h2> | <h2 id="sensitivity">Sensitivity analysis</h2> | ||
− | <p>We performed sensitivity analysis of our model to see the robustness of different parameters in our model. We performed this analysis with aid of Copasi, which has a ready task for it. Further, we performed this analysis based on both parameters/(constants? is it better said like that?) and initial concentrations.</p> | + | <p>We performed sensitivity analysis of our model to see the robustness of different parameters in our model. 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/(constants? is it better said like that?) and initial concentrations.</p> |
<p style="color:gray;">--pic of parameter results--</p> | <p style="color:gray;">--pic of parameter results--</p> |
Revision as of 11:58, 11 August 2015