Difference between revisions of "Team:Aalto-Helsinki/Modeling propane"
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<p style="color:gray;">--pic of concentration results--</p> | <p style="color:gray;">--pic of concentration results--</p> | ||
− | <p>The other results show that not very surprisingly the concentration of | + | <p>The other results show that not very surprisingly the concentration of NADPH (among the known bottleneck concentrations, this could be said better) affects our propane production. To improve this in future, one could add mechanisms of creating these in the cell in higher amounts.</p> |
<h3 id="timecourse">Time course</h3> | <h3 id="timecourse">Time course</h3> | ||
− | <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 | + | <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 calculations 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. <span style="color:gray">Mention about Car?</span></p> |
− | <p> | + | <p>In our Copasi file 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. <span style="color:gray">Reference to particle model?</span></p> |
− | <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>It is good to remember that this doesn’t tell us the exact value of propane produced, rather just an idea of the order of magnitude. We don’t know the amount of enzymes in our cell so we had to estimate it. Also, our model has some simplifications that very possibly affect the outcome.</p> | <p>It is good to remember that this doesn’t tell us the exact value of propane produced, rather just an idea of the order of magnitude. We don’t know the amount of enzymes in our cell so we had to estimate it. Also, our model has some simplifications that very possibly affect the outcome.</p> | ||
− | <p>The predicted amount of propane produced isn't very high. To produce propane more efficiently in the future, we would need to greatly improve the performance of our pathway. This could be done by taking a look into bottlenecks of our pathway and other limiting factors such as | + | <p>The predicted amount of propane produced isn't very high. To produce propane more efficiently in the future, we would need to greatly improve the performance of our pathway. This could be done by taking a look into bottlenecks of our pathway and other limiting factors such as NADPH.</p> |
<h2 id="discussion">Discussion</h2> | <h2 id="discussion">Discussion</h2> | ||
− | <p> | + | <p>Our model isn't perfect. We have made a lot of simplifying assumptions when building the model, maybe the most important of them being irreversibility of reversible reactions. Even though the reactions were quite strongly forward-favored the accuracy might suffer.</p> |
− | <p> | + | <p>We don't know how much we have enzymes in our bacteria so we had to estimate that amount. Although we can find out the reaction rates for all the enzymes the bottleneck situation might change if some enzyme is expressed unusually high amounts. This is however very unlikely and especially since the copy numbers of our backbones are not so different.</p> |
− | <p> | + | <p>We could also have gained more accuracy in modeling were we able to measure the kinetic constants ourselves.</p> |
− | <p> | + | <p>One disadvantage in our model of propane pathway is that it isn't taking into account anything that is happening outside the cell. Right now we have for example NADPH concentration as a constant in the model, but what if its creation is so slow that it becomes a problem? This and similar questions remain unanswered.</p> |
</div> | </div> |
Revision as of 13:39, 17 August 2015