Difference between revisions of "Team:Aalto-Helsinki/Modeling propane"
m |
m |
||
Line 61: | Line 61: | ||
<div class="inner-container"> | <div class="inner-container"> | ||
− | < | + | <h1>Modeling the propane pathway</h1> |
− | < | + | <!-- Introduction --> |
+ | <h2 id="introduction"> 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 CO2 and solar energy. </p> | <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 CO2 and solar energy. </p> | ||
Line 70: | Line 71: | ||
− | < | + | <h2 id="mm">Materials and methods: Building the model / our pathway</h2> |
<p>We built a model of our propane pathway based on Michaelis-Menten enzyme kinetics. It is a basic way to model enzyme reactions that assumes that the change that enzyme causes is faster than the binding of the enzyme and releasing of the substrate.</p> | <p>We built a model of our propane pathway based on Michaelis-Menten enzyme kinetics. It is a basic way to model enzyme reactions that assumes that the change that enzyme causes is faster than the binding of the enzyme and releasing of the substrate.</p> | ||
Line 80: | Line 81: | ||
<p>For modeling this propane pathway we used <a href="http://www.copasi.org/tiki-view_articles.php">Copasi</a> and <a href="http://se.mathworks.com/">Matlab</a>.</p> | <p>For modeling this propane pathway we used <a href="http://www.copasi.org/tiki-view_articles.php">Copasi</a> and <a href="http://se.mathworks.com/">Matlab</a>.</p> | ||
− | < | + | <h2 id="results">Results and implications</h2> |
<p>Here text about our results in all subcategories:</p> | <p>Here text about our results in all subcategories:</p> | ||
− | < | + | <h3 id="caractiv">Car-activation</h3> |
<p>One of the enzymes in our pathway, Car, needs activation before it can function. To further understand how this affects the function of this enzyme we <a href="https://2015.igem.org/Team:Aalto-Helsinki/Car-activation">modeled the reactions governing the activation</a>.</p> | <p>One of the enzymes in our pathway, Car, needs activation before it can function. To further understand how this affects the function of this enzyme we <a href="https://2015.igem.org/Team:Aalto-Helsinki/Car-activation">modeled the reactions governing the activation</a>.</p> | ||
− | < | + | <h3 id="bottlenecks">Bottlenecks: Comparing enzyme rates</h3> |
<p>To know which are the rate limiting steps in our pathway, we compared the rates of the enzyme reactions. This was done by calculating the reaction speeds with different substrate concentrations. The reactions are explained in depth <a href="https://2015.igem.org/Team:Aalto-Helsinki/Kinetics">here</a> and the obtained Michaelis-Menten equations tell us directly the reaction speeds. We implemented the code to plot these with Matlab, it is available here(<- download link).</p> | <p>To know which are the rate limiting steps in our pathway, we compared the rates of the enzyme reactions. This was done by calculating the reaction speeds with different substrate concentrations. The reactions are explained in depth <a href="https://2015.igem.org/Team:Aalto-Helsinki/Kinetics">here</a> and the obtained Michaelis-Menten equations tell us directly the reaction speeds. We implemented the code to plot these with Matlab, it is available here(<- download link).</p> | ||
Line 111: | Line 112: | ||
<p style="color:gray">--pic here--</p> | <p style="color:gray">--pic here--</p> | ||
− | < | + | <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 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>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> | ||
Line 121: | Line 122: | ||
<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> | ||
− | < | + | <h3 id="sensitivity">Sensitivity analysis</h3> |
<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>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> | ||
Line 133: | Line 134: | ||
<p>The other results show that not very surprisingly the concentration of NADP and NADPH (among the known bottleneck concentrations, this could be said better) affect a lot our propane production. To improve this in future, one could add mechanisms of creating these in the cell in higher amounts.</p> | <p>The other results show that not very surprisingly the concentration of NADP and NADPH (among the known bottleneck concentrations, this could be said better) affect a lot our propane production. To improve this in future, one could add mechanisms of creating these in the cell in higher amounts.</p> | ||
− | < | + | <h2 id="discussion">Discussion</h2> |
Revision as of 12:10, 11 August 2015