Difference between revisions of "Basic mevalonate pathway model with limonene synthesis: Construction and Ensemble analysis"
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This model serves as the preliminary MVA pathway framework that we have used as the foundation to debug and design improved MVA models. Although basic, this model was able to provide useful insights into the control of the MVA pathway and suggests strategies for possible engineering. The ensemble analysis carried out for this model have generated a total 8 model generations that have shown a significant improvement in their model scores after each reiteration. A step-by-step ensemble analysis that included scoring the models based on experimental data and identifying influential parameters have found that the proteins that are influential to the pathway are LIMS, MDC, GPPS and IDI. The analysis was also able to shed light on product inhibitions in the pathway that would influence the production of limonene, and also suggests an possible topological engineering design that could accelerate the pathway even more. | This model serves as the preliminary MVA pathway framework that we have used as the foundation to debug and design improved MVA models. Although basic, this model was able to provide useful insights into the control of the MVA pathway and suggests strategies for possible engineering. The ensemble analysis carried out for this model have generated a total 8 model generations that have shown a significant improvement in their model scores after each reiteration. A step-by-step ensemble analysis that included scoring the models based on experimental data and identifying influential parameters have found that the proteins that are influential to the pathway are LIMS, MDC, GPPS and IDI. The analysis was also able to shed light on product inhibitions in the pathway that would influence the production of limonene, and also suggests an possible topological engineering design that could accelerate the pathway even more. | ||
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Revision as of 13:23, 31 January 2018
This model serves as the preliminary MVA pathway framework that we have used as the foundation to debug and design improved MVA models. Although basic, this model was able to provide useful insights into the control of the MVA pathway and suggests strategies for possible engineering. The ensemble analysis carried out for this model have generated a total 8 model generations that have shown a significant improvement in their model scores after each reiteration. A step-by-step ensemble analysis that included scoring the models based on experimental data and identifying influential parameters have found that the proteins that are influential to the pathway are LIMS, MDC, GPPS and IDI. The analysis was also able to shed light on product inhibitions in the pathway that would influence the production of limonene, and also suggests an possible topological engineering design that could accelerate the pathway even more.
The simulation
