Difference between revisions of "Team:Tianjin/Model"

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                                         The model (Figure 14) contained twelve processes (R1-R12) describing all the protein-protein interactions and phosphorylation-dephosphorylation between the Kai proteins. KaiXY represents KaiX and KaiY compound and KaiC* represents fully phosphorylated KaiC. Process R1, R2 and R3 are six aggregations of KaiC protein, two aggregations of KaiA protein and four aggregations of KaiB protein respectively. In process R4, KaiC6 binds KaiA2, forming KaiA<sub>2</sub>C<sub>6</sub> compound. Since KaiA<sub>2</sub> facilitates the autokinase activity of KaiC<sub>6</sub>, KaiA<sub>2</sub>C<sub>6</sub> first converts to partial phosphorylated form, KaiA<sub>2</sub>C<sub>6</sub>C<sub>6</sub>*, by process R5, and then rapidly converts to fully phosphorylated form, KaiA<sub>2</sub>C<sub>6</sub>*, by process R10. Then, fully phosphorylated protein KaiA<sub>2</sub>C<sub>6</sub>* combines with KaiB<sub>4</sub>, forming KaiA<sub>2</sub>B<sub>4</sub>C<sub>6</sub>*, by process R6. In process R7, KaiA<sub>2</sub> is displaced from KaiA<sub>2</sub>B<sub>4</sub>C<sub>6</sub>*. When KaiA<sub>2</sub> no longer exists in KaiA<sub>2</sub>B<sub>4</sub>C<sub>6</sub>*, KaiB<sub>4</sub> dissociates from KaiB<sub>4</sub>C<sub>6</sub>*, by process R8. Process R9, R11, and R12 are depolymerization of KaiC<sub>6</sub>, KaiA<sub>2</sub> and KaiB<sub>4</sub> protein, respectively<sup><a href="#re7">[7]</a></sup>.
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                                         The model (Figure 14) contained twelve processes (R1-R12) describing all the protein-protein interactions and phosphorylation-dephosphorylation between the Kai proteins. KaiXY represents KaiX and KaiY compound and KaiC* represents fully phosphorylated KaiC. Process R1, R2 and R3 are six aggregations of KaiC protein, two aggregations of KaiA protein and four aggregations of KaiB protein respectively. In process R4, KaiC<sub>6</sub> binds KaiA<sub>2</sub>, forming KaiA<sub>2</sub>C<sub>6</sub> compound. Since KaiA<sub>2</sub> facilitates the autokinase activity of KaiC<sub>6</sub>, KaiA<sub>2</sub>C<sub>6</sub> first converts to partial phosphorylated form, KaiA<sub>2</sub>C<sub>6</sub>C<sub>6</sub>*, by process R5, and then rapidly converts to fully phosphorylated form, KaiA<sub>2</sub>C<sub>6</sub>*, by process R10. Then, fully phosphorylated protein KaiA<sub>2</sub>C<sub>6</sub>* combines with KaiB<sub>4</sub>, forming KaiA<sub>2</sub>B<sub>4</sub>C<sub>6</sub>*, by process R6. In process R7, KaiA<sub>2</sub> is displaced from KaiA<sub>2</sub>B<sub>4</sub>C<sub>6</sub>*. When KaiA<sub>2</sub> no longer exists in KaiA<sub>2</sub>B<sub>4</sub>C<sub>6</sub>*, KaiB<sub>4</sub> dissociates from KaiB<sub>4</sub>C<sub>6</sub>*, by process R8. Process R9, R11, and R12 are depolymerization of KaiC<sub>6</sub>, KaiA<sub>2</sub> and KaiB<sub>4</sub> protein, respectively<sup><a href="#re7">[7]</a></sup>.
 
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Revision as of 04:31, 17 October 2018

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MODEL

Overview

The models we built included four parts. First, we established a fluorescent protein model to screen out the most suitable fluorescent protein, the main modeling method here is grayscale analysis. Then, for the large amount of measured OD values, we drew the growth curve of yeasts and it fitted logistic model. It described the growth situation of the yeasts after plasmid introduction, and we compare it with yeasts without any foreign plasmid. The growth curve also offers the best measuring point and the best measuring interval. What’s more, we drew the degradation curve of the fluorescent protein, which helps us know different characteristics of the two chosen fluorescent proteins better. Finally, we constructed a model to illustrate the oscillation of KaiA, KaiB and KaiC protein called Mars Model, it explained the reason why the cycle reduced in yeasts nicely. Modeling work integrated with experiments tightly made our project complete and convincing.