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The system that was already introduced in the project description looks a lot like in the figure below. The Scaffold Construct represents the three functional 14-3-3 monomers. We also described that the Scaffold construct would be a tetramer, but because we mutated the last pocket, the pocket has no function and could be left out of the model. At each functional pockets, an inducer can bind and facilitates the binding of the Binding Partner.<br/> | The system that was already introduced in the project description looks a lot like in the figure below. The Scaffold Construct represents the three functional 14-3-3 monomers. We also described that the Scaffold construct would be a tetramer, but because we mutated the last pocket, the pocket has no function and could be left out of the model. At each functional pockets, an inducer can bind and facilitates the binding of the Binding Partner.<br/> | ||
− | The Binding Partner represents the CT33 | + | The Binding Partner represents the CT33 constructs, with include a strep-tag. The CT33 site can bind in the pockets of the Scaffold construct filled with inducer and the strep-tag site can bind to Strep-tactin, represented as the Center Point. The center point has four sites, which can individually bind to the strep-tag and cause a valency of four. |
<br/><br/> | <br/><br/> | ||
− | In the rule-based-model, we only defined the molecules as described above, with the pockets and where they can bind to. In the simulation, we simplified the visualization of our constructs to the ones shown below. Here, each pocket of the Scaffold construct is already filled with an inducer and the pockets are visualized separately, while in the simulation, three pockets are connected to each other with a certain distance. The same goes for the Center Point and four Binding Partners, they are again (invisibly) connected with each other at a certain distance. In the simulation in 2D, only the binding of a Binding Partner to a pocket of the Protein Scaffold is simulated, making the model less complete and the rule-based-model better. | + | In the rule-based-model, we only defined the molecules as described above, with the pockets and where they can bind to. In the simulation, we simplified the visualization of our constructs to the ones shown below. Here, each pocket of the Scaffold construct is already filled with an inducer and the pockets are visualized separately, while in the simulation, three pockets are connected to each other with a certain distance. The same goes for the Center Point and its four Binding Partners, they are again (invisibly) connected with each other at a certain distance. In the simulation in 2D, only the binding of a Binding Partner to a pocket of the Protein Scaffold is simulated, making the model less complete and the rule-based-model better. |
</h6> | </h6> |
Revision as of 09:05, 30 October 2017