To predict the designed system, iGEM TU Eindhoven developed a model to simulate the designed protein scaffold and its binding partner. The challenge is that there are many options of end products, making it impossible to apply an ordinary ODE-solver with differential equations. There are two approaches that we will introduce. The first is a simulation that we developed ourselves and that visualizes the system in a 2D simulation box.The second approach uses an already developed rule-based-model, which we adapted to our system.
To get a more detailed description, go to the model page of "Simulation in 2D" and "Rule based model", or continue with reading to get a short overview of the molecules that are simulated with the models.
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.
The Binding Partner represents the CT33 constructs, with include a Strep-tag®II. The CT33 site can bind in the pockets of the Scaffold construct filled with inducer and the Strep-tag®II site can bind to Strep-Tactin®XT, represented as the Center Point. The center point has four sites, which can individually bind to the Strep-tag®II and cause a valency of four.
Figure 1: Legend of the Rule Based Model
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.
