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Modeling Results

On this page a summary will be given of the obtained data from the model. Since there are endless combinations possible to fill in the parameters, only a few will be displayed and discussed here. Furthermore, the conclusion that can be extracted from these data will be given.

Linker Simulation

The linker was simulated using a Monte Carlo method. Two membrane proteins were virtually placed on a 2d membrane. Then the linkers connecting the membrane proteins to their corresponding intracellular domain were simulated (For more information, check the approach page). The results for different distances between the membrane proteins are shown in figure 1. These histograms show that for small distances between two membrane proteins, the linker has a strong effect on the distance between the intracellular domains. For larger distances between the membrane proteins, the effect is less. Furthermore, in the last case the effect of the linker on the intracellular distance is more even, almost symmetrical, whilst for the small distance between the membrane proteins, the linker will almost always increase the distance between the intracellular domains. These distances were converted into BRET or FRET efficiencies, to check the linker’s effect on these. Figure 2 shows the effect of the linker on the BRET and FRET efficiency. It shows that for small distances between two membrane proteins, which is for example the case when the clicked aptamers are bound to thrombin, the linker causes a lower BRET and FRET signal, while for larger distances it shows a slight increase in signal intensity.

System Simulation

To estimate how well our sensor works, the increase in BRET or FRET signal on ligand binding was modeled. First the BRET or FRET signal resulting from the binding of aptamers is modeled, using Smoldyn. Then the BRET or FRET signal from the interaction between the unbound membrane proteins is added. This signal is divided by the amount of BRET or FRET found when only unbound membrane proteins are modeled. Two concentrations of the construct were modeled. The results are depicted in figure 3. It shows that on increasing membrane protein concentrations, the range of ligand concentration wherein the sensor shows a response increases, but the signal itself will be weaker.