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Modeling Script

Model input

A short description, the input parameters and output data are explained for the four submodels below:

Linker Simulation (Distance).

This model calculates the effect of the linker on the distance between the intracellular domains. It's output file consists of a list of numbers. Each number represents the distance between the intracellular domains that was calculated in one iteration. The input parameters and used values to obtain our results are shown below:

Linker Simulation (BRET/FRET).

text for model 2

Total System Simulation.

text for model 3

Aptamer Binding Simulation.

text for model 4

Parameters.

• Box Size (nm): The width and height of the simulated 2d membrane, so the total area will be the square. We filled in 188 nm, to obtain an area of 35,344 nm², which is about one hundredth of the area of an E. coli bacterium.
• Amount of Particles: The amount of membrane proteins that will be placed on the 2d area. The amount we used was dependent on the situation
• Radius of Membrane Protein (nm): The radius of the simulated membrane protein. The used membrane protein ompX, has a radius of 2 nm. This was measured by means of its PDB file.
• Length of Linker (nm): The contour length of the modeled linker in nanometers. The value we used for our simulation was 28.4 nm; the linker consists of 71 amino acids that each have a contour length of 0.4 nm [1]
• Persistence Length of Linker (nm): The persistence length that is characteristic for the used material. The value we used to simulate our peptide linker was 0.45 nm [2]
• Radii of the tethered particles (nm): The radii of the two intracellular domains that are tethered to their membrane protein. We filled in 3 nm for both our first domain (Nanoluc) and our second (mNeongreen). These values were measured using PDB files. For Nanoluc a PDB was used that represents a model of the real structure. For mNeongreen, a single beta barrel in the PDB file 4HVF was used. This PDB file describes the x-ray diffraction structure of lanGFP, a relative of lanYFP, the protein which was mutated to mNeongreen. [3]
• Förster Distance (nm): The förster distance of the used BRET or FRET pair. Because this distance was not known for the used pairs, 5 nm was used for this parameter, which is a typical distance [4]
• Max Förster Distance (nm): The maximum distance the membrane proteins may be apart from each other to simulate the BRET or FRET between their intracellular domains. This parameter was set to 12 nm. Figure ? shows that intracellular domains of membrane proteins that are further away than 12 nm of each other, hardly contribute to the total BRET or FRET signal.