Computational modeling was a valuable tool in investigating the properties of encapsulin nanocompartments.
We used GROMACS, CHARMM and VMD software to simulate our encapuslin monomer. The encapsulin monomer is positioned in a box that is attached to a member of the yeast cell membrane using alpha-factor pheromone as a ligand. Under these simulated conditions, the encapsulin monomer is stable.
![Free Encapsulin Monomer](https://static.igem.org/mediawiki/2021/f/f8/T--Michigan--img--modeling1.gif)
Figure 1: Free Encapsulin Monomer
![Encapsulin Monomer Bound to Yeast Plasma Membrane with Alpha Factor Tag](https://static.igem.org/mediawiki/2021/d/d5/T--Michigan--img--modeling2.gif)
Figure 2: Encapsulin Monomer Bound to Yeast Plasma Membrane with Alpha Factor Tag
Due to computational constraints, it was not feasible to simulate the entire protein with alpha-factor pheromones attached to each monomer. Nevertheless, we made the following observations based on the simulated scenarios:
- The N-term of the pheromone is required to be free for binding
- Only the C-term of the encapsulin is available for linkage
- This precludes the fusing of the free C-term of the ligand and the C-term of the encapsulin
- This has implications for primer design and linker positioning when adding the alpha factor sequence