We are interested in oligomeric protein networks and how their transient structures arise to form diffusion traps and scaffolds in the cell. To this end we have created a generalized agent-based simulation framework that makes it easy to specify unique properties (diffusivity, number of binding sites, etc) for individual monomers and the properties of the bonds between them. We can endow these proteins with a specific geometry to approximate the orientation of their binding sites or represent them in their simplest form as spheres. Currently this model is being used to investigate the properties of the Par protein oligomer network that forms near the cortex in polarizing C. elegans embryos.
 |
 |
 |
|---|---|---|
| Oligomerization Domains |
Oligomeric network formed by generic trivalent proteins |
Oligomeric network formed by generic trivalent proteins within meshwork |
 |
||
| Stabilization of actin meshwork by par protein oligomerization network |