Brownian Dynamics simulation of Clathrin Cage Formation

The processes of endo- and exocytosis are associated with the transport of nutrients, hormones and proteins in to and out of living cells. When these molecules enter a cell, they are collected and encapsulated in vesicles for further transport to a destination with the cell. Likewise, the products of organelles are encapsulated before being transported to the edge of the cell. The central protein in the formation process of these vesicles is clathrin.
Clathrins have three long legs that enable them self-assemble into polyhedral cages. We investigate the formation and structure of clathrin cages by means of computer simulations. To achieve this, we have developed a highly coarse-grained patchy particle model by representing a clathrin protein as a rigid triskelion with interaction sites on the legs. To simulate their dynamics, we have implemented a Brownian Dynamics algorithm to describe their translational and rotational motion. We present validation tests of the algorithm to show that both static and dynamic properties are consistent with theory. The model clathrins are observed to self-assemble into cages within several second. These cages are structurally similar to those observed by in vitro experiments.