Multi-component assembly of microcompartments

Many bacteria generate bacterial microcompartments (BMC) in their metabolic processes. These particles are protein-based shells that encapsulate enzymes spontaneously. Using all-atom and coarse-grained molecular dynamics, we study the mechanical properties of protein subunits and the assembly process. We find that the hexamers (PduA) are associated mainly due to the hydrogen bonding, the strength of which exactly corresponds to the region that BMC successfully formed. In addition, we observe cylinder and “samosa” shaped shells coexistent in solution when reducing the pentamer (PduN)-hexamer interaction. We calculate the free energy for each morphology thermodynamically and find that the cargo-hexamer attraction in cylinder/samosa compensates the energy loss of missing pentamers. We also discuss other thermodynamic parameters that can be used to control the shell morphology, which provides a prediction for future experiments.