Figure 2.

Coarse-grained (CG) model and MD simulation results. (A) Illustration of the CG model. The sides of BMC-H and BMC-T are inclined at an angle θ_i = 25° according to their PDB structures (PDB id 3ngk(33) and 4fay(42)). The green beads interact via excluded volume (changed to blue for pentamers); the purple and pink beads are short-range attractive sites representing the arginine hydrogen bonds. The sphere of yellow beads is the cargo, and the yellow beads on the BMC-H and BMC-T proteins are the residues that bind to the cargo. To show the negative (blue) and positive (green) charged sites clearly, all the noncharged sites are shown as semitransparent and in smaller size on the right column. (B–E) Snapshots of CG simulations (the hexamers, pentamers, and cargo are in green, blue, and yellow, respectively): a red dot is marked on the center of BMC-T to distinguish them from BMC-H. Scale bars are 14 nm. (B) A system without BMC-T and with a ratio BMC-H:BMC-P:cargo = 5:3:2 forms shells with icosahedral symmetry (T = 3) resembling in vitro electron micrographs of compartments from Haliangium ochraceum (F) which also form spherical shells with icosahedral symmetry (T = 9). (C, D) Increasing the number of BMC-H or adding BMC-T can enable assembly into polyhedral shapes that resemble the shape of purified MCPs shown in part F. (E) BMC-H proteins alone form cylinders, reproducing observations of the in vitro BMC-H assembly shown in part D. Detailed model parameters for these simulation results are provided in Table S1. Part G is reprinted with permission from ref (20). Copyright 2010 National Academy of Sciences. Parts F and H are reprinted with permission from ref (19). Copyright 2018 American Chemical Society.