Identifying molecular factors of polymorphic bacterial microcompartment assembly through coarse-grained simulations

Bacterial microcompartments (BMCs) are hierarchically self-assembled protein nanoreactors that encapsulate enzymes and improve energy production in bacteria. Metabolic engineers are interested in leveraging BMCs to increase production of high-value chemicals. However, the rational design of BMC monomers remains a challenge because BMC assemblies exhibit polymorphism which makes it non-trivial to isolate how the design of a monomer affects the BMC morphology. In this work, we utilize a bottom-up coarse-grained approach and molecular dynamics to explicitly simulate the assembly pathways of BMC-H and BMC-H² monomers from the Haliangium ochraceum bacteria. BMC-H² is a tandem copy of BMC-H connected by a peptide linker. The linker changes the dominant morphology from rosette sheets to a 25 nm icosahedral shell. We demonstrate that our model captures polymorphic assemblies seen in the results of previous experiments. Furthermore, we test molecular factors (i.e., monomer-monomer interaction strengths and linker rigidity) to isolate their function in assembly. Our data demonstrates that the presence of the linker introduces asymmetric monomer interactions which promote the assembly of icosahedra over rosettes. Our findings suggest that linker engineering is a promising strategy to control BMC morphologies.