Biological nanocompartments are found throughout organisms and have diverse functions and forms, ranging from biomolecular condensates to proteinaceous compartments. Many of these compartments are attractive platforms for nanoreactors, as they can be engineered to host various enzymatic processes. One group of these compartments are encapsulins, proteinaceous cages from prokaryotes that self-assemble from one type of monomer. Encapsulins are durable, compliant to mutations, and can be easily loaded with non-native cargo proteins.1
A critical feature of nanocompartments is the pore, which determines selectivity and permeability through the compartment. If the pore can be tuned for specific substrates, then the compartment can be optimized for new purposes and its cargo protected from damaging or off-target molecules. Mutation of the Thermotoga maritima encapsulin pores for the control of diffusion through the shell has previously been explored but the observed diffusion rates do not appear to neatly correlate with size or charge of the mutation.2
This work describes Molecular Dynamics simulations performed on cryo-EM structures of encapsulin variants to understand how ions diffuse through the pore, both with and without mutations. Analysis of the simulations reveals insights into the dynamic nature of the pore not apparent from the structure alone. The simulations are further contrasted with diffusion rates seen in kinetics experiments of the encapsulin variants. Future steps are considered towards a model for reliably determining mutation effect on pore structure and permeability.