Exploring targeting peptide-shell interactions in encapsulin nanocompartments

Encapsulins are recently discovered protein compartments able to specifically encapsulate cargo proteins in vivo. Encapsulation is dependent on C-terminal targeting peptides (TPs). Here, we characterize and engineer TP-shell interactions in the Thermotoga maritima and Myxococcus xanthus encapsulin systems. Using force-field modeling and particle fluorescence measurements we show that TPs vary in native specificity and binding strength, and that TP-shell interactions are determined by hydrophobic and ionic interactions as well as TP flexibility. We design a set of TPs with a variety of predicted binding strengths and experimentally characterize these designs. This yields a set of TPs with novel binding characteristics representing a potentially useful toolbox for future nanoreactor engineering aimed at controlling cargo loading efficiency and the relative stoichiometry of multiple concurrently loaded cargo proteins.

Automated summary

Researchers characterized and engineered TP-shell interactions in two encapsulin systems, revealing variation in binding specificity and strength of TPs, influenced by hydrophobic and ionic interactions as well as TP flexibility. They designed a set of TPs with predicted binding strengths and experimentally characterized them, creating a toolbox for future nanoreactor engineering to control cargo loading efficiency and the relative stoichiometry of multiple loaded cargo proteins.