Electrostatics-driven peptide-directed encapsulation of nanoparticles into protein cages

Experiments have shown the gold nanoparticles (NPs) which are densely decorated by the short positively-charged ligands and sparsely decorated by longer uncharged cargo-loading peptides (CLPs) could be encapsulated into negatively-charged encapsulin protein cages with high efficiency. We build an experimentally-informed coarse-grained model with explicit ions and a Martini representation of water, and use it to perform molecular dynamics simulations to probe the mechanisms responsible for the encapsulation as the favorable co-assembly product. Experimental observations and simulations reveal three co-assembly states as a function of salt concentration c: for high salt (c > 0.5 M), the binding energy between protomer and NP is weak (~5–10 kBT) which leads to empty cages, for low salt (c < 0.2 M) the protomer-NP attraction is very strong yielding kinetically trapped protomer-NP aggregates, for 0.2 M < c < 0.5 M, NP-encapsulated protein cages are observed which correspond to a binding energy of ~15–20 KBT. Simulations reveal that NP encapsulation at high efficiency is the result of a two-step process: the electrostatic attraction between NPs and protomers driving the NPs into the recruitment zone of protomers, which is followed by the CLPs directing the NPs into the favorable binding region of the protomer.