Fig. 2: Nonviral protein cages: structural diversity and design principles.
From: Nonviral protein cages as tools to decipher and combat viral threats
Surface representations of different protein cages varying in size, symmetry, and the number of constituent capsomers, derived from either naturally occurring (a–d) or computationally designed scaffolds (e–i). a AaLS-wt (PDB 5MPP), a 60-subunit self-assembling cage, served as a template for multiple directed evolution campaigns. b NC-4 (PDB 7A4J) and c AaLS-13 (PDB 5MQ7) are evolved variants of AaLS-wt, optimized to encapsulate their own encoding mRNA55 and toxic proteins167, respectively, with both exhibiting increased diameters. d A variant of human heavy-chain ferritin (PDB 2CEI) with positively charged surface residues was encapsulated within AaLS-13, forming matryoshka-like assemblies168. e OP (PDB 6FDB) was engineered by introducing positive charges onto the lumenal surface of the computationally designed O3-33 cage43. Owing to its positively charged lumen and porous architecture, OP can be efficiently loaded in vitro with a desired oligonucleotide44 or anionic surfactants, forming a hydrophobic core that enables the sequestration of non-polar molecules45. f I3-01 is a 60-subunit icosahedral cage composed exclusively of trimeric subunits. Its variant, mi3, was created by mutating surface-exposed cysteines (Cys76 and Cys100) to alanine169. The SpyTag/SpyCatcher technology170 has been used to encapsulate both proteinaceous and non-proteinaceous cargo within mi3 cages13. g I53-50 (PDB 7SGE) is a 120-subunit icosahedral assembly comprising trimeric (blue) and pentameric (gray) components171. I53-50 has been engineered to encapsulate nucleic acids52 as well as drug-loaded synthetic polymers63. h O42.1 is a 30 nm porous octahedral structure consisting of six tetramers (gray) and 12 dimeric Fc subunits (blue). i Closure of the O42.1 cage’s pores with pH-responsive trimeric plugs (yellow) resulted in the O432 variant. Modifying the interior-facing residues of the trimeric plug to introduce internal charge enabled the packaging of nucleic acid or protein cargo172. All structures were visualized using ChimeraX173,174. O42.1 and O432 were modeled from density maps deposited in the Electron Microscopy Data Bank175 (EMD-29602).
