Symmetry-Directed Design of Protein Cages and Protein Lattices and Their Applications

Noncovalent Self-Assembly of Protein Crystals with Tunable Structures

Engineering noncovalent interactions for assembling nonspherical proteins into supramolecular architectures with tunable morphologies and dynamics is challenging due to the structural heterogeneity and complexity of protein surfaces. Herein, we employed an anisotropic building block l-rhamnulose-1-phosphate aldolase (RhuA) to control supramolecular polymorphism in highly ordered protein assemblies by introducing histidine residues. Histidine-based π-π stacking interactions enabled thermodynamically controlled self-organization of RhuA to form three-dimensional (3D) nanoribbons and crystals. Self-assembly of different 3D crystal phases was kinetically modulated by the strong metal ion-histidine chelation, and double-helical protein superstructures were formed by engineering increased histidine interactions at the RhuA binding surface. Their structural properties and dynamics were determined via fluorescence microscopy, transmission electron microscopy, atomic force microscopy, and small-angle X-ray scattering. This work is aimed at expanding the toolbox for the programming of tunable, highly ordered, protein superstructures and increasing the understanding of the mechanisms of protein interfacial interactions.

Converting histidine-induced 3D protein arrays in crystals into their 3D analogues in solution by metal coordination cross-linking

Histidine (His) residues represent versatile motifs for designing protein-protein interactions because the protonation state of the imidazole group of His is the only moiety in protein to be significantly pH dependent under physiological conditions. Here we show that, by the designed His motifs nearby the C₄ axes, ferritin nanocages arrange in crystals with a simple cubic stacking pattern. The X-ray crystal structures obtained at pH 4.0, 7.0, and 9.0 in conjunction with thermostability analyses reveal the strength of the π-π interactions between two adjacent protein nanocages can be fine-tuned by pH. By using the crystal structural information as a guide, we constructed 3D protein frameworks in solution by a combination of the relatively weak His-His interaction and Ni²⁺-participated metal coordination with Glu residues from two adjacent protein nanocages. These findings open up a new way of organizing protein building blocks into 3D protein crystalline frameworks.

Coiled-Coil-Mediated Assembly of an Icosahedral Protein Cage with Extremely High Thermal and Chemical Stability

The organization of protein molecules into higher-order nanoscale architectures is ubiquitous in Nature and represents an important goal in synthetic biology. Furthermore, the stabilization of enzyme activity has many practical applications in biotechnology and medicine. Here we describe the symmetry-directed design of an extremely stable, enzymatically active, hollow protein cage of M_r ≈ 2.1 MDa with dimensions similar to those of a small icosahedral virus. The cage was constructed based on icosahedral symmetry by genetically fusing a trimeric protein (TriEst) to a small pentameric de novo-designed coiled coil domain, separated by a flexible oligo-glycine linker sequence. Screening a small library of designs in which the linker length varied from 2 to 12 residues identified a construct containing 8 glycine residues (Ico8) that formed well-defined cages. Characterization by dynamic light scattering, negative stain, and cryo-EM and by atomic force and IR-photoinduced force microscopy established that Ico8 assembles into a flexible hollow cage comprising 20 copies of the esterase trimer, 60 protein subunits in total, with overall icosahedral geometry. Notably, the cages formed by Ico8 proved to be extremely stable toward thermal and chemical denaturation: whereas TriEst was unfolded by heating ( T_m ≈ 75 °C) or denatured by 1.5 M guanidine hydrochloride, the Ico8 cages remained folded even at 120 °C or in 8 M guanidine hydrochloride. The increased stability of the cages is a new property that emerges from the higher-order structure of the protein cage, rather than being intrinsic to the components from which it is constructed.

Protein Assemblies: Nature-Inspired and Designed Nanostructures

Ordered protein assemblies are attracting interest as next-generation biomaterials with a remarkable range of structural and functional properties, leading to potential applications in biocatalysis, materials templating, drug delivery and vaccine development. This Review covers ordered protein assemblies including protein nanowires/nanofibrils, nanorings, nanotubes, designed two- and three-dimensional ordered protein lattices and protein-like cages including polyhedral virus-like cage structures. The main focus is on designed ordered protein assemblies, in which the spatial organization of the proteins is controlled by tailored noncovalent interactions (including metal ion binding interactions, electrostatic interactions and ligand–receptor interactions among others) or by careful design of modified (mutant) proteins or de novo constructs. The modification of natural protein assemblies including bacterial S-layers and cage-like and rod-like viruses to impart novel function, e.g. enzymatic activity, is also considered. A diversity of structures have been created using distinct approaches, and this Review provides a summary of the state-of-the-art in the development of these systems, which have exceptional potential as advanced bionanomaterials for a diversity of applications.

On-Axis Alignment of Protein Nanocage Assemblies from 2D to 3D through the Aromatic Stacking Interactions of Amino Acid Residues

Aromatic-aromatic interactions between natural aromatic amino acids Phe, Tyr, and Trp play crucial roles in protein-protein recognition and protein folding. However, the function of such interactions in the preparation of different dimensional, ordered protein superstructures has not been recognized. Herein, by a combination of the directionality of the symmetry axes of protein building blocks and the strength of the aromatic-aromatic interactions coming from a group of aromatic amino acid residues, we built an engineering strategy to construct protein superlattices. Based on this strategy, substitution of single amino acid residue Glu162 around the C₄ rotation axes near the outer surface of 24-mer ferritin nanocage with Phe, Tyr, and Trp, respectively, resulted in 2D and 3D protein superlattices where protein cages are aligned along the C₄ axes, imposing a fixed disposition of neighboring ferritins. The self-assembly of these superlattices is reversible, which can be tuned by external stimuli (salt concentration or pH). Moreover, these superlattices can serve as biotemplates for the fabrication of 2D and 3D inorganic nanoparticle arrays.