Structure-based design of novel polyhedral protein nanomaterials

Abstract

Organizing matter at the atomic scale is a central goal of nanotechnology. Bottom-up approaches, in which molecular building blocks are programmed to assemble via supramolecular interactions, are a proven and versatile route to new and useful nanomaterials. Although a wide variety of molecules have been used as building blocks, proteins have several intrinsic features that present unique opportunities for designing nanomaterials with sophisticated functions. There has been tremendous recent progress in designing proteins to fold and assemble to highly ordered structures. Here we review the leading approaches to the design of closed polyhedral protein assemblies, highlight the importance of considering the assembly process itself, and discuss various applications and future directions for the field. We emphasize throughout the exciting opportunities presented by recent advances as well as challenges that remain.

Figure 1

Structure-based design of novel protein nanomaterials. (a) Example of a rationally designed protein nanomaterial (I53_dn5) [35], highlighting the three distinct surfaces available for modification: (i) interior, (ii) exterior, and (iii) inter-subunit. (b) Most common strategies for the rational design of 3D bound protein materials. Schematic representation and surface maps of successful examples of tetrahedral assemblies resulting from each design strategy (i. PDB ID 3VDX [9], ii. [24], iii. PDB ID 6OT7 [30], iv. PDB ID 4NWN [26]). (c) Survey of structural specifications of well-defined designed assemblies. Outer diameters of the design models (colored polygons and circles: black, natural assemblies; purple, interface design; blue, metal-mediated; orange, genetic fusion; red, coiled-coil, green, edge traversal; pentagons, icosahedral symmetry; squares, octahedral symmetry; triangles, tetrahedral symmetry; circles, other) are plotted from explicitly stated published values, or values estimated from scale images or experimental data. Inner diameters (left end of colored lines) correspond to published values, or are estimated by subtracting the width of the protein component(s) from the outer diameter. Lumen volumes (small gray polygons and circles, designed assemblies; small black polygons, natural assemblies; blue-trimmed black square, metal-redesigned ferritin) are estimated from inner diameter. Black dashed traces plot the relationship between outer diameter and lumen volume for spheres with 2 nm and 5 nm shell thicknesses.

Figure 2

Comparison of controlled and uncontrolled assembly and disassembly. (a) An example of an assembly that is both uncontrolled and non-cooperative, which proceeds simultaneously with protein synthesis, non-specifically encapsulating intracellular contaminants (violet) and resulting in a variety of higher-order structures. A disassembly and purification step is thus required to access the nanomaterial interior and allow for error correction to proceed toward a single target structure that could encapsulate a molecular cargo (blue). Heterogeneity of the assembled product leads to inconsistent cargo protection and release properties. (b) An ideal multi-component assembly is inherently controllable by intentional sequestration and mixing of individually prepared components. Alternatively (or additionally), assembly can be triggered by a physical or biochemical condition, allowing simultaneous assembly and encapsulation. Cooperative assembly yields a uniform product, which prevents premature cargo release.

Figure 3

Selection of current applications of rationally designed polyhedral protein assemblies, grouped by the surface addressed for their realization. Examples are provided for each category: a nanoparticle vaccine based on the two-component icosahedral nanoparticle I53_dn5 displaying genetically fused influenza hemagglutinin (Boyoglu-Barnum et al., bioRxiv doi:10.1101/2020.05.30.125179), the two-component octahedral assembly o42.1, which integrates Fc domains as dimeric components (Divine et al., manuscript submitted), and the two-component icosahedral nanoparticle I53–50-v4 with its mRNA-packaging interior lumen highlighted [50].