Triangular in Vivo Self-Assembling Coiled-Coil Protein Origami

Preorganized cyclic modules facilitate the self-assembly of protein nanostructures

The rational design of supramolecular assemblies aims to generate complex systems based on the simple information encoded in the chemical structure. Programmable molecules such as nucleic acids and polypeptides are particularly suitable for designing diverse assemblies and shapes not found in nature. Here, we describe a strategy for assembling modular architectures based on structurally and covalently preorganized subunits. Cyclization through spontaneous self-splicing of split intein and coiled-coil dimer-based interactions of polypeptide chains provide structural constraints, facilitating the desired assembly. We demonstrate the implementation of a strategy based on the preorganization of the subunits by designing a two-chain coiled-coil protein origami (CCPO) assembly that adopts a tetrahedral topology only when one or both subunit chains are covalently cyclized. Employing this strategy, we further design a 109 kDa trimeric CCPO assembly comprising 24 CC-forming segments. In this case, intein cyclization was crucial for the assembly of a concave octahedral scaffold, a newly designed protein fold. The study highlights the importance of preorganization of building modules to facilitate the self-assembly of higher-order supramolecular structures.

Coiled-Coil Interaction Toolbox for Engineering Mammalian Cells

Protein interactions play a crucial role in a variety of biological processes. Therefore, regulation of these interactions has received considerable attention in terms of synthetic biology tool development. Of those, a toolbox of small peptides known as coiled coils (CCs) represents a unique effective tool for mediating protein-protein interactions because their binding specificity and affinity can be designed and controlled. CC peptides have been used as a building module for designing synthetic regulatory circuits in mammalian cells, construction of fast response to a signal, amplification of the response, and localization and regulation of function of diverse proteins. In this chapter, we describe a designed set of CCs used for mammalian cell engineering and provide a protocol for the construction of CC-mediated logic circuits in mammalian cells. Ultimately, these tools could be used for diverse biotechnological and therapeutic applications.

Streamlined construction of robust heteroprotein complexes by self-induced in-cell disulfide pairing

Biomolecules and their functional subdomains are essential building blocks in the creation of multifunctional nanocomplexes. Methyl-binding domain protein 2 (MBD2) and p66α stand out as small α-helical motifs with an ability to self-assemble into a heterodimeric coiled-coil, making them promising building units. Yet, their practical use is hindered by rapid dissociation upon dilution. In this study, novel fusion tags, MBD2 and p66α variants, were developed to covalently link during co-expression in E. coli SHuffle. Through strategic placement of cysteine at each α-helix's terminus, intracellular crosslinking occurred with high specificity and yield, facilitated by preserved α-helical interactions. This instant disulfide bonding in the oxidative cytoplasm of E. coli SHuffle efficiently overcame the need for inefficient in vitro oxidation and protein extraction prone to creating non-specific adducts and suboptimal bioprocesses. In contrast to their wild-type counterparts, the GFP-mCherry protein complex cross-linked by the fusion tags maintained the heterodimeric state even under extensive dilution. The fusion tags, when combined with the E. coli SHuffle system, allowed for the streamlined co-expression of a stable protein complex through self-induced intracellular cysteine coupling. The approach demonstrated herein holds great promise for producing multifunctional and robust heteroprotein complexes.

Crystal Structure of de Novo Designed Coiled-Coil Protein Origami Triangle

Coiled-coil protein origami (CCPO) uses modular coiled-coil building blocks and topological principles to design polyhedral structures distinct from those of natural globular proteins. While the CCPO strategy has proven successful in designing diverse protein topologies, no high-resolution structural information has been available about these novel protein folds. Here we report the crystal structure of a single-chain CCPO in the shape of a triangle. While neither cyclization nor the addition of nanobodies enabled crystallization, it was ultimately facilitated by the inclusion of a GCN2 homodimer. Triangle edges are formed by the orthogonal parallel coiled-coil dimers P1:P2, P3:P4, and GCN2 connected by short linkers. A triangle has a large central cavity and is additionally stabilized by side-chain interactions between neighboring segments at each vertex. The crystal lattice is densely packed and stabilized by a large number of contacts between triangles. Interestingly, the polypeptide chain folds into a trefoil-type protein knot topology, and AlphaFold2 fails to predict the correct fold. The structure validates the modular CC-based protein design strategy, providing molecular insight underlying CCPO stabilization and new opportunities for the design.

Coiled-Coil Protein Origami: Design, Isolation, and Characterization

Coiled-coil protein origami (CCPO) is a rationally designed de novo protein fold, constructed by concatenating coiled-coil forming segments into a polypeptide chain, that folds into polyhedral nano-cages. To date, nanocages in the shape of a tetrahedron, square pyramid, trigonal prism, and trigonal bipyramid have been successfully designed and extensively characterized following the design principles of CCPO. These designed protein scaffolds and their favorable biophysical properties are suitable for functionalization and other various biotechnological applications. To further facilitate the development, we are presenting a detailed guide to the world of CCPO, starting from design (CoCoPOD, an integrated platform for designing CCPO strictures) and cloning (modified Golden-gate assembly) to fermentation and isolation (NiNTA, Strep-trap, IEX, and SEC) concluding with standard characterization techniques (CD, SEC-MALS, and SAXS).

Creating de novo peptide-based bioactivities: from assembly to origami

DNA origami has created complex structures of various spatial dimensions. However, their versatility in terms of function is limited due to the lower number of the intrinsic building blocks, i.e. nucleotides, compared with the number of amino acids. Therefore, protein origami has been proposed and demonstrated to precisely fabricate artificial functional nanostructures. Despite their hierarchical folded structures, chain-like peptides and DNA share obvious similarities in both structures and properties, especially in terms of chain hybridization; therefore, replacing DNA with peptides to create bioactivities not only has high theoretical feasibility but also provides a new bottom-up synthetic strategy. However, designing functionalities with tens to hundreds of peptide chains using the similar principle of DNA origami has not been reported, although the origami strategy holds great potential to generate more complex bioactivities. In this perspective review, we have reviewed the recent progress in and highlighted the advantages of peptide assembly and origami on the orientation of artificially created bioactivities. With the great potential of peptide origami, we appeal to develop user-friendly softwares in combination with artificial intelligence.

Metal ion-regulated assembly of designed modular protein cages

Coiled-coil (CC) dimers are versatile, customizable building modules for the design of diverse protein architectures unknown in nature. Incorporation of dynamic self-assembly, regulated by a selected chemical signal, represents an important challenge in the construction of functional polypeptide nanostructures. Here, we engineered metal binding sites to render an orthogonal set of CC heterodimers Zn(II)-responsive as a generally applicable principle. The designed peptides assemble into CC heterodimers only in the presence of Zn(II) ions, reversibly dissociate by metal ion sequestration, and additionally act as pH switches, with low pH triggering disassembly. The developed Zn(II)-responsive CC set is used to construct programmable folding of CC-based nanostructures, from protein triangles to a two-chain bipyramidal protein cage that closes and opens depending on the metal ion. This demonstrates that dynamic self-assembly can be designed into CC-based protein cages by incorporation of metal ion-responsive CC building modules that act as conformational switches and that could also be used in other contexts.

Peptide Design and Self-assembly into Targeted Nanostructure and Functional Materials

Peptides have been extensively utilized to construct nanomaterials that display targeted structure through hierarchical assembly. The self-assembly of both rationally designed peptides derived from naturally occurring domains in proteins as well as intuitively or computationally designed peptides that form β-sheets and helical secondary structures have been widely successful in constructing nanoscale morphologies with well-defined 1-d, 2-d, and 3-d architectures. In this review, we discuss these successes of peptide self-assembly, especially in the context of designing hierarchical materials. In particular, we emphasize the differences in the level of peptide design as an indicator of complexity within the targeted self-assembled materials and highlight future avenues for scientific and technological advances in this field.