Design of a hyperstable 60-subunit protein icosahedron

By Y. Hsia, J. Bale, S. Gonen, Dan Shi, W. Sheffler, Kimberly K. Fong, U. Nattermann, Chunfu Xu, Po-Ssu Huang, Rashmi Ravichandran and 5 more. 2016

410 citations recorded by the source corpus.

The icosahedron is the largest of the Platonic solids, and icosahedral protein structures are widely used in biological systems for packaging and transport. There has been considerable interest in repurposing such structures for applications ranging from targeted delivery to multivalent immunogen presentation. The ability to design proteins that self-assemble into precisely specified, highly ordered icosahedral structures would open the door to a new generation of protein containers with properties custom-tailored to specific applications. Here we describe the computational design of a 25-nanometre icosahedral nanocage that self-assembles from trimeric protein building blocks. The designed protein was produced in Escherichia coli, and found by electron microscopy to assemble into a homogenous population of icosahedral particles nearly identical to the design model. The particles are stable in 6.7 molar guanidine hydrochloride at up to 80 degrees Celsius, and undergo extremely abrupt, but reversible, disassembly between 2 molar and 2.25 molar guanidinium thiocyanate. The icosahedron is robust to genetic fusions: one or two copies of green fluorescent protein (GFP) can be fused to each of the 60 subunits to create highly fluorescent ‘standard candles’ for use in light microscopy, and a designed protein pentamer can be placed in the centre of each of the 20 pentameric faces to modulate the size of the entrance/exit channels of the cage. Such robust and customizable nanocages should have considerable utility in targeted drug delivery, vaccine design and synthetic biology.

Subfields: Ecology, Molecular Biology

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Citations in the corpus

Assessing and enhancing foldability in designed proteins (2021, positive): “New methods enable the routine design of new folds [1–4], assemblies [5,6], and new or improved functions [7–13].”
Designing Peptides on a Quantum Computer (2019, methodology): “Rosetta has been used to design new protein topologies ( 2 , 3 ) , large macromolecular assemblies ( 4 – 7 ) , proteins with the ability to bind to toxic small molecules ( 8 , 9 ) or to other proteins of therapeutic interest ( 10 , 11 ) , and enzymes able to catalyze reactions that no known natural…”
De novo protein design, a retrospective (2020, methodology): “This method has been used to create novel cages with varying symmetries including icosahedral assemblies (King et al., 2012; Bale et al., 2016; Hsia et al., 2016).”
Construction, characterization, and immunization of nanoparticles that display a diverse array of influenza HA trimers (2020, background): “Bottom: Cryo-EM structure of I3-01 particle related to mi3 [24] with the locations of SpyCatcher fusion sites indicated by red dots (left) and schematic SpyCatcher-NP (right).”
The coming of age of de novo protein design (2016, methodology): “Protein interface design methods have been used to create one-or two-component assemblies with icosohedral symmetry and 60 subunits 82 or 120 subunits 83 , respectively.”
Illuminating protein space with a programmable generative model (2022, background): “Incorporating symmetry in computational protein generation holds promise in designing large functionalized protein complexes [Hsia et al., 2016].”
AlphaDesign: A de novo protein design framework based on AlphaFold (2021, background): “These applications range from the ﬁrst de novo designed proteins [48] to synthetic vaccines [49, 50], complex assemblies [51, 52] and enzymes [53, 54].”