Four-component protein nanocages designed by programmed symmetry breaking

Sangmin Lee; Ryan D Kibler; Green Ahn; Yang Hsia; Andrew J Borst; Annika Philomin; Madison A Kennedy; Buwei Huang; Barry Stoddard; David Baker

doi:10.1038/s41586-024-07814-1

Four-component protein nanocages designed by programmed symmetry breaking

Nature. 2024 Dec 18. doi: 10.1038/s41586-024-07814-1. Online ahead of print.

Authors

Sangmin Lee^#^{1

2

3

4}, Ryan D Kibler^#^{1

2}, Green Ahn^{1

2}, Yang Hsia^{1

2}, Andrew J Borst^{1

2}, Annika Philomin², Madison A Kennedy^{1

5}, Buwei Huang^{1

2}, Barry Stoddard⁵, David Baker^{6

7

8}

Affiliations

¹ Department of Biochemistry, University of Washington, Seattle, WA, USA.
² Institute for Protein Design, University of Washington, Seattle, WA, USA.
³ Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
⁴ Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea.
⁵ Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA.
⁶ Department of Biochemistry, University of Washington, Seattle, WA, USA. dabaker@uw.edu.
⁷ Institute for Protein Design, University of Washington, Seattle, WA, USA. dabaker@uw.edu.
⁸ Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA. dabaker@uw.edu.

^# Contributed equally.

PMID: 39695226
DOI: 10.1038/s41586-024-07814-1

Abstract

Four, eight or twenty C3 symmetric protein trimers can be arranged with tetrahedral, octahedral or icosahedral point group symmetry to generate closed cage-like structures^1,2. Viruses access more complex higher triangulation number icosahedral architectures by breaking perfect point group symmetry^3-9, but nature appears not to have explored similar symmetry breaking for tetrahedral or octahedral symmetries. Here we describe a general design strategy for building higher triangulation number architectures starting from regular polyhedra through pseudosymmetrization of trimeric building blocks. Electron microscopy confirms the structures of T = 4 cages with 48 (tetrahedral), 96 (octahedral) and 240 (icosahedral) subunits, each with 4 distinct chains and 6 different protein-protein interfaces, and diameters of 33 nm, 43 nm and 75 nm, respectively. Higher triangulation number viruses possess very sophisticated functionalities; our general route to higher triangulation number nanocages should similarly enable a next generation of multiple antigen-displaying vaccine candidates^10,11 and targeted delivery vehicles^12,13.