Caspar, D. L. D. & Klug, A. Physical principles in the construction of regular viruses. Cold Spring Harb. Symp. Quant. Biol. 27, 1–24 (1962).
Johnson, J. E. & Speir, J. A. Quasi-equivalent viruses: a paradigm for protein assemblies. J. Mol. Biol. 269, 665–675 (1997).
Kroto, H. W., Heath, J. R., O’Brien, S. C., Curl, R. F. & Smalley, R. E. C60: buckminsterfullerene. Nature 318, 162–163 (1985).
Shechtman, D., Blech, I., Gratias, D. & Cahn, J. W. Metallic phase with long-range orientational order and no translational symmetry. Phys. Rev. Lett. 53, 1951–1953 (1984).
Kirchhausen, T., Owen, D. & Harrison, S. C. Molecular structure, function, and dynamics of clathrin-mediated membrane traffic. Cold Spring Harb. Perspect. Biol. 6, a016725 (2014).
Hsia, Y. et al. Design of multi-scale protein complexes by hierarchical building block fusion. Nat. Commun. 12, 2294 (2021).
Bale, J. B. et al. Accurate design of megadalton-scale two-component icosahedral protein complexes. Science 353, 389–394 (2016).
Walls, A. C. et al. Elicitation of potent neutralizing antibody responses by designed protein nanoparticle vaccines for SARS-CoV-2. Cell 183, 1367–1382 (2020).
Boyoglu-Barnum, S. et al. Quadrivalent influenza nanoparticle vaccines induce broad protection. Nature 592, 623–628 (2021).
Divine, R. et al. Designed proteins assemble antibodies into modular nanocages. Science 372, eabd9994 (2021).
Yang, E. C. et al. Computational design of non-porous pH-responsive antibody nanoparticles. Nat. Struct. Mol. Biol. 31, 1404–1412 (2024).
Sigl, C. et al. Programmable icosahedral shell system for virus trapping. Nat. Mater. 20, 1281–1289 (2021).
Lee, S. et al. Four-component protein nanocages designed by programmed symmetry breaking. Nature 638, 546–552 (2025).
Dowling, Q. M. et al. Hierarchical design of pseudosymmetric protein nanocages. Nature 638, 553–561 (2025).
Sadoc, J.-F. & Mosseri, R. Geometrical Frustration (Cambridge Univ. Press, 2006).
Perlmutter, J. D. & Hagan, M. F. Mechanisms of virus assembly. Annu. Rev. Phys. Chem. 66, 217–239 (2015).
Wang, S. et al. Bond-centric modular design of protein assemblies. Nat. Mater. 24, 1644–1652 (2025).
Watson, J. L. et al. De novo design of protein structure and function with RFdiffusion. Nature 620, 1089–1100 (2023).
Sahtoe, D. D. et al. Reconfigurable asymmetric protein assemblies through implicit negative design. Science 375, eabj7662 (2022).
Khmelinskaia, A. et al. Local structural flexibility drives oligomorphism in computationally designed protein assemblies. Nat. Struct. Mol. Biol. 32, 1050–1060 (2025).
Schein, S. & Gayed, J. M. Fourth class of convex equilateral polyhedron with polyhedral symmetry related to fullerenes and viruses. Proc. Natl Acad. Sci. USA 111, 2920–2925 (2014).
Morris, K. L. et al. Cryo-EM of multiple cage architectures reveals a universal mode of clathrin self-assembly. Nat. Struct. Mol. Biol. 26, 890–898 (2019).
DiMaio, F., Leaver-Fay, A., Bradley, P., Baker, D. & André, I. Modeling symmetric macromolecular structures in Rosetta3. PLoS ONE 6, e20450 (2011).
Wang, R. Y.-R. et al. Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta. eLife 5, e17219 (2016).
Saito, R., Dresselhaus, G. & Dresselhaus, M. S. Topological defects in large fullerenes. Chem. Phys. Lett. 195, 537–542 (1992).
Pédelacq, J.-D., Cabantous, S., Tran, T., Terwilliger, T. C. & Waldo, G. S. Engineering and characterization of a superfolder green fluorescent protein. Nat. Biotechnol. 24, 79–88 (2006).
Wu, K. et al. Design of intrinsically disordered region binding proteins. Science 389, eadr8063 (2025).
Kubala, M. H., Kovtun, O., Alexandrov, K. & Collins, B. M. Structural and thermodynamic analysis of the GFP:GFP-nanobody complex. Protein Sci. 19, 2389–2401 (2010).
Los, G. V. et al. HaloTag: a novel protein labeling technology for cell imaging and protein analysis. ACS Chem. Biol. 3, 373–382 (2008).
Zakeri, B. et al. Peptide tag forming a rapid covalent bond to a protein, through engineering a bacterial adhesin. Proc. Natl Acad. Sci. USA 109, E690–E697 (2012).
Chen, J., Li, Q. & Wang, J. Topology of human apolipoprotein E3 uniquely regulates its diverse biological functions. Proc. Natl Acad. Sci. USA 108, 14813–14818 (2011).
Huang, B. et al. Designed endocytosis-inducing proteins degrade targets and amplify signals. Nature 638, 796–804 (2025).
Luby-Phelps, K., Taylor, D. L. & Lanni, F. Probing the structure of cytoplasm. J. Cell Biol. 102, 2015–2022 (1986).
Delarue, M. et al. mTORC1 controls phase separation and the biophysical properties of the cytoplasm by tuning crowding. Cell 174, 338–349 (2018).
Hernandez, C. M., Duran-Chaparro, D. C., Van Eeuwen, T., Rout, M. P. & Holt, L. J. Development and Characterization of 50 nanometer diameter genetically encoded multimeric nanoparticles. Preprint at bioRxiv https://doi.org/10.1101/2024.07.05.602291 (2024).
Parry, B. R. et al. The bacterial cytoplasm has glass-like properties and is fluidized by metabolic activity. Cell 156, 183–194 (2014).
Xie, Y. et al. Polysome collapse and RNA condensation fluidize the cytoplasm. Mol. Cell 84, 2698–2716 (2024).
Bindels, D. S. et al. mScarlet: a bright monomeric red fluorescent protein for cellular imaging. Nat. Methods 14, 53–56 (2017).
Cuylen-Haering, S. et al. Chromosome clustering by Ki-67 excludes cytoplasm during nuclear assembly. Nature 587, 285–290 (2020).
Lee, S. et al. Design of one-component quasisymmetric protein nanocages. Nature https://www.doi.org/10.1038/s41586-026-10554-z (2026).
Mojica, M., Alonso, J. A. & Méndez, F. Synthesis of fullerenes. J. Phys. Org. Chem. 26, 526–539 (2013).
Lundberg, E. & Borner, G. H. H. Spatial proteomics: a powerful discovery tool for cell biology. Nat. Rev. Mol. Cell Biol. 20, 285–302 (2019).
Fung, H. K. H. et al. Genetically encoded multimeric tags for subcellular protein localization in cryo-EM. Nat. Methods 20, 1900–1908 (2023).
Volk, M. J. et al. Metabolic engineering: methodologies and applications. Chem. Rev. 123, 5521–5570 (2023).
Sutter, M., Greber, B., Aussignargues, C. & Kerfeld, C. A. Assembly principles and structure of a 6.5-MDa bacterial microcompartment shell. Science 356, 1293–1297 (2017).
Shunzhi, W. QS-2compCage-BBs_Hexagon-Generator. Zenodo https://doi.org/10.5281/zenodo.18892840 (2026).
Dauparas, J. et al. Robust deep learning–based protein sequence design using ProteinMPNN. Science 378, 49–56 (2022).
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).
Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).
Kabsch, W. XDS. Acta Crystallogr. D 66, 125–132 (2010).
Winn, M. D. et al. Overview of the CCP 4 suite and current developments. Acta Crystallogr. D 67, 235–242 (2011).
McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007).
Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010).
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004).
Williams, C. J. et al. MolProbity: more and better reference data for improved all-atom structure validation. Protein Sci. 27, 293–315 (2018).
Mastronarde, D. N. SerialEM: a program for automated tilt series acquisition on tecnai microscopes using prediction of specimen position. Microsc. Microanal. 9, 1182–1183 (2003).
Hagen, W. J. H., Wan, W. & Briggs, J. A. G. Implementation of a cryo-electron tomography tilt-scheme optimized for high resolution subtomogram averaging. J. Struct. Biol. 197, 191–198 (2017).
Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017).
Keegan, S., Fenyö, D. & Holt, L. J. GEMspa: a Napari plugin for analysis of single particle tracking data. Preprint at bioRxiv https://doi.org/10.1101/2023.06.26.546612 (2023).
Meng, E. C. et al. UCSF ChimeraX: tools for structure building and analysis. Protein Sci. 32, e4792 (2023).
Ershov, D. et al. TrackMate 7: integrating state-of-the-art segmentation algorithms into tracking pipelines. Nat. Methods 19, 829–832 (2022).