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De novo design of quasisymmetric two-component protein cages
Caspar, D. L. D. & Klug, A. Physical principles in the construction of regular viruses. Cold Spring Harb. Symp. Quant. Biol. 27, 1–24 (1962).
Google Scholar
Johnson, J. E. & Speir, J. A. Quasi-equivalent viruses: a paradigm for protein assemblies. J. Mol. Biol. 269, 665–675 (1997).
Google Scholar
Kroto, H. W., Heath, J. R., O’Brien, S. C., Curl, R. F. & Smalley, R. E. C60: buckminsterfullerene. Nature 318, 162–163 (1985).
Google Scholar
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).
Google Scholar
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).
Google Scholar
Hsia, Y. et al. Design of multi-scale protein complexes by hierarchical building block fusion. Nat. Commun. 12, 2294 (2021).
Google Scholar
Bale, J. B. et al. Accurate design of megadalton-scale two-component icosahedral protein complexes. Science 353, 389–394 (2016).
Google Scholar
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).
Google Scholar
Boyoglu-Barnum, S. et al. Quadrivalent influenza nanoparticle vaccines induce broad protection. Nature 592, 623–628 (2021).
Google Scholar
Divine, R. et al. Designed proteins assemble antibodies into modular nanocages. Science 372, eabd9994 (2021).
Google Scholar
Yang, E. C. et al. Computational design of non-porous pH-responsive antibody nanoparticles. Nat. Struct. Mol. Biol. 31, 1404–1412 (2024).
Google Scholar
Sigl, C. et al. Programmable icosahedral shell system for virus trapping. Nat. Mater. 20, 1281–1289 (2021).
Google Scholar
Lee, S. et al. Four-component protein nanocages designed by programmed symmetry breaking. Nature 638, 546–552 (2025).
Google Scholar
Dowling, Q. M. et al. Hierarchical design of pseudosymmetric protein nanocages. Nature 638, 553–561 (2025).
Google Scholar
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).
Google Scholar
Wang, S. et al. Bond-centric modular design of protein assemblies. Nat. Mater. 24, 1644–1652 (2025).
Google Scholar
Watson, J. L. et al. De novo design of protein structure and function with RFdiffusion. Nature 620, 1089–1100 (2023).
Google Scholar
Sahtoe, D. D. et al. Reconfigurable asymmetric protein assemblies through implicit negative design. Science 375, eabj7662 (2022).
Google Scholar
Khmelinskaia, A. et al. Local structural flexibility drives oligomorphism in computationally designed protein assemblies. Nat. Struct. Mol. Biol. 32, 1050–1060 (2025).
Google Scholar
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).
Google Scholar
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).
Google Scholar
DiMaio, F., Leaver-Fay, A., Bradley, P., Baker, D. & André, I. Modeling symmetric macromolecular structures in Rosetta3. PLoS ONE 6, e20450 (2011).
Google Scholar
Wang, R. Y.-R. et al. Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta. eLife 5, e17219 (2016).
Google Scholar
Saito, R., Dresselhaus, G. & Dresselhaus, M. S. Topological defects in large fullerenes. Chem. Phys. Lett. 195, 537–542 (1992).
Google Scholar
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).
Google Scholar
Wu, K. et al. Design of intrinsically disordered region binding proteins. Science 389, eadr8063 (2025).
Google Scholar
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).
Google Scholar
Los, G. V. et al. HaloTag: a novel protein labeling technology for cell imaging and protein analysis. ACS Chem. Biol. 3, 373–382 (2008).
Google Scholar
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).
Google Scholar
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).
Google Scholar
Huang, B. et al. Designed endocytosis-inducing proteins degrade targets and amplify signals. Nature 638, 796–804 (2025).
Google Scholar
Luby-Phelps, K., Taylor, D. L. & Lanni, F. Probing the structure of cytoplasm. J. Cell Biol. 102, 2015–2022 (1986).
Google Scholar
Delarue, M. et al. mTORC1 controls phase separation and the biophysical properties of the cytoplasm by tuning crowding. Cell 174, 338–349 (2018).
Google Scholar
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).
Google Scholar
Xie, Y. et al. Polysome collapse and RNA condensation fluidize the cytoplasm. Mol. Cell 84, 2698–2716 (2024).
Google Scholar
Bindels, D. S. et al. mScarlet: a bright monomeric red fluorescent protein for cellular imaging. Nat. Methods 14, 53–56 (2017).
Google Scholar
Cuylen-Haering, S. et al. Chromosome clustering by Ki-67 excludes cytoplasm during nuclear assembly. Nature 587, 285–290 (2020).
Google Scholar
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).
Google Scholar
Lundberg, E. & Borner, G. H. H. Spatial proteomics: a powerful discovery tool for cell biology. Nat. Rev. Mol. Cell Biol. 20, 285–302 (2019).
Google Scholar
Fung, H. K. H. et al. Genetically encoded multimeric tags for subcellular protein localization in cryo-EM. Nat. Methods 20, 1900–1908 (2023).
Google Scholar
Volk, M. J. et al. Metabolic engineering: methodologies and applications. Chem. Rev. 123, 5521–5570 (2023).
Google Scholar
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).
Google Scholar
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).
Google Scholar
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).
Google Scholar
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).
Google Scholar
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).
Google Scholar
McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007).
Google Scholar
Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010).
Google Scholar
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004).
Google Scholar
Williams, C. J. et al. MolProbity: more and better reference data for improved all-atom structure validation. Protein Sci. 27, 293–315 (2018).
Google Scholar
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).
Google Scholar
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).
Google Scholar
Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017).
Google Scholar
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).
Google Scholar
Ershov, D. et al. TrackMate 7: integrating state-of-the-art segmentation algorithms into tracking pipelines. Nat. Methods 19, 829–832 (2022).
Google Scholar