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Design of a symmetry-broken tetrahedral protein cage by a method of internal steric occlusion
Open accessPreprint — published as 10.1002/pro.4973
Abstract
Methods in protein design have made it possible to create large and complex, self-assembling protein cages with diverse applications. These have largely been based on highly symmetric forms exemplified by the Platonic solids. Prospective applications of protein cages would be expanded by strategies for breaking the designed symmetry, e . g ., so that only one or a few (instead of many) copies of an exterior domain or motif might be displayed on their surfaces. Here we demonstrate a straightforward design approach for creating symmetry-broken protein cages able to display singular copies of outward-facing domains. We modify the subunit of an otherwise symmetric protein cage through fusion to a small inward-facing domain, only one copy of which can be accommodated in the cage interior. Using biochemical methods and native mass spectrometry, we show that co-expression of the original subunit and the modified subunit, which is further fused to an outward-facing anti-GFP DARPin domain, leads to self-assembly of a protein cage presenting just one copy of the DARPin protein on its exterior. This strategy of designed occlusion provides a facile route for creating new types of protein cages with unique properties.
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Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764
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- 2022, Metal ion– regulated assembly of designed modular protein cages, Science Advances, 8, eabm8243, 10.1126/sciadv.abm8243 · DOI
- 10.1126/science.aaf8818 · DOI
- 10.1021/jacs.8b13604 · DOI
- 2022, Protein Cages: From Fundamentals to Advanced Applications, Chem. Rev, 122, 9145, 10.1021/acs.chemrev.1c00877 · DOI
- 10.1126/science.1233936 · DOI
- 10.1038/s41586-019-1928-2 · DOI
- Haas RJ de Brunette N , Goodson A , Dauparas J , Yi SY , Yang EC , Dowling Q , Nguyen H , Kang A , Bera AK , et al. (2023) Rapid and automated design of two-component protein nanomaterials using ProteinMPNN. :2023.08.04.551935. Available from: https://www.biorxiv.org/content/10.1101/2023.08.04.551935v1 · DOI
- 10.1126/science.1219364 · DOI
- 10.1038/nature13404 · DOI
- 10.1126/science.1219351 · DOI
- 2014, Structure of a designed protein cage that selfassembles into a highly porous cube, Nature Chem, 6, 1065, 10.1038/nchem.2107 · DOI
- 2019, An ultra-stable goldcoordinated protein cage displaying reversible assembly, Nature, 569, 438, 10.1038/s41586-019-1185-4 · DOI
- Meador K , Castells-Graells R , Aguirre R , Sawaya MR , Arbing MA , Sherman T , Senarathne C , Yeates TO (2023) A Suite of Designed Protein Cages Using Machine Learning Algorithms and Protein Fragment-Based Protocols. :2023.10.09.561468. Available from: https://www.biorxiv.org/content/10.1101/2023.10.09.561468v1 · DOI · Paper page
- 10.1073/pnas.041614998 · DOI
- 2017, Structure and assembly of scalable porous protein cages, Nature Communications, 8, 14663, 10.1038/ncomms14663 · DOI
- 10.1073/pnas.1606013113 · DOI
- 10.1073/pnas.1800527115 · DOI
- 10.1073/pnas.2015183117 · DOI
- 2021, Design of metal-mediated protein assemblies via hydroxamic acid functionalities, Nat Protoc, 16, 3264, 10.1038/s41596-021-00535-z · DOI
- 2017, Geometric Principles for Designing Highly Symmetric Self-Assembling Protein Nanomaterials, Annual Review of Biophysics, 46, 23, 10.1146/annurev-biophys-070816-033928 · DOI
- 10.1038/177473a0 · DOI
- 2020, Structural and functional evaluation of de novo-designed, two-component nanoparticle carriers for HIV Env trimer immunogens, PLOS Pathogens, 16, e1008665, 10.1371/journal.ppat.1008665 · DOI
- 10.1016/j.cell.2021.01.035 · DOI
- 10.1016/j.cell.2019.01.046 · DOI
- 10.1016/j.cell.2020.10.043 · DOI · Paper page
- 10.1126/science.abd9994 · DOI
- 10.3390/biom13071122 · DOI
- 2020, Designed Protein Cages as Scaffolds for Building Multienzyme Materials, ACS Synth. Biol, 9, 381, 10.1021/acssynbio.9b00407 · DOI
- 2023, Tunable In Vivo Colocalization of Enzymes within P22 Capsid-Based Nanoreactors, ACS Appl. Mater. Interfaces, 15, 17705, 10.1021/acsami.3c00971 · DOI
- 2023, Cryo-EM structure determination of small therapeutic protein targets at 3 Å-resolution using a rigid imaging scaffold, Proceedings of the National Academy of Sciences, 120, e2305494120, 10.1073/pnas.2305494120 · DOI · Paper page
- 2019, A 3.8 Å resolution cryo-EM structure of a small protein bound to an imaging scaffold, Nature Communications, 10, 1864, 10.1038/s41467-019-09836-0 · DOI
- 10.1073/pnas.1718825115 · DOI
- 2017, Design of coiled-coil protein-origami cages that self-assemble in vitro and in vivo, Nat Biotechnol, 35, 1094, 10.1038/nbt.3994 · DOI
- Lee S , Kibler RD , Hsia Y , Borst AJ , Philomin A , Kennedy MA , Stoddard B , Baker D (2023) Design of four component T=4 tetrahedral, octahedral, and icosahedral protein nanocages through programmed symmetry breaking. :2023.06.16.545341. Available from: https://www.biorxiv.org/content/10.1101/2023.06.16.545341v1 · DOI
- 10.1002/pro.3802 · DOI
- 10.1016/j.copbio.2011.06.004 · DOI
- 10.1146/annurev-pharmtox-010611-134654 · DOI
- 10.1038/s41598-017-15711-z · DOI
- 10.1073/pnas.1713646115 · DOI
- 2021, Complete and cooperative in vitro assembly of computationally designed selfassembling protein nanomaterials, Nat Commun, 12, 883, 10.1038/s41467-021-21251-y · DOI
- 2022, High-Resolution Native Mass Spectrometry, Chem. Rev, 122, 7269, 10.1021/acs.chemrev.1c00212 · DOI · Paper page
- 10.1038/nmeth.4169 · DOI · Paper page
- 10.1038/nmeth.2089 · DOI · Paper page
Metadata
- Authors
- Gladkov, N., Scott, E. A., Meador, K., Lee, E. J., Laganowsky, A. D., Yeates, T. O., & Castells-Graells, R.
- Affiliations
- University of California, Los Angeles (US)
- Texas A&M University (US)
- Corresponding author
- Yeates, Todd O.
- ORCID
- Venue
- Protein Science
- Publisher
- openRxiv
- Published
- 2023-11-09
- Volume
- 33
- Issue
- 4
- Pages
- e4973-e4973
- ISSN
- 0961-8368 (ISSN-L)
- PMC
- PMC10966355
- OpenAlex
- W4393234111
- Cited by
- 8
- References
- 1
- Citations by year
- 2026: 1 · 2025: 5 · 2024: 2
- FWCI
- 1.09
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- cc-by
- Locations
- Protein Science (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (submittedVersion, cc-by)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- Funders
- U.S. Department of Energy (DEFC0202ER63421, FC02-02ER63421)
- Welch Foundation (A-2106-20220331)
- National Institutes of Health (DE-FC02-02ER63421, RM1GM1454316)
- Office of Science (FC02-02ER63421, 02ER63421, DEFC0202ER63421)
- National Institute of General Medical Sciences (R01GM139876)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biochemical and Structural Characterization
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein purification and stability
- Keywords
- symmetry breaking, steric occlusion, self-assembly, DARPin, Platonic solids
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