{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T15:55:20Z","timestamp":1792598120107,"version":"4.5.0"},"reference-count":51,"publisher":"American Chemical Society (ACS)","issue":"41","license":[{"start":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T00:00:00Z","timestamp":1788739200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T00:00:00Z","timestamp":1788739200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T00:00:00Z","timestamp":1788739200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"DOI":"10.13039\/100031478","name":"NextGenerationEU","doi-asserted-by":"publisher","award":["C005\/24-ED CV1"],"award-info":[{"award-number":["C005\/24-ED CV1"]}],"id":[{"id":"10.13039\/100031478","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002809","name":"Generalitat de Catalunya","doi-asserted-by":"publisher","award":["IU16-014045"],"award-info":[{"award-number":["IU16-014045"]}],"id":[{"id":"10.13039\/501100002809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008105","name":"Fundaci? 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Historically, two main strategies have been used to construct such cages: genetic fusion of oligomeric domains connected by helical linkers, and computational interface design using either physics-based or machine learning-based methods. Here, we extend the original fusion approach using modern AI algorithms and more sophisticated treatments of helix bending to create protein cages with novel architectures composed exclusively of trimeric building blocks arranged in tetrahedral symmetry. Of 15 designs tested experimentally, multiple sequence variants of two of these designs assembled predominantly into soluble, monodisperse particles of the expected size, with native molecular masses of 633 kDa (T33-Fus-1A, B) and 638 kDa (T33-Fus-2). Cryo-electron microscopy (cryo-EM) structures of three distinct sequence variants spanning from 3.0 to 3.9 \u00c5 in resolution confirmed the intended structures in atomic detail, with C-\u03b1 RMSD values over the entire assemblies as low as 2 \u00c5. The predicted modes of helix bending were similarly validated. The results highlight the impact of methodological improvements for achieving a level of regularity and design precision that has largely evaded prior applications of the fusion approach. These findings expand the prospects and accessible design space for self-assembling protein nanomaterials.<\/jats:p>","DOI":"10.1021\/jacs.6c11491","type":"journal-article","created":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T11:01:53Z","timestamp":1788778913000},"page":"44372-44379","source":"Crossref","is-referenced-by-count":0,"title":["Design and Structure\nof Protein Cages Based on Helical\nFusion and Machine Learning"],"prefix":"10.1021","volume":"148","author":[{"given":"Pablo","family":"San Segundo-Acosta","sequence":"first","affiliation":[{"name":"Spanish National Cancer Research Centre (CNIO) , , ,","place":["Madrid, Spain, 28029"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Johanne","family":"Le Coq","sequence":"additional","affiliation":[{"name":"Spanish National Cancer Research Centre (CNIO) , , ,","place":["Madrid, Spain, 28029"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jasminka","family":"Boskovic","sequence":"additional","affiliation":[{"name":"Spanish National Cancer Research Centre (CNIO) , , ,","place":["Madrid, Spain, 28029"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robin A.","family":"Aglietti","sequence":"additional","affiliation":[{"name":"AvimerBio , 9276 Scranton Rd. Suite 500 , , ,","place":["San Diego, California, United States, 92121"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter","family":"Bowers","sequence":"additional","affiliation":[{"name":"AvimerBio , 9276 Scranton Rd. Suite 500 , , ,","place":["San Diego, California, United States, 92121"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Todd O.","family":"Yeates","sequence":"additional","affiliation":[{"name":"AvimerBio , 9276 Scranton Rd. 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Am. Chem.\nSoc."},{"key":"2026102111064332300_cit4","doi-asserted-by":"publisher","DOI":"10.1002\/pro.4973","article-title":"Design of a symmetry-broken\ntetrahedral protein cage by a method of internal steric occlusion","volume":"33","author":"Gladkov","year":"2024","journal-title":"Protein Sci."},{"key":"2026102111064332300_cit5","doi-asserted-by":"publisher","first-page":"1378","DOI":"10.1039\/D5MA00792E","article-title":"Self-assembling protein\ncages: from coiled-coil module to machine learning-driven de novo\ndesign of next-generation biomaterials","volume":"7","author":"Gupta","year":"2026","journal-title":"Mater.\nAdv."},{"key":"2026102111064332300_cit6","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.adu2085","article-title":"Computationally designed\nmRNA-launched protein nanoparticle immunogens elicit protective antibody\nand T cell responses in mice","volume":"17","author":"Hendricks","year":"2025","journal-title":"Sci. Transl. 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Biol."},{"key":"2026102111064332300_cit9","doi-asserted-by":"publisher","DOI":"10.3390\/biom13071122","article-title":"Design\nof Beta-2 Microglobulin\nAdsorbent Protein Nanoparticles","volume":"13","author":"Miller","year":"2023","journal-title":"Biomolecules"},{"key":"2026102111064332300_cit10","doi-asserted-by":"publisher","first-page":"2771","DOI":"10.1039\/D0BM00159G","article-title":"Protein cages\nand virus-like particles: from fundamental\ninsight to biomimetic therapeutics","volume":"8","author":"Steinmetz","year":"2020","journal-title":"Biomater.\nSci."},{"key":"2026102111064332300_cit11","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.abj9424","article-title":"Chemically induced protein\ncage assembly with programmable opening and cargo release","volume":"8","author":"Stupka","year":"2022","journal-title":"Sci. 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M.; et al.\n          De novo design of protein nanoparticles with integrated functional\nmotifs\n          bioRxiv\n          2026\n          10.64898\/2025.12.19.695620.","DOI":"10.64898\/2025.12.19.695620"},{"key":"2026102111064332300_cit31","doi-asserted-by":"publisher","first-page":"546","DOI":"10.1038\/s41586-024-07814-1","article-title":"Four-component protein\nnanocages designed by programmed symmetry breaking","volume":"638","author":"Lee","year":"2025","journal-title":"Nature"},{"key":"2026102111064332300_cit32","doi-asserted-by":"publisher","first-page":"1635","DOI":"10.1038\/s41563-025-02295-7","article-title":"Computational design\nof bifaceted protein nanomaterials","volume":"24","author":"Rankovic","year":"2025","journal-title":"Nat. Mater."},{"key":"2026102111064332300_cit33","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-22276-z","article-title":"Design of multi-scale\nprotein complexes by hierarchical building block fusion","volume":"12","author":"Hsia","year":"2021","journal-title":"Nat. Commun."},{"key":"2026102111064332300_cit34","doi-asserted-by":"publisher","first-page":"687","DOI":"10.1126\/science.aad8036","article-title":"Design of structurally\ndistinct proteins using strategies inspired by evolution","volume":"352","author":"Jacobs","year":"2016","journal-title":"Science"},{"key":"2026102111064332300_cit35","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2015037118","article-title":"Generation of ordered protein assemblies\nusing rigid three-body fusion","volume":"118","author":"Vulovic","year":"2021","journal-title":"Proc. Natl. Acad.\nSci. 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Soc."},{"key":"2026102111064332300_cit39","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.1501855","article-title":"Designing and defining\ndynamic protein cage nanoassemblies in solution","volume":"2","author":"Lai","year":"2016","journal-title":"Sci. Adv."},{"key":"2026102111064332300_cit40","doi-asserted-by":"publisher","first-page":"491","DOI":"10.1093\/protein\/gzv035","article-title":"On the predictability\nof the orientation of protein domains joined by a spanning alpha-helical\nlinker","volume":"28","author":"Lai","year":"2015","journal-title":"Protein Eng., Des. 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Biol."}],"container-title":["Journal of the American\nChemical Society"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/jacs.6c11491","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/jacsat\/article-pdf\/148\/41\/44372\/68401706\/jacs.6c11491.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/jacsat\/article-pdf\/148\/41\/44372\/68401706\/jacs.6c11491.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T15:24:24Z","timestamp":1792596264000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/jacsat\/article\/148\/41\/44372\/5422261\/Design-and-Structure-of-Protein-Cages-Based-on"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,7]]},"references-count":51,"journal-issue":{"issue":"41","published-online":{"date-parts":[[2026,9,7]]},"published-print":{"date-parts":[[2026,10,21]]}},"URL":"https:\/\/doi.org\/10.1021\/jacs.6c11491","relation":{},"ISSN":["0002-7863","1520-5126"],"issn-type":[{"value":"0002-7863","type":"print"},{"value":"1520-5126","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,7]]}}}