Crystal structure of de novo designed coiled-coil protein origami triangle

Satler, Tadej (author), Hadži, San (author), Jerala, Roman (author)

Coiled-coil protein origami (CCPO) uses modular coiled-coil building blocks and topological principles to design polyhedral structures distinct from those of natural globular proteins. While the CCPO strategy has proven successful in designing diverse protein topologies, no high-resolution structural information has been available about these novel protein folds. Here we report the crystal structure of a single-chain CCPO in the shape of a triangle. While neither cyclization nor the addition of nanobodies enabled crystallization, it was ultimately facilitated by the inclusion of a GCN$_2$ homodimer. Triangle edges are formed by the orthogonal parallel coiled-coil dimers P1:P2, P3:P4, and GCN$_2$ connected by short linkers. A triangle has a large central cavity and is additionally stabilized by side-chain interactions between neighboring segments at each vertex. The crystal lattice is densely packed and stabilized by a large number of contacts between triangles. Interestingly, the polypeptide chain folds into a trefoil-type protein knot topology, and AlphaFold2 fails to predict the correct fold. The structure validates the modular CC-based protein design strategy, providing molecular insight underlying CCPO stabilization and new opportunities for the design.

• Language: English
• Keywords: crystal structure, crystals, noncovalent interactions, oligomers, peptides, proteins
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: FKKT - Faculty of Chemistry and Chemical Technology
• Publication status: Published
• Publication version: Version of Record
• Year: 2023
• Number of pages: Str. 16995–17000
• Numbering: Vol. 145, iss. 31
• PID: 20.500.12556/RUL-152674
• UDC: 577
• ISSN on article: 1520-5126
• DOI: 10.1021/jacs.3c05531
• COBISS.SI-ID: 169812995
• Publication date in RUL: 04.12.2023

Record is a part of a journal

• Title: Journal of the American Chemical Society
• Shortened title: J. Am. Chem. Soc.
• Publisher: American Chemical Society
• ISSN: 1520-5126
• COBISS.SI-ID: 512805913

Licences

• License: CC BY 4.0, Creative Commons Attribution 4.0 International
• Link: http://creativecommons.org/licenses/by/4.0/
• Description: This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.

Secondary language

• Language: Slovenian
• Keywords: biokemija, proteinski origami, obvite vijačnice, CCPO, DNK