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Physics-based approach to extend a de novo TIM barrel with rationally designed helix-loop-helix motifs

Title data

Kordes, Sina ; Beck, Julian ; Shanmugaratnam, Sooruban ; Flecks, Merle ; Höcker, Birte:
Physics-based approach to extend a de novo TIM barrel with rationally designed helix-loop-helix motifs.
In: Protein Engineering, Design & Selection. Vol. 36 (2023) . - gzad012.
ISSN 1741-0134
DOI: https://doi.org/10.1093/protein/gzad012

Abstract in another language

Computational protein design promises the ability to build tailor-made proteins de novo. While a range of de novo proteins have been constructed so far, the majority of these designs have idealized topologies that lack larger cavities which are necessary for the incorporation of small molecule binding sites or enzymatic functions. One attractive target for enzyme design is the TIM-barrel fold, due to its ubiquity in nature and capability to host versatile functions. With the successful de novo design of a 4-fold symmetric TIM barrel, sTIM11, an idealized, minimalistic scaffold was created. In this work, we attempted to extend this de novo TIM barrel by incorporating a helix-loop-helix motif into its βα-loops by applying a physics-based modular design approach using Rosetta. Further diversification was performed by exploiting the symmetry of the scaffold to integrate two helix-loop-helix motifs into the scaffold. Analysis with AlphaFold2 and biochemical characterization demonstrate the formation of additional α-helical secondary structure elements supporting the successful extension as intended.

Further data

Item Type: Article in a journal
Refereed: Yes
Keywords: (βα)8-barrel; TIM-barrel; computational protein design; helix-loop-helix
Institutions of the University: Faculties > Faculty of Biology, Chemistry and Earth Sciences > Department of Chemistry > Chair Biochemistry > Chair Biochemistry - Univ.-Prof. Dr. Birte Höcker
Result of work at the UBT: Yes
DDC Subjects: 500 Science > 540 Chemistry
Date Deposited: 14 Nov 2023 08:17
Last Modified: 14 Nov 2023 10:30
URI: https://eref.uni-bayreuth.de/id/eprint/87724