We found a match
Your institution may have access to this item. Find your institution then sign in to continue.
- Title
Physics-based approach to extend a de novo TIM barrel with rationally designed helix-loop-helix motifs.
- Authors
Kordes, Sina; Beck, Julian; Shanmugaratnam, Sooruban; Flecks, Merle; Höcker, Birte
- Abstract
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.
- Subjects
HELIX-loop-helix motifs; SMALL molecules; PROTEIN engineering; BINDING sites; MODULAR design; TISSUE scaffolds
- Publication
PEDS: Protein Engineering, Design & Selection, 2023, Vol 36, p1
- ISSN
1741-0126
- Publication type
Article
- DOI
10.1093/protein/gzad012