ArticleProtein science : a publication of the Protein Society2021
Extension of a de novo TIM barrel with a rationally designed secondary structure element.
Article in Protein science : a publication of the Protein Society, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Customizing the structure of minimal TIM barrels to craft efficient de novo enzymes.Nature chemical biology · 2026Article
- Stability and cooperativity in chimeric de novo TIM barrels via quarter swapping.Protein science : a publication of the Protein Society · 2026Article
- Designing de novo TIM barrels: insights into stabilization, diversification, and functionalization strategies.Biochemical Society transactions · 2026Review
- Diversifying de novo TIM barrels by hallucination.Protein science : a publication of the Protein Society · 2024Article
- Stepwise introduction of stabilizing mutations reveals nonlinear additive effects in de novo TIM barrels.Protein science : a publication of the Protein Society · 2024Article
- Sequence - dynamics - function relationships in protein tyrosine phosphatases.QRB discovery · 2024Article
- Dissecting the stability determinants of a challenging de novo protein fold using massively parallel design and experimentation.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- ProtGPT2 is a deep unsupervised language model for protein design.Nature communications · 2022Article
- What Have We Learned from Design of Function in Large Proteins?Biodesign research · 2022Review
- De Novo Design of a Highly Stable Ovoid TIM Barrel: Unlocking Pocket Shape towards Functional Design.Biodesign research · 2022Article
- Evolution, folding, and design of TIM barrels and related proteins.Current opinion in structural biology · 2021Review
- Extension of a de novo TIM barrel with a rationally designed secondary structure element.Protein science : a publication of the Protein Society · 2021Article
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3 authors.
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Abstract
The ability to construct novel enzymes is a major aim in de novo protein design. A popular enzyme fold for design attempts is the TIM barrel. This fold is a common topology for enzymes and can harbor many diverse reactions. The recent de novo design of a four-fold symmetric TIM barrel provides a well understood minimal scaffold for potential enzyme designs. Here we explore opportunities to extend and diversify this scaffold by adding a short de novo helix on top of the barrel. Due to the size of the protein, we developed a design pipeline based on computational ab initio folding that solves a less complex sub-problem focused around the helix and its vicinity and adapt it to the entire protein. We provide biochemical characterization and a high-resolution X-ray structure for one variant and compare it to our design model. The successful extension of this robust TIM-barrel scaffold opens opportunities to diversify it towards more pocket like arrangements and as such can be considered a building block for future design of binding or catalytic sites.
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