ArticleNature communications2018
Highly active enzymes by automated combinatorial backbone assembly and sequence design.
Article in Nature communications, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Redirecting a Native Ene-Reductase Toward Desaturation With Reverse Enantioselectivity.Angewandte Chemie (International ed. in English) · 2026Article
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- Evolutionary paths that link orthogonal pairs of binding proteins.Cell systems · 2025Article
- Context-dependent design of induced-fit enzymes using deep learning generates well-expressed, thermally stable and active enzymes.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Loop dynamics and the evolution of enzyme activity.Nature reviews. Chemistry · 2023Review
- A novel computationally engineered collagenase reduces the force required for tooth extraction in an ex-situ porcine jaw model.Journal of biological engineering · 2023Article
- Structural and computational design of a SARS-CoV-2 spike antigen with improved expression and immunogenicity.Science advances · 2023Article
- De Novo Computational Design of a Lipase with Hydrolysis Activity towards Middle-Chained Fatty Acid Esters.International journal of molecular sciences · 2023Article
- OSCAR: an extensive repository of chemically and functionally diverse organocatalysts.Chemical science · 2022Article
- Identification and Mutation Analysis of Nonconserved Residues on the TIM-Barrel Surface of GH5_5 Cellulases for Catalytic Efficiency and Stability Improvement.Applied and environmental microbiology · 2022Article
- Assessing and enhancing foldability in designed proteins.Protein science : a publication of the Protein Society · 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
- A PROSS-designed extensively mutated estrogen receptor α variant displays enhanced thermal stability while retaining native allosteric regulation and structure.Scientific reports · 2021Article
- Computational Enzyme Engineering Pipelines for Optimized Production of Renewable Chemicals.Frontiers in bioengineering and biotechnology · 2021Review
- The AbDesign computational pipeline for modular backbone assembly and design of binders and enzymes.Protein science : a publication of the Protein Society · 2021Article
- Tight and specific lanthanide binding in a de novo TIM barrel with a large internal cavity designed by symmetric domain fusion.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Practically useful protein-design methods combining phylogenetic and atomistic calculations.Current opinion in structural biology · 2020Review
- Macromolecular modeling and design in Rosetta: recent methods and frameworks.Nature methods · 2020Review
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Authors and funding
7 authors.
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Abstract
Automated design of enzymes with wild-type-like catalytic properties has been a long-standing but elusive goal. Here, we present a general, automated method for enzyme design through combinatorial backbone assembly. Starting from a set of homologous yet structurally diverse enzyme structures, the method assembles new backbone combinations and uses Rosetta to optimize the amino acid sequence, while conserving key catalytic residues. We apply this method to two unrelated enzyme families with TIM-barrel folds, glycoside hydrolase 10 (GH10) xylanases and phosphotriesterase-like lactonases (PLLs), designing 43 and 34 proteins, respectively. Twenty-one GH10 and seven PLL designs are active, including designs derived from templates with <25% sequence identity. Moreover, four designs are as active as natural enzymes in these families. Atomic accuracy in a high-activity GH10 design is further confirmed by crystallographic analysis. Thus, combinatorial-backbone assembly and design may be used to generate stable, active, and structurally diverse enzymes with altered selectivity or activity.
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