ArticleProtein science : a publication of the Protein Society2012
Robust design and optimization of retroaldol enzymes.
Article in Protein science : a publication of the Protein Society, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
57 citing papers in PubMed.
- Predicting Activation Barriers With Ring and Bond Critical Points in the Kemp Elimination Reaction.Chemphyschem : a European journal of chemical physics and physical chemistry · 2026Article
- Protein engineering: status report.Protein engineering, design & selection : PEDS · 2026Review
- Atom-level enzyme active site scaffolding using RFdiffusion2.Nature methods · 2026Article
- Article
- Modeling protein-small molecule conformational ensembles with PLACER.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Distal mutations enhance catalysis in designed enzymes by facilitating substrate binding and product release.Nature communications · 2025Article
- Modeling protein-small molecule conformational ensembles with PLACER.bioRxiv : the preprint server for biology · 2025Article
- Computation-guided engineering of distal mutations in an artificial enzyme.Faraday discussions · 2024Article
- Article
- Complete Computational Reaction Mechanism for Foldamer-Catalyzed Aldol Condensation.ACS catalysis · 2024Article
- Strategies for designing biocatalysts with new functions.Chemical Society reviews · 2024Review
- Role of mutations in a chemoenzymatic enantiodivergent C(spChemical science · 2023Article
- Protein Dynamics and Enzymatic Catalysis.The journal of physical chemistry. B · 2023Review
- Engineering enzyme activity using an expanded amino acid alphabet.Protein engineering, design & selection : PEDS · 2023Article
- Protein dynamics: The future is bright and complicated!Structural dynamics (Melville, N.Y.) · 2023Article
- Perspective: Path Sampling Methods Applied to Enzymatic Catalysis.Journal of chemical theory and computation · 2022Review
- Design and optimization of enzymatic activity in a de novo β-barrel scaffold.Protein science : a publication of the Protein Society · 2022Article
- Unlocking New Reactivities in Enzymes by Iminium Catalysis.Angewandte Chemie (International ed. in English) · 2022Review
- The road to fully programmable protein catalysis.Nature · 2022Review
- An Approach to the De Novo Synthesis of Life.Accounts of chemical research · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors.
Funding
Abstract
Enzyme catalysts of a retroaldol reaction have been generated by computational design using a motif that combines a lysine in a nonpolar environment with water-mediated stabilization of the carbinolamine hydroxyl and β-hydroxyl groups. Here, we show that the design process is robust and repeatable, with 33 new active designs constructed on 13 different protein scaffold backbones. The initial activities are not high but are increased through site-directed mutagenesis and laboratory evolution. Mutational data highlight areas for improvement in design. Different designed catalysts give different borohydride-reduced reaction intermediates, suggesting a distribution of properties of the designed enzymes that may be further explored and exploited.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.