ArticleResearch (Washington, D.C.)2024
Cytochrome P450 Enzyme Design by Constraining the Catalytic Pocket in a Diffusion Model.
Article in Research (Washington, D.C.), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- A Review of Plant-Derived Diterpenoid Biosynthesis: From Structural Scaffold Diversity and Lineage-Associated Distribution to Enzyme Mining and Discovery Strategies.Molecules (Basel, Switzerland) · 2026Review
- DIMORPH: an integrated multi-omics resource for camptothecin-producing plants.Molecular horticulture · 2026Article
- Multiscale Computational Enzymology of CYP450 Biotransformation of Organic Halogenated Pollutants: Methods and Environmental Perspectives.ACS omega · 2026Review
- Could statistical potential models achieve comparable or better performance than deep learning models?Briefings in bioinformatics · 2026Article
- Design prokaryotic cis-regulatory elements using language model.Nucleic acids research · 2026Article
- DeepCodon: A deep learning codon-optimization model to enhance protein expression.Biodesign research · 2025Article
- Protein design drives synthetic biology research of plant natural products.Biodesign research · 2025Review
- Bacterial Transformation of Adamantane and Its Derivatives: Regioselectivity and Biocatalytic Approaches.Biology · 2025Review
- The biosynthesis and diversity of taxanes: From pathway elucidation to engineering and synthetic biology.Plant communications · 2025Review
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Authors and funding
18 authors.
Funding
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Abstract
Although cytochrome P450 enzymes are the most versatile biocatalysts in nature, there is insufficient comprehension of the molecular mechanism underlying their functional innovation process. Here, by combining ancestral sequence reconstruction, reverse mutation assay, and progressive forward accumulation, we identified 5 founder residues in the catalytic pocket of flavone 6-hydroxylase (F6H) and proposed a "3-point fixation" model to elucidate the functional innovation mechanisms of P450s in nature. According to this design principle of catalytic pocket, we further developed a de novo diffusion model (P450Diffusion) to generate artificial P450s. Ultimately, among the 17 non-natural P450s we generated, 10 designs exhibited significant F6H activity and 6 exhibited a 1.3- to 3.5-fold increase in catalytic capacity compared to the natural CYP706X1. This work not only explores the design principle of catalytic pockets of P450s, but also provides an insight into the artificial design of P450 enzymes with desired functions.
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Registered trials
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