ArticleProceedings of the National Academy of Sciences of the United States of America2020
Allosteric cooperation in a de novo-designed two-domain protein.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 54 citations in OpenAlex.
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- Identification and understanding of allostery hotspots in proteins: Integration of deep mutational scanning and multi-faceted computational analyses.Journal of molecular biology · 2025Review
- Recent advances in de novo designed metallopeptides as tailored enzyme mimics.Current opinion in chemical biology · 2025Review
- Platinum Stabilises a Molten-Globule Conformation of a Small Globular Cytosolic Protein SUMO1.Chemistry, an Asian journal · 2025Article
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- A de novo designed coiled coil-based switch regulates the microtubule motor kinesin-1.Nature chemical biology · 2024Article
- De novo design of proteins housing excitonically coupled chlorophyll special pairs.Nature chemical biology · 2024Article
- An expandable, modular de novo protein platform for precision redox engineering.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Selective Oxidation of Halophenols Catalyzed by an Artificial Miniaturized Peroxidase.International journal of molecular sciences · 2023Article
- Designed Rubredoxin miniature in a fully artificial electron chain triggered by visible light.Nature communications · 2023Article
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- An abiotic, tetrameric, eight-helix bundle.Chemical science · 2023Article
- From peptides to proteins: coiled-coil tetramers to single-chain 4-helix bundles.Chemical science · 2022Article
- De novo protein design of photochemical reaction centers.Nature communications · 2022Article
- Catalysis and Electron Transfer inChemical reviews · 2022Review
- De novo metalloprotein design.Nature reviews. Chemistry · 2022Article
- Rational design of photosynthetic reaction center protein maquettes.Frontiers in molecular biosciences · 2022Article
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Authors and funding
11 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We describe the de novo design of an allosterically regulated protein, which comprises two tightly coupled domains. One domain is based on the DF (Due Ferri in Italian or two-iron in English) family of de novo proteins, which have a diiron cofactor that catalyzes a phenol oxidase reaction, while the second domain is based on PS1 (Porphyrin-binding Sequence), which binds a synthetic Zn-porphyrin (ZnP). The binding of ZnP to the original PS1 protein induces changes in structure and dynamics, which we expected to influence the catalytic rate of a fused DF domain when appropriately coupled. Both DF and PS1 are four-helix bundles, but they have distinct bundle architectures. To achieve tight coupling between the domains, they were connected by four helical linkers using a computational method to discover the most designable connections capable of spanning the two architectures. The resulting protein, DFP1 (Due Ferri Porphyrin), bound the two cofactors in the expected manner. The crystal structure of fully reconstituted DFP1 was also in excellent agreement with the design, and it showed the ZnP cofactor bound over 12 Å from the dimetal center. Next, a substrate-binding cleft leading to the diiron center was introduced into DFP1. The resulting protein acts as an allosterically modulated phenol oxidase. Its Michaelis-Menten parameters were strongly affected by the binding of ZnP, resulting in a fourfold tighter
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