ArticleNature chemical biology2021
Bottom-up de novo design of functional proteins with complex structural features.
Article in Nature chemical biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed, 93 citations in OpenAlex.
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- Multimodal diffusion for joint design of protein sequence and structure.Protein science : a publication of the Protein Society · 2025Article
- A Complementarity-Based Approach to De Novo Binder Design.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- AI Prediction of Structural Stability of Nanoproteins Based on Structures and Residue Properties by Mean Pooled Dual Graph Convolutional Network.Interdisciplinary sciences, computational life sciences · 2025Article
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- Coupling of Spectrin Repeat Modules for the Assembly of Nanorods and Presentation of Protein Domains.ACS nano · 2024Article
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- Protein Design Using Structure-Prediction Networks: AlphaFold and RoseTTAFold as Protein Structure Foundation Models.Cold Spring Harbor perspectives in biology · 2024Review
- Diversifying de novo TIM barrels by hallucination.Protein science : a publication of the Protein Society · 2024Article
- Machine learning for functional protein design.Nature biotechnology · 2024Review
- TIMED-Design: flexible and accessible protein sequence design with convolutional neural networks.Protein engineering, design & selection : PEDS · 2024Article
- Therapeutic drug monitoring of immunotherapies with novel Affimer-NanoBiT sensor construct.Sensors & diagnostics · 2024Article
- Computational Protein Design - Where it goes?Current medicinal chemistry · 2024Review
- Engineering a scalable and orthogonal platform for synthetic communication in mammalian cells.Nature communications · 2023Article
- Rational design of small-molecule responsive protein switches.Protein science : a publication of the Protein Society · 2023Review
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- Transient water wires mediate selective proton transport in designed channel proteins.Nature chemistry · 2023Article
- De novo protein design by inversion of the AlphaFold structure prediction network.Protein science : a publication of the Protein Society · 2023Article
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Authors and funding
15 authors at 5 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
De novo protein design has enabled the creation of new protein structures. However, the design of functional proteins has proved challenging, in part due to the difficulty of transplanting structurally complex functional sites to available protein structures. Here, we used a bottom-up approach to build de novo proteins tailored to accommodate structurally complex functional motifs. We applied the bottom-up strategy to successfully design five folds for four distinct binding motifs, including a bifunctionalized protein with two motifs. Crystal structures confirmed the atomic-level accuracy of the computational designs. These de novo proteins were functional as components of biosensors to monitor antibody responses and as orthogonal ligands to modulate synthetic signaling receptors in engineered mammalian cells. Our work demonstrates the potential of bottom-up approaches to accommodate complex structural motifs, which will be essential to endow de novo proteins with elaborate biochemical functions, such as molecular recognition or catalysis.
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