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Programming protein shape as an explicit design layer via CAD blueprint-guided diffusion
Yilun Qi1, Guoxun Zhang2, Klaus Yserentant2
1Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco; San Francisco, CA, USA.
Biorxiv : the Preprint Server for Biology
|August 1, 2026
Summary
Scientists engineered biomimetic protein architectures using computer-aided design and AI. This programmable approach enables the creation of novel molecular machines with emergent functions, like artificial molecular swimmers.
Area of Science:
- Biophysics
- Computational Biology
- Protein Engineering
Background:
- Industrial design principles link form and function in engineering.
- Global protein shape, curvature, and chirality are crucial for biological processes.
- Generative AI faces challenges in programming these global protein features.
Purpose of the Study:
- To integrate computer-aided design (CAD) blueprints with diffusion models for programmable protein shape engineering.
- To establish protein shape as an explicit, controllable layer in generative AI.
- To engineer novel biomimetic architectures with emergent functions.
Main Methods:
- Integration of CAD blueprints with diffusion models.
- Engineering of diverse protein architectures (single-chain, scaffolds, superhelical assemblies).
- Structural validation using X-ray crystallography and electron microscopy.
- Coupling of fluid-flow-optimized propellers to F1-ATPase for molecular swimmers.
Main Results:
- Successful engineering of tunable protein architectures.
- Structural validation of 31 out of 59 designed protein structures.
- Demonstration of shape-encoded function through ATP-dependent molecular swimmers.
- Translation of industrial design principles to the molecular scale.
Conclusions:
- The developed framework enables programmable engineering of protein shape.
- This approach allows for the creation of biomimetic architectures with novel, emergent functions.
- This work bridges industrial design and molecular engineering for advanced biomolecular design.
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