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Transforming a fragile protein helix into an ultrastable scaffold via a hierarchical AI and chemistry framework
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DOI：10.7554/eLife.109753; 10.7554/eLife.109753.3.sa1; 10.7554/eLife.109753.3.sa2; 10.7554/eLife.109753.3.sa3; 10.7554/eLife.109753.3.sa4.png)
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Abstract
En 中文
The rational design of proteins that maintain structural integrity under concurrent thermal, mechanical, and chemical stress remains a challenge in molecular engineering. We present a hierarchical framework that transforms an alpha-helical domain into an ultrastable scaffold by integrating AI-guided design with foundational chemical principles. This approach progresses from global architectural reinforcement, using multiple AI tools to create a stabilized four-helix bundle, to local chemical tuning, where AlphaFold3 guides the installation of salt bridges and metal-coordination motifs. A computational pipeline using physics-based screening such as molecular dynamics simulations efficiently distilled millions of designs into a minimal candidate set. The resulting alpha-helical proteins exhibit unprecedented multi-axis stability, with mechanical unfolding forces exceeding 200 pN, thermal resilience>100 degrees C, and high resistance to chemical denaturants. By systematically dissecting the contributions of hydrophobic packing, electrostatics, and metal coordination, we establish a general blueprint for imparting extreme robustness. This work bridges AI-driven structural generation with chemical precision, advancing the creation of durable proteins for mechanistic studies and synthetic biology.
Keywords:
protein design
MD simulation
protein stablity
single-molecule force spectroscopy
E. coli
