Bottom-up de novo design of functional proteins with complex structural features

Area of Science:

• Protein engineering
• Synthetic biology
• Biochemistry

Background:

• De novo protein design allows for novel protein structures but struggles with incorporating complex functional sites.
• Designing functional proteins with specific biochemical properties remains a significant challenge.

Purpose of the Study:

• To develop a bottom-up approach for de novo protein design that accommodates structurally complex functional motifs.
• To create novel proteins with tailored functions for biosensing and synthetic signaling.

Main Methods:

• Utilized a bottom-up computational strategy to design de novo proteins.
• Incorporated four distinct binding motifs, including a bifunctional protein, into designed protein folds.
• Validated designs through crystal structures and functional assays in engineered mammalian cells.

Main Results:

• Successfully designed five novel protein folds capable of accommodating complex binding motifs.
• Confirmed atomic-level accuracy of computational designs via X-ray crystallography.
• Demonstrated functionality of designed proteins in biosensors and as orthogonal ligands in synthetic signaling pathways.

Conclusions:

• The bottom-up approach effectively integrates complex structural motifs into de novo proteins.
• This strategy is crucial for imparting elaborate biochemical functions like molecular recognition and catalysis to engineered proteins.
• The designed proteins show promise for applications in biosensing and advanced synthetic biology.