Natural beta-sheet proteins use negative design to avoid edge-to-edge aggregation

Area of Science:

• Protein Biochemistry
• Structural Biology
• Computational Biology

Background:

• Natural beta-sheet proteins are typically soluble, unlike aggregated beta-sheet fragments or designs.
• Beta-sheet edges are prone to aggregation due to their conformation.
• Understanding natural protein design strategies is crucial for de novo protein engineering.

Purpose of the Study:

• To survey and tabulate features that protect natural beta-sheet proteins from aggregation.
• To identify design principles for creating soluble de novo beta structures.
• To investigate strategies for preventing unwanted beta-sheet interactions.

Main Methods:

• Survey of edge strands in a large sample of all-beta proteins.
• Analysis of structural features like beta-bulges, prolines, charges, and loop coverage.
• Comparison of protected edge strands in soluble proteins versus unprotected strands in aggregating structures.

Main Results:

• All free edge strands in natural proteins are protected by multiple, often redundant, mechanisms.
• Diverse strategies are employed, including loop coverage, beta-bulges, prolines, and strategically placed charges.
• Inward-pointing charged side chains on edge strands are effective in preventing aggregation, especially in beta-sandwich proteins.

Conclusions:

• Natural proteins utilize sophisticated and redundant mechanisms to protect beta-sheet edges and maintain solubility.
• A minimal negative-design strategy, such as a single charged side chain, can effectively promote solubility in de novo beta-sheet designs.
• These findings have significant implications for protein design and understanding amyloid formation.