Design and characterization of a protein fold switching network

Area of Science:

• Biochemistry and Molecular Biology
• Structural Biology
• Protein Engineering

Background:

• The relationship between amino acid sequence and protein structure (folding) is complex and not fully understood.
• Existing models struggle to explain the evolution of diverse protein folds from limited sequence space.

Purpose of the Study:

• To investigate how amino acid sequences encode protein structures by creating and analyzing mutational pathways between common protein folds.
• To explore the potential for abrupt protein fold switching and its implications for protein evolution.

Main Methods:

• Engineered mutational pathways connecting three distinct protein folds: 3-alpha (3α), beta-grasp, and alpha/beta-plait (α/β-plait).
• Determined protein structures at key pathway intersections (nodes) using Nuclear Magnetic Resonance (NMR) spectroscopy.
• Analyzed the stability and function of engineered proteins.

Main Results:

• Successfully embedded smaller folds within larger ones, creating protein pairs with different folds (e.g., 3α or β-grasp in smaller, α/β-plait in larger).
• Demonstrated that specific amino acid substitutions can trigger abrupt changes in both protein fold and function.
• Identified critical states within larger folds that facilitate these fold-switching events.

Conclusions:

• The protein folding code exhibits inherent ambiguity, allowing for multiple structures from similar sequences.
• Protein structures can evolve through rapid, abrupt fold switching events, challenging gradual evolutionary models.
• This work provides insights into the fundamental principles governing protein structure determination and evolution.