A Folding Pathway Model of Mini-Protein BBA5

Area of Science:

• Protein folding dynamics
• Computational biophysics
• Molecular modeling

Background:

• Mini-proteins like BBA5 are crucial for understanding fundamental protein folding principles.
• The secondary structure composition (alpha-helix and beta-hairpin) of BBA5 presents an interesting case for folding pathway analysis.

Purpose of the Study:

• To elucidate the folding pathway of the mini-protein BBA5 using advanced simulation techniques.
• To identify key intermediate structures and the sequence of secondary structure formation.
• To compare the folding mechanism of BBA5 with other related proteins.

Main Methods:

• Utilizing action-derived molecular dynamics (ADMD) simulations for enhanced sampling of folding events.
• Performing ten independent ADMD simulations to ensure reproducibility and capture diverse pathways.
• Employing principal component analysis (PCA) to reduce dimensionality and characterize folding dynamics.

Main Results:

• The folding pathway initiates with chain compaction, followed by the formation of a stable C-terminal alpha-helix.
• The N-terminal beta-hairpin formation occurs only after the alpha-helix is stabilized.
• The N-terminal four residues were identified as the most flexible region of BBA5.
• The secondary structure formation sequence in BBA5 differs from the related FSD-1 protein, despite sharing a similar motif.
• PCA effectively described 83.4% of the folding pathway using only three principal components.

Conclusions:

• The folding pathway of BBA5 involves a specific sequence of secondary structure formation, with helical elements stabilizing before hairpin structures.
• Simulation results align with experimental observations of BBA5 mutants exhibiting moderate cooperativity and distinct secondary structure propensities.
• The study provides a detailed, dimensionally reduced model of BBA5 folding dynamics, offering insights into protein self-assembly.