Solvent-Induced Stabilization and Folding Pathways of α-Helical Peptides: A Computational Investigation Using Steered Molecular Dynamics.

Fluorinated polar solvents, such as hexafluoro-2-propanol (HFIP), are known to denature proteins into α-helix-rich structures, a phenomenon of interest in protein engineering and fiber science. Molecular dynamics (MD) simulations offer a valuable approach to explore protein folding mechanisms. In the present study, steered molecular dynamics (SMD) simulations were conducted to stretch the polypeptide models along the α-helix axis in different solvents. The potential of mean force (PMF) associated with nonequilibrium stretching of the polypeptide chain was higher in HFIP than in water and varied depending on amino acid composition and degree of polymerization. HFIP molecules preferentially concentrated in grooves of α-helical polypeptides. Stretching the polypeptides in HFIP resulted in the formation of 310-helix structures, suggesting that local solvation enhances structural stability. Additional SMD simulations of Trp-cage, a mini-protein driven by hydrophobic collapse in protein folding, showed partial unfolding of the α-helix region and global extension of both termini. The resulting PMF profiles indicate that α-helices are formed in the early stages of Trp-cage folding. This study offers an analytical framework that can be extended to more complex amino acid sequences and proteins with diverse structural motifs. HFIP appears to play a central role in the α-helical transformation of higher-order protein structures.