Hydrophobic interactions in the formation of secondary structures in small peptides

Effects of the attractive and repulsive parts of hydrophobic interactions on alpha helices and beta sheets in small peptides are investigated using a simple atomic potential. Typically, a physical spatial range of attraction tends to favor beta sheets, but alpha helices would be favored if the attractive range were more extended. We also found that desolvation barriers favor beta sheets in collapsed conformations of polyalanine, polyvaline, polyleucine, and three fragments of amyloid peptides tested in this study. Our results provide insight into the multifaceted role of hydrophobicity in secondary structure formation, including the alpha to beta transitions in certain amyloid peptides.