Solvent dependence of PII conformation in model alanine peptides

Alanine residues in two model peptides, the pentapeptide AcGGAGGNH ₂ and the 11mer AcO₂A₇O₂NH ₂, have been reported to have substantial PII conformation in water. The PII structure in both peptides is sensitive to solvent. In the presence of the organic solvent TFE, the conformation of the pentamer changes from PII to internally H-bonded γ or β turns, while the chain with seven alanines forms α helix. The PII structure in the 11mer is more stable than that in the shorter peptide as the TFE concentration increases. For the pentamer, a comparison of short-chain aliphatic alcohols to water shows that the PII content decreases in the order water > methanol > ethanol > 2-propanol, linearly according to empirical scales of solvent polarity. Thus, depending on the extent of local solvation as folding progresses, the peptide backbone as modeled by alanine oligomers shifts from PII to internally H-bonded (γ or β turn) conformations and to α helix in longer segments. On the other hand, the PII content of AcO₂A₇O₂NH ₂ increases significantly in the presence of guanidine, as does that of oligoproline peptides, while detergent sodium dodecyl sulfate (SDS) favors α helix in this peptide. The shorter peptide does not show a parallel increase in PII with guanidine.