Free energy surface of the helical peptide Y(MEARA)₆

The folding of the helical peptide Y(MEARA)₆ was studied by a series of molecular dynamics simulations with an implicit solvation model that allowed sampling of a total of more than 4 μs. In the 44 runs at 360 K started from all-coil conformations the peptide assumed an α-helical structure within the first 30 ns, with an average folding time of 10 ns. The free energy surface shows that the coil to helix transition has a small barrier at the helix nucleation step which consists of two to three i,i+4 hydrogen bonds and does not show a strong preference along the sequence. On the helix side of the barrier, there is a very broad basin corresponding to conformations having more than one helical turn. Although the α-helical content is predominant, there is a nonnegligible percentage of conformations with one or more π-helical turns stabilized in part by interactions between Met side chains. Control simulations with two different helical sequences, a 31-residue polyalanine and A₅(AAARA)₃A, did not reveal a significant π-helix population, which indicates that the π-helical content of Y(MEARA)₆ is not an artifact of the force field and solvation model. The folding mechanism and free energy surface presented here are in agreement with previous theoretical models and experimental data on different helical sequences, which suggest that they may be valid for the folding of helical peptides, in general.