Helix unfolding and intramolecular hydrogen bond dynamics in small α-helices in explicit solvent

The dynamics of folding and unfolding of secondary structural motifs found in proteins is crucial to understanding the protein folding problem. In this paper we study the short-time dynamics of loop unfolding and hydrogen bond formation and breaking in the alanine pentapeptide at room temperature, using several constant-energy molecular dynamics simulations of about 4 ns of duration. We analyze the results in terms of time histories of "core" alpha-carbon dihedral angles. We also perform a principal component analysis of the data. We find that the time scale for a considerable deformation of the dihedral angles formed by the alpha-carbons is on the order of 1 ns whereas hydrogen bonds seem to break and form on a shorter time scale.