Studying folding leftrightarrow unfolding dynamics of solvated alanine polypeptides using molecular dynamics

Abstract

The atomistic description of the folding process of a structureless chain of amino acids to a functioning protein is still considered to be a challenge for computational biophysics. An in-depth understanding of protein-folding can be achieved through atomistic dynamics accounting for the solvent effects, combined with the theoretical description of conformational changes in shorter polypeptide chains. The present paper studies the folding transitions in short polypeptide chains consisting of 11 alanine residues in explicit solvent employing all-atom molecular dynamics. The multiple observed folding leftrightarrow unfolding events of the peptide are interpreted as a dynamic process and rationalised through the analysis of the potential energy surface of the system. It is demonstrated that alanine polypeptide folding dynamics is governed by the backbone dihedral angles and involves the formation of spontaneously folded alpha -helices which emerge and live for ca. 1–20 picoseconds. The helical content within the polypeptide at different temperatures was quantified through a statistical mechanics approach, which showed a reasonable agreement with the results of molecular dynamics simulations and experiments performed for alanine-rich peptides.Graphical abstract