Molecular dynamics simulations of the folding of poly(alanine) peptides

The secondary structures and the shapes of long-chain polyalanine (PA) molecules were investigated by all-atom molecular dynamics simulations using a modified Amber force field. Homopolymers of polyaminoacids such as PA are convenient models to study the mechanism of protein folding. It was found that the conformational structures of PA peptides are highly sensitive to the chain length. In the absence of solvent, straight α-helices dominate in short (n ∼ 20) peptides at room temperature. A shape transition occurs at a chain length n of 40–45; the compact helix-turn-helix structure (the double-leg hairpin) becomes favored over a straight α-helix. For n = 60, double-leg and the triple-leg hairpins are the only structures present in PA molecules. An exploration of a chain organization in a cubic cavity revealed a clear predisposition of PA molecules for additional breaks in α-helices and the formation of multifolded hairpins. Furthermore, under confinement the hairpin structure becomes much looser, the antiparallel positions of helical stems are disturbed, and a sizeable proportion of the helical stems are transformed from α-helices into 310-helices.