Comparative Study of the Mechanical Unfolding Pathways of alpha- and beta-Peptides

摘要

Using molecular simulations, we analyze the unfolding pathways of various peptides. We compare the mechanical unfolding of a beta-alanine's octamer (beta-HAla(8)) and an alpha-alanine's decamer (alpha-Ala(10)). Using force-probe molecular-dynamics simulations, to induce unfolding, we show that the 3(14)-helix formed by beta-HAla(8) is mechanically more stable than the alpha-helix formed by alpha-Ala(10), although both structures are stabilized by six hydrogen bonds. Additionally, computations of the potential of mean force validate this result and show that also the thermal stability of the 3(14)-helix is higher. It is demonstrated that beta-HAla(8) unfolds in a two-step fashion with a stable intermediate. This is contrasted with the known single-step scenario of the unfolding of alpha-Ala(10). Furthermore, we present a study of the chain-length dependence of the mechanical unfolding pathway of the 3(14)-helix. The calculation of the dynamic strength for oligomers with chain lengths ranging from 6 to 18 monomers shows that the unfolding pathway of helices with an integer and noninteger number of turns has m + 1 and m energy barriers, respectively, with m being the number of complete turns. The additional barrier for helices with an integer number of turns is shown to be related to the breaking of the N-terminus' hydrogen bond.