posted on 2015-07-02, 00:00authored byLalita Uribe, Jürgen Gauss, Gregor Diezemann
Using molecular simulations, we analyze
the unfolding pathways
of various peptides. We compare the mechanical unfolding of a β-alanine’s
octamer (β-HAla8) and an α-alanine’s
decamer (α-Ala10). Using force-probe molecular-dynamics
simulations, to induce unfolding, we show that the 314-helix
formed by β-HAla8 is mechanically more stable than
the α-helix formed by α-Ala10, 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 314-helix is higher.
It is demonstrated that β-HAla8 unfolds in a two-step
fashion with a stable intermediate. This is contrasted with the known
single-step scenario of the unfolding of α-Ala10.
Furthermore, we present a study of the chain-length dependence of
the mechanical unfolding pathway of the 314-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.