Comparative Study of the Mechanical Unfolding Pathways
of α- and β‑Peptides
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Abstract
Using molecular simulations, we analyze
the unfolding pathways
of various peptides. We compare the mechanical unfolding of a β-alanine’s
octamer (β-HAla<sub>8</sub>) and an α-alanine’s
decamer (α-Ala<sub>10</sub>). Using force-probe molecular-dynamics
simulations, to induce unfolding, we show that the 3<sub>14</sub>-helix
formed by β-HAla<sub>8</sub> is mechanically more stable than
the α-helix formed by α-Ala<sub>10</sub>, 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<sub>14</sub>-helix is higher.
It is demonstrated that β-HAla<sub>8</sub> unfolds in a two-step
fashion with a stable intermediate. This is contrasted with the known
single-step scenario of the unfolding of α-Ala<sub>10</sub>.
Furthermore, we present a study of the chain-length dependence of
the mechanical unfolding pathway of the 3<sub>14</sub>-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 <i>m</i> + 1 and <i>m</i> energy barriers, respectively,
with <i>m</i> 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