title: Mechanical unfolding pathway of a model β-peptide foldamer.
abstract: Foldamers constructed from oligomers of β-peptides form stable secondary helix structures already for small chain lengths, which makes them ideal candidates for the investigation of the (un)folding of polypeptides. Here, the results of molecular simulations of the mechanical unfolding of a β-heptapeptide in methanol solvent revealing the detailed unfolding pathway are reported. The unfolding process is shown to proceed via a stable intermediate even for such a small system. This result is arrived at performing non-equilibrium force ramp simulations employing different pulling velocities and also using standard calculations of the potential of mean force, i.e., the free energy as a function of the helix elongation. It is thus demonstrated that even with the rather large pulling velocities employed in the force ramp simulations relevant information about the equilibrium kinetics can be obtained. The smallness of the system allows a detailed analysis of the unfolding pathway, which is characterized by an opening of the terminal loops followed by the unfolding of the center. This sequence is in accord with the configurational preferences of the system that also are responsible for the stability of the 314-helix. From an analysis of the distributions of rupture forces and the force spectra, the kinetic rates for both transitions were determined and common models were used to extract geometric quantities describing the free energy landscape of the system.
authors.affiliation: Institut für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany.
authors.forename: Lalita
authors.initials: L
authors.lastname: Uribe
authors.affiliation: Institut für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Jaschonek
authors.affiliation: Institut für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany.
authors.forename: Jürgen
authors.initials: J
authors.lastname: Gauss
authors.affiliation: Institut für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany.
authors.forename: Gregor
authors.initials: G
authors.lastname: Diezemann
mesh_terms: D006860:Hydrogen Bonding; D007700:Kinetics; D000432:Methanol / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry*; D017433:Protein Structure, Secondary; D058767:Protein Unfolding; D012997:Solvents / Q000737:chemistry
chemical_list: D010455:Peptides; D012997:Solvents; D000432:Methanol