Kinetics of Helix Unfolding: Molecular Dynamics Simulations with Milestoning

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Abstract
The unfolding process of a helical heteropeptide is studied by computer simulation in explicit solvent. A combination of a functional optimization to determine the reaction coordinate and short time trajectories between “milestones” is used to study the kinetics of the unfolding. One hundred unfolding trajectories along three different unfolding pathways are computed between all nearby milestones, providing adequate statistics to compute the overall first passage time. The radius of gyration is smaller for intermediate configurations compared to the initial and final states, suggesting that the kinetics (but not the thermodynamics) is sensitive to pressure. The transitions are dominated by local bond rotations (the ψ dihedral angle) that are assisted by significant nonmonotonic fluctuations of nearby torsions. The most effective unfolding pathway is via the N-terminal.