Zusammenfassung
Determining protein folding kinetics and thermodynamics from all-atom
molecular dynamics (MD) simulations without using experimental data
represents a formidable scientific challenge because simulations can
easily get trapped in local minima on rough free energy landscapes.
This necessitates the computation of multiple simulation trajectories,
which can be independent from each other or coupled in some manner, as,
for example, in the replica exchange MD method. Here we present results
obtained with a new analysis tool that allows the deduction of faithful
kinetics data from a heterogeneous ensemble of simulation trajectories.
The method is demonstrated on the decapeptide Chignolin for which we
predict folding and unfolding time constants of 1.0 +/- 0.3 and 2.6 +/-
0.4 mu s, respectively. We also derive the energetics of folding, and
calculate a realistic melting curve for Chignolin.
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