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Structured Pathway across the Transition State for Peptide Folding Revealed by Molecular Dynamics Simulations

Figure 9

Time evolution of the minimum distance between all the atoms of the W11 sidechain and all the atoms of the P7 sidechain (maroon) for a representative reactive path.

In addition, the distances between the C atoms of the turn (N6-G9) and central (I4-T12) residues are shown in black and blue, respectively. The shaded region represents the TS. The three histograms at the bottom show the distributions of the minimum distances between the W11 and P7 sidechains for the structures sampled before the TS (prior-to-TS), in the TS (TS) and in the native (F) state evaluated over all forward reactive paths. For the prior-to-TS ensemble the structures occurring within 1 ns prior to the TS along all forward reactive paths are taken.

Figure 9

doi: https://doi.org/10.1371/journal.pcbi.1002137.g009