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

Figure 5

Distribution of turn, middle and end-to-end segments of Peptide 1.

a) Distributions of the distances between the C atoms of residues N6-G9 (top), I4-T12 (middle) and S1-E15(bottom) in the TSE. The corresponding distributions in the F state are shown as green filled bars. b) Distributions of the minimum distances between the atoms of the W11 sidechain and the atoms of the sidechain of two turn residues, namely P7 (top) and G9 (bottom) in the TSE. The corresponding distributions in the F state are shown as green filled bars. Snapshot of TS structure at left shows the key-lock configuration of W11 with P7 and G9 residues, while folded structure at the right has W11 in native configuration.

Figure 5

doi: https://doi.org/10.1371/journal.pcbi.1002137.g005