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

Figure 10

Three-dimensional representation of folding funnel of Peptide 1.

The mechanism by which the peptide crosses TS is shown. The TS is reached with the formation of native end-to-end (red) and turn (green) contacts, with the end-to-end formation appearing at the TS, making it the unique feature of the TS of Peptide 1. However, reaching the folded state from the TS involves W11 sidechain (purple) repositioning and concomitant native arrangement of the central segment (orange) of -hairpin. In “Prior-to-TS” and TS, W11 is in a ‘key-lock’ configuration with turn residues, thus from a dynamic point of view it acts as a chaperone to reach the TS, while the last stage to reach the native state involves ‘correct’ native arrangement of W11 with the central segment of -hairpin (See representative structures).

Figure 10

doi: https://doi.org/10.1371/journal.pcbi.1002137.g010