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

Figure 3

Scenarios for the path reaching and crossing the TS.

a) Schematic diagram showing the possible scenarios for the paths reaching the TS, namely: reactive and non-reactive paths; in the reactive paths, the crossing of the TS can occur either from U to F (forward reactive path) or from F to U (backward reactive path); in non-reactive paths, the peptide falls back into the state of origin (either UTSU or FTSF paths). b) Time evolution of the peptide through the U, TS and F states for six representative paths along the simulations. The three rows in each panel represent the existence of the U (unfolded), T (transition) and F (folded) states. All the four scenarios described in panel a can be observed. The top and middle panels show the forward and backward reactive paths, respectively. The bottom panels show the non-reactive paths, either UTSU or FTSF paths.

Figure 3

doi: https://doi.org/10.1371/journal.pcbi.1002137.g003