Cluster sequence number

Fig. 6.15 Clustering of the combined 100 ns trajectories of two b-hexapeptides in methanol at 298 K. The plot shows the population in percentage per cluster and the portion of structures per cluster that belongs to the trajectory of each of the peptides [19].

Fig. 6.16 Example of folding pathways at 340 K of a b-heptapeptide (see Panel A, Fig. 6.1), one from conformational cluster 2 (left-hand panel) and one from conformational cluster 3 (right-hand panel). The vertical axis indicates the free energy difference with respect to the

helical conformational cluster 1. The transition rate (in ns"1) between consecutive clusters is also indicated. Only the two shortest folding pathways (i.e., those with the minimum number of intermediate clusters) are shown [44].

converged transition rates between conformational clusters very long simulations are required.

Finally, we note that the unfolded state of the b-peptides discussed comprises many fewer conformations than the about 109 theoretically accessible ones [17, 56]. The number of different conformers is rather of the order of 102-103, see Figs. 6.8, 6.13-6.15. This small size of the unfolded state explains why these pep-tides fold on a nanosecond timescale.

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