FIGURE 5.

Polyproline structural content. PP-type conformational probabilities per residue are shown for both A₂₁ (gray) and F_s (black) using the equilibrium sampling (solid lines) and the unfolded state (dashed lines). As described in the text, the AMBER-99 ensembles remain essentially unchanged due to the favoring of extended conformations in that force field. Two parts are shown in panel d to distinguish the PPII content of the unfolded state (top) from that observed in the equilibrium sampling (bottom). Due to the small proportion of highly unfolded configurations in the AMBER-GS ensembles, too few unfolded conformations to quantitatively access PPII presence were analyzed. However, it is clear from the top plot in panel d that unfolded conformations in that force field favor PPII structure to a significant degree.