Pierced Lasso Bundles Are a New Class of Knot-like Motifs
Figure 4
Probability of the formation of helix A.
The plot shows data for Q (a measure of nativeness, between 0–1) versus q(segment) (formation of a particular secondary structure, in this case helix A). The plots display data for reduced (blue) and oxidized (red) protein in the case of the PLBs and the reduced state (black, DD) for the unthreaded proteins (see method section for a full description). The plots are grouped in three boxes according to position in sequence of the covalent loop, dark blue for the C-terminal covalent loop, light blue for the N-terminal covalent loop and grey for the unthreaded proteins. The plots show that the formation of helix A is a late event on the folding landscape as it starts to build its contacts at high Q. The diagonal dashed grey line shows where q(segment) is tracking the overall folding progress. A significant shift is seen between reduced and oxidized N-terminal PLBs where the oxidized state folds faster than the reduced state.