Figure 2.

(A) 2D landscape obtained with ScIMAP for generated RTD-1 conformations with energies no higher than 20 kcal/mol from the global minimum energy obtained. Each point is color-coded according to the cysteine arrangement in corresponding conformation: blue denotes the 4–17 6–15 8–13 native arrangement observed in the NMR ensemble; sky blue denotes at least one native disulfide bond is present, with the rest of the cysteines unpaired; red denotes 4–17 is formed as under native conditions, with the rest scrambled; yellow denotes the 4–6 8–13 15–17 arrangement; green, plum, and orange denote the remaining all-scrambled arrangements. (B) Landscape is color-coded with free energy values (red–blue spectrum indicates high–low values). The lowest free energy state labeled A corresponds to the blue (4–17 6–15 8–13) cluster in A. The second-lowest free energy state labeled B corresponds to the yellow (4–6 8–13 15–17) cluster in A. (C) Plot shows free energy values measured over the first coordinate. The global minimum labeled A is about 10 RT units lower than the local minimum labeled B.