Figure 7.

Conformations associated with lowest free energy states labeled A and B (corresponding to free energy values no higher than 8 kcal/mol) are, respectively, shown in A and B superimposed in transparent with VMD over the minimum potential energy conformation among them. (A) β-Sheets are well-formed as in NMR ensemble, with most of the flexibility located in the loop regions. Cysteines are in the knot motif as in NMR ensemble. (B) There is no significant secondary structure among conformations associated with the second-lowest free energy state. (C) Dark gray line, showing secondary structure probabilities calculated for each amino acid over ensemble in A, reveals well-formed β-sheets. Light gray line, showing probabilities obtained over ensemble in B, reveals negligible secondary structure. (D) Some helicity is observed with low probability in ensemble in A.