Figure 4.

Well-tempered metadynamics simulation with the bias factor of 6. (A) Time-dependent variation of secondary structures of individual residues of αII is shown. The secondary structures were assigned using the DSSP program (46, 47). The x axis is plotted on a logarithmic scale. (B) Estimated free-energy surfaces (kJ/mol) are shown as a function of CVs at different simulation times. Representative native, partially unfolded, and completely unfolded conformations of αII are shown. (C) A schematic of the free-energy landscape of αII in intact IFABP is given, illustrating a native (N), an on-pathway folding intermediate (I), and an unfolded (U) state and sequential filling of individual minima as a function of time. To see this figure in color, go online.