FIGURE 2.

Two-dimensional free energy surface (2D-FES) of Trp-cage native basin as a function of collective coordinates Q₁ and Q₃₇, indicating corresponding similarities to NMR models 1 and 37, was obtained using WHAM in 914 simulation windows (see Methods and Data S1). An all-atom MD simulation of 1.2 ns in duration was carried out in each window. Open circles, marking FES, represent the 38 NMR structures in the Q₁ and Q₃₇ coordinates. Spacing between contour lines is 0.22 kcal/mol (0.37 kT). White rectangles mark the deepest and the second deepest basins corresponding to model 1 (lower right corner) and model 16 (upper left corner), respectively. The difference of ∼0.6 kT in free energy is created by rotation of Tyr-3, cation-π interaction between Arg-16 and Trp-6 and disappearance of 3-10 α-helix.