Figure 4
Free-energy landscape depicted in the 2D space constructed by the FAD-FMN distance and the FMN-heme distance: (A) free-energy landscape for the oxidized state, and (B) that for the reduced state. The free energies were calculated by −kBT ln P, where P represents the probability density obtained from the reweighted data for the last 0.5-μs aMD, and were adjusted so that the lowest free-energy value becomes zero. FMN-heme distance is a predicted one using the CPR-HO complex structure9 (see text), and the center-of-mass distance between the alloxazine ring of FMN and the heme in HO was used. The circle and the square represent the crystal structure of the closed7 and that of the open form9, respectively. MD snapshot structures (triangles in A and B) are shown in the right (the heme and HO are shown in purple; other coloring and the view angle are the same as in Fig. 1A).
