Lateral access mechanism of LPA receptor probed by molecular dynamics simulation
Fig 5
Free energy landscape projected on the plane spanned by the PC1 and PC3 axes.
a) Free energy map projected on the PC1-PC3 plane. In the left panel, the centers of the clusters and the initial structures are plotted as light and dark blue circles, respectively. The sizes of the light blue circles are proportional to the populations of the clusters. In the middle panel, the centers of the clusters are color-coded according to their microstate. In the right panel, the positions of the central structures of the macrostates are indicated by circles. A basin in the free energy map with a small PC1 value corresponds to a dissociated state, that with an intermediate PC1 value represents a partially-bound state to the central region with high energy, and that with a large PC1 value corresponds to a bound state. Macrostate 6 corresponds to a basin with a low PC3 value, and 7 corresponds to a basin with a high PC3 value. b) Relationship between the PC3 value and the distance between the LPA head group and R2817.32. The definition of the distance is the same as in Fig 4.