Figure 3.
Free energy landscapes of Josephin and representative structures. The left panel corresponds to the restrained ensemble. The free energy landscape is projected along two reaction coordinates, the radius of gyration (y axis) and the bending angle (x axis). The energy values are in kBT units. Representative structures within the RDC-CS ensemble for Josephin conformations are also shown on the left panel at small (yellow), intermediate (orange), and large (green) values of the bending angle. The structures are superimposed by using the Cα atoms of the globular subdomain for least square fitting. Individual structures from the bound state are shown by white circles (PDB code 1yzb), red squares (PDB code 3o65), and black triangles (PDB code 2aga). These results illustrate how the compact conformations in the free state resemble those in the bound state. The right panel shows, as a control, the landscape for the unrestrained ensemble. Two representative structures are shown on the top in blue and red having angles of 98° and 115°, respectively. To see this figure in color, go online.