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. 2020 Jan 3;118(3):698–707. doi: 10.1016/j.bpj.2019.12.026

Figure 2.

Figure 2

Left, the free energy landscape over αC-helix swinging distance and activation-loop RMSD to a crystal structure (PDB: 3TL8 (20), chain A) for the unphosphorylated BAK1 kinase domain. The locations of the two structures shown on the right, taken from trajectories, are indicated. The right section shows structures from simulations representing the metastable active-like and inactive free energy basins. Note the cracking of the activation loop and swinging of the αC helix away from the rest of the N-lobe in the inactive structure. Additionally, the αC helix in the inactive structure has partially unfolded. This figure was produced using VMD 1.9.2 (30), Matplotlib 1.5 (47), and Inkscape 0.91 (46). To see this figure in color, go online.