Figure 4.

The distribution of angles LID-CORE ${\theta }_1$ and NMP-CORE ${\theta }_2$ from LT-MD simulations. (a) Starting from the open state without ligand, corresponding to simulations O₁, O₂, and O₃. The green line indicates the transition pathway that LID closed first and then NMP to close. (b) Starting from the closed state without ligand, corresponding to simulations C₁, C₂, and C₃. The red and pink lines indicate two distinctive transition pathways, one is that NMP open first and then LID to open (pink line), and the other one (red line) is in the opposite direction. (c) Starting from the open or the closed state with ligands, corresponding to simulations O-ATP-AMP, O-ATP, O-AMP, and C-ATP-AMP. The crystal structures of PDB 4AKE and PDB 1AKE are marked. The arrows illustrate the conformational transition and pathways as observed in the LT-MD simulations. (Simulation names can be found in Table S3.) To see this figure in color, go online.