Figures & data
Figure 2. The three possible binding sites 1, 2 and 3 predicted by global dockings, in which tubulin protein (1TVK) is shown as ribbon and PLA is shown as stick colored by element.
![Figure 2. The three possible binding sites 1, 2 and 3 predicted by global dockings, in which tubulin protein (1TVK) is shown as ribbon and PLA is shown as stick colored by element.](/cms/asset/7d906019-b710-4f00-a1ee-9d12067c19dd/ienz_a_845816_f0002_b.jpg)
Table 1. The number of conformations and the lowest binding energy in each of the binding sites 1, 2 and 3.
Figure 4. Docking conformations of PLA and corresponding surfaces of tubulin at binding sites 1 (A and B), 2 (C and D) and 3 (E and F), in which the red and blue regions represent oxygen and nitrogen atoms, respectively, whereas gray and white regions represent carbon and hydrogen atoms (as a whole).
![Figure 4. Docking conformations of PLA and corresponding surfaces of tubulin at binding sites 1 (A and B), 2 (C and D) and 3 (E and F), in which the red and blue regions represent oxygen and nitrogen atoms, respectively, whereas gray and white regions represent carbon and hydrogen atoms (as a whole).](/cms/asset/a9d1b003-8154-4bef-ae42-37d5a0c9186a/ienz_a_845816_f0004_b.jpg)
Figure 5. Potential energy (bottom) and total energy (top) evolutions of binding modes 1 (black), 2 (blue) and 3 (red) during the MD simulations (A). RMSD of backbone atoms of β-tubulin (black) and PLA (red) in binding modes 1 (B), 2 (C) and 3 (D), respectively.
![Figure 5. Potential energy (bottom) and total energy (top) evolutions of binding modes 1 (black), 2 (blue) and 3 (red) during the MD simulations (A). RMSD of backbone atoms of β-tubulin (black) and PLA (red) in binding modes 1 (B), 2 (C) and 3 (D), respectively.](/cms/asset/1e51612c-c565-46df-a3d2-7d992cc07227/ienz_a_845816_f0005_b.jpg)
Figure 6. The final (yellow) and initial (gray) structures of binding modes 1(A), 2 (B) and 3 (C) in 12.0 ns MD simulations, respectively.
![Figure 6. The final (yellow) and initial (gray) structures of binding modes 1(A), 2 (B) and 3 (C) in 12.0 ns MD simulations, respectively.](/cms/asset/642a403b-663c-4f6d-bb97-5fd80f328a55/ienz_a_845816_f0006_b.jpg)
Table 2. Binding free energies (kcal/mol) obtained by MM-PBSA method for the 500 snapshots of the last 1.0 ns MD simulations.