Figure 8. Flexibility of β subunit and βM loop during the αβ-tubulin dimer molecular dynamics (MD) simulation.

(A) Mass-weighted positional fluctuations (or root-mean-square fluctuations, Å) by residue for atoms in the β subunit of the αβ-tubulin dimer over the course of 0.6 µs of MD simulation, in the apo form (yellow line) and in complex with baccatin III (green line) or paclitaxel (red dotted line). (B) Evolution of the conformation of the βM loop in the 1.0 µs simulation of the αβ-tubulin dimer free in solution. The Cα root-mean-square deviation is measured with respect to either the initial α-helical structure (blue line) or the extended hairpin conformation that was stabilized at 300 ns (orange line).