Figure 11.

Root mean squared fluctuations (RMSF) of the C_α atoms of (a) p66 and (b) p51 over the concatenated ensemble trajectories of the apo (black), EFV (red) bound and NVP (blue) bound HIV-1 RT simulations. The residues of the NNRTI binding pocket, RnaseH primer grip and active sites are indicated by magenta, dark blue and green dots on the x-axis, respectively. The bars above the graph indicate the locations of the subunits in the sequence; the (F)ingers, (P)alm, (T)humb, (C) connection and (R)NaseH. The p51 αL helix containing residues 395 and 396 in the RNaseH primer grip is indicated by a gray box.