Figure 3.

CTD interaction sites observed during the simulations of the GTase with the 4-heptad pSer5 CTD extended in the N-ter direction (System 6). (A) Locations on the GTase (left) and residues involved in the four CTD interaction sites (panels on the right) reproducibly observed in these simulations. The snapshot shows a representative CTD binding conformation and the positions of the N- and C-terminal heptads are indicated. (B–E) Time-evolution of the minimum distances showing the occupation of each CDS by the respective CTD group (pSer5 or Tyr1) over the duration of the cMD and aMD simulations. Distances obtained in three replicates are shown in orange (replicate 1), blue (replicate 2) and green (replicate 3). The occupation of each site was described by taking representative sidechain minimum distances as follows: (B) CDS1, R330 sidechain nitrogens to the pSer5 phosphate oxygens, (C) CDS2, R411 sidechain nitrogens to the pSer5 phosphate oxygens, (D) CDS–Y1, V372 Cγ atoms to the Tyr1 ring and (E) CDS–Y2, L381 sidechain to the Tyr1 ring. Distances from the CTD groups to other residues in the respective pockets (e.g. R386 and K331 in CDS1) show comparable behaviour.