608385.fig.003a
(a)
608385.fig.003b
(b)
608385.fig.003c
(c)
Figure 3: Structural connectivity between the F-Loop, Bridge Helix, and Link domain. (a) Structure of the complex at the begin of the simulation. The coloring scheme is as described in Figure 2(a). An additional residue, scRPB2 H761, making close contact to the F-Loop is shown in space-filling mode in dark blue. The Bridge Helix N-terminus is fully α-helical and essentially straight. (b) During the molecular dynamics simulation, a kink in BH-HN (red section of the Bridge Helix) occurs and tilts the F-Loop and associated Link domain towards the left. (c) Interpretation of the effects of the structural changes observed in (a) and (b) on the nucleotide insertion site. The removal of the pyrophosphate group after successful incorporation of the nucleotide into the nascent transcript removes a structurally stabilizing contact and may thus influence the spatial position and conformation of the Link domain.