Figure 1

A model for trigger loop hinges, bridge helix hinges and bridge helix bending modes based on all atom molecular dynamics simulations. At the top of the figure, diagrams of the closed TEC, the closed product TEC (after chemistry) and the translocating TEC are shown. DNA is grey; RNA is red; the NTP substrate (or incorporated NMP and pyrophosphate) is blue; the trigger loop (TL) is purple; the bridge helix (BH) is yellow. Interpretations of simulations are shown schematically below. Simulations indicate trigger loop hinges H1 and H2, bridge helix hinges H3 and H4 and bridge helix bend modes B1 (straighter) and B2 (more sharply bent).