Figure 2

The open trigger loop RNAP TEC appears to be the translocating conformation. Vectors describe downstream DNA/DNA and upstream RNA/DNA translocation during simulation. The downstream translocation vector is drawn through DG5 (DNA template dGMP 5) and G37 (RNA GMP 37) 3′ carbons. Translocation is measured as the displacement of an orthogonal projection of DA40 (non-template DNA dAMP 40) 3′ carbon onto the vector relative to the initial structure. The upstream translocation vector is drawn through DT14 (DNA template dTMP 14) and C31 (RNA CMP 31) 3′ carbons. Translocation is measured as the displacement of an orthogonal projection of G33 (RNA GMP 33) 3′ carbon onto the vector relative to the initial structure. Closed-Mg (green) and open (blue) TECs are shown. B) Scatter plot of upstream and downstream translocation (each point represents a 20 ps interval). “X” indicates 10.5 ns time points for the three simulations relative to a (0,0) starting position in the original crystal structures (2O5J for closed; 2PPB for open).