Figure 3.

Active site structures of MD simulations with either a 2′-methoxy or 2′-OH moiety on A−1 and distinct A38 protonation states. (A) Simulation OMe/G8/A38H⁺ retains a crystal structure like arrangement of the active site, which is different from the dominant architecture observed with the native cleavage site A−1(2′-OH). (B) Simulation WT2/G8/A38H⁺ illustrates re-puckering of the A−1 sugar upon introduction of the native A−1(2′-OH). (C) Simulation WT/G8/A38/bsc0 shows a reversible flip-flop of the native A−1(2′-OH) between 2′-endo and 2′-exo. The structures shown (sticks) are averaged over the last ns of the simulation and superimposed (based on the A−1 and G+1 nucleobases) with the starting crystal structure (green lines). Red dashed lines indicate key hydrogen bonds within the active site. (D) Time evolution of hydrogen bonds (the color scale is preserved throughout) involving the A−1(O2′) oxygen over the course of the indicated MD simulations. For clarity, only the first 50 ns of each simulation are shown, however, we note that the arrangement of the active site remains intact in all simulations after these 50 ns.