Fig 7. NTPase substrate-dependent interactions between Arg387 of motif IVa and RNA phosphate groups.

(A) The guanidinium group of Arg387 is observed to transition from the “up” conformation to the “down” conformation, respectively colored blue and orange. (B) Probability densities and (C) free energy surfaces from the US simulations performed to model the “up” to “down” transition of the Arg387 side chain. Short collective variable distances correspond to the “down” conformation. As emphasized by the line colors, the trend of these results show that ssRNA favors the “down” conformation while the other substrate states favor the “up” conformation, suggesting a NTPase substrate-dependence of the Arg387 conformational states.