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. Author manuscript; available in PMC: 2011 Sep 10.
Published in final edited form as: J Mol Biol. 2010 Jul 17;402(1):278–291. doi: 10.1016/j.jmb.2010.07.025

Fig. 5.

Fig. 5

C41 base triple and G40 base triple of DM product undergo minor rearrangements upon C41 protonation. (a, b) Overlays of protonated C41 (blue) and deprotonated C41 (magenta) structural elements (upper panels), along with time evolution of distances between heteroatoms of specified residues (lower panels). Equilibrated structures were obtained from a snapshot after 5 ns of data collection following an extensive equilibration procedure. Overlays were obtained by minimizing RMSD of residues shown (values given in Table 2). Dotted lines (upper panels) and solid lines (lower panels) in the distance plot represent deprotonated and protonated C41 states, respectively. (Note that the trajectories in DM figures are displayed such that the natively folded C41° triple is kept as the upper panel.) Distances (in Å) are between heteroatoms and colored according to the legend. Gold arrows depict key structural rearrangements upon C41 protonation. Independent trajectories are provided in Fig. S6.