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. Author manuscript; available in PMC: 2022 Mar 11.
Published in final edited form as: J Chem Theory Comput. 2010 Nov 9;6(12):3836–3849. doi: 10.1021/ct100481h

Figure 3.

Figure 3.

The MD snapshots (colored by atom types) compared with high-resolution NMR structure (in red) showing structural problems seen in simulations of the UUCG tetraloop (some atoms are not shown for clarity, and important parts are shown as sticks). (A) The disruption of the UL1(O2′)•••GL4(O6) H-bond and formation of a new UL1(O2′)•••UL2(O5′) H-bond observed in all MD simulations with standard χ profiles are highlighted by the blue arrow, while the simultaneous decrease of χ of GL4 leading to a change in the UL1/GL4 propeller is shown by the red arrow. (B) The UL2 phosphate α/γ flip is depicted by the black arrow. See the text for full details.