Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch

Eichhorn, Catherine D.; Feng, Jun; Suddala, Krishna C.; Walter, Nils G.; Brooks, Charles L.; Al-Hashimi, Hashim M.

In general, the REMD simulations predict the NMR data measured for A29C with reduced quality to that noted for WT. Interestingly, the computed absolute S 2 values indicate a global reduction in order for A29C, particularly for residues A27-C33 (Supplementary Figure S8) , whereas NMR relaxation parameters between WT and A29C are more similar, suggesting comparable global order parameters. The REMD simulations reveal enhanced dynamics at C29 consistent with the NMR chemical exchange data. The REMD simulation also suggests increased dynamics at A32, which is not observed experimentally: although slightly reduced, the S 2 rel is within error of A29-A31 values (S 2 rel of 1) (Supplementary Figure S8) . Computed RDCs agree reasonably with measured RDCs, although the C1 0 H1 0 RDCs are opposite in sign as observed in the comparison between WT NMR and REMD-calculated RDCs. The Q-factor comparing the average REMD structure to measured RDCs is 70%; however, removal of A28 C8H8, A30 C2H2 and A30 C1 0 H1 0 RDCs improves the Q-factor significantly. This improvement is observed only for the REMD structure ( Figure 4D ), indicating that these residues, localized about the mutation site, adopt non-Aform conformations and likely experience perturbations from the increased dynamics at C29. The difference in timescales between the REMD simulations and NMR may be another factor leading to the observed discrepancies. Nevertheless, MD and NMR data both indicate significant dynamics at the mutation site with perturbations extending toward the 3 0 end of the ssRNA. ssRNA tail conformation and dynamics optimized for ligand docking in queC aptamer