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.

We subjected the RDCs (excluding RDCs for the two flexible residues from the terminal ends) to an order tensor analysis (47, 69, 70) assuming different input structures including single strands derived from idealized A-form and B-form helices, the REMD-averaged structure, and available ligand-bound X-ray and NMR structures (26, 27) . Despite the relatively small number of RDCs used in this analysis, we clearly observe a better fit with an A-form geometry (Q-factor 4.77%) as compared to all other conformations (Q-factor ! 16%) ( Figure 3B ). This is consistent with independently observed 3 J H1 0 -H2 0 scalar coupling crosspeaks, which indicate a C3 0 -endo sugar conformation for core residues in the tail, suggesting an A-form (and not B-form) helical geometry. The RDCs are in strong disagreement with preQ 1 -bound X-ray and NMR structures (PDBID: 3FU2 and 2L1V) indicating that the tail must undergo a transition from an A-form helical geometry towards the distinct helical conformation observed in the X-ray and NMR structures in which the A-form geometry is perturbed at the hairpin-tail junction, likely due to torsional strain from the ssRNA folding back upon the hairpin. The REMD-averaged structure has a Q-factor of 30%, indicating a better fit than ligand-bound structures, but is still outside the range considered to represent a good fit. Together, these data suggest that, on average, the ssRNA tail adopts an A-form like conformation. The good RDC fit to the A-form structure also suggests that averaging of the RDCs due to internal motions is largely isotropic in nature, causing a semi-uniform attenuation of the RDCs relative to values expected for an A-form structure. The dynamics could involve exchange between a stacked ordered conformation and unstacked highly disordered conformation, or local isotropic motions about the average A-form conformation.