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 also computed the S 2 rel values based on the REMD simulation described above. The REMD simulations reproduce the general trends observed in the experiments; however, the simulations show significantly increased dynamics at the terminal ends compared to experimental values, with S 2 rel values approaching the dynamic limit ( Figure 2B ). Additionally, while experimental values have similar relative order parameters from A28-C33, large variations are observed in the REMD simulation, with A29-A30 being more ordered and A32 less ordered than experimentally observed ( Figure 2B ). These differences may reflect shortcomings in the force field and/or mismatch in the experimental/computational timescales since the REMD simulations likely probe fluctuations that extend beyond the picosecond timescales sensed by spin relaxation data.