Theoretical studies of an exceptionally stable RNA tetraloop: observation of convergence from an incorrect NMR structure to the correct one using unrestrained molecular dynamics.
We report on the results of five independent and unrestrained molecular dynamics simulations of an RNA tetraloop, r(GGACUUCGGUCC), and its related structures with the loop UUCG sugars changed to deoxyribose. Two separate NMR structures have been reported for the loop portion of this molecule, with the second refinement resulting in a slightly different and more accurate conformation for the loop. The root-mean-square deviation (RMSd) between the two NMR structures, for the loop portions only, is 2.5 A. Our simulations, starting from the two NMR structures, demonstrate that this tetraloop is a very stable and rigid structure with both nanosecond length simulations staying very close to the initial structures. Additionally, both simulations preserved most, if not all, of the NMR-derived interactions and violated very few of the nuclear Overhauser effect (NOE)-derived distances used in the structure refinements. However, when the two NMR structures were simulated with deoxyriboses in the loops instead of the native riboses, the flexibility of the systems increased and we observed a conversion from the incorrect to the correct loop conformation in the simulation which started in the incorrect loop conformation. When the riboses were subsequently re-introduced back into the structure which underwent the conversion, the agreement between this simulation and the one starting from the correct NMR structure was a remarkably low 0.5 A, demonstrating an almost complete convergence from the incorrect to the correct structure using unrestrained molecular dynamics.