13C NMR relaxation measurements alone are often not sufficient to describe the motions of small RNA molecules in solution. In the case where the global tumbling time of the RNA is on the same time scale as its internal motions, standard Lipari-Szabo analysis becomes inadequate, and other methods must be used to describe the dynamics. Here, molecular dynamics simulations of the iron-responsive element (IRE) RNA hairpin are analyzed using isotropic reorientational eigenmode dynamics (iRED) to provide a picture of the motions of the RNA. The results show that indeed there is no separability of global and internal motions, and thus the order parameters determined from experimental data cannot be quantitatively accurate. iRED analysis also identifies correlated motions, providing a new picture of the dynamics of the IRE loop.
All Science Journal Classification (ASJC) codes
- Molecular Biology