Using spatial density restraints to fit the structure of an RNA stem-loop (fully flexible at the dihedral angle and sugar pucker levels)

This movie is related to Fig. 2 in the accompanying paper. The heavy atoms of the RNA stem-loop are shown colored from red to blue via green (5' to 3') in stick representation. Faces of sugars and nucleotides bases are colored separately. The movie shows a section of a trajectory (200ns) continuous in geometry, i.e., the REX condition (value of fD) varies and is displayed at the top left. These data are from the run with higher resolution input data. The system is initially trapped in a misfold. By excursion into replicas with low restraint strength, it escapes and enters additional traps (e.g., 20s, 40s), until an extended stay at low fD (50 to 75s) allows it to find a native-like conformation. The favorable restraint energy leads to an immediate drift toward replicas with higher fD.