Figure 5.

Distribution of angles α and β in the low-energy 3D structure of BVDVsegment_180_425. The relative orientation of helices was assessed by a helix-centred representation of RNA 3D structure. As stretched by the relative geometry of green helical segments, angles close to 0° account for parallel stems, whereas angles close to 180° indicate collinear arrangement and can be indicative of coaxial stacking. Analysis of candidate structures from SimRNA simulations of BVDVsegment_180_425 shows that angles between helices are distributed in well-defined intervals. Set 1 and set 2 comprise low-energy structures predicted by SimRNA, whose helices SL IIIf and IIIg are separated by a bulge of 2 and 3 nts, respectively. For set 1, α lies between 37 and 75 degrees, while for set 2, values are distributed between 66 and 149 degrees. This is expected, as a larger bulge allows for more conformational flexibility of the two adjacent helices. Contrary, β falls in a range between 130 and 174 degrees for set 1 and 129 and 173 degrees for set 2. Values for both sets were combined and depicted in blue.