Efficient in silico exploration of RNA interhelical conformations using Euler angles and WExplore.
Bottom Line: Our ensemble achieves similar agreement with experimental NMR data when compared with previous TAR computational studies, and is generated at a fraction of the computational cost.It clearly emerges from configuration space network analysis that the intermittent formation of the A22-U40 base pair acts as a reversible switch that enables sampling of interhelical conformations that would otherwise be topologically disallowed.We find that most previously determined ligand-bound structures are found in similar location in the network, and we use a sample-and-select approach to guide the construction of a set of novel conformations which can serve as the basis for future drug development efforts.
Affiliation: Department of Chemistry, University of Michigan, 930 N University, Ann Arbor, MI 48109, USA.Show MeSH
Mentions: Previous studies from our labs have shown that steric and connectivity constraints imposed by the secondary structure of junctions strongly limit the set of accessible interhelical conformations of an RNA (47,56,57). While these ‘topological’ constraints normally limit 3-nucleotide bulges to only 15% of the Euler angle space, we find that distortions of the junction-closing base pairs could partially alleviate these constraints, expanding the set of allowed conformations (56). We investigate whether breaking of the A22-U40 pair correlates with sampling of otherwise topologically inaccessible states. Comparison to the previously determined set of allowed states shows that 133 of the 438 nodes in the network would be topologically inaccessible, all corresponding to states with broken or highly distorted A22-U40 pairs (Figures 3B and 5B). Figure 5 shows that some of these otherwise topologically disallowed states are strongly selected when a SAS procedure is used to select a subensemble of conformations that show maximal agreement with NMR RDCs (see ‘Sample and select’ below), suggesting that these states play an important role in the natural dynamics of TAR. We also find that all of the states sampled by the A22-U40 restrained simulation fall within the ensemble of topologically allowed 3 nt bulge states. These observations, together with the knowledge that the A22-U40 base pair is known to be unstable in solution (61,69), point to the role of A22-U40 as a reversible entropic gate that can enlarge or contract the space of accessible interhelical configurations.
Affiliation: Department of Chemistry, University of Michigan, 930 N University, Ann Arbor, MI 48109, USA.