Abstract
HIV-1 TAR RNA is a two-helix bulge motif that plays a critical role in HIV viral replication and is an important drug target. However, efforts at designing TAR inhibitors have been challenged by its high degree of structural flexibility, which includes slow large-amplitude reorientations of its helices with respect to one another. Here, we use the recently introduced algorithm WExplore in combination with Euler angles to achieve unprecedented sampling of the TAR conformational ensemble. 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. Collectively, our findings demonstrate the utility of WExplore in combination with suitable order parameters as a method for exploring RNA conformational space.
Highlights
The conformational flexibility of RNA molecules is increasingly recognized as critical to how RNAs carry out their functions [1]
Comparison of sampling ranges in Euler space. It has been previously shown [13,34,48,56,68] that the largescale interhelical dynamics of two-way junctions can be well described by three Euler angles: ␣h, which describes the relative twist of the lower helix about its helical axis; ␥ h, which describes the twist of the upper helix and h, which describes the interhelical bend angle between the two helices
Conventional sampling results are obtained by switching off the cloning and merging operations in the WExplore algorithm, which results in 48 continuous trajectories. 1D Weighted ensemble (WE) simulations use regions defined along a single reaction coordinate, which is the distance of the single axis rotation in Euler space to the initial nuclear magnetic resonance (NMR) structure
Summary
The conformational flexibility of RNA molecules is increasingly recognized as critical to how RNAs carry out their functions [1]. While this flexibility has been characterized experimentally, an atomic-level picture is in many cases lacking. Interhelical motions have been shown to be critical to biological function. Large-scale opening and closing motions of helical domains about higher-order junctions allow ligands to access otherwise buried binding sites [6], and during translation by the ribosome, interhelical dynamics of both tRNA and elements of the ribosomal RNA, like the L1 stalk, facilitate translocation [7,8]
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