Conformations of an RNA Helix-Junction-Helix Construct Revealed by SAXS Refinement of MD Simulations

Abstract

RNA is involved in a broad range of biological processes that extend far beyond translation. Many of RNA's recently discovered functions rely on folding to a specific conformation or transitioning between conformations. The RNA structure contains rigid, short basepaired regions connected by more flexible linkers. Studies of model constructs such as small helix-junction-helix (HJH) motifs are useful in understanding how these elements work together to determine RNA conformation. Here, we reveal the full ensemble of solution structures assumed by a model RNA HJH. We apply small-angle x-ray scattering and an ensemble optimization method to selectively refine models generated by all-atom molecular dynamics simulations. The expectation of a broad distribution of helix orientations, at and above physiological ionic strength, is not met. Instead, this analysis shows that the HJH structures are dominated by two distinct conformations at moderate to high ionic strength. Atomic structures, selected from the molecular dynamics simulations, reveal strong base-base interactions in the junction that critically constrain the conformational space available to the HJH molecule and lead to a surprising re-extension at high salt. These results are corroborated by comparison with previous single-molecule fluorescence resonance energy transfer experiments on the same constructs.

The structural plasticity of nucleic acid duplexes revealed by WAXS and MD

“…Past studies on DNA show the importance of this type of information in deciphering the sequence variability of dsNA molecules, an area that needs further development (35). However, a promising line of study integrates experimental and computational approaches to study RNA conformations (36)(37)(38)(39)(40)(41)(42)(43). Simulations provide atomic-level spatial resolution for macromolecular structure and dynamics while closely correlated experiments can be used to finely tune the simulation parameters (36,38,44) or guide the efficient exploration of conformational space sampled (37,40,43).…”

Nanoscale Structure Determination of Murray Valley Encephalitis and Powassan Virus Non-Coding RNAs

“…Although several attempts have been made to study RNA structures in general [33,34], detailed insight into the structural features of multiple flaviviral strains is lacking. Such insights could provide a platform to develop novel antiviral therapies as well as further our knowledge about viral replication events.…”

Structural analyses of an RNA stability element interacting with poly(A)

“…Three key features of these P(r) curves will be discussed here: 1) the position of the first peak, which reflects the most probable distance between parts of the structure; 2) the appearance of a "shoulder" in P(r) near 40 Å, indicative of a bend in the structure; and 3) the curve's tail, terminating in the maximum linear dimension of the molecule, D max . For duplex-like extended RNA constructs, the most probable pair distance (peak position) represents the averaged diameters of the base-paired stems (19). For each dENE construct, the position of this peak shifts to larger values following the addition of poly(A), indicating that poly(A) binding increases this dimension of the molecules.…”