It can reach atomic resolution for most short RNAs (<30 nt). For example, FARNA/FARFAR ( 34, 35) predicts RNA structures through the assembly of 1–3 nucleotides from known structures via a Monte Carlo procedure. Template-assembly approaches build RNA 3D structures based on the known structural modules ranging from piece-wise fragments to whole structural motifs ( 8, 31–39). The prediction methods result from various coarse-grained levels ( 23–30), such as iFoldRNA ( 27), SimRNA ( 28, 29), and IsRNA ( 30), have the ability to predict RNA structures and folding kinetics, but the accuracy of the predictions can be limited by the large conformational space for some RNAs. RNA 3D structure prediction ( 17–39), on the other hand, has been developed for decades to help in understanding RNA structure-function relationships, as well as to promote the rational design of RNA-based molecular systems. Combined with a novel energy function for the positioning of stems and loops, the model can predict RNA 3D structures. Ernwin ( 16), a coarse-grained helix-centered model as another example, explores global arrangements of helices and loops within RNA structures. For example, guided by the knowledge-based statistical potentials for bending and torsional degrees of freedom of the internal loop and radius of gyration, graph theory-based tool (RAG) ( 14, 15) can efficiently sample the global helical topologies (as represented by graphs) in 3D space. Conformational analysis based on TOPRNA ( 6) and MC-sym ( 7, 8) showed that RNA global conformation is largely defined by topological constraints of RNA secondary structure while the electrostatics, intra- and inter-loop and other interactions select specific conformations from the accessible conformational ensemble.ĭifferent approaches have been developed to investigate the impact of RNA 2D structural constraint on 3D conformations. Stochastic dynamics simulations and small-angle X-ray scattering experiments showed that the HJH junction topology can further significantly reduce the conformational space and influence the preferred location and orientation of the adjoining helices. studied two helices joined by flexible single- or double-stranded polyethylene glycol tethers ( 5). For the helix-junction-helix (HJH) motif, Chu et. performed a grid search for all the potential conformers for a dinucleotide, and found that hard sphere steric exclusion and bond connectivity can restrict torsion angles in nucleic acids to <5% of all the possible conformations ( 4). Understanding the degree to which RNA structural topology restricts RNA 3D conformational space (i.e. topological constraints) can improve the accuracy of structure prediction as well as our understanding for RNA folding principles.Ĭompared with the protein backbone, RNA contains more rotatable bonds per residue, contributing to the substantial conformational flexibility. Different RNA 2D structural motifs show different linkages between helices.
Chain (bond) connectivity, excluded volume, and the linkage between the different helices, play an essential role in shaping the RNA conformational space and the global topology of the native structure ( 4–16).
Most RNAs fold in a hierarchical pathway, with the folding of secondary structures typically preceding the formation of tertiary interactions ( 1–3). This approach can be further combined with structure probing methods to expand the capability of computational prediction for large RNA folds. Furthermore, based on the topological constraints encoded in the 2D structure and the 3D templates, we develop a 3D structure prediction approach. Moreover, the analysis indicates that (cross-linked) tertiary contacts can cause much stronger topological constraints on RNA global fold than non-cross-linked base pairs. The result shows that a viable conformational space is predominantly determined by the motif type, helix size, and loop size, indicating a strong topological coupling between helices and loops in RNA tertiary motifs. We quantitatively analyze the topological constraints on RNA 3D conformational space, in particular, on the distribution of helix orientations, for pseudoknots and loop-loop kissing structures. The linkage between the helices plays an essential role in determining the structural topology, which restricts RNA local and global folds, especially for RNA tertiary structures involving cross-linked base pairs. An RNA global fold can be described at the level of helix orientations and relatively flexible loop conformations that connect the helices.