RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme

Abstract

RNA-Puzzles is a collective experiment in blind 3D RNA structure prediction. We report here a third round of RNA-Puzzles. Five puzzles, 4, 8, 12, 13, 14, all structures of riboswitch aptamers and puzzle 7, a ribozyme structure, are included in this round of the experiment. The riboswitch structures include biological binding sites for small molecules (S-adenosyl methionine, cyclic diadenosine monophosphate, 5-amino 4-imidazole carboxamide riboside 5 ′ -triphosphate, glutamine) and proteins (YbxF), and one set describes large conformational changes between ligand-free and ligand-bound states. The Varkud satellite ribozyme is the most recently solved structure of a known large ribozyme. All puzzles have established biological functions and require structural understanding to appreciate their molecular mechanisms. Through the use of fast-track experimental data, including multidimensional chemical mapping, and accurate prediction of RNA secondary structure, a large portion of the contacts in 3D have been predicted correctly leading to similar topologies for the top ranking predictions. Template-based and homologyderived predictions could predict structures to particularly high accuracies. However, achieving biological insights from de novo prediction of RNA 3D structures still depends on the size and complexity of the RNA. Blind computational predictions of RNA structures already appear to provide useful structural information in many cases. Similar to the previous RNA-Puzzles Round II experiment, the prediction of non-Watson-Crick interactions and the observed high atomic clash scores reveal a notable need for an algorithm of improvement. All prediction models and assessment results are available at http://ahsoka.ustrasbg.fr/rnapuzzles/.

RNA structure inference through chemical mapping after accidental or intentional mutations

“…After testing the mechanism of the M2-seq signal, we evaluated the general applicability of the method across diverse structured RNA molecules. We chose several RNAs that have challenged prior structure modeling efforts: the P4-P6 RNA, the catalytic domain of RNase P, and the thiamine pyrophosphate (TPP) riboswitch aptamer, which were the three test cases for an earlier RING-MaP study (20,21); and the GIR1 ribozyme, riboswitch aptamers for adenosylcobalamin (AdoCbl) and cyclic-di-AMP, and an Xrn1-exonuclease-resistant domain from the Zika virus, four targets of the RNA-puzzle community-wide trials whose secondary structures were particularly challenging for most groups and algorithms to model (Tables S1 and S2) (12,13,24). M2-seq gave visually apparent signals for helices in all of these cases (Fig.…”

“…For example, models of the 9-kb HIV-1 RNA genome have been repeatedly revised with updates to the selective 2′-OH acylation by primer extension (SHAPE) protocol, data processing, and computational assumptions (2,(9)(10)(11), and the majority of this RNA's helices remain uncertain. Even for small RNA domains, SHAPE and dimethyl sulfate (DMS) (methylation of N1 and N3 atoms at A and C) have produced misleading secondary structures for ribosomal domains and blind modeling challenges that have been falsified through crystallography or mutagenesis (3,7,12,13). In alternative approaches based on photoactivated cross-linkers, many helix detections appear to be false positives, based on ribosome data in vitro and in vivo (14,15).…”

F-RAG: Generating Atomic Coordinates from RNA Graphs by Fragment Assembly

“…al. in [54], as also used in the RNA-Puzzles exercise [59, 60, 61]: Specificity (PPV), Sensitivity (STY), Interaction Network Fidelity (INF), and Deformation Index (DI). In brief, PPV is the percentage of base pairing and stacking interactions in the predicted atomic model that are found in the reference structure; STY is the percentage of interactions in the reference structure that are found in the predicted atomic model.…”

Surprising Sequence Effects on GU Closure of Symmetric 2 × 2 Nucleotide RNA Internal Loops

“…16-23 Accurate modeling of the intermolecular interactions important for RNA folding would hasten determination of both secondary and 3D structure, but such modeling is still challenging. 24-28 RNAPuzzles, a blind competition to predict RNA 3D structure, demonstrated the importance of accurate RNA secondary structure prediction for 3D prediction and the need for improvements, especially in modeling of noncanonical motifs. 25, 28 Thus, detailed structural analysis of RNA loops with idiosyncratic stabilities can provide insight into structure-energetics relationships in RNA and contribute to development of de novo prediction rules.…”