Automated 3D RNA Structure Prediction Using the RNAComposer Method for Riboswitches1

Purzycka, Katarzyna J.; Popenda, Mariusz; Szachniuk, Marta; Antczak, Maciej; Łukasiak, Piotr; Błażewicz, Jacek; Adamiak, Ryszard W.

doi:10.1016/bs.mie.2014.10.050

Cited by 41 publications

(43 citation statements)

References 52 publications

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“…The crystals used for the structure determination were soaked with osmium or gold salts, but the structure was finally solved by the molecular replacement method since the very low derivation with these salts did not allow exploiting these data sets by the SAD or SIRAS methods. The molecular replacement was achieved using a model constructed with RNAcomposer (31) and the data from the crystal soaked with the osmium salt. The native structure was obtained by phasing the non-isomorphous native data (from crystals obtained in an earlier stage of the project) with the Os model.…”

Section: Resultsmentioning

confidence: 99%

“…Data sets were collected from the native crystals and crystals soaked for several hours either with osmium hexamine (2 mM) or with gold (KAu[III]Cl 4 , 10 mM) in a solution containing 40% PEG 1000 prior to flash-freezing. The structure was solved by molecular replacement using PHASER with a model built using RNAcomposer (31) and the Au-derived crystal data set, exploiting the approach described by Robertson et al. (2010) (32).…”

Section: Methodsmentioning

confidence: 99%

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The crystal structure of the 5′ functional domain of the transcription riboregulator 7SK

et al. 2017

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In vertebrates, the 7SK RNA forms the scaffold of a complex, which regulates transcription pausing of RNA-polymerase II. By binding to the HEXIM protein, the complex comprising proteins LARP7 and MePCE captures the positive transcription elongation factor P-TEFb and prevents phosphorylation of pausing factors. The HEXIM-binding site embedded in the 5΄-hairpin of 7SK (HP1) encompasses a short signature sequence, a GAUC repeat framed by single-stranded uridines. The present crystal structure of HP1 shows a remarkably straight helical stack involving several unexpected triples formed at a central region. Surprisingly, two uridines of the signature sequence make triple interactions in the major groove of the (GAUC)2. The third uridine is turned outwards or inward, wedging between the other uridines, thus filling the major groove. A molecular dynamics simulation indicates that these two conformations of the signature sequence represent stable alternatives. Analyses of the interaction with the HEXIM protein confirm the importance of the triple interactions at the signature sequence. Altogether, the present structural analysis of 7SK HP1 highlights an original mechanism of swapping bases, which could represent a possible ‘7SK signature’ and provides new insight into the functional importance of the plasticity of RNA.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

The crystal structure of the 5′ functional domain of the transcription riboregulator 7SK

et al. 2017

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“…The prediction fidelity of RNAComposer depends critically on the accuracy of the RNA secondary structure, used as an input (Popenda et al 2012;Purzycka et al 2015). Therefore, secondary structures predicted in silico using tools integrated in the RNAComposer system were adjusted according to experimental data, if available.…”

Section: Adamiak Groupmentioning

confidence: 99%

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

Miao

Adamiak

Antczak

et al. 2017

RNA

185

209

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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/.

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“…RNAComposer was used for prediction of RNA 3D structural models (http://rnacompo ser.cs.put.poznan.pl/). This is a fully automated RNA structure modeling server that predicts RNA 3D structures based on sequence and secondary structure [61][62][63].…”

Section: Rna Structure Predictionmentioning

confidence: 99%

Retroviral-like determinants and functions required for dimerization of Ty1 retrotransposon RNA

et al. 2019

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During replication of long terminal repeat (LTR)-retrotransposons, their proteins and genome (g) RNA assemble into virus-like particles (VLPs) that are not infectious but functionally related to retroviral virions. Both virions and VLPs contain gRNA in a dimeric form, but contrary to retroviruses, little is known about how gRNA dimerization and packaging occurs in LTR-retrotransposons. The LTR-retrotransposon Ty1 from Saccharomyces cerevisiae is an informative model for studying LTR-retrotransposon and retrovirus replication. Using structural, mutational and functional analyses, we explored dimerization of Ty1 genomic RNA. We provide direct evidence that interactions of self-complementary PAL1 and PAL2 palindromic sequences localized within the 5′UTR are essential for Ty1 gRNA dimer formation. Mutations disrupting PAL1-PAL2 complementarity restricted RNA dimerization in vitro and Ty1 mobility in vivo. Although dimer formation and mobility of these mutants was inhibited, our work suggests that Ty1 RNA can dimerize via alternative contact points. In contrast to previous studies, we cannot confirm a role for PAL3, tRNAiMet as well as recently proposed initial kissing-loop interactions in dimer formation. Our data also supports the critical role of Ty1 Gag in RNA dimerization. Mature Ty1 Gag binds in the proximity of sequences involved in RNA dimerization and tRNAiMet annealing, but the 5′ pseudoknot in Ty1 RNA may constitute a preferred Gag-binding site. Taken together, these results expand our understanding of genome dimerization and packaging strategies utilized by LTR-retroelements.

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Automated 3D RNA Structure Prediction Using the RNAComposer Method for Riboswitches1

Cited by 41 publications

References 52 publications

The crystal structure of the 5′ functional domain of the transcription riboregulator 7SK

The crystal structure of the 5′ functional domain of the transcription riboregulator 7SK

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

Retroviral-like determinants and functions required for dimerization of Ty1 retrotransposon RNA

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