RNA structure refinement using NMR solvent accessibility data

Hartlmüller, Christoph; Günther, Johannes; Wolter, Antje C.; Wöhnert, Jens; Sattler, Michael; Madl, Tobias

doi:10.1038/s41598-017-05821-z

Cited by 27 publications

(33 citation statements)

References 57 publications

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“…They found that the inclusion of sPRE data during structural refinement significantly enhanced the quality of the resulting NMR ensemble. (30) Their findings, along with the results of our benchmarking studies, strongly suggest that experimentally-derived SASA contains sufficient restraining power to infer structural ensembles of RNAs. We envision, therefore, that the SASA-based reweighting approach we utilize in this study will emerge as a simple yet robust strategy for using experimentally-derived SASA data to infer atomistic ensembles.…”

Section: Discussionmentioning

confidence: 51%

Structural Ensembles of Ribonucleic Acids From Solvent Accessibility Data: Application to the S-Adenosylmethionine (SAM)-Responsive Riboswitch

Xie

Frank

2020

Preprint

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Riboswitches are regulatory ribonucleic acid (RNA) elements that act as ligand-dependent conformational switches. In the apo form, the aptamer domain, the region of a riboswitch that binds to its cognate ligand, is dynamic, thus requiring an ensemble-representation of its structure. Analysis of such ensembles can provide molecular insights into the sensing mechanism and capabilities of riboswitches. Here, as a proof-of-concept, we constructed a pair of atomistic ensembles of the well-studied S-adenosylmethionine (SAM)responsive riboswitch in the absence (-SAM) and presence (+SAM) of SAM. To achieve this, we first generated a large conformational pool and then reweighted conformers in the pool using solvent accessible surface area (SASA) data derived from recently reported light-activated structural examination of RNA (LASER) reactivities, measured in the -SAM and +SAM states of the riboswitch. The di↵erences in the resulting -SAM and +SAM ensembles are consistent with a SAM-dependent reshaping of the free landscape of the riboswitch. Interestingly, within the -SAM ensemble, we identified a conformer that harbors a hidden binding pocket, which was discovered using ensemble docking. The method we have applied to the SAM riboswitch is general, and could, therefore, be used to construct atomistic ensembles for other riboswitches, and more broadly, other classes of structured RNAs.

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Section: Discussionmentioning

confidence: 51%

Structural Ensembles of Ribonucleic Acids From Solvent Accessibility Data: Application to the S-Adenosylmethionine (SAM)-Responsive Riboswitch

Xie

Frank

2020

Preprint

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“…Removing the salt increases the strength of the interactions between the nanodiscs and G‐quadruplexes and consequently increases the PRE effect (Figure ). This interesting result suggests that DOTA functionalized nanodiscs could potentially be used to structurally and dynamically probe surfaces of biomolecules similar to previously applied solvent PRE techniques …”

Section: Figurementioning

confidence: 66%

Metal‐Chelated Polymer Nanodiscs for NMR Studies

et al. 2019

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Paramagnetic relaxation enhancement (PRE) is commonly used to speed up spin lattice relaxation time (T1) for rapid data acquisition in NMR structural studies. Consequently, there is significant interest in novel paramagnetic labels for enhanced NMR studies on biomolecules. Herein, we report the synthesis and characterization of a modified poly(styrene‐co‐maleic acid) polymer which forms nanodiscs while showing the ability to chelate metal ions. Cu2+‐chelated nanodiscs are demonstrated to reduce the T1 of protons for both polymer and lipid‐nanodisc components. The chelated nanodiscs also decrease the proton T1 values for a water‐soluble DNA G‐quadruplex. These results suggest that polymer nanodiscs functionalized with paramagnetic tags can be used to speed‐up data acquisition from lipid bilayer samples and also to provide structural information from water‐soluble biomolecules.

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“…The sPRE restraints afford better refined RNA tetraloop structure The 14-mer RNA tetraloop hairpin has often been used as a model system (Borkar et al 2016;Duchardt and Schwalbe 2005;Hartlmuller et al 2017). For its short length and simple secondary structure, even with only the hydrogen-bonding and knowledge-based restraints for the A-form RNA hairpin, the 14-mer RNA structure can already be calculated to a root-mean-square (RMS) deviation of 1.59 Å for all heavy atoms ( Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Since the secondary and tertiary structures of an RNA molecule are often intertwined, the incorporation of sPRE restraints is particularly important for RNAs with complex topologies. Note that the previous use of sPRE data for RNA structure refinement (Hartlmuller et al 2017) was demonstrated with two relatively simple RNA structures, and their secondary structures can be readily predicted. In comparison, the secondary structure prediction does not work for the pseudoknot and four-way junction tRNA, the two RNA systems used in Fig.…”

Section: Discussionmentioning

confidence: 99%

Refining RNA solution structures with the integrative use of label-free paramagnetic relaxation enhancement NMR

Gong

Yang

et al. 2019

Biophys Rep

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NMR structure calculation is inherently integrative, and can incorporate new experimental data as restraints. As RNAs have lower proton densities and are more conformational heterogenous than proteins, the refinement of RNA structures can benefit from additional types of restraints. Paramagnetic relaxation enhancement (PRE) provides distance information between a paramagnetic probe and protein or RNA nuclei. However, covalent conjugation of a paramagnetic probe is difficult for RNAs, thus limiting the use of PRE NMR for RNA structure characterization. Here, we show that the solvent PRE can be accurately measured for RNA labile imino protons, simply with the addition of an inert paramagnetic cosolute. Demonstrated on three RNAs that have increasingly complex topologies, we show that the incorporation of the solvent PRE restraints can significantly improve the precision and accuracy of RNA structures. Importantly, the solvent PRE data can be collected for RNAs without isotope enrichment. Thus, the solvent PRE method can work integratively with other biophysical techniques for better characterization of RNA structures.

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RNA structure refinement using NMR solvent accessibility data

Cited by 27 publications

References 57 publications

Structural Ensembles of Ribonucleic Acids From Solvent Accessibility Data: Application to the S-Adenosylmethionine (SAM)-Responsive Riboswitch

Structural Ensembles of Ribonucleic Acids From Solvent Accessibility Data: Application to the S-Adenosylmethionine (SAM)-Responsive Riboswitch

Metal‐Chelated Polymer Nanodiscs for NMR Studies

Refining RNA solution structures with the integrative use of label-free paramagnetic relaxation enhancement NMR

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