RNA structure refinement using NMR solvent accessibility data

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

doi:10.1038/s41598-017-05821-z

Abstract

NMR spectroscopy is a powerful technique to study ribonucleic acids (RNAs) which are key players in a plethora of cellular processes. Although the NMR toolbox for structural studies of RNAs expanded during the last decades, they often remain challenging. Here, we show that solvent paramagnetic relaxation enhancements (sPRE) induced by the soluble, paramagnetic compound Gd(DTPA-BMA) provide a quantitative measure for RNA solvent accessibility and encode distance-to-surface information that correlates well with RNA structure and improves accuracy and convergence of RNA structure determination. Moreover, we show that sPRE data can be easily obtained for RNAs with any isotope labeling scheme and is advantageous regarding sample preparation, stability and recovery. sPRE data show a large dynamic range and reflect the global fold of the RNA suggesting that they are well suited to identify interaction surfaces, to score structural models and as restraints in RNA structure determination.

Highlights

In the last decades, ribonucleic acids (RNAs) have been found to be key regulators for numerous important cellular processes including transcription, translation, splicing, cell differentiation as well as cell death and proliferation[1]
We show that solvent paramagnetic relaxation enhancements (sPRE) data are efficient NMR observables to probe RNA structure. sPRE data obtained with the paramagnetic compound Gd(DTPA-BMA) yield quantitative information of solvent accessibility as they correlate well with RNA structure, provide structural information for both buried and surface-exposed atoms and can be used as restraints to drive molecular dynamics-based structure determination of RNAs
Since sPRE data reflect the global fold of a RNA they are well suited to identify tertiary contacts or map interaction surfaces with other molecules[32], for example, in RNA-protein complexes

Summary

Introduction

Ribonucleic acids (RNAs) have been found to be key regulators for numerous important cellular processes including transcription, translation, splicing, cell differentiation as well as cell death and proliferation[1]. The RNA backbone is defined by several torsion angles, requiring a large set of restraints to obtain an accurate structural model. To overcome these limitations, different labeling strategies, including for example specific or uniformly 13C- and/or 15N-labeling and segmental labelling of RNAs were developed to reduce spectral complexity and signal overlap[9,10,11,12,13,14,15,16,17,18,19,20,21,22]. SPRE data are obtained by titrating the RNA sample with Gd(DTPA-BMA), a soluble, well-characterized Gd3+ chelating paramagnetic contrast agent that was originally developed for MRI imaging[31, 36]

Methods

Results

Conclusion