Combining NMR and EPR to Determine Structures of Large RNAs and Protein–RNA Complexes in Solution

Duss, Olivier; Yulikov, Maxim; Allain, Frédéric H.‐T.; Jeschke, Gunnar

doi:10.1016/bs.mie.2015.02.005

Cited by 40 publications

(35 citation statements)

References 132 publications

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“…Furthermore, the RNA-binding orientation with respect to an RNA-binding protein can be determined (Mackereth et al, 2011), and protein-RNA distances can be obtained and used for structure calculation and validation (Allen, Varani, & Varani, 2001). Another chapter in this book describes the labeling of RNA and its use in EPR measurements to derive restraints for structure calculations (Duss, Yulikov, Allain, & Jeschke, 2015).…”

Section: Spin Labeling Of Protein-rna Complexesmentioning

confidence: 99%

Structural Analysis of Protein–RNA Complexes in Solution Using NMR Paramagnetic Relaxation Enhancements

Hennig

Warner

Simon

et al. 2015

Methods in Enzymology

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Section: Spin Labeling Of Protein-rna Complexesmentioning

confidence: 99%

Structural Analysis of Protein–RNA Complexes in Solution Using NMR Paramagnetic Relaxation Enhancements

Hennig

Warner

Simon

et al. 2015

Methods in Enzymology

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“…The structure of the 70 kDa protein/RNA complex RmsE/RmsZ was modelled with a CYANA-based protocol [58] from 4664 intramolecular NOE restraints for the protein, ∼850 intramolecular NOE restraints for the RNA, and 21 distance distribution restraints between RNA stem loops [59]. Underlying assumptions and technical issues have been discussed in detail [60]. The structure consists of three rigid protein domains and a 72 nucleotide long non-coding RNA that binds to the protein via four stem loops.…”

Section: Integrative Modellingmentioning

confidence: 99%

The contribution of modern EPR to structural biology

Jeschke

2018

Emerging Topics in Life Sciences

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133

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Electron paramagnetic resonance (EPR) spectroscopy combined with site-directed spin labelling is applicable to biomolecules and their complexes irrespective of system size and in a broad range of environments. Neither short-range nor long-range order is required to obtain structural restraints on accessibility of sites to water or oxygen, on secondary structure, and on distances between sites. Many of the experiments characterize a static ensemble obtained by shock-freezing. Compared with characterizing the dynamic ensemble at ambient temperature, analysis is simplified and information loss due to overlapping timescales of measurement and system dynamics is avoided. The necessity for labelling leads to sparse restraint sets that require integration with data from other methodologies for building models. The double electron-electron resonance experiment provides distance distributions in the nanometre range that carry information not only on the mean conformation but also on the width of the native ensemble. The distribution widths are often inconsistent with Anfinsen's concept that a sequence encodes a single native conformation defined at atomic resolution under physiological conditions.

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“…However, these methodologies are often challenged by the size of the RNA to be studied, or the inherent problems in the preparation of stable ribonucleoprotein complexes (Duss et al 2015).…”

Section: Introductionmentioning

confidence: 99%

Fingerprinting the junctions of RNA structure by an open-paddlewheel diruthenium compound

Lozano

Jiménez‐Aparicio

Herrero

et al. 2016

RNA

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RNA function is determined by its structural organization. The RNA structure consists of the combination of distinct secondary structure motifs connected by junctions that play an essential role in RNA folding. Selective 2 ′ -hydroxyl acylation analyzed by primer extension (SHAPE) probing is an established methodology to analyze the secondary structure of long RNA molecules in solution, which provides accurate data about unpaired nucleotides. However, the residues located at the junctions of RNA structures usually remain undetected. Here we report an RNA probing method based on the use of a novel open-paddlewheel diruthenium (OPW-Ru) compound [Ru 2 Cl 2 (µ-DPhF) 3 (DMSO)] (DPhF = N,N ′ -diphenylformamidinate). This compound has four potential coordination sites in a singular disposition to establish covalent bonds with substrates. As a proof of concept, we have analyzed the reactivity of OPW-Ru toward RNA using two viral internal ribosome entry site (IRES) elements whose function depends on the structural organization of the molecule. Our study suggests that the compound OPW-Ru preferentially attacks at positions located one or two nucleotides away from junctions or bulges of the RNA structure. The OPW-Ru fingerprinting data differ from that obtained by other chemical reagents and provides new information about RNA structure features.

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Combining NMR and EPR to Determine Structures of Large RNAs and Protein–RNA Complexes in Solution

Cited by 40 publications

References 132 publications

Structural Analysis of Protein–RNA Complexes in Solution Using NMR Paramagnetic Relaxation Enhancements

Structural Analysis of Protein–RNA Complexes in Solution Using NMR Paramagnetic Relaxation Enhancements

The contribution of modern EPR to structural biology

Fingerprinting the junctions of RNA structure by an open-paddlewheel diruthenium compound

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