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Schlundt, A. ; Tants, J.-N. ; Sattler, M.

Integrated structural biology to unravel molecular mechanisms of protein-RNA recognition.

Methods 118, 119-136 (2017)
Postprint DOI PMC
Open Access Green
Recent advances in RNA sequencing technologies have greatly expanded our knowledge of the RNA landscape in cells, often with spatiotemporal resolution. These techniques identified many new (often non-coding) RNA molecules. Large-scale studies have also discovered novel RNA binding proteins (RBPs), which exhibit single or multiple RNA binding domains (RBDs) for recognition of specific sequence or structured motifs in RNA. Starting from these large-scale approaches it is crucial to unravel the molecular principles of protein-RNA recognition in ribonucleoprotein complexes (RNPs) to understand the underlying mechanisms of gene regulation. Structural biology and biophysical studies at highest possible resolution are key to elucidate molecular mechanisms of RNA recognition by RBPs and how conformational dynamics, weak interactions and cooperative binding contribute to the formation of specific, context-dependent RNPs. While large compact RNPs can be well studied by X-ray crystallography and cryo-EM, analysis of dynamics and weak interaction necessitates the use of solution methods to capture these properties. Here, we illustrate methods to study the structure and conformational dynamics of protein-RNA complexes in solution starting from the identification of interaction partners in a given RNP. Biophysical and biochemical techniques support the characterization of a protein-RNA complex and identify regions relevant in structural analysis. Nuclear magnetic resonance (NMR) is a powerful tool to gain information on folding, stability and dynamics of RNAs and characterize RNPs in solution. It provides crucial information that is complementary to the static pictures derived from other techniques. NMR can be readily combined with other solution techniques, such as small angle X-ray and/or neutron scattering (SAXS/SANS), electron paramagnetic resonance (EPR), and Förster resonance energy transfer (FRET), which provide information about overall shapes, internal domain arrangements and dynamics. Principles of protein-RNA recognition and current approaches are reviewed and illustrated with recent studies.
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Publication type Article: Journal article
Document type Scientific Article
Keywords Integrated Structural Biology ; Molecular Dynamics ; Multi-domain Proteins ; Nuclear Magnetic Resonance ; Rna-protein Complex ; Small Angle Scattering; Double-stranded-rna; Macromolecular Nmr-spectroscopy; Single-nucleotide Resolution; Nucleic Acid Interactions; Splicing Factor U2af65; Small-angle Scattering; U4/u6.u5 Tri-snrnp; Cryo-em Structure; Vts1p Sam Domain; Messenger-rna
Language
Publication Year 2017
HGF-reported in Year 2017
ISSN (print) / ISBN 1046-2023
e-ISSN 1095-9130
Journal Methods
Quellenangaben Volume: 118, Issue: , Pages: 119-136 Article Number: , Supplement: ,
Publisher Elsevier
Publishing Place Amsterdam [u.a.]
Reviewing status Peer reviewed
Institute(s) Institute of Structural Biology (STB)
POF-Topic(s) 30203 - Molecular Targets and Therapies
Research field(s) Enabling and Novel Technologies
PSP Element(s) G-503000-001
DOI 10.1016/j.ymeth.2017.03.015
WOS ID WOS:000401052800013
Scopus ID 85018292861
PubMed ID 28315749
Erfassungsdatum 2017-03-23
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