ArticleJournal of biomolecular NMR2013
Combining NMR and small angle X-ray and neutron scattering in the structural analysis of a ternary protein-RNA complex.
Article in Journal of biomolecular NMR, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 52 citations in OpenAlex.
- Article
- A novel experimental approach for nanostructure analysis: simultaneous small-angle X-ray and neutron scattering.Journal of applied crystallography · 2020Article
- Evolving SAXS versatility: solution X-ray scattering for macromolecular architecture, functional landscapes, and integrative structural biology.Current opinion in structural biology · 2019Review
- Review
- Small-Angle Scattering as a Structural Probe for Nucleic Acid Nanoparticles (NANPs) in a Dynamic Solution Environment.Nanomaterials (Basel, Switzerland) · 2019Review
- Size-exclusion chromatography small-angle X-ray scattering of water soluble proteins on a laboratory instrument.Journal of applied crystallography · 2018Article
- The role of small-angle scattering in structure-based screening applications.Biophysical reviews · 2018Review
- HnRNP A1 Alters the Structure of a Conserved Enterovirus IRES Domain to Stimulate Viral Translation.Journal of molecular biology · 2017Article
- The First Crystal Structure of the UP1 Domain of hnRNP A1 Bound to RNA Reveals a New Look for an Old RNA Binding Protein.Journal of molecular biology · 2015Article
- Efficient segmental isotope labeling of multi-domain proteins using Sortase A.Journal of biomolecular NMR · 2015Article
- Emerging applications of small angle solution scattering in structural biology.Protein science : a publication of the Protein Society · 2015Review
- Small-angle X-ray scattering: a bridge between RNA secondary structures and three-dimensional topological structures.Current opinion in structural biology · 2015Review
- Methods for SAXS-based structure determination of biomolecular complexes.Advanced materials (Deerfield Beach, Fla.) · 2014Article
- Article
- The dynamic duo: combining NMR and small angle scattering in structural biology.Protein science : a publication of the Protein Society · 2014Review
- Protein modeling: what happened to the "protein structure gap"?Structure (London, England : 1993) · 2013Review
- NMR studies on protein-nucleic acid interaction.Journal of biomolecular NMR · 2013Article
- Chemical shift-based methods in NMR structure determination.Progress in nuclear magnetic resonance spectroscopyReview
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Authors and funding
5 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Many processes in the regulation of gene expression and signaling involve the formation of protein complexes involving multi-domain proteins. Individual domains that mediate protein-protein and protein-nucleic acid interactions are typically connected by flexible linkers, which contribute to conformational dynamics and enable the formation of complexes with distinct binding partners. Solution techniques are therefore required for structural analysis and to characterize potential conformational dynamics. Nuclear magnetic resonance spectroscopy (NMR) provides such information but often only sparse data are obtained with increasing molecular weight of the complexes. It is therefore beneficial to combine NMR data with additional structural restraints from complementary solution techniques. Small angle X-ray/neutron scattering (SAXS/SANS) data can be efficiently combined with NMR-derived information, either for validation or by providing additional restraints for structural analysis. Here, we show that the combination of SAXS and SANS data can help to refine structural models obtained from data-driven docking using HADDOCK based on sparse NMR data. The approach is demonstrated with the ternary protein-protein-RNA complex involving two RNA recognition motif (RRM) domains of Sex-lethal, the N-terminal cold shock domain of Upstream-to-N-Ras, and msl-2 mRNA. Based on chemical shift perturbations we have mapped protein-protein and protein-RNA interfaces and complemented this NMR-derived information with SAXS data, as well as SANS measurements on subunit-selectively deuterated samples of the ternary complex. Our results show that, while the use of SAXS data is beneficial, the additional combination with contrast variation in SANS data resolves remaining ambiguities and improves the docking based on chemical shift perturbations of the ternary protein-RNA complex.
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