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Nat Chem Biol. 2016 Mar;12(3):146-52. doi: 10.1038/nchembio.1997. Epub 2016 Jan 4.

The solution structural ensembles of RNA kink-turn motifs and their protein complexes.

Author information

1
Department of Biochemistry, Stanford University, Stanford, California, USA.
2
Nucleic Acid Structure Research Group, School of Life Sciences, University of Dundee, Dundee, UK.
3
ChEM-H, Stanford University, Stanford, California, USA.
4
Department of Chemistry, Stanford University, Stanford, California, USA.
5
Department of Chemical Engineering, Stanford University, Stanford, California, USA.

Abstract

With the growing number of crystal structures of RNA and RNA-protein complexes, a critical next step is understanding the dynamic solution behavior of these entities in terms of conformational ensembles and energy landscapes. To this end, we have used X-ray scattering interferometry (XSI) to probe the ubiquitous RNA kink-turn motif and its complexes with the canonical kink-turn binding protein L7Ae. XSI revealed that the folded kink-turn is best described as a restricted conformational ensemble. The ions present in solution alter the nature of this ensemble, and protein binding can perturb the kink-turn ensemble without collapsing it to a unique state. This study demonstrates how XSI can reveal structural and ensemble properties of RNAs and RNA-protein complexes and uncovers the behavior of an important RNA-protein motif. This type of information will be necessary to understand, predict and engineer the behavior and function of RNAs and their protein complexes.

PMID:
26727239
PMCID:
PMC4755865
DOI:
10.1038/nchembio.1997
[Indexed for MEDLINE]
Free PMC Article

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