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

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

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Interferometry
  • Molecular Dynamics Simulation
  • Molecular Sequence Data
  • Nucleic Acid Conformation*
  • Nucleotide Motifs*
  • RNA / chemistry
  • Scattering, Radiation
  • X-Rays

Substances

  • RNA