title: The solution structural ensembles of RNA kink-turn motifs and their protein complexes.
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.
authors.affiliation: Department of Biochemistry, Stanford University, Stanford, California, USA.
authors.forename: Xuesong
authors.initials: X
authors.lastname: Shi
authors.affiliation: Nucleic Acid Structure Research Group, School of Life Sciences, University of Dundee, Dundee, UK.
authors.forename: Lin
authors.initials: L
authors.lastname: Huang
authors.affiliation: Nucleic Acid Structure Research Group, School of Life Sciences, University of Dundee, Dundee, UK.
authors.forename: David M J
authors.initials: DM
authors.lastname: Lilley
authors.affiliation: Department of Biochemistry, Stanford University, Stanford, California, USA.|ChEM-H, Stanford University, Stanford, California, USA.
authors.forename: Pehr B
authors.initials: PB
authors.lastname: Harbury
authors.affiliation: Department of Biochemistry, Stanford University, Stanford, California, USA.|ChEM-H, Stanford University, Stanford, California, USA.|Department of Chemistry, Stanford University, Stanford, California, USA.|Department of Chemical Engineering, Stanford University, Stanford, California, USA.
authors.forename: Daniel
authors.initials: D
authors.lastname: Herschlag
mesh_terms: D001483:Base Sequence; D007368:Interferometry; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs; D012313:RNA / Q000737:chemistry; D012542:Scattering, Radiation; D014965:X-Rays
chemical_list: D012313:RNA