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

Xuesong Shi (Lead / Corresponding author), Lin Huang, David M. J. Lilley, Pehr B. Harbury (Lead / Corresponding author), Daniel Herschlag (Lead / Corresponding author)

Research output: Contribution to journalArticle

19 Citations (Scopus)
77 Downloads (Pure)

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.

Original languageEnglish
Pages (from-to)146-152
Number of pages7
JournalNature Chemical Biology
Volume12
Issue number3
Early online date4 Jan 2016
DOIs
Publication statusPublished - Mar 2016

Fingerprint

Amino Acid Motifs
Interferometry
RNA
X-Rays
RNA Probes
Nucleotide Motifs
Proteins
Protein Binding
Carrier Proteins
Ions

Keywords

  • Base sequence
  • Interferometry
  • Molecular dynamics simulation
  • Molecular sequence data
  • Nucleic acid conformation
  • Nucleotide motifs
  • RNA
  • Scattering, Radiation
  • X-Rays
  • Journal article
  • Research support, N.I.H., Extramural
  • Research support, Non-U.S. Gov't

Cite this

Shi, Xuesong ; Huang, Lin ; Lilley, David M. J. ; Harbury, Pehr B. ; Herschlag, Daniel. / The solution structural ensembles of RNA kink-turn motifs and their protein complexes. In: Nature Chemical Biology. 2016 ; Vol. 12, No. 3. pp. 146-152.
@article{c9fd8da4b54b405eb312ea0026b53ea5,
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.",
keywords = "Base sequence, Interferometry, Molecular dynamics simulation, Molecular sequence data, Nucleic acid conformation, Nucleotide motifs, RNA, Scattering, Radiation, X-Rays, Journal article, Research support, N.I.H., Extramural, Research support, Non-U.S. Gov't",
author = "Xuesong Shi and Lin Huang and Lilley, {David M. J.} and Harbury, {Pehr B.} and Daniel Herschlag",
year = "2016",
month = "3",
doi = "10.1038/nchembio.1997",
language = "English",
volume = "12",
pages = "146--152",
journal = "Nature Chemical Biology",
issn = "1552-4450",
publisher = "Nature Publishing Group",
number = "3",

}

The solution structural ensembles of RNA kink-turn motifs and their protein complexes. / Shi, Xuesong (Lead / Corresponding author); Huang, Lin; Lilley, David M. J.; Harbury, Pehr B. (Lead / Corresponding author); Herschlag, Daniel (Lead / Corresponding author).

In: Nature Chemical Biology, Vol. 12, No. 3, 03.2016, p. 146-152.

Research output: Contribution to journalArticle

TY - JOUR

T1 - The solution structural ensembles of RNA kink-turn motifs and their protein complexes

AU - Shi, Xuesong

AU - Huang, Lin

AU - Lilley, David M. J.

AU - Harbury, Pehr B.

AU - Herschlag, Daniel

PY - 2016/3

Y1 - 2016/3

N2 - 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.

AB - 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.

KW - Base sequence

KW - Interferometry

KW - Molecular dynamics simulation

KW - Molecular sequence data

KW - Nucleic acid conformation

KW - Nucleotide motifs

KW - RNA

KW - Scattering, Radiation

KW - X-Rays

KW - Journal article

KW - Research support, N.I.H., Extramural

KW - Research support, Non-U.S. Gov't

U2 - 10.1038/nchembio.1997

DO - 10.1038/nchembio.1997

M3 - Article

C2 - 26727239

VL - 12

SP - 146

EP - 152

JO - Nature Chemical Biology

JF - Nature Chemical Biology

SN - 1552-4450

IS - 3

ER -