Visualizing spatially correlated dynamics that directs RNA conformational transitions.

Visualizing spatially correlated dynamics that directs RNA conformational transitions. Research Abstract Details 

Research Abstract Table of Contents

Jump to the:

Visualizing spatially correlated dynamics that directs RNA conformational transitions. Abstract Text:

Qi Zhang,Andrew C Stelzer,Charles K Fisher,Hashim M Al-Hashimi,Qi Zhang,Andrew C Stelzer,Charles K Fisher,Hashim M Al-Hashimi,Qi Zhang,Andrew C Stelzer,Charles K Fisher,Hashim M Al-Hashimi,

RNAs fold into three-dimensional (3D) structures that subsequently undergo large, functionally important, conformational transitions in response to a variety of cellular signals. RNA structures are believed to encode spatially tuned flexibility that can direct transitions along specific conformational pathways. However, this hypothesis has proved difficult to examine directly because atomic movements in complex biomolecules cannot be visualized in 3D by using current experimental methods. Here we report the successful implementation of a strategy using NMR that has allowed us to visualize, with complete 3D rotational sensitivity, the dynamics between two RNA helices that are linked by a functionally important trinucleotide bulge over timescales extending up to milliseconds. The key to our approach is to anchor NMR frames of reference onto each helix and thereby directly measure their dynamics, one relative to the other, using 'relativistic' sets of residual dipolar couplings (RDCs). Using this approach, we uncovered super-large amplitude helix motions that trace out a surprisingly structured and spatially correlated 3D dynamic trajectory. The two helices twist around their individual axes by approximately 53 degrees and 110 degrees in a highly correlated manner (R = 0.97) while simultaneously (R = 0.81-0.92) bending by about 94 degrees . Remarkably, the 3D dynamic trajectory is dotted at various positions by seven distinct ligand-bound conformations of the RNA. Thus even partly unstructured RNAs can undergo structured dynamics that directs ligand-induced transitions along specific predefined conformational pathways.

Visualizing spatially correlated dynamics that directs RNA conformational transitions. Publishing Authors By Initials

Q Zhang,AC Stelzer,CK Fisher,HM Al-Hashimi,Q Zhang,AC Stelzer,CK Fisher,HM Al-Hashimi,Q Zhang,AC Stelzer,CK Fisher,HM Al-Hashimi,

For similar abstracts research abstracts see: abstracts research

PUBMED ID PMID:

MEDLINE DATE:

Visualizing spatially correlated dynamics that directs RNA conformational transitions. Journal Published:

PUBLICATION TYPE: Journal Article

Journal: Nature

VOLUME: 450

Page Numbers: 1263-7

Journal Abbreviation: Nature

ISSN: 1476-4687

DAY: 20

MONTH: Dec

YEAR: 2007

Visualizing spatially correlated dynamics that directs RNA conformational transitions. Information

Number of References:

LANGUAGE: eng

NlmUniqueID: 410462

Visualizing spatially correlated dynamics that directs RNA conformational transitions. Keywords Mesh Terms:

KEYWORDS:

MESH TERMS:

Chemical & Substance for Abstract: Visualizing spatially correlated dynamics that directs RNA conformational transitions. Information

Substance Name:

Registry Number:

Grant and Affiliation Information for Visualizing spatially correlated dynamics that directs RNA conformational transitions.

AFFILIATION: Department of Chemistry and Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, USA.

Country: England

AGENCY:

GRANT:

ACRONYM:

MEDLINETA: Nature

REFSOURCE:

DATABASENAME:

ACCESSION NUMBER:

Number Hits: 0

Visualizing spatially correlated dynamics that directs RNA conformational transitions Related Publications

• Bilateral hippocampal hyperintensities: a new finding in MR imaging of heat stroke.
• Characterizing complex dynamics in the transactivation response element apical loop and motional correlations with the bulge by NMR, molecular dynamics, and mutagenesis.
• Characterizing the relative orientation and dynamics of RNA A-form helices using NMR residual dipolar couplings.
• Dynamics of large elongated RNA by NMR carbon relaxation.
• Extending the NMR spatial resolution limit for RNA by motional couplings.
• Impact of static and dynamic A-form heterogeneity on the determination of RNA global structural dynamics using NMR residual dipolar couplings.
• In vitro effect of different non-steroidal anti-inflammatory drugs on human polymorphonuclear leukocyte activity measured by luminol-dependent chemiluminescence of the whole blood.
• NMR studies of RNA dynamics and structural plasticity using NMR residual dipolar couplings.
• Probing Na(+)-induced changes in the HIV-1 TAR conformational dynamics using NMR residual dipolar couplings: new insights into the role of counterions and electrostatic interactions in adaptive recognition.
• Probing motions between equivalent RNA domains using magnetic field induced residual dipolar couplings: accounting for correlations between motions and alignment.
• Resolving fast and slow motions in the internal loop containing stem-loop 1 of HIV-1 that are modulated by Mg2+ binding: role in the kissing-duplex structural transition.
• Structural plasticity and Mg2+ binding properties of RNase P P4 from combined analysis of NMR residual dipolar couplings and motionally decoupled spin relaxation.
• Visualizing spatially correlated dynamics that directs RNA conformational transitions.