A general method for constructing atomic-resolution RNA ensembles using NMR residual dipolar couplings: the basis for interhelical motions revealed.
Journal Article (Journal Article)
The ability to modulate alignment and measure multiple independent sets of NMR residual dipolar couplings (RDCs) has made it possible to characterize internal motions in proteins at atomic resolution and with time scale sensitivity ranging from picoseconds up to milliseconds. The application of such methods to the study of RNA dynamics, however, remains fundamentally limited by the inability to modulate alignment and by strong couplings between internal and overall motions that complicate the quantitative interpretation of RDCs. Here, we address this problem by showing that RNA alignment can be generally modulated, in a controlled manner, by variable elongation of A-form helices and that the information contained within the measured RDCs can be extracted even in the presence of strong couplings between motions and overall alignment via structure-based prediction of alignment. Using this approach, four RDC data sets, and a broad conformational pool obtained from a 8.2 μs molecular dynamics simulation, we successfully construct and validate an atomic resolution ensemble of human immunodeficiency virus type I transactivation response element RNA. This ensemble reveals local motions in and around the bulge involving changes in stacking and hydrogen-bonding interactions, which are undetectable by traditional spin relaxation and drive global changes in interhelical orientation. This new approach broadens the scope of using RDCs in characterizing the dynamics of nucleic acids.
Full Text
Duke Authors
Cited Authors
- Salmon, L; Bascom, G; Andricioaei, I; Al-Hashimi, HM
Published Date
- April 10, 2013
Published In
Volume / Issue
- 135 / 14
Start / End Page
- 5457 - 5466
PubMed ID
- 23473378
Pubmed Central ID
- PMC3676943
Electronic International Standard Serial Number (EISSN)
- 1520-5126
Digital Object Identifier (DOI)
- 10.1021/ja400920w
Language
- eng
Conference Location
- United States