Dataset Information

A general method for constructing atomic-resolution RNA ensembles using NMR residual dipolar couplings: the basis for interhelical motions revealed.

ABSTRACT: 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 ?s 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.

SUBMITTER: Salmon L

PROVIDER: S-EPMC3676943 | biostudies-literature | 2013 Apr

REPOSITORIES: biostudies-literature

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A general method for constructing atomic-resolution RNA ensembles using NMR residual dipolar couplings: the basis for interhelical motions revealed.

Salmon Loïc L Bascom Gavin G Andricioaei Ioan I Al-Hashimi Hashim M HM

Journal of the American Chemical Society 20130328 14

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 qu ...[more]

PMID: 23473378

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Project description:A growing number of studies employ time-averaged experimental data to determine dynamic ensembles of biomolecules. While it is well-known that different ensembles can satisfy experimental data to within error, the extent and nature of these degeneracies, and their impact on the accuracy of the ensemble determination remains poorly understood. Here, we use simulations and a recently introduced metric for assessing ensemble similarity to explore degeneracies in determining ensembles using NMR residual dipolar couplings (RDCs) with specific application to A-form helices in RNA. Various target ensembles were constructed representing different domain-domain orientational distributions that are confined to a topologically restricted (<10%) conformational space. Five independent sets of ensemble averaged RDCs were then computed for each target ensemble and a "sample and select" scheme used to identify degenerate ensembles that satisfy RDCs to within experimental uncertainty. We find that ensembles with different ensemble sizes and that can differ significantly from the target ensemble (by as much as ∑Ω ∼ 0.4 where ∑Ω varies between 0 and 1 for maximum and minimum ensemble similarity, respectively) can satisfy the ensemble averaged RDCs. These deviations increase with the number of unique conformers and breadth of the target distribution, and result in significant uncertainty in determining conformational entropy (as large as 5 kcal/mol at T = 298 K). Nevertheless, the RDC-degenerate ensembles are biased toward populated regions of the target ensemble, and capture other essential features of the distribution, including the shape. Our results identify ensemble size as a major source of uncertainty in determining ensembles and suggest that NMR interactions such as RDCs and spin relaxation, on their own, do not carry the necessary information needed to determine conformational entropy at a useful level of precision. The framework introduced here provides a general approach for exploring degeneracies in ensemble determination for different types of experimental data.

Dataset Information

A general method for constructing atomic-resolution RNA ensembles using NMR residual dipolar couplings: the basis for interhelical motions revealed.

Publications

A general method for constructing atomic-resolution RNA ensembles using NMR residual dipolar couplings: the basis for interhelical motions revealed.

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