RRM
2006
Rustbelt RNA Meeting
RRM
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Talk abstracts
Abstract:
An understanding of structural dynamics is essential to the full characterization of any biomolecule, but is especially relevant with respect to RNA for which dynamics is used in myriad ways to achieve functional complexity that would otherwise be inaccessible based on a rigid framework composed of only four chemically similar nucleotides. Due to experimental difficulties in resolving the manifold of motional modes that pervade RNA structures, their dynamical properties remain poorly understood. Solution NMR is one of the most powerful tools for the characterization of structural dynamics, as it provides atomic level detail on a variety of timescales.
Spin relaxation measurements can provide information on motions occurring at ps to ns timescales. This includes bond librations, local base and sugar fluctuations, and global movements of helical domains. Traditionally, spin relaxation data is interpreted using to the Model Free formalism. At the crux of this formalism is the assumption that internal motions are not correlated to overall rotational diffusion. Owing to their extended architecture and prevalence of motions occurring at timescales approaching overall rotational diffusion, this approximation often breaks down for RNA often rendering interpretation of relaxation data intractable. It was recently shown that a domain elongation strategy can be used to eliminate couplings between internal motions and overall diffusion (Zhang et al., Science (2006) 311, 653-656). Using N-15 relaxation data measured in Watson-Crick residues, diffusion limited inter-domain motions were observed in the transactivation response element (TAR) from HIV-1 that evade detection in non-elongated constructs.
Here we have used domain-elongation in conjunction with C-13 relaxation measurements in both sugar and base moieties to characterize motional modes inaccessible by N-15 relaxation data. Model free analysis of these results using spectral density functions that account for asymmetric CSAs and anisotropic tumbling (i) reaffirm the existence of domain motions occurring at nanosecond diffusion limited timescales and (ii) reveal extremely large variations in the amplitude of local motions with unprecedented degrees of mobility observed for bulge residues that act as the hinge site for domain motions. The site-specific dynamical parameters are quantitatively interpreted in terms of TAR’s ability to adopt different conformations following adaptive recognition.
References:
Zhang et al., Science (2006) 311, 653-656
Keywords: NMR Relaxation, Dynamics, ModelFree
