Biomedical Engineering Reference
In-Depth Information
conformations of TAR, further supporting that adaptive recognition may
proceed via 'conformational selection' [Figure 9.5(D)]. Comparison of the
HIV-1 and HIV-2 TAR dynamic ensembles revealed that reducing the length
of the bulge leads to a significant reduction in local motions of the A22-U40
junctional base pair and bulge residues U23 and U25, and this ordering likely
drives the reduction in the amplitude of inter-helical motions. The ensemble
revealed that the WC base pairs within A-form helices adopt a stable geometry
consistent with an idealised A-form helix structure.
More recently, the RDC-derived TAR dynamics ensemble was subjected to
computational screening.
15
This provided one avenue for overcoming the
difficulty in computationally modeling changes in RNA structure that take
place on small molecule binding and resulted in the de novo discovery of six
small molecules that bind TAR, one of which inhibited HIV replication in T-
cell lines in vivo with an IC
50
of y20 mM.
15
Thus, RDC studies of RNA
dynamics are already being translated into important biomedical applications.
RDCs have also been used to characterise the dynamic and structural
characteristics of highly flexible single-stranded RNA. By combining spin
relaxation measurements and MD simulations, Eichhorn and co-workers were
able to show that the 12-nt adenine-rich single-stranded tail derived from the
prequeuosine riboswitch maintained a high degree of order in the polyadenine
core, despite a high level of internal dynamics. RDCs fit extremely well to an
A-form helix, suggesting rapid exchange between an isotropically unfolded and
stacked, A-form-like conformation.
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These studies suggest that RDCs may
provide the much-needed experimental parameters needed to characterise the
poorly understood conformation of highly disordered single-stranded RNA—
the RNA equivalent of intrinsically disordered proteins.
9.7 Summary and Future Perspectives
Methods for measuring and interpreting RDCs in terms of RNA dynamics
have matured significantly over the past five years and can now be applied
broadly to study the dynamic properties of RNA structure. There are
nevertheless still some key areas that will require further developments in the
future. First, robust approaches for varying RNA alignment need to be
developed in order to extract the full dynamics information contained within
RDCs. Second, more practical approaches need to be developed to measure
RDCs of the sugar and phosphodiester backbone. Third, the application of
RDC dispersion, as implemented for proteins,
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should enable the
characterisation of transient structures of nucleic acids and open an entirely
new direction of RDC-driven dynamics studies. Finally, methods must
continue to be devised to combine RDCs with additional experimental
measurements and computational techniques—only then will it be possible to
unravel the dazzling complexity of RNA dynamics.
Thus far, RDC studies of RNA dynamics have mostly focused on model
systems. This has proven to be quite fruitful, resulting in the discovery ofgeneral
