Biomedical Engineering Reference
In-Depth Information
mentioned above, one case in which this is feasible is magnetic-field-induced
alignment. Here, the overall x-tensor can be predicted for a given RNA
conformer based on a tensor summation over all x-tensors associated with
individual nucleobases.
52,85,121
Furthermore, one can write expressions relating
the overall x-tensor in terms of the x-tensors of individual helices and their
relative orientation. By taking advantage of this simple relationship, Zhang
and co-workers showed that couplings between inter-helical motions and the
overall alignment can be explicitly treated in the case of magnetic field
alignment.
121
This study revealed that RDCs measured in the presence of
motional couplings, in fact, carry greater information regarding the underlying
dynamics compared to RDCs measured under the decoupling limit. This
provides great motivation to apply approaches for predicting overall alignment
in ordering media in the dynamic analysis of RDCs measured in RNA.
Though several studies have shown that the alignment of RNA in phage can be
accurately computed based on the RNA structure, further benchmark studies
are required to establish the accuracy of such predictions under a range of ionic
strength conditions and for a variety of RNA tertiary contexts.
9.6 Example Applications in Studies of RNA Dynamics
From RDCs
The application of RDCs in studies of RNA dynamics has yielded
fundamental new insights into the dynamic behavior of RNA. Many early
studies identified dynamic hot-spots as regions with RDCs that could not
readily be satisfied using a single static structure.
23
Many of these residues were
localised within flexible junctions that tether helices together and in many
cases,
independent
evidence
for
flexibility
could
be
obtained
based
on
measurements of spin relaxation data.
An early example is a study by Sibille and co-workers which used RDCs and
MD simulations to refine the global and local structure of the theophylline-
binding RNA aptamer-ligand complex from an existing NOE-based NMR
structure.
147
The inclusion of RDCs measured in the nucleobase of a flexible
internal loop residue C27 in the structure refinement resulted in several
different conformations for this residue suggesting a contribution from
motional averaging
147
[Figure 9.5(A)]. In other studies, dynamic hot-spots
were identified by examining the fit of measured RDCs to a known X-ray
structure of the RNA. For example, deviations between RDCs measured in the
unbound 84-nt guanine riboswitch and values predicted from an X-ray
structure of the ligand-bound form were observed for a sub-set of residues that
form the binding pocket, indicating that while the overall riboswitch structure
is preformed, the binding pocket is locally disordered.
148
RDCs have also provided fundamental insights into global motions
involving the collective movements of helical elements. Some of the earliest
applications of RDCs to RNA provided evidence for large-amplitude (y45u)
collective inter-helical motions in HIV-1 TAR RNA that occur about a flexible
