One of the best investigated RNA structures with respect to conformational transitions is the HIV-1
transactivation response element (TAR). The TAR RNA is highly flexible and adopts rather different
conformations upon binding of different ligands. The decoupling of internal and overall motions of the
TAR RNA revealed that the unbound TAR RNA undergoes dynamical changes that sample the known ligand
bound conformations along specific conformation pathways [1-3]. The movie on the right side shows a simulated
pathway linking the conformations of the PDB-IDs 1ARJ, 1QD3, 1UTS, 1UUI, 1LVJ, 1UUD, and 1ARJ, respectively,
as suggested by Al-Hashimi and co-workers. The experimental determined structures are shown in orange and
the generated ones along the pathway in blue.
Graphics is from work of Simone Fulle, Dan Farrell and M.F. Thorpe. (unpublished)
Al-Hashimi, H. M., Gosser, Y., Gorin, A., Hu, W., Majumdar, A. & Patel, D. J. (2002). Concerted motions in HIV-1 TAR RNA may allow access to bound state conformations: RNA dynamics from NMR residual dipolar couplings. Journal of Molecular Biology 315, 95-102.
Zhang, Q., Sun, X., Watt, E. D. & Al-Hashimi, H. M. (2006). Resolving the motional modes that code for RNA adaptation. Science 311, 653-656.