Al-Hashimi et al. Review: Movies of RNA dynamics
Provided are links to movies and animations of experimentally determined RNA dynamics
that have been published in conjunction with studies, most of which are discussed in the
review text.
HDV ribozyme
Ke, A., Zhou, K., Ding, F., Cate, J.H. & Doudna, J.A. A conformational switch controls
hepatitis delta virus ribozyme catalysis. Nature 429, 201–205 (2004).
This animation highlights the crystallographically observed conformational rearrangements of
the HDV ribozyme that occur after substrate cleavage.
http://rna.berkeley.edu/Research/Movies/hdv-rbz-conf-change.qt
HIV-TAR motions
Zhang, Q., Stelzer, A.C., Fisher, C.K. & Al-Hashimi, H.M. Visualizing spatially correlated
dynamics that directs RNA conformational transitions. Nature 450, 1263–1267 (2007).
These animations highlight the interhelical motions of the three-nucleotide bulge of HIV TAR
captured by NMR and show a comparison between these motions and different protein and
ligand bound TAR crystal structures.
http://www.nature.com/nature/journal/v450/n7173/extref/nature06389-s2.mov
http://www.nature.com/nature/journal/v450/n7173/extref/nature06389-s3.mov
Frank, A.T., Stelzer, A.C., Al-Hashimi, H.M. & Andricioaei, I. Constructing RNA dynamical
ensembles by combining MD and motionally decoupled NMR RDCs: new insights into RNA
dynamics and adaptive ligand recognition. Nucleic Acids Res 37, 3670–3679 (2009).
This movie captures the conformational dynamics of HIV-1 TAR determined through
molecular dynamics and NMR-RDCs through a sample and select (SAS) approach.
http://hashimi.biop.lsa.umich.edu/index.php?q=node/5
Ribosome motions
Frank, J. & Agrawal, R.K. A ratchet-like inter-subunit reorganization of the ribosome during
translocation. Nature 406, 318–322 (2000).
This animation provides the first demonstration of ribosomal inter-subunit ratcheting,
captured by a comparison of free and EF-G bound cryo-EM structures of the ribosome.
http://www.nature.com/nature/journal/v406/n6793/extref/406318ai1.mov
Ogle, J.M., Murphy, F.V., Tarry, M.J. & Ramakrishnan, V. Selection of tRNA by the
ribosome requires a transition from an open to a closed form. Cell 111, 721–732 (2002).
A comparison between crystal structures of the ribosome in free and cognate anticodon stemloop bound states reveals ‘domain closure’ conformational changes of the 30S subunit upon
formation of a cognate codon-anticodon minihelix. The closed ribosomal conformation is
further stabilized by paromomycin.
http://download.cell.com/mmcs/journals/0092-8674/PIIS0092867402010863.mmc2.gif
http://download.cell.com/mmcs/journals/0092-8674/PIIS0092867402010863.mmc6.gif
Valle, M. et al. Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron
microscopy. Nature Struct. Biol. 10, 899–906 (2003).
Comparisons between cryo-EM reconstructions of the ribosome bound by the EF-Tu•tRNA
ternary complex, with tRNA in the A/T site, and fully A-site accommodated tRNA reveal
conformational changes of the tRNA anticodon stem involved in tRNA recognition and
ribosome-incorporation.
http://www.nature.com/nsmb/journal/v10/n11/extref/nsb1003-S2.mov
http://www.nature.com/nsmb/journal/v10/n11/extref/nsb1003-S3.mov
Blaha, G., Stanley, R.E., & Steitz, T.A. Formation of the first peptide bond: the structure of
EF-P bound to the 70S ribosome. Science 325, 966–970 (2009).
The high degree of mobility of the L1 ribosomal stalk is illustrated by this animation that
morphs between two crystallographically observed stalk conformations.
http://www.sciencemag.org/content/suppl/2009/08/20/325.5943.966.DC1/1175800s1.mov
Schmeing, T.M. et al. The crystal structure of the ribosome bound to EF-Tu and aminoacyltRNA. Science 326, 688–694 (2009).
An animation highlighting crystallographically observed conformational changes of both the
ribosome and tRNA that are involved in tRNA selection and accommodation by the
ribosome.
http://www.sciencemag.org/content/suppl/2009/10/15/1179700.DC1/1179700s1.mov
Zhang, W., Dunkle, J.A., & Cate, J.H. Structures of the ribosome in intermediate states of
ratcheting. Science 325, 1014–1017 (2009).
Comparisons between crystal structures of the ribosome in different ratcheted intermediates
highlight the inter- and intra-subunit conformational rearrangements involved in
translocation.
http://www.sciencemag.org/content/suppl/2009/08/20/325.5943.1014.DC1/1175275S1.mov
http://www.sciencemag.org/content/suppl/2009/08/20/325.5943.1014.DC1/1175275S2.mov
Fischer, N., Konevega, A.L., Wintermeyer, W., Rodnina, M.V. & Stark, H. Ribosome
dynamics and tRNA movement by time-resolved electron cryomicroscopy. Nature 466, 329–
333 (2010).
This movie captures tRNA retrotranslocation through the ribosome and associated ribosome
conformational changes as seen through cryo-electron microscopy reconstructions.
http://www.nature.com/nature/journal/v466/n7304/extref/nature09206-s3.mpg
Ratje, A.H. et al. Head swivel on the ribosome facilitates translocation by means of intrasubunit tRNA hybrid sites. Nature 468, 713–716 (2010).
Comparisons between subclassifications of cryo-EM structures of EF-G bound ribosomes
reveals ‘head swiveling’ of the 30S subunit that is associated with tRNA translocation.
http://www.nature.com/nature/journal/v468/n7324/extref/nature09547-s2.gif
http://www.nature.com/nature/journal/v468/n7324/extref/nature09547-s3.gif
http://www.nature.com/nature/journal/v468/n7324/extref/nature09547-s4.gif
Dunkle, J.A. et al. Structures of the bacterial ribosome in classical and hybrid states of tRNA
binding. Science 332, 981–984 (2011).
Animations show the crystallographically observed changes in tRNA conformation as it
transits through the ribosome and changes in helix 69 of the 23S rRNA during ribosome
ratcheting.
http://www.sciencemag.org/content/suppl/2011/05/18/332.6032.981.DC1/1202692s1.mov
http://www.sciencemag.org/content/suppl/2011/05/18/332.6032.981.DC1/1202692s2.mov