Magnesium dependence of the amplified conformational switch in the trans-acting hepatitis delta virus ribozyme

Biochemistry
Rebecca A TinsleyNils G Walter

Abstract

The ability of divalent metal ions to participate in both structure formation and catalytic chemistry of RNA enzymes (ribozymes) has made it difficult to separate their cause and effect in ribozyme function. For example, the recently solved crystal structures of precursor and product forms of the cis-cleaving genomic hepatitis delta virus (HDV) ribozyme show a divalent metal ion bound in the active site that is released upon catalysis due to an RNA conformational change. This conformational switch is associated with a repositioning of the catalytically involved base C75 in the active-site cleft, thus controlling catalysis. These findings confirm previous data from fluorescence resonance energy transfer (FRET) on a trans-acting form of the HDV ribozyme that found a global conformational change to accompany catalysis. Here, we further test the conformational switch model by measuring the Mg(2+) dependence of the global conformational change of the trans-acting HDV ribozyme, using circular dichroism and time-resolved FRET as complementary probes of secondary and tertiary structure formation, respectively. We observe significant differences in both structure and Mg(2+) affinity of the precursor and product forms, in the presence an...Continue Reading

References

Jan 1, 1997·Annual Review of Biophysics and Biomolecular Structure·P Brion, E Westhof
Mar 22, 2000·Antisense & Nucleic Acid Drug Development·P DeschênesJ P Perreault
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May 22, 2003·Journal of Molecular Biology·Prashanth Rangan, Sarah A Woodson
Sep 2, 2003·Journal of Molecular Biology·Christine M DunhamWilliam G Scott
Nov 13, 2003·Journal of the American Chemical Society·Rebecca A TinsleyNils G Walter

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Citations

Apr 7, 2005·Current Opinion in Chemical Biology·Sarah A Woodson
Mar 31, 2009·Journal of the American Chemical Society·Debapriya MazumdarYi Lu
Oct 26, 2005·RNA·Meredith Newby LambertNils G Walter
Feb 28, 2006·Biophysical Journal·Meredith Newby LambertNils G Walter
Jan 30, 2015·Physical Chemistry Chemical Physics : PCCP·Kamali N SripathiNils G Walter
Aug 18, 2010·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Fabrice Leclerc
Jan 4, 2018·Chemical Reviews·Jiří ŠponerMichal Otyepka
Jan 12, 2007·The Journal of Physical Chemistry. B·Haining LiuJames W Gauld

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