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@article{1200026,
author = {Sripathi, Kamali N. and Tay, Wendy W. and Banáš, Pavel and Otyepka, Michal and Šponer, Jiří and Walter, Nils G.},
article_location = {Cold Spring Harbor},
article_number = {7},
doi = {http://dx.doi.org/10.1261/rna.044982.114},
keywords = {HEPATITIS-DELTA-VIRUS; MOLECULAR-DYNAMICS SIMULATIONS; SELF-CLEAVING RIBOZYMES; ACID-BASE CATALYSIS; MULTICHANNEL REACTION-MECHANISM; LOCAL CONFORMATIONAL-CHANGES; DIVALENT METAL-IONS; GENERAL ACID; HAIRPIN RIBOZYME; GENOMIC RIBOZYME},
language = {eng},
issn = {1355-8382},
journal = {RNA},
title = {Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape},
url = {http://rnajournal.cshlp.org/content/20/7/1112.long},
volume = {20},
year = {2014}
}
TY - JOUR
ID - 1200026
AU - Sripathi, Kamali N. - Tay, Wendy W. - Banáš, Pavel - Otyepka, Michal - Šponer, Jiří - Walter, Nils G.
PY - 2014
TI - Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape
JF - RNA
VL - 20
IS - 7
SP - 1112-1128
EP - 1112-1128
PB - Cold Spring Harbor Laboratory Press
SN - 13558382
KW - HEPATITIS-DELTA-VIRUS
KW - MOLECULAR-DYNAMICS SIMULATIONS
KW - SELF-CLEAVING RIBOZYMES
KW - ACID-BASE CATALYSIS
KW - MULTICHANNEL REACTION-MECHANISM
KW - LOCAL CONFORMATIONAL-CHANGES
KW - DIVALENT METAL-IONS
KW - GENERAL ACID
KW - HAIRPIN RIBOZYME
KW - GENOMIC RIBOZYME
UR - http://rnajournal.cshlp.org/content/20/7/1112.long
L2 - http://rnajournal.cshlp.org/content/20/7/1112.long
N2 - The hepatitis delta virus (HDV) ribozyme is a member of the class of small, self-cleaving catalytic RNAs found in a wide range of genomes from HDV to human. Both pre- and post-catalysis (precursor and product) crystal structures of the cis-acting genomic HDV ribozyme have been determined. These structures, together with extensive solution probing, have suggested that a significant conformational change accompanies catalysis. A recent crystal structure of a trans-acting precursor, obtained at low pH and by molecular replacement from the previous product conformation, conforms to the product, raising the possibility that it represents an activated conformer past the conformational change. Here, using fluorescence resonance energy transfer (FRET), we discovered that cleavage of this ribozyme at physiological pH is accompanied by a structural lengthening in magnitude comparable to previous trans-acting HDV ribozymes. Conformational heterogeneity observed by FRET in solution appears to have been removed upon crystallization. Analysis of a total of 1.8 mu sec of molecular dynamics (MD) simulations showed that the crystallographically unresolved cleavage site conformation is likely correctly modeled after the hammerhead ribozyme, but that crystal contacts and the removal of several 2'-oxygens near the scissile phosphate compromise catalytic in-line fitness. A cis-acting version of the ribozyme exhibits a more dynamic active site, while a G-1 residue upstream of the scissile phosphate favors poor fitness, allowing us to rationalize corresponding changes in catalytic activity. Based on these data, we propose that the available crystal structures of the HDV ribozyme represent intermediates on an overall rugged RNA folding free-energy landscape.
ER -
SRIPATHI, Kamali N., Wendy W. TAY, Pavel BANÁŠ, Michal OTYEPKA, Jiří ŠPONER and Nils G. WALTER. Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape. \textit{RNA}. Cold Spring Harbor: Cold Spring Harbor Laboratory Press, 2014, vol.~20, No~7, p.~1112-1128. ISSN~1355-8382. Available from: https://dx.doi.org/10.1261/rna.044982.114.
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