J 2014

Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape

SRIPATHI, Kamali N., Wendy W. TAY, Pavel BANÁŠ, Michal OTYEPKA, Jiří ŠPONER et. al.

Basic information

Original name

Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape

Authors

SRIPATHI, Kamali N. (840 United States of America), Wendy W. TAY (840 United States of America), Pavel BANÁŠ (203 Czech Republic), Michal OTYEPKA (203 Czech Republic), Jiří ŠPONER (203 Czech Republic, guarantor, belonging to the institution) and Nils G. WALTER (840 United States of America)

Edition

RNA, Cold Spring Harbor, Cold Spring Harbor Laboratory Press, 2014, 1355-8382

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10403 Physical chemistry

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

Impact factor

Impact factor: 4.936

RIV identification code

RIV/00216224:14740/14:00076675

Organization unit

Central European Institute of Technology

UT WoS

000338271200016

Keywords in English

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

Tags

International impact, Reviewed
Změněno: 11/3/2015 08:08, Martina Prášilová

Abstract

V originále

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.

Links

ED1.1.00/02.0068, research and development project
Name: CEITEC - central european institute of technology