Long-distance communication in the HDV ribozyme: insights from molecular dynamics and experiments.

Journal of Molecular Biology
Narayanan VeeraraghavanSharon Hammes-Schiffer

Abstract

The hepatitis delta virus ribozyme is a small, self-cleaving RNA with a compact tertiary structure and buried active site that is important in the life cycle of the virus. The ribozyme's function in nature is to cleave an internal phosphodiester bond and linearize concatemers during rolling circle replication. Crystal structures of the ribozyme have been solved in both pre-cleaved and post-cleaved (product) forms and reveal an intricate network of interactions that conspire to catalyze bond cleavage. In addition, extensive biochemical studies have been performed to work out a mechanism for bond cleavage in which C75 and a magnesium ion catalyze the reaction by general acid-base chemistry. One issue that has remained unclear in this ribozyme and in other ribozymes is the nature of long-distance communication between peripheral regions of the RNA and the buried active site. We performed molecular dynamics simulations on the hepatitis delta virus ribozyme in the product form and assessed communication between a distal structural portion of the ribozyme-the protonated C41 base triple-and the active site containing the critical C75. We varied the ionization state of C41 in both the wild type and a C41 double mutant variant and deter...Continue Reading

References

Jan 1, 1995·Annual Review of Biochemistry·M M Lai
Feb 1, 1996·Journal of Molecular Graphics·W HumphreyK Schulten
Aug 1, 1997·European Journal of Biochemistry·M D Been, G S Wickham
Mar 1, 1985·Physical Review A: General Physics·W G Hoover
Sep 13, 2002·Journal of Molecular Biology·Paul L NixonDavid P Giedroc
Dec 24, 2003·Biopolymers·Philip C BevilacquaRieko Yajima
Jan 13, 2006·Nature Chemical Biology·Subha R Das, Joseph A Piccirilli
Jun 8, 2006·Annual Review of Biochemistry·Sharon Hammes-Schiffer, Stephen J Benkovic
Aug 29, 2006·Current Opinion in Chemical Biology·Philip C Bevilacqua, Rieko Yajima
Sep 23, 2006·Science·Kourosh Salehi-AshtianiJack W Szostak
Mar 16, 2007·Structure·Ailong KeJennifer A Doudna
Dec 8, 2009·Science·Chiu-Ho T WebbAndrej Lupták

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Citations

Jul 8, 2011·Accounts of Chemical Research·Jennifer L WilcoxPhilip C Bevilacqua
Feb 26, 2011·Biochemistry·Narayanan VeeraraghavanBarbara L Golden
Jun 8, 2011·The Journal of Physical Chemistry. B·Narayanan VeeraraghavanSharon Hammes-Schiffer
Sep 25, 2012·The Journal of Physical Chemistry. B·Pavel BanášMichal Otyepka
Jan 21, 2014·The Journal of Chemical Physics·Jiawen ChenWenbing Zhang
Nov 20, 2016·Wiley Interdisciplinary Reviews. RNA·Jiří ŠponerMichal Otyepka
Jan 4, 2018·Chemical Reviews·Jiří ŠponerMichal Otyepka
Jan 5, 2014·Journal of the American Chemical Society·Abir GangulySharon Hammes-Schiffer
Dec 14, 2011·The Journal of Physical Chemistry Letters·Abir GangulySharon Hammes-Schiffer
Dec 27, 2011·The Journal of Physical Chemistry Letters·Tai-Sung LeeDarrin M York
Dec 7, 2018·Biochemistry·Pratul K Agarwal
Mar 26, 2013·Journal of Chemical Theory and Computation·Garrett B GohCharles L Brooks
Feb 26, 2013·Journal of the American Chemical Society·Jennifer L Wilcox, Philip C Bevilacqua

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