| KRASOVSKA, Maryna, Jana SEVCIKOVA, Kamila REBLOVA, Bohdan SCHNEIDER, Walter NILS a Jiri SPONER. Cations and Hydration in Catalytic RNA: Molecular Dynamics of the Hepatitis Delta Virus Ribozyme. Biophysical Journal. USA: Biophysical Society, 2006, roč. 91, -, s. 626-638, 16 s. ISSN 0006-3495. |
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@article{638687,
author = {Krasovska, Maryna and Sevcikova, Jana and Reblova, Kamila and Schneider, Bohdan and Nils, Walter and Sponer, Jiri},
article_location = {USA},
article_number = {-},
keywords = {molecular dynamics simulations; ribozyme; hydration; cations;},
language = {eng},
issn = {0006-3495},
journal = {Biophysical Journal},
title = {Cations and Hydration in Catalytic RNA: Molecular Dynamics of the Hepatitis Delta Virus Ribozyme},
volume = {91},
year = {2006}
}
TY - JOUR
ID - 638687
AU - Krasovska, Maryna - Sevcikova, Jana - Reblova, Kamila - Schneider, Bohdan - Nils, Walter - Sponer, Jiri
PY - 2006
TI - Cations and Hydration in Catalytic RNA: Molecular Dynamics of the Hepatitis Delta Virus Ribozyme
JF - Biophysical Journal
VL - 91
IS - -
SP - 626-638
EP - 626-638
PB - Biophysical Society
SN - 00063495
KW - molecular dynamics simulations
KW - ribozyme
KW - hydration
KW - cations;
N2 - The hepatitis delta virus (HDV) ribozyme is an RNA enzyme from the human pathogenic HDV. Cations play a crucial role in self-cleavage of the HDV ribozyme, by promoting both folding and chemistry. Experimental studies have revealed limited but intriguing details on the location and structural and catalytic functions of metal ions. Here, we analyze a total of ;200 ns of explicit-solvent molecular dynamics simulations to provide a complementary atomistic view of the binding of monovalent and divalent cations as well as water molecules to reaction precursor and product forms of the HDV ribozyme. Our simulations nd that an Mg21 cation binds stably, by both inner- and outer-sphere contacts, to the electronegative catalytic pocket of the reaction precursor, in a position to potentially support chemistry. In contrast, protonation of the catalytically involved C75 in the precursor or articial placement of this Mg21 into the product structure result in its swift expulsion from the active site. These ndings are consistent with a concerted reaction mechanism in which C75 and hydrated Mg21 act as general base and acid, respectively. Monovalent cations bind to the active site and elsewhere assisted by structurally bridging long-residency water molecules, but are generally delocalized.
ER -
KRASOVSKA, Maryna, Jana SEVCIKOVA, Kamila REBLOVA, Bohdan SCHNEIDER, Walter NILS a Jiri SPONER. Cations and Hydration in Catalytic RNA: Molecular Dynamics of the Hepatitis Delta Virus Ribozyme. \textit{Biophysical Journal}. USA: Biophysical Society, 2006, roč.~91, -, s.~626-638, 16 s. ISSN~0006-3495.
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