The role of an active site Mg2+ in HDV ribozyme self-cleavage: insights from QM/MM calculations

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68081707%3A_____%2F15%3A00442423" target="_blank" >RIV/68081707:_____/15:00442423 - isvavai.cz</a>
Alternative codes found
RIV/61989592:15310/15:33156519 RIV/00216224:14740/15:00082202
Result on the web
<a href="http://dx.doi.org/10.1039/c4cp03857f" target="_blank" >http://dx.doi.org/10.1039/c4cp03857f</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1039/c4cp03857f" target="_blank" >10.1039/c4cp03857f</a>

Result language
angličtina
Original language name
The role of an active site Mg2+ in HDV ribozyme self-cleavage: insights from QM/MM calculations
Original language description
The hepatitis delta virus (HDV) ribozyme is a catalytic RNA motif embedded in the human pathogenic HDV RNA. It catalyzes self-cleavage of its sugar-phosphate backbone with direct participation of the active site cytosine C75. Biochemical and structural data support a general acid role of C75. Here, we used hybrid quantum mechanical/molecular mechanical (QM/MM) calculations to probe the reaction mechanism and changes in Gibbs energy along the ribozyme's reaction pathway with an N3-protonated C75H(+) in the active site, which acts as the general acid, and a partially hydrated Mg2+ ion with one deprotonated, inner-shell coordinated water molecule that acts as the general base. We followed eight reaction paths with a distinct position and coordination of the catalytically important active site Mg2+ ion. For six of them, we observed feasible activation barriers ranging from 14.2 to 21.9 kcal mol(-1), indicating that the specific position of the Mg2+ ion in the active site is predicted to st
Czech name
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Czech description
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Type
J<sub>x</sub> - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)
CEP classification
BO - Biophysics
OECD FORD branch
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Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year
2015
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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