Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989592%3A15310%2F14%3A33152333" target="_blank" >RIV/61989592:15310/14:33152333 - isvavai.cz</a>
Alternative codes found
RIV/00216224:14740/14:00076678
Result on the web
<a href="http://pubs.acs.org/doi/pdf/10.1021/ct401015e" target="_blank" >http://pubs.acs.org/doi/pdf/10.1021/ct401015e</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1021/ct401015e" target="_blank" >10.1021/ct401015e</a>

Result language
angličtina
Original language name
Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme
Original language description
We have analyzed the capability of state-of-the-art multiscale computational approaches to provide atomic-resolution electronic structure insights into possible catalytic scenarios of the g hairpin ribozyme by evaluating potential and free energy surfaces 4 of the reactions by various hybrid QM/MM methods. The hairpin ribozyme is a unique catalytic RNA that achieves rate acceleration similar to other small self-cleaving ribozymes but without direct metal ion participation. Guanine 8 (G8) and adenine 38(A38) have been identified as the catalytically essential nucleobases. However, their exact catalytic roles are still being investigated. In line with the available experimental data, we considered two reaction scenarios involving protonated A38H(+) as ageneral acid Which is further assisted by either canonical G8 or deprotonated G8(-) forms. We used the spin-component scaled Moller-Plesset (SCS-MP2) method at the complete basis set limit as the reference method. The semiempirical AM1/d
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
CF - Physical chemistry and theoretical chemistry
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
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)<br>S - Specificky vyzkum na vysokych skolach

Publication year
2014
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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