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

Kód výsledku v 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>

Nalezeny alternativní kódy

RIV/00216224:14740/14:00076678

Výsledek na webu

<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>

Jazyk výsledku

angličtina

Název v původním jazyce

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

Popis výsledku v původním jazyce

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

Název v anglickém jazyce

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

Popis výsledku anglicky

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

Druh

J_x - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)

CEP obor

CF - Fyzikální chemie a teoretická chemie

OECD FORD obor

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Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)<br>S - Specificky vyzkum na vysokych skolach

Rok uplatnění

2014

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Journal of Chemical Theory and Computation

ISSN

1549-9618

e-ISSN

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Svazek periodika

10

Číslo periodika v rámci svazku

4

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

15

Strana od-do

1608-1622

Kód UT WoS článku

000334571900024

EID výsledku v databázi Scopus

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