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

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About: Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme Goto Sponge NotDistinct Permalink

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
rdfs:seeAlso	http://pubs.acs.org/doi/abs/10.1021/ct401015e
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 a general 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. 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 a general 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. (en)
Title	Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme (en)
skos:prefLabel	Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme (en)
skos:notation	RIV/00216224:14740/14:00076678!RIV15-MSM-14740___
http://linked.open...avai/riv/aktivita	P S
http://linked.open...avai/riv/aktivity	P(ED1.1.00/02.0068), P(ED2.1.00/03.0058), P(EE2.3.20.0017), P(EE2.3.20.0058), P(GAP208/12/1878), P(GPP301/11/P558), S
http://linked.open...iv/cisloPeriodika	4
http://linked.open...vai/riv/dodaniDat	2015
http://linked.open...aciTvurceVysledku	Šponer, Jiří
http://linked.open.../riv/druhVysledku	J - Článek v odborném periodiku
http://linked.open...iv/duvernostUdaju	S - Úplné a pravdivé údaje nepodléhající ochraně podle zvláštních právních předpisů
http://linked.open...titaPredkladatele	Masarykova univerzita / Středoevropský technologický institut
http://linked.open...dnocenehoVysledku	8001
http://linked.open...ai/riv/idVysledku	RIV/00216224:14740/14:00076678
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	MOLECULAR-DYNAMICS SIMULATIONS; DELTA-VIRUS RIBOZYME; ACID-BASE CATALYSIS; TRANSITION-STATE STABILIZATION; DENSITY-FUNCTIONAL THEORY; ACTIVE-SITE ADENINE; ENZYME CATALYSIS; ALKALINE-PHOSPHATASE; SELF-CLEAVAGE; ELECTROSTATIC INTERACTIONS (en)
http://linked.open.../riv/klicoveSlovo	DENSITY-FUNCTIONAL THEORY MOLECULAR-DYNAMICS SIMULATIONS ACID-BASE CATALYSIS TRANSITION-STATE STABILIZATION ACTIVE-SITE ADENINE ALKALINE-PHOSPHATASE DELTA-VIRUS RIBOZYME ELECTROSTATIC INTERACTIONS ENZYME CATALYSIS SELF-CLEAVAGE
http://linked.open...odStatuVydavatele	US - Spojené státy americké
http://linked.open...ontrolniKodProRIV	[8EEF074D7467]
http://linked.open...i/riv/nazevZdroje	Journal of Chemical Theory and Computation
http://linked.open...in/vavai/riv/obor	CF
http://linked.open...ichTvurcuVysledku	1 (xsd:int)
http://linked.open...cetTvurcuVysledku	6 (xsd:int)
http://linked.open...vavai/riv/projekt	Catalytic strategies of RNA and RNP enzymes studied by multi-scale computational approach Central european institute of technology Regional Centre of Advanced Technologies and Materials Research team development of the Regional Centre of Advanced Technologies and Materials Integration of Regional Centre of Advanced Technologies and Materials into International Networks of Nanotechnological and Optical Research. Mechanism of catalytical self-cleavage of two non-coding RNAs of human patogens
http://linked.open...UplatneniVysledku	2014
http://linked.open...v/svazekPeriodika	10
http://linked.open...iv/tvurceVysledku	Otyepka, Michal Šponer, Jiří Banáš, Pavel Mlýnský, Vojtěch Mulholland, Adrian J. van der Kamp, Marc W.
http://linked.open...ain/vavai/riv/wos	000334571900024
issn	1549-9618
number of pages	15 (xsd:int)
http://bibframe.org/vocab/doi	10.1021/ct401015e
http://localhost/t...ganizacniJednotka	14740

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