About: Computational study of the dimethylphosphate hydrolysis as the reference system for the understanding of the restriction endonucleases mechanism

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About: Computational study of the dimethylphosphate hydrolysis as the reference system for the understanding of the restriction endonucleases mechanism Goto Sponge NotDistinct Permalink

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
Description	Understanding enzymatic mechanisms is essential knowledge for further medicine and biotechnology development. Our long-standing effort is aimed at the explanation of the reaction mechanism of endonucleases (enzymes cleaving DNA chain(s)) using computational approaches. According to the published experimental and theoretical results, the suggested mechanism is SN2 hydrolysis of the phosphate backbone. [1] Presented work is focused on the study of simplified model of the enzymatic reaction. This model consists of dimethylphosphate and the nucleophile (water, hydroxyl ion) attacking the phosphodiester bond. The hydrolysis was simulated using Car Parrinello Molecular Dynamics (CPMD) [2] in vacuum and in water. The reaction free energy profiles were evaluated using metadynamics [3] and obtained results were compared to the experimental data [4]. The model serves as a reference system for the upcoming simulation of the enzymatic reactions. Understanding enzymatic mechanisms is essential knowledge for further medicine and biotechnology development. Our long-standing effort is aimed at the explanation of the reaction mechanism of endonucleases (enzymes cleaving DNA chain(s)) using computational approaches. According to the published experimental and theoretical results, the suggested mechanism is SN2 hydrolysis of the phosphate backbone. [1] Presented work is focused on the study of simplified model of the enzymatic reaction. This model consists of dimethylphosphate and the nucleophile (water, hydroxyl ion) attacking the phosphodiester bond. The hydrolysis was simulated using Car Parrinello Molecular Dynamics (CPMD) [2] in vacuum and in water. The reaction free energy profiles were evaluated using metadynamics [3] and obtained results were compared to the experimental data [4]. The model serves as a reference system for the upcoming simulation of the enzymatic reactions. (en)
Title	Computational study of the dimethylphosphate hydrolysis as the reference system for the understanding of the restriction endonucleases mechanism Computational study of the dimethylphosphate hydrolysis as the reference system for the understanding of the restriction endonucleases mechanism (en)
skos:prefLabel	Computational study of the dimethylphosphate hydrolysis as the reference system for the understanding of the restriction endonucleases mechanism Computational study of the dimethylphosphate hydrolysis as the reference system for the understanding of the restriction endonucleases mechanism (en)
skos:notation	RIV/00216224:14740/11:00050025!RIV12-GA0-14740___
http://linked.open...avai/riv/aktivita	P S Z
http://linked.open...avai/riv/aktivity	P(GD301/09/H004), P(LC06030), S, Z(MSM0021622413)
http://linked.open...vai/riv/dodaniDat	2012
http://linked.open...aciTvurceVysledku	Štěpán, Jakub Kulhánek, Petr Střelcová, Zora Koča, Jaroslav
http://linked.open.../riv/druhVysledku	O - Ostatní výsledky nezařaditelné do žádného z výše uvedených druhů výsledku
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	191521
http://linked.open...ai/riv/idVysledku	RIV/00216224:14740/11:00050025
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	enzyme catalyses MutH ab-inito dynamics CPMD dimethylphosphate metadynamics PMF lib (en)
http://linked.open.../riv/klicoveSlovo	enzyme catalyses MutH ab-inito dynamics CPMD dimethylphosphate metadynamics PMF lib
http://linked.open...ontrolniKodProRIV	[0B0272BC3884]
http://linked.open...in/vavai/riv/obor	CF
http://linked.open...ichTvurcuVysledku	4 (xsd:int)
http://linked.open...cetTvurcuVysledku	5 (xsd:int)
http://linked.open...vavai/riv/projekt	Molecular and structural biology of selected antitumor drugs. From mechanistic studies to chemotherapy of tumors Biomolecular centre
http://linked.open...UplatneniVysledku	2011
http://linked.open...iv/tvurceVysledku	Carloni, Paolo Koča, Jaroslav Kulhánek, Petr Střelcová, Zora Štěpán, Jakub
http://linked.open...n/vavai/riv/zamer	Proteiny v metabolismu a při interakci organismů s prostředím
http://localhost/t...ganizacniJednotka	14740

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