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Original title:
Interdoménové a intradoménové interakce u motorové podjednotky EcoR124I: Výpočetní studie
Authors: SINHA, Dhiraj
Document type: Doctoral theses
Year: 2016
Language: eng
Abstract: EcoR124I is a Type I restrictionmodification (RM) enzyme and as such forms multifunctional pentameric complexes with DNA cleavage and ATP-dependent DNA translocation activities located on the motor subunit HsdR. When non-methylated invading DNA is recognized by the complex, two HsdR endonuclease/motor subunits start to translocate dsDNA without strand separation activity up to thousands base pairs towards the stationary enzyme while consuming ~1 molecule of ATP per base pair advanced. Whenever translocation is stalled the HsdR subunits cleave the dsDNA nonspecifically far from recognition site. The X-ray crystal structure of HsdR of EcoR124I bound to ATP gave a first insight of structural/functional correlation in the HsdR subunit. The four domains within the subunit were found to be in a square planer arrangement. Computational modeling including molecular dynamics in combination with crystallography, point mutations, in vivo and in vitro assays reveals how interactions between these four domains contribute to ATP-dependent DNA translocation, DNA cleavage or inter-domain communication between the translocase and endonuclease activities.
Keywords: Domain motions; EcoR124I; Endonuclease activity; Helicases; Interactions; Molecular dynamics; Motor subunit; Pentameric complex; Principal component analysis; Signal transfer; Translocase activity; Type I RM system
Citation: SINHA, Dhiraj. Interdoménové a intradoménové interakce u motorové podjednotky EcoR124I: Výpočetní studie. N. Hrady, 2016. disertační práce (Ph.D.). JIHOČESKÁ UNIVERZITA V ČESKÝCH BUDĚJOVICÍCH. Přírodovědecká fakulta
Institution: University of South Bohemia in České Budějovice (web)
Document availability information: Fulltext is available in the Digital Repository of University of South Bohemia.
Original record: http://www.jcu.cz/vskp/45938
Permalink: http://www.nusl.cz/ntk/nusl-263281
The record appears in these collections:
Universities and colleges > Public universities > University of South Bohemia in České Budějovice
Academic theses (ETDs) > Doctoral theses
Authors: SINHA, Dhiraj
Document type: Doctoral theses
Year: 2016
Language: eng
Abstract: EcoR124I is a Type I restrictionmodification (RM) enzyme and as such forms multifunctional pentameric complexes with DNA cleavage and ATP-dependent DNA translocation activities located on the motor subunit HsdR. When non-methylated invading DNA is recognized by the complex, two HsdR endonuclease/motor subunits start to translocate dsDNA without strand separation activity up to thousands base pairs towards the stationary enzyme while consuming ~1 molecule of ATP per base pair advanced. Whenever translocation is stalled the HsdR subunits cleave the dsDNA nonspecifically far from recognition site. The X-ray crystal structure of HsdR of EcoR124I bound to ATP gave a first insight of structural/functional correlation in the HsdR subunit. The four domains within the subunit were found to be in a square planer arrangement. Computational modeling including molecular dynamics in combination with crystallography, point mutations, in vivo and in vitro assays reveals how interactions between these four domains contribute to ATP-dependent DNA translocation, DNA cleavage or inter-domain communication between the translocase and endonuclease activities.
Keywords: Domain motions; EcoR124I; Endonuclease activity; Helicases; Interactions; Molecular dynamics; Motor subunit; Pentameric complex; Principal component analysis; Signal transfer; Translocase activity; Type I RM system
Citation: SINHA, Dhiraj. Interdoménové a intradoménové interakce u motorové podjednotky EcoR124I: Výpočetní studie. N. Hrady, 2016. disertační práce (Ph.D.). JIHOČESKÁ UNIVERZITA V ČESKÝCH BUDĚJOVICÍCH. Přírodovědecká fakulta
Institution: University of South Bohemia in České Budějovice (web)
Document availability information: Fulltext is available in the Digital Repository of University of South Bohemia.
Original record: http://www.jcu.cz/vskp/45938
Permalink: http://www.nusl.cz/ntk/nusl-263281
The record appears in these collections:
Universities and colleges > Public universities > University of South Bohemia in České Budějovice
Academic theses (ETDs) > Doctoral theses
Record created 2017-02-15, last modified 2023-01-15