About: DNA basepair step deformability inferred from molecular dynamics simulations.

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About: DNA basepair step deformability inferred from molecular dynamics simulations. Goto Sponge NotDistinct Permalink

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
Description	The sequence-dependent DNA deformability at the basepair step level was investigated using large-scale atomic resolution molecular dynamics simulation of two 18-bp DNA oligomers: d( GCCTATAAACGCCTATAA) and d( CTAGGTGGATGACTCATT). From an analysis of the structural fluctuations, the harmonic potential energy functions for all 10 unique steps with respect to the six step parameters have been evaluated. In the case of roll, three distinct groups of steps have been identified: the flexible pyrimidine-purine (YR) steps, intermediate purine-purine (RR), and stiff purine-pyrimidine (RY). The YR steps appear to be the most flexible in tilt and partially in twist. Increasing stiffness from YR through RR to RY was observed for rise, whereas shift and slide lack simple trends. A proposed measure of the relative importance of couplings identifies the slide-rise, twist-roll, and twist-slide couplings to play a major role. The sequence-dependent DNA deformability at the basepair step level was investigated using large-scale atomic resolution molecular dynamics simulation of two 18-bp DNA oligomers: d( GCCTATAAACGCCTATAA) and d( CTAGGTGGATGACTCATT). From an analysis of the structural fluctuations, the harmonic potential energy functions for all 10 unique steps with respect to the six step parameters have been evaluated. In the case of roll, three distinct groups of steps have been identified: the flexible pyrimidine-purine (YR) steps, intermediate purine-purine (RR), and stiff purine-pyrimidine (RY). The YR steps appear to be the most flexible in tilt and partially in twist. Increasing stiffness from YR through RR to RY was observed for rise, whereas shift and slide lack simple trends. A proposed measure of the relative importance of couplings identifies the slide-rise, twist-roll, and twist-slide couplings to play a major role. (en)
Title	DNA basepair step deformability inferred from molecular dynamics simulations. DNA basepair step deformability inferred from molecular dynamics simulations. (en)
skos:prefLabel	DNA basepair step deformability inferred from molecular dynamics simulations. DNA basepair step deformability inferred from molecular dynamics simulations. (en)
skos:notation	RIV/68081707:_____/03:17033295!RIV/2004/MSM/A17004/N
http://linked.open.../vavai/riv/strany	2872;2883
http://linked.open...avai/riv/aktivita	P Z
http://linked.open...avai/riv/aktivity	P(LN00A032), Z(AV0Z4040901), Z(AV0Z5004920)
http://linked.open...iv/cisloPeriodika	5
http://linked.open...vai/riv/dodaniDat	2004
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	Biofyzikální ústav AV ČR, v. v. i.
http://linked.open...dnocenehoVysledku	604235
http://linked.open...ai/riv/idVysledku	RIV/68081707:_____/03:17033295
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	molecular dynamics simulations; DNA basepair step deformability (en)
http://linked.open.../riv/klicoveSlovo	molecular dynamics simulations DNA basepair step deformability
http://linked.open...odStatuVydavatele	US - Spojené státy americké
http://linked.open...ontrolniKodProRIV	[ADD915637EBA]
http://linked.open...i/riv/nazevZdroje	Biophysical Journal
http://linked.open...in/vavai/riv/obor	BO
http://linked.open...ichTvurcuVysledku	1 (xsd:int)
http://linked.open...cetTvurcuVysledku	4 (xsd:int)
http://linked.open...ocetUcastnikuAkce	0 (xsd:int)
http://linked.open...nichUcastnikuAkce	0 (xsd:int)
http://linked.open...vavai/riv/projekt	Structure and dynamics of complex molecular systems and biomolecules
http://linked.open...UplatneniVysledku	2003
http://linked.open...v/svazekPeriodika	85
http://linked.open...iv/tvurceVysledku	Šponer, Jiří Cheatham III, T. E. Lankaš, Filip Langowski, J.
http://linked.open...n/vavai/riv/zamer	Objasňování zákonitostí vztahů struktury a vlastností - zejména dynamiky a chemické reaktivity - látek a molekulárních systémů Biophysical properties of living systems and their changes under the influence of environmental factors
issn	0006-3495
number of pages	12 (xsd:int)

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