About: Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale

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Attributes	Values
rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
rdfs:seeAlso	http://nar.oxfordjournals.org/content/41/4/2723.long
Description	The human telomeric DNA sequence with four repeats can fold into a parallel-stranded propeller-type topology. NMR structures solved under molecular crowding experiments correlate with the crystal structures found with crystal-packing interactions that are effectively equivalent to molecular crowding. This topology has been used for rationalization of ligand design and occurs experimentally in a number of complexes with a diversity of ligands, at least in the crystalline state. Although G-quartet stems have been well characterized, the interactions of the TTA loop with the G-quartets are much less defined. To better understand the conformational variability and structural dynamics of the propeller-type topology, we performed molecular dynamics simulations in explicit solvent up to 1.5 mu s. The analysis provides a detailed atomistic account of the dynamic nature of the TTA loops highlighting their interactions with the G-quartets including formation of an A: A base pair, triad, pentad and hexad. The human telomeric DNA sequence with four repeats can fold into a parallel-stranded propeller-type topology. NMR structures solved under molecular crowding experiments correlate with the crystal structures found with crystal-packing interactions that are effectively equivalent to molecular crowding. This topology has been used for rationalization of ligand design and occurs experimentally in a number of complexes with a diversity of ligands, at least in the crystalline state. Although G-quartet stems have been well characterized, the interactions of the TTA loop with the G-quartets are much less defined. To better understand the conformational variability and structural dynamics of the propeller-type topology, we performed molecular dynamics simulations in explicit solvent up to 1.5 mu s. The analysis provides a detailed atomistic account of the dynamic nature of the TTA loops highlighting their interactions with the G-quartets including formation of an A: A base pair, triad, pentad and hexad. (en)
Title	Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale (en)
skos:prefLabel	Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale (en)
skos:notation	RIV/00216224:14740/13:00068737!RIV14-MSM-14740___
http://linked.open...avai/predkladatel	Středoevropský technologický institut
http://linked.open...avai/riv/aktivita	I P
http://linked.open...avai/riv/aktivity	I, P(ED1.1.00/02.0068), P(GAP208/11/1822)
http://linked.open...iv/cisloPeriodika	4
http://linked.open...vai/riv/dodaniDat	2014
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	66723
http://linked.open...ai/riv/idVysledku	RIV/00216224:14740/13:00068737
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	MOLECULAR-DYNAMICS; CRYSTAL-STRUCTURE; B-DNA; FORCE-FIELD; NUCLEIC-ACIDS; CENTER-DOT; SIMULATIONS; STABILITY; RNA; RECOGNITION (en)
http://linked.open.../riv/klicoveSlovo	CENTER-DOT CRYSTAL-STRUCTURE STABILITY FORCE-FIELD RNA B-DNA NUCLEIC-ACIDS RECOGNITION MOLECULAR-DYNAMICS SIMULATIONS
http://linked.open...odStatuVydavatele	GB - Spojené království Velké Británie a Severního Irska
http://linked.open...ontrolniKodProRIV	[239F5827D45F]
http://linked.open...i/riv/nazevZdroje	Nucleic Acids Research
http://linked.open...in/vavai/riv/obor	CF
http://linked.open...ichTvurcuVysledku	1 (xsd:int)
http://linked.open...cetTvurcuVysledku	7 (xsd:int)
http://linked.open...vavai/riv/projekt	Central european institute of technology Structure and dynamics of DNA. Advanced computational studies.
http://linked.open...UplatneniVysledku	2013
http://linked.open...v/svazekPeriodika	41
http://linked.open...iv/tvurceVysledku	Šponer, Jiří Neidle, Stephen Haider, Shozeb Islam, Barira Laughton, Charlie Orozco, Modesto Sgobba, Miriam
http://linked.open...ain/vavai/riv/wos	000318062000059
issn	0305-1048
number of pages	13 (xsd:int)
http://bibframe.org/vocab/doi	10.1093/nar/gks1331
http://localhost/t...ganizacniJednotka	14740

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