Structural dynamics of human telomeric G-quadruplex loops studied by molecular dynamics simulations.

Loops which are linkers connecting G-strands and supporting the G-tetrad core in G-quadruplex are important for biological roles of G-quadruplexes. TTA loop is a common sequence which mainly resides in human telomeric DNA (hTel) G-quadruplex. A series of molecular dynamics (MD) simulations were carr...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Hong Zhu, Shiyan Xiao, Haojun Liang
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/79eb64632fad471db5b923427a906540
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:79eb64632fad471db5b923427a906540
record_format	dspace
spelling	oai:doaj.org-article:79eb64632fad471db5b923427a9065402021-11-18T09:00:34ZStructural dynamics of human telomeric G-quadruplex loops studied by molecular dynamics simulations.1932-620310.1371/journal.pone.0071380https://doaj.org/article/79eb64632fad471db5b923427a9065402013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23951152/?tool=EBIhttps://doaj.org/toc/1932-6203Loops which are linkers connecting G-strands and supporting the G-tetrad core in G-quadruplex are important for biological roles of G-quadruplexes. TTA loop is a common sequence which mainly resides in human telomeric DNA (hTel) G-quadruplex. A series of molecular dynamics (MD) simulations were carried out to investigate the structural dynamics of TTA loops. We found that (1) the TA base pair formed in TTA loops are very stable, the occupied of all hydrogen bonds are more than 0.95. (2) The TA base pair makes the adjacent G-quartet more stable than others. (3) For the edgewise loop and the diagonal loop, most loop bases are stacking with others, only few bases have considerable freedom. (4) The stabilities of these stacking structures are distinct. Part of the loops, especially TA base pairs, and bases stacking with the G-quartet, maintain certain stable conformations in the simulation, but other parts, like TT and TA stacking structures, are not stable enough. For the first time, spontaneous conformational switches of TTA edgewise loops were observed in our long time MD simulations. (5) For double chain reversal loop, it is really hard to maintain a stable conformation in the long time simulation under present force fields (parm99 and parmbsc0), as it has multiple conformations with similar free energies.Hong ZhuShiyan XiaoHaojun LiangPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 8, p e71380 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Hong Zhu Shiyan Xiao Haojun Liang Structural dynamics of human telomeric G-quadruplex loops studied by molecular dynamics simulations.
description	Loops which are linkers connecting G-strands and supporting the G-tetrad core in G-quadruplex are important for biological roles of G-quadruplexes. TTA loop is a common sequence which mainly resides in human telomeric DNA (hTel) G-quadruplex. A series of molecular dynamics (MD) simulations were carried out to investigate the structural dynamics of TTA loops. We found that (1) the TA base pair formed in TTA loops are very stable, the occupied of all hydrogen bonds are more than 0.95. (2) The TA base pair makes the adjacent G-quartet more stable than others. (3) For the edgewise loop and the diagonal loop, most loop bases are stacking with others, only few bases have considerable freedom. (4) The stabilities of these stacking structures are distinct. Part of the loops, especially TA base pairs, and bases stacking with the G-quartet, maintain certain stable conformations in the simulation, but other parts, like TT and TA stacking structures, are not stable enough. For the first time, spontaneous conformational switches of TTA edgewise loops were observed in our long time MD simulations. (5) For double chain reversal loop, it is really hard to maintain a stable conformation in the long time simulation under present force fields (parm99 and parmbsc0), as it has multiple conformations with similar free energies.
format	article
author	Hong Zhu Shiyan Xiao Haojun Liang
author_facet	Hong Zhu Shiyan Xiao Haojun Liang
author_sort	Hong Zhu
title	Structural dynamics of human telomeric G-quadruplex loops studied by molecular dynamics simulations.
title_short	Structural dynamics of human telomeric G-quadruplex loops studied by molecular dynamics simulations.
title_full	Structural dynamics of human telomeric G-quadruplex loops studied by molecular dynamics simulations.
title_fullStr	Structural dynamics of human telomeric G-quadruplex loops studied by molecular dynamics simulations.
title_full_unstemmed	Structural dynamics of human telomeric G-quadruplex loops studied by molecular dynamics simulations.
title_sort	structural dynamics of human telomeric g-quadruplex loops studied by molecular dynamics simulations.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/79eb64632fad471db5b923427a906540
work_keys_str_mv	AT hongzhu structuraldynamicsofhumantelomericgquadruplexloopsstudiedbymoleculardynamicssimulations AT shiyanxiao structuraldynamicsofhumantelomericgquadruplexloopsstudiedbymoleculardynamicssimulations AT haojunliang structuraldynamicsofhumantelomericgquadruplexloopsstudiedbymoleculardynamicssimulations
_version_	1718421030095028224

Structural dynamics of human telomeric G-quadruplex loops studied by molecular dynamics simulations.

Ejemplares similares