Hairpins participating in folding of human telomeric sequence
quadruplexes studied by standard and T-REMD simulations

J 2015

Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations

STADLBAUER, Petr, Petra KUHROVÁ, Pavel BANÁŠ, Jaroslav KOČA, Giovanni BUSSI et. al.

Basic information

Original name

Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations

Authors

STADLBAUER, Petr (203 Czech Republic), Petra KUHROVÁ (203 Czech Republic), Pavel BANÁŠ (203 Czech Republic), Jaroslav KOČA (203 Czech Republic, belonging to the institution), Giovanni BUSSI (380 Italy), Lukáš TRANTÍREK (203 Czech Republic, belonging to the institution), Michal OTYEPKA (203 Czech Republic) and Jiří ŠPONER (203 Czech Republic, guarantor, belonging to the institution)

Edition

Nucleic Acids Research, Oxford, Oxford University Press, 2015, 0305-1048

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10600 1.6 Biological sciences

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 9.202

RIV identification code

RIV/00216224:14740/15:00086621

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1093/nar/gkv994

UT WoS

000366410000016

Keywords in English

MOLECULAR-DYNAMICS SIMULATIONS; INTRAMOLECULAR DNA QUADRUPLEXES; PARTICLE MESH EWALD; AMBER FORCE-FIELD; G-TRACT LENGTH; NUCLEIC-ACIDS; REPLICA-EXCHANGE; K+ SOLUTION; ENERGY LANDSCAPE; STRUCTURAL DYNAMICS

Abstract

V originále

DNA G-hairpins are potential key structures participating in folding of human telomeric guanine quadruplexes (GQ). We examined their properties by standard MD simulations starting from the folded state and long T-REMD starting from the unfolded state, accumulating similar to 130 mu s of atomistic simulations. Antiparallel G-hairpins should spontaneously form in all stages of the folding to support lateral and diagonal loops, with sub-mu s scale rearrangements between them. We found no clear predisposition for direct folding into specific GQ topologies with specific syn/anti patterns. Our key prediction stemming from the T-REMD is that an ideal unfolded ensemble of the full GQ sequence populates all 4096 syn/anti combinations of its four G-stretches. The simulations can propose idealized folding pathways but we explain that such few-state pathways may be misleading. In the context of the available experimental data, the simulations strongly suggest that the GQ folding could be best understood by the kinetic partitioning mechanism with a set of deep competing minima on the folding landscape, with only a small fraction of molecules directly folding to the native fold. The landscape should further include non-specific collapse processes where the molecules move via diffusion and consecutive random rare transitions, which could, e.g. structure the propeller loops.

Links

ED1.1.00/02.0068, research and development project

Name: CEITEC - central european institute of technology

Files attached

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Citovat

STADLBAUER, Petr, Petra KUHROVÁ, Pavel BANÁŠ, Jaroslav KOČA, Giovanni BUSSI, Lukáš TRANTÍREK, Michal OTYEPKA and Jiří ŠPONER. Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations. Nucleic Acids Research. Oxford: Oxford University Press, 2015, vol. 43, No 20, p. 9626-9644. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkv994.

@article{1335876,
   author = {Stadlbauer, Petr and Kuhrová, Petra and Banáš, Pavel and Koča, Jaroslav and Bussi, Giovanni and Trantírek, Lukáš and Otyepka, Michal and Šponer, Jiří},
   article_location = {Oxford},
   article_number = {20},
   doi = {http://dx.doi.org/10.1093/nar/gkv994},
   keywords = {MOLECULAR-DYNAMICS SIMULATIONS; INTRAMOLECULAR DNA QUADRUPLEXES; PARTICLE MESH EWALD; AMBER FORCE-FIELD; G-TRACT LENGTH; NUCLEIC-ACIDS; REPLICA-EXCHANGE; K+ SOLUTION; ENERGY LANDSCAPE; STRUCTURAL DYNAMICS},
   language = {eng},
   issn = {0305-1048},
   journal = {Nucleic Acids Research},
   title = {Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations},
   url = {http://nar.oxfordjournals.org/content/43/20/9626.full.pdf+html},
   volume = {43},
   year = {2015}
}

TY  - JOUR
ID  - 1335876
AU  - Stadlbauer, Petr - Kuhrová, Petra - Banáš, Pavel - Koča, Jaroslav - Bussi, Giovanni - Trantírek, Lukáš - Otyepka, Michal - Šponer, Jiří
PY  - 2015
TI  - Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations
JF  - Nucleic Acids Research
VL  - 43
IS  - 20
SP  - 9626-9644
EP  - 9626-9644
PB  - Oxford University Press
SN  - 03051048
KW  - MOLECULAR-DYNAMICS SIMULATIONS
KW  - INTRAMOLECULAR DNA QUADRUPLEXES
KW  - PARTICLE MESH EWALD
KW  - AMBER FORCE-FIELD
KW  - G-TRACT LENGTH
KW  - NUCLEIC-ACIDS
KW  - REPLICA-EXCHANGE
KW  - K+ SOLUTION
KW  - ENERGY LANDSCAPE
KW  - STRUCTURAL DYNAMICS
UR  - http://nar.oxfordjournals.org/content/43/20/9626.full.pdf+html
L2  - http://nar.oxfordjournals.org/content/43/20/9626.full.pdf+html
N2  - DNA G-hairpins are potential key structures participating in folding of human telomeric guanine quadruplexes (GQ). We examined their properties by standard MD simulations starting from the folded state and long T-REMD starting from the unfolded state, accumulating similar to 130 mu s of atomistic simulations. Antiparallel G-hairpins should spontaneously form in all stages of the folding to support lateral and diagonal loops, with sub-mu s scale rearrangements between them. We found no clear predisposition for direct folding into specific GQ topologies with specific syn/anti patterns. Our key prediction stemming from the T-REMD is that an ideal unfolded ensemble of the full GQ sequence populates all 4096 syn/anti combinations of its four G-stretches. The simulations can propose idealized folding pathways but we explain that such few-state pathways may be misleading. In the context of the available experimental data, the simulations strongly suggest that the GQ folding could be best understood by the kinetic partitioning mechanism with a set of deep competing minima on the folding landscape, with only a small fraction of molecules directly folding to the native fold. The landscape should further include non-specific collapse processes where the molecules move via diffusion and consecutive random rare transitions, which could, e.g. structure the propeller loops.
ER  -

STADLBAUER, Petr, Petra KUHROVÁ, Pavel BANÁŠ, Jaroslav KOČA, Giovanni BUSSI, Lukáš TRANTÍREK, Michal OTYEPKA and Jiří ŠPONER. Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations. \textit{Nucleic Acids Research}. Oxford: Oxford University Press, 2015, vol.~43, No~20, p.~9626-9644. ISSN~0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkv994.

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