Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68081707%3A_____%2F17%3A00485734" target="_blank" >RIV/68081707:_____/17:00485734 - isvavai.cz</a>
Alternative codes found
RIV/61989592:15310/17:73584502
Result on the web
<a href="http://dx.doi.org/10.1021/acs.jctc.7b00226" target="_blank" >http://dx.doi.org/10.1021/acs.jctc.7b00226</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1021/acs.jctc.7b00226" target="_blank" >10.1021/acs.jctc.7b00226</a>
Alternative languages
Result language
angličtina
Original language name
Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations
Original language description
We have carried out a series of extended unbiased molecular dynamics (MD) simulations (up to 10 its long, similar to 162 mu s in total) complemented by replica-exchange with the collective variable tempering (RECT) approach for several human telomeric DNA G-quadruplex (GQ) topologies with TTA propeller loops. We used different AMBER DNA force-field variants and also processed simulations by Markov State Model (MSM) analysis. The slow conformational transitions in the propeller loops took place on a scale of a few,us, emphasizing the need for long simulations in studies of GQ dynamics. The propeller loops sampled similar ensembles for all GQtopologies and for all force field dihedral-potential variants. The outcomes of standard and RECT simulations were consistent and captured similar spectrum of loop conformations. However, the most common crystallographic loop conformation was very unstable with all force-field versions. Although the loss of canonical gamma-trans state of the first propeller loop nucleotide could be related to the indispensable bsc0 alpha/gamma dihedral potential, even supporting this particular dihedral by a bias was insufficient to populate the experimentally dominant loop conformation. In conclusion, while our simulations were capable of providing a reasonable albeit not converged sampling of the TTA propeller loop conformational space, the force-field description still remained far from satisfactory.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10403 - Physical chemistry
Result continuities
Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)
Others
Publication year
2017
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Journal of Chemical Theory and Computation
ISSN
1549-9618
e-ISSN
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Volume of the periodical
13
Issue of the periodical within the volume
6
Country of publishing house
US - UNITED STATES
Number of pages
23
Pages from-to
2458-2480
UT code for WoS article
000403530100010
EID of the result in the Scopus database
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