Effect of Monovalent Ion Parameters on Molecular Dynamics Simulations of G-Quadruplexes
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68081707%3A_____%2F17%3A00485606" target="_blank" >RIV/68081707:_____/17:00485606 - isvavai.cz</a>
Alternative codes found
RIV/00216224:14740/17:00100461 RIV/61989592:15310/17:73584494
Result on the web
<a href="http://dx.doi.org/10.1021/acs.jctc.7b00267" target="_blank" >http://dx.doi.org/10.1021/acs.jctc.7b00267</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1021/acs.jctc.7b00267" target="_blank" >10.1021/acs.jctc.7b00267</a>
Alternative languages
Result language
angličtina
Original language name
Effect of Monovalent Ion Parameters on Molecular Dynamics Simulations of G-Quadruplexes
Original language description
G-quadruplexes (GQs) are key noncanonical DNA and RNA architectures stabilized by desolvated monovalent cations present in their central channels. We analyze extended atomistic molecular dynamics simulations (similar to 580 mu s in total) of GQs with 11 monovalent cation parametrizations, assessing GQ overall structural stability, dynamics of internal cations, and distortions of the G-tetrad geometries. Majority of however, test simulations with TIP3P and OPC water models simulations were executed with the SPC/E water model, are also reported. The identity and parametrization of ions strongly affect behavior of a tetramolecular d[GGG](4) GQ, which is unstable with, several ion parametrizations. The remaining studied RNA and DNA GQs are structurally stable, though the G-tetrad geometries are always deformed by bifurcated H-bonding in a parametrization-specific manner. Thus, basic 10-mu s-scale simulations of fully folded GQs can be safely done with a number of cation,parametrization. However, there are patametrization-specific differences and basic force-field errors affecting the quantitative description of ion-tetrad interactions,, which may significantly affect studies of the ion-binding processes and description of the GQ folding landscape. Our d[GGG]4 simulations indirectly suggest that such studies will also be sensitive to the water models. During exchanges with bulk water, the Na+ ions move inside the GQs in a concerted manner, While larger relocations of the K+ ions are typically separated. We suggest that the Joung-Cheatham SPC/E K+ parameters represent a safe choice in simulation studies of GQs, though variation of ion parameters can be used for specific simulation goals.
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
8
Country of publishing house
US - UNITED STATES
Number of pages
16
Pages from-to
3911-3926
UT code for WoS article
000407522100040
EID of the result in the Scopus database
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