Matches in SemOpenAlex for { <https://semopenalex.org/work/W2724349047> ?p ?o ?g. }
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- W2724349047 abstract "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 (∼580 μs 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 simulations were executed with the SPC/E water model; however, test simulations with TIP3P and OPC water models 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-μs-scale simulations of fully folded GQs can be safely done with a number of cation parametrizations. However, there are parametrization-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." @default.
- W2724349047 created "2017-07-14" @default.
- W2724349047 creator A5016773569 @default.
- W2724349047 creator A5026399646 @default.
- W2724349047 creator A5028187203 @default.
- W2724349047 creator A5041529029 @default.
- W2724349047 creator A5065501960 @default.
- W2724349047 date "2017-07-17" @default.
- W2724349047 modified "2023-10-16" @default.
- W2724349047 title "Effect of Monovalent Ion Parameters on Molecular Dynamics Simulations of G-Quadruplexes" @default.
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