FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2469383222> ?p ?o ?g. }

• W2469383222 endingPage "7391" @default.
• W2469383222 startingPage "7380" @default.
• W2469383222 abstract "Most molecular dynamics (MD) simulations of DNA quadruplexes have been performed under minimal salt conditions using the Åqvist potential parameters for the cation with the TIP3P water model. Recently, this combination of parameters has been reported to be problematic for the stability of quadruplex DNA, especially caused by the ion interactions inside or near the quadruplex channel. Here, we verify how the choice of ion parameters and water model can affect the quadruplex structural stability and the interactions with the ions outside the channel. We have performed a series of MD simulations of the human full-parallel telomeric quadruplex by neutralizing its negative charge with K+ ions. Three combinations of different cation potential parameters and water models have been used: (a) Åqvist ion parameters, TIP3P water model; (b) Joung and Cheatham ion parameters, TIP3P water model; and (c) Joung and Cheatham ion parameters, TIP4Pew water model. For the combinations (b) and (c), the effect of the ionic strength has been evaluated by adding increasing amounts of KCl salt (50, 100, and 200 mM). Two independent simulations using the Åqvist parameters with the TIP3P model show that this combination is clearly less suited for the studied quadruplex with K+ as counterions. In both simulations, one ion escapes from the channel, followed by significant deformation of the structure, leading to deviating conformation compared to that in the reference crystallographic data. For the other combinations of ion and water potentials, no tendency is observed for the channel ions to escape from the quadruplex channel. In addition, the internal mobility of the three loops, torsion angles, and counterion affinity have been investigated at varied salt concentrations. In summary, the selection of ion and water models is crucial as it can affect both the structure and dynamics as well as the interactions of the quadruplex with its counterions. The results obtained with the TIP4Pew model are found to be closest to the experimental data at all of the studied ion concentrations." @default.
• W2469383222 created "2016-07-22" @default.
• W2469383222 creator A5019849798 @default.
• W2469383222 creator A5021992046 @default.
• W2469383222 creator A5026399646 @default.
• W2469383222 creator A5071845719 @default.
• W2469383222 creator A5087678650 @default.
• W2469383222 date "2016-07-26" @default.
• W2469383222 modified "2023-10-16" @default.
• W2469383222 title "Molecular Dynamics Simulation Study of Parallel Telomeric DNA Quadruplexes at Different Ionic Strengths: Evaluation of Water and Ion Models" @default.
• W2469383222 cites W1575740340 @default.
• W2469383222 cites W1676032689 @default.
• W2469383222 cites W1889327264 @default.
• W2469383222 cites W1942920752 @default.
• W2469383222 cites W1967737979 @default.
• W2469383222 cites W1976499671 @default.
• W2469383222 cites W1978498560 @default.
• W2469383222 cites W1981021420 @default.
• W2469383222 cites W1981225934 @default.
• W2469383222 cites W1984760060 @default.
• W2469383222 cites W1986961755 @default.
• W2469383222 cites W1998617042 @default.
• W2469383222 cites W1999900311 @default.
• W2469383222 cites W2001785938 @default.
• W2469383222 cites W2007634776 @default.
• W2469383222 cites W2007812774 @default.
• W2469383222 cites W2009231552 @default.
• W2469383222 cites W2011727914 @default.
• W2469383222 cites W2015625843 @default.
• W2469383222 cites W2016133492 @default.
• W2469383222 cites W2024726841 @default.
• W2469383222 cites W2026823636 @default.
• W2469383222 cites W2029667189 @default.
• W2469383222 cites W2034512710 @default.
• W2469383222 cites W2040413013 @default.
• W2469383222 cites W2042285588 @default.
• W2469383222 cites W2046159224 @default.
• W2469383222 cites W2049475242 @default.
• W2469383222 cites W2051564720 @default.
• W2469383222 cites W2053058099 @default.
• W2469383222 cites W2053492014 @default.
• W2469383222 cites W2053586924 @default.
• W2469383222 cites W2054531267 @default.
• W2469383222 cites W2057477511 @default.
• W2469383222 cites W2063702714 @default.
• W2469383222 cites W2067174909 @default.
• W2469383222 cites W2078843953 @default.
• W2469383222 cites W2081693079 @default.
• W2469383222 cites W2082168427 @default.
• W2469383222 cites W2083308932 @default.
• W2469383222 cites W2083370569 @default.
• W2469383222 cites W2087596773 @default.
• W2469383222 cites W2087984168 @default.
• W2469383222 cites W2089527788 @default.
• W2469383222 cites W2092449862 @default.
• W2469383222 cites W2095447252 @default.
• W2469383222 cites W2108843451 @default.
• W2469383222 cites W2121006786 @default.
• W2469383222 cites W2121069954 @default.
• W2469383222 cites W2122199548 @default.
• W2469383222 cites W2123768693 @default.
• W2469383222 cites W2128572087 @default.
• W2469383222 cites W2132306213 @default.
• W2469383222 cites W2133038385 @default.
• W2469383222 cites W2136729627 @default.
• W2469383222 cites W2137500638 @default.
• W2469383222 cites W2144727118 @default.
• W2469383222 cites W2155773930 @default.
• W2469383222 cites W2160544821 @default.
• W2469383222 cites W2161536471 @default.
• W2469383222 cites W2163661389 @default.
• W2469383222 cites W2164876360 @default.
• W2469383222 cites W2167230638 @default.
• W2469383222 cites W2172060739 @default.
• W2469383222 cites W2174254251 @default.
• W2469383222 cites W2316421631 @default.
• W2469383222 cites W2324216403 @default.
• W2469383222 cites W2337120805 @default.
• W2469383222 cites W2343350205 @default.
• W2469383222 cites W2410310292 @default.
• W2469383222 cites W3104468196 @default.
• W2469383222 doi "https://doi.org/10.1021/acs.jpcb.6b06485" @default.
• W2469383222 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/27379924" @default.
• W2469383222 hasPublicationYear "2016" @default.
• W2469383222 type Work @default.
• W2469383222 sameAs 2469383222 @default.
• W2469383222 citedByCount "28" @default.
• W2469383222 countsByYear W24693832222016 @default.
• W2469383222 countsByYear W24693832222017 @default.
• W2469383222 countsByYear W24693832222018 @default.
• W2469383222 countsByYear W24693832222019 @default.
• W2469383222 countsByYear W24693832222020 @default.
• W2469383222 countsByYear W24693832222021 @default.
• W2469383222 countsByYear W24693832222022 @default.
• W2469383222 countsByYear W24693832222023 @default.
• W2469383222 crossrefType "journal-article" @default.
• W2469383222 hasAuthorship W2469383222A5019849798 @default.
• W2469383222 hasAuthorship W2469383222A5021992046 @default.

• next