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• W2891153952 endingPage "5026" @default.
• W2891153952 startingPage "5011" @default.
• W2891153952 abstract "The NMR solution structures of human telomeric (Htel) G-quadruplexes (GQs) are characterized by the presence of two lateral loops complemented by either diagonal or propeller loops. Bases of a given loop can establish interactions within the loop as well as with other loops and the flanking bases. This can lead to a formation of base alignments above and below the GQ stems. These base alignments are known to affect the loop structures and relative stabilities of different Htel GQ folds. We have carried out a total of 217 μs of classical (unbiased) molecular dynamics (MD) simulations starting from the available solution structures of Htel GQs to characterize structural dynamics of the lateral and diagonal loops, using several recent AMBER DNA force-field variants. As the loops are involved in diverse stacking and H-bonding interactions, their dynamics is slow, and extended sampling is required to capture different conformations. Nevertheless, although the simulations are far from being quantitatively converged, the data suggest that multiple 10 μs-scale simulations can provide a quite good assessment of the loop conformational space as described by the force field. The simulations indicate that the lateral loops may sample multiple coexisting conformations, which should be considered when comparing simulations with the NMR models as the latter include ensemble averaging. The adenine–thymine Watson–Crick arrangement was the most stable base pairing in the simulations. Adenine–adenine and thymine–thymine base pairs were also sampled but were less stable. The data suggest that the description of lateral and diagonal GQ loops in contemporary MD simulations is considerably more realistic than the description of propeller loops, though definitely not flawless." @default.
• W2891153952 created "2018-09-27" @default.
• W2891153952 creator A5009175551 @default.
• W2891153952 creator A5016773569 @default.
• W2891153952 creator A5026399646 @default.
• W2891153952 creator A5028187203 @default.
• W2891153952 creator A5037269329 @default.
• W2891153952 creator A5065501960 @default.
• W2891153952 date "2018-09-05" @default.
• W2891153952 modified "2023-10-16" @default.
• W2891153952 title "Structural Dynamics of Lateral and Diagonal Loops of Human Telomeric G-Quadruplexes in Extended MD Simulations" @default.
• W2891153952 cites W1632349675 @default.
• W2891153952 cites W1784617990 @default.
• W2891153952 cites W1889327264 @default.
• W2891153952 cites W1915004688 @default.
• W2891153952 cites W1921820043 @default.
• W2891153952 cites W1942920752 @default.
• W2891153952 cites W1967366836 @default.
• W2891153952 cites W1969189143 @default.
• W2891153952 cites W1972820538 @default.
• W2891153952 cites W1978685619 @default.
• W2891153952 cites W1979860914 @default.
• W2891153952 cites W1980263741 @default.
• W2891153952 cites W1981225934 @default.
• W2891153952 cites W1981888951 @default.
• W2891153952 cites W1987046124 @default.
• W2891153952 cites W1991827974 @default.
• W2891153952 cites W1993152080 @default.
• W2891153952 cites W2001785938 @default.
• W2891153952 cites W2001828972 @default.
• W2891153952 cites W2002025936 @default.
• W2891153952 cites W2002730194 @default.
• W2891153952 cites W2006496261 @default.
• W2891153952 cites W2007812774 @default.
• W2891153952 cites W2009186918 @default.
• W2891153952 cites W2009231552 @default.
• W2891153952 cites W2009846643 @default.
• W2891153952 cites W2011428226 @default.
• W2891153952 cites W2015037479 @default.
• W2891153952 cites W2018900810 @default.
• W2891153952 cites W2023735050 @default.
• W2891153952 cites W2029667189 @default.
• W2891153952 cites W2037146644 @default.
• W2891153952 cites W2040413013 @default.
• W2891153952 cites W2044480512 @default.
• W2891153952 cites W2045571168 @default.
• W2891153952 cites W2053586924 @default.
• W2891153952 cites W2055717669 @default.
• W2891153952 cites W2057429923 @default.
• W2891153952 cites W2058197513 @default.
• W2891153952 cites W2062724831 @default.
• W2891153952 cites W2067174909 @default.
• W2891153952 cites W2068727176 @default.
• W2891153952 cites W2079438618 @default.
• W2891153952 cites W2082168427 @default.
• W2891153952 cites W2082633296 @default.
• W2891153952 cites W2083370569 @default.
• W2891153952 cites W2089527788 @default.
• W2891153952 cites W2089619525 @default.
• W2891153952 cites W2092449862 @default.
• W2891153952 cites W2095447252 @default.
• W2891153952 cites W2095900421 @default.
• W2891153952 cites W2098085059 @default.
• W2891153952 cites W2121069954 @default.
• W2891153952 cites W2122199548 @default.
• W2891153952 cites W2128856714 @default.
• W2891153952 cites W2130272241 @default.
• W2891153952 cites W2133038385 @default.
• W2891153952 cites W2136729627 @default.
• W2891153952 cites W2144100895 @default.
• W2891153952 cites W2145344158 @default.
• W2891153952 cites W2166630132 @default.
• W2891153952 cites W2168839470 @default.
• W2891153952 cites W2171830519 @default.
• W2891153952 cites W2172060739 @default.
• W2891153952 cites W2181156889 @default.
• W2891153952 cites W2229724153 @default.
• W2891153952 cites W2230812641 @default.
• W2891153952 cites W2278099513 @default.
• W2891153952 cites W2315961248 @default.
• W2891153952 cites W2321647501 @default.
• W2891153952 cites W2322862858 @default.
• W2891153952 cites W2327806745 @default.
• W2891153952 cites W2332712348 @default.
• W2891153952 cites W2344252179 @default.
• W2891153952 cites W2398201425 @default.
• W2891153952 cites W2407404800 @default.
• W2891153952 cites W2417212801 @default.
• W2891153952 cites W2433523887 @default.
• W2891153952 cites W2503315900 @default.
• W2891153952 cites W2561564177 @default.
• W2891153952 cites W2570104014 @default.
• W2891153952 cites W2571150331 @default.
• W2891153952 cites W2591101673 @default.
• W2891153952 cites W2595859407 @default.
• W2891153952 cites W2610750301 @default.
• W2891153952 cites W2614205362 @default.
• W2891153952 cites W2621961850 @default.

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