A nanosecond molecular dynamics study of antiparallel d(G)7 quadruplex structures: effect of the coordinated cations

Journal of Biomolecular Structure & Dynamics
S Chowdhury, M Bansal

Abstract

Nanosecond scale molecular dynamics simulations have been performed on antiparallel Greek key type d(G7) quadruplex structures with different coordinated ions, namely Na+ and K+ ion, water and Na+ counter ions, using the AMBER force field and Particle Mesh Ewald technique for electrostatic interactions. Antiparallel structures are stable during the simulation, with root mean square deviation values of approximately 1.5 A from the initial structures. Hydrogen bonding patterns within the G-tetrads depend on the nature of the coordinated ion, with the G-tetrad undergoing local structural variation to accommodate different cations. However, alternating syn-anti arrangement of bases along a chain as well as in a quartet is maintained through out the MD simulation. Coordinated Na+ ions, within the quadruplex cavity are quite mobile within the central channel and can even enter or exit from the quadruplex core, whereas coordinated K+ ions are quite immobile. MD studies at 400K indicate that K+ ion cannot come out from the quadruplex core without breaking the terminal G-tetrads. Smaller grooves in antiparallel structures are better binding sites for hydrated counter ions, while a string of hydrogen bonded water molecules are observed w...Continue Reading

References

Feb 25, 1975·Journal of Molecular Biology·S B ZimmermanD R Davies
Nov 1, 1992·Proceedings of the National Academy of Sciences of the United States of America·P V ScariaR H Shafer
Aug 11, 1992·Nucleic Acids Research·P BalagurumoorthyV Sasisekharan
Apr 18, 1991·Nature·E H Blackburn
Dec 1, 1990·Journal of Biomolecular Structure & Dynamics·W GuschlbauerD Thiele
Feb 1, 1989·Journal of Biomolecular Structure & Dynamics·D Bhattacharyya, M Bansal
Apr 28, 1988·Nature·T R Cech
Jan 16, 1986·Nature·D Eisenberg, A D McLachlan
Aug 1, 1974·The Biochemical Journal·S ArnottC M Marttila
Dec 8, 1995·Journal of Molecular Biology·A KettaniD J Patel
Apr 28, 1995·Journal of Molecular Biology·T MiuraG J Thomas
Jan 1, 1994·Annual Review of Biophysics and Biomolecular Structure·J R Williamson
Jun 1, 1993·Journal of Molecular Graphics·M L Connolly
Apr 15, 1993·Proceedings of the National Academy of Sciences of the United States of America·W I Sundquist, S Heaphy
Apr 15, 1993·Proceedings of the National Academy of Sciences of the United States of America·R F MacayaJ Feigon
Jan 26, 1996·Journal of Molecular Biology·H Deng, W H Braunlin
Nov 21, 1997·Journal of Molecular Biology·K PhillipsB Luisi
Jan 8, 1999·Journal of Molecular Biology·N V HudJ Feigon
Apr 9, 1999·Biochemistry·V M Marathias, P H Bolton
Apr 27, 1999·Journal of Biomolecular Structure & Dynamics·T E CheathamP A Kollman

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Citations

Jan 5, 2002·Expert Opinion on Investigational Drugs·P J PerryT C Jenkins
Jun 1, 2016·Physical Chemistry Chemical Physics : PCCP·Kaushik ChakrabortySanjoy Bandyopadhyay
Sep 8, 2009·Journal of Chemical Theory and Computation·Eva FadrnáJiří Šponer
Jun 19, 2002·Accounts of Chemical Research·Emmanuel Giudice, Richard Lavery
Dec 22, 2006·The Journal of Physical Chemistry. B·Manuela CavallariRosa Di Felice

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