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Effect of coordinated ions on structure and flexibility of parallel G-quadruplexes: A molecular dynamics study

Chowdhury, Shibasish and Bansal, Manju (2000) Effect of coordinated ions on structure and flexibility of parallel G-quadruplexes: A molecular dynamics study. In: Journal of Biomolecular Structure & Dynamics, 18 (1). pp. 11-28.

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Abstract

ingle tract guanine residues can associate to form stable parallel quadruplex structures in the presence of certain cations. Nanosecond scale molecular dynamics simulations have been performed on fully solvated fibre model of parallel d(G(7)) quadruplex structures with Na+ or K+ ions coordinated in the cavity formed by the O6 atoms of the guanine bases. The AMBER 4.1 force field and Particle Mesh Ewald technique for electrostatic interactions have been used in all simulations. There quadruplex structures are stable during the simulation, with the middle four base tetrads showing root mean square deviation values between 0.5 to 0.8 Angstrom from the initial structure as well the high resolution crystal structure. Even in the absence of any coordinated ion in the initial structure, the G-quadruplex structure remains intact throughout the simulation. During the 1.1 ns MD simulation, one Nai counter ion from the solvent as well as several water molecules enter the central cavity to occupy the empty coordination sites within the parallel quadruplex and help stabilize the structure. Hydrogen bonding pattern depends on the nature of the coordinated ion, with the G-tetrad undergoing local structural variation to accommodate cations of different sizes. in the absence of any coordinated ion. due to strong mutual repulsion, O6 atoms within G-tetrad are forced farther apart from each other, which leads to a considerably different hydrogen bonding scheme within the G-tetrads and very favourable interaction energy between the guanine bases constituting a G-tetrad. However, a coordinated ion between G-tetrads provides extra stacking energy for the G-tetrads and makes the quadruplex structure more rigid. Na+ ions, within the quadruplex cavity, are more mobile than coordinated K+ ions. A number of hydrogen bonded water molecules are observed within the grooves of all quadruplex structures.

Item Type: Journal Article
Additional Information: Copyright of this article belongs to Adenine Press.
Department/Centre: Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited: 09 Aug 2010 10:50
Last Modified: 19 Sep 2010 06:13
URI: http://eprints.iisc.ernet.in/id/eprint/31068

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