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Volume 5   Issue 2   Year 2010
Application of the RISM Method to Estimate the Relative Gibbs Free Energies of 4',6-Diamidino-2-phenylindole Binding Within the Minor Groove of a DNA Along Simulation Trajectory

Sobolev E.V., Tikhonov D.A., Freedman H., Truong T.N.

Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
Department of Chemistry, Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, USA

Abstract. The efficient parallel algorithm for solving RISM equations in infinity dilution limit and estimate of solvation free energy was applied to study the relative binding energies of sequence-specific binding modes of 4',6-diamidino-2-phenylindole (DAPI) within the minor groove of a DNA duplex. The speedy implementation allows solvation free energies to be calculated at all points along a given simulation trajectory, leading to a more accurate representation of the solute than in the usual RISM approach considering the solute molecule as frozen.

Keywords: thermodynamics, solvation of macromolecule, Gibbs free energy, integral equations of theory of liquids, RISM, DNA.

Table of Contents Original Article
Math. Biol. Bioinf.
doi: 10.17537/2010.5.98
published in Russian

Abstract (rus.)
Abstract (eng.)
Full text (rus., pdf)


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