Hydration of nucleic acid fragments: comparison of theory and experiment for high-resolution crystal structures of RNA, DNA, and DNA-drug complexes

Biophysical Journal
G HummerD M Soumpasis

Abstract

A computationally efficient method to describe the organization of water around solvated biomolecules is presented. It is based on a statistical mechanical expression for the water-density distribution in terms of particle correlation functions. The method is applied to analyze the hydration of small nucleic acid molecules in the crystal environment, for which high-resolution x-ray crystal structures have been reported. Results for RNA [r(ApU).r(ApU)] and DNA [d(CpG).d(CpG) in Z form and with parallel strand orientation] and for DNA-drug complexes [d(CpG).d(CpG) with the drug proflavine intercalated] are described. A detailed comparison of theoretical and experimental data shows positional agreement for the experimentally observed water sites. The presented method can be used for refinement of the water structure in x-ray crystallography, hydration analysis of nuclear magnetic resonance structures, and theoretical modeling of biological macromolecules such as molecular docking studies. The speed of the computations allows hydration analyses of molecules of almost arbitrary size (tRNA, protein-nucleic acid complexes, etc.) in the crystal environment and in aqueous solution.

Citations

Jan 5, 2002·Biopolymers·P Auffinger, E Westhof
Jun 19, 1998·Current Opinion in Structural Biology·B M PettittB K Andrews
Jan 17, 2012·Journal of the American Chemical Society·Elizabeth J Denning, Alexander D MacKerell
Mar 18, 1997·Proceedings of the National Academy of Sciences of the United States of America·T I OpreaA E Garcia
Sep 18, 1997·Proceedings of the National Academy of Sciences of the United States of America·M L VerkhovskayaM Wikström
Apr 30, 2013·Journal of Biomolecular NMR·Marc van DijkAlexandre M J J Bonvin
Mar 26, 2011·Biophysical Chemistry·Kunitsugu SodaMakoto Taiji
Sep 8, 2010·Biophysical Journal·Jouko J VirtanenKarl F Freed
Oct 28, 1998·Biophysical Journal·B SchneiderH M Berman
Dec 7, 2000·Biophysical Journal·V A MakarovB M Pettitt
Jun 17, 2008·Chembiochem : a European Journal of Chemical Biology·Jozica DolencWilfred F van Gunsteren
Jan 1, 1996·Faraday Discussions·G HummerD M Soumpasis
May 1, 1996·Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics·S GardeM E Paulaitis
Jan 1, 1995·Progress in Biophysics and Molecular Biology·B P SchoenbornR Knott
Mar 27, 2003·Journal of the American Chemical Society·Srabani Taraphder, Gerhard Hummer

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