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Improved Parametrization of Li+, Na+, K+, and Mg2+ Ions for All-Atom Molecular Dynamics Simulations of Nucleic Acid Systems

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    Macromolecules, Soft Matter

    Improved Parametrization of Li+, Na+, K+, and Mg2+ Ions for All-Atom Molecular Dynamics Simulations of Nucleic Acid Systems
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    † ‡ †Department of Physics and ‡Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
    *E-mail: [email protected]
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    The Journal of Physical Chemistry Letters

    Cite this: J. Phys. Chem. Lett. 2012, 3, 1, 45–50
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    https://doi.org/10.1021/jz201501a
    Published December 6, 2011
    Copyright © 2011 American Chemical Society
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    Abstract

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    Atomic-scale modeling of compacted nucleic acids has the ability to reveal the inner workings of spectacular biomolecular machines, yet the outcome of such modeling efforts sensitively depends on the accuracy of the underlying computational models. Our molecular dynamics simulations of an array of 64 parallel duplex DNA revealed considerable artifacts of cation–DNA phosphate interactions in CHARMM and AMBER parameter sets: both the DNA arrangement and the pressure inside the DNA arrays were found to be in considerable disagreement with experiment. To improve the models, we fine-tuned van der Waals interaction parameters for specific ion pairs to reproduce experimental osmotic pressure of binary electrolyte solutions of biologically relevant ions. Repeating the DNA array simulations using our parameters produced results consistent with experiment. Our improved parametrization can be directly applied to molecular dynamics simulations of various charged biomolecular systems, including nucleic acids, proteins, and lipid bilayer membranes.

    Copyright © 2011 American Chemical Society

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    Detailed description of the setup and procedures used in our MD simulations, discussion of the force field choices and our treatment of magnesium, complete account of the fitting procedures, and sample parameter files with NBFIX corrections. This material is available free of charge via the Internet at http://pubs.acs.org.

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    Cite this: J. Phys. Chem. Lett. 2012, 3, 1, 45–50
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    https://doi.org/10.1021/jz201501a
    Published December 6, 2011
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