J. Yoo and A. Aksimentiev.
Improved parametrization of Li+, Na+,
K+, and Mg2+.
Journal of Physical Chemistry Letters, 3:45-50, 2012.
YOO2012-AA
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.
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