We demonstrate that the crystallization system of the protein thaumatin in the presence of
tartrate ions can be studied with GROMACS molecular dynamics simulations. We show that
the OPLS all-atom force field can be used to model L- and D-tartrate with some modifications
to the partial atomic charges and the short-range electrostatic forces. Additionally, our
models of L- and D-tartrate can bind to arginine residues, as they do in thaumatin crystals, if a
constraint is placed upon the location of the hydroxyl protons. We find that both L- and Dtartrate
preferentially bind to arginine and lysine residues on thaumatin, as expected based on
experimental data and these residues’ partial positive charge. We show that the thaumatintartrate
system and the difference between L- and D-tartrate may be studied effectively using
molecular dynamics models.
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