Using Molecular Dynamics to Study the Crystallization of Thaumatin

Abstract

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.