A Charge Moving Algorithm for Molecular Dynamics Simulations of Gas-Phase Proteins.

A method for moving charges in a coarse-grained simulation of gas-phase proteins is presented which uses a Monte Carlo approach to move charges between charge sites. The method is used to study the role of charge movement in the dissociation mechanism of protein complexes in order to better understand experimentally observed mass spectra from CID studies. The charge hopping process is analyzed using energy distributions and a pair correlation plot. Hopping rates, charge distributions, and structural parameters (radius of gyration and RMSD) are also calculated. The importance of charge movement for the unfolding of protein complexes is demonstrated. The algorithm is implemented in the GROMACS molecular dynamics software package. In this study, transthyretin (TTR) tetramer is used with the MARTINI force field as a model system, and comparisons to experiments are made. The hopping and unfolding are found to be controlled by the Coulomb repulsion among the charges in the complex.