Comparison of reduced point charge models of proteins: Molecular Dynamics simulations of Ubiquitin

Reduced point charge models of amino acids are used to model Ubiquitin (PDB: 1UBQ). They are designed (i) from local extremum positions in charge density (CD) distribution functions built from the Poisson equation applied to smoothed molecular electrostatic potential functions, or (ii) from local maximum positions in promolecular electron density distribution (ED) functions. Charge values are fitted versus all-atom Amber99 molecular electrostatic potentials. The program GROMACS is used to generate molecular dynamics trajectories of the protein, under various implementation schemes, solvation, and temperature conditions. Point charges that are not located on atoms are considered as virtual sites with a null mass and radius. The results illustrate that secondary structure is best preserved with the CD-based model at low temperatures and in vacuum. This indicates that local potential energy wells are consistent with the all-atom model. However, at room temperature, the structure is best conserved when point charges are forced to be located on atoms, due to a better description of the Coulomb 1–4 energy terms. The ED-based model, generated at a lower resolution, led to the largest discrepancies versus the all-atom case. The CD-based model allows the formation of protein-water H-bonds with geometrical properties similar to the all-atom ones. Contrarily, intra-molecular H-bonds are not well described. Structural, thermodynamical, and dynamical properties of proteins modelled with reduced point charge models are also significantly affected by the choice of the solvent force field.