Polarization effect within a protein crystal: A molecular dynamics simulation study

Abstract Systematical molecular dynamics with different force fields are performed to simulate the structure and dynamics of crystal of hen egg-white lysozyme, including AMBER and three versions of protein-specific charge, PPC. The electrostatic polarization within the crystal is studied with the comparison among four 250 ns trajectories under them. Results show that under appropriate parameterized PPC, the protein can be stable during simulations, indicated by both smaller root-mean-square deviation and closer crystallographic B-factors to the experimental values. This work also shows how the selection of dielectric constant affects the results of utilizing PPC.