Treatment of Hydrogen Bonds in Protein Simulations

Abstract

The hydrogen bond plays an essential role in maintaining the secondary structures of protein, and an accurate description of hydrogen bond interaction is critical in protein folding simulation. Modern classical force fields treat hydrogen bonding as nonbond‐ ed interaction, which is dominated by electrostatic interaction. However, in the widely used nonpolarizable force fields, atomic charges are fixed and are determined in a mean-field fashion. Applying nonpolarizable AMBER force field in the folding simulations of some short peptides, the native structure cannot be well populated. When polarization effect is introduced into the simulation by utilizing either the onthe-fly charge fitting or the polarizable hydrogen bond model, the native structure becomes prominent in the free energy landscape. These studies highlight the necessity of electrostatic polarization effect in protein simulation.