Comparative Analysis of Polarizable and Nonpolarizable CHARMM Family Force Fields for Proteins with Flexible Loops and High Charge Density.

Electrostatic interactions are fundamental to biomolecular structure, stability, and function. While these interactions are traditionally modeled using fixed-charge force fields, such approaches are not transferable among different molecular environments. Polarizable force fields, such as DRUDE, address this limitation by explicitly incorporating the polarization effect. However, their performance does not uniformly surpass that of nonpolarizable force fields since multiple factors such as bonded terms, dihedral correction maps, and solvent screening also modulate biomolecular dynamics. In this work, we study the Im7 protein to evaluate the structural and dynamic behaviors of nonpolarizable (CHARMM36m) and polarizable (DRUDE2019) force fields relative to NMR experiments. Our simulations show that DRUDE2019 better stabilizes α-helices than CHARMM36m, including shorter ones that contain helix-breaking residues. However, both force fields underestimate loop dynamics, particularly in the loop I region, mainly due to restricted dihedral angle sampling. Moreover, salt bridge analysis reveals that DRUDE2019 and CHARMM36m preferentially stabilize different salt bridges, driven by ionic interactions, charge screening by the environment, and neighboring residue flexibility Additionally, the latest DRUDE2019 variant, featuring updated NBFIX and NBTHOLE parameters for ion-protein interactions, demonstrated improved accuracy in modeling Na+-protein interactions. These findings are further supported by simulations of CBD1, a protein with a β-sheet and flexible loops, which exhibited similar trends of stable structured regions and restricted loop dynamics across both force fields. These findings highlight the need to balance bonded and nonbonded interactions along with dihedral correction maps while incorporating polarization effects to improve the accuracy of force fields to model protein structure and dynamics.