Electronic polarization effects on protein pdb 2khk.

Abstract

Standard AMBER charge model with non-polarized force fields and polarized protein-specific charge (PPC) charge model with polarized force fields were employed to study Molecular Dynamics (MD) simulations and their effects on Protein Data Bank (PDB) entry 2KHK which consists of 53 amino acids, b30 to 82 domain of F1Fo ATP synthases in Escherichia coli. Our study reveals that the protein structure obtained under PPC simulation is similar to the native state discovered by NMR method and it corresponds to the lowest-energy conformation of the protein. Whereas for AMBER simulation, denatured protein was observed and the structure deviates much from the native state. Moreover energy conformation of the denatured protein is much higher than that of the native structure. Hence indicating that under the influence of PPC, the native conformations of these proteins are dynamically more stable. This presents strong evidence that polarization effect plays a significant role in stabilizing the native conformations of proteins.