Effect of polarization on the stability of a helix dimer

Abstract

Molecular dynamics (MD) simulations have been carried out to study helix–helix interaction using both standard AMBER and polarized force fields. Comparison of the two simulations shows that electrostatic polarization of intra-protein hydrogen bonds plays a significant role in stabilizing the structure of helix dimer. This stabilizing effect is clearly demonstrated by examining the monomer structure, helix crossing angle and stability of backbone hydrogen bonds under AMBER and PPC. Since reliable prediction of protein–protein structure is a significant challenge, the current study should help shed light on the importance of electrostatic polarization of protein in helix–helix interaction and helix bundle structures.