Antigen–antibody interactions are critical for understanding antigen–antibody associations in immunology. To shed further light on this que stion, we studied a dissociation of the 19D9D6-HCV core protein antibody complex structure. However, forced separations in single molecule experiments are difficult, and therefore molecular
simulation techniqueswere applied in our study. The stretching, that is, the distance between the center of mass of theHCV core protein and the 19D9D6 antibody, has been studied using the potential ofmean force calculations based on molecular dynamics and the explicit water model. Our simulations indicate that the 7 residues Gly70, Gly72, Gly134, Gly158, Glu219, Gln221 and Tyr314, the interaction region (antibody), and the 14 interprotein molecular hydrogen bonds might play important roles in the antigen–antibody interaction, and this findingmay be useful for protein engineering of this antigen–antibody structure. In addition, the 3 residues Gly134, Gly158 and Tyr314 might be more important in the development of bioactive antibody analogs.
