Binding in Human Antibody-DNA Interface: A Computer-Simulation Study

The stretching, that is, the distance between the centre of mass of the ssDNA and the antibody, has been studied using the potential of mean force calculations based on molecular dynamics and the explicit water model. Our simulations indicate that the 6 residues Gln43, Gly44, Arg98, Tyr100, Val136 and Thr137, pair interactions of antibody-ssDNA, and the 5 interprotein molecular hydrogen bonds might play important roles in the antibody-ssDNA interaction, and this finding may be useful for protein engineering of this antibody-ssDNA structure. In addition, the 6 residues Gln43, Gly44, Arg98, Tyr100, Val136 and Thr137 might be more important in the development of bioactive antibody analogues.