Author_Institution :
Dept. of Inf. Manage., Chia Nan Univ. of Pharmacy & Sci., Tainan, Taiwan
Abstract :
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.
Keywords :
DNA; biology computing; molecular dynamics method; proteins; Arg98; Gln43; Gly44; Thr137; Tyr100; Yal136; antibody-ssDNA interaction; antibody-ssDNA structure; bioactive antibody analogues; centre of mass; computer-simulation study; explicit water model; human antibody-DNA interface; interprotein molecular hydrogen bonds; mean force calculations; molecular dynamics; protein engineering; Biological system modeling; Computational modeling; DNA; Force; Hydrogen; Proteins; Simulation; Antibody; Antigen; Molecular dynamics; Potential of mean force;
