Xue X. Yao, Chang G. Ji, Dai Q. Xie and John Z.H. Zhang
The combined use of a quantum-based, polarized, protein-specific charge (PPC) for protein and a polarized, nucleic, acid-specific charge (PNC) for DNA is employed in a molecular dynamics simulation to study the interaction dynamics between INTDBD and DNA. The protein-DNA structure is stabilized by polarization, and the calculated protein-DNA binding free energy is in good agreement with the experimental data. The image shows the structure of the INT-DBD-DNA binding complex, in which the secondary structure elements are labeled as L, loop; T, turn; and β, beta strand.