Molecular dynamics study of DNA binding by INT-DBD under a polarized force field

Xue X. Yao, Chang G. Ji, Dai Q. Xie, John Z.H. Zhang

Research output: Contribution to journalArticlepeer-review


The DNA binding domain of transposon Tn916 integrase (INT-DBD) binds to DNA target site by positioning the face of a three-stranded antiparallel β-sheet within the major groove. As the negatively charged DNA directly interacts with the positively charged residues (such as Arg and Lys) of INT-DBD, the electrostatic interaction is expected to play an important role in the dynamical stability of the protein-DNA binding complex. In the current work, the combined use of quantum-based polarized protein-specific charge (PPC) for protein and polarized nucleic acid-specific charge (PNC) for DNA were employed in molecular dynamics simulation to study the interaction dynamics between INT-DBD and DNA. Our study shows that the protein-DNA structure is stabilized by polarization and the calculated protein-DNA binding free energy is in good agreement with the experimental data. Furthermore, our study revealed a positive correlation between the measured binding energy difference in alanine mutation and the occupancy of the corresponding residue's hydrogen bond. This correlation relation directly relates the contribution of a specific residue to protein-DNA binding energy to the strength of the hydrogen bond formed between the specific residue and DNA.

Original languageEnglish (US)
Pages (from-to)1136-1142
Number of pages7
JournalJournal of Computational Chemistry
Issue number13
StatePublished - May 15 2013


  • PBSA
  • binding energy
  • elestrostatic interaction
  • force field
  • hydrogen bond
  • polarization
  • protein-DNA

ASJC Scopus subject areas

  • General Chemistry
  • Computational Mathematics


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