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

Bibliographische Detailangaben
Veröffentlicht in:	Journal of computational chemistry. - 1984. - 34(2013), 13 vom: 15. Mai, Seite 1136-42
1. Verfasser:	Yao, Xue X (VerfasserIn)
Weitere Verfasser:	Ji, Chang G, Xie, Dai Q, Zhang, John Z H
Format:	Online-Aufsatz
Sprache:	English
Veröffentlicht:	2013
Zugriff auf das übergeordnete Werk:	Journal of computational chemistry
Schlagworte:	Journal Article Research Support, Non-U.S. Gov't DNA 9007-49-2 Integrases EC 2.7.7.-

Beschreibung
Zusammenfassung:	Copyright © 2013 Wiley Periodicals, Inc. 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
Beschreibung:	Date Completed 02.07.2014 Date Revised 09.04.2013 published: Print-Electronic Citation Status MEDLINE
ISSN:	1096-987X
DOI:	10.1002/jcc.23244