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

Journal of Computational Chemistry - Tập 34 Số 13 - Trang 1136-1142 - 2013
Xue X. Yao1,2, Chang G. Ji3, Dai Qian Xie2, John Z. H. Zhang4,3
1College of Engineering, Nanjing Agricultural University, Nanjing 210031，China
2Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
3State Key Laboratory of Precision Spectroscopy, Department of Physics, Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China
4Department of Chemistry, New York University, New York, NY 10003

Tóm tắt

AbstractThe 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. © 2013 Wiley Periodicals, Inc.

Từ khóa


Tài liệu tham khảo

10.1038/7603

10.1038/799

10.1006/jmbi.2000.3888

10.1021/bi0269355

10.1021/bi026936x

10.1021/bi048907n

10.1021/bi026937p

10.1002/jmr.658

10.1016/S0959-440X(00)00196-2

10.1088/0953-8984/21/33/333102

10.1002/jcc.1161

10.1016/j.bbamem.2011.09.016

10.1021/jp053182y

10.1021/ct700167b

10.1021/ct700146x

10.1021/ct800239q

10.1021/jp1092338

10.1016/j.bpj.2008.09.048

10.1021/jp901088g

10.1039/b910574c

10.1021/jp907999e

10.1021/jp809774q

10.1529/biophysj.108.131110

10.1073/pnas.96.25.14330

10.1021/ja807374x

10.1021/ja901650r

10.1063/1.3089723

10.1021/ja206212a

10.1002/jcc.22969

10.1021/jp205907h

10.1021/j100142a004

10.1002/jcc.540161106

10.1021/ja00074a030

10.1002/jcc.20290

10.1063/1.464397

10.1002/jcc.540120405

10.1002/(SICI)1097-0282(199603)38:3<305::AID-BIP4>3.0.CO;2-Y

10.1021/j100265a018

10.1038/nature08473

10.1093/nar/gkp608

10.1021/ci100275a

10.1021/ja0779250

10.1021/ja909575j

10.1529/biophysj.108.130542

Thông tin
Thông tin xuất bản

Journal of Computational Chemistry

Tập 34 Số 13

1136-1142

Thông tin tác giả