Insights into the thermal stabilization and conformational transitions of DNA by hyperthermophile protein Sso7d: molecular dynamics simulations and MM-PBSA analysis.
In the assembly of DNA-protein complex, the DNA kinking plays an important role in nucleoprotein structures and gene regulation. Molecular dynamics (MD) simulations were performed on specific protein-DNA complexes in this study to investigate the stability and structural transitions of DNA depending on temperature. Furthermore, we introduced the molecular mechanics/Poisson-Boltzmann surface area (MM-PBSA) approach to analyze the interactions between DNA and protein in hyperthermophile. Focused on two specific Sso7d-DNA complexes (PDB codes: 1BNZ and 1BF4), we performed MD simulations at four temperatures (300, 360, 420, and 480 K) and MM-PBSA at 300 and 360 K to illustrate detailed information on the changes of DNA. Our results show that Sso7d stabilizes DNA duplex over a certain temperature range and DNA molecules undergo B-like to A-like form transitions in the binary complex with the temperature increasing, which are consistent with the experimental data. Our work will contribute to a better understanding of protein-DNA interaction.
State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, 130023, P.R. China.
Lin
L
Chen
Qing-Chuan
QC
Zheng
Li-Ying
LY
Yu
Wen-Ting
WT
Chu
Ji-Long
JL
Zhang
Qiao
Q
Xue
Hong-Xing
HX
Zhang
Chia-Chung
CC
Sun
D019843:Archaeal Proteins / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry*; D020862:GC Rich Sequence; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013499:Surface Properties; D013816:Thermodynamics
D019843:Archaeal Proteins; D004268:DNA-Binding Proteins; D009838:Oligodeoxyribonucleotides; C093228:Sso7d protein, Sulfolobus