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Interaction between cytochrome c and DNA: conformation, peroxidase activity and molecular dynamics simulation

Citation

Hong, Jun et al. (2020), Interaction between cytochrome c and DNA: conformation, peroxidase activity and molecular dynamics simulation, Dryad, Dataset, https://doi.org/10.5061/dryad.59zw3r25h

Abstract

A mixed system of cytochrome c (Cyt c, a typical hemoprotein) and DNA was constructed and the interaction between Cyt c and DNA were analyzed by experiment and molecular dynamics (MD) simulation methods, respectively. On the one hand, the experimental results showed: 1. The peroxidase activity of the mixed system was significantly enhanced relative to the Cyt c in 50 mM phosphate buffer solution at 25ºC. 2. UV-Vis spectra study found that, compared with the Cyt c solution, the absorbance of the Cyt c-DNA mixed system increased significantly at 280 nm, while the absorbance decreased at 405 nm, indicating that the overall structure of Cyt c in the mixed system became loose, and the structure around heme group became more compact. 3. Circular Dichroism (CD) studies showed that there was a weak interaction between DNA and Cyt c in the mixed system, which had little effects on the secondary structures of Cyt c. On the other hand, MD simulation results showed: 1. DNA and Cyt c were combined by hydrogen bonding and non-bonding interactions in the mixed system. 2. During the simulation process, N-Terminal α-Helix changed, and Lys13-Cys17 opened, exposing the active center (heme structure) of Cyt c, which may increase the binding of the mixed system to the substrate. 3. The bond length of Fe-N (N in His18 and Fe in heme group) became slightly shorter after equilibrium in the presence of DNA. 4. The Cyt c became loose after binding with DNA. 5. The total binding free energy between Cyt c and DNA was calculated to be -141.9 kJ/mol. The Cyt c-DNA system was in a relatively stable state from energy perspective. The results of the research on the structure and function of the Cyt c-DNA mixed system using experimental method and MD simulation method were consistent. The combination of experimental method and simulation method may provide useful research ideas and effective research methods for further studying the interaction mechanism between hemeprotein and DNA.

Usage Notes

Horse heart Cyt c, 2,2’-Azino-bis(3-Ethylbenzthiazoline-6-Sulfonic Acid) (ABTS), herring sperm DNA (DNA, <50 bp), sodium dihydrogen phosphate and disodium hydrogen phosphate were purchased from Sigma (St. Louis, MO, USA).

PDB file of crystal structure of Cyt c (PDB ID:1HRC) was achieved from the Protein Data Bank (http://www.rcsb.org).

All Softwares used in this paper were from free sources:

Ambertools: http://ambermd.org/

Gromacs: http://www.gromacs.org/

Pymol:  https://pymol.org/#opensource

Vmd https://www.ks.uiuc.edu/Research/vmd/

APBS http://www.poissonboltzmann.org/

LigPlot https://www.ebi.ac.uk/thornton-srv/software/LigPlus/

Funding

Natural Science Foundation of Henan Province, Award: 182300410217