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Conformation and molecular dynamics simulation of the interaction between cytochrome c and DNA

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Abstract

Cytochrome c (Cyt c) is a key molecule involved in mitochondria-mediated apoptosis. Cyt c is released into the cytoplasm to bind to apoptotic enzyme activating factor 1 (Apaf-1) and then forms an apoptotic complex and activated Caspase-9 to further activate Caspase-3/6/7, thereby inducing apoptosis. Among them, the caspase-activated deoxyribonuclease causes DNA fragmentation. In this paper, the interactions between Cyt c and DNA are studied by UV, circular dichroism (CD), isothermal titration calorimetry (ITC), and molecular dynamics (MD) simulation methods. The results show that each 50 bp DNA fragment could bind about 8 Cyt c molecules on average, and the peroxidase activity of Cyt c is significantly enhanced when it interacts with DNA. The conformation around the alpha-helix (K13-C17) is slightly opened, the exposure of the active center (heme group) is slightly increased, and the average bond length of Fe-S (S in M80, Fe in heme group) is shortened, which may enhance the affinity between Cyt c and the substrate. The study also shows that lysine residues (especially K86, K87, and K88) may play a key role in the interaction between Cyt c and DNA.

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Acknowledgements

The supports of the National Natural Science Foundation of China (NSFC, 32161143021), the Iran National Science Foundation (INSF, 4001873), and the Natural Science Foundation of Henan Province (182300410217) are gratefully acknowledged.

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Authors and Affiliations

  1. School of Life Sciences, Henan University, JinMing Road, Kaifeng, 475000, China

    Bao-Lin Xiao, Xin-Xin Ma, Yang-Yang Li & Jun Hong

  2. Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran

    Ali Akbar Moosavi-Movahedi

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Correspondence to Jun Hong or Ali Akbar Moosavi-Movahedi.

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Xiao, BL., Ma, XX., Li, YY. et al. Conformation and molecular dynamics simulation of the interaction between cytochrome c and DNA. J IRAN CHEM SOC 20, 2747–2756 (2023). https://doi.org/10.1007/s13738-023-02872-0

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