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

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.