Evaluation of Cyc protein stability in Acidithiobacillus ferrooxidans bacterium after E121D mutation by molecular dynamics simulation to improve electron transfer.

Cyc (Cytochrome c) is a protein in the electron transport chain of the Acidithiobacillus ferrooxidans (Af) bacteria which obtain their energy from oxidation Fe to Fe. The electrons are directed through Cyc, RCY (rusticyanin), Cyc and Cox aa proteins to O. Cyc protein consists of two chains, A and B. In the present study, a novel mutation (E121D) in the A chain of Cyc protein was selected due to electron receiving from Histidine 143 of RCY. Then, the changes performed in the E121D mutant were evaluated by MD simulations analyzes. Cyc and RCY proteins were docked by a Patchdock server. By E121D mutation, the connection between Zn 1388 of chain B and aspartate 121 of chain A weaken. Asp 121 gets farther from Zn 1388. Therefore, the aspartate gets closer to Cu 1156 of the RCY leading to the higher stability of the RCY/Cyc complex. Further, an acidic residue (Glu121) becomes a more acidic residue (Asp121) and improves the electron transfer to Cyc protein. The results of RMSF analysis showed further ligand flexibility in mutation. This leads to fluctuation of the active site and increases redox potential at the mutation point and the speed of electron transfer. This study also predicts that in all respiratory chain proteins, electrons probably enter the first active site via glutamate and exit histidine in the second active site of each respiratory chain protein.