| Title | Evaluation of Cyc1 protein stability in Acidithiobacillus ferrooxidans bacterium after E121D mutation by molecular dynamics simulation to improve electron transfer |
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| Author | Mahnaz Shojapour1, Somayeh Farahmand1*, Faezeh Fatemi2, and Marzieh Dehghan Shasaltaneh3 |
| Address | 1Department of Biology, Faculty of Sciences, Payame Noor University, Tehran 19395-4697, Iran, 2Materials and Nuclear Fuel Research School, Nuclear Science and Technology Research Institute, Tehran 14155-1339, Iran, 3Department of Biology, Faculty of Sciences, University of Zanjan, Zanjan 45371-38791, Iran |
| Bibliography | Journal of Microbiology, 60(5),526–532, 2022, |
| DOI | 10.1007/s12275-022-1645-7 |
| Key Words | Acidithiobacillus ferrooxidans, E121D mutation, MD simulation, RCY/Cyc1 complex, respiratory chain |
| Abstract | Cyc1 (Cytochrome c552) is a protein in the electron transport chain of the Acidithiobacillus ferrooxidans (Af) bacteria which obtain their energy from oxidation Fe2+ to Fe3+. The electrons are directed through Cyc2, RCY (rusticyanin), Cyc1, and Cox aa3 proteins to O2. Cyc1 protein consists of two chains, A and B. In the present study, a novel mutation (E121D) in the A chain of Cyc1 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. Cyc1 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/ Cyc1 complex. Further, an acidic residue (Glu121) becomes a more acidic residue (Asp121) and improves the electron transfer to Cyc1 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. |