- Evaluation of Cyc1 protein stability in Acidithiobacillus ferrooxidans bacterium after E121D mutation by molecular dynamics simulation to improve electron transfer
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Mahnaz Shojapour , Somayeh Farahmand , Faezeh Fatemi , Marzieh Dehghan Shasaltaneh
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J. Microbiol. 2022;60(5):526-532. Published online March 14, 2022
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DOI: https://doi.org/10.1007/s12275-022-1645-7
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 Abstract
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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.
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Citations
Citations to this article as recorded by  - Carnosic Acid as a Potent Ag85C Inhibitor Identified Through Integrated Pharmacokinetic Evaluation and Molecular Modeling in Mycobacterium Tuberculosis Drug Discovery
Somayeh Farahmand, Saber SamadiAfshar, Reza HajiHosseini, Toktam Babari
Journal of Pharmaceutical Innovation.2025;[Epub] CrossRef - Point mutation consideration in CcO protein of the electron transfer chain by MD simulation
Mahnaz Shojapour, Somayeh Farahmand
Journal of Molecular Graphics and Modelling.2022; 117: 108309. CrossRef
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