Bioinformatics
Somayeh Farahmand; Marzieh Dehghan Shasaltaneh; Faezeh Fatemi; Mahnaz Shojapour
Volume 1, Issue 1 , March 2025, , Pages 17-31
Abstract
Iron-rusticyanin reductase (Cyc2) is the first protein in the respiratory chain of Acidithiobacillus ferrooxidans (Af), which plays a crucial role in electron transfer. Cytochrome c (cytC) is located in the bacterial outer membrane (OM) and functions as the first electron carrier inside the respiratory ...
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Iron-rusticyanin reductase (Cyc2) is the first protein in the respiratory chain of Acidithiobacillus ferrooxidans (Af), which plays a crucial role in electron transfer. Cytochrome c (cytC) is located in the bacterial outer membrane (OM) and functions as the first electron carrier inside the respiratory ferrous iron oxidation pathway is encoded by the Cyc2 gene. The present computational research examines the effect of a novel Cyc2 mutation (F312Y) to enhance conformational flexibility of the mentioned protein for target recognition. Molecular dynamic simulations (MD) of wild and mutant types of Cyc2 protein were carried out. By analyzing RMSD, RMSF, SASA, Rg, H Bond, DSSP, PCA, ED, DCCM, FEL and EM the conformational variations of mutated protein were studied. The results of the RMSF analysis represent an increase in the flexibility of the ligand after mutant. Eventually, the flexibility of the active site probably improves electron transfer by increasing the amount of Eo at the mutation point. Our results confirm that the mutated protein retains its stability during the simulation. With the conversion of Phenylalanine 312 into Tyrosine, an alpha-amino acid with hydrophobic and nonpolar side chains changes to a polar side group with an extra -OH group. This resulted in more intracellular hydrogen bonds. Furthermore, the mutant variant was more stable than the wild-type. Findings from the present study indicate that an interface between the F312Y mutation and rusticyanin activation could improve the electron transfer rate and yield fruitful insight into site-specific mutagenesis studies.
