Shojapour Mahnaz, Fatemi Faezeh, Farahmand Somayeh, Shasaltaneh Marzieh Dehghan
Department of Biology, Faculty of Sciences, Payame Noor University, Tehran, Iran.
Materials and Nuclear Fuel Research School, Nuclear Science and Technology Research Institute, Tehran, Iran.
J Mol Graph Model. 2021 Jun;105:107864. doi: 10.1016/j.jmgm.2021.107864. Epub 2021 Feb 9.
Acidithiobacillus ferrooxidans (Af) is an acidophilic bacterium that grows in rigid surroundings and gets its own energy from the oxidation of Fe to Fe. These bacteria are involved in the bioleaching process. Cyc is a periplasmic protein with a crucial role in electron transportation in the respiratory chain. His53 of the Cyc protein, involved in electron transfer to CoxB, was selected for mutation and bioinformatics studies. His53 was substituted by Ile using PyMol software. Molecular dynamics simulations were performed for wild and mutant types of Cyc protein. The conformational changes of mutated protein were studied by analyzing RMSD, RMSF, SASA, Rg, H Bond, and DSSP. The results of the RMSF analysis indicated an increase in the flexibility of the ligand in the mutant. Finally, active site instability leads to an increase in the value of E at the mutation point and improving electron transfer. On the other, His53 in Cyc is interconnected to Glu126 in CoxB through the water molecule (W76) and hydrogen bonding. In the H53I mutation, there was a decrease in the distance between H2O 2030, 2033, and isoleucine 53, and subsequently, the distance to the water molecule 76 between the two proteins was reduced and strengthens the hydrogen bond between Cyc and CoxB, finally improves electron transfer and the bioleaching process.
氧化亚铁硫杆菌（Af）是一种嗜酸细菌，生长在坚硬的环境中，通过将Fe氧化为Fe来获取自身能量。这些细菌参与生物浸出过程。Cyc是一种周质蛋白，在呼吸链的电子传递中起关键作用。参与向CoxB进行电子转移的Cyc蛋白的His53被选用于突变和生物信息学研究。使用PyMol软件将His53替换为Ile。对野生型和突变型Cyc蛋白进行了分子动力学模拟。通过分析均方根偏差（RMSD）、均方根波动（RMSF）、溶剂可及表面积（SASA）、回旋半径（Rg）、氢键（H Bond）和二级结构预测（DSSP）来研究突变蛋白的构象变化。RMSF分析结果表明突变体中配体的灵活性增加。最后，活性位点的不稳定性导致突变点处的E值增加并改善电子转移。另一方面，Cyc中的His53通过水分子（W76）和氢键与CoxB中的Glu126相互连接。在H53I突变中，H2O 2030、2033与异亮氨酸53之间的距离减小，随后，两种蛋白质之间到水分子76的距离缩短，增强了Cyc与CoxB之间的氢键，最终改善了电子转移和生物浸出过程。
