Homology modeling and evolutionary trace analysis of superoxide dismutase from extremophile Acidithiobacillus ferrooxidans |
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Authors: | Liu Yuan-dong Wang Hai-dong and Qiu Guan-zhou |
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Affiliation: | (1) School of Resources Processing and Bioengineering, Central South University, Changsha, 410083, China |
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Abstract: | The gene sod in Acidithiobacillus ferrooxidans may play a crucial role in its tolerance to the extremely acidic, toxic and oxidative environment of bioleaching. For insight
into the anti-toxic mechanism of the bacteria, a three-dimensional (3D) molecular structure of the protein encoded by this
gene was built by homology modeling techniques, refined by molecular dynamics simulations, assessed by PROFILE-3D and PROSTAT
programs and its key residues were further detected by evolutionary trace analysis. Through these procedures, some trace residues
were identified and spatially clustered. Among them, the residues of Asn38, Gly103 and Glu161 are randomly scattered throughout
the mapped structure; interestingly, the other residues are all distinctly clustered in a subgroup near Fe atom. From these
results, this gene can be confirmed at 3D level to encode the Fe-depending superoxide dismutase and subsequently play an anti-toxic
role. Furthermore, the detected key residues around Fe binding site can be conjectured to be directly responsible for Fe binding
and catalytic function.
Foundation item: Project(2004CB619201) supported by the National Basic Research Program of China; Project (50321402) supported by the National
Natural Science Foundation of China |
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Keywords: | bioleaching superoxide dismutase Acidithiobacillus ferrooxidans homology modeling evolutionary trace molecular dynamics |
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