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Application of principal component analysis to determine the key structural features contributing to iron superoxide dismutase thermostability

Authors

  • Yanrui Ding,

    Corresponding author
    1. Key Laboratory of Advanced Process Control for Light Industry, Jiangnan University, Wuxi, People's Republic of China
    2. Department of Computer Science and Technology, Jiangnan University, Wuxi, Jiangsu, People's Republic of China
    • Key Laboratory of Advanced Process Control for Light Industry, Jiangnan University, Wuxi, People's Republic of China
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  • Yujie Cai,

    1. Key Laboratory of Industrial Biotechnology, Jiangnan University, Wuxi, Jiangsu, People's Republic of China
    2. School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, People's Republic of China
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  • Yonggang Han,

    1. Department of Computer Science and Technology, Jiangnan University, Wuxi, Jiangsu, People's Republic of China
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  • Bingqiang Zhao,

    1. Department of Computer Science and Technology, Jiangnan University, Wuxi, Jiangsu, People's Republic of China
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  • Lei Zhu

    1. Department of Computer Science and Technology, Jiangnan University, Wuxi, Jiangsu, People's Republic of China
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  • This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

Abstract

Iron superoxide dismutase (Fe-SOD) is predominantly found in bacteria and mitochondria. The thermal stability of Fe-SOD from different sources can vary dramatically. We have studied the influence of structural parameters on Fe-SOD thermostability by principal component analysis (PCA). The results show that an increased α-helical and turn content, an increased α-helix and loop length, an increase in the number of main-main chains and charged-uncharged hydrogen bonds, a decrease in the 310-helix content, and a decreased β-strand and loop length are all important factors for Fe-SOD thermostability. Interestingly, the use of charged residues to form salt bridges is tendentious in thermophilic Fe-SOD. Negatively charged Arg and positively charged Glu are efficiently used to form salt bridges. The cooperative action of the exposed area, the hydrogen bonds, and the secondary structure plays a crucial role in resisting high temperatures, which demonstrates that the increased stability of thermophilic Fe-SOD is provided by several structural factors acting together. © 2012 Wiley Periodicals, Inc. Biopolymers 97:864–872, 2012.

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