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Conformational dynamics of xylanase a from Streptomyces lividans: Implications for TIM-barrel enzyme thermostability

Authors

  • Yanrui Ding,

    Corresponding author
    1. Key Laboratory of Industrial Biotechnology, Ministry of Education, Wuxi, Jiangsu, People's Republic of China
    • Department of Computer Science and Technology, Jiangnan University, Wuxi, Jiangsu, People's Republic of China
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  • Yujie Cai

    1. Key Laboratory of Industrial Biotechnology, Ministry of Education, Wuxi, Jiangsu, People's Republic of China
    2. School of Biotechnology, 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

Correspondence to: Yanrui Ding; e-mail: yr_ding@jiangnan.edu.cn

ABSTRACT

The conformational dynamics of xylanase A from Streptomyces lividans (Sl-XlnA) were studied using Molecular Dynamics (MD) simulation to identify the thermally sensitive regions. Sl-XlnA begins to unfold at loop4 and this unfolding expands to the loops near the N-terminus. The high flexibility of loop6 during the 300 K simulation is related to its function. The intense movements of the 310-helices also affect the structural stability. The interaction between the α4β5-loop and the neighboring α5β6-loop plays a crucial role in stabilizing the region from the α4β5-loop to α6. The most thermally sensitive region is from β3 to loop4. The high mobility of the long loop4 easily transfers to the adjacent β4 and α4 and causes β4 and α4 to fluctuate. And, salt bridges ASP124-ARG79, ASP200-ARG159, and ASP231-LYS166 formed a “clamp” to stabilize the region including α4, β4, β5, β6, and β7. © 2013 Wiley Periodicals, Inc. Biopolymers 99: 594–604, 2013.

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