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Author:

Shao, Qi (Shao, Qi.) | Han, Zhongjie (Han, Zhongjie.) | Cheng, Jingmin (Cheng, Jingmin.) | Wang, Qiankun (Wang, Qiankun.) | Gong, Weikang (Gong, Weikang.) | Li, Chunhua (Li, Chunhua.) (Scholars:李春华)

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EI Scopus SCIE

Abstract:

Aminoacyl-tRNA synthetases (aaRSs), a family of ubiquitous and essential enzymes, can bind target tRNAs and catalyze the aminoacylation reaction in genetic code translation. In this work, we explore the dynamic properties and allosteric communication of human mitochondrial phenylalanyl-tRNA synthetase (hmPheRS) in free and bound states to understand the mechanisms of its tRNA(Phe) recognition and allostery using molecular dynamics simulations combined with the torsional mutual information-based network model. Our results reveal that hmPheRS's residue mobility and inter-residue motional coupling are significantly enhanced by tRNA(Phe) binding, and there occurs a strong allosteric communication which is critical for the aminoacylation reaction, suggesting the vital role of tRNA(Phe) binding in the enzyme's function. The identified signaling pathways mainly make the connections between the anticodon binding domain (ABD) and catalytic domain (CAD), as well as within the CAD composed of many functional fragments and active sites, revealing the co-regulation role of them to act coordinately and achieve hmPheRS's aminoacylation function. Besides, several key residues along the communication pathways are identified to be involved in mediating the coordinated coupling between anticodon recognition at the ABD and activation process at the CAD, showing their pivotal role in the allosteric network, which are well consistent with the experimental observation. This study sheds light on the allosteric communication mechanism in hmPheRS and can provide important information for the structure-based drug design targeting aaRSs.

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Author Community:

  • [ 1 ] [Shao, Qi]Beijing Univ Technol, Fac Environm & Life Sci, Beijing 100124, Peoples R China
  • [ 2 ] [Han, Zhongjie]Beijing Univ Technol, Fac Environm & Life Sci, Beijing 100124, Peoples R China
  • [ 3 ] [Cheng, Jingmin]Beijing Univ Technol, Fac Environm & Life Sci, Beijing 100124, Peoples R China
  • [ 4 ] [Wang, Qiankun]Beijing Univ Technol, Fac Environm & Life Sci, Beijing 100124, Peoples R China
  • [ 5 ] [Gong, Weikang]Beijing Univ Technol, Fac Environm & Life Sci, Beijing 100124, Peoples R China
  • [ 6 ] [Li, Chunhua]Beijing Univ Technol, Fac Environm & Life Sci, Beijing 100124, Peoples R China

Reprint Author's Address:

  • 李春华

    [Li, Chunhua]Beijing Univ Technol, Fac Environm & Life Sci, Beijing 100124, Peoples R China

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Source :

JOURNAL OF PHYSICAL CHEMISTRY B

ISSN: 1520-6106

Year: 2021

Issue: 28

Volume: 125

Page: 7651-7661

3 . 3 0 0

JCR@2022

ESI Discipline: CHEMISTRY;

ESI HC Threshold:96

JCR Journal Grade:3

Cited Count:

WoS CC Cited Count: 5

SCOPUS Cited Count: 5

ESI Highly Cited Papers on the List: 0 Unfold All

WanFang Cited Count:

Chinese Cited Count:

30 Days PV: 0

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