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Author:

Zhang Shan (Zhang Shan.) | Gong Weikang (Gong Weikang.) | Han Zhongjie (Han Zhongjie.) | Liu Yang (Liu Yang.) | Li Chunhua (Li Chunhua.)

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Abstract:

Understanding generic mechanisms of functions shared by the secretory phospholipase A2 (sPLA2) family involved in the lipid metabolism and cell signaling and the molecular basis of function specificity for family members is an intriguing but challenging problem for biologists. Here, we explore the issue through extensive analyses using a combination of structure-based methods and bioinformatics tools on130 sPLA2 family members. The principal component analysis of the structure ensemble reveals that the enzyme has an open-close motion which helps widen the substrate binding channel, facilitating its binding to phospholipid. Performing elastic network model and sequence analyses found that the residues critical for family functions, such as cysteine and catalytic residues, are highly conserved and undergo minimal movements, which is evolutionarily essential as their perturbation would impact the function, while the four residue regions involved in the association with the calcium ion/membrane are lowly conserved and of high mobility and large variations in low-to-intermediate frequency modes, which reflects the specificity of members. The analyses from perturbation response scanning also reveal that the above four regions with high sensitivity to an external perturbation are member-specific, suggesting their different roles in allosteric modulation, while the minimal sensitive residues are the shared characteristics across family members, which play an important role in maintaining structural stability as the folding core. This study is helpful for understanding how sequences, structures, and dynamics of sPLA2 family members evolve to ensure their common and specific functions and can provide a guide for accurate design of proteins with finely tuned activities.

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Author Community:

  • [ 1 ] [Zhang Shan]Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
  • [ 2 ] [Gong Weikang]Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
  • [ 3 ] [Han Zhongjie]Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
  • [ 4 ] [Liu Yang]Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
  • [ 5 ] [Li Chunhua]Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China

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Source :

The journal of physical chemistry. B

ISSN: 1520-5207

Year: 2021

Issue: 13

Volume: 125

Page: 3353-3363

Cited Count:

WoS CC Cited Count: 0

SCOPUS Cited Count: 6

ESI Highly Cited Papers on the List: 0 Unfold All

WanFang Cited Count:

Chinese Cited Count:

30 Days PV: 0

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