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Comprehensive Folding Variations for Protein Folding
  • +8
  • Jiaan Yang,
  • Wen Xiang,
  • Xiao Fei Zhao,
  • Gang Wu,
  • Shi Tong,
  • Qiyue Hu,
  • Hu Ge,
  • Qianshan Qin,
  • Xinshen Jin,
  • Lianshan Zhang,
  • Peng Zhang
Jiaan Yang
Chinese Academy of Sciences Shenzhen Institutes of Advanced Technology

Corresponding Author:jiaanyang@yahoo.com

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Wen Xiang
Chinese Academy of Sciences Shenzhen Institutes of Advanced Technology
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Xiao Fei Zhao
Micro Biotech Ltd Shanghai 200123 China
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Gang Wu
Huazhong University of Science and Technology Tongji Medical College
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Shi Tong
Shenzhen Hua Ying Kang Gene Technology Co Ltd Shenzhen Guangdong 518057 China
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Qiyue Hu
Shanghai Hengrui Pharmaceutical CoLtd Shanghai 200245 China
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Hu Ge
Shanghai Hengrui Pharmaceutical CoLtd Shanghai 200245 China
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Qianshan Qin
Shanghai Hengrui Pharmaceutical CoLtd Shanghai 200245 China
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Xinshen Jin
Shanghai Hengrui Pharmaceutical CoLtd Shanghai 200245 China
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Lianshan Zhang
Shanghai Hengrui Pharmaceutical CoLtd Shanghai 200245 China
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Peng Zhang
Chinese Academy of Sciences Shenzhen Institutes of Advanced Technology
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Abstract

The revelation of protein folding is a challenging subject in both discovery and description. Except acquirement of accurate 3D structure for protein stable state, another big hurdle is how to discover structural flexibility for protein innate character. Even if a huge number of flexible conformations are known, difficulty is how to describe these conformations. A novel approach, protein structure fingerprint, has been developed to expose the comprehensive local folding variations, and then construct folding conformations for entire protein. The backbone of 5 amino acid residues was identified as a universal folden, and then a set of Protein Folding Shape Code (PFSC) was derived for completely covering folding space in alphabetic description. Sequentially, a database was created to collect all possible folding shapes of local folding variations for all permutation of 5 amino acids. Successively, Protein Folding Variation Matrix (PFVM) assembled all possible local folding variations along sequence for a protein, which possesses several prominent features. First, it showed the fluctuation with certain folding patterns along sequence which revealed how the protein folding was related the order of amino acids in sequence. Second, all folding variations for an entire protein can be simultaneously apprehended at a glance within PFVM. Third, all conformations can be determined by local folding variations from PFVM, so total number of conformations is no longer ambiguous for any protein. Finally, the most possible folding conformation and its 3D structure can be acquired according PFVM for protein structure prediction. Therefore, the protein structure fingerprint approach provides a significant means for investigation of protein folding problem.
16 Feb 2022Submitted to PROTEINS: Structure, Function, and Bioinformatics
16 Feb 2022Submission Checks Completed
16 Feb 2022Assigned to Editor
16 Feb 2022Reviewer(s) Assigned
28 Mar 2022Review(s) Completed, Editorial Evaluation Pending
30 Mar 2022Editorial Decision: Revise Major
12 Apr 20221st Revision Received
13 Apr 2022Submission Checks Completed
13 Apr 2022Assigned to Editor
13 Apr 2022Reviewer(s) Assigned
21 Apr 2022Review(s) Completed, Editorial Evaluation Pending
22 Apr 2022Editorial Decision: Accept
Nov 2022Published in Proteins: Structure, Function, and Bioinformatics volume 90 issue 11 on pages 1851-1872. 10.1002/prot.26381