Expose flexible conformations for intrinsically disordered protein
The folding conformation of native protein has flexibility in different degrees, which may bring difficulty in presenting the structures, and also it causes complexity in understanding the relationship between structure and functions. Although many methods and databases provide information for intri...
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| Format: | Article |
| Language: | English |
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Elsevier
2025-12-01
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| Series: | Current Research in Structural Biology |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2665928X25000078 |
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| author | Jiaan Yang Wenxin Ji Wen Xiang Cheng Gang Wu Si Tong Sheng Peng Zhang Jun Lin Xiaojia Chen Qiong Shi |
| author_facet | Jiaan Yang Wenxin Ji Wen Xiang Cheng Gang Wu Si Tong Sheng Peng Zhang Jun Lin Xiaojia Chen Qiong Shi |
| author_sort | Jiaan Yang |
| collection | DOAJ |
| description | The folding conformation of native protein has flexibility in different degrees, which may bring difficulty in presenting the structures, and also it causes complexity in understanding the relationship between structure and functions. Although many methods and databases provide information for intrinsically disordered protein (IDP), they are mainly limited to determining the intrinsically disordered regions (IDR) lacking knowledge of possible folding patterns. To overcome the barrier, the protein structure fingerprint technology has been developed, which includes PFSC (Protein Folding Shape Code) (Yang, 2008) and PFVM (Protein Folding Variation Matrix) (Yang et al., 2022) algorithms as well as FiveFold (Yang et al., 2025) approach for protein structure prediction, which are able explicitly to expose the possible conformational structures for intrinsically disordered protein. Three proteins, human cellular tumor antigen P53, human alpha-synuclein, and human protamine-2, are taken as samples for demonstration of how to obtain their folding conformation structures for intrinsically disordered proteins. The folding features for intrinsically disordered proteins with given structures may be revealed by the alignment of PFSC strings, and the folding possibility for intrinsically disordered proteins without a given structure can be exhibited by the local folding variations in PFVM. Furthermore, the multiple conformational 3D structures for intrinsically disordered protein can be predicted by FiveFold approach, which provides a significant tool further to understand the intrinsic disorder of proteins. |
| format | Article |
| id | doaj-art-5d9c2f8446c44d728cb863a2f6dc6149 |
| institution | Kabale University |
| issn | 2665-928X |
| language | English |
| publishDate | 2025-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Current Research in Structural Biology |
| spelling | doaj-art-5d9c2f8446c44d728cb863a2f6dc61492025-08-20T03:29:10ZengElsevierCurrent Research in Structural Biology2665-928X2025-12-011010017010.1016/j.crstbi.2025.100170Expose flexible conformations for intrinsically disordered proteinJiaan Yang0Wenxin Ji1Wen Xiang Cheng2Gang Wu3Si Tong Sheng4Peng Zhang5Jun Lin6Xiaojia Chen7Qiong Shi8Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; Micro Biotech, Ltd., Shanghai, 200123, China; Corresponding author. Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, ChinaShenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, ChinaSchool of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, ChinaHYK High-throughput Biotechnology Institute, Shenzhen, 518057, ChinaShenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; Faculty of Biomedical Engineering, Shenzhen University of Advanced Technology, Shenzhen, 518060, ChinaShanghai Ginspire Biologics Co., Ltd., Shanghai, 200131, ChinaInstitute of Biomedicine & Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangdong, 510632, China; National Engineering Research Center of Genetic Medicine, Guangdong, 510632, ChinaCollege of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518057, ChinaThe folding conformation of native protein has flexibility in different degrees, which may bring difficulty in presenting the structures, and also it causes complexity in understanding the relationship between structure and functions. Although many methods and databases provide information for intrinsically disordered protein (IDP), they are mainly limited to determining the intrinsically disordered regions (IDR) lacking knowledge of possible folding patterns. To overcome the barrier, the protein structure fingerprint technology has been developed, which includes PFSC (Protein Folding Shape Code) (Yang, 2008) and PFVM (Protein Folding Variation Matrix) (Yang et al., 2022) algorithms as well as FiveFold (Yang et al., 2025) approach for protein structure prediction, which are able explicitly to expose the possible conformational structures for intrinsically disordered protein. Three proteins, human cellular tumor antigen P53, human alpha-synuclein, and human protamine-2, are taken as samples for demonstration of how to obtain their folding conformation structures for intrinsically disordered proteins. The folding features for intrinsically disordered proteins with given structures may be revealed by the alignment of PFSC strings, and the folding possibility for intrinsically disordered proteins without a given structure can be exhibited by the local folding variations in PFVM. Furthermore, the multiple conformational 3D structures for intrinsically disordered protein can be predicted by FiveFold approach, which provides a significant tool further to understand the intrinsic disorder of proteins.http://www.sciencedirect.com/science/article/pii/S2665928X25000078Intrinsically disordered proteinProtein foldingProtein conformationProtein structure prediction |
| spellingShingle | Jiaan Yang Wenxin Ji Wen Xiang Cheng Gang Wu Si Tong Sheng Peng Zhang Jun Lin Xiaojia Chen Qiong Shi Expose flexible conformations for intrinsically disordered protein Current Research in Structural Biology Intrinsically disordered protein Protein folding Protein conformation Protein structure prediction |
| title | Expose flexible conformations for intrinsically disordered protein |
| title_full | Expose flexible conformations for intrinsically disordered protein |
| title_fullStr | Expose flexible conformations for intrinsically disordered protein |
| title_full_unstemmed | Expose flexible conformations for intrinsically disordered protein |
| title_short | Expose flexible conformations for intrinsically disordered protein |
| title_sort | expose flexible conformations for intrinsically disordered protein |
| topic | Intrinsically disordered protein Protein folding Protein conformation Protein structure prediction |
| url | http://www.sciencedirect.com/science/article/pii/S2665928X25000078 |
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