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WU XUE, FU TING, XIU ZHILONG, YIN LIU, WANG JINGUANG, LI GUOHUI. COMPARING FOLDING MECHANISMS OF DIFFERENT PRION PROTEINS BY Gō MODEL. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2013. [DOI: 10.1142/s0219633613410046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Prions are associated with neurodegenerative diseases induced by transmissible spongiform encephalopathies. The infectious scrapie form is referred to as PrP Sc , which has conformational change from normal prion with predominant α-helical conformation to the abnormal PrP Sc that is rich in β-sheet content. Neurodegenerative diseases have been found from both human and bovine sources, but there are no reports about infected by transmissible spongiform encephalopathies from rabbit, canine and horse sources. Here we used coarse-grained Gō model to compare the difference among human, bovine, rabbit, canine, and horse normal (cellular) prion proteins. The denatured state of normal prion has relation with the conversion from normal to abnormal prion protein, so we used all-atom Gō model to investigate the folding pathway and energy landscape for human prion protein. Through using coarse-grained Gō model, the cooperativity of the five prion proteins was characterized in terms of calorimetric criterion, sigmoidal transition, and free-energy profile. The rabbit and horse prion proteins have higher folding free-energy barrier and cooperativity, and canine prion protein has slightly higher folding free-energy barrier comparing with human and bovine prion proteins. The results from all-atom Gō model confirmed the validity of C α-Gō model. The correlations of our results with previous experimental and theoretical researches were discussed.
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Affiliation(s)
- XUE WU
- School of Life Science and Biotechnology, Dalian University of Technology, Linggong Road 2, Dalian 116024, P. R. China
- Laboratory of Molecular Modeling and Design, State key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science 457, Zhongshan Road, Dalian, Liaoning, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - TING FU
- School of Life Science and Biotechnology, Dalian University of Technology, Linggong Road 2, Dalian 116024, P. R. China
- Laboratory of Molecular Modeling and Design, State key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science 457, Zhongshan Road, Dalian, Liaoning, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - ZHI-LONG XIU
- School of Life Science and Biotechnology, Dalian University of Technology, Linggong Road 2, Dalian 116024, P. R. China
| | - LIU YIN
- Oncology Department in the 1st Affiliated Hospital of Dalian, Medical University, 222 Zhongshan Road, Liaoning Province, Dalian 116011, P. R. China
| | - JIN-GUANG WANG
- Thoracic Surgery Department in the 1st Affiliated Hospital of Dalian, Medical University, 222 Zhongshan Road, Liaoning Province, Dalian 116011, P. R. China
| | - GUO-HUI LI
- Laboratory of Molecular Modeling and Design, State key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science 457, Zhongshan Road, Dalian, Liaoning, P. R. China
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