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Journal article
Thermodynamics of protein folding using a modified Wako-Sait-Muoz-Eaton model
Journal of biological physics, v 38(4), pp 543-571
01 Sep 2012
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
Herein, we propose a modified version of the Wako-Sait-Muoz-Eaton (WSME) model. The proposed model introduces an empirical temperature parameter for the hypothetical structural units (i.e., foldons) in proteins to include site-dependent thermodynamic behavior. The thermodynamics for both our proposed model and the original WSME model were investigated. For a system with beta-hairpin topology, a mathematical treatment (contact-pair treatment) to facilitate the calculation of its partition function was developed. The results show that the proposed model provides better insight into the site-dependent thermodynamic behavior of the system, compared with the original WSME model. From this site-dependent point of view, the relationship between probe-dependent experimental results and model's thermodynamic predictions can be explained. The model allows for suggesting a general principle to identify foldon behavior. We also find that the backbone hydrogen bonds may play a role of structural constraints in modulating the cooperative system. Thus, our study may contribute to the understanding of the fundamental principles for the thermodynamics of protein folding.
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Details
- Title
- Thermodynamics of protein folding using a modified Wako-Sait-Muoz-Eaton model
- Creators
- Min-Yeh Tsai - National Yang Ming Chiao Tung UniversityJian-Min Yuan - Drexel UniversityYoshiaki Teranishi - National Yang Ming Chiao Tung UniversitySheng Hsien Lin - National Yang Ming Chiao Tung University
- Publication Details
- Journal of biological physics, v 38(4), pp 543-571
- Publisher
- Springer Nature
- Number of pages
- 29
- Grant note
- National Science Council (Taiwan); Ministry of Science and Technology, Taiwan
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Physics
- Web of Science ID
- WOS:000310193000001
- Scopus ID
- 2-s2.0-84867864943
- Other Identifier
- 991019168586504721
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- Collaboration types
- Domestic collaboration
- International collaboration
- Web of Science research areas
- Biophysics