標題: | Thermodynamics of protein folding using a modified Wako-Sait-Muoz-Eaton model |
作者: | Tsai, Min-Yeh Yuan, Jian-Min Teranishi, Yoshiaki Lin, Sheng Hsien 交大名義發表 National Chiao Tung University |
關鍵字: | WSME model;Protein;Beta-hairpin;Backbone hydrogen bond;Thermodynamics;Probe-dependent thermodynamic behavior;Site-dependent behavior;Foldon |
公開日期: | 1-Sep-2012 |
摘要: | 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. |
URI: | http://dx.doi.org/10.1007/s10867-012-9271-y http://hdl.handle.net/11536/20483 |
ISSN: | 0092-0606 |
DOI: | 10.1007/s10867-012-9271-y |
期刊: | JOURNAL OF BIOLOGICAL PHYSICS |
Volume: | 38 |
Issue: | 4 |
起始頁: | 543 |
結束頁: | 571 |
Appears in Collections: | Articles |
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