Title: Thermodynamics of protein folding using a modified Wako-Sait-Muoz-Eaton model
Authors: Tsai, Min-Yeh
Yuan, Jian-Min
Teranishi, Yoshiaki
Lin, Sheng Hsien
National Chiao Tung University
Keywords: WSME model;Protein;Beta-hairpin;Backbone hydrogen bond;Thermodynamics;Probe-dependent thermodynamic behavior;Site-dependent behavior;Foldon
Issue Date: 1-Sep-2012
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.
URI: http://dx.doi.org/10.1007/s10867-012-9271-y
ISSN: 0092-0606
DOI: 10.1007/s10867-012-9271-y
Volume: 38
Issue: 4
Begin Page: 543
End Page: 571
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