title: Thermodynamics of protein folding using a modified Wako-Saitô-Muñoz-Eaton model.
abstract: Herein, we propose a modified version of the Wako-Saitô-Muñoz-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.
authors.affiliation: National Chiao Tung University, 1001 Ta Hsuen Road, Hsinchu, Taiwan, Republic of China, mytsai886@gmail.com.
authors.forename: Min-Yeh
authors.initials: MY
authors.lastname: Tsai
authors.forename: Jian-Min
authors.initials: JM
authors.lastname: Yuan
authors.forename: Yoshiaki
authors.initials: Y
authors.lastname: Teranishi
authors.forename: Sheng Hsien
authors.initials: SH
authors.lastname: Lin
mesh_terms: D002151:Calorimetry; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry; D017510:Protein Folding; D017433:Protein Structure, Secondary; D013696:Temperature; D013816:Thermodynamics
chemical_list: D010455:Peptides