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Journal of Biological Physics

, Volume 38, Issue 4, pp 543–571 | Cite as

Thermodynamics of protein folding using a modified Wako-Saitô-Muñoz-Eaton model

  • Min-Yeh TsaiEmail author
  • Jian-Min Yuan
  • Yoshiaki Teranishi
  • Sheng Hsien Lin
Original Paper

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.

Keywords

WSME model Protein Beta-hairpin Backbone hydrogen bond Thermodynamics Probe-dependent thermodynamic behavior Site-dependent behavior Foldon 

Notes

Acknowledgements

We wish to thank the National Science Council (Taiwan) for financial support. We also appreciate the help from Dr. Oleksandr Morozov from Florida International University for providing useful suggestions about this paper.

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Copyright information

© Springer Science+Business Media B.V. 2012

Authors and Affiliations

  • Min-Yeh Tsai
    • 1
    • 2
    Email author
  • Jian-Min Yuan
    • 3
  • Yoshiaki Teranishi
    • 1
  • Sheng Hsien Lin
    • 1
  1. 1.National Chiao Tung UniversityHsinchuRepublic of China
  2. 2.Department of ChemistryNational Taiwan UniversityTaipeiRepublic of China
  3. 3.Department of PhysicsDrexel UniversityPhiladelphiaUSA

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