Browsing by Author "Yuan, Jian-Min"

Now showing 1 - 6 of 6

Folding Thermodynamics of a Beta-Hairpin Peptide: A Theoretical Study
(2012-01-31)
Tsai, Min-Yeh
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Yuan, Jian-Min
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Teranishi, Yoshiaki
;
Lin, Sheng-Hsien
;
交大名義發表
Kinetic Ising Model Study of Protein Aggregation
(2014-01-28)
Tsai, Min-Yeh
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Yuan, Jian-Min
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Lin, Sheng-Hsien
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應用化學系
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Department of Applied Chemistry
Molecular Dynamics Insight into the Diverse Thermodynamic Behavior of a Beta-Hairpin Peptide
(2013-07-01)
Tsai, Min-Yeh
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Yuan, Jian-Min
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Yamaki, Masahiro
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Lin, Chih-Kai
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Lin, Sheng Hsien
The b-hairpin is a building block in the -sheet structure. Understanding the formation of the -hairpin may provide insight into the formation of -sheet structures in, for example, protein amyloids. In this study, we performed molecular dynamics (MD) simulations to investigate the temperature-dependent transition behaviors of the GB1 -hairpin peptide. The simulated results are analysed in terms of distances between pairs of peptide bonds and site-dependent dihedral angles. Our results show that the properties of the hairpin can be site-dependent and that the dependency is primarily associated with the hairpin's geometrical shape and specific interactions, such as hydrophobic clustering. Thus our study provides a foundation for the interpretation of probe-dependent experimental results.
Thermodynamic Insight into Protein Aggregation Using a Kinetic Ising Model
(2015-01-01)
Tsai, Min-Yeh
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Yuan, Jian-Min
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Lin, Sheng-Hsien
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應用化學系
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Department of Applied Chemistry
In this work, we present a kinetic analysis for protein aggregation using the kinetic Ising model, which serves as a new application of a previously proposed model [Liang et al., J. Chin. Chem. Soc. 2003, 50, 335]. Considering protein as a single spin unit, we map two states of a unit to the aggregation-prone (AP) and the fibril (F) states. This work shows that the model can successfully capture the nucleation-growth features of protein aggregation from experiments, which offers thermodynamic interpretations of aggregation properties, such as lag-time and fibril stability.
Thermodynamics of protein folding using a modified Wako-Sait-Muoz-Eaton model
(2012-09-01)
Tsai, Min-Yeh
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Yuan, Jian-Min
;
Teranishi, Yoshiaki
;
Lin, Sheng Hsien
;
交大名義發表
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.
Thermodynamics of Protein Folding using a Modified Wako-Saito-Munoz-Eaton Model
(2013-01-29)
Tsai, Min-Yeh
;
Yuan, Jian-Min
;
Teranishi, Yoshiaki
;
Lin, Sheng Hsien
;
交大名義發表