Browsing by Author "Tsai, Min-Yeh"

Now showing 1 - 8 of 8

Folding Thermodynamics of a Beta-Hairpin Peptide: A Theoretical Study
(2012-01-31)
Tsai, Min-Yeh
;
Yuan, Jian-Min
;
Teranishi, Yoshiaki
;
Lin, Sheng-Hsien
;
交大名義發表
Intrinsic coordination for revealing local structural changes in protein folding-unfolding
(2016-01-28)
Shiu, Ying-Jen
;
Hayashi, Michitoshi
;
Shih, Orion
;
Su, Charlene
;
Tsai, Min-Yeh
With a deformed object of a rigid rod inside, the local dislocations may be tracked relatively easily with respect to the internal rigid rod. We apply this concept on protein folding-unfolding to track the internal structural changes of an unfolded protein in solution. Proposed here is a protein internal coordination based on the major axis X of an ellipsoidal protein and the stable intrinsic transition dipole moment mu of the protein during unfolding. In this methodology, small-angle X-ray scattering (SAXS) is used to provide the protein global morphologies in the native and unfolded states. Furthermore, time-resolved fluorescence anisotropy (TRFA) provides the relative orientation between X and mu of Trp59 of the model protein cytochrome c. Hence observed in the protein unfolding with denaturants, acid, urea, or GuHCl, is the elongation of the native protein conformation along a reoriented protein major axis; accompanied are the different extents of relocations of the terminal a helices and loop structures of the protein in the corresponding unfolding.
Kinetic Ising Model Study of Protein Aggregation
(2014-01-28)
Tsai, Min-Yeh
;
Yuan, Jian-Min
;
Lin, Sheng-Hsien
;
應用化學系
;
Department of Applied Chemistry
Molecular Dynamics Insight into the Diverse Thermodynamic Behavior of a Beta-Hairpin Peptide
(2013-07-01)
Tsai, Min-Yeh
;
Yuan, Jian-Min
;
Yamaki, Masahiro
;
Lin, Chih-Kai
;
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.
Theoretical Study on Structure and Sum-Frequency Generation (SFG) Spectroscopy of Styrene-Graphene Adsorption System
(2013-01-31)
Lin, Chih-Kai
;
Shih, Chun-Chi
;
Niu, Yingli
;
Tsai, Min-Yeh
;
Shiu, Ying-Jen
In this theoretical study, we aimed to simulate the sum-frequency generation (SFG) spectroscopy of a thin polystyrene layer physically adsorbed on the graphene sheet and to figure out the orientation distribution of the phenyl units. To simplify the problem, we started the investigation by constructing molecular models with styrene and ethylbenzene monomers and styrene oligomers up to four units adsorbed on a finite-sized graphene hexagon. Geometric optimization results showed that the phenyl rings of the adsorbate always orientate close to the surface normal with a small tilt angle. The adsorption is weak but not negligible. SFG spectra have been simulated based on these calculated structures, vibrational frequencies, and dipole and polarizability derivatives to compare with experimental reports of polystyrene adsorbed on other surfaces.
Thermodynamic Insight into Protein Aggregation Using a Kinetic Ising Model
(2015-01-01)
Tsai, Min-Yeh
;
Yuan, Jian-Min
;
Lin, Sheng-Hsien
;
應用化學系
;
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
;
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