Browsing by Author "Shiu, Ying-Jen"

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Global and Local Structural Changes of Protein Unfolding
(2009)
Shiu, Ying-Jen
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Jeng, U-Ser
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Lin, Sheng-Hsien
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應用化學系
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應用化學系分子科學碩博班
In the mean-field Ising model, the folding-unfolding behavior of a protein is regarded as an ensemble of units reduced from, presumably, peptide bonds or amino acid residues. Units of similar thermodynamic properties are further classified into groups that are related to, for instance, alpha-helices or beta-sheets. Units of the same group are assumed to unfold collectively, whereas those of different groups may undergo either sequential or coupled unfolding. The introduction of unfolding groups facilitates the description of non-collective local structural changes experimentally observed via a multi-group unfolding. We incorporate denaturants and temperature effects into the free energy expression of the protein upon dissolution in a specific environment at thermal equilibrium, and a model protein, cytochrome c, was examined. Results indicate that there are at least four unfolding groups induced unfolding of cytochrome c: two are related to the prosthetic heme group, whereas another two groups are a-helices and global nearly group, which largely account for global changes in protein morphology. The extracted thermodynamic parameters, on the basis of the Ising model, can closely predict unfolding behaviors of the proteins in compounded denaturing environments.
Intrinsic coordination for revealing local structural changes in protein folding-unfolding
(2016-01-28)
Shiu, Ying-Jen
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Hayashi, Michitoshi
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Shih, Orion
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Su, Charlene
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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.
Mesostructured Arrays of Nanometer-spaced Gold Nanoparticles for Ultrahigh Number Density of SERS Hot Spots
(2014-05-01)
Lai, Ying-Huang
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Chen, Shiaw-Woei
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Hayashi, Michitoshi
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Shiu, Ying-Jen
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Huang, Chiao-Cheng
A novel one-trough synthesis via an air-water interface is demonstrated to provide hexagonally packed arrays of densely spaced metallic nanoparticles (NPs). In the synthesis, a mesostructured polyoxometalate (POM)-silicatropic template (PSS) is first self-assembled at the air-water interface; upon UV irradiation, anion exchange cycles enable the free-floating PSS film to continuously uptake gold precursors from the solution subphase for diffusion-controlled and POM-site-directed photoreduction inside the silica channels. NPs approximate to 2 nm can hence be homogeneously formed inside the silica-surfactant channels until saturation. As revealed via X-ray diffraction, small-angle X-ray scattering (SAXS), grazing incidence SAXS, and transmission electron microscopy, the Au NPs directed by the PSS template are arrayed into a 2D hexagonal lattice with inter-channel spacing of 3.2 nm and a mean along-channel NP spacing of 2.8 nm. This corresponds to an ultra-high number density (approximate to 10(19) NPs cm(-3)) of narrowly spaced Au NPs in the Au-NP@PSS composite, leading to 3D densely deployed hot-spots along and across the mesostructured POM-silica channels for surface-enhanced Raman scattering (SERS). Consequently, the Au-NP@PSS composite exhibits prominent SERS with 4-mercaptobenzoic acid (4-MBA) adsorbed onto Au NPs. The best 4-MBA detection limit is 5 nm, with corresponding SERS enhancement factors above 10(8).
Theoretical Study on Structure and Sum-Frequency Generation (SFG) Spectroscopy of Styrene-Graphene Adsorption System
(2013-01-31)
Lin, Chih-Kai
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Shih, Chun-Chi
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Niu, Yingli
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Tsai, Min-Yeh
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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.
Theory of time-resolved sum-frequency generation and its applications to vibrational dynamics of water
(2007-09-20)
Hayashi, Michitoshi
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Shiu, Ying-Jen
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Liang, Kuo Kan
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Lin, Sheng Hsien
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Shen, Yuan Ron
A molecular theory of time-resolved sum-frequency generation (SFG) has been developed. The theoretical framework is constructed using the coupled-oscillator model in the adiabatic approximation. This theory can treat not only the vibrational spectroscopy but also vibrational dynamics. An application of this theory is also provided for estimation of the time constants of the intermolecular vibrational energy transfer between water molecules. This approach can be used for molecular analysis of the experimental results of Shen at al. on the SFG studies of vibrational dynamics of water.