• Rapid Communication in Photoscience
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• v.4 no.1
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• pp.1-8
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• 2015

For understanding molecular mechanisms of photochemical reactions, in particular reactions of proteins with biological functions, it is important to elucidate both the initial reactions from the photoexcited states and the series of subsequent chemical reactions, e.g., conformation, intermolecular interactions (hydrogen bonding, hydrophobic interactions), and inter-protein interactions (oligomer formation, dissociation reactions). Although time-resolved detection of such dynamics is essential, these dynamics have been very difficult to track by traditional spectroscopic techniques. Here, relatively new approaches for probing the dynamics of protein photochemical reactions using time-resolved transient grating (TG) are reviewed. By using this method, a variety of spectrally silent dynamics can be detected and such data provide a valuable description about the reaction scheme. Herein, a blue light sensor protein TePixD is the exemplar. The initial photochemistry for TePixD occurs around the chromophore and is detected readily by light absorption, but subsequent reactions are spectrally silent. The TG experiments revealed conformational changes and changes in inter-protein interactions, which are essential for TePixD function. The TG experiments also showed the importance of fluctuations of the intermediates as the driving force of the reaction. This technique is complementary to optical absorption detection methods. The TG signal contains a variety of unique information, which is difficult to obtain by other methods. The advantages and methods for signal analyses are described in detail in this review.

• Journal of Soil and Groundwater Environment
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• v.10 no.5
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• pp.61-69
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• 2005

Changes in pyrene binding by dissolved and kaolinite-associated humic substances (HS) due to HS adsorptive fractionation processes were examined using purified Aldrich humic acid (PAHA) at different pH (4, 7 and 9). Irrespective of solution pH, molecular weight (MW) fractionation occurred upon adsorption of PAHA onto kaolinite, resulting in the deviation of residual PAHA MW from the original MW prior to sorption. Variation in $K_{OC}$ by bulk PAHA was observed at different pH due to relative contributions of partitioning and size exclusion effects (i.e., specific interactions). For all pH conditions investigated, carbon-normalized pyrene binding coefficients for nonadsorbed, residual fractions $(K_{OC}(res))$ were different from the original dissolved PAHA $K_{OC}$ value $(K_{OC}(orig))$ prior to contact with the kaolinite suspensions. Positive correlations between pyrene $(K_{OC}(res))$ and weight-average molecular weight $(MW_W)$ for residual PAHA fractions were observed for pH 7 and 9. However, such a positive correlation was not found at pH 4 due to the absence of the dramatic fractionation observed for high pH conditions (i.e., exclusive fractionation with respect to higher MW), suggesting that actual MW distribution pattern is more important for sorption-fractionated HS than the composite MW value. For adsorbed PAHA, conformational changes of PAHA upon adsorption seem to be important for the extent of pyrene binding. At relatively high pH (7 and 9), lower extent of pyrene binding was observed for adsorbed PAHA versus nonadsorbed PAHA. The conformation effects were more pronounced at higher pH.

• Bulletin of the Korean Chemical Society
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• v.32 no.9
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• pp.3433-3436
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• 2011

Some of metal nanoparticles have the potential for use as colorimetric assays for estimating solution properties, such as pH and temperature due to localized surface plasmon (LSP) phenomena. This report describes the use of silver nanoparticles (AgNP) conjugated with cytochrome c (Cyt c) for the colorimetric determination of solution pHs. When the pH of a solution decreases, the Cyt c immobilized on the AgNP undergoes a conformational change, leading to a decrease in the interparticle distance between Cyt c-AgNP probes and consequent red-shift in LSP. As a result, the color of the Cyt c-AgNP probe solution changes from yellow to red and finally to a grayish blue in the pH range from 11 to 3. This gradual color change can be used to determine the pH of a solution over a wide pH range, compared to other colorimetric methods that use gold nanoparticles.

• Molecules and Cells
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• v.38 no.2
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• pp.105-111
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• 2015

The beta2-adrenergic receptor (${\beta}2AR$) belongs to the G protein coupled receptor (GPCR) family, which is the largest family of cell surface receptors in humans. Extra attention has been focused on the human GPCRs because they have been studied as important protein targets for pharmaceutical drug development. In fact, approximately 40% of marketed drugs directly work on GPCRs. GPCRs respond to various extracellular stimuli, such as sensory signals, neurotransmitters, chemokines, and hormones, to induce structural changes at the cytoplasmic surface, activating downstream signaling pathways, primarily through interactions with heterotrimeric G proteins or through G-protein independent pathways, such as arrestin. Most GPCRs, except for rhodhopsin, which contains covalently linked 11 cis-retinal, bind to diffusible ligands, having various conformational states between inactive and active structures. The first human GPCR structure was determined using an inverse agonist bound ${\beta}2AR$ in 2007 and since then, more than 20 distinct GPCR structures have been solved. However, most GPCR structures were solved as inactive forms, and an agonist bound fully active structure is still hard to obtain. In a structural point of view, ${\beta}2AR$ is relatively well studied since its fully active structure as a complex with G protein as well as several inactive structures are available. The structural comparison of inactive and active states gives an important clue in understanding the activation mechanism of ${\beta}2AR$. In this review, structural features of inactive and active states of ${\beta}2AR$, the interaction of ${\beta}2AR$ with heterotrimeric G protein, and the comparison with ${\beta}1AR$ will be discussed.

• The Journal of the Korea Contents Association
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• v.5 no.4
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• pp.71-77
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• 2005

On contraction of the muscles, marked changes in X-ray reflections are observed, suggesting that conformational changes of contractile molecules and the movement of myosin heads during muscle contraction. It was found that the successive twitches decreased not only the time needed to the peak tension after the onset of stimulation but also the time needed to the maximum change of the X-ray intensity. However, the difference of the time between the peak tension and the maximum intensity change$(T_i-I_i)$ is nearly the same at any twitch.

• Bulletin of the Korean Chemical Society
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• v.29 no.8
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• pp.1510-1518
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• 2008

Results of intrinsic and extrinsic fluorescence studies on choline oxidase revealed that the enzyme at high alkaline pH values has more accessible hydrophobic patches relative to acidic pH. Fluorescence quenching studies with acrylamide confirm these changes. The quenching constants were also determined at different pH(s) by using the Stern-Volmer equation. CD studies showed that at higher pH a transition from $\alpha$-helix to $\beta$- structure was appeared while at lower pH the content of $\alpha$-helix structure was increased. Furthermore, analysis of the spectral data using chemometric method gave evidence for existence of intermediate components at very high pH(s). Results of thermal denaturation evaluated that the enzyme has the most instability at higher pH(s). Altogether low and high pH values caused significant alteration on secondary and tertiary structures of choline oxidase via inducing of an intermediate.

• Bulletin of the Korean Chemical Society
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• v.27 no.5
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• pp.642-648
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• 2006

Mushroom tyrosinase (MT) structural changes in the presence of $Cu ^{2+}$ and $Ni ^{2+}$ were studied separately. Far-UV CD spectra of the incubated MT with the either of the metal ions indicated reduction of the well-ordered secondary structure of the enzyme. Increasing in the maximum fluorescence emission of anilinonaphthalene-8-sulfonic acid (ANS) was also revealing partial unfolding caused by the conformational changes in the tertiary structure of MT. Thermodynamic studies on the chemical denaturation of MT by dodecyl trimethylammonium bromide (DTAB) showed decrease in the stability of MT in the presence of $Cu ^{2+}$ or $Ni ^{2+}$ using their activation concentrations. Both activities of MT were also assessed in the presence of different concentrations of these ions, separately, with various monophenols and their corresponding diphenols. Kinetic studies revealed that cresolase activity on p-coumaric acid was boosted in the presence of either of the metal ions, but inhibited when phenol, L-tyrosine, or 4-[(4-methylphenyl)azo]-phenol was substrate. Similarly, catecholase activity on caffeic acid was enhanced in the presence of $Cu ^{2+}$ or $Ni ^{2+}$, but inhibited when catechol, L-DOPA, or 4-[(4-methylbenzo)azo]-1,2-benzenediol was substrate. Results of this study suggest that both cations make MT more fragile and less active. However, the effect of the substrate structure on the MT allosteric behavior can not be ignored.

• Journal of Plant Biology
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• v.39 no.3
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• pp.173-177
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• 1996

A novel calcium binding protein (CaBP) was purified to electrophoretic homogeneity from Dunaliella salina. In the course of purification experiment, this CaBP was identified as a monomer and its molecular weight was about 21 kDand isoelectric point (pI) value was about 4.1 using isoelectrofocusing. This CaBP was able to bind Ca2+ even in the pressence of an excess MgCl2 and KCI both in solution. In the SDS-PAGE, the Ca2+-bound form was slower than the Ca2+-free form in the nondenaturing PAGE. This means that the CaBP undergoes conformational change in the Ca2+-bound condition. Furthermore, UV absorption spectrum and fluorescence intensity of this CaBP was investigated. UV absorption peak was appeared at about 258 nm and decreased somewhat in Ca2+-bound condition. In the measurement of fluorescence, maximum intensity was appeared at 303 nm and decreased in Ca2+-bound state, similarly as UV absorption spectrum. These show distinct changes upon Ca2+-binding, which indicate of structural and/or dynamic changes largely reminiscent of other members of the EF-hand Ca2+-binding protein family.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.42 no.3
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• pp.232-237
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• 2009

Norovirus surrogate (feline calicivirus) was inactivated by treatment at 50,000 psi for 60 sec by 6.8-$log_{10}TCID_{50}mL^{-1}$. Tissue obtained from oyster (digestive gland, gill and mantle) was qualitatively destroyed and distorted by treatment at pressure greater than 5,000 psi for 60 sec. High pressure treatment induced progressive changes in the color of the oyster adductor muscle. High pressure treatment effectively reduced norovirus surrogate but induced conformational changes in the tissue and color of oyster flesh.

• Proceedings of the Korean Fiber Society Conference
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• 2003.10a
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• pp.81-82
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• 2003

Two antibiotics, doxycycline (doxy) and ciprofloxacin (cipro) were applied under a variety of conditions to silk, and to silk that had previously been hydrolyzed. FTIR-ATR analyses indicated that the drastic increase in sorption of antibiotics by hydrolyzed silk was attributable to both chemical and conformational changes that occurred on hydrolysis. A high sorption of doxy by hydrolyzed silk did not necessarily give a more infection-resistant material as determined by a zone of inhibition test. Conversely, the same hydrolysis considerably increased both sorption of cipro and zone of inhibition of cipro-treated silk dyed at 65$^{\circ}C$ and 85$^{\circ}C$.