• Journal of Plant Biotechnology
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• v.33 no.1
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• pp.1-9
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• 2006

Peroxiredoxins (Prxs) are ubiquitously distributed and play important functions in diverse cellular signaling systems. The proteins are largely classified into three groups, such as typical 2-Cys Prx, atypical 2-Cys Prx, and 1-Cys Prx, that are distinguished by their catalytic mechanisms and number of Cys residues. From the three classes of Prxs, the typical 2-Cys Prx containing the two-conserved Cys residues at its N-terminus and C-terminus catalyzes $H_2O_2$ with the use of thioredoxin (Trx) as an electron donor. During the catalytic cycle, the N-terminal Cys residue undergoes a peroxide-dependent oxidation to sulfenic acid, which can be further oxidized to sulfinic acid at the presence of high concentrations of $H_2O_2$ and a Trx system containing Trx, Trx reductase, and NADPH. The sulfinic acid form of 2-Cys Prx is reduced by the action of sulfiredoxin which requires ATP as an energy source. Under the strong oxidative or heat shock stress conditions, 2-Cys Prx in eukaryotes rapidly switches its protein structure from low-molecular-weight species to high-molecular-weight protein structures. In accordance with its structural changes, the protein concomitantly triggers functional switching from a peroxidase to a molecular chaperone, which can protect its substrate denaturation from external stress. In addition to its N-terminal active site, the C-terminal domain including 'YF-motif' of 2-Cys Prx plays a critical role in the structural changes. Therefore, the C-terminal truncated 2-Cys Prxs are not able to regulate their protein structures and highly resistant to $H_2O_2$-dependent hyperoxidation, suggesting that the reaction is guided by the peroxidatic Cys residue. Based on the results, it may be concluded that the peroxidatic Cys of 2-Cys Prx acts as an '$H_2O_2$-sensor' in the cells. The oxidative stress-dependent regulation of 2-Cys Prx provides a means of defense systems in cells to adapt stress conditions by activating intracellular defense signaling pathways. Particularly, 2-Cys Prxs in plants are localized in chloroplasts with a dynamic protein structure. The protein undergoes conformational changes again oxidative stress. Depending on a redox-potential of the chloroplasts, the plant 2-Cys Prx forms super-molecular weight protein structures, which attach to the thylakoid membranes in a reversible manner.

• BMB Reports
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• v.49 no.12
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• pp.681-686
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• 2016

Fructose 1,6-bisphosphate aldolase (FBA) is important for both glycolysis and gluconeogenesis in life. Class II (zinc dependent) FBA is an attractive target for the development of antibiotics against protozoa, bacteria, and fungi, and is also widely used to produce various high-value stereoisomers in the chemical and pharmaceutical industry. In this study, the crystal structures of class II Escherichia coli FBA (EcFBA) were determined from four different crystals, with resolutions between $1.8{\AA}$ and $2.0{\AA}$. Native EcFBA structures showed two separate sites of Zn1 (interior position) and Zn2 (active site surface position) for $Zn^{2+}$ ion. Citrate and TRIS bound EcFBA structures showed $Zn^{2+}$ position exclusively at Zn2. Crystallographic snapshots of EcFBA structures with and without ligand binding proposed the rationale of metal shift at the active site, which might be a hidden mechanism to keep the trace metal cofactor $Zn^{2+}$ within EcFBA without losing it.

• Proceedings of the Korean Vacuum Society Conference
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• 2010.08a
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• pp.259-259
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• 2010

Periodically polarity inverted (PPI) ZnO structures on (0001) Al2O3 substrates are demonstrated by plasmas assisted molecular beam epitaxy. The patterning and re-growth methods are used to realize the PPI ZnO by employing the polarity controlling method. For the in-situ polarity controlling of ZnO films, Cr-compound buffer layers are used.[1, 2] The region with the CrN intermediate layer and the region with the Cr2O3 and Al2O3 substrate were used to grow the Zn- and O-polar ZnO films, respectively. The growth behaviors with anisotropic properties of PPI ZnO heterostructures are investigated. The periodical polarity inversion is evaluated by contrast images of piezo-response microscopy. Structural and optical interface properties of PPI ZnO are investigated by the transmission electron microcopy (TEM) and micro photoluminescence ($\mu$-PL). The inversion domain boundaries (IDBs) between the Zn and the O-polar ZnO regions were clearly observed by TEM. Moreover, the investigation of spatially resolved local photoluminescence characteristics of PPI ZnO revealed stronger excitonic emission at the interfacial region with the IDBs compared to the Zn-polar or the O-polar ZnO region. The possible mechanisms will be discussed with the consideration of the atomic configuration, carrier life time, and geometrical effects. The successful realization of PPI structures with nanometer scale period indicates the possibility for the application to the photonic band-gap structures or waveguide fabrication. The details of application and results will be discussed.

• Bulletin of the Korean Chemical Society
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• v.13 no.3
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• pp.268-274
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• 1992

An attempt to improve the second harmonic generation (SHG) efficiency of MAP (methyl (2,4-dinitrophenyl)aminopropanoate) by modifying the substituents on the amino group of MAP is described. Several MAP analogues have been prepared using optically active amino acids alanine, phenylalanine and serine, and their SHG efficiencies measured. None of the MAP analogues exhibited SHG efficiencies as high as that of MAP. X-ray crystal structures of three MAP analogues have been determined. In the crystal structures of two of them, which were the derivatives of phenylalanine, two crystallographically-independent molecules existing in the asymmetric unit are aligned almost antiparallel. These structures are consistent with the very low SHG efficiencies of these compounds. On the other hand, the crystal structure of a serine derivative reveals substantial alignment of the dinitroaniline chromophore along the polar axis. However, the angle of 86.2° between the molecular charge tranfer axis and the polar axis of the crystal is still far away from the optimum value of 54.74° for the phase-matchable SHG. The structure is consistent with the SHG efficiency of this compound which is much higher than those of the phenylalanine derivatives but still lower than that of MAP. This study demonstrates the importance of the orientation of molecules in the crystal lattice in determining secod-order nonlinear optical properties of crystalline materials.

• Journal of Microbiology and Biotechnology
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• v.13 no.6
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• pp.926-936
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• 2003

Overexpression of human Bcl-2 protein in recombinant Chinese hamster ovary (rCHO) cells producing humanized antibody (SH2-0.32) considerably suppressed sodium butyrate (NaBu)-induced apoptosis during batch culture by using commercially available serum-free medium, which extended the culture longevity. Due to the extended culture longevity provided by the anti-apoptotic effect of Bcl-2 overexpression, the final antibody concentration of 14C6-bcl-2 culture (Bcl-2 high producer, $23\;\mu\textrm{g}\;ml^{-1}$) was 2 times higher than that of the $SH2-0.32-{\Delta}bcl-2$ culture (cells transfected with bcl-2-deficient plasmid, $10.5\;\mu\textrm{g}\;ml^{-1}$) in the presence of NaBu. To determine the effect of NaBu/Bcl-2 overexpression on the molecular integrity of protein products, antibodies purified from 14C6-bcl-2 and $SH2-0.32-{\Delta}bcl-2$ cultures in the presence of NaBu were characterized by using various molecular assay systems. For comparison, antibody purified from the parental rCHO cell culture (SH2-0.32) in the absence of NaBu was also characterized. No significant changes in molecular weight of antibodies could be observed by SDS-PAGE. From GlycoSep-N column analysis, it was found that the core oligosaccharide structure ($GlcNAc_2Man_3GlcNAc_2$) was not affected by NaBu/Bcl-2 overexpression, while the microheterogeneity of N-linked oligosaccharide structure was slightly affected. Compared with the antibody produced in the absence of NaBu, the proportion of neutral oligosaccharides was increased from 10% (14C6-bcl-2) to 16% ($SH2-0.32-{\Delta}bcl-2$) in the presence of NaBu, which was accompanied by the reduced proportion of acidic oligosaccharides, especially of monosialylated and disialylated forms. The changes in microheterogeneous oligoformal structures of antibody in turn affected the mobility of antibody isoforms in isoelectric focusing (IEF), resulting in the occurrence of some more basic antibody isoforms produced in the presence of NaBu. However, the antigen-antibody binding properties were not changed by alteration of glycosylation pattern. The competitive enzyme-linked immunosorbent assay (ELISA) showed that the antibody produced by NaBu/Bcl-2 overexpression maintained its antigen-antibody binding properties with binding affinity of about $2.5{\times}10^9{\;}M^{-1}$. Taken together, no significant effects of NaBu/Bcl-2 overexpression on the molecular integrity of antibodies, produced by using serum-free medium, could be observed by the molecular assay systems.

• Applied Chemistry for Engineering
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• v.28 no.3
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• pp.263-271
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• 2017

The application of mass spectrometry to polymer science has rapidly increased since the development of MALDI-TOF MS. This review summarizes current polymer analysis methods using MALDI-TOF MS, which has been extensively applied to analyze the average molecular weight of biopolymers and synthetic polymers. Polymer sequences have also been analyzed to reveal the structures and composition of monomers. In addition, the analysis of unknown end-groups and the determination of polymer concentrations are very important applications. Hyphenated techniques using MALDI-tandem MS have been used for the analysis of fragmentation patterns and end-groups, and also the combination of SEC and MALDI-TOF MS techniques is recommended for the analysis of complex polymers. Moreover, MALDI-TOF MS has been utilized for the observation of polymer degradation. Ion mobility MS, TOF-SIMS, and MALDI-TOF-imaging are also emerging technologies for polymer characterization because of their ability to automatically fractionate and localize polymer samples. The determination of polymer characteristics and their relation to the material properties is one of the most important demands for polymer scientists; the development of software and instrument for higher molecular mass range (> 100 kD) will increase the applications of MALDI-TOF MS for polymer scientists.

• Journal of Applied Biological Chemistry
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• v.50 no.1
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• pp.1-5
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• 2007

Chemical properties of spray-dried powders separated based on molecular weight from crude protein binding polysaccharide (CP-SD) of Agraricus blazei were examined. Contents of ${\beta}$-glucan in SD-1, SD-2 and SD-3 were 18.67%, 48.24%, and 37.15% respectively, and SD-2 (10-150 kDa) showed the highest molecular weight. Obtained ${\beta}$-glucans were not pure glucan, but was determined to be an acidic proteo-heteroglycan with a large amount of glucose (74.46-80.05%), galactose (8.91-15.2%), and mannose (4.9-5.46%). Composition of their amino acids was mainly aspartic and glutamic acids. FT-IR spectrum revealed SD-1, SD-2 and SD-3 were structures of ${\beta}$-1,3-glucans and ${\alpha}$-1,6-glucans at 890 and 930 $cm^{-1}$, respectively, signals of ${\alpha}$-1,6-glucans for CP-SD was not found. Useful CP-SD was recovered from A. blazei for preparation of three powder types as food materials.

• ALGAE
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• v.19 no.3
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• pp.175-190
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• 2004

The morphological and molecular characteristics of Pachydictyon coriaceum (Holmes) Okamura (1899) are described. Plants are collected from Korea all year round and have maximum height from August to September. The monthly variability of thallus growth is in the way with that of the seawater temperature. Two types of thallus structures, thick cortical layer tallus type and thin cortical cell layer type, are distinguished according to growing seasons. The habit of Korean plants is also classified into two thallus types, slender type and wide type, based on the length and the width of internodes, but this distinction between two types is not supported by either anatomical or molecular characteristics. P. coriaceum shares typical morphology in branching pattern and morphogenetic processes with the other species of Dictyota: 1) multi-cellular cortical and medullar layer in the partial of thallus, 2) same development of thallus from apical meristem cell, and 3) sub-lineage within Dictyota species lineage in rbcL, psaA and psbA gene sequences analyses. These characteristics lead to propose the new combination of Dictyota coriacea (Homes) I.K. Hwang, H.S. Kim et W.J. Lee, comb. nov.

• Molecules and Cells
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• v.43 no.11
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• pp.899-908
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• 2020

Intrinsically disordered proteins or regions (IDPs or IDRs) are widespread in the eukaryotic proteome. Although lacking stable three-dimensional structures in the free forms, IDRs perform critical functions in various cellular processes. Accordingly, mutations and altered expression of IDRs are associated with many pathological conditions. Hence, it is of great importance to understand at the molecular level how IDRs interact with their binding partners. In particular, discovering the unique interaction features of IDRs originating from their dynamic nature may reveal uncharted regulatory mechanisms of specific biological processes. Here we discuss the mechanisms of the macromolecular interactions mediated by IDRs and present the relevant cellular processes including transcription, cell cycle progression, signaling, and nucleocytoplasmic transport. Of special interest is the multivalent binding nature of IDRs driving assembly of multicomponent macromolecular complexes. Integrating the previous theoretical and experimental investigations, we suggest that such IDR-driven multiprotein complexes can function as versatile allosteric switches to process diverse cellular signals. Finally, we discuss the future challenges and potential medical applications of the IDR research.

• Bulletin of the Korean Chemical Society
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• v.33 no.3
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• pp.848-854
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• 2012

We have studied the oligomerization of a fibril-forming segment of ${\alpha}$-Synulcein using a replica exchange molecular dynamics (REMD) simulation. The simulation was performed with trimers and tetramers of a 12 amino acid residue stretch (residues 71-82) of ${\alpha}$-Synulcein. From extensive REMD simulations, we observed the spontaneous formation of both trimer and tetramer, demonstrating the self-aggregating and fibril-forming properties of the peptides. Secondary structure profile and clustering analysis illustrated that antiparallel ${\beta}$-sheet structures are major species corresponding to the global free energy minimum. As the size of the oligomer increases from a dimer to a tetramer, conformational stability is increased. We examined the evolution of simple order parameters and their free energy profiles to identify the process of aggregation. It was found that the degree of aggregation increased as time passed. Tetramer formation was slower than trimer formation and a transition in order parameters was observed, indicating the full development of tetramer conformation which is more stable than that of the trimer. The shape of free energy surface and change of order parameter distributions indicate that the oligomer formation follows a dock-and-lock process.