• Applied Biological Chemistry
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• 제31권2호
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• pp.137-142
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• 1988

Saccharomycopsis lipolytica ATCC 44601에서 정제한 isocitrate lyase 반응산물의 축합반응과 개열반응은 $30^{\circ}C$, pH 7.0에서 분석되었다. Glyoxylate와 succinate의 축합반응에서 Km값은 각각 0.06 mM과 0.21 mM이었고, 개열 반응에서 glyoxylate는 직선적인 경쟁적 저해를, succinate는 직선적인 비경쟁적 저해를 나타내었으며 이때 Ki 값은 각각 0.22 mM과 0.82 mM이었다. 그러므로 이 kinetic분석은 이 효소가 축합 반응에서 glyoxylate가 succinate보다 먼저 결합하는 정서반응기구인 것을 나타내었다. 3-Bromopyruvate(BrP)의 불활성화는 포화 kinetics를 나타내면서 효소를 불가역적으로 불활성화하였으며 반감기는 0.15분이고 $K_{BrP}$는 0.032 mM이었으며, 기질과 반응생성물들을 불활성화에 대하여 보호작용이 있었다.

• The Plant Pathology Journal
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• 제33권4호
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• pp.370-381
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• 2017

Rathayibacter tritici, which is a Gram positive, plant pathogenic, non-motile, and rod-shaped bacterium, causes spike blight in wheat and barley. For successful pathogenesis, R. tritici is associated with Anguina tritici, a nematode, which produces seed galls (ear cockles) in certain plant varieties and facilitates spread of infection. Despite significant efforts, little research is available on the mechanism of disease or bacteria-nematode association of this bacterium due to lack of genomic information. Here, we report the first complete genome sequence of R. tritici NCPPB 1953 with diverse features of this strain. The whole genome consists of one circular chromosome of 3,354,681 bp with a GC content of 69.48%. A total of 2,979 genes were predicted, comprising 2,866 protein coding genes and 49 RNA genes. The comparative genomic analyses between R. tritici NCPPB 1953 and R. toxicus strains identified 1,052 specific genes in R. tritici NCPPB 1953. Using the BlastKOALA database, we revealed that the flexible genome of R. tritici NCPPB 1953 is highly enriched in 'Environmental Information Processing' system and metabolic processes for diverse substrates. Furthermore, many specific genes of R. tritici NCPPB 1953 are distributed in substrate-binding proteins for extracellular signals including saccharides, lipids, phosphates, amino acids and metallic cations. These data provides clues on rapid and stable colonization of R. tritici for disease mechanism and nematode association.

• 한국진공학회:학술대회논문집
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• 한국진공학회 2013년도 제45회 하계 정기학술대회 초록집
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• pp.204.2-204.2
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• 2013

Wide band gap II-VI semiconductors have attracted the interest of many research groups during the past few years due to the possibility of their applications in light-emitting diodes and laser diodes. Among the II-VI semiconductors, ZnO is an important optoelectronic device material for use in the violet and blue regions because of its wide direct band gap (Eg ~3.37 eV) and large exciton binding energy (60 meV). F-doped ZnO (FZO) and undoped ZnO thin films were grown onto quartz substrate by the sol-gel spin-coating method. The doping level in the solution, designated by F/Zn atomic ratio of was varied from 0 to 5 in 1 steps. To investigate the effects of the structure and optical properties of FZO thin films were investigated using X-ray diffraction (XRD), UV-visible spectroscopy, and photoluminescence (PL). In the XRD, the residual stress, FWHM, bond length, and average grain size were changed with increasing the doping concentration. For the PL spectra, the high INBE/IDLE ratio of the FZO thin films doping concentration at 1 at.% than the other samples.

• Molecules and Cells
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• 제43권9호
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• pp.784-792
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• 2020

Arginine kinase (AK), a bioenergy-related enzyme, is distributed widely in invertebrates. The role of highly conserved histidines in AKs is still unascertained. In this study, the highly conserved histidine 284 (H284) in AK of Daphnia magna (DmAK) was replaced with alanine to elucidate the role of H284. We examined the alteration of catalytic activity and structural changes of H284A in DmAK. The catalytic activity of H284A was reduced dramatically compared to that in wild type (WT). Thus the crystal structure of H284A displayed several structural changes, including the alteration of D324, a hydrogen-bonding network around H284, and the disruption of π-stacking between the imidazole group of the H284 residue and the adenine ring of ATP. These findings suggest that such alterations might affect a conformational change of the specific loop consisting of G310-V322 at the antiparallel β-sheet region. Thus, we speculated that the H284 residue might play an important role in the conformational change of the specific loop when ATP binds to the substrate-binding site of DmAK.

• 방사선산업학회지
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• 제3권1호
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• pp.25-29
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• 2009

Microarrays can be used to screen thousands of binding events in a parallel and high throughput fashion and are of major importance in disease diagnosis and drug discovery. The use of radioisotope is conventionally regarded as one of the most sensitive detection methods. Atherosclerosis is a common disorder affecting arterial blood vessels. It happens when fat, cholesterol, and other substances made in the arterial blood vessels form a hard substances called plaque. Lipoprotein-associated phospholipase $A_2$ ($Lp-PLA_2$), a phospholipase $A_2$ enzyme, is used as a marker for cardiac disease. The detection of $Lp-PLA_2$ was accomplished by using radioactive [$^3H-acetyl$] PAF as a substrate and a feasibility study on RI biochip application to detection of $Lp-PLA_2$, a risk factors of atherosclerosis was performed. Inhibitive activity of a native plant extract was also determined by using the RI biochip. It was found to be applicable to a high-throughput screening of inhibitors for developing atherosclerosis therapeutic agents.

• Journal of Microbiology and Biotechnology
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• 제29권2호
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• pp.244-255
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• 2019

Xylose isomerase (XI; E.C. 5.3.1.5) catalyzes the isomerization of xylose to xylulose, which can be used to produce bioethanol through fermentation. Therefore, XI has recently gained attention as a key catalyst in the bioenergy industry. Here, we identified, purified, and characterized a XI (PbXI) from the psychrophilic soil microorganism, Paenibacillus sp. R4. Surprisingly, activity assay results showed that PbXI is not a cold-active enzyme, but displays optimal activity at $60^{\circ}C$. We solved the crystal structure of PbXI at $1.94-{\AA}$ resolution to investigate the origin of its thermostability. The PbXI structure shows a $({\beta}/{\alpha})_8$-barrel fold with tight tetrameric interactions and it has three divalent metal ions (CaI, CaII, and CaIII). Two metal ions (CaI and CaII) located in the active site are known to be involved in the enzymatic reaction. The third metal ion (CaIII), located near the ${\beta}4-{\alpha}6$ loop region, was newly identified and is thought to be important for the stability of PbXI. Compared with previously determined thermostable and mesophilic XI structures, the ${\beta}1-{\alpha}2$ loop structures near the substrate binding pocket of PbXI were remarkably different. Site-directed mutagenesis studies suggested that the flexible ${\beta}1-{\alpha}2$ loop region is essential for PbXI activity. Our findings provide valuable insights that can be applied in protein engineering to generate low-temperature purpose-specific XI enzymes.

• Journal of Microbiology and Biotechnology
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• 제29권9호
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• pp.1375-1382
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• 2019

Phenylalanine hydroxylase from Chromobacterium violaceum (CvPAH) is a monomeric enzyme that converts phenylalanine to tyrosine. It shares high amino acid identity and similar structure with a subunit of human phenylalanine hydroxylase that is a tetramer, resulting in the latent application in medications. In this study, semirational design was applied to CvPAH to improve the catalytic ability based on molecular dynamics simulation analyses. Four N-terminal truncated variants and one single point variant were constructed and characterized. The D267P variant showed a 2.1-fold increased thermal stability compared to the wild type, but lower specific activity was noted compared with the wild type. The specific activity of all truncated variants was a greater than 25% increase compared to the wild type, and these variants showed similar or slightly decreased thermostability with the exception of the $N-{\Delta}9$ variant. Notably, the $N-{\Delta}9$ variant exhibited a 1.2-fold increased specific activity, a 1.3-fold increased thermostability and considerably increased catalytic activity under the neutral environment compared with the wild type. These properties of the $N-{\Delta}9$ variant could advance medical and pharmaceutical applications of CvPAH. Our findings indicate that the N-terminus might modulate substrate binding, and are directives for further modification and functional research of PAH and other enzymes.

• Biomolecules & Therapeutics
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• 제30권6호
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• pp.520-528
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• 2022

Mast cells are an effector cell that plays a pivotal role in type I hypersensitive immune responses. Mast cells exist in connective tissues, such as skin and mucosal tissue, and contain granules which contain bioactive substances such as histamine and heparin in cells. The granules of mast cells are secreted by antigen stimulation to cause the type I allergic hypersensitivity. In addition, stimulated by antigen, mast cells synthesize and secrete various eicosanoids and cytokines. While AT9283 is known to have anticancer effects, the therapeutic effect of AT9283 on allergic disorders is completely unknown. In this study, it was found that AT9283 reversibly inhibited antigen-IgE binding-induced degranulation in mast cells (IC₅₀, approx. 0.58 μM) and suppressed the secretion of the inflammatory cytokines IL-4 (IC₅₀, approx. 0.09 μM) and TNF-α (IC₅₀, approx. 0.19 μM). For a mechanism of mast cell inhibition, while not inhibiting Syk phosphorylation, AT9283 suppressed the activation of LAT, a downstream substrate protein of Syk, in a dose-dependent manner. As expected, AT9283 also inhibited the activation of PLCγ1 and Akt, downstream signaling molecules of Syk/LAT, and MAP kinases such as JNK, Erk1/2, and P38. In an in vitro protein tyrosine kinase assay, AT9283 directly inhibited Syk activity. Next, AT9283 dose-dependently inhibited passive cutaneous anaphylaxis (PCA), an IgE-mediated allergic acute response, in mice (ED50, approx. 34 mg/kg, p.o.). These findings suggest that AT9283 has potential to use as a new drug for alleviating the symptoms of IgE-mediated allergic disorders.

• 한국미생물·생명공학회지
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• 제49권1호
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• pp.65-74
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• 2021

Serine proteases are the most versatile proteolytic enzymes with tremendous applications in various industrial processes. This study was designed to investigate the biochemical properties, critical residues, and the catalytic potential of alkaline serine protease using in-silico approaches. The primary sequence was analyzed using ProtParam, SignalP, and Phyre2 tools to investigate biochemical properties, signal peptide, and secondary structure, respectively. The three-dimensional structure of the enzyme was modeled using the MODELLER program present in Discovery Studio followed by Molecular Dynamics simulation using GROMACS 5.0.7 package with CHARMM36m force field. The proteolytic potential was measured by performing docking with casein- and keratin-enriched residues, while the effect of the inhibitor was studied using phenylmethylsulfonyl fluoride, (PMSF) applying GOLDv5.2.2. Molecular weight, instability index, aliphatic index, and isoelectric point for serine protease were 39.53 kDa, 27.79, 82.20 and 8.91, respectively. The best model was selected based on the lowest MOLPDF score (1382.82) and DOPE score (-29984.07). The analysis using ProSA-web revealed a Z-score of -9.7, whereas 88.86% of the residues occupied the most favored region in the Ramachandran plot. Ser327, Asp138, Asn261, and Thr326 were found as critical residues involved in ligand binding and execution of biocatalysis. Our findings suggest that bioengineering of these critical residues may enhance the catalytic potential of this enzyme.

• Journal of Yeungnam Medical Science
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• 제9권2호
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• pp.288-301
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• 1992

소의 중추신경계의 신경전달인자에 의한 세포막에서의 정보전달 과정에 관여하는 PLC 활성화에 G-단백질의 관여 여부를 관찰하기 위하여 소의 뇌조직의 PLC ${\beta}$, ${\gamma}$ 및 ${\delta}$를 얻어 각 isozyme의 특성을 관찰하였다. 기질용액에 phosphatidyl choline(PC)을 첨가시 PLC 각 isozyme 마다 정도의 차이는 있으나 증가 양상을 보였으며 PLC ${\delta}$는 $100{\mu}M$ $Ca^{2+}$ 농도에서 높은 활성도 증가를 보였다. 세포막 소포체를 형성하기 위하여 $PIP_2$기질과 PC에 detergent로 cholate와 deoxycholate 농도에 따른 PLC 효과 관찰에서 cholate 농도 0.2%에서 1%까지 증가할 때 효소 활성도의 지속적인 상승이 관찰되었고, deoxycholate는 농도가 0.2%에서 높았다가 0.4%에서 낮아졌고 1%까지 증가함에 따라 PLC 효소 활성도는 약간 증가하였다. 기질액에 뇌추출액을 첨가하여 cholic acid 농도에 따른 PLC의 효과를 관찰한 결과 cholic acid 농도 0.2%에서 보다 1%에서 각 isozyme 모두에서 PLC활성도가 증가하였다. 소의 여러 장기에서 PLC isozyme의 분포정도를 방사면역측정방법으로 관찰하였을 때 뇌조직에 가장 많이 분포하고 있으며 특히 PLC ${\beta}$, ${\gamma}$가 많았고, PLC ${\delta}$는 부신에서 가장 많이 분포하였다. 다음으로 PLC ${\beta}$는 부신과 위, PLC${\gamma}$는 부신과 폐순이었다. PLC 효소가 활성화될 때 G-단백질의 관여 여부에 관하여 cholate 0.2%와 0.1%에서 G-단백질과 GTPrS 및 PLC의 결합정도의 관찰은 조직분쇄시료를 소의 뇌 및 부신조직을 이용하여 $^{35}S$-GTPrS 첨가시와 단세포군 항체를 이용한 경우 모두에서 1.49% 이하의 낮은 결합 정도를 관찰하였다. 그래서 정제된 PLC isozyme과 G-단백질 $Go{\alpha}$, $G{\beta}{\gamma}$, Gmix, $Gi{\alpha}$ 및 $Gt{\alpha}$ 각각에 대한 효과 관찰에 서 $Go{\alpha}$와 $G{\beta}{\gamma}$는 PLC ${\beta}$와 ${\delta}$의 활성도를 증가시켰고, PLC ${\gamma}$는 별 영향이 없었으며 Gmix에서는 세효소 모두 증가시켰다. $Gi{\alpha}$는 PLC ${\beta}$와 ${\gamma}$에서만 증가하였다. $Gt{\alpha}$는 PLC ${\beta}$ 및 ${\gamma}$에서 억제하였고 PLC ${\delta}$에서는 증가 양상을 보였다. 그러므로 PLC 활성화에 G-단백질의 관여가 인지되며 PLC isozyme과 G-단백질의 종류에 따라 대개의 경우 증가하는 경향이나 일부는 억제 내지는 별 영향이 없는 것으로 나타났다.