• Proceedings of the Korean Society for Applied Microbiology Conference
• /
• 2001.06a
• /
• pp.35-39
• /
• 2001

The Integration Host factor (IHF) of Escherichia coli is a small, basic protein that is required for a variety of functions including site-specific recombination, transposition, gene regulation, plasmid replication, and DNA packaging. It ,is composed of two subunits that are encoded by the ihfA ($\alpha$-subunit) and ihjB ($\beta$-subunit) genes. IHF binding sites are composed of three elements called the WATCAR, TTG, and poly (dAT) elements. We have characterized IHF binding to the H site of bacteriophage λ. We have isolated suppressors that bind to altered H' sites using a challenge phage selection. Two different suppressors were isolated that changed the adjacent $\alpha$P64 and $\alpha$K65 residues. The suppressors recognized both the wild-type site and a site with a change in the WATCAR element. Three suppressors were isolated at $\beta$-E44. These suppressors bound the wild-type and a mutant site with a T：A to A：T change (H44A) in the middle of the TIR element. Site-directed mutagenesis was used to make several additional changes at $\beta$E44. The wild-type and $\beta$E44D mutant could not bind the wild-type site but were able to bind the H44A mutant site. Other mutants with neutral, polar, or a positive charge at $\beta$E44 were able to repress both the wild-type and H44A sites. Examination of the IHF crystal structure suggests that the ability of the wild-type and $\beta$E44D proteins to discriminate between the T：A and A：T basepairs is due to indirect interactions. The $\beta$-E44 residue does not contact the DNA directly. It imposes binding specificity indirectly by interactions with residues that contact the DNA. Details of the proposed interactions are discussed.

• Korean Journal of Pharmacognosy
• /
• v.31 no.3
• /
• pp.273-279
• /
• 2000

Leukotriene $B_4\;(LTB_4)$ is a pro-inflammatory mediator synthesized in myeloid cells from arachidonic acid. Elevated levels of $LTB_4$ have been found in a number of inflammatory diseases and levels are related to disease activity in some of these. Because $LTB_4$ interacts with cells through specific cell surface receptors, $LTB_4$ receptor blockade is the most specific approach to reduce the pathogenic role of $LTB_4$. In order to find $LTB_4$ receptor antagonist from plants, we screened the $LTB_4$ receptor antagonistic activity of the methanol extract and solvent fractions of herbal drugs. The ability of samples to inhibit specific binding of $[^3H]-LTB_4$ to human peripheral neutrophils was used as assay to evaluate the antagonistic activity of plant materials. Among the tested methanol extracts of herbal drugs, Mori Radicis Cortex, Perillae Semen, Armeniacae Semen and Sophorae subprostratae Radix showed potent inhibitory activity above 70% at the concentration of $100\;{mu}g/ml$. The inhibitory activities of $LTB_4$ binding to human neutrophils were evaluated for several solvent fractions at three different concentrations. Especially, hexane soluble fractions of Anemarrhenae Rhizoma and Embeliae Radix, and ethyl acetate soluble fractions of Aristolochiae Fructus, Magnoliae Cortex and Zingiberis Rhizoma crudus showed moderate activity at $25\;{mu}g/ml$. These fractions were promising candidates for the study of the activity-guided chromatographic purification of active compounds. Silica gel column chromatography of hexane soluble fractions of Anemarrhenae Rhizoma and Embeliae Radix gave very active sub-fractions, AA-4 and ES-4, and their inhibition activities of $LTB_4$ binding to human neutrophil at $30\;{mu}g/ml$ were 78% and 62%, respectively. From these results we could anticipate new $LTB_4$ receptor antagonist from herbal drugs, and the block of $LTB_4$ effects may provide beneficial in neutrophil mediated diseases such as inflammation and bronchial asthma.

• Journal of Applied Biological Chemistry
• /
• v.50 no.3
• /
• pp.109-114
• /
• 2007

Sar1p is a ras-related GTP-binding protein that functions in intracellular protein transport between the endoplasmic reticulum (ER) and the Golgi complex. The effector domain of Ras family proteins is highly conserved and this domain is functionally interchangeable in plant, yeast and mammalian Sar1. Using a recombinant Brassica sar1 protein (Bsar1p) harboring point mutations in its effector domain, we here investigated the ability of Sar1p to bind and hydrolyze GTP and to interact with the two sar1-specific regulators, GTPase activating protein (GAP) and guanine exchange factor (GEF). The T51A and T55A mutations impaired Bsar1p intrinsic GTP-binding and GDP-dissociation activity. In contrast, mutations in the switch domain of Bsar1 did not affect its intrinsic GTPase activity. Moreover, the P50A, P54A, and S56A mutations affected the interaction between Bsar1p and GAP. P54A mutant protein did not interact with two regulating proteins, GEF and GAP, even though the mutation didn't affect the intrinsic GTP-binding, nucleotide exchange or GTPase activity of Bsar1p.

• The Korean Journal of Ecology
• /
• v.28 no.1
• /
• pp.7-13
• /
• 2005

In the present study, we investigated the tolerance of Commelina communis to growth in Cu-contaminated soil and water We examined the germination rate, root and shoot growth of seedlings, fresh biomass in soil and water, and ability to eliminate Cu. We found that C. communis eliminated 41% of Cu in soil containing 50 mg Cu/kg and removed over 50% of Cu from water containing 100 mg Cu/L Cu. In addition, the plants could accumulate 90 mg Cu/g when grown in soil containing 50 mg Cu/kg and 140 mg Cu/g when grown in soil containing 100 mg Cu/kg thus higher levels of Cu removal were observed in soils containing higher Cu concentrations. In water, the maximal accumulation rate was 4.9 mg Cu/g root and 1.2 mg Cu/g shoot in water containing 20 mg Cu/L, and 7 days after exposure, Cu absorption saturated. Further, the growth rate of C. communis was not affected by up to 100 mg Cu/kg in the soil. Therefore, the phytotoxic effect of Cu on plants increased as the concentration of Cu was raised, although to different extents depending on whether the Cu was in soil or water. Overall, Cu removal from soil by C. communis was most effective at 100 mg Cu/kg in soil and 10 mg Cu/L in water. Finally, we identified two peaks of Cu-binding ligands in C. communis. Which is a high molecular weight peak (HMWL) at 60 kDa (Fraction 17 to 25) and a Cu binding peptide peak at <1 kDa (Very low molecular weight ligand: VLMWL). Cu-binding peptide (Cu-BP) was observed to have an amino acid composition typical of phytochelations.

• BMB Reports
• /
• v.41 no.7
• /
• pp.511-515
• /
• 2008

The nucleocapsid (NC) protein of the Human Immunodeficiency Virus-1 plays a key role in viral genomic packaging by specifically recognizing the Psi($\Psi$) RNA sequence within the HIV-1 genome RNA. Recently, a novel cell-based assay was developed to probe the specific interactions in vivo between the NC and $\Psi$-RNA using E.coli cells (J. Virol. 81: 6151-55, 2007). In order to examine the extendibility of this cell-based assay to RNAs other than $\Psi$-RNA, this study tested the RNA aptamers isolated in vitro using the SELEX method, but whose specific binding ability to NC in a living cellular environment has not been established. The results demonstrate for the first time that each of those aptamer RNAs can bind specifically to NC in a NC zinc finger motif dependent manner within the cell. This confirms that the cell-based assay developed for NC-$\Psi$interaction can be further extended and applied to NC-binding RNAs other than $\Psi$-RNA.

• Journal of Ginseng Research
• /
• v.17 no.1
• /
• pp.1-12
• /
• 1993

The Preventive effect of the saponin fraction of Panax ginseng C.A. Meyer against hyperchole- sterolemia was demonstrated by assaying the cholesterol and triacylglyceride level of the blood serum and liver of rats fed high-cholesterol diet with and/or without ginsenoside. To understand the mechanism of the preventive action of ginsenoside, ginsenoside effect on LDL receptor binding ability, cholesterol level, and cAMP level of Chinese hamster ovary (CHO) cells cultured under various conditions were examined. When LDL (20 $\mu$g/ml) was added to the culture medium for CHO cell culture, LDL receptor binding activity of the cell was suppressed down to 58% of that of normal group. Ginsenosides at 10--2% and 10-3% level (w/v) were shown to exert an appreciable stimulatory effect on CHO cell LDL receptor activity, which partially overcame the suppression due to the presence of LDL (20 $\mu\textrm{g}$/ml) in the medium. Ginsenosides also reduced the increased cholesterol level of test group almost to that of normal group, and it increased cAMP level, which was usually reduced to 55% of that of the normal group due to the presence of LDL in the medium. Comparison of Kd and Bmax value of CHO cells cultured under different conditions revealed that this stimulation was due not to the receptor's binding affinity but to its number. Addition of ginsenoside (10-2%) decreased the uptake of taurocholic acid as much as 20% at the actively transporting everted ileal sacs, but it failed to form a large mixed micelles with taurocholic acid, which was one of the proposed mechanisms by which ginsenoside inhibits bile acid reabsorption. From the above results, it seemed likely that ginsenoside prevented hypercholestrolemia by decreasing cholesterol level in cells thereby relieving the inhibition of LDL receptor synthesis by cholesterol and also by inhibiting bile acid reabsorption from the small intestine.

• Childhood Kidney Diseases
• /
• v.20 no.1
• /
• pp.23-28
• /
• 2016

Purpose: We investigated whether serum levels of insulin growth factor-1 (IGF-1) and insulin growth factor binding protein-3 (IGFBP-3) are valuable in predicting clinical outcomes or are correlated with other laboratory findings in children with Henoch-$Sch{\ddot{o}}nlein$ purpura (HSP). Methods: We examined 27 children who were consecutively admitted to our hospital with HSP between January 2011 and February 2012. Blood tests (C-reactive protein, white blood cell count, platelet count, erythrocyte sedimentation rate, albumin, immunoglobulin A, complement C3, antineutrophil cytoplasmic antibody, IGF-1, IGFBP-3) and urine tests were performed upon admission. IGF-1 and IGFBP-3 were resampled in the recovery phase. Controls included 473 children whose IGF-1 and IGFBP-3 were sampled for evaluating their growth, at the outpatient department of pediatric endocrinology in our hospital. IGF-1 and IGFBP-3 were compared between the HSP children and controls, and between the acute and recovery phases in HSP children. The ability of these values to predict clinical outcomes including renal involvement was analyzed using bivariate logistic regression analysis (BLRA). Results: IGF-1 and IGFBP-3 were not different between the HSP children and controls ($148.7{\pm}117.6$ vs. $69.2{\pm}96.9$, P=0.290: $3465.9{\pm}1290.9$ vs. $3597.2{\pm}1,127.6$, P=0.560, respectively). There was no significant difference in IGF-1 or IGFBP-3 between acute and recovery phases. Based on the BLRA, no variable, including IGF-1 and IGFBP-3, could predict clinical outcomes including the presence of nephritis Conclusion: We concluded that IGF-1 and IGFBP-3 do not predict clinical outcomes of HSP, including renal involvement, in this study.

• Journal of Radiation Industry
• /
• v.10 no.1
• /
• pp.7-12
• /
• 2016

Ikaros, a transcription factor containing zinc-finger motif, has known as a critical regulator of hematopoiesis in immune system. Ikaros protein modulates the transcription of target genes via binding to the regulatory elements of the genes promoters. However the regulatory function of Ikaros in other organelle except nuclear remains to be determined. This study explored radiation-induced modulatory function of Ikaros in cytoplasm. The results showed that Ikaros protein lost its DNA binding ability after LDIR (low-dose ionizing radiation) exposure. Cell fractionation and Western blot analysis showed that Ikaros protein was translocated into cytoplasm from nuclear by LDIR. This was confirmed by immunofluorescence assay. We identified Autotaxin as a novel protein which potentially interacts with Ikaros through in vitro protein-binding screening. Co-immunoprecipitation assay revealed that Ikaros and Autotaxin are able to bind each other. Autotaxin is a crucial enzyme generating lysophosphatidic acid (LPA), a phospholipid mediator, which has potential regulatory effects on immune cell growth and motility. Our results indicate that LDIR potentially regulates immune system via protein-protein interaction of Ikaros and Autotaxin.

• Genomics & Informatics
• /
• v.18 no.4
• /
• pp.43.1-43.13
• /
• 2020

The coronavirus disease 2019 is a contagious disease and had caused havoc throughout the world by creating widespread mortality and morbidity. The unavailability of vaccines and proper antiviral drugs encourages the researchers to identify potential antiviral drugs to be used against the virus. The presence of RNA binding domain in the nucleocapsid (N) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) could be a potential drug target, which serves multiple critical functions during the viral life cycle, especially the viral replication. Since vaccine development might take some time, the identification of a drug compound targeting viral replication might offer a solution for treatment. The study analyzed the phylogenetic relationship of N protein sequence divergence with other 49 coronavirus species and also identified the conserved regions according to protein families through conserved domain search. Good structural binding affinities of a few natural and/or synthetic phytocompounds or drugs against N protein were determined using the molecular docking approaches. The analyzed compounds presented the higher numbers of hydrogen bonds of selected chemicals supporting the drug-ability of these compounds. Among them, the established antiviral drug glycyrrhizic acid and the phytochemical theaflavin can be considered as possible drug compounds against target N protein of SARS-CoV-2 as they showed lower binding affinities. The findings of this study might lead to the development of a drug for the SARS-CoV-2 mediated disease and offer solution to treatment of SARS-CoV-2 infection.

• Journal of the Korea institute for structural maintenance and inspection
• /
• v.26 no.5
• /
• pp.119-126
• /
• 2022

This study proposed a BCM(Binding Column Method) that can reinforce the insufficient seismic force of piloti buildings that are not designed for seismic resistance. In addition, 4 reinforcement specimens and 1 reference specimen were manufactured for the proposed seismic reinforcement method. The effect of improving seismic performance before and after reinforcement was examined through repeated loading tests. As a result of experiment, seismic reinforcement specimen with BCM system showed hysteretic characteristics of a large ellipse with great energy dissipation ability and increased strength and stiffness, while reference specimen showed rapid reduction in strength and brittle shear failure column. In addition, it can be seen that the reinforcing effect is improved as the gap is narrow, the torque is large, and the thickness of the L-shaped steel sheet is thicker. The SC4 specimen showed the best seismic performance reinforcement effect.