• Molecules and Cells
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• v.37 no.3
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• pp.264-269
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• 2014

The molecular interaction between tumor suppressor p53 and the anti-apoptotic Bcl-2 family proteins plays an essential role in the transcription-independent apoptotic pathway of p53. In this study, we investigated the binding of p53 DNA-binding domain (p53DBD) with the anti-apoptotic Bcl-2 family proteins, Bcl-w, Mcl-1, and Bcl-2, using GST pull-down assay and NMR spectroscopy. The GST pull-down assays and NMR experiments demonstrated the direct binding of the p53DBD with Bcl-w, Mcl-1, and Bcl-2. Further, NMR chemical shift perturbation data showed that Bcl-w and Mcl-1 bind to the positively charged DNA-binding surface of p53DBD. Noticeably, the refined structural models of the complexes between p53DBD and Bcl-w, Mcl-1, and Bcl-2 showed that the binding mode of p53DBD is highly conserved among the anti-apoptotic Bcl-2 family proteins. Furthermore, the chemical shift perturbations on Bcl-w, Mcl-1, and Bcl-2 induced by p53DBD binding occurred not only at the p53DBD-binding acidic region but also at the BH3 peptide-binding pocket, which suggests an allosteric conformational change similar to that observed in Bcl-$X_L$. Taken altogether, our results revealed a structural basis for a conserved binding mechanism between p53DBD and the anti-apoptotic Bcl-2 family proteins, which shed light on to the molecular understanding of the transcription-independent apoptosis pathway of p53.

• Korean Journal of Microbiology
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• v.55 no.3
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• pp.181-190
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• 2019

In Escherichia coli, DicA protein is involved in cell division control. DicA protein is known to bind DNA better at $25^{\circ}C$ than at $37^{\circ}C$. However, the molecular cause of the temperature dependent binding is not clear. In this study, we investigated how DicA binds DNA and why its DNA binding activity depends on temperature. An unique in vivo DNA binding assay developed in this laboratory showed that unlike the homologous proteins such as RovA or SlyA, DicA uses its N-terminal domain for DNA binding. The in vivo DNA binding assay of DicA also demonstrated that the temperature-dependent DNA binding activity does not come from Cnu or H-NS that is known to bind DNA better at $25^{\circ}C$ than at $37^{\circ}C$. Electrophoretic Mobility Shift Assay (EMSA), when performed with purified DicA protein, did not show temperature-dependent DicA binding activity. However when EMSA was performed with crude protein from WT E. coli cells, temperature-dependent DicA binding activity was observed, suggesting that there is a factor(s) that confers temperature DNA binding activity of DicA in vivo.

• Toxicological Research
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• v.16 no.2
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• pp.141-146
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• 2000

Phthalate esters are used extensively as a plasticizer in the manufacture of plastic products such as PVC bags and medical devices. Recently, phthalate esters have been shown to induce endocrine system mediated responses. However. only a Jew studies have been conducted for estrogenic activity of phthalate esters. In this study estrogenic activities of seven phthalate esters. butyl benzyl phthalate (BBP), di(2-ethylhexyl) phthalate (DEHP), di-n-butylphthalate (DBP), diethylphthalate (DEP), di-n-pentylphthalate (DPP), di-n-propylphthalate (DPrP) and dicyclohexylphthalate (DCHP), were examined in vitro using E-screen assay and competitive binding assay. From the E-screen assay, BBP. DEHP. DBP and DEP showed weak estrogenic activity at the concentration of 5 $\mu\textrm{M}$. The relative proliferative effect (RPE) and the relative proliferative potency (RPP) were 50~70% and 0.01%. respectively, when compared with 500 pM of 17$\beta$-estradiol (E2). In competitive binding assay with the rat uterine estrogen receptor (ER), BBP and DEP showed weak binding potency ［(l/$10^4$~1/$10^5$ of E2］ while DEHP and DBP scarcely bound to ER. These results suggest that some phthalate esters have weak estrogenic activities in vitro.

• Journal of Korean Dental Science
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• v.4 no.1
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• pp.6-13
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• 2011

Purpose: Craniosynostosis (CS), one of the most common congenital craniofacial deformities, is the premature closure of cranial sutures. NELL-1 is a novel molecule overexpressed during premature cranial suture closure in human CS. From a functional perspective, NELL-1 has been reported to accelerate chondrocyte maturation and modulate calvarial osteoblast differentiation and apoptosis pathways. The mechanism through which NELL-1 induces these phenomena, however, remains unclear. The purpose of this study is to identify the NELL-1 binding protein(s) through which the biologic mechanism of NELL-1 can be further investigated. Materials and Methods: Far-Western and Immunoprecipitation (IP) assays were performed, independently and in sequence, followed by mass spectrometry to identify the NELL-1 binding proteins. Reverse IP was used to verify and confirm candidate binding protein. Results: The only confirmative protein from current experimentation was vimentin. Vimentin is the major structural component of the intermediate filaments. Conclusion: The present study identified and confirmed vimentin as a NELL-1 binding protein, which opened up a new window to mechanistically facilitate studies on this CS-associated molecule.

• Language and Information
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• v.14 no.1
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• pp.67-91
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• 2010

Present study examines L1 transfer effect and UG involvement in the acquisition of binding properties of Korean as second language (L2). The study especially investigates i) whether knowledge from different L1s (English and Chinese) affect the interpretation of binding in Korean as L2 and ii) whether L2 learners of Korean differentiate two Korean anaphors like Korean monolinguals do, based on their knowledge of universal form-function correlation of anaphors. 53 post-puberty L2 learners of Korean with English or Chinese L1, together with 30 Korean monolinguals, were tested over Truth Value Judgment Task with stories, composed of Korean sentences representing various types of binding with two Korean reflexives - caki and caki-casin. The results showed some effect of L1 transfer, though not always. Overall, late L2 learners of Korean seem to know the difference between the two anaphors in their properties related to form-function correlation, though their performance level was lower compared to Korean monolinguals. Detailed pattern of the results and the role of UG in the interpretations of Korean reflexives are also discussed.

• Bulletin of the Korean Chemical Society
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• v.32 no.1
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• pp.162-168
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• 2011

Many ligands have been experimentally designed and tested for their activities as inhibitors against bacterial enoyl-ACP reductase (FabI), ENR. Here the binding energies of the reported ligands with the E. coli ENR-$NAD^+$ were calculated, analyzed and compared, and their molecular dynamics (MD) simulation study was performed. IDN, ZAM and AYM ligands were calculated to have larger binding energies than TCL and IDN has the largest binding energy among the considered ligands (TCL, S54, E26, ZAM, AYM and IDN). The contribution of residues to the ligand binding energy is larger in E. coli ENR-NAD+-IDN than in E. coli ENR-$NAD^+$-TCL, while the contribution of $NAD^+$ is smaller for IDN than for TCL. The large-size ligands having considerable interactions with residues and $NAD^+$ have many effective functional groups such as aromatic $\pi$ rings, acidic hydroxyl groups, and polarizable amide carbonyl groups in common. The cation-$\pi$ interactions have large binding energies, positively charged residues strongly interact with polarisable amide carbonyl group, and the acidic phenoxyl group has strong H-bond interactions. The residues which have strong interactions with the ligands in common are Y146, Y156, M159 and K163. This study of the reported inhibitor candidates is expected to assist the design of feasible ENR inhibitors.

• The Korean Journal of Physiology and Pharmacology
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• v.24 no.3
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• pp.277-286
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• 2020

Polycystic kidney disease 2-like-1 (PKD2L1), also known as polycystin-L or TRPP3, is a non-selective cation channel that regulates intracellular calcium concentration. Calmodulin (CaM) is a calcium binding protein, consisting of N-lobe and C-lobe with two calcium binding EF-hands in each lobe. In previous study, we confirmed that CaM is associated with desensitization of PKD2L1 and that CaM N-lobe and PKD2L1 EF-hand specifically are involved. However, the CaM-binding domain (CaMBD) and its inhibitory mechanism of PKD2L1 have not been identified. In order to identify CaM-binding anchor residue of PKD2L1, single mutants of putative CaMBD and EF-hand deletion mutants were generated. The current changes of the mutants were recorded with whole-cell patch clamp. The calmidazolium (CMZ), a calmodulin inhibitor, was used under different concentrations of intracellular. Among the mutants that showed similar or higher basal currents with that of the PKD2L1 wild type, L593A showed little change in current induced by CMZ. Co-expression of L593A with CaM attenuated the inhibitory effect of PKD2L1 by CaM. In the previous study it was inferred that CaM C-lobe inhibits channels by binding to PKD2L1 at 16 nM calcium concentration and CaM N-lobe at 100 nM. Based on the results at 16 nM calcium concentration condition, this study suggests that CaM C-lobe binds to Leu-593, which can be a CaM C-lobe anchor residue, to regulate channel activity. Taken together, our results provide a model for the regulation of PKD2L1 channel activity by CaM.

• Journal of Periodontal and Implant Science
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• v.29 no.3
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• pp.663-676
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• 1999

Porphyromonas gingivalis, a Gram negative, anaerobic, asaccharolytic rod, is one of the most frequently implicated pathogens in human periodontal disease and has a requirement for hemin for growth. A 30 kDa (heated 24 kDa) hemin-binding protein whose expression is both hemin and iron regulated has recently been purified and characterized in this oral pathogen. This study has identified a hemin-binding P. gingivalis protein by expression of a P. gingivalis genomic library in Escherichia coli, a bacterium which does not require or transport exogenous hemin. A library of genomic DNA fragments from P. gingivalis was constructed in plasmid pUC18, transformed into Escherichia coli strain $DH5{\alpha}$ , and screened for recombinant clones with hemin-binding activity by plating onto hemin-containing agar. Of approximately 10,000 recombinant E. coli colonies screened on LB-amp-hemin agar, 10 exhibited a clearly pigmented phenotype. Each clone contained various insert DNA. The Hind III fragment transferred to the T7 RNA polymerase/promoter expression vector system produced a sligltly smaller (21 kDa) protein, a precursor form, immunoreactive to the antibody against the 24 kDa protein, suggesting that the cloned DNA fragment probably carried an entire gene for the 24 kDa hemin-binding protein.

• Journal of Applied Biological Chemistry
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• v.56 no.3
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• pp.147-156
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• 2013

The objectives of this study were to investigate the effect of Lactobacillus paracasei subsp. tolerans JG22 isolated from pepper leaf jangajji on the mutagenic activity of N-methyl, N'-nitro, N-nitrosoguanidine (MNNG) and 2-nitrofluene (2-NF) and to evaluate the effect of physico-chemical pretreatment on the antimutagenic activity of the strain. The viable cells of JG22 strain displayed a significantly high (p <0.05) antimutagenic activity against both mutagens tested. The antimutagenic effect of JG22 strain seems to be positively correlated with the amounts of the cells in the incubation time. This strain produced the antimutagenic activity of the maximum levels after preincubation for 30 min. The binding of this strain against the mutagenic compounds might be mainly present in the cell wall fraction rather than the cytosol fraction. Pretreatment with proteolytic enzymes and simulated gastric and intestinal juices and at different pH values had no significant effect on two mutagens removal by the viable cells. However, the binding activity of the mutagen by the strain seems to be affected by heating, enzymes including $\alpha$-amylase and lysozyme, divalent ions, and sodium metaperiodate. Thus, carbohydrates consisting of the cell walls may be important elements responsible for the binding of MNNG and 2-NF by this strain. In conclusion, the binding of the mutagens to cells of JG 22 strain may play a vital role in suppressing the process of mutagenesis induced by mutagens.

• Asian-Australasian Journal of Animal Sciences
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• v.19 no.10
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• pp.1484-1489
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• 2006

This study was carried out to investigate the effect of high pressure and the addition of non-meat proteins on the physico-chemical and binding properties of restructured pork. Pressurizations were carried out at up to 200 MPa and non-meat proteins used as a binder were isolated soy protein (ISP), sodium caseinate (SC), whey protein concentrate (WPC) and egg white powder (EWP). The pH values of all treatments were affected by the level of pressure. $L^*$-value of all treatments increased significantly (p<0.05), while both $a^*$-value and $b^*$-value of all treatments showed a significant decrease (p<0.05) with increasing pressure level. Binders could contribute only additive effects on both pH and color of the treatments. It was found that high pressure improved the water binding capacities and binding strength of the treatments. Binders also improved the binding strength of restructured pork. However, SC and WPC had no effect on water binding properties under high pressure. These results indicate that the application of high pressure had more significant effect on restructuring meat than binders.