• Journal of Microbiology and Biotechnology
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• 제26권4호
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• pp.659-665
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• 2016

The oligosaccharides in human milk constitute a major innate immunological mechanism by which breastfed infants gain protection against infectious diarrhea. Clostridium difficile is the most important cause of nosocomial diarrhea, and the C-terminus of toxin A with its carbohydrate binding site, TcdA-f2, demonstrates specific abolishment of cytotoxicity and receptor binding activity upon diethylpyrocarbonate modification of the histidine residues in TcdA. TcdA-f2 was cloned and expressed in E. coli BL21 (DE3). A human milk oligosaccharide (HMO) mixture displayed binding with TcdA-f2 at 38.2 respond units (RU) at the concentration of 20 μg/ml, whereas the eight purified HMOs showed binding with the carbohydrate binding site of TcdA-f2 at 3.3 to 14 RU depending on their structures via a surface plasma resonance biosensor. Among them, Lacto-N-fucopentaose V (LNFPV) and Lacto-N-neohexaose (LNnH) demonstrated tight binding to TcdA-f2 with docking energy of −9.48 kcal/mol and −12.81 kcal/mol, respectively. It displayed numerous hydrogen bonding and hydrophobic interactions with amino acid residues of TcdA-f2.

• Bulletin of the Korean Chemical Society
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• 제34권11호
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• pp.3429-3443
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• 2013

Chemokine receptor (CCR2) is a G protein-coupled receptor that contains seven transmembrane helices. Recent pharmaceutical research has focused on the antagonism of CCR2 and candidate drugs are currently undergoing clinical studies for the treatment of diseases like arthritis, multiple sclerosis, and type 2 diabetes. In this study, we analyzed the time dependent behavior of CCR2 docked with a potent 4-azetidinyl-1-aryl-cyclohexane (4AAC) derivative using molecular dynamics simulations (MDS) for 20 nanoseconds (ns). Homology modeling of CCR2 was performed and the 4AAC derivative was docked into this binding site. The docked model of selected conformations was then utilized to study the dynamic behavior of the 4AAC enzyme complexes inside lipid membrane. MDS of CCR2-16b of 4AAC complexes allowed us to refine the system since binding of an inhibitor to a receptor is a dynamic process and identify stable structures and better binding modes. Structure activity relationships (SAR) for 4AAC derivatives were investigated and reasons for the activities were determined. Probable binding pose for some CCR2 antagonists were determined from the perspectives of binding site. Initial modeling showed that Tyr49, Trp98, Ser101, Glu291, and additional residues are crucial for 4AAC binding, but MDS analysis showed that Ser101 may not be vital. 4AAC moved away from Ser101 and the hydrogen bonding between 4AAC and Ser101 vanished. The results of this study provide useful information regarding the structure-based drug design of CCR2 antagonists and additionally suggest key residues for further study by mutagenesis.

• Bulletin of the Korean Chemical Society
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• 제34권4호
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• pp.1300-1302
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• 2013

• Bulletin of the Korean Chemical Society
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• 제20권11호
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• pp.1319-1322
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• 1999

Leucine zipper dynamically tunes the degree of bifurcation of the DNA binding segments in the basic region of the Fos-Jun bZIP complex. Molecular dynamics simulation indicated that site-specific mutagenesis of conserved leucine residues inside the leucine zipper domain caused the change of dynamic behavior of the basic region, and efficient DNA binding occurs only within a certain range of distance between the two DNA binding segments in the basic region. Distribution of α-helices in the hinge region is also suggested to influence the bifurcation of the DNA binding segments.

• Natural Product Sciences
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• 제25권1호
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• pp.28-33
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• 2019

A popular approach for the study of estrogen receptor ${\alpha}$ inhibition is to investigate the protein-protein interaction between the estrogen receptor (ER) and the coactivator surface. In our study, we investigated phytochemicals from Rubus coreanus that were able to disrupt $ER{\alpha}$ and coactivator interaction with an $ER{\alpha}$ antagonist. The E-screen assay and molecular docking analysis were performed to evaluate the effects of the estrogenic activity of R. coreanus extract and its constituents on the MCF-7 human breast cancer cell line. At $100{\mu}g/mL$, R. coreanus extract significantly stimulated cell proliferation ($574.57{\pm}8.56%$). Sanguiin H6, which was isolated from R. coreanus, demonstrated the strongest affinity for the $ER{\alpha}$ coactivator-binding site in molecular docking analysis, with a binding energy of -250.149. The initial results of the study indicated that sanguiin H6 contributed to the estrogenic activity of R. coreanus through the activation of the $ER{\alpha}$ coactivator-binding site.

• BMB Reports
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• 제54권3호
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• pp.176-181
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• 2021

Bcl-x, a member of the Bcl-2 family, plays a key role in apoptosis. Alternative splicing of Bcl-x pre-mRNA through alternative 5' splice-site selection produces an anti-apoptotic mRNA isoform that includes exon 2b and a pro-apoptotic Bcl-x mRNA isoform that excludes exon 2b. Here we used Bcl-x minigene and identified SRSF2 and SRSF6 as two regulatory factors of 5' splice-site selection of Bcl-x pre-mRNA. We selected binding clusters closer to 5' splice-sites from multiple potential binding sites of SRSF2 and SRSF6 to perform loss of functions analysis through site-directed mutagenesis. Our results demonstrated that these mutations did not abolish regulatory functions of SRSF2 or SRSF6, indicating that a single binding motif or a cluster was not a functional target of these proteins in Bcl-x pre-mRNA splicing. Random deletion mutagenesis did not disrupt the role of SRSF2 and SRSF6. Importantly, mutagenesis of 5' splice-site to a conserved or a weaker score demonstrated that the weaker strength of the target 5' splice-site or higher strength of the other 5' splice-site strength limited the role of SRSF2 and SRSF6 in 5' splice-site activation.

• BMB Reports
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• 제36권3호
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• pp.305-311
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• 2003

A modified actinomycin D was prepared with a hydroxyl group that replaced the amino group at the chromophore 2-position, a substitution known to strongly reduce affinity for double-stranded DNA. Interactions of the modified drug on single-stranded DNAs of the defined sequence were investigated. Competition assays showed that 2-hydroxyactinomycin D has low affinity for two oligonucleotides that have high affinities ($K_a\;=\;5-10{\times}10^6\;M^{-1}$ oligomer) for 7-aminoactinomycin D and actinomycin D. Primer extension inhibition assays performed on several single-stranded DNA templates totaling around 1000 nt in length detected a single high affinity site for 2-hydroxyactinomycin D, while many high affinity binding sites of unmodified actinomycin D were found on the same templates. The sequence selectivity of 2-hydroxyactinomycin D binding is unusually high and approximates the selectivity of restriction endonucleases. Binding appears to require a complex structure, including residues well removed from the polymerase pause site.

• 한국건축시공학회:학술대회논문집
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• 한국건축시공학회 2014년도 추계 학술논문 발표대회
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• pp.156-157
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• 2014

Inorganic binding material was made by recycled resource and its applicability as pile-filling material was examined. The result was that the material had same liquidity with the liquidity of OPC and high reactivity with site soil. According to dynamic/static loading tests by site test-construction, the inorganic binding material met both design bearing capacity and settlement. Since the inorganic binding material showed same or better performance than OPC, the utilization possibility of the inorganic binding material made of recycled resource as pile-filling material was verified.

• 한국건축시공학회:학술대회논문집
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• 한국건축시공학회 2013년도 추계 학술논문 발표대회
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• pp.8-10
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• 2013

Inorganic binding material was made by recycled resource and its applicability as pile-filling material was examined. The result was that the material had same liquidity with the liquidity of OPC and high reactivity with site soil. According to dynamic/static loading tests by site test-construction, the inorganic binding material met both design bearing capacity and settlement. Since the inorganic binding material showed same or better performance than OPC, the utilization possibility of the inorganic binding material made of recycled resource as pile-filling material was verified.

• BMB Reports
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• 제29권2호
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• pp.169-174
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• 1996

Yeast cytochrome c (cyt c) was modified at cysteine-102 with a thiol-specific spin label and its interaction with liposomes containing acidic phospholipids was studied by electron paramagnetic resonance (EPR) spectroscopy. Association of cyt c with liposomes resulted in a significant reduction in the mobility of the spin label and a fraction of cyt c even seemed to be immobilized. Based on a large spectral change upon binding and the proximity of the spin-label to lysine-86 and -87, we propose these two residues to be the potential binding site at neutral pH. The interaction is electrostatic in nature because the spectral changes were reversed by addition of anions. Dissociation of the bound cyt c by anions, however, became less effective as the lipid/protein ratio increased. This suggests a repulsive lateral interaction among the bound cyt c. Unlabeled cyt c molecules added to preformed cyt c-liposome complex displaced the bound (spin labeled) cyt c and the process was competitive and reversible.