• Bulletin of the Korean Chemical Society
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• v.35 no.5
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• pp.1279-1284
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• 2014

The binding of TATA-binding protein (TBP) to the TATA-box containing promoter region is aided by many other transcriptional factors including TFIIA and TFIIB. The mechanistic insight into the assembly of RNA polymerase II preinitation complex (PIC) has been gained by either directly altering a function of target protein or perturbing molecular interactions using drugs, RNAi, or aptamers. Aptamers have been found particularly useful for studying a role of a subset of PIC on transcription for their ability to inhibit specific molecular interactions. One major hurdle to the wide use of aptamers as specific inhibitors arises from the difficulty with traditional assays to validate and determine specificity, affinity, and binding epitopes for aptamers against targets. Here, using a technique called the bio-layer interferometry (BLI) designed for a label-free, real-time, and multiplexed detection of molecular interactions, we studied the assembly of a subset of PIC, TBP binding to TATA DNA, and two distinct classes of aptamers against TPB in regard to their ability to inhibit TBP binding to TFIIA or TATA DNA. Using BLI, we measured not only equilibrium binding constants ($K_D$), which were overall in close agreement with those obtained by electrophoretic mobility shift assay, but also kinetic constants of binding ($k_{on}$ and $k_{off}$), differentiating aptamers of comparable KDs by their difference in binding kinetics. The assay developed in this study can readily be adopted for high throughput validation of candidate aptamers for specificity, affinity, and epitopes, providing both equilibrium and kinetic information for aptamer interaction with targets.

• Korean Journal of Microbiology
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• v.55 no.3
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• pp.199-205
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• 2019

Yeast two-hybrid (Y2H) technique has been used to study protein-protein interactions, but its application particularly to a large-scale analysis of protein interaction networks, is limited by the fact that the technique is labor-intensive, based on scoring colonies on plate. Here, we develop a new reporter for the measurement of the protein-protein interactions by flow cytometry. The yeast harboring interacting proteins can also be enriched by fluorescence-activated cell sorting (FACS) or magnetic-activated cell sorting (MACS). When two interacting proteins are present in the same yeast cell, a reporter protein containing 10 tandem repeats of c-myc epitope becomes localized on the surface of the cell wall, without affecting cell growth. We successful measured the surface display of c-myc epitope upon interacting p53 with SV40 T antigen by flow cytometry. Thus, the newly developed Y2H assay based on the display of c-myc repeat on yeast cell wall could be used to the simultaneous analysis of multiple protein-protein interactions without laborious counting colonies on plate.

• Journal of The Korean Astronomical Society
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• v.37 no.4
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• pp.223-224
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• 2004

The Tycho supernova remnant (SNR), as one of the few historical SNRs, has been widely studied in various wavebands and previous observations have shown evidence that Tycho is interacting with a dense ambient medium toward the northeast direction, In this paper, we report our high-resolution (16') $^{12}CO$ observation of the remnant using the Nobeyama 45m radio telescope. The Nobeyama data shows that a large molecular cloud surrounds the SNR along the northeastern boundary. We suggest that the Tycho SNR and the molecular cloud are both located in the Perseus arm and that the dense medium interacting with the SNR is possibly the molecular cloud. We also discuss the possible connection between the molecular cloud and the Balmer-dominated optical filaments, and suggest that the preshock gas may be accelerated within the cosmic ray and/or fast neutral precursor.

• Bulletin of the Korean Chemical Society
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• v.34 no.6
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• pp.1814-1822
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• 2013

By using density functional theory calculations, we have performed a systemic study on the electronic structures and topological properties of interactions between N-butylpyridinium nitrate ($[BPY]^+[NO_3]^-$) and thiophene (TS), benzothiophene (BT), dibenzothiophene (DBT), naphthalene (NAP). The most stable structure of $[BPY]^+[NO_3]^-$ ion pair indicates that hydrogen bonding interactions between oxygen atoms on $[NO_3]^-$ anion and C2-H2 on pyridinium ring play a dominating role in the formation of ion pair. The occurrence of hydrogen bonding, ${\pi}{\cdots}$H-C, and ${\pi}{\cdots}{\pi}$ interactions between $[BPY]^+[NO_3]^-$ and TS, BT, DBT, NAP has been corroborated at the molecular level. But hydrogen bonding and ${\pi}{\cdots}{\pi}$ interactions between $[BPY]^+[NO_3]^-$ and NAP are weak in terms of structural properties and NBO, AIM analyses. DBT is prior to adsorption on N-butylpyridinium nitrate ionic liquid.

• Textile Coloration and Finishing
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• v.22 no.2
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• pp.83-87
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• 2010

Crystal structure of coumarin 6 has been solved by X-ray diffraction. The crystals are triclinic, space group P-1, with a=8.823(2) ${\AA}$, b=8.898(2) ${\AA}$, c=11.025(9) ${\AA}$, ${\alpha}$=86.41(3)$^{\circ}$, ${\beta}$=85.39(3)$^{\circ}$, ${\gamma}$=76.23(3)$^{\circ}$, Mr=350.42, V=837.1(3) ${\AA}^3$, Z=2 and R=0.0516. The molecules are packed parallel to each other by weaker ${\pi}{\cdots}{\pi}$ and C-H${\cdots}{\pi}$ interactions. The detailed geometry of C-H${\cdots}{\pi}$ interactions were discussed. The hydrogen bonds and non-traditional C-H${\cdots}O$ interactions join the no-parallel molecules together. All the molecules packed wall-like with the molecular brick.

• Proceedings of the Korean Vacuum Society Conference
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• 2011.02a
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• pp.302-302
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• 2011

Fabrications of metal-organic hybrid networks attracted much attention due to possible applications in gas storages, heterogeneous catalyses, information storages, and opto-electronic devices. One way to construct three-dimensional hybrid structures is to make the arrays of planar or linear metal-organic hybrid structures which are linked through electrostatic interactions. As a model study, we fabricated the arrays of one-dimensional hybrid chains and investigated inter-chain interactions between adjacent hybrid chains using scanning tunneling microscopy (STM) and spectroscopy (STS) on Ag(111). Brominated anthracene molecules were used to grow the arrays of hybrid chains on Ag(111). We proposed atomic models for the observed structures. Linear chains are made of repetition of Ag-anthracene units. Br atoms are attached to anthracene molecules through Br-H structures which mediate inter-chain interactions. Two different apparent heights were observed in anthracene molecules. Molecules having a Br-H connection look brighter than those with two connections due to electronic effect. When a chain is laterally manipulated with STM tip, Br atoms move together with the chain implying that Br-H inter-chain interactions are quite strong.

• The Plant Pathology Journal
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• v.40 no.3
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• pp.251-260
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• 2024

Flavobacterium is a genus within the phylum Bacteroidota that remains relatively unexplored. Recent analyses of plant microbiota have identified the phylum Bacteroidota as a major bacterial group in the plant rhizosphere. While Flavobacterium species within the phylum Bacteroidota have been recognized as pathogens in the aquatic habitats, microbiome analysis and the characterization of novel Flavobacterium species have indicated the great diversity and potential of their presence in various environments. Many Flavobacterium species have positively contribute to plant health and development, including growth promotion, disease control, and tolerance to abiotic stress. Despite the well-described beneficial interactions of the Flavobacterium species with plants, the molecular mechanisms and bacterial determinants underlying these interactions remain unclear. To broaden our understanding of the genus Flavobacterium's role in plant health, we review the recent studies focusing on their ecological niche, functional roles, and determinants in plant-beneficial interactions. Additionally, this review discusses putative mechanisms explaining the interactions between plants and Flavobacterium. We have also introduced the importance of future research on Flavobacterium spp. and its potential applications in agriculture.

• The Korean Journal of Nuclear Medicine
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• v.38 no.2
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• pp.115-120
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• 2004

Molecular imaging is a rapidly growing field due to the advances in molecular biology and imaging technologies. With the introduction of imaging reporter genes into the cell, diverse cellular processes can be monitored, quantified and imaged non-invasively in vivo. These precesses include the gene expression, protein-protein interactions, signal transduction pathways, and monitoring of cells such as cancer cells, immune cells, and stem cells. In the near future, molecular imaging analysis will allow us to observe the incipience and progression of the disease. These will make us easier to give a diagnosis in the early stage of intractable diseases such as canter, neuro-degenerative disease, and immunological disorders. Additionally, molecular imaging method will be a valuable tool for the real-time evaluation of cells in molecular biology and the basic biological studies. As newer and more powerful molecular imaging tools become available, it will be necessary to corporate clinicians, molecular biologists and biochemists for the planning, interpretation, and application of these techniques to their fullest potential. in order for such a multidisciplinary team to be effective, it is essential that a common understanding of basic biochemical and molecular biologic techniques is achieved. Basic molecular techniques for molecular imaging methods are presented in this paper.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.6
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• pp.3735-3742
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• 2013

Background: Cardamom (Elettaria cardamom), also known as "Queen of Spices", has been traditionally used as a culinary ingredient due to its pleasant aroma and taste. In addition to this role, studies on cardamom have demonstrated cancer chemopreventive potential in in vitro and in vivo systems. Nevertheless, the precise poly-pharmacological nature of naturally occurring chemo-preventive compounds in cardamom has still not been fully demystified. Methods:In this study, an effort has been made to identify the proapoptopic, anti-inflammatory, anti-proliferative, anti-invasive and anti-angiogenic targets of Cardamom's bioactive principles (eucalyptol, alpha-pinene, beta-pinene, d-limonene and geraniol) by employing a dual reverse virtual screening protocol. Experimentally proven target information of the bioactive principles was annotated from bioassay databases and compared with the virtually screened set of targets to evaluate the reliability of the computational identification. To study the molecular interaction pattern of the anti-tumor action, molecular docking simulation was performed with Auto Dock Pyrx. Interaction studies of binding pose of eucalyptol with Caspase 3 were conducted to obtain an insight into the interacting amino acids and their inter-molecular bondings. Results:A prioritized list of target proteins associated with multiple forms of cancer and ranked by their Fit Score (Pharm Mapper) and descending 3D score (Reverse Screen 3D) were obtained from the two independent inverse screening platforms. Molecular docking studies exploring the bioactive principle targeted action revealed that H- bonds and electrostatic interactions forms the chief contributing factor in inter-molecular interactions associated with anti-tumor activity. Eucalyptol binds to the Caspase 3 with a specific framework that is well-suited for nucleophilic attacks by polar residues inside the Caspase 3 catalytic site. Conclusion:This study revealed vital information about the poly-pharmacological anti-tumor mode-of-action of essential oils in cardamom. In addition, a probabilistic set of anti-tumor targets for cardamom was generated, which can be further confirmed by in vivo and in vitro experiments.

• Bulletin of the Korean Chemical Society
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• v.32 no.8
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• pp.2695-2699
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• 2011

${\beta}$ Ketoacyl acyl carrier protein synthase III (KAS III) initiates fatty acid synthesis in bacteria and is a key target enzyme to overcome the antibiotic resistance problem. In our previous study, we found flavonoid inhibitors of Enterococcus faecalis KAS III and proposed three potent antimicrobial flavonoids against Enterococcus faecalis and Vancomycin-resistant Enterococcus faecalis with MIC values in the range of 128-512 ${\mu}g/mL$ as well as high binding affinities on the order from $10^6$ to $10^7\;M^{-1}$. Using these series of flavonoids, we conducted biological assays as well as docking study to find potent flavonoids inhibitors of Staphylococcus aureus KAS III with specificities against Staphylococcus aureus and Methicillin-resistant Staphylococcus aureus. Here, we propose that naringenin (5,7,4'-trihydroxyflavanone) and eriodictyol (5,7,3',4'-tetrahydroxyflavanone) are potent antimicrobial inhibitors of Staphylococcus aureus KAS III with binding affinity of $3.35{\times}10^5$ and $2.01{\times}10^5\;M^{-1}$, respectively. Since Arg38 in efKAS III is replaced with Met36 in saKAS III, this key difference caused one hydrogen bond missing in saKAS III compared with efKAS III, resulting in slight discrepancy in their binding interactions as well as decrease in binding affinities. 4'-OH and 7-OH of these flavonoids participated in hydrogen bonding interactions with backbone carbonyl of Phe298 and Ser152, respectively. In particular, these flavonoids display potent antimicrobial activities against various MRSA strains in the range of 64 to 128 ${\mu}M$ with good binding affinities.