• Proceedings of the Korean Society of Applied Pharmacology
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• 1995.10a
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• pp.9-15
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• 1995

When quiescent cells ate stimulated to enter the cell cycle, the thymidine kinase(TK) gene is transcriptionally activated at the border of Gl and 5. In this report we show that the human TK promoter contains multiple protein-binding sites. By site-directed mutagenesis, we identified a protein-binding site on the human TK promoter requited for conferring Gl-S-regulated transcription to a heterologous promoter and dissociated it functionally from an adjacent protein-binding domain containing an inverted CCAAT motif requited for high basal level expression. Substitution-mutation of this site results in constitutive expression of the neo reporter gene in serum-stimulated fibroblasts, as well as in cells arrested in mid-Gl by a temperature-sensitive mutation. The regulatory domains for the human TK promoter exhibit interesting symmetrical features, including a set of CCAAT motifs and sites similar to the novel Yi protein-binding site recently discovered in the mouse TK promoter. Thus, components of the hTK complex is important for hTK gene regulation.

• Archives of Pharmacal Research
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• v.23 no.6
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• pp.633-636
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• 2000

Translationally controlled tumor protein (TCTP), also known as IgE-dependent histamine-releasing factor, is a growth-related tumor protein. Although the primary sequence of rat TCTP does not reveal any recognizable $Ca^{2+}$ -binding motif, previous studies have demonstrated that rat TCTP consisting of 172 amino acids is a $Ca^{2+}$ -binding protein. However. the region of TCTP required for $Ca^{2+}$ interaction has not been mapped to the molecule. Here, we reported that the $Ca^{2+}$ binding region of TCTP which was mapped by using a combination of deletion constructs of rat TCTP and $^{45}Ca^{2+}$-overlay assay. was confined to amino acid residues 81-112. This binding domain did not show any peculiar loop of calcium- binding motif such as CaLB domain and EF hand motif and it seems to be constituted of random coil regions neighboring the a helix. Thus, our data confirm that TCTP is a novel family of $Ca^{2+}$ -binding protein.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.9 no.5
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• pp.1218-1224
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• 2008

Located on the upstream of a gene, the promoter region that plays a very important role in the control of gene expression as a signal part has various binding sites for transcription factors. These binding sites are present in various parts of the promoter region and assume an aspect of highly conserved consensus sequence pattern. This paper deals with the introductions of search methods for consensus pattern, including Wataru method, EM algorithm, MEME algorithm, Genetic algorithm and Phylogenetic Footprinting method, and intends to give future prospects of research on this field.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2006.02a
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• pp.125-126
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• 2006

NimbleGen has developed strategies to use its high-density oligonucleotide microarray platform (385,000 probes per array) to map both promoter binding sites and copy number variation at very high-resolution in the human genome. Here we describe a genome-wide map of active promoters determined by experimentally locating the sites of transcription imitation complex binding throughout the human genome using microarrays combined with chromatin immunoprecipitation. This map defines 10,567 active promoters corresponding to 6,763 known genes and at least 1,196 un-annotated transcriptional units. Microarray-based comparative genomic hybridisation (CGH) is animportant research tool for investigating chromosomal aberrations frequently associated with complex diseases such as cancer, neuropsychiatric disorders, and congenital developmental disorders. NimbleGen array CGH is an ultra-high resolution (0.5-50 Kb) oligo array platform that can be used to detect amplifications and deletions and map the associated breakpoints on the whole-genome level or with custom fine-tiling arrays. For whole-genome array CGH, probes are tiled through genic and intergenic regions with a median probe spacing of 6 Kb, which provides a comprehensive, unbiased analysis of the genome.

• Journal of the Korean Magnetic Resonance Society
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• v.18 no.2
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• pp.52-57
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• 2014

The TCP domain is a DNA-binding domain present in plant transcription factors and plays important roles in various biological functions. The hydrogen exchange rate constants of the imino protons were determined for the three DNA duplexes containing the DNA-binding sites for the TCP11, TCP15, and TCP20 transcription factors using NMR spectroscopy. The M11 duplex displays unique hydrogen exchange property of the five base pairs in the first binding site (5'-GTGGG-3'). However, the M15 and M20 duplexes lead to clear changes in thermal stabilities of these five base pairs. The unique dynamic features of the five base pairs in the first binding site might play crucial roles in the sequence-specific DNA binding of the class I TCP transcription factors.

• Proceedings of the Microbiological Society of Korea Conference
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• 2000.10a
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• pp.15-23
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• 2000

The subcellular localization of the SopB protein, which is encoded by the Escherichia coli F plasmid and is involved in the partition of the single-copy plasmid, was directly visualized through the expression of the protein fused to the jellyfish green fluorescent protein (GFP). The fusion protein was found to localize to positions close but not at the poles of exponentially growing cells. Examination of derivatives of the fusion protein lacking various regions of SopB suggests that the signal for the cellular localization of SopB resides in a region close to its N terminus. Overexpression of SopB led to silencing of genes linked to, but well-separated from, a cluster of SopB-binding sites termed sopC. In this SopB-mediated repression of sopC-linked genes, all but the N-terminal 82 amino acids of SopB can be replaced by the DNA-binding domain of a sequence-specific DNA -binding protein, provided that the sopC locus is also replaced by the recognition sequence of the DNA-binding domain. These results suggest a mechanism of gene silencing: patches of closely packed DNA-binding protein is localized to specific cellular sites; such a patch can capture a DNA carrying the recognition site of the DNA -binding domain and sequestrate genes adjacent to the recognition site through nonspecific binding of DNA.

• Biomolecules & Therapeutics
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• v.2 no.4
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• pp.361-368
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• 1994

The nature of the muscarinic receptors in bovine adrenal medulla was investigated in this study. [$^3$H]Quinuclidinyl benzilate(QNB) specifically bound to a single class of muscarinic receptor with a $K_{D}$ value of about 70 pM in bovine adrenal medullary, cardiac ventricular and ileal homogenates. Pirenzepine inhibition curves of [$^3$H]QNB binding to cardiac ventricular and ileal homogenates were steep, indicating the presence of a single class of binding site for pirenzepine with a Ki value of 990 nM and 508 nM, respectively. However, pirenzepine/[$^3$H]QNB competition binding curves in adrenal medulla suggested the presence of two binding sites (Hill coefficient=0.59) with a high( $M_1$) and a low( $M_2$) affinity. Respective Ki values for pirenfepine were 16 nM and 633 nM, with 44% of total sites having a high affinity( $M_1$). Gallamine, which is selective to cardiac $M_2$-receptor, inhibited [$^3$H]QNB binding to adrenal medullary, cardiac ventricular and ileal homogenates with Ki values of 12 $\mu$M, 6 $\mu$M and 13 $\mu$M, respectively. Thus, the binding affinities of pirenzepine and gallamine for $M_2$-receptor in adrenal medulla were similar to those in ileum, which contains the $M_3$-receptor. These results indicate that the $M_1$- and $M_3$- muscarinic receptor subtypes coexist in the bovine adrenal medulla.a.

• Bulletin of the Korean Chemical Society
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• v.10 no.4
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• pp.339-343
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• 1989

The interaction of cationic surfactants, n-alkyltrimethylammonium bromide ($C_nTAB$; n = 12, 14, 16) with anionic polyelectrolyte, poly(styrenesulfonate) (PSS) has been studied by surface tension measurement. In the absence of added salt, the cationic surfactants bind to PSS quantitatively up to ca. 60% coverage of anionic sites of the polyanion and the complexes were surface inactive. Further binding of the surfactant cations on PSS caused a sharp conformational transition of the surfactant/ PSS complexes to surface active complexes and accompanied precipitation. The binding showed a biphasic behavior in the presence of NaCl and cooperativity of the binding became less as the concentration of NaCl increased. Binding of the cationic surfactants on poly(vinylsulfonate) also showed the biphasic behavior and the cooperativity of the binding was much less even in the absence of NaCl. The binding of surfactant to PSS provided hydrophobic environment to solubilized pyrene and reduced the viscosity of the solution greatly even at surfactant concentrations well below cmc. This study indicated that the surfactant bound to PSS up to $60{\%}$ coverage of PSS sites are present as surfactant aggregates which are wrapped up with PSS chains, and hydrophobic interaction is an important factor in the binding of the surfactants to PSS.

• Molecules and Cells
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• v.45 no.7
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• pp.444-453
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• 2022

Multivalent macromolecular interactions underlie dynamic regulation of diverse biological processes in ever-changing cellular states. These interactions often involve binding of multiple proteins to a linear lattice including intrinsically disordered proteins and the chromosomal DNA with many repeating recognition motifs. Quantitative understanding of such multivalent interactions on a linear lattice is crucial for exploring their unique regulatory potentials in the cellular processes. In this review, the distinctive molecular features of the linear lattice system are first discussed with a particular focus on the overlapping nature of potential protein binding sites within a lattice. Then, we introduce two general quantitative frameworks, combinatorial and conditional probability models, dealing with the overlap problem and relating the binding parameters to the experimentally measurable properties of the linear lattice-protein interactions. To this end, we present two specific examples where the quantitative models have been applied and further extended to provide biological insights into specific cellular processes. In the first case, the conditional probability model was extended to highlight the significant impact of nonspecific binding of transcription factors to the chromosomal DNA on gene-specific transcriptional activities. The second case presents the recently developed combinatorial models to unravel the complex organization of target protein binding sites within an intrinsically disordered region (IDR) of a nucleoporin. In particular, these models have suggested a unique function of IDRs as a molecular switch coupling distinct cellular processes. The quantitative models reviewed here are envisioned to further advance for dissection and functional studies of more complex systems including phase-separated biomolecular condensates.

• YAKHAK HOEJI
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• v.30 no.1
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• pp.42-46
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• 1986

The binding characteristics of five cephalosporins, cefamandole, ceftriaxone, cefoxitin, latamoxef, and cefotetan to bovine serum albumin (BSA) was examined by UV difference spectrophotometry. 2-(4'-hydroxybenzeneazo) benzoic acid was used as the spectrophotometric probe. Competitive bindings between the probe and cephalosporins were observed. Based on the Scatchard plot, the BSA appeared to have two classes of binding sites in BSA binding with cephalosporins. The number of primary binding sites appears to be one, secondary binding sites appears to be three. The binding constants were found as follows: BSA-HBAB; $K_1^{obs}$=8.39$\times$$10^4$ $M^{-1}$, $K_2^{obs}$=1.60$\times$$10^4$ $M^{-1}$, BSA-Cefamandole; $K_1^{obs}$=5.44$\times$$10^3$ $M^{-1}$, $K_2^{obs}$=0.74$\times$$10^3$ $M^{-1}$, BSA-Cefotriaxone; $K_1^{obs}$=6.78$\times$$10^3$ $M^{-1}$, $K_2^{obs}$=0.88$\times$$10^3$ $M^{-1}$, BSA-Cefoxitin; $K_1^{obs}$=7.24$\times$$10^3$ $M^{-1}$, $K_2^{obs}$=1.13$\times$$10^3$ $M^{-1}$, BSA-Latamoxef; $K_1^{obs}$=8.87$\times$$10^3$ $M^{-1}$, $K_2^{obs}$=1.92$\times$$10^3$ $M^{-1}$, BSA-Cefotetan; $K_1^{obs}$=15.41$\times$$10^3$ $M^{-1}$, $K_2^{obs}$=2.7$\times$$10^3$ $M^{-1}$.