• Journal of the Korean Wood Science and Technology
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• v.29 no.3
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• pp.104-111
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• 2001

There are some evidence that active enzymatic proteins, e.g. fungal laccase, exist in the naturally occured soil humus. This study was performed to investigate the covalent binding of fungal laccase to the humic acid-iron complex, and to measure laccase activity of immobilized ones. Seven methods were adopted to form the covalent binding of fungal laccase with soil humic acids complexed with iron. Using these seven methods it was possible to change the dimension of spacer arm between laccase and support, and also to regulate the mode of covalent binding of this enzyme. The spacer arm was regulated from 2C to 11C. There was not observed any straight relationship between the spacer arm longitude and the laccase activity after immobilization, but the binding mode more effective than the former. Three out of the seven methods gave the high activity of immobilized laccase, and which active products of laccase immobilization was stable up to 10 days after the process. It is indicated that natural soil condition might be prevented the laccase activation by the toxic influence of some phenolic humic compounds. It was shown, for the first time, the possibilities to obtain the high activity of fungal laccase by binding to humic acids, and especially in complex with iron.

• Journal of Microbiology and Biotechnology
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• v.16 no.1
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• pp.109-117
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• 2006

The Rev binding to Rev Responsive Element (RRE) of HIV-1 mRNA plays an important role in the HIV-I viral replication cycle. The disruption of the Rev-RRE interaction has been studied extensively in order to develop a potential antiviral drug. In order to provide the basis for a more promising approach to develop a Rev-RRE binding inhibitor against HIV-I infection, it is necessary to understand the binding modes of the aminoglycoside antibiotics to RRE. In the present study, the binding mode of a modified antibiotic, a neamine conjugated with pyrene and arginine (NCPA), to RRE has been studied by the methods of $T_m$ measurement and spectroscopic analysis of RRE with or without antibiotics. The results confirmed that NCPA competes with Rev in binding to RRE.

• Journal of Microbiology and Biotechnology
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• v.15 no.3
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• pp.537-543
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• 2005

Subtilisin (EC 3.4.21.14) is the major extracellular alkaline serine protease of Bacillus species. Previously, we found that subtilisins did not migrate in the electrophoretic field in the Laemmili buffer system due to their high pI values (over 8.8); however, it formed a 'binding mode' at the top of the separating gel [5]. Utilizing this characteristic, four subtilisins from Bacillus sp. strains (e.g., B. subtilis 168, B. subtilis KCTC 1021, B. amyloliquefaciens KCTC 3002, and Bacillus sp. DJ-1 and DJ-4) were easily and quickly identified by an over-running electrophoretic technique with a miniscale culture supernatant (less than 20 ml) without any column chromatographic steps. Two subtilisins (DJ-l and a recombinant version) from Bacillus sp. DJ-l were characterized, and the enzymatic properties were determined by SDS-fibrin zymography and densitometric analysis. Based on this observation, the recombinant pro-subtilisin DJ-l showed the same 'binding mode,' similar to native subtilisin DJ-l. On the other hand, mature subtilisin DJ -1 without pro-peptide showed no enzymatic activity.

• Journal of Microbiology
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• v.33 no.3
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• pp.191-195
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• 1995

IciA protein has been shown as an inhibitor for the initiation of E. coli chromosomal DNA replication at oriC. IciA protein binds the AT-rich region in oriC and then blocks the initiation of chromosomal DNA replication. Two binding sites for IciA protein were identified in dnaA gene, encoding the initiator for the E. coli chromosomal replication, promoter region by gel-shift assay and DNase I footprinting, One, named as IciA site I, is located upstream of the dnaA promoter 1P. The other, named as IciA site II, is located downstream of the dnaA promoter 2P. The sequence comparison of the regions protected from the DNase I cleavage did not result in a clear consensus sequence for the binding of IciA protein, suggesting that IciA protein may be a member of multimeric complex dsDNA binding proteins. This study provided information about the binding mode of IciA protein. Even though the IciA site II and IciA binding site in oriC seem to be composed of two IciA binding units, one binding unit is likely enough to cause the binding of IciA protein to the IciA site I. The binding of IciA protein to the dna4 promoter implies that IciA protein may involve not only the control of the initiation of chromosomal DNA replication but also the control of the dna4 gene expression.

• YAKHAK HOEJI
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• v.49 no.5
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• pp.428-436
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• 2005

DNA topoisomerase I(TOP1) helps the control of DNA replication, transcription and recombination by assist­ing breaking and rejoining of DNA double strand. Camptothecin (CPT) and its derivative, topotecan, are known to inhibit TOP1 by intercalating into TOP1-DNA complex. Recently various non-CPT intercalators are synthesized for a new class of TOP1 inhibitors. In this study, six compounds isolated from Poria cocos were investigated for their interaction with TOP1­DNA complex using the flexible docking program, FlexiDock. The binding modes were analyzed and compared with the TOP1 inhibition activities. The compounds that showed potent activity were intercalated between the + 1/-1 base pairs of DNA, located near the active site phosphotyrosine723 and formed hydrogen bonds with active site residues. On the other hand, compounds with no activity were not docked at all. The binding modes were well correlated with the inhibition activity, suggesting the possibility that potent inhibitors can be designed from the information presented by the docking study.

• Bulletin of the Korean Chemical Society
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• v.29 no.5
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• pp.953-958
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• 2008

A novel anthraquinone diamino-bridged bis($\beta$ -cyclodextrin) 2 was synthesized. The inclusion complexation behaviors of the native $\beta$ -cyclodextrin 1 and the novel bis($\beta$ -cyclodextrin) 2 with guests, such as acridine red (AR), neutral red (NR), ammonium 8-anilino-1-naphthalenesulfonate (ANS), sodium 2-(p-toluidinyl) naphthalenesulfonate (TNS) and rhodamine B (RhB) were investigation by fluorescence, circular dichroism and 2D NMR spectroscopy. The spectral titrations were performed in phosphate buffer (pH 7.20) at 25 ${^{\circ}C}$ to give the complex stability constants (Ks) and Gibbs free energy changes (−${\Delta}G^0$) for the stoichiometric 1:1 inclusion complexation of host 1 and 2 with guests. The results indicated that the novel bis($\beta$ -cyclodextrin) 2 greatly enhanced the original binding affinity of the native $\beta$ -cyclodextrin 1. Typically, bis($\beta$ -cyclodextrin) 2 showed the highest binding constant towards ANS up to 34.8 times higher than that of 1. The 2D NMR spectra of bis($\beta$ -cyclodextrin) 2 with RhB and TNS were performed to confirm the binding mode. The increased binding affinity and molecular selectivity of guests by bis($\beta$ -cyclodextrin) 2 were discussed from the viewpoint of the size/shape-fit concept and multipoint recognition mechanism.

• Journal of the Korean Chemical Society
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• v.58 no.2
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• pp.153-159
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• 2014

Herein, the cyclic voltammetric (CV) investigations of structurally similar bisnitrocompounds (N3, N4, N5, N6, having different-$CH_2$-spacer length) is presented. CV study offered interesting interactional possibilities of bisnitrocompounds with chicken blood ds.DNA at physiological pH 4.7 and human body temperature, 310 K. The results indicated strong interaction by these symmetric molecules with ds.DNA and strength of binding is found to depend on length of $CH_2$ spacer group in their molecular structure. Thermodynamics derived from electrochemical binding parameters also favored the irreversible interactions. Moreover, threading intercalation mode of binding is suggested based on thermodynamic and kinetic binding parameters extracted from CV studies.

• Bulletin of the Korean Chemical Society
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• v.35 no.7
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• pp.2114-2122
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• 2014

The association of silybin with ${\beta}$-cyclodextrin and its influence on silybin's binding with bovine serum albumin are reported. The stoichiometry, binding constant, and the structure of silybin-${\beta}$-cyclodextrin inclusion complex are reported. The titrations of silybin with bovine serum albumin in the absence and presence of ${\beta}$-cyclodextrin are carried out and the differences in binding strengths are discussed. Molecular modeling is used to optimize the sites and mode of binding of silybin with bovine serum albumin. F$\ddot{o}$rster resonance energy transfer is calculated and the proximity of interacting molecules is reported in the presence and absence of ${\beta}$-cyclodextrin.

• YAKHAK HOEJI
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• v.58 no.1
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• pp.16-20
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• 2014

KR-31064 was developed for the strong angiotensin II receptor antagonist among the one of pyridyl imidazol series compounds. To investigate the receptor-ligand binding characteristics of this nonpeptide antagonist, binding experiments were deployed in various conditions and ex vivo contractile responses were tested toward the standard compound, losartan. Receptor binding experiments with radiolabeled angiotensin II, the $IC_{50}$ value for KR-31064 resulted 0.67 nM without any activities toward type 2 angiotensin II receptor. The comparative potency against losartan was more than 18 fold and the specific activity in type 1 angiotensin II receptor was more than 10,000 fold comparing to the type 2 receptor. Scatchard analysis of saturation binding data showed KR-31064 acted on the receptor in a competitive mode. KR-31064 inhibited the contractile response derived by angiotensin II ($pK_B$: 9.86) similar to that of losartan with decreased maximum signals. As a potent and specific type 1 angiotensin II receptor antagonist, KR-31064 may have possibilities for the development of diagnostic ligands that can be used as tools for various biochemical research experiments and non-invasive diagnostics.

• Molecules and Cells
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• v.40 no.8
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• pp.533-541
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• 2017

Engineered DNA-binding domains provide a powerful technology for numerous biomedical studies due to their ability to recognize specific DNA sequences. Zinc fingers (ZF) are one of the most common DNA-binding domains and have been extensively studied for a variety of applications, such as gene regulation, genome engineering and diagnostics. Another novel DNA-binding domain known as a transcriptional activator-like effector (TALE) has been more recently discovered, which has a previously undescribed DNA-binding mode. Due to their modular architecture and flexibility, TALEs have been rapidly developed into artificial gene targeting reagents. Here, we describe the methods used to design these DNA-binding proteins and their key applications in biomedical research.