• Journal of Microbiology
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• v.42 no.2
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• pp.126-132
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• 2004

A single chain variable fragment (scFv) specific towards B. pseudomallei exotoxin had previously been generated from an existing hybridoma cell line (6E6AF83B) and cloned into the phage display vector pComb3H. In this study, the scFv was subcloned into the pComb3X vector to facilitate the detection and purification of expressed antibodies. Detection was facilitated by the presence of a hemagglutinin (HA) tag, and purification was facilitated by the presence of a histidine tag. The culture was grown at 30$^{\circ}C$ until log phase was achieved and then induced with 1 mM IPTG in the absence of any additional carbon source. Induction was continued at 30$^{\circ}C$ for five h. The scFv was discerned by dual processes-direct enzyme-linked immunosorbent assays (ELISA), and Western blotting. When compared to E. coli strains ER2537 and HB2151, scFv expression was observed to be highest in the E. coli strain Topl0F'. The expressed scFv protein was purified via nickel-mediated affinity chromatography and results indicated that two proteins a 52 kDa protein, and a 30 kDa protein were co-purified. These antibodies, when blotted against immobilized exotoxin, exhibited significant specificity towards the exotoxin, com-pared to other B. pseudomallei antigens. Thus, these antibodies should serve as suitable reagents for future affinity purification of the exotoxin.

• Genomics & Informatics
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• v.21 no.3
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• pp.32.1-32.11
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• 2023

Resistance to anti-tuberculosis drugs, especially ethambutol (EMB), has been widely reported worldwide. EMB resistance is caused by mutations in the embB gene, which encodes the arabinosyl transferase enzyme. This study aimed to detect mutations in the embB gene of Mycobacterium tuberculosis from Papua and to evaluate their impact on the effectiveness of EMB. We analyzed 20 samples of M. tuberculosis culture that had undergone whole-genome sequencing, of which 19 samples were of sufficient quality for further bioinformatics analysis. Mutation analysis was performed using TBProfiler, which identified M306L, M306V, D1024N, and E378A mutations. In sample TB035, the M306L mutation was present along with E378A. The binding affinity of EMB to arabinosyl transferase was calculated using AutoDock Vina. The molecular docking results revealed that all mutants demonstrated an increased binding affinity to EMB compared to the native protein (-0.948 kcal/mol). The presence of the M306L mutation, when coexisting with E378A, resulted in a slight increase in binding affinity compared to the M306L mutation alone. The molecular dynamics simulation results indicated that the M306L, M306L + E378A, M306V, and E378A mutants decreased protein stability. Conversely, the D1024N mutant exhibited stability comparable to the native protein. In conclusion, this study suggests that the M306L, M306L + E378A, M306V, and E378A mutations may contribute to EMB resistance, while the D1024N mutation may be consistent with continued susceptibility to EMB.

• Biotechnology and Bioprocess Engineering:BBE
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• v.10 no.4
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• pp.334-340
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• 2005

Lectin is a cell-agglutinating and carbohydrate-binding protein present in many plants. The lectin of Canavalia ensiformis shoot with specific affinity for D-glucose was purified by affinity chromatography using Sephadex G-100, and some of its biochemical characterizations were studied. Lectin was purified 8.87-fold and exhibited final specific activity of 225.74 units/mg protein with a $2.3\%$ yield. SDS-PAGE analysis demonstrated that the purified shoot lectin exists as a tetramer of 102 kD, composed of two subunits with molecular weight of 29 and 22 kD. The purified lectin was observed to agglutinate rabbit blood cell. The optimal temperature for the activity of this lectin was $40^{\circ}C$, and this lectin was relatively stable to heat with the highest activity at $50{\~}60^{\circ}C$. The maximal activity was observed at pH 7.2.

• Textile Coloration and Finishing
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• v.14 no.4
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• pp.208-213
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• 2002

In dyeing PET/Spandex blends with disperse dyes, many disperse dyes are absorbed more readily into Spandex than PET. Inorganic/organic(I/O) values can characterize the affinity of disperse dyes for Spandex and PET fibers. As I/O values of disperse dyes approach that of Spandex, the dye uptake in Spandex increases. On the contrary, the disperse dyes of higher I/O values are absorbed more into PET than Spandex. The dye uptake in PET increases with increasing I/O values of disperse dyes. As I/O values of disperse dyes increase, the rate of dyeing become slower in the dyeing of PET/Spandex blends. Hence, the affinity and the compatibility of disperse dyes in PET/Spandex blends dyeing can be evaluated with I/O value.

• Interdisciplinary Bio Central
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• v.2 no.2
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• pp.6.1-6.5
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• 2010

Fragment molecular orbital (FMO) method provides a novel tool for ab initio calculations of large biomolecules. This method overcomes the size limitation difficulties in conventional molecular orbital methods and has several advantages compared to classical force field approaches. While there are many features in this method, we here focus on explaining the issues related to protein-ligand binding: FMO method provides useful interaction-analysis tools such as IFIE, CAFI and FILM. FMO calculations can provide not only binding energies, which are well correlated with experimental binding affinity, but also QSAR descriptors. In addition, FMO-derived charges improve the descriptions of electrostatic properties and the correlations between docking scores and experimental binding affinities. These calculations can be performed by the ABINIT-MPX program and the calculation results can be visualized by its proper BioStation Viewer. The acceleration of FMO calculations on various computer facilities is ongoing, and we are also developing methods to deal with cytochrome P450, which belongs to the family of drug metabolic enzymes.

• Proceedings of the Korean Vacuum Society Conference
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• 2013.02a
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• pp.84-84
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• 2013

FcBP consisting of 13 amino acids specifically binds to Immunoglobulin G Fc domain. Initially, we utilized this peptide for preparation of antibody chip as a PEG composite for enhanced solubility. After then, the peptide conjugate was immobilized on agarose resin, resulting in highly efficient affinity column for antibody purification. The efficiency was comparable to commercial Protein A column. Recently, this peptide was conjugated with cell penetratingpeptide (CPP) on a backbone of GFP, affording antibody transducer, which carries antibody into live cells by simple mixing of antibody and the transducer in cell culture media. Antibody transduction into cells was monitored by live cell imaging. More recently, the FcBP was fused to ferritin cage, which consists of 24 ferritin protein molecules. The FcBP-ferritin cage showed greatly increased binding affinity to human IgG. Its binding was analyzed by QCM and SPR analysis. Finally, it was selectively delivered by Herceptin to SKBR3, a breast cancer cell, over MCF10A, non-tumorigenic cells.

• Textile Coloration and Finishing
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• v.21 no.5
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• pp.21-26
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• 2009

In order to analyze numerically the hydrophobicity of the new dyes synthesized for unmodified pure polypropylene fibers, the octanol-water partition coefficient (logP), which is one of molecular descriptors representing hydrophobicity of organic compounds, was obtained by a semi-empirical method using Chem3D software. For the dyes of higher logP than around 5, the affinity of the dyes towards unmodified polypropylene fiber was substantial. In contrast to the new dyes for polypropylene, conventional disperse dyes have logP values lower than 5 and exhibited poor affinity.

• 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.

• Microbiology and Biotechnology Letters
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• v.31 no.2
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• pp.201-204
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• 2003

Glycopeptide antibiotics, teicoplanin was purified from a mutant strain of Actinoplanes teichomyceticus ATCC31121, A. teichomyceticus MSL2211. We developed a simple procedure to separate and purify the teicoplanin from the fermentation broth. Teicoplanin was purified by two-step purification system, hydrophobic adsorption and sugar affinity chromatography in combination with HPLC analysis based on the properties of hydrophobic acyl chain and sugar moiety in teicoplanin. Teicoplanin was separated from the culture broth by Diaion HP-20 and further purified by concanavalin A affinity column chromatography. As an adsorbent resin, Diaion HP-20 in broth eliminated toxic effects on growth, reduced feedback repression of teicoplanin production, and assisted In rapid recovery of teicoplanin. The teicoplanin displayed the final yield of 80% and 95% of purity.

• BMB Reports
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• v.45 no.1
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• pp.14-19
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• 2012

A feruloyl esterase encoding gene (designated fae6), derived from a leachate metagenomic library, was cloned and the nucleotide sequence of the insert DNA determined. Translational analysis revealed that fae6 consists of a 515 amino acid poly-peptide, encoding a 55 kDa pre-protein. The Fae6 primary structure contained the G-E-S-A-G sequence, which corresponds well with a typical catalytic serine sequence motif (G-x-S-x-G). The fae6 gene was successfully over-expressed in E. coli and the recombinant protein was purified to 8.4 fold enrichment with 17% recovery. The $K_M$ data showed Fae6 has a high affinity to methyl sinapate while thermostability data indicated that fae6 was thermolabile with a half life ($T_{1/2}$) < 30 min at $50^{\circ}C$. High affinity for Fae6 against methyl sinapate, methyl ferulate and ethyl ferulate suggest that the enzyme can be useful in hydrolyzing ferulated polysaccharides in a biorefinery process.