• Korean Journal of Computational Design and Engineering
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• v.11 no.2
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• pp.97-106
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• 2006

Voronoi diagrams have been known for numerous important applications in science and engineering including CAD/CAM. Especially, the Voronoi diagram for 3D spheres has been known as very useful tool to analyze spatial structural properties of molecules or materials modeled by a set of spherical atoms. In this paper, we present two algorithms, the edge-tracing algorithm and the region-expansion algorithm, for constructing the Voronoi diagram of 3D spheres and applications to protein structure analysis. The basic scheme of the edge-tracing algorithm is to follow Voronoi edges until the construction is completed in O(mn) time in the worst-case, where m and n are the numbers of edges and spheres, respectively. On the other hand, the region-expansion algorithm constructs the desired Voronoi diagram by expanding Voronoi regions for one sphere after another via a series of topology operations, starting from the ordinary Voronoi diagram for the centers of spheres. It turns out that the region-expansion algorithm also has the worst-case time complexity of O(mn). The Voronoi diagram for 3D spheres can play key roles in various analyses of protein structures such as the pocket recognition, molecular surface construction, and protein-protein interaction interface construction.

• Environmental Engineering Research
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• v.20 no.2
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• pp.163-169
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• 2015

In this study, we attempted to solubilize protein in slaughter blood (SB) using ultrasonic technology. The application of ultrasonic technology can make enzymatic degradation of SB more effective, which has no comparable alternative for treatment. The SB was homogenized by grinding it for 10 minutes at 10,000 rpm as a pretreatment for preventing its clotting, and then ultrasonic treatment was attempted to solubilize protein in SB. To maximize the efficiency of ultrasonic treatment for SB, the optimum condition of ultrasonic frequency (UF) was determined to be 20 kHz. To optimize the operation conditions of ultrasonification with 20 kHz of frequency, we used response surface methodology (RSM) based on ultrasonic density (UD) and ultrasonification time (UT). The solubilization rate (SR) of protein (%) was calculated to be $101.304-19.4205X_1+0.0398X_2+7.9411X_1{^2}+0.0001X_2{^2}+0.0455X_1X_2$. From the results of the RSM study, the optimum conditions of UD and UT were determined at 0.5 W/mL and 22 minutes, respectively, and SB treated under these conditions was estimated to have a 95% SR. Also, experimentally, a 95.53% SR was observed under same conditions, accurately reflecting the theoretical prediction of 95%.

• Korean Chemical Engineering Research
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• v.44 no.2
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• pp.166-171
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• 2006

In this study, in using a piezoelectric material of $Pb(Mg_{1/3}Nb_{2/3})O_3-PbTiO_3$ (PMN-PT), which has a high electromechanical coupling coefficient, we have tried to study about this material can be practically available as a new biosensor to detect protein by using surface acoustic wave (SAW). As the results, the filtering of the center frequency of the PMN-PT substrate is a superior result to that of the $LiTaO_3$ (LT) substrate, but the result was not completely satisfactory. Also this study attempts to develop a sensing method to detect mismatched DNA in order to diagnose cancer. We could directly immobilize the MutS to the NTA using the EDC solution. But, we immobilized MutS using nickel and it is judged that is more effective method to detect mismatched DNA.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.12
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• pp.5115-5118
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• 2015

Background: The $p16^{INK4a}$ is a protein that expressed in Liquid-based cervical cytology specimens and has been proved link to cervical cancer. The $p16^{INK4a}$ could be detection by piezoelectric immunosensor and the immobilization of the $p16^{INK4a}$ antibody influence the sensitivity of the piezoelectric immunosensor. Materials and Methods: $5{\mu}L$ mouse polyclonal antibody against $p16^{INK4a}$ was bound onto the surface of immonosensor through two methods. (directly immobilized method; protein A method). Absorb of the $p16^{INK4a}$ antibody on the surface of immonosensor caused a shift in the resonant frequency of the immunosensor and The frequency changes recorded showed a better reproducibility. The activity of the immobilization antibody with the directly method and protein A method was tested with $p16^{INK4a}$ antigen. Results: The resonant frequency for different antibody immobilization methods were different, and the sensitivity for $p16^{INK4a}$ detection also different. Conclusions: The protein A method was found to be much more better than the directly method for the immobilization of the p16INK4A antibody on the gold electrode of the quartz crystal for cervical lesion detection. The Protein A method created more reproducible and stable immobilization antibody layers with p16INK4A antigen.

• Journal of Microbiology and Biotechnology
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• v.24 no.2
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• pp.188-196
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• 2014

Extracellular production of recombinant human bone morphogenetic protein-7 (rhBMP-7) was carried out through the fermentation of Bacillus subtilis. Three significant fermentation conditions and medium components were selected and optimized to enhance the rhBMP-7 production by using the response surface methodology (RSM). The optimum values of the three variables for the maximum extracellular production of rhBMP-7 were found to be 2.93 g/l starch, 5.18 g/l lactose, and a fermentation time of 34.57 h. The statistical optimization model was validated with a few fermentations of B. subtilis in shake flasks under optimized and unoptimized conditions. A 3-L jar fermenter using the shake-flask optimized conditions resulted in a higher production (413 pg/ml of culture medium) of rhBMP-7 than in a shake flask (289.1 pg/ml), which could be attributed to the pH being controlled at 6.0 and constant agitation of 400 rpm with aeration of 1 vvm.

• Journal of Microbiology and Biotechnology
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• v.29 no.3
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• pp.419-428
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• 2019

Phytases are enzymes that can hydrolyze phytate and its salts into inositol and phosphoric acid, and have been utilized to increase the availability of nutrients in animal feed and mitigate environmental pollution. However, the enzymes' low thermostability has limited their application during the feed palletization process. In this study, a combination of B-value calculation and protein surface engineering was applied to rationally evolve the heat stability of Escherichia coli phytase. After systematic alignment and mining for homologs of the original phytase from the histidine acid phosphatase family, the two models 1DKL and 1DKQ were chosen and used to identify the B-values and spatial distribution of key amino acid residues. Consequently, thirteen potential amino acid mutation sites were obtained and categorized into six domains to construct mutant libraries. After five rounds of iterative mutation screening, the thermophilic phytase mutant P56214 was finally yielded. Compared with the wild-type, the residual enzyme activity of the mutant increased from 20% to 75% after incubation at $90^{\circ}C$ for 5 min. Compared with traditional methods, the rational engineering approach used in this study reduces the screening workload and provides a reference for future applications of phytases as green catalysts.

• 한국생물공학회:학술대회논문집
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• 2005.04a
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• pp.18-18
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• 2005

Photoinduced electron transport process in nature such as photoelectric conversion and long-range electron transfer in photosynthetic organisms are known to occur not only very efficiently but also unidirectionally through the functional groups of biomolecules. The basic principles in the development of new functional devices can be inspired from the biological systems such as molecular recognition, electron transfer chain, or photosynthetic reaction center. By mimicking the organization of the biological system, molecular electronic devices can be realized $artificially^{1)}$. The nano-fabrication technology of biomolecules was applied to the development of nano-protein chip for simultaneously analyzing many kinds of proteins as a rapid tool for proteome research. The results showed that the self-assembled protein layer had an influence on the sensitivity of the fabricated bio-surface to the target molecules, which would give us a way to fabricate the nano-protein chip with high sensitivity. The results implicate that the biosurface fabrication using self-assembled protein molecules could be successfully applied to the construction of nanoscale bio-photodiode and nano-protein chip based on electrical detection.

• Biotechnology and Bioprocess Engineering:BBE
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• v.9 no.3
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• pp.179-183
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• 2004

A biocompatible polyelectrolyte complex multilayer (PECML) film consisting of poly-L-lysine (PLL) as a polycation and hyaluronic acid (HA) as a polyanion was developed to test its use for surface modification to prevent cell attachment and protein drug delivery. The formation of PECML through the electrostatic interaction of HA and PLL was confirmed by contact angle measurement, ESCA analysis, and HA content analysis. HA content increased rapidly up to 8 cycles for HA/PLL deposition and then slightly increased with an increasing number of deposition cycle. In vitro release of PLL in the PECML continued up to 4 days and ca. 25% of HA remained on the chitosan-coated cover glass after in vitro release test for 7 days. From the results, PECML of HA and PLL appeared to be stable for about 4 days. The surface modification of the chitosan-coated cover glass with PECML resulted in drastically reduced peripheral blood mononuclear cell (PBMC) attachment. Concerned with its use for protein drug delivery, we confirmed that bovine serum albumin (BSA) as a model protein could be incorporated into the PECML and its release might be triggered by the degradation of HA with hyaluronidase.

• Journal of Biomedical Engineering Research
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• v.10 no.1
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• pp.43-52
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• 1989

We modified polymer surfaces, polyethylene, polystyrene and polyester, to improve cellcompatibility. For surface modification of the polymers, we used various surface treatment methods; physicochemical oxidation methods such as plasma discharge, corona discharge, sulfuric acid and chloric acid treatments, and biological methods such as adsorption of plasma protein and fibronectin onto the polymer surfaces. The treated polymer surfaces were characterized by electron spectroscopy for chemical analysis ( ESCA ). The physicochemically treated polymers showed different surface chemical structures depending on the treated methods. The sulfuric acid-treated surfaces showed greater carboxyl groups than those of plasma- or corona- treated surfaces, while the chloric acid-treated one showed high density of hydroxyl group on the surface. By the biological treatments, the surfaces were uniformly coated with proteins. The fibronectin adsorbed on the surface seems to have unique properties for cell binding.

• BMB Reports
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• v.33 no.3
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• pp.242-248
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• 2000

Phage display of proteins is a powerful tool for protein engineering since a vast library of sequences can be rapidly screened for a specific property. In this study, we develop da new phage display vector that was derived from a pET-25b(+) vector. The pET-25b(+) was modified in order that the expressed protein would have a T7-tag at the amino terminus and GpS (a major coat protein of M13 phage) at the carboxyl terminus. Another vector without the gp8 gene was also constructed. The newly developed phagemid vectors have several advantageous features. First, it is easy to examine whether or not the target proteins are functional and faithfully transported into the periplasmic space. This feature is due to the fact that recombinant proteins are produced abundantly in the pET system. Second, the T7-tag makes it possible to detect any target proteins that are displayed on the surface of filamentous bacteriophage. To verify the utility of the vector, the clones containing the glutathione S-transferase (GST) gene as a target were examined. The result showed that the GST produced from the recombinant vector was successfully transported into the periplasmic space and had the anticipated enzyme activity. Western blot analysis using a T7-tag antibody also showed the presence of the target protein displayed on the surface of the phage. The phages prepared from the recombinant clones were able to bind to glutathione-Sepharose and then eluted with glutathione. These results showed that the new vectors developed in this study are useful for the phage display of proteins.