• Journal of Life Science
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• v.32 no.9
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• pp.729-733
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• 2022

Aggregation of normally soluble proteins can cause disease-related problems. Tryptophan synthase α-subunit (αTS) in E. coli adopts one of most popular structural scaffolds, the TIM barrel fold. Previous mutagenesis of the αTS gene resulted in many aggregation-prone mutant proteins. Here, Y173F (Tyr at residue 173 to Phe) substitution, which imparts increased stability, was tested for its ability to suppress aggregation of aggregation-prone mutant proteins (Y4C, S33L, P28L, P28S, G44S, D46N, P96L, and P96S). Aggregation was suppressed in all eight severe aggregate-forming mutants (all differing in their mutation positions), by the Y173F replacement. P28L αTS, which was available in pure form, was further analyzed and showed reduced secondary structure content, lower stability, and a looser structure with more exposed hydrophobic surface compared to the wild type protein. A double mutant P28L/Y173F protein showed almost no indication of these changes compared to the wild type protein. We hypothesized that Tyr at position 173 in αTS is positioned at the hydrophobic core and may serve to suppress the aggregation of this protein caused by other residues. Important residue (s) could be working widely in the prevention/suppression of protein aggregation.

• Interdisciplinary Bio Central
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• v.1 no.1
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• pp.3.1-3.6
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• 2009

Introduction: GTPases known as translation factor play a vital role as ribosomal subunit assembly chaperone. The bacterial Obg proteins ($Spo{\underline{0B}}$-associated ${\underline{G}}TP$-binding protein) belong to the subfamily of P-loop GTPase proteins and now it is considered as one of the new target for antibacterial drug. The majority of bacterial Obgs have been commonly found to be associated with ribosome, implying that these proteins may play a fundamental role in ribosome assembly or maturation. In addition, one of the experimental evidences suggested that Bacillus subtilis Obg (BsObg) protein binds to the L13 ribosomal protein (BsL13) which is known to be one of the early assembly proteins of the 50S ribosomal subunit in Escherichia coli. In order to investigate binding mode between the BsObg and the BsL13, protein-protein docking simulation was carried out after generating 3D structure of the BsL13 structure using homology modeling method. Materials and Methods: Homology model structure of BsL13 was generated using the EcL13 crystal structure as a template. Protein-protein docking of BsObg protein with ribosomal protein BsL13 was performed by DOT, a macro-molecular docking software, in order to predict a reasonable binding mode. The solvated energy minimization calculation of the docked conformation was carried out to refine the structure. Results and Discussion: The possible binding conformation of BsL13 along with activated Obg fold in BsObg was predicted by computational docking study. The final structure is obtained from the solvated energy minimization. From the analysis, three important H-bond interactions between the Obg fold and the L13 were detected: Obg:Tyr27-L13:Glu32, Obg:Asn76-L13:Glu139, and Obg:Ala136-L13:Glu142. The interaction between the BsObg and BsL13 structures were also analyzed by electrostatic potential calculations to examine the interface surfaces. From the results, the key residues for hydrogen bonding and hydrophobic interaction between the two proteins were predicted. Conclusion and Prospects: In this study, we have focused on the binding mode of the BsObg protein with the ribosomal BsL13 protein. The interaction between the activated Obg and target protein was investigated with protein-protein docking calculations. The binding pattern can be further used as a base for structure-based drug design to find a novel antibacterial drug.

• Proceedings of the Korean Vacuum Society Conference
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• 2016.02a
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• pp.102-102
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• 2016

Water, which is most abundant in Earth surface and very closely related to all forms of living organisms, has a simple molecular structure but exhibits very unique physical and chemical properties. Even though tremendous effort has been paid to understand this nature's core substance, there amazingly still lefts much room for scientist to explore its novel behaviors. Especially, as the scale goes down to nano-regime, water shows extraordinary properties that are not observable in bulk state. One of such interesting features is the formation of nanoscale bubbles showing unusual long-term stability. Nanobubbles can be spontaneously formed in water on hydrophobic surface or by decompression of gas-saturated liquid. In addition, the nanobubbles can be generated during electrochemical reaction at normal hydrogen electrode (NHE), which possibly distorts the standard reduction potential at NHE as the surface nanobubble screens the reaction with electrolyte solution. However, the real-time evolution of these nanobubbles has been hardly studied owing to the lack of proper imaging tools in liquid phase at nanoscale. Here we demonstrate, for the first time, that the behaviors of nanobubbles can be visualized by in situ transmission electron microscope (TEM), utilizing graphene as liquid cell membrane. The results indicate that there is a critical radius that determines the long-term stability of nanobubbles. In addition, we find two different pathways of nanobubble growth: i) Ostwald ripening of large and small nanobubbles and ii) coalescence of similar-sized nanobubbles. We also observe that the nucleation and growth of nanoparticles and the self-assembly of biomolecules are catalyzed at the nanobubble interface. Our finding is expected to provide a deeper insight to understand unusual chemical, biological and environmental phenomena where nanoscale gas-state is involved.

• Proceedings of the Korea Water Resources Association Conference
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• 2005.09b
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• pp.1189-1192
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• 2005

Due to their slow degradation properties, hydrophobic organic contaminants in estuarine sediment have been a concern for risks to human health and aquatic organisms. Studies of fate and transport of these contaminants in estuaries are further complicated by the fact that hydrodynamics and sediment transport processes in these regions are complex, involving processes with various temporal and spatial scales. In order to simulate and quantify long-term attenuation of Polycyclic Aromatic Hydrocarbons (PAH) in the Elizabeth River, VA, we develop a modeling approach, which employs the U.S. Environmental Protection Agency's water quality model, WASP, and encompasses key physical and chemical processes that govern long-term fate and transport of PAHs in the river. In this box-model configuration, freshwater inflows mix with ocean saline water and tidally averaged dispersion coefficients are obtained by calibration using measured salinity data. Sediment core field data is used to estimate the net deposition/erosion rate, treating only either the gross resuspension or deposition rate as the calibration parameter. Once calibrated, the model simulates fate and transport PAHs following the loading input to the river in 1967, nearly 4 decades ago. Sediment PAH concentrations are simulated over 1967-2022 and model results for Year 2002 are compared with field data measured at various locations of the river during that year. Sediment concentrations for Year 2012 and 2022 are also projected for various remedial actions. Since all the model parameters are based on empirical field data, model predictions should reflect responses based on the assumptions that have been governing the fate and sediment transport for the past decades.

• Journal of the Korean Electrochemical Society
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• v.11 no.4
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• pp.304-308
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• 2008

Noble Poly (lithium 2-acrylamido-2-methyl propane sulfonate) and its copolymer with N-vinyl formamide based on trihexyl (tetradecyl) phosphonium acetate [$(C_6H_{13})_3$ P ($C_{14}H_{29}$) $CH_3COO$; $P_{66614}$ $CH_3COO$] and trihexyl (tetradecyl)phosphonium bis(trifluoromethane sulfonyl) amide ([$(C_6H_{13})_3P(C_{14}H_{29})$] [TFSA];$P_{66614}TFSA$) were prepared and analyzed to determine their characteristics and properties. The ionic conductivity of a copolymer based $P_{66614}TFSA$ ionic liquid system exhibits a higher conductivity ($8.9{\times}10^{-5}Scm^{-1}$) than that of a copolymer based $P_{66614}CH_3COO$ system ($1.57{\times}10^{-5}Scm^{-1})$. The charge on the TFSA anion is spread very diffusely through the S-N-S core and particularly in the trifluoromethane groups, and this diffusion results in a decreased interaction between the cation and the anion. The viscosity of $P_{66614}TFSA$ (39 cP at 343 K) and $P_{66614}CH_3COO$ (124 cP at 343 K), which is very hydrophobic, was fairly high. High viscosity leads to a slow rate of diffusion of redox species. The ionic conductivity of copolymer of a phosphonium ionic liquid system also exhibits higher conductivity than that of a homopolymer system. Phosphonium ionic liquids were thermally stable at temperatures up to $400^{\circ}C$.

• Proceedings of the Korean Society of Applied Pharmacology
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• 2001.11a
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• pp.94-94
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• 2001

Prostaglandin endoperoxide H synthase (PGHS) catalyzes the committed step in prostaglandins and thromboxane A$_2$-- oxygenation of arachidonic acid to the hydroperoxy endoperoxide PGG$_2$, followed by reduction PGG$_2$to the alcohol PGH$_2$. The two reactions by PGHS -- cyclooxygenase and peroxidase -- occur at distinct but structurally and functionally interconnected sites. The peroxidase reaction occurs at a heme-containing active site located near the protein surface. The cyclooxygenase reaction occurs in a hydrophobic channel in the core of the enzyme. Initially a peroxide reacts with the heme group, yielding Compound I and an alcohol derived from the oxidizing peroxide. Compound I next undergoes an intramolecular reduction by a single electron traveling from Tyr385 along the peptide chain to the proximal heme ligand, His388, and finally to the heme group. Following the binding of arachidonic acid, Tyr385 tyrosyl radical initiates the cyclooxygenase reaction by abstracting the 13-pro(5) hydrogen atom to give an arachidonyl radical, which sequentially reacts with two molecules of oxygen to yield PGG$_2$. In order to characterize PGHS peroxidase active site, we examined various lipid peroxides with purified recombinant ovine PGHS proteins and determined the rate constants. The results have shown that twenty-carbon unsaturated fatty acid hydroperoxides have similar efficiency in peroxidation by PGHS, irrespective of either the location of hydroperoxy group or the number of double bonds. It was also confirmed by the subsequent study with PGHS peroxidase active site mutants.

• Korean Journal of Microbiology
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• v.55 no.1
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• pp.9-16
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• 2019

Acetoin is generated by numerous microorganisms using ${\alpha}$-acetolactate decarboxylase (ALDC) to prevent overacidification of cells and their environment and to store remaining energy. Because acetoin has been used as a safe flavor enhancer in food products, industries have been interested in biotechnological production of acetoin using ALDC. ALDC is a metal-dependent enzyme that produces acetoin from ${\alpha}$-acetolactate through decarboxylation reaction. Here, we report the crystal structure of ALDC from Bacillus subtilis subspecies spizizenii (bssALDC) at $1.7{\AA}$ resolution. bssALDC folds into a two-domain ${\alpha}/{\beta}$ structure where two ${\beta}$-sheets form a central core. bssALDC assembles into a dimer through central hydrophobic interactions and peripheral hydrophilic interactions. bssALDC coordinates a zinc ion using three histidine residues and three water molecules. Based on comparative analyses of ALDC structures and sequences, we propose that the active site of bssALDC includes the zinc ion and its neighboring bssALDC residues.

• KSBB Journal
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• v.18 no.3
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• pp.211-216
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• 2003

The removal yield of dissolved organic matter in drinking water by biological activated carbon (BAC) process was investigated. The tested processes wer raw water-AC process (BAC1), raw water-ozonation-BAC process (BAC2), and raw water-ozonation-coagulation/sedimentation-BAC process (BAC3). The amounts of organic matter was measured as dissolved organic carbon (DOC), ulta-violet radiation at 254 nm wavelength ($UV_{254}$), total nitrogen (T-N), ammonia nitrogen (NH_3$-N), and total phosphate (T-P). As a results, 30.7% DOC was removed by BAC2 process, which showed higher removal efficiency than BAC1 or BAC3 processes. The removal yield of $UV_{254}$ in BAC1, BAC2, and BAC3 processes were observed as 45.3%, 44.6%, 58.4%, respectively. And the removal yield of ammonia nitrogen were 66%, 81%, 29% in each BAC processes. The optimal empty bed contact time (EBCT) of BAC processes was estimated as 10 minute. This study has shown that BAC process combined with ozone treatment was efficient for removing dissolved organic matter in water.

• Journal of the Society of Cosmetic Scientists of Korea
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• v.33 no.2
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• pp.93-97
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• 2007

Even in the moderately concentrated anionic surfactant system, some special encapsulation method can shield the papain enzyme from proteolytic attacks. The stabilization of enzyme has been a major issue for successful therapies. In this study, we first stabilized an enzyme, papain in the microcapsules by using polyols, polyethyleneglycol (PEG), poly-propyleneglycol (PPG), and PEG-PPG-PEG block copolymer. In the analysis of EDS and CLSM, it was demonstrated that polyols are effectively located in the interface of papain and polymer. Polyols located in the interface had an ability to buffer the external triggers by hydrophobic partitioning, preventing consequently the catalytic activity of papain in the micro-capsules. Second. we introduced multi-layer capsulation methods containing ion complex. Such a moderately concentrated anionic surfactant system as wash-off cleansers, surfactants and waters can cause instability of entrapped enzymes. Surfactants and water in our final products swell the surface of enzyme capsules and penetrate into the core so easily that we can not achieve the effect of enzyme, papain. In this case, the ion complex multi-layer capsule composed of sodium lauroyl sarcosinate and polyquaternium-6 could effectively prevent water from penetration into the core enzyme, followed by in vivo test, and evaluate the stratum corneum (SC) turn-over speed.

• Polymer(Korea)
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• v.36 no.2
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• pp.177-181
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• 2012

This study presents the preparation of double emulsions in a poly(dimethylsiloxane) (PDMS)-based microfluidic device. To improve the wettability of hydrophilic continuous phase onto a hydrophobic PDMS microchannel, the surface was modified with 3-(trimethoxysilyl) propyl methacrylate (TPM) and then sequentially reacted with acrylic acid monomer solution, which produced selective covalent bonding between acrylic acids and methacrylate groups. For the proof of selective surface modification, tolonium chloride solution was used to identify the modified region and we confirmed that the approach was successfully performed. When water containing 0.5% w/w sodium dodecyl sulfate and 1% w/w Span80 with hexadecane were loaded into the selectively modified microfluidic channels, we can produce stable double emulsion. Based on the spreading coefficients, we predict the morphology of double emulsions. Our proposed method efficiently produces monodisperse double emulsions having 48.5 ${\mu}m$(CV:1.6%) core and 65.1 ${\mu}m$ (CV:1.6%) shell. Furthermore, the multiple emulsions having different numbers of core were easily prepared by simple control of flow rates.