• BMB Reports
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• 제49권6호
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• pp.349-354
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• 2016

The archaeon Sulfolobus solfataricus P1 carboxylesterase is a thermostable enzyme with a molecular mass of 33.5 kDa belonging to the mammalian hormone-sensitive lipase (HSL) family. In our previous study, we purified the enzyme and suggested the expected amino acids related to its catalysis by chemical modification and a sequence homology search. For further validating these amino acids in this study, we modified them using site-directed mutagenesis and examined the activity of the mutant enzymes using spectrophotometric analysis and then estimated by homology modeling and fluorescence analysis. As a result, it was identified that Ser151, Asp244, and His274 consist of a catalytic triad, and Gly80, Gly81, and Ala152 compose an oxyanion hole of the enzyme. In addition, it was also determined that the cysteine residues are located near the active site or at the positions inducing any conformational changes of the enzyme by their replacement with serine residues.

• 한국미생물·생명공학회지
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• 제28권1호
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• pp.26-32
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• 2000

Electrostatic forces contribute to the high degree of enzyme transition state complementarity in enzyme catalyzed reaction and such forces are modified by the solvent through its dielectric constant and polar properties. The contributions of electrostatic interaction to the formation of ES complex and the stabilization of transition state of the trypsin catalyzed reaction were probed by kinetic studied with high pressure and solvent dielectric constant. A good correlation has been observed between the increase of catalytic efficiency of trypsin and the decrease of solvent dielectric constant. Activation volume linearly decreased as the dielectric constant of solvent decreased, which means the increase in the reaction rae. Moreover, the decrease of activation volume by lowering the solvent dielectric constant implies a solvent penetration of the active with and a reduction of electrostatic energy for the formation of dipole of the active site oxyanion hole. When the 야electric constant of the solvents was lowered to 4.7 unit, the loss of activation energy and that of free energy of activation were 2.262 KJ/mol and 3.169 KJ/mol, respectively. The results of this study indicate that the high pressure kinetics combined with solvent effects can provide unique information on enzyme reaction mechanisms, and the controlling the solvent dielectric constant can stabilize the transition state of the trypsin-catalyzed reaction.

• Journal of Microbiology and Biotechnology
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• 제12권1호
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• pp.31-38
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• 2002

Bacteria have evolved various types of resistance mechanism to toxic heavy metals, such as arsenic and antimony. An arsenical and antimonial resistant bacterium was isolated from a shallow creek draining a coal-mining area near Taebaek City, in Kangwon-Do, Korea. The isolated bacterium was identified and named as Pseudomonas sp. KM20 after biochemical and physiological studies were conducted. A plasmid was identified and its function was studied. Original cells harboring the plasmid were able to grow in the presence of 15 mM sodium arsenite, while the plasmid-cured (plasmidless) strain was sensitive to as little as 0.5 mM sodium arsenate. These results indicated that the plasmid of Pseudomonas sp. KM20 does indeed encode the arsenic resistance determinant. In growth experiments, prior exposure to 0.1 mM arsenate allowed immediate growth when they were challenged with 5 mM arsenate, 5 mM arsenite, or 0.1 mM antimonite. These results suggested that the arsenate, arsenite, and antimonite resistance determinants of Pseudomonas sp. KM20 plasmid were indeed inducible. When induced, plasmid-bearing resistance cells showed a decreased accumulation $of\;73^As$ and showed an enhanced efflux $of\;^73As$. These results suggested that plasmid encoded a transport system that extruded the toxic metalloids, resulting in the lowering of the intracellular concentration of toxic oxyanion. In a Southern blot study, hybridization with an E. coli R773 arsA-specific probe strongly suggested the absence of an arsA cistron in the plasmid-associated arsenical and antimonial resistance determinant of Pseudomonas sp. KM20.

• Bulletin of the Korean Chemical Society
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• 제14권4호
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• pp.491-496
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• 1993

A class A ${\beta}$-lactamase from Staphylococcus aureus PC1 complexed with 3R,5R-clavulanate is studied. The starting geometry for the computation is the crystal structure of the ${\beta}$-lactamase. Docking of the clavulanate to the enzyme is done exploiting the requirements of electrostatic and shape complementarity between the enzyme and clavulanate. This structure is then hydrated by water molecules and refined by energy minimization and short molecular dynamics simulation. In the energy refined structure of this complex, the carboxyl group of the clavulanate is hydrogen bonded to Lys-234, and the the carbonyl carbon atom of the clavulanate is adjacent to the $O_{\gamma}$ of Ser-70. It is found that a crystallographic water molecule initially located at the oxyanion hole, which is formed by the two -NH group of Ser-70 and Gln-237, is replaced by the carbonyl oxygen atom of the 3R,5R-clavulanate after docking and energy reginement. The crystallographic water molecules are proved to be important in ligand binding. Glu-166 residue is found to be repulsive to the binding of clavulanate, which is in agreement with experimental observation. Arg-244 residue is found to be important to the binding of clavulanate as well as to interaction with C2 side chain of the clavulanate. The electron density redistribution of the clavulanate on binding to the ${\beta}$-lactamase in studied by an ab initio quantum-mechanical calculation. A significant redistribution of electron density of the clavulanate is induced by the enzyme, toward the enzyme, toward the transition state of the enzymatic reaction.

• 자원환경지질
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• 제55권4호
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• pp.377-388
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• 2022

제강슬래그를 이용한 광물탄산화 공정 이후 발생하는 잔사슬래그의 비소(As) 제거 기작 규명을 위해, 전로제강슬래그(blast oxygen furnace slag: BOF)에 직접 및 간접탄산화 공정이 각각 적용된 두 종류의 잔사슬래그를 대상으로 실험실 규모의 실험을 실시하였다. 광물탄산화 공정은 잔사슬래그의 화학적-광물학적 조성변화, 용출수의 pH 저감, 표면 미세공극 형성 등 기존 제강슬래그의 특성을 변화시키는 것으로 밝혀졌다. 다양한 pH 범위의 As 인공오염수(초기농도: 203.6 mg/L)에 잔사슬래그를 반응시킨 배치실험에서, RDBOF (직접탄산화 후 BOF)는 초기 pH가 감소할수록 As 제거효율이 증가하는 경향을 보이며 초기 pH가 1인 환경에서 99.3%의 As 제거효율을 나타냈다. 이는 RDBOF 표면을 피복하던 CaCO₃가 낮은 초기 pH 환경에서 용해되어 RDBOF 표면에서 철산화물의 노출 면적을 증가시킴으로 인해, 철산화물의 As 음이온 표면 흡착을 촉진한 것에서 기인한 것으로 판단되었다. 반면 RIBOF (간접탄산화 후 BOF)는 초기 pH가 높은 환경일수록 As 제거효율이 증가하며 초기 pH 10의 As 오염수에서 70.0%의 가장 높은 As 제거효율을 보였다. RIBOF의 영전하점(pH 4.5)을 고려할 때, 초기 pH 4-10 조건에서 음전하를 띠는 RIBOF의 표면에 As 음이온의 전기적 인력에 의한 표면 흡착은 발생하기 어려울 것으로 예상되었다. 다만 수용액 내 용존하는 Ca²⁺, Mn²⁺, Fe²⁺와 같은 2가 양이온들에 의해 As 음이온이 RIBOF 내 철산화물에 간접적으로 고정되는 양이온 가교효과(cation bridge effect)가 발생하였고, 초기 pH가 높은 환경일수록 슬래그 표면이 더 강한 음전하를 띠며 양이온 가교효과가 가속화되어, 결과적으로 많은 As가 흡착된 것으로 판단되었다. 하지만 강알칼리 (pH 10-11 이상) 조건에서는 RIBOF 표면에 생성된 칼슘침전물이 철산화물을 피복함으로써 철산화물에 의한 As 음이온 표면 흡착을 저해하는 현상이 발생하였다. 또한 배치실험 이후 회수된 잔사슬래그에 TCLP 시험을 수행한 결과, RDBOF와 RIBOF 모두 2% 미만의 As 탈착률을 보여 안정적인 형태로 As가 고정되어 있음이 확인되었다. 본 연구 결과를 통해, 잔사슬래그가 기존에 As 제거제로 활용되던 제강슬래그의 단점인 수계의 급격한 pH 상승을 억제하는 동시에, 높은 As 제거효율 및 안정성을 나타내는 저비용-친환경의 As 제거제로서의 활용 가능성을 입증하였다.

• Carbon letters
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• 제26권
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• pp.31-42
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• 2018

Adsorption is one of the best methods for wastewater purification. The fact that water quality is continuously decreasing requires the development of novel, effective and cost available adsorbents. Herein, a simple procedure for the preparation of a magnetic adsorbent from agricultural waste biomass and ferrofluid has been introduced. Specifically, ferrofluid mixed with wheat straw was directly pyrolyzed either by microwave irradiation (900 W, 30 min) or by conventional heating ($550^{\circ}C$, 90 min). Magnetic biochars were characterized by X-ray powder diffraction, $M{\ddot{o}}ssbauer$ spectroscopy, textural analysis and tested as adsorbents of As(V) oxyanion and cationic methylene blue, respectively. Results showed that microwave pyrolysis produced char with high adsorption capacity of As(V) ($Q_m=25.6mg\;g^{-1}$ at pH 4), whereas conventional pyrolysis was not so effective. In comparison to conventional pyrolysis, one-step microwave pyrolysis produced a material with expressive microporosity, having a nine times higher value of specific surface area as well as total pore volume. We assumed that sorption properties are also caused by several iron-bearing composites identified by $M{\ddot{o}}ssbauer$ spectroscopy ([super] paramagnetic $Fe_2O_3$, ${\alpha}-Fe$, non-stoichiometric $Fe_3C$, ${\gamma}-Fe_2O_3$, ${\gamma}-Fe$) transformed from nano-maghemite presented in the ferrofluid. Methylene blue was also more easily removed by magnetic biochar prepared by microwaves ($Q_m=144.9mg\;g^{-1}$ at pH 10.9) compared to using conventional techniques.

• KSBB Journal
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• 제20권4호
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• pp.311-316
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• 2005

EH의 catalytic nucleophile residue, His-Asp로 구성된 charge relay system, oxyanion hole 등의 EH 관련 conserved domain의 아미노산 공통 서열을 참고로 하여 G. westfalica megaplasmid로부터 putative EH를 선별할 수 있었다. Bioinformatics를 기반으로 스크리닝한 G. westfalica에 의한 라세믹 styrene oxide 기질에 대한 입체선택성 가수분해 반응에 있어 중요 반응 parameter들인, pH 및 온도 등이 초기 가수분해반응속도에 미치는 영향을 분석하고, 최적 회분식 반응조건을 결정하였다. 최적 반응조건인 pH 7, 반응 온도 $30^{\circ}C$, 생촉매량 40 mg의 조건에서 약 5시간 20분간 반응을 통해 20 mM 라세믹 기질로부터 광학순도 $100\%$ ee인 (S)-styrene oxide를 $36.5\%$의 수율로 얻을 수 있었다.

• Journal of Microbiology and Biotechnology
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• 제15권1호
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• pp.155-160
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• 2005

Abstract A direct approach was used to retrieve active lipases from Paenibacillus polymyxa genome databases. Twelve putative lipase genes were tested using a typical lipase sequence rule built on the basis of a consensus sequence of a catalytic triad and oxyanion hole. Among them, six genes satisfied the sequence rule and had similarity (about 25%) with known bacterial lipases. To obtain the six lipase proteins, lipase genes were expressed in E. coli cells and lipolytic activities were measured by using tributyrin plate and pnitrophenyl caproate. One of them, contig 160-26, was expressed as a soluble and active form in E. coli cell. After purifying on Ni-NTA column, its detailed biochemical properties were characterized. It had a maximum hydrolytic activity at $30^{\circ}C$ and pH 7- 8, and was stable up to $40^{\circ}C$ and in the range of pH 5- 8. It most rapidly hydrolyzed pNPC$_6$ among various PNPesters. The other contigs were expressed more or less as soluble forms, although no lipolytic activities were detected. As they have many conserved regions with lipase 160-26 as well as other bacterial lipases throughout their equence, they are suggested as true lipase genes.

• Journal of Microbiology and Biotechnology
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• 제15권3호
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• pp.587-594
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• 2005

The contribution of electrostriction of water molecules to the stabilization of the negatively charged tetrahedral transition state of a lipase-catalyzed reaction was examined by means of kinetic studies involving high-pressure and solvent dielectric constant. A good correlation was observed between the increased catalytic efficiency of lipase and the decreased solvent dielectric constant. When the dielectric constant of solvents was lowered by 5.00 units, the losses of activation energy and free energy of activation were 7.92 kJ/mol and 11.24 kJ/mol, respectively. The activation volume for $k_{cat}$ decreased significantly as the dielectric constant of solvent decreased, indicating that the degree of electrostriction of water molecules around the charged tetrahedral transition state has been enhanced. These observations demonstrate that the increase in the catalytic efficiency of the lipase reaction with decreasing dielectric constant resulted from the stabilization of electrostatic energy for the formation of an oxyanion hole, and that this stabilization was caused by the increase of electrostricted water around the charged tetrahedral transition state. Therefore, we conclude that the control of solvent dielectric constant can stabilize the tetrahedral transition state, thus lowering the activation energy.

• Corrosion Science and Technology
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• 제9권1호
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• pp.20-28
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• 2010

According to the bipolar model, ion selectivity of some species in the passive film is important factor to control the passivation. An increase of cation selectivity of outer layer of the passive film can stabilize the film and improves the corrosion resistance. Therefore, the formation and roles of ionic species in the passive film should be elucidated. In this work, two types of solution (hydrochloric or sulfuric acid) were used to test high N and Mo-bearing stainless steels. The objective of this work was to investigate the formation of oxyanions in the passive film and the roles of oxyanions in passivation of stainless steel. Nitrogen exists as atomic nitrogen, nitric oxide, nitro-oxyanions (${NO_x}^-$), and N-H species, not nitride in the passive film. Because of its high mobility, the enriched atomic nitrogen can act as a reservoir. The formation of N-H species buffers the film pH and facilitates the formation of oxyanions in the film. ${NO_x}^-$ species improve the cation selectivity of the film, increasing the oxide content and film density. ${NO_x}^-$ acts similar to a strong inhibitor both in the passive film and at active sites. This facilitates the formation of chromium oxide. Also, ${NO_x}^-$ can make more molybdate and nitric oxide by reacting with Mo. The role of Mo addition on the passivation characteristics of stainless steel may differ with the test environment. Mo exists as metallic molybdenum, molybdenum oxide, and molybdate and the latter facilitates the oxide formation. When nitrogen and molybdenum coexist in stainless steel, corrosion resistance in chloride solutions is drastically increased. This synergistic effect of N and Mo in a chloride solution is mainly due to the formation of nitro-oxyanions and molybdate ion. Oxyanions can be formed by a 'solid state reaction' in the passive film, resulting in the formation of more molybdate and nitric oxide. These oxyanions improve the cation selectivity of the outer layer and form more oxide and increase the amount of chromium oxide and the ratio of $Cr_2O_3/Cr(OH)_3$ and make the film stable and dense.