• 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.

• Journal of the Mineralogical Society of Korea
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• v.30 no.2
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• pp.45-57
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• 2017

Two single crystals of fully dehydrated $Cd^{2+}$-exchanged zeolites Y were prepared by the exchange of ${\mid}Na_{75}{\mid}[Si_{117}Al_{75}O_{384}]-FAU$ ($Na_{75}-Y$, Si/Al = 1.56) with aqueous $0.05M\;Cd(NO_3)_2$ (pH = 3.65) at 294 K, followed by vacuum dehydration at 723 K (crystal 1) and a second crystal, similarly prepared, was exposed to zeolitically dried benzene for 72 hours at 294 K and evacuated (crystal 2). Their structures were determined crystallographically using synchrotron X-rays and were refined to the final error indices using $F_o$>$4{\sigma}(F_o)$ of $R_1/wR_2=0.040/0.121$ and 0.052/0.168, respectively. In crystal $1({\mid}Cd_{36}H_3{\mid}[Si_{117}Al_{75}O_{384}]-FAU)$, $Cd^{2+}$ ions primarily occupy sites I and II, with additional $Cd^{2+}$ ions at sites I', II', and a second site II. In crystal $2({\mid}Cd_{35}(C_6H_6)_{24}H_5{\mid}[Si_{117}Al_{75}O_{384}]-FAU)$, $Cd^{2+}$ ions occupy five crystallographic sites. The 24 benzene molecules are found at two distinct positions within the supercages. The 17 benzene molecules are found on the 3-fold axes in the supercages where each interacts facially with one of site IIa $Cd^{2+}$ ions. The remaining 7 benzene molecules lie on the planes of the 12-rings where each is stabilized by multiple weak electrostatic and van der Waals interactions with framework oxygens.

• Journal of the Mineralogical Society of Korea
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• v.22 no.3
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• pp.177-189
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• 2009

Iron (oxyhydr)oxides commonly form as secondary minerals of high reactivity and large surface area resulting from alteration and weathering of primary minerals, and they are efficient sorbents for inorganic and organic contaminants. Accordingly, they have a great potential in industrial applications and are also of substantial interest in environmental sciences. Goethite (${\alpha}$-FeOOH) is one of the most ubiquitous and stable forms of iron (oxyhydr)oxides in terrestrial soils, sediments, and ore deposits, as well as a common weathering product in rocks of all types. This study focused on adsorption reaction as a main mechanism in scavenging arsenic using goethite. Goethite was synthesized in the laboratory to get high purity, and a variety of mineralogical and physicochemical features of goethite were measured and related to adsorption characteristics of arsenic. To compare differences in adsorption reactions between arsenic species, in addition, a variety of experiments to acquire adsorption isotherm, adsorption edges, and adsorption kinetics were accomplished. The point of zero charge (PZC) of the laboratory-synthesized goethite was measured to be 7.6, which value seems to be relatively higher, compared to those of other iron (oxyhydr)oxides. Its specific surface area appeared to be $29.2\;m^2/g$ and it is relatively smaller than those of other (oxyhydr)oxides. As a result, it was speculated that goethite shows a smaller adsorption capacity. It is likely that the affinity of goethite is much more larger for As(III) (arsenite) than for As(V) (arsenate), because As(III) was observed to be much more adsorbed on goethite than As(V) in equivalent pH conditions. When the adsorption of each arsenic species onto goethite was characterized in various of pH, the adsorption of As(III) was largest in neutral pH range (7.0~9.0) and decreased in both acidic and alkaline pH conditions. In the case of As(V), the adsorption appeared to be highest in the lowest pH condition, and then decreased with an increase of pH. This peculiarity of arsenic adsorption onto goethite might be caused by macroscopic electrostatic interactions due to variation in chemical speciation of arsenic and surface charge of goethite, and also it is significantly affected by change in pH. Parabolic diffusion model was adequate to effectively evaluate arsenic adsorption on goethite, and the regression results show that the kinetic constant of As(V) is larger than that of As(III).

• Journal of Sensor Science and Technology
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• v.7 no.3
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• pp.179-187
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• 1998

A neutral particle energy analyzer, which has the carbon stripping foil and the $90^{\circ}$ cylindrical electrostatic deflection plate, was designed and constructed for measuring of ion temperature in plasma. The energy calibration and energy resolution were studied in detail for a hydrogen ion at the $0.5{\sim}3.0\;keV$ energy using a duoplasmatron ion source. An energy of hydrogen ion to the deflection plate voltage at the peak ion count rate could be fitted by the expression $E_{o}(keV)$=3.83V(kV). The measured energy resolution, which was about 2 % at the energy of 3.0 keV and 9 % at the energy of 0.5keV, was better for the increased hydrogen ion energy. For the charge exchanged hydrogen atom due to the carbon stripping foil, the energy calibration, energy loss and resolution were measured to the $0.5{\sim}2.0{\mu}g/cm^{2}$ thickness of the carbon stripping foil. An energy of the charge exchanged hydrogen atom as a function of the deflection plate voltage and carbon foil thickness could be fitted by the expression $E_{o}(keV)=(0.53d+4.4){\cdot}V(kV)$. The energy loss was $0.23{\sim}0.89\;keV $ to the $0.5{\sim}2.0{\mu}g/cm^{2}$ carbon foil thickness and the $0.5{\sim}3.0\;keV$ energy of the incident neutral hydrogen atom, it could be fitted by the expression ${\Delta}E=(0.12d+0.27){\cdot}{E_{o}}^{1/2}(keV)$. The measured energy resolution for the neutral hydrogen atom, which was between 7 % and 35 % in this experiment region, was increased for the increasing neutral hydrogen atom energy and the decreasing carbon stripping foil thickness.

• Journal of the Mineralogical Society of Korea
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• v.26 no.2
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• pp.101-110
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• 2013

Due to the large specific surface area and great reactivity toward environmental contaminants, nanocrystalline mackinawite (FeS) has been widely applied for the remediation of contaminated groundwater and soil. Furthermore, nanocrystalline FeS is rather thermodynamically stable against anoxic corrosion, and its reactivity can be regenerated continuously by the activity of sulfate-reducing bacteria. However, nanocrystalline mackinawite is prone to either spread out along the groundwater flow or cause pore clogging in aquifers by particle aggregation. Accordingly, this mineral should be modified for the application of permeable reactive barriers (PRBs). In this study, coating methods were investigated by which mackinawite nanoparticles were deposited on the surface of alumina or activated alumina. The amount of FeS coating was found to significantly vary with pH, with the highest amount occurring at pH ~6.9 for both minerals. At this pH, the surfaces of mackinawite and alumina (or activated alumina) were oppositely charged, with the resultant electrostatic attraction making the coating highly effective. At this pH, the coating amounts by alumina and activated alumina were 0.038 and 0.114 $mmol{\cdot}FeS/g$, respectively. Under anoxic conditions, arsenite sorption experiments were conducted with uncoated alumina, uncoated activated alumina, and both minerals coated with FeS at the optimal pH for comparison of their reactivity. Uncoated activated alumina showed the higher arsenite removal compared to uncoated alumina. Notably, the arsenite sorption capacity of activated alumina was little changed by the coating with FeS. This might be attributed to the abundance of highly reactive hydroxyl functional groups (${\equiv}$AlOH) on the surface of activated alumina, making the arsenite sorption by the coated FeS unnoticeable. In contrast, the arsenite sorption capacity of alumina was found to increase substantially by the FeS coating. This was due to the consumption of the surface hydroxyl functional groups on the alumina surface and the subsequent occurrence of As(III) sorption by the coated FeS. Alumina, on the surface area basis, has about 8 times higher FeS coating amount and higher As(III) sorption capacity than silica. This study indicates that alumina is a better candidate than silica for the coating of nanocrystalline mackinawite.

• The Korean Journal of Pesticide Science
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• v.8 no.3
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• pp.151-161
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• 2004

Three dimensional quantitative structure-activity relationships (3D-QSAR) studies for the protox inhibition activities against root and shoot of rice plant (Orysa sativa L.) and barnyardgrass (Echinochloa crus-galli) by a series of new A=3,4,5,6-tetrahydrophthalimino, B=3-chloro-4,5,6,7-tetrahydro-2H-indazolyl and C=3,4-dimethylmaleimino group, and R-group substituted on the phenyl ring in 1-(5-methyl-3-phenylisoxazolin-5-yl)methoxy-2chloro-4-fluorobenzene derivatives were performed using comparative molecular field analyses (CoMFA) methodology with Gasteiger-Huckel charge. Four CoMFA models for the protox inhibition activities against root and shoot of the two plants were generated using 46 molecules as training set and the predictive ability of the each models was evaluated against a test set of 8 molecules. And the statistical results of these models with combination (SIH) of standard field, indicator field and H-bond field showed the best predictability of the protox inhibition activities based on the cross-validated value $r^2_{cv.}$ $(q^2=0.635\sim0.924)$, conventional coefficient $(r^2_{ncv.}=0.928\sim0.977)$ and PRESS value $(0.091\sim0.156)$, respectively. The activities exhibited a strong correlation with steric $(74.3\sim87.4%)$, electrostatic $(10.10\sim18.5%)$ and hydrophobic $(1.10\sim8.30%)$ factors of the molecules. The steric feature of molecule may be an important factor for the activities. We founded that an novel selective and higher protox inhibitors between the two plants may be designed by modification of X-subsitutents for barnyardgrass based upon the results obtained from CoMFA analyses.

• The Korean Journal of Pesticide Science
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• v.9 no.1
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• pp.26-34
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• 2005

3D-QSAR studies for the fungicidal activities against resistance phytophthora blight (RPC; 95CC7303) and sensitive phytophthora blight (Phytopthora capsici) (SPC; 95CC7105) by a series of new 2-alkoxyphenyl-3-phenylthioisoindoline-1-one derivatives (A & B) were studieded using comparative molecular similarity indices analyses (CoMSIA) methodology. From the based on the results, the two CoMSIA models, R5 and S1: as the best models were derivated. The statistical results of the models showed the best predictability and fitness for the fungicidal activities based on the cross- validated value ($q^2=0.714{\sim}0.823$) and non cross-validated, value ($r^2_{ncv.}=0.918{\sim}0.954$), respectively. The model R5 for fungicidal activity of RPC generated from the field fit alignment and combination of electrostatic field, H-bond acceptor field and LUMO molecular orbital field. The model S1 (or S5) for fungicidal activity of SPC generated from the atom based fit alignment and combination of steric field and HOMO molecular orbital field. The models also shows that inclusion of H-bond acceptor field (A) improved the statistical significance of the models. From the based graphical analyses of CoMSIA contribution maps, it was revealed that the novel selective character for fungicidal activities between the two fungi by modify of X-sub-stituent on the N-phenyl group and R-substituent on the S-phenyl group will be able to achivement.

• Journal of the Society of Cosmetic Scientists of Korea
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• v.30 no.3 s.47
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• pp.353-359
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• 2004

The extent of silica flocculation can be modified by varying the silica concentration, aqueous phase pH, salt and polvmer concentration. High volume fraction W/O emulsion stabilized by hydrophobic silica was established with various aqueous phase conditions for cosmetic application. By increasing the silica concentration up to $1.0\;wt\%,$ the size of droplet decreased. A high silica concentration increased the viscosity of continuous oil phase by network formation, which resulted in target size of droplet. The stability of W/O emulsion is improved as increasing the aqueous phase pH. At low and intermediate pH, the emulsions became more stable by adding salt $(0.083\;mol\;dm^{-3}\;MgSO_4).$ At high PH, the presence of salt caused significant destabilization. The gelation behavior of the emulsion indicates that the effect of salt on silica-stabilized emulsion is derived from an electrostatic attraction. The addition of xanthan gum in aqueous phase increased the mono-dispersity of the W/O emulsion by making water more hydrophobic and hindering the recombination of droplets. In conclusion, these results indicate that very stable emulsifier-free, finely dispersed W/O emulsion can be achieved for cosmetic application by changing the aqueous phase composition.

• Polymer(Korea)
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• v.33 no.6
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• pp.555-560
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• 2009

Sulfonic acid of the sulfonated 6FDA-based polyimides were exchanged with the monovalent ($Li^+$, $Na^+$, $K^+$) and divalent ($Mg^{2+}$, $Ca^{2+}$, $Ba^{2+}$) ions. The effect of metal cations exchanged sulfonated polyimides was investigated in terms of gas permeability and selectivity for $CO_2$, $O_2$ and $N_2$ gases. Thermogravimetric analysis showed that thermal stability of sulfonated polyimide was improved by exchanged metal cations. The permeabilities of monovalent cation-exchanged, sulfonated polyimide were reduced as the ion radius reduced [$Li^+$(0.059 nm)>$Na^+$(0.102 nm)>$K^+$(0.138 nm)], and those of divalent cations exchanged were determined by the ionic radii and electrostatic crosslinking between the polymer and metal cations, whereas the selectivities of all the metal cation-exchanged, sulfonated polyimides for $CO_2/N_2$ and $O_2/N_2$, were higher than those of sulfonated polyimide membranes. The sulfonated polyimide exchanged with the potassium cation showed the $O_2$ permeability of 89.98 Barrer [$1\times10^{-10}\;cm^3$(STP) $cm/cm^2{\cdot}s{\cdot}cmHg$] and the sulfonated polyimide exchanged with the lithium cation showed the $O_2/N_2$ selectivity of 12.9.

• Journal of Life Science
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• v.26 no.8
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• pp.875-880
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• 2016

The plasma membrane plays a crucial role in relaying signals from the outside environment to the inside of the cells. In eukaryotic cells, the inner leaflets of the plasma membrane are composed mostly of phospholipids, including phosphatidylethanolamine (PE), phosphatidylserine (PS), and phosphatidylinositides (PIs). In this study, we tried to analyze the morphological changes induced by EGFP-fused membrane binding proteins, which are targeted to the plasma membrane via specific phospholipids binding. As a result, we found that overexpression of EGFP-P4M-SidM, a specific PI4P binding protein, or EGFP alone, did not induce any morphological changes. On the other hand, overexpression of EGFP-PLCδ1(PH), which is a specific PI(4,5)P₂ binding protein, EGFP-AKT1(PH) which binds to PI(3,4,5)P₃, or EGFP-OSH2(PH)×2 which binds to PI4P and PI(4,5)P₂, could induce the filopodia and lamilapodia formation as well as cell shrinkage. Overexpression of Lact-C2-EGFP which is a specific PS-binding probe, EGFP fused Aplysia phosphodiesterase 4 (ApPDE4) long-form (L(N20)-EGFP) which is localized to the plasma membrane via hydrophobic interaction, or EGFP fused Aplysia PDE4 short-form (S(N-UCR1-2)-EGFP) which is localized to the plasma membrane via electrostatic interaction, could induce cell shrinkage, but not filopodia or lamilapodia formation. Taken together, our data support that the different phospholipid bindings in the plasma membrane could induce different characteristic morphological changes. Thus, we can analyze, characterize, and classify the cellular morphological changes induced by the various phospholipid binding proteins.