• 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.

• 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.

• 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.

• Journal of the Mineralogical Society of Korea
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• v.20 no.4
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• pp.313-325
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• 2007

In order to have better insights into adsorption of organic molecules on kaolinite surfaces, we performed quantum chemical calculations of interaction between three different model clusters of kaolinite siloxane surfaces and benzyl alcohol, with emphasis on the effect of size and lattice topology of the cluster on the variation of electron density and magnetic shielding tensor. Model cluster 1 is an ideal silicate tetrahedral surface that consists of 7 hexagonal rings, and model cluster 2 is composed of 7 ditrigonal siloxane rings with crystallographically distinct basal oxygen atoms in the cluster, and finally model cluster 3 has both tetrahedral and octahedral layers. The Mulliken charge analysis shows that siloxane surface of model cluster 3 undergoes the largest electron density transfer after the benzyl alcohol adsorption and that of model cluster 1 is apparently larger than that of model cluster 2. The difference of Mulliken charges of basal oxygen atoms before and after the adsorption is positively correlated with hydrogen bond strength. NMR chemical shielding tensor calculation of clusters without benryl alcohol shows that three different basal oxygen atoms (O3, O4, and O5) in model cluster 2 have the isotropic magnetic shielding tensor as $228.2{\pm}3.9,\;228.9{\pm}3.4,\;and\;222.3{\pm}3.0ppm$, respectively. After the adsorption, the difference of isotropic chemical shift varies from 1 to 5.5 ppm fer model cluster 1 and 2 while model cluster 2 apparently shows larger changes in isotropic chemical shift. The chemical shift of oxygen atoms is also positively correlated with electron density transfer. The current results show that the adsorption of benzyl alcohol on the kaolinite siloxane surfaces can largely be dominated by a weak hydrogen bonding and electrostatic force (charge-charge interaction) and demonstrate the importance of the cluster site and the lattice topology of surfaces on the adsorption behavior of the organic molecules on clay surfaces.