• Proceedings of the Korean Biophysical Society Conference
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• 2003.06a
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• pp.45-45
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• 2003

We isolated a novel ankyrin-repeat containing protein, rSIAP (rSlo Interacting Ankyrin-repeat Protein), as an interacting protein to the cytosolic domain of the alpha-subunit of rat large-conductance Ca$\^$2+/-activated K$\^$+/ channel (rSlo) by yeast two-hybrid screening. Affinity pull-down assay showed the direct and specific interaction between rSIAP and rSlo domain. The channel-binding proteins can be classified into several categories according to their functional effects on the channel proteins, i.e. signaling adaptors, scaffolding net, molecular tuners, molecular chaperones, etc. To obtain initial clues on its functional roles, we investigated the cellular localization of rSIAP using immunofluorescent staining. The results showed the possible co-localization of rSlo and rSIAP protein near the plasma membrane, when co-expressed in CHO cells. We then investigated the functional effects of rSIAP on the rSlo channel using electrophysiological means. The co-expression of rSIAP accelerated the activation of rSlo channel. These effects were initiated at the micromolar [Ca$\^$2+/]$\_$i/ and gradually increased as [Ca$\^$2+/]$\_$i/ raised. Interestingly, rSIAP decreased the inactivation kinetics of rSlo channel at micromolar [Ca$\^$2+/]$\_$i/, while the rate was accelerated at sub-micromolar [Ca$\^$2+/]$\_$i/. These results suggest that rSIAP may modulate the activity of native BK$\_$Ca/ channel by altering its gating kinetics depending on [Ca$\^$2+/]$\_$i/. To localize critical regions involved in protein-protein interaction between rSlo and rSIAP, a series of sub-domain constructs were generated. We are currently investigating sub-domain interaction using both of yeast two-hybrid method and in vitro binding assay.

• Archives of Pharmacal Research
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• v.13 no.3
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• pp.221-226
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• 1990

A physiological pharmacokinetic hybrid model was developed in order to predict the disposition kinetics of diphenylhydantoin (DPH) in the brain from the plasma conentration data of DPH. The model was constructed under the assumptions of well-stirred, plasma flow-limited and lienar tissue diposition kinetics of DPH. DPH was administered intravenously to the rats at a dose of 10 mg/kg together with/without sodium salicylate (SA;10 mg/kg) and the DPH concentrations in the plasma and brain were determined. Plasma protein binding of DPH concentrations in the plasma and brain were determined. Plasma protein binding of DPH was also determined using equilibrium dialysis technique. Then the model was tested for its predictability of DPH concentrations in the brian from the plasma data of DPH. It was found that the predicted values of DPH concentrations in the brian were in fair agreement with the experimental values in the rats of both treatments. The 2-fold increase in the brain concentration of DPH by SA-coadinistration was predicted well from the plasma concentration and plasma free fraction ($f_p$) data of DPH using the model. Therefore, the hybrid model was concluded to be very useful for the prediction of the concentrations of DPH in the brain from the plasma concentration data. Finally, DPH concentrations in the human brian was calculated using this model from plasma DPH data in the literature, yet the scale-up of this model to the human is not convinced.

• Bulletin of the Korean Chemical Society
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• v.35 no.5
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• pp.1279-1284
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• 2014

The binding of TATA-binding protein (TBP) to the TATA-box containing promoter region is aided by many other transcriptional factors including TFIIA and TFIIB. The mechanistic insight into the assembly of RNA polymerase II preinitation complex (PIC) has been gained by either directly altering a function of target protein or perturbing molecular interactions using drugs, RNAi, or aptamers. Aptamers have been found particularly useful for studying a role of a subset of PIC on transcription for their ability to inhibit specific molecular interactions. One major hurdle to the wide use of aptamers as specific inhibitors arises from the difficulty with traditional assays to validate and determine specificity, affinity, and binding epitopes for aptamers against targets. Here, using a technique called the bio-layer interferometry (BLI) designed for a label-free, real-time, and multiplexed detection of molecular interactions, we studied the assembly of a subset of PIC, TBP binding to TATA DNA, and two distinct classes of aptamers against TPB in regard to their ability to inhibit TBP binding to TFIIA or TATA DNA. Using BLI, we measured not only equilibrium binding constants ($K_D$), which were overall in close agreement with those obtained by electrophoretic mobility shift assay, but also kinetic constants of binding ($k_{on}$ and $k_{off}$), differentiating aptamers of comparable KDs by their difference in binding kinetics. The assay developed in this study can readily be adopted for high throughput validation of candidate aptamers for specificity, affinity, and epitopes, providing both equilibrium and kinetic information for aptamer interaction with targets.

• Journal of Soil and Groundwater Environment
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• v.16 no.6
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• pp.79-94
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• 2011

Black carbon (BC), a kind of high surface area carbonaceous material (HSACM), was isolated from Andong lake sediment. Sorption and desorption kinetics of naphthalene (Naph) and phenanthrene (Phen) in organic carbon (OC) and BC in the Andong lake sediment were investigated. Several kinetic models such as one-site mass transfer model (OSMTM), two-compartment first-order kinetic model (TCFOKM), and a newly proposed modified two-compartment first-order kinetic model (MTCFOKM) were used to describe the sorption and desorption kinetics. The MTCFOKM was the best fitting model. The MTCFOKM for sorption kinetics showed that i) the sorbed amounts of PAHs onto BC were higher than those onto OC, consistent with BET surface area; ii) the equilibration time for sorption onto BC was longer than those onto OC due to smaller size of micropore ($11.67{\AA}$) of BC than OC ($38.18{\AA}$); iii) initial sorption velocity of BC was higher than OC; and iv) the slow sorption velocity in BC caused the later equilibrium time than OC even though the fast sorption velocity was early completed in both BC and OC. The MTCFOKM also described the desorption of PAHs from the OC and BC well. After desorption, the remaining fractions of PAHs in BC were higher than those in OC due to stronger PAHs-BC binding. The remaining fractions increased with aging for both BC and OC.

• Bulletin of the Korean Chemical Society
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• v.26 no.2
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• pp.260-264
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• 2005

The nature of the active site of Tobacco acetohydroxyacid synthase (AHAS) in the substrate- and cofactorbinding was studied by kinetics and fluorescence spectroscopy. The substrate saturation curve does not follow Michaelis-Menten kinetics at different temperatures (7, 21 and 37 ${^{\circ}C}$), pH (6.5, 7.5 and 8.5) and buffers (Tris-HCl and MOPS). The concentration of one half of the maximum velocity ($S_{0.5}$) decreased in the following order: pyruvate $\gt$ ThDP $\approx$$Mg^{+2}$ $\gt$ FAD. However, the catalytic efficiency (K$_{cat}/S_{0.5}$) inversely decreased in the following order; FAD $\gt$ $Mg^{+2}$ $\approx$ThDP $\gt$ pyruvate, indicating that the cofactors by in decreasing order; FAD, $Mg^{+2}$, ThDP, affect the catalysis of AHAS. The dissociation constant ($K_d$) of the intrinsic tryptophan fluorescence decreased with the same tendency of the concentration of one half of the maximum velocity ($S_{0.5}$) decreasing order. This data provides evidence that the substrate and cofactor binding natures of the active site, as well as its activation characteristics, resemble those of other ThDP-dependent enzymes.

• Bulletin of the Korean Chemical Society
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• v.33 no.2
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• pp.426-432
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• 2012

The activity of an antimicrobial peptide, protegrin-1 (PG-1), on lipid membranes was investigated using solidstate NMR and a new sampling method that employed mechanically aligned bilayers between thin glass plates. At 95% hydration and full hydration, the peptide respectively disrupted 25% and 86% of the aligned 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphotidylcholine (POPC) bilayers at a P/L (peptide-to-lipid) ratio of 1/20 under the new experimental conditions. The kinetics of the POPC bilayers disruption appeared to be diffusioncontrolled. The presence of cholesterol at 95% hydration and full hydration reduced the peptide disruption of the aligned POPC bilayers to less than 10% and 35%, respectively. A comparison of the equilibrium states of heterogeneously and homogeneously mixed peptides and lipids demonstrated the importance of peptide binding to the biomembrane for whole membrane disruption.

• Bulletin of the Korean Chemical Society
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• v.25 no.7
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• pp.1031-1035
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• 2004

The adsorption kinetics of ${\beta}$-casein on a hydrophobic surface has been studied by means of the quartz crystal microbalance (QCM). The self assembled monolayer of 1-octadecanethiol on a gold coated quartz crystal was used as a hydrophobic surface for adsorption. The adsorption kinetics was monitored in different solution conditions. Formation of monolayer is observed in most cases. At high concentration of protein, micelle formation which is interrupted by high ionic strength of solution is observed. Casein binding cations such as $Ca^{2+},\;Ba^{2+}\;and\;Al^{3+}$ increase the hydrophobicity of the protein and the multiple layer adsorption occurs. The strong and weak points of the QCM method in the study of protein adsorption are discussed.

• BMB Reports
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• v.29 no.3
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• pp.210-214
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• 1996

The pH dependence of the kinetic parameters of mutant O-acetylserine sulfhydrylase (OASS) from Salmonella typhimurium LT-2 has been determined in order to obtain information on the chemical mechanism. The initial velocity pattern obtained by varying the concentrations of OAS at several fixed concentrations of TNB, shows an intersection on the left of the ordinate at pH 7.0, indicating that the kinetic mechanism is a sequential mechanism in which substrate inhibition by OAS is observed while the wild type enzyme showed a ping pong mechanism. The values of $V/E_t$, $V/K_{OAS}E_{t}$ and $V/K_{TNB}E_{t}$ decreased by about 68%, 14% and 16% as compared with the wild type enzyme. The $V/K_{OAS}E_{t}$ is a pK of 6.5 on the acid side of the pH profile, and the $V/K_{TNB}$ is pH independent. As compared with the wild type enzyme, the pKs in the V/K profiles are shifted, reflecting that binding of the cofactor in free E:OAS is less asymmetric.

• Microbiology and Biotechnology Letters
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• v.25 no.2
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• pp.173-177
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• 1997

Glycerol-3-phosphate cytidylyltransferase from Bacillus subtilis was modified with various chemical modifiers to determine the active sites of the enzyme. Treatment of the enzyme with group-specific reagents diethylpyrocarbonate, N-bromosuccinimide, or carbodiimide resulted in complete loss of enzyme activity, which shows histidine, tryptophan, and glutamic acid or aspartic acid residues are at or near the active site. In each case, inactivation followed pseudo first-order kinetics. Inclusion of glycerol-3-phosphate and/or CTP prevented the inactivation, indicating the presence of tryptophan and glutamic acid or aspartic acid residues at the substrate binding site. Analysis of kinetics of inactivation showed that the loss of enzyme activity was due to modification of a two histidine residues, single tryptophan residue, and two glutamic acid or aspartic acid residues.

• Proceedings of the Korean Biophysical Society Conference
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• 1996.07a
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• pp.13-13
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• 1996

Aggregation of human $\alpha$$_1$-antitrypsin ($\alpha$$_1$-AT) during folding occurs both in vitro and in vivo. In vivo aggregates of mutant $\alpha$$_1$-AT such as $M_{malton}$ (Phe52 deleted) and Z (Glu342 longrightarrowLys) variants have pathological consequences. In order to analyze the process of $\alpha$$_1$-AT aggregation in detail, the folding-unfolding kinetics of $\alpha$$_1$-AT was examined by monitoring intrinsic Trp fluorescence and ANS binding. (omitted)