• Biotechnology and Bioprocess Engineering:BBE
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• v.10 no.4
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• pp.309-314
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• 2005

We performed a basic experiment for the rapid, on-line, real-time measurement of hepatitis B surface antigen using a surface plasmon resonance biosensor. We immobilized anti­HBsAg (hepatitis B surface antigen) polyclonal antibody, as a ligand, to the dextran layer on a CM5 chip surface that had previously been activated by N-hydroxysuccinimide. A sample solution containing HBsAg was fed through a microfluidic channel, and the reflecting angle change due to the mass increase from the binding was detected. The binding characteristics between HBsAg and its polyclonal antibody followed the typical monolayer adsorption isotherm. When the entire immobilized antibody had interacted, no additional, non-specific binding occurred, suggesting the immunoreaction was very specific. The bound antigen per unit mass of the antibody was independent of the immobilized ligand density. No significant steric hindrance was observed at an immobilization density of approximately $17.6 ng/mm^2$. The relationship between the HBsAg concentration in the sample solution and the antigen bound to the ligand was linear up to ca. $40{\mu}g$/mL. This linearity was much higher than that of the ELISA method. It appeared the anti­gen-antibody binding increased as the immobilized ligand density increased. In summary, this study showed the potential of this SPR biosensor-based method as a rapid, simple and multi­sample on-line assay. Once properly validated, it may serve as a more efficient method for HBsAg quantification for replacing the ELISA.

• Journal of Radiopharmaceuticals and Molecular Probes
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• v.4 no.2
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• pp.73-79
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• 2018

In our previous study, tricarbonyl $^{99m}Tc$-labeled TSPO-binding ligand, named $^{99m}Tc$-CB256, having positively charge (+1) was investigated but did not show promising results in in vivo environment despite of a nanomolar binding affinity for TSPO. Because the overall positively charge of $^{99m}Tc$-CB256 would likely interrupt its target protein uptake, we herein designed the neutral tricarbonyl-$^{99m}Tc$ labeled TSPO-binding ligand ($^{99m}Tc$-CB257, 1). $^{99m}Tc$-CB257 was prepared by the facile incorporation of the $[^{99m}Tc(CO)_3]^+$ into a N-(hydroxycarbonylmethyl)-2-picoly moiety in CB257. The radiochemical yield of $^{99m}Tc$-CB257 after HPLC purification was $54.1{\pm}2.4%$ (decay corrected, n = 3). The authentic Re-CB257 (2) was synthesized by using $(NEt_4)_2[Re(CO)_3Br_3]$ in 69.0% yield. The binding affinity of 2 for TSPO was measured in leukocyte and showed approximately 280 times higher than that observed for the positively charged (+1) ligand, Re-CB256 ($K_i=0.57{\pm}0.06nM$ versus $159.3{\pm}8.7nM$, respectively). Our results indicated that 1 can be considered potentially as a new SPECT radiotracer for TSPO-rich cancer and provides the foundation for further in vivo evaluation related with abnormal TSPO-overexpression environments.

• Journal of Integrative Natural Science
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• v.3 no.3
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• pp.143-147
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• 2010

Since it is of great importance to know how a ligand binds to a receptor, there have been a lot of efforts to improve the quality of prediction of docking poses. Earlier efforts were focused on improving search algorithm and scoring function in a docking program resulting in a partial improvement with a lot of variations. Although these are basically very important and essential, more tangible improvements came from the reduction of search space. In a normal docking study, the approximate active site is assumed to be known. After defining active site, scoring functions and search algorithms are used to locate the expected binding pose within this search space. A good search algorithm will sample wisely toward the correct binding pose. By careful study of receptor structure, it was possible to prioritize sub-space in the active site using "receptor-based pharmacophores" or "hot spots". In a sense, these techniques reduce the search space from the beginning. Further improvements were made when the bound ligand structure is available, i.e., the searching could be directed by molecular similarity using ligand information. This could be very helpful to increase the accuracy of binding pose. In addition, if the biological activity data is available, docking program could be improved to the level of being useful in affinity prediction for a series of congeneric ligands. Since the number of co-crystal structures is increasing in protein databank, "Ligand-Guided Docking" to reduce the search space would be more important to improve the accuracy of docking pose prediction and the efficiency of virtual screening. Further improvements in this area would be useful to produce more reliable docking programs.

• Proceeding of EDISON Challenge
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• 2014.03a
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• pp.63-74
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• 2014

Predicting protein loop structures is an important modeling problem since protein loops are often involved in diverse biological functions by participating in enzyme active sites, ligand binding sites, etc. However, loop structure prediction is difficult even when structures of homologous proteins are known due to large sequence and structure variability among loops of homologous proteins. Therefore, an ab initio approach is necessary to solve loop modeling problems. One of the difficulties in the development of ab initio loop modeling method is to derive an accurate scoring function that closely approximates the true free energy function. In particular, entropy as well as energy contribution have to be considered adequately for loops because loops tend to be flexible compared to other parts of protein. In this study, the contribution of conformational entropy is considered in scoring loop conformations by employing "colony energy" which was previously proposed to estimate the free energy for an ensemble of conformations. Loop conformations were generated by using two EDISON_Chem programs GalaxyFill and GalaxySC, and colony energy was designed for this sampling by tuning relevant parameters. On a test set of 40 loops, the accuracy of predicted loop structure improved on average by scoring with the colony energy compared to scoring by energy alone. In addition, high correlation between colony energy and deviation from the native structure suggested that more extensive sampling can further improve the prediction accuracy. In another test on 6 ligand-binding loops that show conformational changes by ligand binding, both ligand-free and ligand-bound states could be identified by using colony energy when no information on the ligand-bound conformation is used.

• Bulletin of the Korean Chemical Society
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• v.33 no.2
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• pp.717-720
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• 2012

• Biomolecules & Therapeutics
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• v.6 no.4
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• pp.337-344
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• 1998

The objective of the present study was to investigate the effect of senescence on the binding properties of muscarinic receptors in the neostriatum of young (3 months), middle-aged (18 months) and aged (33 months) male Fischer 344 x Brown Norway hybrid rats by employing direct binding of selective radiolabeled antagonists. Using the selective M, muscarinic receptor antagonist, $[^3H]$AF-DX384, as the ligand, no significant difference in the maximal receptor density (Bmax) was observed in the neostriatum among any age-groups. In contrast, with the selective M, receptor antagonist, $[^3H]$4-DAMP, a significant increase in the number of muscarinic receptors was observed in neostriatal membrane fractions prepared from the aged animals relative to that observed in the young rats. For each ligand there was no age-related change in its affinity (Kd) for the muscarinic receptors. These results indicate that the observed age-related changes in the muscarinic receptor density may not be necessarily decremuntal and depend upon the muscarinic receptor subtype examined.

• Bulletin of the Korean Chemical Society
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• v.27 no.10
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• pp.1648-1650
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• 2006

The synthesis of a new C,N-bipyrazolic ligand with a functionalized donor-group is reported. The binding properties of the ligand and two other ligand of similar structures towards heavy metal ions ($Hg^{2+}$, $Cd^{2+}$, $Pb^{2+}$, $Zn^{2+}$, $Cu^{2+}$) and alkaline metal ions ($K^+$, $Na^{+}$, $Li^+$) were studied by a liquid-liquid extraction process and the extracted cation percentage was determined by atomic absorption measurements. The selectivity of the ligand to Hg(II) has been mentioned in the abstract.

• The Korean Journal of Pharmacology
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• v.23 no.2
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• pp.101-111
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• 1987

We investigated the binding properties of $(^3H)$ QNB and $(^3H)$ NMS to mAchR to elucidate the characterstics of mAchR in rat brain by using two different preparations (homogemates & intact brain cell aggregates). The binding properties of both ligands demonstrated high affinity and saturability in both experiments, however $(^3H)$ QNB showed a significantly higher maximal binding capacity than tha ot $(^3H)$ NMS 1. In rat brain homogenates; Displacement of both lignands with several mAchR antagonists resulted in competition curves in accoradnce with the law of massaction for QNB, atropine & scopolamine in thie preparation, also a similar profile was found for the quaternary ammonium analogs of atropine & scopolamine (methyl atropine & methylscopolamine) when $(^3H)$ NMS was used to label the receptors in rat brain. But when these hydrophillic antagonists were used to displace $(^3H)$ QNB, they showed interaction with high- and low-affinity binding sites in brain homogenates. Pirenzepine, the nonclassical mAchR antagonist, was able to displace both ligands from binding sites in this preparation. 2. In intact rat brain cell aggregates; Intact bain cell aggregates were used to elucidate the binding characteristics of $(^3H)$ NMS to mAchR in rat. The magnitude of binding of this ligand was related linearly to the amount of cell protein in the binding assay with a high ratio of total to nonspecific binding. mAchR antagonists displaced specific $(^3H)$ NMS binding according to the law of mass-action, while it was possible to resolve displacement curves using mAchR agonist into high-& low-affinity component. 3. Our results indicate that more hydrophilic receptor ligand $(^3H)$ QNB, displacement experiments in both tissues demonstrated that the lipid solubility of a particulr mAchR ligand might play an important role in determining its profile of binding to the mAchR, and the concentrations of mAchR in rat brain are both on the cell surface (membrane-bound receptor) and in the intracelluar membrane (intermembrane-bound receptor). 4. The results are discussed in terms of the usefulness of dissociated intact rat brain cells in studying mAchR in central nervous system.

• BMB Reports
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• v.36 no.2
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• pp.207-213
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• 2003

Peroxisome proliferator-activated receptors (PPARs) are orphan nuclear hormone receptors that are known to control the expression of genes that are involved in lipid homeostasis and energy balance. PPARs activate gene transcription in response to a variety of compounds, including hypolipidemic drugs. Most of these compounds have high affinity to the ligand-binding domain (LBD) of PPARs and cause a conformational change within PPARs. As a result, the receptor is converted to an activated mode that promotes the recruitment fo co-activators such as the steroid receptor co-activator-1 (SRC-1). Based on the activation mechanism of PPARs (the ligand binding to $PPAR{\gamma}$ induces interactions of the receptor with transcriptional co-activators), we performed Western blot and ELISA. These showed that the indomethacin, a $PPAR{\gamma}$ ligand, increased the binding between $PPAR{\gamma}$ and SRC-1 in a ligand dose-dependent manner. These results suggested that the in vitro conformational change of $PPAR{\gamma}$ by ligands was also induced, and increased the levels of the ligand-dependent interaction with SRC-1. Collectively, we developed a novel and useful ELISA system for the mass screening of $PPAR{\gamma}$ ligands. This screening system (based on the interaction between $PPAR{\gamma}$ and SRC-1) may be a promising system in the development of drugs for metabolic disorders.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.48 no.6
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• pp.913-919
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• 2015

In vertebrates, the vitamin D receptor (VDR), a member of the nuclear receptor superfamily, binds the biologically active ligand $1{\alpha},25-(OH)_2$-vitamin $D_3$ (1,25 $D_3$). Nearly all vertebrates, including Agnatha, possess a VDR with high ligand selectivity for 1,25 $D_3$ and related metabolites. Although a putative ancestral VDR gene is present in the genome of the chordate invertebrate Ciona intestinalis, the functional characteristics of marine invertebrate VDR are still obscure. To elucidate the ascidian Halocynthia roretzi VDR (HrVDR), we cloned full-length HrVDR cDNA and investigated the transcriptional activity of HrVDR in HEK293 cells. HrVDR consists of 1,680 nucleotides (559 amino acids [aa]), including a short N-terminal region (A/B domain; 26 aa), DNA-binding domain (C domain; 72 aa), hinge region (D domain; 272 aa), and C-terminal ligand-binding domain (E domain; 161 aa). The amino acid sequence identity of HrVDR was greatest to that of C. intestinalis VDR (56%). In the luciferase reporter assays, the transcriptional activity of HrVDR was not significantly increased by 1,25 $D_3$, whereas the farnesoid X receptor agonist GW4064 increased the transactivation of HrVDR. These results suggest the presence of a novel ligand for and a distinct ligand-binding domain in ascidian VDR.