• Journal of the Korean Magnetic Resonance Society
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• v.15 no.1
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• pp.80-89
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• 2011

3D structures of STAM1 UIM-ubiquitin complex were presented to predict and analyze the interaction between UIM and ubiquitin. To generate the protein-peptide complex structure, the RosettaDock method was used with and without NMR restraints. High resolution complex structure was acquired successfully and evaluated electrostatic interaction in the protein-peptide binding with several charged residues at the binding site. From docking results, the Rosettadock method could be useful to acquire essential information of protein-protein or protein-peptide interaction with minimal biological evidences.

• Journal of the Korean Physical Society
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• v.73 no.12
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• pp.1908-1917
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• 2018

The binding affinity between the T-cell receptors (TCRs) and antigenic peptides mainly determines immunological recognition. It is not a trivial task that T cells identify the digital sequences of peptide amino acids by simply relying on the integrated binding affinity between TCRs and antigenic peptides. To address this problem, we examine whether the affinity-based discrimination of peptide sequences is learnable and generalizable by artificial neural networks (ANNs) that process the digital experimental amino acid sequence information of receptors and peptides. A pair of TCR and peptide sequences correspond to the input for ANNs, while the success or failure of the immunological recognition correspond to the output. The output is obtained by both theoretical model and experimental data. In either case, we confirmed that ANNs could learn the immunological recognition. We also found that a homogenized encoding of amino acid sequence was more effective for the supervised learning task.

• Bulletin of the Korean Chemical Society
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• v.33 no.2
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• pp.583-588
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• 2012

Functional interaction between Drosophila orphan receptor FTZ-F1 (NR5A3) and a segmentation gene product fushi tarazu (FTZ) is crucial for regulating genes related to define the identities of alternate segmental regions in the Drosophila embryo. FTZ binding to the ligand-binding domain (LBD) of FTZ-F1 is of essence in activating its transcription process. We determined solution structures of the cofactor peptide ($FTZ^{PEP}$) derived from FTZ by NMR spectroscopy. The cofactor peptide showed a nascent helical conformation in aqueous solution, however, the helicity was increased in the presence of TFE. Furthermore, $FTZ^{PEP}$ formed ${\alpha}$-helical conformation upon FTZ-F1 binding, which provides a receptor bound structure of $FTZ^{PEP}$. The solution structure of $FTZ^{PEP}$ in the presence of FTZ-F1 displays a long stretch of the ${\alpha}$-helix with a bend in the middle of helix.

• Bulletin of the Korean Chemical Society
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• v.31 no.12
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• pp.3703-3706
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• 2010

Biomolecules specific to explosives can be exploited as chemical sensors. Peptides specific to immobilized dinitrotoluene (DNT) were identified using a phage display library. A derivative of DNT that contained an extended amine group, 4-(2,4-dinitrophenyl)butan-1-amine, was synthesized and immobilized using a self-assembled monolayer surface on gold. Filamentous M13 phages displaying random sequences of 12-mer peptides specific to the immobilized DNT-derivate were isolated from the M13 phage library by biopanning. A common peptide sequence was identified from the isolated phages and the synthesized peptides showed selective binding to DNT. When the peptide was immobilized on a quartz crystal microbalance (QCM) chip, it showed a binding signal to DNT, while toluene barely showed significant binding to the QCM chip. These results demonstrate that peptides screened by biopanning against immobilized DNT can be useful for quick and accurate detection of DNT.

• 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.

• Journal of Environmental Science International
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• v.6 no.2
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• pp.189-194
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• 1997

Toxic peptides from hornet venom, mastoparan and mastoparan-B were synthesized us- ing the solid phase peptide synthesis method and investigated the interaction of them with phospholipid bilayer, antibacterial activity, and hemolytic activity. Both toxic peptides could induce dye release at a low concentration in neutral liposome. The binding affinity of mastoparan-B for neutral liposome was smaller than that for acidic one. Mastoparan and mastoparan-B had strong antibacterial activity for gram-positive bacteria, but weak or potent activity for gram-negative ones, respectively. Mastoparan and mastoparan-B lysed erythrocyte very little up to 5 $\mu$M.

• Animal cells and systems
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• v.6 no.3
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• pp.253-261
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• 2002

Although cardiac distribution of specific receptors for atrial natriuretic peptide (ANP) was mainly observed in the ventricular endocardium, the modulation of ANP receptors in relation to cardiac development is not defined. The present study was undertaken to investigate ANP receptor modulation in rat during development. In the developmental stages examined (fetus, after postnatal 3-days, 1-, 2-, 3-, 4-, and 8-week-old Sprague Dawley rats) specific ANP binding sites were localized in the right and left ventricular endo-cardia by quantitative in vitro receptor autoradiography using (equation omitted)-rat ANP as labeled ligand. The specific bindings to endocardium were much higher in the right than the left ventricle. The binding affinities of ANP were much higher in the right than the left ventricular endocardium. The difference of these binding affinities among various developmental stages was not observed in the right ventricle, whereas the binding affinity in left ventricle was gradually increased with aging and reached the peak value at 8 weeks. No significant difference in maximal binding capacities of endocardial bindings was observed in the right and left ventricular endocardia during developmental stages. Also, cGMP production via activation of particulate guanylyl cyclase-coupled receptor subtypes in the ventricular membranes was gradually decreased with close relationship to aging. Therefore, the present study show that the endocardial ANP receptor is modulated with close relationship to cardiac development in the left ventricle rather than the right ventricle, and may be involved in regulating myocardial contractility in left heart.

• Bulletin of the Korean Chemical Society
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• v.27 no.4
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• pp.529-534
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• 2006

Chemical modification of the S. cerevisiae farnesyl protein transferase (FPT) with CMC, phenylglyoxal and DEPC resulted in enzyme inactivation, depending upon the reagent concentration. The peptide substrate GST-PEP-I, a GST-fused undecapeptide mimicking the C-terminus of $p21^{Ki-ras}$, protected the enzyme against inactivation by CMC which is specific to either aspartate or glutamate, while the other substrate farnesyl pyrophosphate (FPP) showed protection against phenylglyoxal which is the specific modifier of arginine residues, dependent on the substrate concentrations. Neither of the two substrates protected the enzyme against histidine inactivation by DEPC. It is suggested that there is at least one aspartate or glutamate residue at the peptide substrate binding site, and that at least one arginine residue is located at the binding site of FPP. There also seems to be at least one histidine residue which is critical for enzymic activity and is exposed toward the bulk solution, excluded from the substrate binding sites.

• Journal of Radiation Industry
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• v.7 no.2_3
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• pp.127-134
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• 2013

Bombesin receptors are overexpressed in many kinds of human tumors. In particular, the gastrin releasing peptide receptor (GRPR) which is also called bombesin receptor subtype 2, has been identified in prostate cancer. In the present study, we developed a bombesin antagonist-based $^{177}Lu$-labeled peptide, $^{177}Lu$-DOTA-$Ala(SO_3H)$-Aminooctanoyl-Gln-Trp-Ala-Val-N methyl Gly-His-Statine-Leu-$NH_2$ (DOTA-sBBNA). DOTA-sBBNA was prepared using a solid phase synthesis method. It was labeled with $^{177}Lu$ by a high radiolabeling yield (>98%), and its Log P value was -2.05. The radiolabeled peptide was highly stable in serum incubation at $37^{\circ}C$ for 48 hr. A competitive displacement of $^{125}I-[Tyr^4]$-Bombesin on the PC-3 human prostate carcinoma cells revealed that the $IC_{50}$ value of the peptide was 6.76 nM indicating a highly nanomolar binding affinity for GRPR. These results suggest that $^{177}Lu$-DOTA-sBBNA can be a potential candidate for targeting prostate cancer, and further studies to evaluate its biological characteristics are needed.

• BMB Reports
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• v.42 no.11
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• pp.737-742
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• 2009

Hypoxia-inducible factor-$1{\alpha}/{\beta}$ (HIF-$1{\alpha}/{\beta}$) is a heterodimeric transcriptional activator that mediates gene expression in response to hypoxia. HIF-$1{\alpha}$ has been noted as an effective therapeutic target for ischemic diseases such as myocardiac infarction, stroke and cancer. By using a yeast two-hybrid system and a random peptide library, we found a 16-mer peptide named F29 that directly interacts with the bHLH-PAS domain of HIF-$1{\alpha}$. We found that F29 facilitates the interaction of the HIF-$1{\alpha/\beta}$ heterodimer with its target DNA sequence, hypoxia-responsive element (HRE). The transient transfection of an F29-expressing plasmid increases the expression of both an HRE-driven luciferase gene and the endogenous HIF-1 target gene, vascular endothelial growth factor (VEGF). Taken together, we conclude that F29 increases the DNA-binding ability of HIF-$1{\alpha}$, leading to increased expression of its target gene VEGF. Our results suggest that F29 can be a lead compound that directly targets HIF-$1{\alpha}$ and increases its activity.