• Journal of Adhesion and Interface
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• v.25 no.1
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• pp.157-161
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• 2024

Amphiphilic gold nanoparticles, synthesized by the simultaneous binding of hydrophilic and hydrophobic ligands on their surfaces, find diverse applications in energy, bio, optical, electronic technologies, and various other fields. Particularly, these amphiphilic gold nanoparticles possess both hydrophilic and hydrophobic characteristics, enabling them to activate interface at the interface of immiscible fluids and form organized structures. The surface properties of gold nanoparticles play a crucial role in influencing the behaviors of amphiphilic gold nanoparticles at the interface of two fluids. Therefore, this study investigated the adsorption behaviors of gold nanoparticles at the organic solvent-water interface based on the surface characteristics of amphiphilic gold nanoparticles and the type of organic solvents. It was observed that the amount of adsorbed gold nanoparticles at the interface increased with the length of hydrocarbon chains in hydrophobic ligands and increased with shorter hydrocarbon chains in the organic solvent. Furthermore, using the Langmuir isotherm model, the study confirmed the formation of a monolayer by amphiphilic gold nanoparticles and obtained significant thermodynamic parameters simultaneously.

• Molecules and Cells
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• v.20 no.1
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• pp.1-16
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• 2005

The peptidyl transferase center (PTC) is located in a protein free environment, thus confirming that the ribosome is a ribozyme. This arched void has dimensions suitable for accommodating the 3'ends of the A-and the P-site tRNAs, and is situated within a universal sizable symmetry-related region that connects all ribosomal functional centers involved in amino-acid polymerization. The linkage between the elaborate PTC architecture and the A-site tRNA position revealed that the A-to P-site passage of the tRNA 3'end is performed by a rotatory motion, which leads to stereochemistry suitable for peptide bond formation and for substrate mediated catalysis, thus suggesting that the PTC evolved by genefusion. Adjacent to the PTC is the entrance of the protein exit tunnel, shown to play active roles in sequence-specific gating of nascent chains and in responding to cellular signals. This tunnel also provides a site that may be exploited for local co-translational folding and seems to assist in nascent chain trafficking into the hydrophobic space formed by the first bacterial chaperone, the trigger factor. Many antibiotics target ribosomes. Although the ribosome is highly conserved, subtle sequence and/or conformational variations enable drug selectivity, thus facilitating clinical usage. Comparisons of high-resolution structures of complexes of antibiotics bound to ribosomes from eubacteria resembling pathogens, to an archaeon that shares properties with eukaryotes and to its mutant that allows antibiotics binding, demonstrated the unambiguous difference between mere binding and therapeutical effectiveness. The observed variability in antibiotics inhibitory modes, accompanied by the elucidation of the structural basis to antibiotics mechanism justifies expectations for structural based improved properties of existing compounds as well as for the development of novel drugs.

• Bulletin of the Korean Chemical Society
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• v.32 no.6
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• pp.2008-2014
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• 2011

Serotonin or 5-hydroxytryptamine subtype 2C ($5-HT_{2C}$) receptor belongs to class A amine subfamily of G-protein-coupled receptor (GPCR) super family and its ligands has therapeutic promise as anti-depressant and -obesity agents. So far, bovine rhodopsin from class A opsin subfamily was the mostly used X-ray crystal template to model this receptor. Here, we explained homology model using beta 2 adrenergic receptor (${\beta}$2AR), the model was energetically minimized and validated by flexible ligand docking with known agonists and antagonists. In the active site Asp134, Ser138 of transmembrane 3 (TM3), Arg195 of extracellular loop 2 (ECL2) and Tyr358 of TM7 were found as important residues to interact with agonists. In addition to these, V208 of ECL2 and N351 of TM7 was found to interact with antagonists. Several conserved residues including Trp324, Phe327 and Phe328 were also found to contribute hydrophobic interaction. The predicted ligand binding mode is in good agreement with published mutagenesis and homology model data. This new template derived homology model can be useful for further virtual screening based lead identification.

• Journal of the Korean Society of Clothing and Textiles
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• v.20 no.4
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• pp.655-666
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• 1996

The effect of protease (subtilisin Carlsberg) on the removal of hemoglobin as protein soil was studied. The relation between the renloval and the hydrolysis of hemoglobin by subtilisin Carlsberg was discussed. The soiled babric was prepared by spotting of hemoglobin solution evenly on the cotton fabric and was denatured by steaming. The soiled fabric was washed by using Terg-0-Tometer at various conditions. The removal efficiency was evaluated by analysis of protein on the fabrics before and after washing by means of copper-Folin method. 1. The removal of hemoglobin was increased in proportion to increasing of the enzyme concentration up to a certain point, but it began to decrease above the point. 2. The hemoglobin was removed effectively by adding of subtilisin Carlsberg, and more effectively removed by adding of AOS in the enzyme solution. 3. The removal of hemoglobin deviated from the first order reaction in detergency. 4. The renloval of hemoglobin was highest at $50^{\circ}C$ in detergency, Even at low temperature the removal efficiency of enzyme was relatively higher compared with the hydrolysis of hemoglobin by the enzyme. However the removal of hemoglobin was apparently decreased with the increase of temperature over $60^{\circ}C$. 5. The removal of hemoglobin was relatively high at pH 7.0~8.0 and increased continuously with the increase of pH in detergency 6. In detergency, the removal mechanism of hemoglobin by subtilisin Carlsberg could be explained as follows: Fisrt of all, the enzyme hydrolyzed hemoglobin substrates partially by forming E-S complex at the surface of hemoglobin on the cotton fiber, and decomposed cooperative binding of hemoglobin. Subsequently, the fragments of hemoglobin were easily removed by washing. According as the enzyme penetrated to inner part of hemoglobin gradually, the hemoglobin on the cotton fiber was effectively removed by the repetition of these process. The removal of hemoglobin was more effectively increased by adding both the enzyme and AOS in the washing solution. Therefore, it was regarded that AOS molecules were adsorbed at the hydrophobic surface of denatured hemoglobin, subsequently, decomposed more effectively cooperative binding of hemoglobin, and the fragments of hemoglobin were removed more efficiently by means of the interfacial reaction of AOS.

• Journal of Microbiology and Biotechnology
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• v.28 no.5
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• pp.671-678
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• 2018

Papiliocin, isolated from the swallowtail butterfly (Papilio xuthus), is an antimicrobial peptide with high selectivity against gram-negative bacteria. We previously showed that the N-terminal helix of papiliocin (PapN) plays a key role in the antibacterial and anti-inflammatory activity of papiliocin. In this study, we measured the selectivity of PapN against multidrug-resistant gram-negative bacteria, as well as its anti-inflammatory activity. Interactions between Trp2 of PapN and lipopolysaccharide (LPS), which is a major component of the outer membrane of gram-negative bacteria, were studied using the Trp fluorescence blue shift and quenching in LPS micelles. Furthermore, using circular dichroism, we investigated the interactions between PapN and LPS, showing that LPS plays critical roles in peptide folding. Our results demonstrated that Trp2 in PapN was buried deep in the negatively charged LPS, and Trp2 induced the ${\alpha}$-helical structure of PapN. Importantly, docking studies determined that predominant electrostatic interactions of positively charged arginine residues in PapN with phosphate head groups of LPS were key factors for binding. Similarly, hydrophobic interactions by aromatic residues of PapN with fatty acid chains in LPS were also significant for binding. These results may facilitate the development of peptide antibiotics with anti-inflammatory activity.

• The Plant Pathology Journal
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• v.35 no.6
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• pp.564-574
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• 2019

Like many fungal pathogens, the conidium and appressorium play key roles during polycyclic dissemination and infection of Magnaporthe oryzae. Ran-binding protein microtubule-organizing center (RanBPM) is a highly conserved nucleocytoplasmic protein. In animalia, RanBPM has been implicated in apoptosis, cell morphology, and transcription. However, the functional roles of RanBPM, encoded by MGG_00753 (named MoRBP9) in M. oryzae, have not been elucidated. Here, the deletion mutant ΔMorbp9 for MoRBP9 was generated via homologous recombination to investigate the functions of this gene. The ΔMorbp9 exhibited normal conidial germination and vegetative growth but dramatically reduced conidiation compared with the wild type, suggesting that MoRBP9 is involved in conidial production. ΔMorbp9 conidia failed to produce appressoria on hydrophobic surfaces, whereas ΔMorbp9 still developed aberrantly shaped appressorium-like structures at hyphal tips on the same surface, suggesting that MoRBP9 is involved in the morphology of appressorium-like structures from hyphal tips and is critical for development of appressorium from germ tubes. Taken together, our results indicated that MoRBP9 played a pleiotropic role in polycyclic dissemination and infection-related morphogenesis of M. oryzae.

• Bulletin of the Korean Chemical Society
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• v.35 no.8
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• pp.2523-2528
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• 2014

In the present study, at first, azo Schiff base ligand of (N,N'-bis(5-phenylazosalicylaldehyde)-ethylenediamine) ($H_2L$) has been synthesized by condensation reaction of 5-phenylazosalicylaldehyde and ethylenediamine in 2:1 molar ratio, respectively. Then, its cobalt complex (CoL) was synthesized by reaction of $Co(OAc)_2{\cdot}4H_2O$ with ligand ($H_2L$) in 1:1 molar ratio in ethanol solvent. This ligand and its cobalt complex containing azo functional groups were characterized using elemental analysis, $^1H$-NMR, UV-vis and IR spectroscopies. Subsequently, the interaction between native calf thymus deoxyribonucleic acid (ct-DNA) and CoL complex was investigated in 10 mM Tris/HCl buffer solution, pH = 7 using UV-vis absorption, thermal denaturation technique and viscosity measurements. From spectrophotometric titration experiments, the binding constant of CoL complex with ct-DNA was found to be $(2.4{\pm}0.2){\times}10^4M^{-1}$. The thermodynamic parameters were calculated by van't Hoff equation.The enthalpy and entropy changes were $5753.94{\pm}172.66kcal/mol$ and $43.93{\pm}1.18cal/mol{\cdot}K$ at $25^{\circ}C$, respectively. Thermal denaturation experiments represent the increasing of melting temperature of ct-DNA (about $0.93^{\circ}C$) due to binding of CoL complex. The results indicate that the process is entropy-driven and suggest that hydrophobic interactions are the main driving force for the complex formation.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.1
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• pp.51-55
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• 2016

Phytochemical investigation of Pistacia integerrima has highlighted isolation of two known compounds naringenin (1) and dihydrokaempferol (2). A crude extract and these isolated compounds were here evaluated for their effects on reversion of multidrug resistance (MDR) mediated by P-glycoprotein (P-gp). The multidrug resistance P-glycoprotein is a target for chemotherapeutic drugs from cancer cells. In the present study rhodamine-123 exclusion screening test on human mdr1 gene transfected mouse gene transfected L5178 and L5178Y mouse T-cell lymphoma cells showed excellent MDR reversing effects in a dose dependent manner. In-silico molecular docking investigations demonstrated a common binding site for Rhodamine123, and compounds naringenin and dihydrokaempferol. Our results showed that the relative docking energies estimated by docking softwares were in satisfactory correlation with the experimental activities. Preliminary interaction profile of P-gp docked complexes were also analysed in order to understand the nature of binding modes of these compounds. Our computational investigation suggested that the compounds interactions with the hydrophobic pocket of P-gp are mainly related to the inhibitory activity. Moreover this study s a platform for the discovery of novel natural compounds from herbal origin, as inhibitor molecules against the P-glycoprotein for the treatment of cancer.

• Parasites, Hosts and Diseases
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• v.46 no.4
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• pp.209-216
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• 2008

A monoclonal antibody against Toxoplasma gondii of Tg556 clone (Tg556) blotted a 29 kDa protein, which was localized in the dense granules of tachyzoites and secreted into the parasitophorous vacuolar membrane (PVM) after infection to host cells. A cDNA fragment encoding the protein was obtained by screening a T. gondii cDNA expression library with Tg556, and the full-length was completed by 5'-RACE of 2,086 bp containing an open reading frame (ORF) of 669 bp. The ORF encoded a polypeptide of 222 amino acids homologous to the revised GRA3 but not to the first reported one. The polypeptide has 3 hydrophobic moieties of an N-terminal stop transfer sequence and 2 transmembrane domains (TMD) in posterior half of the sequence, a cytoplasmic localization motif after the second TMD and an endoplasmic reticulum (ER) retrival motif in the C-terminal end, which suggests GRA3 as a type III transmembrane protein. With the ORF of GRA3, yeast two-hybrid assay was performed in HeLa cDNA expression library, which resulted in the interaction of GRA3 with calcium modulating ligand (CAMLG), a type II transmembrane protein of ER. The specific binding of GRA3 and CAMLG was confirmed by glutathione S-transferase (GST) pull-down and immunoprecipitation assays. The localities of fluorescence transfectionally expressed from GRA3 and CAMLG plasmids were overlapped completely in HeLa cell cytoplasm. In immunofluorescence assay, GRA3 and CAMLG were shown to be co-localized in the PVM of host cells. Structural binding of PVM-inserted GRA3 to CAMLG of ER suggested the receptor-ligand of ER recruitment to PVM during the parasitism of T. gondii.

• Bulletin of the Korean Chemical Society
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• v.29 no.5
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• pp.921-927
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• 2008

Discovery of $\alpha$-glucosidase inhibitors has been actively pursued with the aim to develop therapeutics for the treatment of diabetes and the other carbohydrate mediated diseases. As a method for the discovery of new novel inhibitors of $\alpha$-glucosidase, we have addressed the performance of the computer-aided drug design protocol involving the homology modeling of $\alpha$-glucosidase and the structure-based virtual screening with the two docking tools: FlexX and the automated and improved AutoDock implementing the effects of ligand solvation in the scoring function. The homology modeling of $\alpha$-glucosidase from baker’s yeast provides a high-quality 3-D structure enabling the structure-based inhibitor design. Of the two docking programs under consideration, AutoDock is found to be more accurate than FlexX in terms of scoring putative ligands to the extent of 5-fold enhancement of hit rate in database screening when 1% of database coverage is used as a cutoff. A detailed binding mode analysis of the known inhibitors shows that they can be stabilized in the active site of $\alpha$- glucosidase through the simultaneous establishment of the multiple hydrogen bond and hydrophobic interactions. The present study demonstrates the usefulness of the automated AutoDock program with the improved scoring function as a docking tool for virtual screening of new $\alpha$-glucosidase inhibitors as well as for binding mode analysis to elucidate the activities of known inhibitors.