• Proceedings of the Korea Information Processing Society Conference
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• 2005.11a
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• pp.15-18
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• 2005

A ribonucleic acid (RNA) is one of the two types of nucleic acids found in living organisms. An RNA molecule represents a long chain of monomers called nucleotides. The sequence of nucleotides of an RNA molecule constitutes its primary structure, and the pattern of pairing between nucleotides determines the secondary structure of an RNA. Non-coding RNA genes produce transcripts that exert their function without ever producing proteins. Predicting the secondary structure of non-coding RNAs is very important for understanding their functions. We focus on Nussinov's algorithm as useful techniques for predicting RNA secondary structures. We introduce a new traceback matrix and scoring table to improve above algorithm. And the improved prediction algorithm provides better levels of performance than the originals.

• Journal of Microbiology and Biotechnology
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• v.15 no.3
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• pp.656-659
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• 2005

Small peptides synthesized by nonribosomal peptide synthetases (NRPSs) genes are found in bacteria and fungi. While some microbial taxa have few, others make a large number and variety. However, biochemical characterization of the products synthesized by NPRS demands a great deal of efforts. Since the completion of genome projects of numerous microorganisms, the numbers of available NRPSs genes are being expanded. Prediction of the peptides encoded by NRPS could save time and efforts. We chose the NRPS gene from Bradyrhizobium japonicum as a model to predict the peptide structure encoded by NRPS genes. Using computational analyses, the domain structure of this gene was defined, and the structure of a peptide synthesized by this NRPS was deduced. It was found that it encoded a tripeptide consisting of proline-serine-phenylalanine. This method would be helpful to predict the structure of small peptides with various NPRS genes from the genome sequence.

• Bulletin of the Korean Chemical Society
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• v.24 no.9
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• pp.1256-1260
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• 2003

Two O-methyltransferases, OMTII-1 and OMTII-4 of meadow rue Thalictrum tuberosum showed a high sequence identity. Of 364 amino acids only one residue is not the same, which is Tyr21 or Cys21. Even if the 21st residues in these OMTs are not included in the binding sites of the enzymes, binding affinities of the enzyme homodimers over the same substrate are very different. While the binding affinity of one homodimer over caffeic acid is 100%, that of the other is 25%. Authors tried to predict the three-dimensional structures of Thalictrum tuberosum O-methyltransferases using homology-based modelling by a comparison with caffeic acid O-methyltransferase, and explain the reason of the phenomenon mentioned above based on their three dimensional structural studies. In the enzyme homodimer, the better binding affinity may be caused by the shorter distance between the 21st residue and the binding site of the other monomer.

• Bulletin of the Korean Chemical Society
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• v.30 no.8
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• pp.1839-1844
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• 2009

A 20-residue hybrid peptide CA(1-8)-MA(1-12) (CAMA) incorporating residues 1-8 of cecropin A (CA) and residues 1-12 of magainin 2 (MA) has high antimicrobial activity without toxicity. To investigate the effects of the total positive charges of CAMA on the antibacterial activity and toxicity, a hybrid peptide analogue (CAMA-syn) was designed with substitutions of $Ile^{10}\;and\;Ser^{16}$ with Lys. According to CD spectra, structure of CAMA-syn with increase of cationicity was very similar to that of CAMA in DPC micelle. CAMA-syn showed antimicrobial activity similar with CAMA while CAMA-syn has no hemolytic activity and much lower cytotoxicity against RAW 264.7 macrophage cells than CAMA. Also, CAMA and CAMA-syn significantly inhibited NO production by LPSstimulated RAW264.7 macrophage at 10.0∼20.0 $\mu$M. CAMA-syn displayed salt resistance on antimicrobial activity against Escherichia coli at the physiological concentrations of $CaCl_2\;and\;MgCl_2$. The combination studies of peptides and antibiotics showed that CAMA-syn has synergistic effects with synthetic compound and flavonoid against Enterococcus faecalis and VREF. CAMA-syn can be a good candidate for the development of new antibiotics with potent antibacterial and synergistic activity but without cytotoxicity.

• Food Science of Animal Resources
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• v.30 no.3
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• pp.359-364
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• 2010

Lactobacillus acidophilus A12 was isolated from chicken feces for use as an immunostimulating livestock probiotic. The purpose of this study was to optimize the production of L. acidophilus A12 using response surface methodology (RSM). Initially, the influence of growth medium was studied in terms of carbon sources (glucose, fructose, lactose, glycerol, sucrose, ethanol, and mannitol), nitrogen sources (beef extract, yeast extract, malt extract, and tryptone), and inorganic salts ($CaCl_2$, $MgSO_4$, $KH_2PO_4$, $(NH_4)_2SO_4$, $FeSO_4$, and NaCl). Through one factor-at-a time experiment, lactose, yeast extract, and $CaCl_2$ were determined to be the best sources of carbon, nitrogen, and inorganic salt, respectively. The optimum composition was found to be 17.7 g/L lactose, 18.6 g/L yeast extract, and 0.9 g/L $CaCl_2$. Under these conditions, a maximum cell density of 9.33 Log CFU/mL was produced, similar to the predicted value.

• Bulletin of the Korean Chemical Society
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• v.35 no.9
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• pp.2787-2790
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• 2014

Quercetin is a major dietary flavonoid found in onions, apples, tea, and red wine, and potentially has beneficial effects on disease prevention. We carried out this study to investigate the effect of quercetin on UVB-induced matrix metalloproteinase-1 (MMP-1) expression in human keratinocyte HaCaT cells and to further understand the mechanisms of its action. The anti-inflammatory activity of quercetin was investigated and quercetin significantly suppressed the NO production in LPS-stimulated RAW264.7 mouse macrophages. Post treatment of quercetin decreased UV irradiation-induced phosphorylation of JNK, p38 MAPK, and ERK by 91%, 21%, and 17%, respectively. MMP-1 is mainly responsible for the degradation of dermal collagen during the aging process of human skin and quercetin suppressed the UVB-induced MMP-1 by 94%. Binding studies revealed that quercetin binds to p38 with high binding affinity ($1.85{\times}10^6M^{-1}$). The binding model showed that the 4'-hydroxy groups of the B-ring of quercetin participated in hydrogen bonding interactions with the side chains of Lys53, Glu71, and Asp168 and the 5-hydroxy group of the A-ring formed a hydrogen bond with the backbone amide of Met109. The major finding of this study shows that quercetin inhibits phosphorylation of JNK, p38 MAPK, and ERK pathway leading to the prevention of MMP-1 expression in human keratinocyte HaCaT cells. Therefore, our findings suggested the potentials of quercetin as a skin anti-photoaging agent.

• Journal of Microbiology and Biotechnology
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• v.25 no.5
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• pp.589-597
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• 2015

It has been reported that overexpression of MUC5AC induced by excessive inflammation leads to airway obstruction in respiratory diseases such as chronic obstructive pulmonary disease and asthma. 15-Hydroxyeicosatetraenoic acid (15-HETE) has been reported to have anti-inflammatory effects, but the role of 15-HETE in respiratory inflammation has not been determined. Therefore, the aim of this study was to investigate the effects of 15-HETE on MUC5AC expression and related pathways. In this study, phorbol-12-myristate-13-acetate (PMA) was used to stimulate NCI-H292 bronchial epithelial cells in order to examine the effects of 15-HETE. 15-HETE inhibited PMA-induced expression of MUC5AC mRNA and secretion of MUC5AC protein. Moreover, 15-HETE regulated matrix metallopeptidase 9 (MMP-9), mitogen-activated protein kinase kinase (MEK), and extracellular signal-regulated kinase (ERK). In addition, 15-HETE decreased the nuclear translocation of specificity protein-1 (Sp-1) transcription factor and nuclear factor κB (NF-κB). Furthermore, 15-HETE enhanced the transcriptional activity of peroxisome proliferator-activated receptor gamma (PPARγ) as a PPARγ agonist. This activity reduced the phosphorylation of protein kinase B (PΚB/Akt) by increasing the expression of phosphatase and tensin homolog (PTEN). In conclusion, 15-HETE regulated MUC5AC expression via modulating MMP-9, MEK/ERK/Sp-1, and PPARγ/PTEN/Akt signaling pathways in PMA-treated respiratory epithelial cells.

• Bulletin of the Korean Chemical Society
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• v.32 no.8
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• pp.2695-2699
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• 2011

${\beta}$ Ketoacyl acyl carrier protein synthase III (KAS III) initiates fatty acid synthesis in bacteria and is a key target enzyme to overcome the antibiotic resistance problem. In our previous study, we found flavonoid inhibitors of Enterococcus faecalis KAS III and proposed three potent antimicrobial flavonoids against Enterococcus faecalis and Vancomycin-resistant Enterococcus faecalis with MIC values in the range of 128-512 ${\mu}g/mL$ as well as high binding affinities on the order from $10^6$ to $10^7\;M^{-1}$. Using these series of flavonoids, we conducted biological assays as well as docking study to find potent flavonoids inhibitors of Staphylococcus aureus KAS III with specificities against Staphylococcus aureus and Methicillin-resistant Staphylococcus aureus. Here, we propose that naringenin (5,7,4'-trihydroxyflavanone) and eriodictyol (5,7,3',4'-tetrahydroxyflavanone) are potent antimicrobial inhibitors of Staphylococcus aureus KAS III with binding affinity of $3.35{\times}10^5$ and $2.01{\times}10^5\;M^{-1}$, respectively. Since Arg38 in efKAS III is replaced with Met36 in saKAS III, this key difference caused one hydrogen bond missing in saKAS III compared with efKAS III, resulting in slight discrepancy in their binding interactions as well as decrease in binding affinities. 4'-OH and 7-OH of these flavonoids participated in hydrogen bonding interactions with backbone carbonyl of Phe298 and Ser152, respectively. In particular, these flavonoids display potent antimicrobial activities against various MRSA strains in the range of 64 to 128 ${\mu}M$ with good binding affinities.

• Journal of Microbiology and Biotechnology
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• v.20 no.3
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• pp.494-500
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• 2010

Bacterial blight, an important and potentially destructive bacterial disease in rice, is caused by Xanthomonas oryzae. Recently, this organism has developed resistance to available antibiotics, prompting scientists to find a suitable alternative. This study focused on secondary metabolites of Phomopsis longicolla to target X. oryzae. Five bioactive compounds were isolated by activity-guided fractionation from ethyl acetate extracts of mycelia and were identified by LC/MS and NMR spectroscopy as dicerandrol A, dicerandrol B, dicerandrol C, deacetylphomoxanthone B, and fusaristatin A. This is the first time fusaristatin A has been isolated from Phomopsis sp. Deacetylphomoxanthone B showed a higher antibacterial effect against X. oryzae KACC 10331 than the positive control (2,4-diacetyphloroglucinol). Dicerandrol A also showed high antimicrobial activity against Gram-positive bacteria (Staphylococcus aureus, Bacillus subtilis) and yeast (Candida albicans). In addition, high production yields of these compounds were obtained at the stationary and death phases.

• Bulletin of the Korean Chemical Society
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• v.35 no.1
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• pp.39-44
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• 2014

Glass discs functionalized with alkynyl (GDA) terminated monolayers were prepared and incubated in $AgNO_3$ solution (GDA-Ag). The modified functional glass surfaces were characterized by X-ray photoelectron microscopy (XPS). The potential of GDA and GDA-Ag as antimicrobial surfaces was investigated. Anti-microbial efficacies of GDA against Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, Bacillus cereus, and Candida albicans was relatively low ranging from 4.67 to 17.00%. However, the GDA-Ag was very effective and its antimicrobial efficacy ranged from 99.90 to 99.99% against the same set of microbial strains except for C. albicans where it was 95.50%. The durability of the Ag bonded to the terminal alkynyl groups was studied by placing the GDA-Ag in PBS buffer solution (pH 7.4) for two weeks. Initially, the silver release was relatively fast, with 40.05 ppb of silver released in first 24 h followed by a very slow and constant release. To study the potential of GDA-Ag for medical applications, in vitro cytotoxicity of GDA-Ag against Human Embryonic Kidney 293 (HEK293) cell lines was studied using WST-assay. The cytotoxicity of the GDA-Ag was very low (5%) and was almost comparable to the control (blank glass disc) indicating that GDA-Ag has a promising potential for medical applications.