• Journal of Microbiology and Biotechnology
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• v.26 no.12
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• pp.2019-2029
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• 2016

Zinc finger proteins are among the most extensively applied metalloproteins in the field of biotechnology owing to their unique structural and functional aspects as transcriptional and translational regulators. The classical zinc fingers are the largest family of zinc proteins and they provide critical roles in physiological systems from prokaryotes to eukaryotes. Two cysteine and two histidine residues ($Cys_2His_2$) coordinate to the zinc ion for the structural functions to generate a ${\beta}{\beta}{\alpha}$ fold, and this secondary structure supports specific interactions with their binding partners, including DNA, RNA, lipids, proteins, and small molecules. In this account, the structural similarity and differences of well-known $Cys_2His_2$-type zinc fingers such as zinc interaction factor 268 (ZIF268), transcription factor IIIA (TFIIIA), GAGA, and Ros will be explained. These proteins perform their specific roles in species from archaea to eukaryotes and they show significant structural similarity; however, their aligned amino acids present low sequence homology. These zinc finger proteins have different numbers of domains for their structural roles to maintain biological progress through transcriptional regulations from exogenous stresses. The superimposed structures of these finger domains provide interesting details when these fingers are applied to specific gene binding and editing. The structural information in this study will aid in the selection of unique types of zinc finger applications in vivo and in vitro approaches, because biophysical backgrounds including complex structures and binding affinities aid in the protein design area.

• Journal of Microbiology and Biotechnology
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• v.24 no.7
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• pp.925-935
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• 2014

A cold-adapted carbohydrate esterase, CEST, belonging to the carbohydrate esterase family 6, was cloned from Microbulbifer thermotolerans DAU221. CEST was composed of 307 amino acids with the first 22 serving as a secretion signal peptide. The calculated molecular mass and isoelectric point of the mature enzyme were 31,244 Da and pH 5.89, respectively. The catalytic triad consisted of residues Ser37, Glu192, and His281 in the conserved regions: GQSNMXG, QGEX(D/N), and DXXH. The three-dimensional structure of CEST revealed that CEST belongs to the ${\alpha}/{\beta}$-class of protein consisted of a central six-stranded ${\beta}$-sheet flanked by eight ${\alpha}$-helices. The recombinant CEST was purified by His-tag affinity chromatography and the characterization showed its optimal temperature and pH were $15^{\circ}C$ and 8.0, respectively. Specifically, CEST maintained up to 70% of its enzyme activity when preincubated at $50^{\circ}C$ or $60^{\circ}C$ for 6 h, and 89% of its enzyme activity when preincubated at $70^{\circ}C$ for 1 h. The results suggest CEST belongs to group 3 of the cold-adapted enzymes. The enzyme activity was increased by $Na^+$ and $Mg^{2+}$ ions but was strongly inhibited by $Cu^+$ and $Hg^{2+}$ ions, at all ion concentrations. Using p-nitrophenyl acetate as a substrate, the enzyme had a $K_m$ of 0.278 mM and a $k_{cat}$ of $1.9s^{-1}$. Site-directed mutagenesis indicated that the catalytic triad (Ser37, Glu192, and His281) and Asp278 were essential for the enzyme activity.

• Journal of the Korean Society of Food Science and Nutrition
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• v.45 no.9
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• pp.1293-1301
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• 2016

Hulled oat (Chohan) and naked oat (Choyang) flours were analyzed according to particle size to investigate nutritional components and physicochemical properties. Particle size of naked oat flours was larger than that of hulled oat flours. As the mesh of the crushed ones decreased, particle sizes increased in value. The content of total ${\beta}$-glucan was highest in hulled oat flour (4.23%) with 60 mesh and in naked oat flour (4.26%) with 100 mesh. Most total ${\beta}$-glucan was soluble ${\beta}$-glucan in both flours (over 76%). Total starch of hulled oat flours (63.64~69.82%) was higher than that of naked oat flours (52.45~63.71%). Whereas amylose contents showed a negative correlation with total starch contents. Contents of free amino acids increased according to particle size, and each component was dependent on each type of amino acid. Moreover, while fatty acid composition was not significant, the content of most naked oats was higher than that of hulled oats. Besides, the ratio of unsaturated fatty acids (oleic acid and linoleate) in both types of oat flours was relatively higher than that of other grains. The pasting properties of peak viscosity, trough, and breakdown showed the highest value in both oats with 100 mesh. Further, the values of final viscosity and the setback were higher with relatively larger particle size. In addition, peak time exhibited a lower value with larger particle size, whereas it showed the opposite value for pasting temperature. Starch digestibility did not show any specific trend according to particle size, whereas expected glycemic index of hulled oats was lower than that of naked oats. Moreover, lower values were investigated at larger particle sizes. The results of this study provide basic useful information for processing of oat products to improve consumption of oats grown in Korea.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.29 no.1
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• pp.51-63
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• 1996

In order to investigate the food quality of Korean chum salmon (Oncorhynchus keta) the composition of extractive nitrogenous components including the free amino acids, oligopeptides, nucleotides and related compounds, guanidino compounds, and quaternary ammonium bases were analyzed. The extractive nitrogen from the muscle ranged from 478 to 649 mg/100 g with little discrepancies by sex, sampling seasons and areas. The large amount of anserine was noted with fairly low level of taurine, alanine, glycine, glutamic acid and lysine in each extract. After Hydrolysis of the entracts remarkable increases were found in $\pi-methylhistidine,\;\beta-alanine$ from anserine and carnosine. The sum of nucleotides and related compounds of the muscle was $3.32\~9.22\;{\mu}mol/g$, and predominant compound was the inosine 5'-monophosphate. The lower glycinebetaine, $\beta-alaninebetaine$ and homarine were also found in some samples. The trimethylamine oxide content of the muscle was ranged from 107 to 148 mg, and the trimethylamine content was no move than 11 mg in all the collections. The concentrations of creatine in the muscle extracts ranged from 477 to 642 mg, and $8\~11mg$ for creatinine, respectively. The total nitrogens of the compounds analyzed for each samples accounted for more than $90\%$ of the extractive nitrogen in this study.

• KSBB Journal
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• v.23 no.5
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• pp.425-430
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• 2008

Hydrogen sulfide ($H_2S$) is a by-product of metabolism of amino acids including sulfur and alcoholic fermentation, it is generally thought of in terms of a poisonous gas. Though $H_2S$ can have a negative impact on the perceived quality of fermented drinks due to an undesirable aroma, it plays prominent roles as a neuromodulator in the mammalian brain as well as a smooth muscle relaxant. Nowadays studies on the proteins which produce $H_2S$ are carried out in various fields such as structure, function, and metabolism. Here we propose to develop a simple and rapid $H_2S$ forming assay method, which will lead to speed up preparing the $H_2S$ forming proteins for identification by MALDI-TOF MS analysis. We detected three kinds of proteins which produce $H_2S$ in the crude extract of Saccharomyces cerevisiae. Those proteins were cystathionie $\beta$-synthase, O-acetylserine sulfhydrylase, and cystathionine $\gamma$-lyase.

• Korean Journal of Microbiology
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• v.46 no.1
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• pp.38-45
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• 2010

The study performed to identify the type of ESBL against strains which are producing extendedspectrum ${\beta}$-lactamases and isolated from sewage in Suyeong sewage disposal plant, Busan Environmental Corporation. By the standard activated sludge method, Suyeong sewage disposal plant purify living and lavatory sewage gathering from the northeast Busan and the facility purify total 550,000 tons of living sewage disposal a day. 14 strains were isolated by double disk synergy test and the third generation cepha-antibiotics test. Indole, methyl-red, Voges-Proskauer, Simmon's citrate, decarboxylasedihydrolase and sugar-fermentation tests identified as Klebsiella pneumoniae (n=4) and Escherichia coli (n=10). Plasmid-mediated transmission test against isolated 14 strains proved 11 strains transmitted resistance to recipient E. coli J53 (sodium $azide^R$, $ceftazidime^S$). 9 strains of conjugant were expressed ESBL genes transferred from parental strain but 2 conjugants did not expressed. The type of ESBL from each strain was determined by isoelectric focusing points, DNA and amino acids sequencing. The results indicated that the types of ESBL transmitted to recipient E. coli J53 were TEM-1, the parental TEM type and SHV-12 type.

• Journal of Web Engineering
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• v.14 no.19
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• pp.4103-4118
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• 2022

The physiological or dietary advantages of germinated grains have been the subject of numerous discussions over the past decade. Around 23 million tons of oats are consumed globally, making up a sizeable portion of the global grain market. Oat seedlings contain more protein, beta-glucan, free amino acids, and phenolic compounds than seeds. The progressive neurodegenerative disorder of Alzheimer's is accompanied by worsening memory and cognitive function. A key indicator of this disorder is the unusual buildup of amyloid-beta protein (or Aβ) in human brains. In this context, oat seedling extract (OSE) has been identified as a new therapeutic candidate for AD, due to its antioxidant activity and AD-specific mechanism of action. This study directly investigated how OSE affected AD and its impacts by examining the cognitive function and exploring the inflammatory response mechanism. The dried oat seedlings were grounded finely with a grinder, inserted with 50% fermented ethanol 10 times (w/v), and extracted by stirring for 10 h at 45 ℃. After filtering the extract by 0.22 um filter, some of it was used for UHPLC analysis. The results indicated that the treatment with OSE protects against Aβ25-35-induced cytotoxicity in BV2 cells. Tg-5Xfad AD mice had strong deposition of Aβ throughout their brains, while WT mice did not exhibit any such deposition within their brains. A drastic reduction was observed in terms of numbers, as well as the size, of Aβ plaques within Tg-5Xfad AD mice exposed to OSE. This study indicated OSE's neuroprotective impacts against neurodegeneration, synaptic dysfunction, and neuroinflammation induced by amyloid-beta. Our results suggest that OSE acts as a neuroprotective agent to combat AD-specific apoptotic cell death, neuroinflammation, amyloid-beta accumulation, as well as synaptic dysfunction in AD mice's brains. Furthermore, the study indicated that OSE treatment affects JNK/ERK/p38 MAPK signaling, with considerable inhibition in p-JNK, p-p38, and p-ERK levels seen in the brain of OSE-treated Tg-5Xfad AD mice.

• Journal of Mushroom
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• v.18 no.2
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• pp.151-163
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• 2020

Antioxidant activities and contents of β-glucan and amino acids of wild mushrooms collected from Geosan, Boeun, Eumseong, and Bonghwa in Korea were investigated. Phaeolus schweinitzii (OK1165) displayed the highest 2,2-diphenyl-1-picrylhydrazyl radical scavenging activity (60.3%), ferric reducing antioxidant power (3.84), reducing power (1.05), nitrite scavenging activity (96.4%), total polyphenol content (54.7 mg gallic acid equivalent/g), and flavonoid content (19.98 mg quercetin equivalent/g). The β-glucan content of Pycnoporus cinnabarinus (OK1172) of 51.9% was higher than the contents of the other mushrooms. P. schweinitzii (OK1165) displayed the highest total amino acid (1,373.9 mg/kg) and essential amino acid (515.0 mg/kg) contents among the wild mushrooms. The findings confirmed that wild mushrooms could be a high-value resource for functional foods with pronounced antioxidant activity. The results also provide fundamental data for extracting useful compounds from wild mushrooms.

• Asian-Australasian Journal of Animal Sciences
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• v.22 no.5
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• pp.681-685
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• 2009

L-carnitine promotes mitochondrial ${\beta}$-oxidation of long chain fatty acids and their subsequent transport across the inner mitochondrial membrane. Although the role of L-carnitine in fatty acid metabolism has been extensively studied, its role in live performance and carcass responses of commercial broilers is less understood. The objective of this research was to determine if Lcarnitine fed at various levels in diets differing in CP and amino acids impacted on live performance and carcass characteristics of commercial broilers. Two floor pen experiments were conducted to assess the effect of dietary L-carnitine in grower diets. In Exp. 1, Ross${\times}$Hubbard Ultra Yield broilers were placed in 48 floor pens (12 birds/pen) and fed common diets to d 14. A two (0 or 50 ppm Lcarnitine) by three (173, 187, and 202 g/kg CP) factorial arrangement of treatments was employed from 15 to 35 d of age (8 replications/treatment). An interaction (p<0.05) in carcass yield indicated that increasing CP (187 g/kg) resulted in improved yield in the presence of L-carnitine. Increasing CP from 173 to 202 g/kg increased (p<0.05) BW gain and decreased (p<0.05) feed conversion and percentage abdominal fat. Feeding dietary L-carnitine increased back-half carcass yield which was attributable to an increase (p<0.05) in thigh, but not drumstick, yield relative to carcass. In Exp. 2, $Ross{\times}Ross$ 708 broilers were fed common diets until 29 d. From 30 to 42 d of age, birds were fed one of seven diets: i) 200 g/kg CP, 0 ppm L-carnitine; ii) 200 g/kg CP, 40 ppm L-carnitine; iii) 180 g/kg CP, 0 ppm L-carnitine; iv) 180 g/kg CP, 10 ppm L-carnitine; v) 180 g/kg CP, 20 ppm L-carnitine; vi) 180 g/kg CP, 30 ppm L-carnitine; and vii) 180 g/kg CP, 40 ppm L-carnitine (6 replications of 12 birds each). BW gain, feed conversion, mortality (30 to 42 d), and carcass traits (42 d) were measured on all birds by pen. There were no treatment differences (p<0.05). However, the addition of 40 ppm L-carnitine in the 200 g CP/kg diet increased (p = 0.06) thigh yields relative to BW in comparison to birds fed diets without L-carnitine, which was further confirmed via a contrast analysis (0 vs. 40 ppm L-carnitine in the 200 and 180 g CP/kg diets; p<0.05). These results indicated that dietary L-carnitine may heighten metabolism in dark meat of commercial broilers resulting in increased relative thigh tissue accretion without compromising breast accretion.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.41 no.6
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• pp.427-434
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• 2008

Processing of collagen from yellowfin tuna (Thunnus albacares) abdominal skins was optimized by response surface methodology and central composite design. The values of independent variables at optimal conditions were NaOH concentration: 0.5 N, NaOH treatment time: 36.2 hr, pepsin concentration: 1:4.9 ratio (0.245%, w/v), and digestion time: 48.1 hr, respectively. The collagen content estimated under optimal conditions was 33.1%, and the actual experimental collagen content was 32.3%. Physicochemical properties of collagen from yellowfin tuna abdominal skin were investigated by amino acids analysis, SDS-PAGE, FT-IR, viscosity and denaturation temperature. Amino acids content of the collagen was 21.0%. SDS-PAGE pattern of the collagen showed two different $\alpha$-chain (${\alpha}_1$- and ${\alpha}_2$- chain), $\beta$-component and $\gamma$-component. The spectrum of FT-IR of the collagen showed wavenumber at 3,434, 1,650, 1,542 and $1,235\;cm^{-1}$ representing the regions of amide A, I, II and III, respectively. Relative viscosity of the collagen decreased continuously on heating up to $32^{\circ}C$, and the rate of decrease was retarded in the temperature range of $35-50^{\circ}C$. Denaturation temperature (Td) of the collagen solution (0.06%, w/v) was $31^{\circ}C$ and was lower than calf skin collagen ($35^{\circ}C$).