• Journal of Microbiology and Biotechnology
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• v.24 no.7
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• pp.954-958
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• 2014

Succinic semialdehyde dehydrogenase (SSADH) catalyzes the oxidation of succinic semialdehyde (SSA) into succinic acid in the final step of ${\gamma}$-aminobutyric acid degradation. Here, we characterized Bacillus subtilis SSADH (BsSSADH) regarding its cofactor discrimination and substrate inhibition. BsSSADH showed similar values of the catalytic efficiency ($k_{ca}t/K_m$) in both $NAD^+$ and $NADP^+$ as cofactors, and exhibited complete uncompetitive substrate inhibition at higher SSA concentrations. Further analyses of the sequence alignment and homology modeling indicated that the residues of catalytic and cofactor-binding sites in other SSADHs were highly conserved in BsSSADH.

• Journal of Korean Society on Water Environment
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• v.33 no.3
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• pp.311-325
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• 2017

Habitat suitability index (HSI) of 17 benthic macroinvertebrate taxa, which were lotic insects of generic category except Potamanthidae in mayfly, was developed for three physical habitat factors (current velocity, water depth and substrate) based on an ecological monitoring in a Korean stream (Gapyeong). Weibull model was used as a probability density function to analyze the distribution of individual abundance related with physical factors, which showed it was so available. Number of species and total individual abundance increased along with the increase of current velocity and the mean diameter of substrate, and decreased along with the increase of water depth. Most taxa showed a clear preference for a fast current velocity, shallow water depth and coarse substrate except Ephemera, Potamanthidae (mayfly), and Plectrocnemia (caddisfly) which were rheophobic, potamophilic and lithophobious. Based on the canonical correspondence analysis, the relative importance of each factor was determined as follows: current velocity > substrate > water depth.

• KSII Transactions on Internet and Information Systems (TIIS)
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• v.10 no.2
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• pp.522-541
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• 2016

Network virtualization provides an effective way to overcome the Internet ossification problem. As one of the main challenges in network virtualization, virtual network embedding refers to mapping multiple virtual networks onto a shared substrate network. However, existing heuristic embedding algorithms evaluate the embedding potential of the nodes simply by the product of different resource attributes, which would result in an unbalanced embedding. Furthermore, ignoring the hops of substrate paths that the virtual links would be mapped onto may restrict the ability of the substrate network to accept additional virtual network requests, and lead to low utilization rate of resource. In this paper, we introduce and extend five node attributes that quantify the embedding potential of the nodes from both the local and global views, and adopt the technique for order preference by similarity ideal solution (TOPSIS) to rank the nodes, aiming at balancing different node attributes to increase the utilization rate of resource. Moreover, we propose a novel two-stage virtual network embedding algorithm, which maps the virtual nodes onto the substrate nodes according to the node ranks, and adopts a shortest path-based algorithm to map the virtual links. Simulation results show that the new algorithm significantly increases the long-term average revenue, the long-term revenue to cost ratio and the acceptance ratio.

• Korean Journal of Environmental Biology
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• v.39 no.3
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• pp.383-389
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• 2021

The Erythropeltidales are a common group of small, mostly epiphytic, marine red algae. However, they are little known in Korea. Many of the described species of Erythropeltidales differ subtly in morphology, and often the morphological differences are due to the substrate or environmental changes. Integration of molecular data with standardized culture conditions has been recommended to account for these algae. A Madagascaria species was first collected from the western coast of Korea and was identified as Madagascaria erythrocladioides based on the morphological and molecular characteristics. Morphological characteristics conformed well with its original description, and the phylogenetic analysis based on rbcL sequence showed Korean M. erythrocladioides nests in the same clade with the original species described in Japan with a genetic distance of 0.0-0.1%. This species was isolated from a red alga, Pterocladiella capillacea, in laboratory culture. The thallus ontogeny and host preference were examined by a co-culture with 13 different species of algae. Results showed a relatively broad host preference in mono-spore attachment and epiphyte development of Madagascaria erythrocladioides. Mono-spores of M. erythrocladioides attached to most of the red algal hosts' surfaces but no crustose thalli developed on some of the algal hosts even after one month of co-culture.

• Journal of Korean Society on Water Environment
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• v.34 no.1
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• pp.10-25
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• 2018

This study was conducted to estimate the habitat suitability of 17 benthic macroinvertebrate taxa in the Hwayang stream. Habitat Suitability Index (HSI) of benthic macroinvertebrates from the Hwayang stream was developed based on three physical habitat factors which include current velocity, water depth, and the substrate. The Weibull model was used as a probability density function to analyze the distribution of individual abundance by physical factors. The number of species and the total individual abundance increased along with the increase in current velocity. By means of Canonical Correspondence Analysis (CCA), the relative importance of each factor was determined in the following order: current velocity, water depth, and the mean diameter. The results depicted that, the most influential factor in the growth of benthic macroinvertebrates in the Hwavang system was current velocity. After comparing the analyzed results from the Hwayang stream with the resukts from the Gapyeong stream, the integrated HSI was drawn. The results indicated that current velocity and substrate had similar distributions of HSI in the two streams. This was due to the addition of unmeasured data from previous surveys, or the fact that benthic macroinvertebrates adapted to deeper waters in the Hwayang Stream. Most taxa showed a clear preference for a fast current velocity, deep water depth and coarse substrate except Baetiella, Epeorus, (mayflies), and Hydropsyche (caddisfly).

• Journal of Microbiology and Biotechnology
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• v.28 no.4
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• pp.597-605
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• 2018

Acyl-CoA oxidases (ACOXs) play important roles in lipid metabolism, including peroxisomal fatty acid ${\beta}$-oxidation by the conversion of acyl-CoAs to 2-trans-enoyl-CoAs. The yeast Yarrowia lipolytica can utilize fatty acids as a carbon source and thus has extensive biotechnological applications. The crystal structure of ACOX3 from Y. lipolytica (YlACOX3) was determined at a resolution of $2.5{\AA}$. It contained two molecules per asymmetric unit, and the monomeric structure was folded into four domains; $N{\alpha}$, $N{\beta}$, $C{\alpha}1$, and $C{\alpha}2$ domains. The cofactor flavin adenine dinucleotide was bound in the dimer interface. The substrate-binding pocket was located near the cofactor, and formed at the interface between the $N{\alpha}$, $N{\beta}$, and $C{\alpha}1$ domains. Comparisons with other ACOX structures provided structural insights into how YlACOX has a substrate preference for short-chain acyl-CoA. In addition, the structure of YlACOX3 was compared with those of medium- and long-chain ACOXs, and the structural basis for their differences in substrate specificity was discussed.

• Archives of Pharmacal Research
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• v.8 no.3
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• pp.149-157
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• 1985

The HCL hydrolyzate of the non-histone protein fractionated from the rat liver nuclei which have been incubated inthe presence of S-adenosyl-L-[methyl-$^{14}C$ ]-methionine shows at least four unidentified radioactive peaks on a basic amino acid analysis chromatogram. One of these unknown compounds (designated as compound 3) is also formed by the rat liver homogenated with the exogenous addition of an appropriate protein substrate. Since boiled rat liver homogenate or fresh homogenate in the absence of an exogenous protein substrate failed to form compound 3, its formation can be considered to be enzyme-catalyzed. The enzyme which yields compound 3 shows a preference of protein substrate in the order of reductively methylated hemoglobin > native > histone type II-A. The rat enzyme is nuclear in location associated with chromatin, and exhibits the highest activity in the liver among various rat organs. A compound 3-forming enzyme is also present in Neurospora crassa, since endogenous formation of the compound 3 can be demonstrated with the crude extract of this mold. The chemical identity of compound 3 is not yet known. However, it resisted to the following treatments; 6 N HCL and 0.1 N Na NaOH hydrolysis at $110^{\circ}C$, OR L-amino acid oxidase.

• Journal of Microbiology and Biotechnology
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• v.33 no.3
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• pp.387-397
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• 2023

Cytochrome P450 (CYP) is a heme-containing enzyme that catalyzes hydroxylation reactions with various substrate molecules. Steroid hydroxylases are particularly useful for effectively introducing hydroxyl groups into a wide range of steroids in the pharmaceutical industry. This study reports a newly identified CYP steroid hydroxylase (BaCYP106A6) from the bacterium Bacillus sp. and characterizes it using an in vitro enzyme assay and structural investigation. Bioconversion assays indicated that BaCYP106A1 catalyzes the hydroxylation of progesterone and androstenedione, whereas no or low conversion was observed with 11β-hydroxysteroids such as cortisol, corticosterone, dexamethasone, and prednisolone. In addition, the crystal structure of BaCYP106A6 was determined at a resolution of 2.8 Å to investigate the configuration of the substrate-binding site and understand substrate preference. This structural characterization and comparison with other bacterial steroid hydroxylase CYPs allowed us to identify a unique Arg295 residue that may serve as the key residue for substrate specificity and regioselectivity in BaCYP106A6. This observation provides valuable background for further protein engineering to design commercially useful CYP steroid hydroxylases with different substrate specificities.

• Journal of Microbiology and Biotechnology
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• v.20 no.12
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• pp.1653-1663
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• 2010

The first gene (${\alpha}$-gal1) encoding an extracellular ${\alpha}$-Dgalactosidase from the thermophilic fungus Talaromyces emersonii was cloned and characterized. The ${\alpha}$-gal1 gene consisted of an open reading frame of 1,792 base pairs interrupted by six introns that encoded a mature protein of 452 amino acids, including a 24 amino acid secretory signal sequence. The translated protein had highest identity with other fungal ${\alpha}$-galactosidases belonging to glycosyl hydrolase family 27. The ${\alpha}$-gal1 gene was overexpressed as a secretory protein with an N-terminal histidine tag in the methylotrophic yeast Pichia pastoris. Recombinant ${\alpha}$-Gal1 was secreted into the culture medium as a monomeric glycoprotein with a maximal yield of 10.75 mg/l and purified to homogeneity using Hisbinding nickel-agarose affinity chromatography. The purified enzyme was maximally active at $70^{\circ}C$, pH 4.5, and lost no activity over 10 days at $50^{\circ}C$. ${\alpha}$-Gal1 followed Michaelis-Menten kinetics ($V_{max}\;of\;240.3{\mu}M/min/mg,\;K_m\;of\;0.294 mM$) and was inhibited competitively by galactose ($K_m{^{obs}}$ of 0.57 mM, $K_i$ of 2.77 mM). The recombinant T. emersonii ${\alpha}$-galactosidase displayed broad substrate preference, being active on both oligo- and polymeric substrates, yet had strict specificity for the ${\alpha}$-galactosidic linkage. Owing to its substrate preference and noteworthy stability, ${\alpha}$-Gal1 is of particular interest for possible biotechnological applications involving the processing of plant materials.

• BMB Reports
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• v.32 no.1
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• pp.39-44
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• 1999

Pyruvate decarboxylase (PDC) catalyzes the conversion of pyruvate to acetaldehyde as the penultimate step in alcohol fermentation. The enzyme requires two cofactors, thiamin diphosphate (ThDP) and $Mg^{2+}$, for activity. Zymomonas mobilis PDC shows a strong preference for pyruvate although it will use the higher homologues 2-ketobutyrate and 2-ketovalerate to some extent. We have investigated the effect of mutagenesis of valine 111 and leucine 112 on the substrate specificity. V111 was replaced by glycine, alanine, leucine, and isoleucine while L112 was replaced by alanine, valine, and isoleucine. With the exception of L112I, all mutants retain activity towards pyruvate with $k_{cat}$ values ranging from 40% to 139% of wild-type. All mutants show changes from wild-type in the affinity for ThDP, and several (V111A, L112A, and L112V) show decreases in the affinity for $Mg^{2+}$. Two of the mutants, V111G and V111A, show an increase in the $K_m$ for pyruvate. The activity of each mutant towards 2-ketobutyrate and 2-ketovalerate was investigated and some changes from wild-type were found. For the V111 mutants, the most notable of these is a 3.7-fold increase in the ability to use 2-ketovalerate. However, the largest effect is observed for the L112V mutation which increases the ability to use both 2-ketobutyrate (4.3-fold) and 2-ketovalerate (5.7-fold). The results suggest that L112 and, to a lesser extent, V111 are close to the active site and may interact with the alkyl side-chain of the substrate.