• KSBB Journal
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• v.19 no.1
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• pp.42-49
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• 2004

A gene coding for epoxide hydrolase (EH) of Aspergillus niger LK, a fungus possessing the enantioselective hydrolysis activity for racemic epoxides, was characterized by phylogenetic analysis. The deduced protein of A. niger LK epoxide hydrolase shares significant sequence similarity with several bacterial EHs and mammalian microsomal EHs (mEH) and belongs to the a/${\beta}$ hydrolase fold family. EH from A. niger LK had 90.6% identity with 3D crystal structure of lqo7 in Protein Data Bank. Sequence comparison with other source EHs suggested that Asp$\^$l92/, Asp$\^$374/ and His$\^$374/ constituted the catalytic triad. Based on the multiple sequence comparison of the functional and structural domain sequence, the phylogenetic tree between relevant epoxide hydrolases from various species were reconstructed by using Neighbor-Joining method. Genetic distances were so far as 1.841-2.682 but characteristic oxyanion hole and catalytic triad were highly conserved, which means they have diverged from a common ancestor.

• Analytical Science and Technology
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• v.13 no.4
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• pp.494-503
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• 2000

A 21-residue peptide corresponding to amino acids 84-104 of $p16^{INK4A}$, the tumor suppressor, has been synthesized and its structure was studied by Circular Dichroism, $^1H$ NMR spectroscopy and molecular modeling. A p16-derived peptide (84-104 amino acids) forming stable complex with CDK4 and CDK6 inhibits the ability of CDK4/6 to phosphorylate pRb in vitro, and blocks cell-cycle progression through G1/S phase as shown in the function of the full-length p16. Its NMR spectral data including NOEs, $^3J_{NH-H{\alpha}}$ coupling constants, $C_{\alpha}H$ chemical shift, the average amplitude of amide chemical shift oscillation and temperature coefficients indicate that the secondary structure of a p16-derived peptide is similar to that of the same region of full-length p16, which consists of helix-turn-helix structure. The 3-D distance geometry structure based on NOE-hased distance and torsion angle restraints is characterized by ${\gamma}$-turn conformation between residues $Gly^{89}-Leu^{91}$(${\varphi}_{i+1}=-79.8^{\circ}$, ${\varphi}_{i+1}=60.2^{\circ}$) as evidenced in a single crystal structure for the corresponding region of p18 or p19, but is undefined at both the N and C termini. This compact and rigid ${\gamma}$-turn region is considered to stabilize the structure of p16-derived peptide and serve as a site recognizing cyelin dependent kinase, and this well-defined ${\gamma}$-turn structure could be utilized for the design of anti-cancer drug candidates.

• Proceedings of the Korean Society for Information Management Conference
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• 2013.08a
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• pp.11-14
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• 2013

본 연구의 목적은 바이오인포매틱스 분야의 회색문헌과 백색문헌의 초록을 대상으로 단어 동시출현(word co-occurrence)네트워크 분석을 통해 해당 분야의 연구 동향을 비교 분석하고자 하였다. 이를 위해 2010년부터 2012년까지 발표된 회색문헌인 회의자료(proceeding)와 백색문헌인 학술논문(journal article)의 초록을 SCOPUS, IEEEXplore, Microsoft academic search에서 수집하였다. 단어 동시출현 네트워크를 분석한 결과 회색문헌의 주요 연구는 분석도구 및 방법으로, 백색문헌의 주요 연구는 바이오인포매틱스의 주요 연구대상인 유전자 발현, 단백질 서열 및 구조 등으로 나타났다.

• Journal of the Korean Chemical Society
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• v.42 no.2
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• pp.143-149
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• 1998

When anesthetics were added to a bacteriorhodopsin (bR) in the purple membranes, the 570 nm absorption band shifts to 480 nm. This anesthetic-induced spectroscopic change is reversible. The apparent pKa (6.3) of this equilibrium depends on the nature of the anesthetics in which bR is dispersed. The electric orientation measurements showed that the native bR is easily achieved by relatively small electric field which is oriented at $60^\circ$, while anesthetic-treated bR is not the case. These results demonstrate that the subtle changes in the chromophore and the protein structure surrounding the chromophore by anesthetics influence the spatial orientation of the charged residues in the protein matrix surrounding chromophore.

• Applied Biological Chemistry
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• v.38 no.1
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• pp.49-54
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• 1995

To understand the molecular structure and pathogenesis mechanism of Korean garlic viruses, we have isolated cDNA clones for garlic viruses. The partial nucleotide sequences of 24 cDNA clones were determined and those of five clones containing poly(A) tail were compared with sequences of other plant viruses. One of these clones, V9, has a primary structure similar to the carlavirus group, suggesting that the clone V9 derived from a part of garlic latent virus (GLV). Northern blot analysis with the clone V9 as a probe demonstrated that GLV genome is 8.5 knt long and has a poly(A) tail. The clone V9 encodes coat protein (CP) of 33 kDa and nucleic acid binding protein of 10 kDa in different reading frame. The hexanucleotide motif, 5'-ACCUAA, which is conserved in the 3' noncoding region arid was proposed to be a cis-acting element involved in the production of negative strand genomic RNA was noticed. Complementary sequence to the hexanucleotide motif, 5'-TTAGGT, is also found in the positive strand of V9 RNA. The putative CP gene was cloned into the pRSET-A expression vector and expressed in E. coli BL21. The expressed recombinant V9CP protein was purified by $Ni^{2+}$ NTA affinity chromatography. The anti-V9CP antibody recognizes 34 kDa polypeptide which could be CP of GLV in infected garlic leaf extract. Immunoblot and Northern blot analysis of various cultivars shows wide occurrence of GLV in Korean garlic plants.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.22 no.4
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• pp.483-492
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• 2021

Agastachis Herba (AH) to treat anorexia and nausea and its antidiabetic efficacy was recently reported. This study examined the antioxidant activities and chemical constituents of AH and predicted the target proteins of each compound using in silico approaches. The results showed that EC50 values of AH methanol extract for DPPH and ABTS radical scavenging were 78.6 ㎍/mL and 31.0 ㎍/mL, respectively. Compared to the EC50 values of ascorbic acid (9.9 ㎍/mL, 5.2 ㎍/mL), the AH methanol extract possessed excellent antioxidant activities. Rosmarinic acid, tilianin, agastachoside, and acetin were confirmed as the major compounds of extracts by qualitative analysis performed with HPLC-PDA-MS/MS. The antidiabetic target proteins of these compounds were predicted by applying a structural similarity and inverse docking methodology using a DIA-DB server. The resulting target proteins were PPAR-γ, DPP IV, glucokinase, α-glucosidase, SGLT2, aldose reductase, and corticosteroid 11-beta-dehydrogenase, some of which have already been proven experimentally as target proteins. Therefore, the in silico methods can be considered valid. Finally, AH were extracted with various solvents to determine the optimal conditions for the extraction of active components. Methanol among organic solvents and 80% ethanol in ethanol-water mixtures were identified as the most effective solvent for the extraction.

• Journal of Life Science
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• v.12 no.3
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• pp.264-273
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• 2002

We have isolated and artificially expressed three cDNA clones of Capsicum annuum PR5 genes for elucidating the antifungal activity against Phytophthora capsici which contracted a hot pepper root rot in field condition. Three divergent PR5 proteins from hot pepper were designated as CAPR5-1 and CAPR5-2 from susceptible cultivar (Subicho) as well as CAPR5-3 from resistant cultivar (CM331) in response to P. capsici. The cDNA similarity was found over 80% of identity among the three CAPR5s, and deduced amino acid sequence was characterized that all of CAPR5s contained 16 cysteine residues which possibly had a significant role in the structural formation. The result of genomic DNA blot showed that CAPR5-1 and CAPR5-2 existed as single copy in the Subicho genome. Three recombinant CPARs in E. coli were identified by SDS-PACE, and each expressed protein was treated on the PDA medium which contained cultured pathogens. Although three CAPR5 proteins did not affected the hyphal growth of Glomerella glycines and Colletotrichum fagenarium, CAPR5-1, CAPR5-2, and CAPR5-3 showed a specific antifungal activities against P. capsici.

• Journal of Radiation Protection and Research
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• v.22 no.1
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• pp.23-27
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• 1997

Radiation effects on carbohydrate moiety of chicken ovomucoid, a protease inhibitor as a typical allergenic glycoprotein of egg white, was observed. The trypsin inhibitory activity of chicken ovomucoid decreased exponentially and the inactivation was more significant irradiated in $N_2$ than in $O_2$. From the protein blotting, radiation caused protein degradation in $O_2$ and protein aggregation also in $N_2$. The patterns of carbohydrate blotting were also similar with that of protein blotting. Sugar chains in low molecular weight fraction (MW<5,000) were released by radiation and those in $O_2$ were higher than in $N_2$. From the HPLC patterns of the degradation of sugar chains, all peaks of oligosaccharides have the tendency to decrease with the increase of radiation dose and more remarkable in $O_2$ than in $N_2$. These results suggest that ionising radiation could cause the overall conformational changes of ovomucoid by the degradation and release of oligosaccharides.

• Microbiology and Biotechnology Letters
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• v.17 no.6
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• pp.539-544
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• 1989

Campylobacter jejuni, bacterial agent causing human diarrhea, were studied for their disinfection effects with chlorine and monochloramine. The cells treated with the chemical agents were observed by scanning electron microscopy to know their morphological and structural changes. The proteins and DNA in the chemical-treated cells were also examined by gel electrophoresis for structural changes. When C. jejuni were chlorinated at concentrations of 0.5 and 1.0 mg/l for 15 minutes, the organisms were disinfected by 4 and 6 log, respectively. Those disinfection effects were higher at acidic pH, while lowered at neutral and alkaline values of pH. The effects of monochloramine were lower than those of chlorine at the game concentration for the same period of reaction time. The shapes of C. jejuni cells treated with the agents appeared to be deformed from spiral rod into spherical forms, showing some destruction in surface structure of the cells. Some of the proteins and DNA of the chlorinated cells did not appear in the gel electrophoresis when the chlorination was at concentration of 10 mg/l or higher.

• Journal of Life Science
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• v.32 no.8
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• pp.659-665
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• 2022

Chlorella vulgaris is an important freshwater alga that is widely used as a food source by humans and animals. Recently, Chlorella has received considerable attention with regard to its potential application in aquaculture and the production of biofuels, nutrients, and therapeutic proteins. Recently, our laboratory acquired a new strain of C. vulgaris, PKVL7422, characterized by fast growth, ease of culture, and cultivability under dark conditions. However, the genes involved in its nitrogen assimilation are unknown. In this work, we identified the nitrate reductase (NR) gene of C. vulgaris PKVL7422 using rapid amplification of cDNA ends and genome walking. The NR gene of C. vulgaris PKVL7422 is approximately 8 kb long and composed of 18 introns and 19 exons, which encode 877 amino acids. An alignment analysis of the NR gene showed that it possesses the five domains and several invariant residues found in plant NRs. These results provide new insight into the molecular organization of the NR gene in algae.