• Journal of Plant Biotechnology
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• v.29 no.3
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• pp.161-170
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• 2002

For the hairy root of Panax ginseng, we have got mass spectrums from MALDI/TOF/MS analysis and Tandem mass spectrums from ESI/Q-TOF/MS analysis. While mass spectrum provides the molecular weights of peptide fragments digested by protease such as trypsin, tandem mass spectrum produces amino acid sequence of digested peptides. Each amino acid sequences can be a query sequence in BLAST search to identify proteins. For the specimens of animals or plants of which genome sequences were known, we can easily identify expressed proteins from mass spectrums with high accuracy. However, for the other specimens such as ginseng, it is difficult to identify proteins with accuracy since all the protein sequences are not available yet. Here we compared the mass spectrums and the peptide amino acid sequences with ginseng expressed sequence tag (EST) DB. The matched EST sequence was used as a query in BLAST search for protein identification. They could offer the correct protein information by the sequence alignment with EST sequences. 90% of peptide sequences of ESI/Q-TOF/MS are matched with EST sequences. Comparing 68% matches of the same sequences with the nr database of NCBI, we got more matches by 22% from ginseng EST sequence search. In case of peptide mass fingerprinting from MALDI/TOF/MS, only about 19% (9 proteins of 47 spots) among peptide matches from nr DB were correlated with ginseng EST DB. From these results, we suggest that amino acid sequencing using tandem mass spectrum analysis may be necessary for protein identification in ginseng proteome analysis.

• Journal of Mushroom
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• v.19 no.4
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• pp.285-293
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• 2021

The purpose of this study was to identify and characterize the laccase genes of Flammulina velutipes var. lupinicola. Five laccase genes (g1934, g1937, g2415, g2539, g5858) were selected based on the copper binding site and signal peptide analysis results using the laccase gene selected from the F. velutipes var. lupinicola genome. The size of the laccase genes of F. velutipes var. lupinicola were 1,488 bp~1,662 bp. As a result of cDNA sequence analysis, 14 to 17 introns were identified in the laccase genes. The cleavage site predicted as the signal peptide of the laccase gene was found to be located between 20 bp and 34 bp from the N-terminus. In addition, separation and purification were performed to characterize the F. velutipes var. lupinicola laccases, and the optimal activity of the separated and purified proteins were analyzed by pH, temperature and time. Five bands with laccase activity were found from zymogram analysis. The optimal pH of the reaction was 5.5, the optimal temperature was found to be 40℃. Therefore, characterization of the laccase genes identified in this study should help in better understanding the biomass decomposition of F. velutipes var. lupinicola.

• Proceedings of the Korea Information Processing Society Conference
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• 2007.05a
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• pp.71-74
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• 2007

오늘날 생물학 데이터베이스 시스템은 끊임없이 증가하고 복잡하게 연결되는 데이터를 처리해야 할 필요성과 데이터양의 증가만큼이나 빨리 성장하는 사용자들의 요구에 부응해야 하는 필요성에 직면해 있다. 이 논문에서는 기존의 생물학 데이터베이스 시스템의 특징을 살펴본 후, 현재 당뇨 관련 데이터베이스가 존재하지 않으므로 당뇨 연구를 위한 포괄적인 정보 제공과 사용의 편의를 제공하기 위하여 생물학 관련 데이터베이스를 교차 참조한 당뇨 연구용 데이터베이스를 설계하였다. 본 논문에서 설계한 데이터베이스는 Genetic Information, Protein Information, In Silico digestion, 그리고 Chemical Information 4개의 메뉴로 구성하였다. Genetic Information과 Protein Information은 Cross-Reference를 통한 관련 데이터베이스와 연결시켰고, Protein Information에서 PDB 코드가 존재할 경우 3차원 분자 구조를 제공한다. 아울러 단백질 동정시에 활용할 수 있는 선택된 효소처리 후의 펩타이드의 이론적 질량값을 계산하도록 구현(In Silico Digestion)하였으며, 당뇨 관련 주요 단백질의 화합물들의 구조를 제공하였다.

• Journal of the Korean Society of Food Science and Nutrition
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• v.30 no.4
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• pp.594-599
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• 2001

This study was attempted to isolate and identify the strain revealing high angiotensin converting enzyme (ACE) inhibitory activity from various soy fermented foods, i.e. meju, soybean paste and soy sauce. Forty-two strains with morphologically different characteristics were selected and the ACE inhibitory and proteolytic activities were examined. Of the strains tested, SS103 which was isolated from soy sauce showed the highest ACE inhibitory and proteolytic activities and was finally selected for further studies. The SS103 strain showed motility, rod form and ellipsoidal spores. The shape of colonies on the agar media was irregular, mucoidal and surface dull. The strain could grow under aerobic conditions of pH 5~9 and 10~$50^{\circ}C$. Main cellular fatty acid was $C_{15:0}$ anteiso, $C_{17:0}$ cis and $C_{17:0}$ iso, which was 33.9%, 18.8% and 16.5%, respectively. Based upon these morphological, biochemical and cultural properties, SS103 was identified as a Bacillus subtilis. Optimum cultural condition of Bacillus subtilis SS103 was pH 8.0, $37^{\circ}C$ and 48 hr.48 hr.

• Journal of Mushroom
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• v.19 no.1
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• pp.33-40
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• 2021

The genome sequence of various Flammulina species has recently been reported, thereby revealing a diverse genetic repertoire. In this study, we identified laccase genes and analyzed their structural characteristics in Flammulina elastica (F. elastica) genome. Through genome analysis and bioinformatics approaches, three laccase genes (Fe-lac1, -lac2, and -lac3) were identified, ranging from 1,548 to 1,602 bp in length. These genes contained a copper ion-binding region with ten histidine residues and one cysteine residue and a disulfide bond-forming region with four cysteine residues. Full-length cDNA sequencing analysis revealed that laccase genes contain 12 to 16 introns and signal peptides between 17 and 22 bp in the N-terminus. Structural characterization of the laccase genes identified in this study should help in better understanding the biomass decomposition of F. elastica.

• Journal of KIISE:Software and Applications
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• v.34 no.10
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• pp.889-899
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• 2007

In proteomics, recent advancements In mass spectrometry technology and in protein extraction and separation technology made high-throughput analysis possible. This leads to thousands to hundreds of thousands of MS/MS spectra per single LC-MS/MS experiment. Such a large amount of data creates significant computational challenges and therefore effective data analysis methods that make efficient use of computational resources and, at the same time, provide more peptide identifications are in great need. Here, SIFTER system is designed to avoid inefficient processing of shotgun proteomic data. SIFTER provides software tools that can improve throughput of mass spectrometry-based peptide identification by filtering out poor-quality tandem mass spectra and estimating a Peptide charge state prior to applying analysis algorithms. SIFTER tools characterize and assess spectral features and thus significantly reduce the computation time and false positive rates by localizing spectra that lead to wrong identification prior to full-blown analysis. SIFTER enables fast and in-depth interpretation of tandem mass spectra.

• Analytical Science and Technology
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• v.30 no.6
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• pp.348-354
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• 2017

In this study, patterns of proteome expression were monitored and specifically expressed proteins in human milk were detected in collected human milk after 1 week, 3 weeks, and 6 weeks from delivery. A quantitative shotgun proteomic approach was used to identify human milk proteins and reveal their relative expression amounts. For each sample, two independent human milk samples from two mothers were pooled, and then three replicated shotgun proteomic analyses were carried out. Casein, which is a highly abundant protein in human milk, was removed, and then trypsin was treated to produce a digested peptide mixture. The peptides were loaded in the home-made reversed-phase C18 fused-silica capillary column, and then the eluted peptides were analyzed by using a linear ion-trap mass spectrometer. The relative quantitation of proteins was performed by the normalized spectral count method. For each sample, 81-109 non-redundant proteins were identified. The identified proteins consisted of glycoproteins, metabolic enzyme, and chaperon enzymes such as lactoferrin, carboxylic ester hydrolase, and clusterin. The comparative analysis for the 63 proteins, which were reproducibly identified in all three replications, revealed that 25 proteins were statically significant differentially expressed. Among the differentially expressed proteins, Ig lambda-7 chain C region and tenascin drastically decreased with the delivery time.

• Journal of Dairy Science and Biotechnology
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• v.30 no.1
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• pp.45-53
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• 2012

Lactobacillus acidophilus isolated from the feces of a 7-day-old breast-fed infant was characterized to examine the scope of its commercial use. Forty-three Lactobacillus strains, which could grow at pH 5.5, were isolated. From these Lactobacillus isolates, 14 Lactobacillus strains were selected, which demonstrated more than 80% viability and homofermentative lactic fermentation. Finally, 9 L. acidophilus strains (NB 201~NB 209) were identified as candidate strains based upon biochemical properties, carbohydrate utilization, and cellular fatty acid composition. L. acidophilus isolates demonstrated a survival rate of more than 80% when exposed to pH 2.5 for 2 h. In particular, L. acidophilus NB 204 showed a strong acid tolerance, with a 71% survival rate even at pH 2.0. L. acidophilus isolates also manifested high bile acid tolerance; more than 87% of the cells survived on agar containing 1% bile extract, except for L. acidophilus NB 206, which showed a 73% survival rate. All L. acidophilus isolates were confirmed to have proteolytic activity; L. acidophilus NB 204 and NB 209 yielded higher levels of TCA-soluble peptides and free amino acids. The ${\beta}$-galactosidase activity of the L. acidophilus isolates was in the range of 1.97~2.45 units/mL.

• Journal of Fisheries and Marine Sciences Education
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• v.26 no.3
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• pp.543-552
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• 2014

Papain family중 하나인 cysteine protease는 근골격계 질환 치료를 위한target molecule로 인식 되어왔으며 Cathepsin B 는 단백질 분해의 초기과정에 관여하는 cysteine proteases 중 하나이다. 본 연구는 넙치의 cathepsin B 유전자의 발현 양상과 넙치 cathepsin B(PoCtB)의 클로닝, 발현 및 효소특성을 분석하였다. cDNA Library Screening을 이용하여 넙치의 cDNA를 클로닝하였다. 넙치의 동정된 cathepsin B 유전자는 993bp의 open reading frame과 330개의 아미노산으로 이루어져있다. Cathepsin B의 propeptide region 내에 GNFD motif와 occluding loop 가 존재함으로써 이것이 명백하게 cathepsin B group이라는 것을 보여주며, 계통 유전학적 분석 결과 다른 종의 cathepsin B에 비해 초창기에 분화되어 나온 것으로 사료된다. mature enzyme인 maPoCtB은 fusion protein인 glutathione S-transferase를 포함하는 pGEX-4T-1 vector에 삽입하여 E.coli 균주인 $DH5{\alpha}$ 내에 발현시켰다. 재조합 단백질인 PoCtB을 과발현 시킨 결과 53kDa의 분자량을 가진다. 넙치 cathepsin B 활성은 Z-Arg-Arg-AMC와 같은 fluorogenic 펩타이드 기질을 이용하여 측정되었고 적정 pH는 pH.7.5 이다.

• Journal of Life Science
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• v.15 no.4 s.71
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• pp.528-535
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• 2005

The non-enzymatic anti-oxidants and lunasin peptide from the extracts of the pepper were examined in order to utilize the discovery in natural products as cancer chemopreventive agents. The DPPH (1,1-diphenyl-2-picryl-hydrazyl) free radical scavenging activity on the fruit parts of the pepper was higher than that of the seed, but the difference was low. The Inhibition activity of xanthine/ xanthine oxidase in extracts of the seed was higher than that of the fruit and that of the seed on 20 days after flowering was the highest at the growing period. These were identified as fatty acids and phenolic compounds such as 1-eicosanol, palmitic acid, linoleic acid, linolenic acid and benzonitrile. The contents of fatty acids and phenolic compounds increased according to the time passing at the growing period. Peroxidase (POD) activity of the fruit at middle stage was high than that of other growing stages and that of the seed was the highest at later growing period. Though superoxide dismutase (SOD) activities in fruit were hish by passage of Slowing stage, the activity in seed was low. Lunasin was searched from seeds of the peppers by coomassie blue staining and western blot among them and we just found lunasin peptide from extracted protein of the pepper by western blot. In addition, we observed the contents of lunasin after flowering and confirmed to appear the lunasin at 35 days after flowering. We confirmed that lunasin is complex protein of maturing seeds. 100nM lunasin peptide in pepper showed inhibition effect on colony formation in $2\~12$ cells.