• Proceedings of the PSK Conference
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• 2001.04a
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• pp.235.2-236
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• 2001

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2002.06a
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• pp.35-47
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• 2002

2D-PAGE/MALDI-TOF는 프로-테옴 연구의 중요한 실험 기법중의 하나이다. 이는 단백질의 발현 분석을 위한 방법으로, 2D-PAGE 결과로 얻어진 영상 데이터의 분석에 대한 정확도가 단백질 발현에 대한 분석 결과의 질을 결정하는 중요한 요인으로 작용한다. 2D Electrophoresis에 의한 Gel Protein Database는 현재 많은 연구자들에 의해 생산되고 있으며, 대단히 많은 데이터들이 인터넷을 통하여 접근이 가능하다. 이러한 대량 정보의 Database 활용이 가능한 상황은 2D-PAGE에 의해 생산된 Gel Image의 상호 비교에 대한 요구를 도출하였다. 본 발표에서는 영상처리 및 형태인식 기술과 2D-PAGE 연구의 결합을 주제로 하여, 2D-PAGE Gel 영상 처리 및 비교에 관련되는 전처리 (preprocessing), spot detection, feature extraction, spot matching 및 image comparison 기술을 소개한다.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.3
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• pp.307-312
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• 2007

The present study was carried out to investigate differentially expressed chicken muscle proteins using proteomics approach. More than 300 protein spots were investigated for the muscle samples in 2DE gels and the differentially expressed protein spots between pectoralis and peroneus longus muscles from Cornish and White Leghorn breeds were characterized by MALDI-TOF. In pectoralis muscles, PGAM1 protein was detected as differentially expressed between White Leghorn and Cornish breeds. On the other hand, 4 protein spots (SP22, nxf-2, SOD1, TNNI2) were differentially expressed between White Leghorn and Cornish breeds in peroneus longus muscles. These proteins assumed to be related with muscle development, growth, stress, and movements in chicken. In this experimental process, 2D reference map of the chicken muscle proteins was needed and 25 proteins, which were commonly expressed in both pectoralis and peroneus longus muscles in both breeds, were selected and characterized. Upon finishing the exact roles of the differentially expressed proteins, the identified 5 proteins will be used as valuable information for the fundamental mechanisms of muscle biology and underline genetics.

• Journal of Embryo Transfer
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• v.25 no.4
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• pp.281-286
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• 2010

This study was to evaluate the protein profile of seminal plasma using 2-DE in Hanwoo. Seminal plasma was harvested from five mature Hanwoo, and seminal plasma protein was extracted by M-PER Mammalian Protein Extraction Reagent. Proteins were refined by clean-up kit and quantified by Bradford method until total protein was $300\;{\mu}l$. Immobilized pH gradient (IPG) strip was used 18 cm and 3~11 NL. SDS-PAGE was used 12% acrylamide gel. Each gels were visualized by comassie brilliant blue and silver staining. These spots were analyzed by MALDI-TOF MS and searched on NCBInr. The result, 20 proteins of 36 protein spots were searched through peptide sequencing on the NCBInr. 8 proteins profiled by 2-DE were proved through previous bovine studies and the name of each protein was albumin, nucleobindin, clusterin, TIMP-2, spermadhesin Z13, spermadhesin-1 and BSP proteins (BSP 30 kDa and BSP A1/A2). 12 new proteins were ATP synthase, protein MAK16 homolog, Transmembrane protein 214, E3 ubiquitin-protein ligase BRE1A, dual serine/threonine and tyrosine protein kinase, tissue factor pathway inhibitor 2, alpha-actinin-4, RUN domain-containing protein 3B, catenin alpha-1, protein-glutamine gamma-glutamyltransferase 2, plakophilin-1 and inter-alpha-trypsin inhibitor heavy chain H1 has not been previously described in the bovine seminal plasma study. These proteins may be contribute to define the type of proteins affecting fertility of male and improve the fertilizing ability of semen in Hanwoo.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.9 no.3
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• pp.800-806
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• 2008

The strain HK-12 was enriched and isolated from naturally fermented soybean for the production of fibrinolytic enzyme and the proteome of this enzyme induced during the incubation period was analyzed. The activity of fibrinolytic enzyme derived from supernatants of the HK-12 culture was performed by fibrin plate method for solid fibrinolytic activity. As the result, the fibrinolytic activity of HK-12 grown on the nutrient agar media was about 2.3 times greater than that of plasmin used as standard. The purified enzyme was prepared by a series of purification process including ammonium sulfate precipitation, DEAE-cellulose, Sephadex chromatography. The molecular weight of the enzyme was determined to approximately 23kDa with SDS-PAGE. In order to examine which strain HK-12 proteins increased or decreased during the incubation period, 2-DE analysis was performed. Protein spot #1 significantly expressed on the 2-DE gel of bacteria cultivated for 36-hrs was analysed. As the result of protein sequence analysis using MALDI-TOF MS, one protein was identified as serine protein kinase (PrkA).

• Journal of Microbiology and Biotechnology
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• v.16 no.6
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• pp.946-951
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• 2006

To study the effect of iron on Saccharomyces cerevisiae, whole-cell proteins of Saccharomyces cerevisiae were extracted and subjected to two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), and differentially expressed proteins were identified. The proteins separated were further identified by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry and were compared with a protein database. Of more than 300 spots separated by molecular weight and isoelectric points, 27 differentially expressed spots were identified. Ten proteins were found to be differentially expressed at high iron concentration. Triosephosphate isomerase (TPI), YDR533C hypothetical protein, superoxide dismutase (SOD), 60 kDa heat-shock protein (HSP60), pyruvate dehydrogenase beta subunit 1 (PDB1), and old yellow enzyme 2 (OYE2) were upregulated, whereas thiol-specific antioxidant (TSA), regulatory particle non-ATPase subunit 8 (RPN8), thiol-specific peroxiredoxin 1 (AHP1), and fructose-1, 6-bisphosphate adolase (FBA) were downregulated by iron. Based on the result, we propose that SOD upregulated by iron would protect the yeast from oxidative stress by iron, and that TSA downregulated by iron would render cells hypersensitive to oxidative stress.

• 한국생물공학회:학술대회논문집
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• 2002.04a
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• pp.558-561
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• 2002

In this study, a method for the localization of pregnancy-specific proteins from cow urine on 2-D gel have been established. The proteins were digested with trypsin in gel and then analyzed with MALDI- TOF or transferred to a membrane and microsequenced. To examine the pregnancy associated protein spot 2 as a diagnosis marker in bovine urine 2-D western blotting was performed. This antibody was reacted specifically in the protein of pregnant cow’s urine. Consequently spot 2 was identified and found to be good candidates for developing cow pregnancy detection assay kit.

• Journal of Industrial and Engineering Chemistry
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• v.68
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• pp.6-13
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• 2018

Well-modified amino-appended ${\beta}$-cyclodextrin ($AA-{\beta}-CD$) with an amino group at the primary face of the ${\beta}-CD$ was synthesized and used in the catalytic synthesis of chromeno pyrimido[1,2-b]indazol as supramolecular catalysts in water for the first time. $AA-{\beta}-CD$ was characterized by FT-IR, NMR, MALDI-TOF mass spectrometry, and SEM analysis. A possible reaction mechanism featuring molecular complexation was suggested based on 2D NMR (ROESY) spectroscopy, FE-SEM, DSC, and FT-IR. Advantages such as operational simplicity, recyclability of the catalysts, and accessibility in aqueous medium render this protocol eco-friendly.

• BMB Reports
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• v.37 no.3
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• pp.298-303
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• 2004

In general, a SYPRO Ruby dye is well known as a sensitive fluorescence-based method for detecting proteins by one-or two-dimensional SDS-PAGE (1-DE or 2-DE). Based on the SYPRO Ruby dye system, the combined two-dimensional fibrin zymography (2-D FZ) with SYPRO Ruby staining was newly developed to identify the Bacillus sp. proteases. Namely, complex protein mixtures from Bacillus sp. DJ-4, which were screened from Doen-Jang (Korean traditional fermented food), showed activity on the zymogram gel. The gel spots on the SYPRO Ruby gel, which corresponded to the active spots showing on the 2-D FZ gel, were analyzed by a matrix-assisted laser desorption ionization time of flight (MALDI-TOF) mass spectrometric analysis. Five intracellular fibrinolytic enzymes of Bacillus sp. DJ-4 were detected through 2-D FZ. The gel spots on the SYPRO Ruby dye stained 2-D gel corresponding to 2-D FZ were then analyzed by MALID TOF MS. Three of the five gel spots proved to be quite similar to the ATP-dependent protease, extracellular neutral metalloprotease, and protease of Bacillus subtilis. Also, the extracellular proteases of Bacillus sp. DJ-4 employing this combined system were identified on three gels (e.g., casein, fibrin, and gelatin) and the proteolytic maps were established. This combined system of 2-D zymography and SYPRO Ruby dye should be useful for searching the specific protease from complex protein mixtures of many other sources (e.g., yeast and cancer cell lines).

• Bulletin of the Korean Chemical Society
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• v.32 no.12
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• pp.4337-4340
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• 2011

The vitamin D receptor binding peptide, VDRBP, was overexpressed as a fused form with the ubiquitin molecule in Rosetta(DE3)pLysS, a protein production strain of Escherichia coli harboring an induction controller plasmid. The fusion protein was bound to the immobilized metal ions, and the denaturation and renaturation of the fusion protein were performed as a part of the purification procedure. After the elution of the fusion protein, the peptide hormone was released from its fusion partner by using yeast ubiquitin hydrolase (YUH), and subsequently purified by reverse phase chromatography. The purity of the resulting peptide fragment was checked by MALDI-TOF mass and NMR spectroscopy. The final yields of the target peptide were around 5 and 2 mg per liter of LB and minimal media, respectively. The recombinant expression and purification of this peptide will enable structural and functional studies using multidimensional NMR spectroscopy and X-ray crystallography.