• Genomics & Informatics
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• v.4 no.2
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• pp.87-93
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• 2006

With the rapid development of MS technologiesy, the demands for a more sophisticated MS interpretation algorithm haves grown as well. We have developed a new protein fingerprinting method using a binomial distribution, (fBIND). With the fBIND, we improved the performance accuracy of protein fingerprinting up to the maximum 49% (more than MOWSE) and 2% than(at a previous binomial distribution approach studied by of Wool et al.) as compared to the established algorithms. Moreover, we also suggest a the statistical approach to define the significance of transcription factors and motifs in the identified proteins based on the Gene Ontology (GO). Abbreviations: fBIND, fingerprinting using binomial distribution; GO, Gene Ontology; MS, Mass Spectrometry; PMF, peptide mass fingerprinting; nr, nonredundant; SGD, Saccharomyces Genome Database

• Genomics & Informatics
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• v.4 no.2
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• pp.65-70
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• 2006

Peptide mass mapping is the matching of experimentally generated peptides masses with the predicted masses of digested proteins contained in a database. To identify proteins by matching their constituent fragment masses to the theoretical peptide masses generated from a protein database, the peptide mass fingerprinting technique is used for the protein identification. Thus, it is important to know the theoretical mass distribution of the database. However, few researches have reported the peptide mass distribution of a database. We analyzed the peptide mass distribution of non-redundant protein sequence database in the NCBI after digestion with 15 different types of enzymes. In order to characterize the peptide mass distribution with different digestion enzymes, a power law distribution (Zipfs law) was applied to the distribution. After constructing simulated digestion of a protein database, rank-frequency plot of peptide fragments was applied to generalize a Zipfs law curve for all enzymes. As a result, our data appear to fit Zipfs law with statistically significant parameter values.

• Journal of Life Science
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• v.19 no.3
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• pp.397-402
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• 2009

To isolate bacteria secreting protease, which can dissolve fibrin efficiently, we prepared chunggukjang using rice straw and isolated, preliminarily, approximately 100 bacterial stains. Their capabilities to dissolve milk protein as well as fibrin included in media were then examined and finally, five strains named J1 - J5 were selected. Among them, J-4, which is close to bacillus subtilis, showed highest activity for fibrin dissolution. Proteases secreted from the J-4 strain were partially purified from culture supernatant using DEAE-sepharose column chromatography and identified with SDS-polyacrylamide gel electrophoresis. Three proteins were subjected to analysis with MALDI-TOF and PMF (Peptide Mass Fingerprinting). 41.9 kDa protein was identified as a neutral protease. On the other hand, 45 kDa protein turned out to be bacillopeptidase F, with a molecular mass of 91.7 kDa, indicating that partially purified peptide is a degradation product.

• Preventive Nutrition and Food Science
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• v.7 no.4
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• pp.432-436
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• 2002

A proteomic map of Hanwoo loin was obtained using 2-D SDS-PAGE and mass spectrometric analysis: 27 bovine proteins plus 2 proteins having similarities to other mammal proteins out of 52 proteins analyzed. The identified proteins consisted of 50 % basic house keeping proteins involved in metabolism, 30% muscle proteins, and other miscellaneous proteins. Many proteins on the 2-D gel with different molecular weights and isoelectric points were identified as same proteins due to posttranslational modification. As many of the identified house keeping proteins showed the high sequence similarities to other mammal equivalent proteins, searching the mammal databases could confirm the annotation. The preliminary identification of the proteome in bovine loin tissue could reveal the functions of proteins at over 50 % of chance with high fidelities. Using the established loin proteome map, proteomic difference between 1 yr and 2 yr Hanwoo loin tissues were compared on 2D gel. Regardless of the difficulty normalizing protein concentrations and sample-to-sample variations, three unidentified proteins and myoglobin were selected as up-regulated proteins during the fat deposition period. This study contributes to a move thorough and holistic understanding of beef meat, helping to build the basis for future identification of new markers for good quality meat.

• Korean Journal of Microbiology
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• v.48 no.2
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• pp.87-92
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• 2012

The purpose of this study was to examine the cellular response of Salmonella typhimurium exposed to tea polyphenols (TPP) extracted from Korean green tea (Camellia sinensis L.). TPP showed a dose-dependent bactericidal effect on S. typhimurium. Analysis of cell membrane fatty acids of S. typhimurium cultures treated with TPP identified unique changes in saturated and unsaturated fatty acids, while scanning electron microscopic analysis demonstrated the presence of perforations and irregular rod forms with wrinkled surfaces in cells treated with TPP. Two-dimensional polyacrylamide gel electrophoresis of soluble protein fractions from S. typhimurium cultures showed 16 protein spots increased by TPP. These up-regulated proteins including proteins involved in antioxidants and chaperons, transcript and binding proteins, energy and DNA metabolism were identified by peptide mass fingerprinting using MALDI-TOF. These results provide clues for understanding the mechanism of TPP induced stress and cytotoxicity on S. typhimurium.

• BMB Reports
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• v.37 no.1
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• pp.59-74
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• 2004

The study of whole patterns of changes in protein expression and their modifications, or proteomics, presents both technological advances as well as formidable challenges to biological researchers. Nutrition research and the food sciences in general will be strongly influenced by the new knowledge generated by the proteomics approach. This review examines the different aspects of proteomics technologies, while emphasizing the value of consideration of "traditional" aspects of protein separation. These include the choice of the cell, the subcellular fraction, and the isolation and purification of the relevant protein fraction (if known) by protein chromatographic procedures. Qualitative and quantitative analyses of proteins and their peptides formed by proteolytic hydrolysis have been substantially enhanced by the development of mass spectrometry technologies in combination with nanoscale fluidics analysis. These are described, as are the pros and cons of each method in current use.

• Journal of the Korea Institute of Information and Communication Engineering
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• v.11 no.10
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• pp.1880-1885
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• 2007

In this paper, we propose the method that improve the performance of the Mowse. Mowse is the tool of the peptide mass fingerprinting that is used the identification of protein. In Mowse, frequency factor matrix is generated to regular interval for protein and peptide mass and the value of each elements is calculated to frequency of peptide. We propose new method for calculation of exact scoring value maintaining same size of matrix. The proposed method is that decide interval of matrix considering distribution of protein database. That is, interval of matrix is decided to small in many value of protein mass and is decided to large in few value of protein mass. We present the performance result both Mowse scoring method and the proposed scoring method.

• Current Research on Agriculture and Life Sciences
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• v.32 no.1
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• pp.34-42
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• 2014

Soy and fermented soy are popular and recognized as a health food among Koreans. Since soy proteins are known to be protease resistant, even to pepsin and pancreatin, it is hypothesized that soy proteins may interact with the intestinal tract and trigger certain physiological reactions. To test this hypothesis, mice were fed diets supplemented with soy, Chunkukjang, or casein. The differentially expressed proteins were analyzed using 2-D gels and identified by peptide mass fingerprinting using mass spectrometry. The majority of the differentially expressed proteins could be functionally grouped into metabolic enzymes and calcium-binding proteins. The differential protein expression by the soy-fed groups was also verified based on a representative protein, tropomyosin, using a Western blotting analysis. In addition, the soy-fed groups exhibited a taller villi structure. Therefore, this study suggests that soy proteins can be an effective nutrient and physiological stimulant for the intestines.

• 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.

• Molecules and Cells
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• v.22 no.1
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• pp.36-43
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• 2006

Mesenchymal stem cells (MSCs) are promising candidates for cell therapy and tissue engineering, but their application has been impeded by lack of knowledge of their core biological properties. In order to identify MSC-specific proteins, the hydrophobic protein fraction was individually prepared from two different umbilical cord blood (UCB)-derived MSC populations; these were then subjected to two-dimensional (2D) gel electrophoresis and peptide mass fingerprinting matrix-assisted laser desorption/ionization (MALDI)-time of flight (TOF)-mass spectrometry (MS). Although the 2D gel patterns differed somewhat between the two samples, computer-assisted image analysis identified shared protein spots. 35 spots were reliably identified corresponding to 32 different proteins, many of which were chaperones. Based on their primary sub-cellular locations the proteins could be grouped into 6 categories: extracellular, cell surface, endoplasmic reticular, mitochondrial, cytoplasmic and cytoskeletal proteins. This map of the water-insoluble proteome may provide valuable insights into the biology of the cell surface and other compartments of human MSCs.