• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.313-318
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• 2005

Estimating the reliability of protein-protein interaction data sets obtained by high-throughput technologies such as yeast two-hybrid assays and mass spectrometry is of great importance. We develop a maximum likelihood estimation method that uses both protein localization and gene expression data to estimate the reliability of protein interaction data sets. By integrating protein localization data and gene expression data, we can obtain more accurate estimates of the reliability of various interaction data sets. We apply the method to protein physical interaction data sets and protein complex data sets. The reliability of the yeast two-hybrid interactions by Ito et al. (2001) is 27%, and that by Uetz et at.(2000) is 68%. The reliability of the protein complex data sets using tandem affinity purification-mass spec-trometry (TAP) by Gavin et at. (2002) is 45%, and that using high-throughput mass spectrometric protein complex identification (HMS-PCI) by Ho et al. (2002) is 20%. The method is general and can be applied to analyze any protein interaction data sets.

• Journal of Nutrition and Health
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• v.28 no.8
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• pp.782-790
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• 1995

The longitudinal changes in protein secretion from 27 lactating women(primiparae = 10, multiparae=17) and protein intake of infants have been studied from 0.5 to 6 months postpartum in Chungju and Anseong area. The protein contents o breast milk in primiparae appeared significantly higher than in multipaae at 0.5 and 1 month postpartum. The protein secretion of primiparae and multiparae was not significantly different. In breast-feeding period, there was a tendency that protein secretion from 0.5 to 2 months postpartum was higher than thereafter. Average protein intake of boys from milk from 0.5 to 6 months postpartum was significantly higher than that of girls(p<0.05), because volume of milk intake of boys was much more than that of girls. In the amount of protein intake per infant weight, there was no significant difference between boys and girls. Protein intakes per infant weight decreased during lactation. Mean energy consumption of lactating women was 2,327㎉/day, which was 93.1% of recommended energy allowance for Koreans. Mean dietary protein consumption of lactating women was 81g/day, which was 101.3% of recemmended protein allowance for Koreans. Energy ratio of carbohydrate : protein : lipid was appeared to 68.8 : 13.9 : 17.3.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.28-31
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• 2000

We describe a hidden Markov model, HMMTIR, for general protein sequence based on the I-sites library of sequence-structure motifs. Unlike the linear HMMs used to model individual protein families, HMMSTR has a highly branched topology and captures recurrent local features of protein sequences and structures that transcend protein family boundaries. The model extends the I-sites library by describing the adjacencies of different sequence-structure motifs as observed in the database, and achieves a great reduction in parameters by representing overlapping motifs in a much more compact form. The HMM attributes a considerably higher probability to coding sequence than does an equivalent dipeptide model, predicts secondary structure with an accuracy of 74.6% and backbone torsion angles better than any previously reported method, and predicts the structural context of beta strands and turns with an accuracy that should be useful for tertiary structure prediction. HMMSTR has been incorporated into a public, fully-automated protein structure prediction server.

• BMB Reports
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• v.33 no.1
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• pp.82-88
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• 2000

A homologous gene to alanine racemase was cloned from a hyperthermophilic bacterium, Aquifex pyrophilus. The cloned gene encodes a protein of 341 amino acids, which has a significant homology to alanine racemase of Bacillus stearothermophilus, Lactobacillus brevis, and E. coli. When the gene was expressed in Escherichia coli, it produced a 40 kDa protein. The purified protein contains one mole pyridoxal 5-phosphate per one mole of protein, which is essential for catalytic activity of alanine racemase. The purified protein catalyzed racemization of L-alanine to D-alanine, or vice versa, indicating that the cloned gene encoded alanine racemase. It also showed significant racemization activity against L-serine and ${\alpha}-aminobutylic$ acid. The A. pyrophilus alanine racemase showed strong thermostability, and it maintained catalytic activity in the presence of organic solvents.

• Parasites, Hosts and Diseases
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• v.37 no.4
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• pp.277-283
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• 1999

To investigate the development of a subunit vaccine against theileriosis in cattle, the DNA fragments encoding piroplasm surface protein (p33) of Theileria sergenti of a Korean isolate were expressed in baculoviruses. The expressed p33 was characterized by indirect fluorescent antibody (IFA) and western blotting analysis. The expression of p33 was mainly detected on the surface of infected Sf21 cells by IFA. The immunoblotting analysis revealed the presence of a same molecular weight protein band of p33. The antigenicity of expressed polypeptide was further examined through the inoculation of a guinea pig. The sera of guinea pigs immunized with p33 expressed cell Iysate showed similar fluorescent antibody patterns and reacted with the same molecular weight protein of T. sergenti in immunoblotting analysis, thus indicating that this protein can be a promising candidate for a subunit vaccine in the future.

• Clinical and Experimental Reproductive Medicine
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• v.26 no.2
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• pp.225-230
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• 1999

In mouse, the heat shock protein 70-2 (hsp70-2) is found to have special function in spermatogenesis. Based on the observation, the hypothesis that human hspA2 (human gene; 98.2% amino acid homology with hsp70-2) might have important function in spermatogenesis in human testes was proposed. To test the hypothesis, we examined the expression of hspA2 in human tissues. Expression vector pDMC4 for expression of the human hspA2 protein using pTricHisB (invitrogen, USA) was constructed and the expressed hspA2 protein was cross-reacted with antiserum 2A raised against mouse hsp70-2 protein. Based on the cross-reactivity, we determined the expression level of hspA2 protein in human tissues by western blot analysis using the antiserum 2A. We demonstrated that antiserum 2A antibodies detected human hspA2 protein with specificity which was produced in the E.coli expression system. On Western blot analyses, significant hspA2 expression was observed in testes with normal spermatogenesis, whereas a low level of hspA2 was expressed in testis with Sertoli-cell only syndrome. Also, a small amount of hspA2 was detected in breast, stomach, prostate, colon, liver, ovary, and epididymis. These results demonstrate that the hspA2 protein is highly expressed in male specific germ cells, which in turn suggests that hspA2 protein might playa specific role during meiosis in human testes as suggested in the murine model. However, further studies should be attempted to determine the function of hspA2 protein in human spermatogenesis.

• Journal of Periodontal and Implant Science
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• v.29 no.3
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• pp.663-676
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• 1999

Porphyromonas gingivalis, a Gram negative, anaerobic, asaccharolytic rod, is one of the most frequently implicated pathogens in human periodontal disease and has a requirement for hemin for growth. A 30 kDa (heated 24 kDa) hemin-binding protein whose expression is both hemin and iron regulated has recently been purified and characterized in this oral pathogen. This study has identified a hemin-binding P. gingivalis protein by expression of a P. gingivalis genomic library in Escherichia coli, a bacterium which does not require or transport exogenous hemin. A library of genomic DNA fragments from P. gingivalis was constructed in plasmid pUC18, transformed into Escherichia coli strain $DH5{\alpha}$ , and screened for recombinant clones with hemin-binding activity by plating onto hemin-containing agar. Of approximately 10,000 recombinant E. coli colonies screened on LB-amp-hemin agar, 10 exhibited a clearly pigmented phenotype. Each clone contained various insert DNA. The Hind III fragment transferred to the T7 RNA polymerase/promoter expression vector system produced a sligltly smaller (21 kDa) protein, a precursor form, immunoreactive to the antibody against the 24 kDa protein, suggesting that the cloned DNA fragment probably carried an entire gene for the 24 kDa hemin-binding protein.

• Journal of Microbiology
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• v.37 no.4
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• pp.229-233
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• 1999

The mitochondrial plasmid pMLP1 from a white-rot fungus, Pleurotus ostreatus, is a double-stranded DNA containing 381 bp terminal inverted repeat (TIR) whose 5'-ends are covalently bound by terminal proteins. The plasmid contains two major open reading frames (ORFs), encoding putative DNA and RNA polymerases, and a minor ORF encoding a small, highly basic protein. To identify the DNA binding activity that recognizes the TIR region of pMLP1, gel retardation assays were performed with mitochondrial extracts. A specific protein binding to a region between 123 and 248 nt within TIR was observed. We examined whether the gene product of mORF1 bindes to this region specifically. E. coli cell extract which contains an overproduced mORF1 protein formed a complex specific to the region between 123 and 248 nt. Inclusion of mORF1 protein in the specific complex formed between P. ostreatus mitochondrial extract and TIR was confirmed by a supershift assay using polyclonal antibodies against the mORF1 protein. Our result suggest that the product of mORF1 may function as a terminal region recognition factor (TRF), recognizing an internal region in TIR.

• 한국생물공학회:학술대회논문집
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• 2005.04a
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• pp.47-47
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• 2005

There are many different surface technologies currently applied for preparation of protein chips. However, it requires innovative surface chemistry for capture proteins to be immobilized on chip surface keeping their conformation and activity intact and their orientation right, while they bind tightly and densely in a given array spot. Proteogen has developed 'ProteoChip BP' coated with novel proprietary linker molecules $(ProLinker^{TM})$ for efficient and robust immobilizations of capture proteins by improving surface properties of molecular captures. It was demonstrated that $ProLinker^{TM}$ gave the best surface performance in preparation of protein microarray chip base plates among others currently available on the market. In particular, the $ProLinker^{TM}-based$ surface chemistry has demonstrated to provide excellent performance in preparation of 'Antibody Chip' for analysis of biomarkers as well as proteome expression profiles. The linker molecule has also shown to be well applicable for development of biosensors and micro-beads as well as protein microarray and nano-array. ProteoChip BP can be used either for preparation of high-density array by using a microarrayer or for preparation of 'Well-on-a-Chip' with low density array, which is better applicable for quantitative analysis of biomarkers or protein-protein interactions. The biomarker assay can be performed either by direct or sandwich methods of fluorescence immunoassay. Application of ProteoChip BP has been well demonstrated by the extensive studies of 1) tumor-marker assays, 2) new drug screening by using 'Integrin Chip' and 3) protein expression profile analysis. Some of experimental results will be presented.

• Korean Journal of Food Science and Technology
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• v.20 no.1
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• pp.34-39
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• 1988

The possibility of using sodium dodecylsulfate-polyacrylamide gel electrophoresis was studied to detect specific proteins and their content in meat products such as beef, pork, fish, soybean, fish paste, ham and fish sausage. Many complicated bands were observed in the total protein fractions of the tested samples. The number of protein bands in the low salt-soluble protein fractions was considerably lesser and showed more specific bands in comparison with total protein fractions. Actone-insoluble fractions of non-meat proteins showed different patterns from meat proteins. A heating procedure seemed to be a cause for the diminished number and quantity of resolved protein bands in sausages. The results suggest that the discgel electrophoresis can be used to detect specific proteins and their content in protein foods, if a selective extraction method is emplyed.