• Parasites, Hosts and Diseases
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• v.47 no.1
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• pp.31-36
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• 2009

Cockroaches have been recognized as a major cause of asthma. Bla g 4 is one of the most important German cockroach allergens. The aim of this study is to investigate IgE reactivity to the recombinant Bla g 4 (rBla g 4) in the sera of allergic patients and identify linear IgE binding epitope. For protein expression, full-length Bla g 4 (EF202172) was divided into 5 overlapping peptide fragments (E1: aa 1-100, E2: aa 34-77, E3: aa 74-117, E4: aa 114-156, and E5: aa 153-182). The full-length and 5 peptide fragments of Bla g 4 was generated by PCR and over-expressed in E. coli BL21 (DE3). The IgE binding reactivities of the full-length and peptide fragments were measured by ELISA using 32 serum samples of cockroach allergy. The sera of 8 patients (25%) reacted with rBla g 4. Four sera (100%) showed IgE-binding reactivity to full-length and peptide fragment 4, and 2 sera (50%) reacted with peptide fragment 2. One (20%) serum reacted with peptide fragment 3. The results of ELISA using overlapping recombinant fragments indicated that the epitope region was located at amino acid sequences 34-73 and 78-113, and major IgE epitope of Bla g 4 was located at amino acid sequences 118-152 of C-terminal. B-cell epitope analysis of German cockroach allergen Bla g 4 could contribute to the strategic development of more specific and potentially efficacious immunotherapy.

• Mass Spectrometry Letters
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• v.4 no.4
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• pp.71-74
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• 2013

In the present study, we report that the charge-directed (assisted) peptide dissociation products, such as b- and y-type peptide backbone fragments, were the major products in MS/MS and $MS^3$ applications of some o-TEMPO-Bz-C(O)-peptide ions, while radical-driven dissociation products, such as a/x and c/z-type fragments, were previously shown to be the major products in the free radical initiated peptide sequencing mass spectrometry (FRIPS MS). Those o-TEMPO-Bz-C(O)-peptides share a common feature in their sequences, that is, the peptides do not include an arginine residue that has the highest proton affinity among free amino acids. The appearance of b- and y-type fragments as major products in FRIPS MS can be understood in terms of the so-called "mobile-proton model". When the proton is highly mobilized by the absence of arginine, the chare-directed peptide dissociation pathways appear to be more competitive than the radical-driven dissociation pathways, in our FRIPS experiments.

• The Korean Journal of Physiology
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• v.24 no.1
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• pp.131-144
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• 1990

It is well known that the atrial natriuretic peptide (ANP) has a prepro-hormone of 151 amino-acids which loses their hydrophobic signal peptide to form 126 amino acid prohormone. The whole prohormone is released and then cleaved by proteases into more than one circulating forms. Recently, Winters et al. (1988a, b) reported that high concentrations of N-terminal fragments of prepro-ANP $(26{\sim}55),\;(56{\sim}92)\;and\;(104{\sim}123)$ were detected in human plasma. However, their physiological roles have not been established. The present study was conducted to determine whether the N-terminal fragments of pro-ANP have any effect on the renal function and to compare the effect with those of G-terminal fragments of pro-ANP The results indicate that intrarenal arterial infusions of prepro-ANP $(26{\sim}41),\;(26{\sim}55),\;(56{\sim}92)\;and\;(104{\sim}123)$ induced no significant changes in renal function. Whereas ${\alpha}-human$ ANP $(prepro-ANP,\;124{\sim}151)$ and pro-ANP caused a significant increase in urine volume, renal plasma flow, glomerular filtration rate, urinary excretions of sodium, chloride and potassium, and fractional excretion of sodium. These results suggest that the N-terminal fragments of pro-ANP are ineffective, while the C-terminal fragments retain the natriuretic and diuretic activities.

• Preventive Nutrition and Food Science
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• v.4 no.2
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• pp.145-151
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• 1999

Apolipoprotein B-100 (apo B-100) is an important component in plasma low density lipoproteins (LDL). It function as the ligand for the LDL receptor in peripheral cells. The LDLs are removed from the circulation by both high-affinity receptor-mediated and receptor-independant pathways. LDLs are heterogeneous in their lipid content, size and density and certain LDL subspecies increase risk of atherosclerosis due to differences in the conformation of apo B in the particle. In the present study , surface and core peptide fraction of Apo B-100 have been characterized by comparing peptide-mapping and fluorescence spectroscopy. Surface fragments of apo B-100 were generated by digestion of LDL with either trypsin , pronase, or pancreatin elastase. Surface fractions were fractionated on a Sephadex G-50 column. The remaining core fragments were delipidated and redigested with the above enzymes, and the resulting core peptides were compared with surface peptides. Results from peptide-mapping by HPLC showed pronase-digestion was more extensive than trypsin -digestion to remove surface peptide fraction from LDL. Fluorescence spectra showed that core fractions contained higher amount of tryptophan than surface fractions, and it indicated that core fraction wa smore hydrophobic than surface fractions. A comparison of the behavior of the core and surface provided informations about the regions of apo B-100 involved in LDL metabolism and also about the structural features concerning the formation of atherosclerosis.

• 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.

• Parasites, Hosts and Diseases
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• v.46 no.4
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• pp.243-246
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• 2008

Bla g 2 is a cockroach allergen of great importance, This study was conducted to identify IgE-binding epitope(s) of Bla g 2 using the recombinant protein technique, Approximately 50% of tested sera showed IgE reactivity to Pichia-expressed Bla g 2 (PrBla g 2) and E. coli-expressed Bla g 2 (ErBla g 2), Only 5,3% of serum samples showed stronger reactivity to PrBla g 2 than ErBla g 2, indicating that serum was reactive to conformational or carbohydrate epitopes. The full-length and 5 peptide fragments of Bla g 2 were produced in E. coli. All fragments showed IgE-binding activity to the cockroach-allergy patients' sera. Specifically, peptide fragments of amino acid residue 1-75 and 146-225 appeared to be important for IgE-binding. The information about the IgE-binding epitope of Bla g 2 can aid in the diagnosis and treatment for cockroach allergies.

• Bulletin of the Korean Chemical Society
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• v.18 no.7
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• pp.687-689
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• 1997

• Journal of Microbiology and Biotechnology
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• v.11 no.1
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• pp.153-159
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• 2001

In order to clone the peptide synthetase gene form Lysobacter lactamgenus IFO 14,288, the gene fragments were amplified using primers for the adenylation domain and the thionylation domain of the peptide synthetase genes in other organisms by polymerase chain reaction (PCR). The resulting 0.5-kb fragment was cloned in a pGEM-T vector, and the nucleotide sequences were determined. Six different PCR products were obtained; three were identified to be a part of L-$\alpha$-aminoadipyl-L-cysteinyl-D-valine (ACV) synthetase and three to be other peptide synthetases. Using each of the two different classes of PCR products as mixed probes, a cosmid library of L. lactamgenus chromosomal DNA constructed in a pHC79 vector was screened by an in situ hybridization procedure, and one positive clone was selected which was bound by peptide synthetase gene fragments as well as ACV synthetase gene fragments. The partial sequence analysis formt he obtained pPTS-5 cosmid showed th presence of more than two open reading frames. These were for two putative membrane transporters, which were homologous with several integral membrane proteins including the ABC transporter ATP-binding protein of E. coli (YbjZ) and the metal ion uptake protein of Bacillus subtilis (YvrN). A 45% homology was also found between the two transporter proteins at the carboxy terminus. Through a hydropathy analysis and transmembrane analysis. 4-5 transmembrane domains were found in these two proteins. When the genes were expressed in Escherichia coli, the gene products inhibited the hose cell growth, probably due to the disturbance of the membrane transport system.

• Proceedings of the Korean Information Science Society Conference
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• 2012.06b
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• pp.426-428
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• 2012

In order to identify proteins that are present in biological samples, these samples are separated and analyzed under the sequential procedure as follows: protein purification and digestion, peptide fragmentation by tandem mass spectrometry (MS/MS) which breaks peptides into fragments, peptide identification, and protein identification. One of the widely used methods for protein identification is based on probabilistic approaches such as ProteinProphet and BaysPro. However, they do not consider the difference in peptide identification probabilities according to their length. Here, we propose a probabilistic graphical model-based approach to protein identification from MS/MS data considering peptide identification probabilities, number of sibling peptides, and peptide length. We compared our approach with ProteinProphet using a yeast MS/MS dataset. As a result, our model identified 27 more proteins than ProteinProphet at 1% of FDR (false discovery rate), confirming the importance of peptide length information in protein identification.

• YAKHAK HOEJI
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• v.40 no.2
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• pp.193-201
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• 1996

In order to study the role of C-terminal aromatic region of T4 endonuclease V in the interaction with substrate DNA, NMR and Fluorescence spectrum were recorded. Analysis of flu orescence emission spectra showed that C-terminal region of T4 endonuclease V is in or very near the binding site. In the HSQC spectrum of $^{15}N$-Tyr-labeled T4 endonuclease V*DNA complex, the broadening of a peak was observed. It is presumed that this peak corresponds to one among three tyrosine residues which belong to the WYKYY segment of C-terminal region of T4 endonuclease V. Interactions of peptide fragments consisting of C-terminal residues of T4 endonuclease V with DNAs(TT-, T^T-DNA) were investigated by NMR and Fluorescence experiment. The results suggest that two peptide fragments themselves bind to DNAs and their binding pattern is not an intercalation mode.