• KIISE Transactions on Computing Practices
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• v.22 no.1
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• pp.56-60
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• 2016

Peptide identification in tandem mass spectrometry is usually done by searching the spectra against target databases consisting of reference protein sequences. To control false discovery rates for high-confidence peptide identification, spectra are also searched against decoy databases constructed by permuting reference protein sequences. In this case, a peptide of the same sequence could be included in both the target and the decoy databases or multiple entries of a same peptide could exist in the decoy database. These phenomena make the protein identification problem complicated. Thus, it is important to minimize the number of such redundant peptides for accurate protein identification. In this regard, we examined two popular methods for decoy database generation: 'pseudo-shuffling' and 'pseudo-reversing'. We experimented with target databases of varying sizes and investigated the effect of the maximum number of missed cleavage sites allowed in a peptide (MC), which is one of the parameters for target and decoy database generation. In our experiments, the level of redundancy in decoy databases was proportional to the target database size and the value of MC, due to the increase in the number of short peptides (7 to 10 AA). Moreover, 'pseudo-reversing' always generated decoy databases with lower levels of redundancy compared to 'pseudo-shuffling'.

• 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.

• Journal of Life Science
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• v.25 no.7
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• pp.833-838
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• 2015

Multidrug-resistant super bacterial, fungal, viral, and parasitic infections are major health threaten pathogens. However, to overcome the present healthcare situation, among the leading alternatives to current drugs are antimicrobial peptides (AMPs), which are abundantly produced via various species in nature. AMPs, small host defense proteins, are in charge of the innate immunity for the protection of multicellular organisms such as fish, amphibian, reptile, plants and animals from infection. The number of AMPs identified per year has increased steadily since the 1980s. Over 2,000 natural AMPs from bacteria, protozoa, fungi, plants, and animals have been listed into the antimicrobial peptide database (APD). The majority of these AMPs (>86%) possess 11–50 amino acids with a net charge from 0 to +7 and hydrophobic percentages between 31–70%. This report classified AMP into several categories including biological source, biological functions, peptide properties, covalent bonding pattern, and 3D structure. AMP functions not only antimicrobial activity but facilitates cell biological activity such as chemotatic activity. In addition, fibroblastic reticular cell (FRC) originated from mouse lymph node stroma induced the expression of AMP in inflammatory condition. AMP induced from FRC contained whey acidic protein (WAP) domain. It suggests that the classification of AMP will be done by protein domain.

• Applied Chemistry for Engineering
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• v.22 no.2
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• pp.119-124
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• 2011

Currently, people are exposed to many harmful diseases. Therefore, there are many schemes, such as automation of productive facilities, development of information and communication technology, enhanced the quality of human life and wealth. However, these processes lead to weakened immune system. Thus, people are more vulnerable to infections from pathogens and environmental stress. Misuse and abuse of drugs resulted in the rapid emergence of multidrug-resistant microbes and tumors, therefore, to find new antibiotics are urgently needed. One of them is a peptide-antibiotic, that is not or less occurred a drug-resistance, comparing to conventional drugs. Peptides with various antibiotic activities have been identified from life organisms. The present review provides an overview of activities and application of peptide antibiotics.

• Proceedings of the KAIS Fall Conference
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• 2012.05a
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• pp.269-273
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• 2012

본 연구는 알려진 녹차의 다양한 항산화, 항염 효능이 있는 Polyphenol 류 이외의 생물학적 활성을 가지는 펩타이드 및 당단백질 소재에 대한 특성과 분석을 위하여 연구되었다. 녹차에서 수용성 성분을 추출 후 알콜 침전방법을 사용하여 단백질과 펩타이드류를 분리하여 실험에 사용하였다. 전체 추출물 중에는 Glutamic acid가 14073.9ug/g, (39.11%)로 가장 높게 분석되었으며, GPC 분석결과 Mn 886, Mw 25218, Mp 890, Mw/Mn 28.46으로 분석이 되었으며, 전체적으로 3개의 피크로 분석되었다. 함유된 펩타이드를 분석하기 위하여 HPLC를 이용하여 RT 16.148min의 Fraction을 분리하여 펩타이드 분석결과 녹차에서 유래한 TNTLSN이라는 hexapeptide를 동정하였다. 이러한 펩타이드는 친수성이며, 안정도가 높은 특징을 가지고 있고, 분자량이 1000이하로 피부 흡수도가 높을 것으로 기대되며, Biodegradable하며, Renewable 한 자연 친화적인 화장품 소재로서 널리 활용될 수 있을 것으로 판단된다.

• Bioinformatics and Biosystems
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• v.1 no.2
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• pp.109-114
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• 2006

In proteomics research, proteins are digested into peptides by an enzyme and in mass spectrometer, these peptides break into fragment ions to generate tandem mass spectra. The tandem mass spectral data obtained from the mass spectrometer consists of the molecular weights of the precursor ion and fragment ions. The precursor ion mass of tandem mass spectrum is the first value that is fetched to sort the candidate peptides in the database search. We look far the peptide sequences whose molecular weight matches with precursor ion mass of the mass spectrum. Then, we choose one peptide sequence that shows the best match with fragment ions information. The precursor ion mass of the tandem mass spectrum is compared with that of the digested peptides of protein database within the mass tolerance that is assigned by users according to the mass spectrometer accuracy. In this study, we used reversed sequence database method to analyze the molecular weight distribution of precursor ions of the tandem mass spectra obtained by the FT LTQ mass spectrometer for human plasma sample. By reinterpreting the precursor ion mass distribution, we could compute the experimental accuracy and we suggested a method to improve the protein identification performance.

• Journal of Sericultural and Entomological Science
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• v.50 no.2
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• pp.145-149
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• 2012

Cecropin is a well-studied antimicrobial peptide that play important role as key factor in insect humoral immunity. In this study, cecropin-like antimicrobial peptide was isolated and purified from the larval haemolymph of immune-challenged japanese oak silkworm, Antheraea yamamai. To isolate antimicrobial peptide, we separated and compared acidic extracted hemolymph protein bends between control and immune-challenged larvae using SDS-PAGE analysis. In the immune hemolymph extract, but not of non-immune hemolymph, we detected differential expressed peptide band with molecular mass 4,223.01 Da. To understand this peptide better, we successfully purified this peptide using cation exchange chromatography and gel permeation chromatography. Its N-terminal amino acid sequence obtained by Edman degradation evidenced a significant degree of identity with other lepidopteran cecropins. The purified A. yamamai cecropin-like peptide showed a broad spectrum of activity against fungi, Gram-negative and Gram-positive bacteria.

• Journal of Life Science
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• v.15 no.3 s.70
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• pp.427-433
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• 2005

With the completely discovery of the Drosophila genome sequence, the next great challenge is to extract its biological information by systematic expression and to perform functional analysis of the gene. Here we reported a proteome analysis of D. melanogaster with two-dimensional electrophoresis (2-DE) and matrix-assisted laser desorption ionization time-of-flight mass spectrometer (MALDI-TOF-MS). The cell extracts of D. melanogaster, $200{\mu}g$ were resolved to more than 400 silver-stained spots by 2-DE. The most abundant protein spots were ranged from 4.0-7.5 of pI and from 15-90 kDa of molecular weight. The excised spots were destained and in-gel digested by trypsin. The masses of the resulting peptide mixtures were measured by MALDI-TOF-MS. Identified proteins were compared with measured peptide mass and a dynamic peptide searching database which is accessible via the internet. The results revealed that identified proteins were produced by 59 genes derived from 65 protein spots.

• Korean Journal Plant Pathology
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• v.12 no.1
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• pp.80-84
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• 1996

토양에서 분리한 방선균류(actinomycetes) GT103 균주의 배양여액 및 균체추출물은 담배의 주요 병원균인 담배 줄기속마름병균(Erwinia carotovora subsp. carotovora), 담배 탄저병균(Colletotrichum tabacum), 담배역병균(Phytophthora nicotianae var. nicotianae)등에 강한 항균활성을 보였다. 항균활성물질은 용매 추출, silica gel chromatography, HPLC 등을 실시하여 분리.정제하였으며 UV, IR, FAB-MS, \ulcornerH-NMR, \ulcornerC-NMR 분석결과 actinomycin group의 펩타이드계 항생 물질인 actinomycin C\ulcorner로 동정되었다. 이 활성물질의 담배 탄저병에 대한 방제효과는 50$\mu\textrm{g}$/ml 농도에서 100%, 10$\mu\textrm{g}$/ml 농도에서 90%의 방제효과를 보였다.

• Journal of the Society of Cosmetic Scientists of Korea
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• v.45 no.3
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• pp.299-306
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• 2019

Ginseng berry (GB) contains Ginsenoside Re and has anti-inflammatory and anti-wrinkle properties. In this study, TLC fractions 1, 2, and 4 of the ginseng berry amino acid complex were identified and analyzed by HPLC. And identified a peptide (AP-1) by LC/MASS analysis of fraction 1. The anti-inflammatory activity was confirmed by investigating the inhibitory effect of AP-1 on NO production. In addition, collagen synthesis using procollagen type I C-peptide (PIP) ELISA kit was 50% higher effective than that of the control group. From these results, the peptide isolated from ginseng berry amino acid complex is considered to have anti-inflammatory and anti-wrinkle effect, and may be useful as an anti-inflammatory and anti-aging cosmetic raw material.