• Journal of the Korean Data and Information Science Society
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• 제16권3호
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• pp.683-693
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• 2005

This paper presents a new transmembrane Protein topology prediction method which is an attempt to model the topological rules governing the topogenesis of transmembrane proteins. Context-dependent structural regions of the transmembrane protein are used as basic modeling units in order to effectively represent their topogenic roles during transmembrane protein assembly. These modeling units are modeled by means of a tied-state hidden Markov model, which can express the position-specific effect of amino acids during ransmembrane protein assembly. The performance of prediction improves with these modeling approaches. In particular, marked improvement of orientation prediction shows the validity of the proposed modeling. The proposed method is available at http://bioroutine.com/TRAPTOP.

• Molecules and Cells
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• 제39권9호
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• pp.692-698
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• 2016

Advances in next generation sequencing (NGS) technologies have enabled population-level studies for many animals to unravel the relationships between genotypic differences and traits of specific populations. The objective of this study was to perform evolutionary analysis of single nucleotide polymorphisms (SNP) in genes of Korean native cattle Hanwoo in comparison to SNP data from four other cattle breeds (Jersey, Simmental, Angus, and Holstein) and four related species (pig, horse, human, and mouse) obtained from public databases through NGS-based resequencing. We analyzed population structures and differentiation levels for the five cattle breeds and estimated species-specific SNPs with their origins and phylogenetic relationships among species. In addition, we identified Hanwoo-specific genes and proteins, and determined distinct changes in protein-protein interactions among five species (cattle, pig, horse, human, mouse) in the STRING network database by additionally considering indirect protein interactions. We found that the Hanwoo population was clearly different from the other four cattle populations. There were Hanwoo-specific genes related to its meat trait. Protein interaction rewiring analysis also confirmed that there were Hanwoo-specific protein-protein interactions that might have contributed to its unique meat quality.

• 센서학회지
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• 제17권5호
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• pp.380-386
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• 2008

Quartz crystal microbalance immunosensor has a capacity to perform a label-free and real time detection of a trace amount of analyte through the specific interaction between antibody and antigen. However, immobilization of antibody molecules on the sensor surface is a troublesome procedure for researchers who are not experienced in chemistry. Protein G has a specific affinity to antibody and would serve as a capturing agent for antibody when immobilized on the sensor surface. In this work, we prepared a protein G sensor chip by immobilizing protein G on the surface of quartz crystal microbalance and examined its capability to detect human haptoglobin or human transferrin with unpurified corresponding antiserum. Specific and dose dependent response was observed when the protein G chip was used for detection of antigens after saturated with antiserum. We also verified several advantageous aspects of the protein G chip such as improved flexibility and sensitivity.

• 한국동물학회지
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• 제37권1호
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• pp.130-136
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• 1994

Although alteration in protein phosphorylation by specific protein kinases is of importance in transducing cellular signals in a variety of neural/endocrine systems, little is known about protein phosphorylation in the hvpothalamus. The present study aims to explore whether activation of the second messenger-dependent protein kinases affects phosphorylation of specific proteins using a cell free phosphorylation system followed by SDS-polvacrylamide gel electrophoresis. Cytoplasmic fractions derived from hvpothalami of immature rats were used as substrates and several activators and/or inhibitors of CAMP-, phosphatidylinositol- and Ca2+-calmodulin-dependent protein kinases were assessed. Many endogenous proteins were extensively phosphorylated and depending on the signal transduction pathways, phosphorvlation profiles were markedly different. The present data indicate that extracellular signals may affect cellular events through protein phosphorylation by second messengers-protein kinases in the rat hypothalamus.

• 한국양식학회지
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• 제11권2호
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• pp.271-278
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• 1998

전복의 난황단백질의 특성을 조사하기 위하여 성숙한 참전복 암컷의 난소난 추출물로부터 sepharose Cl-4B gel chromatography을 사용하여 난황단백질을 분리하였다. 암컷과 수컷의 혈청과 난소난 추출물에 대한 항혈청을 이용하여 암수혈청과 난소난 추출물을 면역전기영동과 Ouchterlony 면역확산을 한 결과, 성숙한 암컷 혈청에는 암컷 특이 혈청 단백질(female specific serum protein) 이 존재하였으며, 이것은 난소난 추출물과 동일한 항원성을 가지고 있었다. 한 종류의 난황단백질이 난소난 추출물로부터 분리되었으며, 이 난황단백질은 SDS 전기영동에 의해 분자량이 각각 181kDa과 113kDa이 되는 2개의 subuit로 구성되어 있었다. 이들 난황단백질에 대한 항혈청은 성숙한 암컷 특이 혈청단백질과 간췌장 추출액과 침강반응을 보였으며 서로 교차반응이 일어났으나, 성숙한 수컷 간췌장 추출물에 대해서는 반응이 일어나지 않았다.

• 한국잠사곤충학회지
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• 제34권1호
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• pp.30-34
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• 1992

누에의 성충특이체액단백질(adult specific protein : ASP)의 생리 생화학적 특성 및 성충화 발육에 따른 기능을 구명하기 위한 연구의 일환으로 ASP의 분리·정제 및 분자적 특성을 조사하였다. ASP는 Sephadex G-100 gel 여과 및 CM52 ion exchange chromatography에 의해 분리·정제되었으며, 정제된 단백질의 순도는 native-PAGE 및 면역전기영동에 의해 확인되었다. ASP는 분자량 19.5kDa 및 17.5kDa으로 추정되는 2종류의 subunits으로 구성되어 있고 또한 당 및 지질을 포함하지 않는 단순단백질임이 밝혀졌다.

• 한국동물학회지
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• 제26권3호
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• pp.181-192
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• 1983

이차원 전긱영동법에 의하여 A. proteus의 tD strain과 tD strain이 박테리아와 공생에 의해 유도된 xD strain의 단백질 양성을 비교하였다. Silver stain에 의해 비교 가능한 200여개의 주요 단백질 가운데 tD strain에서 분자량 45,000, 동전점 5.9의 특이성 단백질이, xD strain의 세포액과 공생낭에서는 분자량 29,000, 동전점 5.5의 공생 특이성 단백질이 탐지되었다. 공생 특이성 단백질은 아메바 고은 배양 및 실험 공생 아메바를 이용한 실험 결과 박테리아와 직접 연관 되어 있었다. 탐지된 두 특이성 단백질에 대하여 종전의 세포 핵 이식 및 배양 실험을 통해서 얻어진 결과에 비추어 이들 단백질 상호 연관 및 세포내의 기능에 관하여 논의하였다.

• Journal of Plant Biology
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• 제36권4호
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• pp.377-382
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• 1993

벼(Oryza sativa L.) 캘러스는 2.0 mg/L 2,4-D와 0.5 mg/L kinetin이 첨가된 MS 배지에서 성숙종자로부터 유도되었으며 embryogenic callus(EC)와 nonembryogenic callus(NEC)는 색깔과 외부형태에 의해 경시적으로 선별되었다. EC와 NEC의 전체 단백질로부터 SDS-PAGE와 등전점 전기영동에 의한 전기영동적 분석은 EC와 NEC의 각각에 대해 특이적, 양적인 차이를 보여주었다. 또한 EC와 NEC의 2차원 전기영동 분석은 약 20여개 이상의 EC 특이단백질과 10여개의 NEC 특이 단백질 양상을 보여주었으며, 아울러 EC 특이적인 90, 65, 50 kD의 단백질은 microheterogeneity를 보여주는 반면, NEC에서는 분자량의 변이가 큰 일련의 산성 이질단백질군을 보여주었다.

• Bioinformatics and Biosystems
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• 제2권1호
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• pp.28-32
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• 2007

The protein phosphorylation is one of the important processes in the cell signaling pathway. A variety of protein kinase families are involved in this process, and each kinase family phosphorylates different kinds of substrate proteins. Many methods to predict the kinase-specific phosphoryrated sites or different types of phosphorylated residues (Serine/Threonine or Tyrosin) have been developed. We employed Supprot Vector Machine (SVM) to attempt the prediction of protein kinase specific phosphorylation sites. 10 different kinds of protein kinase families (PKA, PKC, CK2, CDK, CaM-KII, PKB, MAPK, EGFR) were considered in this study. We defined 9 residues around a phosphorylated residue as a deterministic instance from which protein kinases determine whether they act on. The subsets of PSI-BALST profile was converted to the numerical vectors to represent positive or negative instances. When SVM training, We took advantage of multiple SVMs because of the unbalanced training sets. Representative negative instances were drawn multiple times, and generated new traing sets with the same positive instances in the original traing set. When testing, the final decisions were made by the votes of those multiple SVMs. Generally, RBF kernel was used for the SVMs, and several parameters such as gamma and cost factor were tested. Our approach achieved more than 90% specificity throughout the protein kinase families, while the sensitivities recorded 60% on average.

• Journal of Microbiology
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• 제37권4호
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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.