• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2002년도 제1차워크샵
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• pp.5-23
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• 2002

Motivation: Protein-protein interaction plays a critical role in the biological processes. The identification of interacting proteins by bioinformatical methods can provide new lead In the functional studies of uncharacterized proteins without performing extensive experiments. Results: Protein-protein interactions are predicted by a computational algorithm based on the weighted scoring system for domain interactions between interacting protein pairs. Here we propose potential interaction domain (PID) pairs can be extracted from a data set of experimentally identified interacting protein pairs. where one protein contains a domain and its interacting protein contains the other. Every combinations of PID are summarized in a matrix table termed the PID matrix, and this matrix has proposed to be used for prediction of interactions. The database of interacting proteins (DIP) has used as a source of interacting protein pairs and InterPro, an integrated database of protein families, domains and functional sites, has used for defining domains in interacting pairs. A statistical scoring system. named "PID matrix score" has designed and applied as a measure of interaction probability between domains. Cross-validation has been performed with subsets of DIP data to evaluate the prediction accuracy of PID matrix. The prediction system gives about 50% of sensitivity and 98% of specificity, Based on the PID matrix, we develop a system providing several interaction information-finding services in the Internet. The system, named PreDIN (Prediction-oriented Database of Interaction Network) provides interacting domain finding services and interacting protein finding services. It is demonstrated that mapping of the genome-wide interaction network can be achieved by using the PreDIN system. This system can be also used as a new tool for functional prediction of unknown proteins.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2004년도 The 3rd Annual Conference for The Korean Society for Bioinformatics Association of Asian Societies for Bioinformatics 2004 Symposium
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• pp.265-271
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• 2004

The interaction network of protein -protein plays an important role to understand the various biological functions of cells. Currently, the high -throughput experimental techniques (two -dimensional gel electrophoresis, mass spectroscopy, yeast two -hybrid assay) provide us with the vast amount of data for protein-protein interaction at the proteome scale. In order to recognize the role of each protein in their network, the efficient bioinformatical and computational analysis methods are required. We propose a systematic and mathematical method which can analyze the protein -protein interaction network rigorously and enable us to capture the biological and physical essence of a topological character and stability of protein -protein network, and sensitivity of each protein along the biological pathway of their network. We set up a Laplacian matrix of spectral graph theory based on the protein-protein network of yeast proteome, and perform an eigenvalue analysis and apply a perturbation method on a Laplacian matrix, which result in recognizing the center of protein cluster, the identity of hub proteins around it and their relative sensitivities. Identifying the topology of protein -protein network via a Laplacian matrix, we can recognize the important relation between the biological pathway of yeast proteome and the formalism of master equation. The results of our systematic and mathematical analysis agree well with the experimental findings of yeast proteome. The biological function and meaning of each protein cluster can be explained easily. Our rigorous analysis method is robust for understanding various kinds of networks whether they are biological, social, economical...etc

• Preventive Nutrition and Food Science
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• 제16권4호
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• pp.291-298
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• 2011

Yam extracts (Dioscorea batatas) have been reported to possess a variety of functions. However, studies on its osteogenic properties are limited. In this study, we investigated the effect of ethanol and water extracts on osteoblast proliferation and bone matrix protein synthesis, type I collagen and alkaline phosphatase (ALP), using osteoblastic MC3T3-E1 cell model. MC3T3-E1 cells were cultured with yam ethanol and water extracts (0~30 mg/L) within 39 days of osteoblast differentiation period. Cell proliferation was measured by MTT assay. Bone matrix proteins were assessed by the accumulation of type I collagen and ALP activity by staining the cell layers for matrix staining. Also, the secreted (media) matrix protein concentration (type I collagen) and enzyme activity (ALP) were measured colorimetrically. Yam ethanol and water extracts stimulated cell proliferation within the range of 15~30 mg/L at 15 day treatment. The accumulation of type I collagen in the extracellular matrix, as well as secreted collagen in the media, increased with increasing doses of yam ethanol (3~15 mg/L) and water (3~30 mg/L) extracts. ALP activity was not affected by yam ethanol extracts. Our results demonstrated that yam extracts stimulated osteoblast proliferation and enhanced the accumulation of the collagenous bone matrix protein type I collagen in the extracellular matrix. These results suggest that yam extracts may be a potential activator for bone formation by increasing osteoblast proliferation and increasing bone matrix protein type I collagen. Before confirming the osteogenic action of yam, further studies for clarifying how and whereby yam extracts can stimulate this ostegenesis action are required.

• International Journal of Industrial Entomology and Biomaterials
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• 제3권1호
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• pp.1-6
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• 2001

Silk protein has been investigated by many researchers to apply to biomedical field. We reviewed biomedical applications of silk protein such as matrix of wound dressing and drug delivery system. Since silk fibroin/ poly (ethylene glycol) (PEG) semi-interpenetrating polymer networks showed good mechanical properties and wound healing phenomena, it can be used as wound dressing materials. Sericin nanoparticles pre- pared by conjugation with PEG and silk protein/ poloxamer mixture gel are expected to become a deliv- ery as matrix for hydrophobic drug.

• Preventive Nutrition and Food Science
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• 제10권1호
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• pp.40-45
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• 2005

Age-related changes in bone metabolism are well established by biochemical markers of bone matrix in serum and urine, but analysis of the residual bone matrix, which is still turning over, has not been investigated. In the present study, we measured in vivo rates of bone protein synthesis using a precursor-product method based on the exchange of ²H from ²H₂O into amino acids. Four percent ²H₂O was administered to mice in drinking water after intraperitonial (i.p) bolus injection of 99.9% ²H₂O. Mice were divided into the two groups: growing young mice were administered 4% ²H₂O for 12 weeks after an i.p bolus injection at 5 week of age, whereas weight stable adult mice started drinking 4% ²H₂O 8 weeks later than the growing group and continued 4% ²H₂O drinking for 8 weeks. Mass isotopomer abundance in alanine from bone protein was analyzed by gas chromatography/mass spectrometry. Body ²H₂O enrichments were in the range of 1.88-2.41% over the labeling period. The fractional synthesis rates (ks) of bone protein were 2.000±0.071%/d for growing mice and 0.243±0.014%/d for adult mice. These results demonstrate that the bone protein synthesis rate decreases with age and present direct evidence of age-related changes in bone protein synthesis.

• 대한화장품학회:학술대회논문집
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• 대한화장품학회 2003년도 IFSCC Conference Proceeding Book I
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• pp.590-600
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• 2003

The matrix metalloproteinases (MMPs) are a family of enzymes responsible for degrading connective tissue. MMPs catalyze the breakdown of collagen from the extracellular matrix, leading to wrinkle formation and accelerated skin aging. Furthermore, ultraviolet irradiation causes increased expression of certain MMPs. In the extracellular matrix turnover, MMPs are interacting with endogenous regulators named tissue inhibitors of metalloproteinases (TIMPs). Using peptide substrate assays, it has been demonstrated that TIMP-MMP complexes interact highly specifically with $K_{i}$ values of 10$^{-9}$ -10$^{-16}$ M. Therefore applications for TIMP as inhibitor of collagen degradation are suggested for cosmetic anti-aging products to prevent wrinkle formation and loss of elasticity. To date four TIMP proteins (TIMP-1, TIMP-2, TIMP-3 and TIMP-4) have been identified which show a high degree in sequence similarity. The production of human TIMP-2, a 194-residue nonglycosylated protein, was performed by fed-batch culture of Escherichia coli. TIMP-2 accumulated in the bacterial cells in an insoluble form as inclusion bodies. The inclusion bodies were solubilized and the protein refolded to yield the native TIMP-2 in the active form. The integrity of the protein was confirmed by mass analysis, Edman sequencing and gel shift experiments with authentic samples. The inhibitory activity of the refolded and purified TIMP-2 was demonstrated with MMP-1 and MMP-2 assays using synthetic fluorogenic peptide substrates.s.

• BMB Reports
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• 제55권12호
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• pp.627-632
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• 2022

Dickkopf-1 (DKK1) is a secreted protein that acts as an antagonist of the canonical WNT/β-catenin pathway, which regulates osteoblast differentiation. However, the role of DKK1 on osteoblast differentiation has not yet been fully clarified. Here, we investigate the functional role of DKK1 on osteoblast differentiation. Primary osteoprogenitor cells were isolated from human spinal bone tissues. To examine the role of DKK1 in osteoblast differentiation, we manipulated the expression of DKK1, and the cells were differentiated into mature osteoblasts. DKK1 overexpression in osteoprogenitor cells promoted matrix mineralization of osteoblast differentiation but did not promote matrix maturation. DKK1 increased Ca⁺ influx and activation of the Ca⁺/calmodulin-dependent protein kinase II Alpha (CAMK2A)-cAMP response element-binding protein 1 (CREB1) and increased translocation of p-CREB1 into the nucleus. In contrast, stable DKK1 knockdown in human osteosarcoma cell line SaOS2 exhibited reduced nuclear translocation of p-CREB1 and matrix mineralization. Overall, we suggest that manipulating DKK1 regulates the matrix mineralization of osteoblasts by Ca⁺-CAMK2A-CREB1, and DKK1 is a crucial gene for bone mineralization of osteoblasts.

• Mass Spectrometry Letters
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• 제4권1호
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• pp.21-23
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• 2013

The effects of trifluoroacetic acid (TFA) were evaluated on the generation of multiply charged ions of cytochrome c in a 2-nitrophloroglucinol (2-NPG) matrix in high-vacuum, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The presence of 1% TFA in the 2-NPG matrix solution was more effective in generating multiply charged protein ions than matrix solutions containing 0.1% or 0% TFA. Regarding the matrix itself, with 1% TFA, 2-NPG was significantly more effective in generating multiply charged ions than 2,5-dihydroxybenzoic acid (2,5-DHB). The maximum charge state of cytochrome c was +8 when using a 2-NPG matrix containing 1% TFA.

• Journal of Animal Science and Technology
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• 제62권4호
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• pp.533-542
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• 2020

The objective of this study was to observe the interactions between salt-soluble proteins extracted from beef and elephant foot yam (Amorphophallus campanulatus) flour in heat-induced gel matrix development. The effect of salt concentration; 0.5%, 1.0%, 1.5%, and 2.0% in weight/weight basis (w/w), during protein extraction on pH, salt-soluble protein concentration and myofibril fractions of beef extract was determined firstly, and no significant effect was found. The beef salt-soluble proteins extracted using salt solution at different concentrations were then added with elephant foot yam flour at 5%, 10%, and 15% w/w, gelatinized at 90℃ for 20 min, and cooled down at 4℃ for 12 h. The interactions between beef salt-soluble proteins and elephant foot yam flour resulted in an improved gel strength (p < 0.01) and the addition level of elephant foot yam flour affected the pH, instrumental color, moisture, crude protein, and ash content significantly. The addition of elephant foot yam flour also reduced the size of the pores in the gel matrix as shown by scanning electron microscope (SEM) photographs. These suggest that elephant foot yam flour well interacts with beef salt-soluble proteins to form gel matrix.

• 정보처리학회논문지D
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• 제14D권7호
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• pp.743-752
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• 2007

단백질은 다른 물질과의 결합하여 기능을 수행하기 때문에 활성 사이트가 유사한 단백질은 유사한 기능을 가진다. 따라서 단백질의 바인딩 영역을 식별함으로써 단백질의 기능을 추론할 수 있다. 이 논문은 MCL (Markov Cluster) 알고리즘을 이용하여 단백질의 바인딩 영역을 추출하는 새로운 방법을 제시한다. 이를 위하여 단백질의 표면 잔기 거리를 나타내는 distance matrix를 생성하고, 여기에 MCL 프로세스를 적용한다. 제시한 방법을 평가하기 위해 Catalytic Site Atlas (CSA) 데이터를 사용하였다. CSA 데이터 (94개의 단일 체인 단백질)를 이용한 실험 결과, 알고리즘은 91개 단백질의 활성 사이트 주변의 바인딩 영역을 검출하였다. 이 논문은 단백질 활성 사이트를 분석하기 위한 새로운 기하학적 특징을 제시하였고, 활성 사이트와 관련이 없는 잔기를 제거함으로써 단백질 표면의 분석의 시간을 줄일 수 있는 장점이 있다.