• Journal of Microbiology
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• 제38권3호
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• pp.176-179
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• 2000

A challenge phage system was used to study the DNA-protein interaction between C4-dicarboxylic acid transport protein D(DCTD) or $\sigma$54, and a $\sigma$54 -dependent promoter, dctAp. R. meliloti dctA promoter regulatory region replaced the Omnt site on the phage. S. typhimurium strains overproducing either DCTD or $\sigma$54 directed this challenge phage towards lysogency, indicating that DCTD or E$\sigma$54 recognized the dctA promoter on the phage and repressed transcription of the ant gene. These challenge phage constructs will be useful for examining interactions between DCTD(or $\sigma$54) and the dctA promoter region.

• 한국자기공명학회논문지
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• 제10권1호
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• pp.96-104
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• 2006

The gene coding for APG8a (At4g21980), a protein from Arabidopsis thaliana, is involved in the autophagy process. The protein is an interesting candidate for structure determination by NMR spectroscopy. Toward this end, APG8a has been produced recombinantly in Escherichia coli and typical NMR experiments such as $^{15}N-HSQC$, HNCA, HN(CO)CA, CBCA(CO)NH, HCCH-TOCSY, HNCO were performed. The backbone resonances, HN, N, CA, CB, and C' were sequence-specifically assigned, and the secondary structures including 3 $\alpha$ helices and $4\beta$ strands were deduced based on the assignments. Due to the intrinsic flexibility or the effect of the denaturant, the backbone resonances were not fully observed. Since the structure calculation by NMR data was not possible, the 3-dimensional model was built based on the sequence homology, and compared with the NMR results. The overall structure of the model could explain and complement the NMR derived secondary structures.

• 한국자기공명학회논문지
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• 제18권1호
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• pp.36-40
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• 2014

Predicting secondary structure of protein through assigned backbone chemical shifts has been used widely because of its convenience and flexibility. In spite of its usefulness, chemical shift based analysis has some defects including isotopic shifts and solvent interaction. Here, it is shown that corrected chemical shift analysis for secondary structure of protein. It is included chemical shift correction through consideration of deuterium isotopic effect and calculate chemical shift index using probability-based methods. Enhanced method was applied successfully to one of the proteins from Mycobacterium tuberculosis. It is suggested that correction of chemical shift analysis could increase accuracy of secondary structure prediction of protein and small molecule in solution.

• Mass Spectrometry Letters
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• 제6권2호
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• pp.31-37
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• 2015

Phosphorylation upon protein is well known to a key regulator that implicates in modulating many cellular processes like growth, migration, and differentiation. Up to date, grafting of multidimensional separation techniques onto advanced mass spectrometry (MS) has emerged as a promising tool for figuring out the biological functions of phosphorylation in a cell. However, advanced MS-based phosphoproteomics is still challenging, due to its intrinsic issues, i.e., low stoichiometry, less susceptibility in positive ion mode, and low abundance in biological sample. To overcome these bottlenecks, diverse techniques (e.g., SCX, HILIC, ERLIC, IMAC, TiO₂, etc.) are continuously developed for on-/off-line enrichment of phosphorylated protein (or peptide) from biological samples, thereby helping qualitative/quantitative determination of phosphorylated protein and its phosphorylated sites. In this review, we introduce to the overall views of enrichment tools that are universally used to selectively isolate targeted phosphorylated protein (or peptide) from ordinary ones before MS-based phospoproteomic analysis.

• 대한방사성의약품학회지
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• 제2권2호
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• pp.69-72
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• 2016

Since the translocator protein (TSPO) is involved in neurodegeneration diseases, many scientists' interest has been focused on the development of a ligand targeting TSPO. A novel compound based on pyrazolo[1,5 -a] pyrimidine structure, DPA-714, has been studied and considered as a TSPO ligand with high affinity. In this highlight review, several researches for the novel radioligand for the translocator protein are illustrated.

• 통합자연과학논문집
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• 제9권1호
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• pp.35-40
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• 2016

Protein phosphatase manganese dependent 1D (PPM1D) is one of the Ser/Thr protein phosphatases belongs to the PP2C family. They play an important role in cancer tumorigenesis of various tumors including neuroblastoma, pancreatic adenocarcinoma, medulloblastoma, breast cancer, prostate cancer and ovarian cancer. Even though PPM1D is involved in the pathophysiology of various tumors, the three dimensional protein structure is still unknown. Hence in the present study, homology modelling of PPM1D was performed. 20 different models were modelled using single- and multiple-template based homology modelling and validated using different techniques. Best models were selected based on the validation. Three models were selected and found to have similar structures. The predicted models may be useful as a tool in studying the pathophysiological role of PPM1D.

• 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

• KSBB Journal
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• 제22권6호
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• pp.393-400
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• 2007

현재 많은 대학과 기업에서 다양한 방법으로 상용화가 가능한 protein microarray의 개발을 위해 많은 연구를 집중하고 있다. Protein microarray의 제작 및 분석 조건을 최적화하기 위한 연구도 진행되고 있지만 protein microarray로 부터 얻은 분석 결과를 모든 연구자들이 공유하고 통합하기 위한 노력이 절실한 실정이다. 뿐만 아니라, PCR 같은 무한 확장 방법이 존재하지 않는 단백질의 특성을 고려할 때, 좀 더 실용적인 protein microarray를 많이 만들기 위해서는 수많은 단백질들과 결합할 수 있는 특이성이 높고 결합력이 강한 capture molecule들을 개발하는 것이 필수이다. 그러나 이러한 장애에도 불구하고 protein microarray는 아주 적은 시료량으로 high-throughput assay가 가능하다는 장점 때문에 현재의 생명과학의 발전 추세로 볼 때 앞으로 protein microarray가 조만간 실용화될 것이며 이의 시장성은 매우 클 것으로 기대된다. 보다 빠른 실용화를 위해서는 protein microarray의 개발에 필요한 기반 기술의 개발과 동시에 이를 활용하기 위한 contents의 개발도 절실히 요구된다.

• Genomics & Informatics
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• 제19권4호
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• pp.43.1-43.12
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• 2021

Campylobacter jejuni is one of the most prevalent organisms associated with foodborne illness across the globe causing campylobacteriosis and gastritis. Many proteins of C. jejuni are still unidentified. The purpose of this study was to determine the structure and function of a non-annotated hypothetical protein (HP) from C. jejuni. A number of properties like physiochemical characteristics, 3D structure, and functional annotation of the HP (accession No. CAG2129885.1) were predicted using various bioinformatics tools followed by further validation and quality assessment. Moreover, the protein-protein interactions and active site were obtained from the STRING and CASTp server, respectively. The hypothesized protein possesses various characteristics including an acidic pH, thermal stability, water solubility, and cytoplasmic distribution. While alpha-helix and random coil structures are the most prominent structural components of this protein, most of it is formed of helices and coils. Along with expected quality, the 3D model has been found to be novel. This study has identified the potential role of the HP in 2-methylcitric acid cycle and propionate catabolism. Furthermore, protein-protein interactions revealed several significant functional partners. The in-silico characterization of this protein will assist to understand its molecular mechanism of action better. The methodology of this study would also serve as the basis for additional research into proteomic and genomic data for functional potential identification.

• Fisheries and Aquatic Sciences
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• 제1권2호
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• pp.255-259
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• 1998

This study was designed to evaluate the economic analysis of channel catfish production in 1998 based on fish value and total feed cost. Catfish received higher protein feeds with lesser amount based on the dietary protein levels, but received the constant total protein input for all treatments. Weight gain per pond for treatment 1 $(28\%\;protein,\;100\%\;of\;satiation)$ was higher (P<0.10) than for treatment 3 $(36\%\;protein,\;77.8\%\;of\;satiation)$, but not significantly higher than for treatment 2 $(32\%\;protein,\;87.5\%\;of\;satiation)$ at constant DE. At constant DE/P (treatments 4, 2 and 5), weight gain per pond for treatment 5 $(36\%\;protein,\;77.8\%\;of\;satiation)$ was lower (P<0.10) than for treatment 2, but not significantly lower than for treatment 4 $(28\%\;protein,\;100\%\;of\;satiation)$. At constant DE, feed conversion slightly improved as dietary protein level increased from $28\%\;to\;32\%$ and feed allowance decreased by $12.5\%$, but did not improve further as dietary protein level increased from $28\%\;to\;36\%$ and feed allowance decreased by $22.2\%$. At constant DE/P, feed conversion improved as dietary protein level increased from $28\%\;to\;32\%$ increased and feed allowance decreased by $12.5\%$, but did not improve as dietary protein level increased from $28\%\;to\;36\%$ and feed allowance decreased by $22.2\%$ Total feed cost for treatment 1 was slightly, but not significantly higher than for treatments 2 and 3 at constant DE. At constant DE/P, total feed cost for treatment 5 was higher (P<0.05) than for treatment 2, but not significantly higher than for treatment 4. Total value of fish ($ /ha) produced for treatment 1 was highest and lowest was for treatment 5. Return above feed cost was highest for treatment 1 and nearly the same as treatment 2. Return over feed cost for treatments 3 and 4 were slightly lower than for treatments 1 and 2. Economic analysis showed that feeding fish the diet containing $28\%$ protein and 3.08 kcal/g DE to satiation and the diet containing $32\%$ protein and 3.08 kcal/g DE to $87.5\%$ of satiation produced the highest profit to farmer.