• Biomedical Science Letters
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• v.13 no.4
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• pp.305-311
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• 2007

cAMP-dependent protein kinase A (PKA) is the best-characterized protein kinases and has served as a model of the structure and regulation of cAMP-binding protein as well as of protein kinases. To determine the function of PKA in development, we employed the yeast two-hybrid system to screen for catalytic subunit of PKA $(C\alpha)$ interacting partners in a cDNA library from mouse embryo. A Testis-brain RNA-binding protein (TB-RBP), specifically bound to $C\alpha$. This interaction was verified by several biochemical analysis. Our findings indicate that $C\alpha$ can modulate nucleic acid binding proteins of TB-RBP and provide insights into the diverse role of PKA.

• Journal of The Korean Society of Integrative Medicine
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• v.8 no.2
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• pp.53-61
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• 2020

Purpose : We investigated the correlation between body composition and lung function in healthy adults. Methods : This study included 204 healthy adults in whom all measurements were obtained once, and all data were analyzed using the SPSS software for Windows, version 22.0. Pearson's correlation analysis was performed to determine the correlation between body composition (represented by the total body water, protein mass, soft lean mass, mineral mass, basal metabolic rate, fat-free mass, skeletal muscle mass, and body fat percentage) and lung function (represented by the forced vital capacity [FVC], forced expiratory volume in 1 second [FEV₁], the FEV₁/FVC ratio, maximum voluntary ventilation [MVV], maximum expiratory pressure [MEP], and the maximum inspiratory pressure [MIP]). All measurements were obtained by two investigators to improve reliability. A significance level of α=.05 was used to verify statistical significance. Results : Among the lung function measurements obtained in both men and women, the FVC, FEV₁, MVV, and MIP were positively correlated with the total body water, protein mass, soft lean mass, mineral mass, basal metabolic rate, fat-free mass, and skeletal muscle mass in men (p<.05). The FEV₁/FVC ratio was negatively correlated with the total body water, soft lean mass, mineral mass, basal metabolic rate, fat-free mass and the body fat percentage (p<.05). Notably, the FVC, FEV₁, and MVV were positively correlated with the total body water, protein mass, soft lean mass, mineral mass, basal metabolic rate, fat-free mass, and skeletal muscle mass in women (p<.05). Conclusion : This study showed a significant correlation between body composition and lung function in healthy adults. In combination with future studies on lung function, our results can provide objective evidence regarding the importance of prevention of lung disease, and our data can be utilized in rehabilitation programs for patients with respiratory diseases.

• Journal of Life Science
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• v.14 no.6 s.67
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• pp.991-996
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• 2004

This paper deals with an integrated system that facilitates researchers to do motif and domain search effectively and systematically. The system we developed is constructed on the basis of the integration of various resources related to motif, domain, and protein family. Those resources that can be classified into databases and search programs are dispersed to be available in Internet. In order to develop this system, we extracted core contents of diverse databases, which are required to analyze the protein function in terms of motifs or domains, to construct local databases and installed motif or domain search programs on our server, which corresponding database has as its own search program. Diverse utilities and CGI (Common Gateway Interface) programs make the databases and the search programs interlocked and web-based graphical user interfaces integrate all the components of our system. Employing our integrated system, end-users can receive its one-stop service to do protein function analysis systematically and effectively, without surfing many sites in Internet and wasting time over integrating search results.

• KIPS Transactions on Software and Data Engineering
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• v.3 no.4
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• pp.163-168
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• 2014

In a protein molecule, ${\alpha}$-helices are important for protein structure, function, and binding to other proteins, so the analysis on the structure of helices has been researched. Since an interaction between two helices is evaluated based on their axes, massive errors in protein structure analysis would be caused if a curved or kinked long ${\alpha}$-helix is considered as a linear one. In this paper, we present an algorithm to reconstruct ${\alpha}$-helices in a protein molecule as a sequence of straight helices under given threshold.

• Journal of Microbiology and Biotechnology
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• v.19 no.2
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• pp.194-203
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• 2009

$HpaG_{Xooc}$, from rice pathogenic bacterium Xanthomonas oryzae pv. oryzicola, is a member of the harpin group of proteins, eliciting hypersensitive cell death in non-host plants, inducing disease and insect resistance in plants, and enhancing plant growth. To express and secret the $HpaG_{Xooc}$ protein in Bacillus subtilis, we constructed a recombinant expression vector pM43HF with stronger promoter P43 and signal peptide element nprB. The SDS-PAGE and Western blot analysis demonstrated the expression of the protein $HpaG_{Xooc}$ in B. subtilis. The ELISA analysis determined the optimum condition for $HpaG_{Xooc}$ expression in B. subtilis WBHF. The biological function analysis indicated that the protein $HpaG_{Xooc}$ from B. subtilis WBHF elicits hypersensitive response(HR) and enhances the growth of tobacco. The results of RT-PCR analysis revealed that $HpaG_{Xooc}$ induces expression of the pathogenesis-related genes PR-1a and PR-1b in plant defense response.

• Animal cells and systems
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• v.7 no.2
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• pp.159-164
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• 2003

The RAD3 gene of Saccharomyces cerevisiae is required for excision repair and is essential for cell viability. The RAD3 encoded protein possesses a single stranded DNA-dependent ATPase and DNA and DNA-RNA helicase activities. To examine the extent of conservation of structure and function of a S. pombe RAD3 during eukaryotic evolution, the RAD3 homolog gene was isolated by screening of genomic DNA library. The isolated gene was designated as HRD3 (homolog of RAD3 gene). Southern blot analysis confirmed that S. pombe chromosome contains the same DNA as HRD3 gene and this gene exists as a single copy in S. pombe. The transcript of 2.8 kb was detected by Northern blot analysis, The level of transcripts increased by ultraviolet (UV) irradiation, indicating that HRD3 is one of the UV-inducible genes in S. pombe. Furthermore, the predicted partial sequence of HRD3 protein has 60％ identity to S. cerevisiae RAD3 gene. This homology was particularly striking in the regions identified as being conserved in a group of DNA helicases. Gene deletion experiments indicate that the HRD3 gene is essential for viability and DNA repair function. These observations suggest evolutionary conservation of other protein components with which HRD3 might interact in mediating its DNA repair and viability functions.

• Journal of Microbiology and Biotechnology
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• v.17 no.2
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• pp.359-363
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• 2007

Because of the importance of the type III protein-secretion system in bacteria-plant interaction, its function in bacterial pathogenesis of plants has been intensively studied. To identity bacterial proteins interacting with Xanthomonas hrp gene products that are involved in pathogenicity, we performed the glutathione-bead binding analysis of Xanthomonas lysates containing GST-tagged Hrp proteins. Analysis of glutathione-bead bound proteins by 1-DE and MALDI-TOF has demonstrated that Avr proteins, RecA, and several components of the type III secretion system interact with HrpB protein. This proteomic approach could provide a powerful tool in finding interaction partners of Hrp proteins whose roles in host-pathogen interaction need further studies.

• Journal of the Korean Magnetic Resonance Society
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• v.23 no.2
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• pp.56-60
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• 2019

Study on the structure and dynamics of molecules at the atomic level is of great significance for understanding their function and stability as well as roles for various chemico-physical and biological processes. $^{17}O$ NMR spectroscopy has appeared as an elegant technique for investigating of the physicochemical and structural properties of oxygen-containing compounds such as metal organic frameworks and nanosized oxides. This method has drawn much attention as it provides unique insights into the properties of targets based on atomistic information of local oxygen environments which is otherwise difficult to obtain using other methods. In this mini review, we introduce and discuss the recent study and developments of $^{17}O$ NMR techniques which are tailored for the investigation on the structure and dynamics of water and inorganic materials.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.60 no.1
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• pp.114-122
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• 2015

Soybean is very useful crop to supply vegetable protein for human. However, cultivation arear of this economically important crop is gradually diminished in upland field. Hence, cultivation area of soybean is increased in paddy field. During the growth duration of soybean, excessive moisture injury is serious problem for sustainable production and supply. We investigated protein expression according to different period of seed soaking and germination after seed soaking. For comparison on expression of protein according to different condition, we performed two-dimensional electrophoresis. After electrophoresis analysis, we selected differentially expressed protein spots according to different condition such as soaking period and germination after soaking to identify protein function by using MALDI-TOF. Results revealed that pattern of expression of protein according to soaking period and germination after soaking were generally not different in major spots. However, degree of expression of protein in some protein spots was increased in accordance with decrease of soaking period. Especially, in Hwangkeum-Kong, Danyeop-Kon, and Pecking, the degree of expression of protein was remarkably increased for 4 days after soaking. But, according to germination after soaking, degree of expression of protein in germinated seeds of all cultivars was higher than un-germinated seeds. In results of MALDI-TOF analysis, specific proteins were identified by different soaking period such as Allergen Gly m Bd 28K, P24 oleosin isoform B. Also, in accordance with germination, degree of protein expression of the related protein, Gibberellin was increased in un-germinated seeds of Iksan-Kong. In ungerminated seeds of Sinpaldal-kong, proteins were identified as down-regulated by soaking such as ATP binding and Inhibitor II', proteinase.

• Journal of Ginseng Research
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• v.46 no.6
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• pp.750-758
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• 2022

Background: Mild cognitive impairment (MCI) is a transitional condition between normality and dementia. Ginseng is known to have effects on attenuating cognitive deficits in neurogenerative diseases. Ginsenosides are the main bioactive component of ginseng, and their protein targets have not been fully understood. Furthermore, no thorough analysis is reported in ginsenoside-related protein targets in MCI. Methods: The candidate protein targets of ginsenosides in brain tissues were identified by drug affinity responsive target stability (DARTS) coupled with label-free liquid chromatography-mass spectrometry (LC-MS) analysis. Network pharmacology approach was used to collect the therapeutic targets for MCI. Based on the above-mentioned overlapping targets, we built up a proteineprotein interaction (PPI) network in STRING database and conducted gene ontology (GO) enrichment analysis. Finally, we assessed the effects of ginseng total saponins (GTS) and different ginsenosides on mitochondrial function by measuring the activity of the mitochondrial respiratory chain complex and performing molecular docking. Results: We screened 2526 MCI-related protein targets by databases and 349 ginsenoside-related protein targets by DARTS. On the basis of these 81 overlapping genes, enrichment analysis showed the mitochondria played an important role in GTS-mediated MCI pharmacological process. Mitochondrial function analysis showed GTS, protopanaxatriol (PPT), and Rd increased the activities of complex I in a dose-dependent manner. Molecular docking also predicted the docking pockets between PPT or Rd and mitochondrial respiratory chain complex I. Conclusion: This study indicated that ginsenosides might alleviate MCI by targeting respiratory chain complex I and regulating mitochondrial function, supporting ginseng's therapeutic application in cognitive deficits.