• Bulletin of the Korean Chemical Society
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• 제31권12호
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• pp.3521-3524
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• 2010

MTH1880 is a hypothetical protein derived from Methanobacterium thermoautotrophicum, thermophilic methanogen. The solution structure determined by NMR spectroscopy showed that it has a novel $\alpha+\beta$-fold with a highly acidic ligand binding pocket. Since MTH1880 maintains its ultra-stable structural characteristics at both high temperature and pressure, it has been considered as an excellent model for studying protein folding. To initiate the structural and folding study of MTH1880 in proving its unusual stability, we performed the site directed mutagenesis and biochemical analysis of MTH1880 mutants. Data from circular dichroism and NMR spectroscopy suggest that the point mutations perturbed the structural stability of protein even though the secondary structure is retained. This study will provide the useful information in understanding the role of participating residues during folding-unfolding process and our result will be used in designing further folding experiments for hyper-thermopile proteins like MTH1880.

• Journal of Microbiology
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• 제45권4호
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• pp.326-332
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• 2007

In order to understand the functional role of CPRl in Saccharomyces cerevisiae KNU5377 with regard to its multi-tolerance characteristics against high temperatures, inorganic acids, and oxidative stress conditions, whole cellular proteins were analyzed via liquid chromatography electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS). This procedure was followed by two-dimensional (2-D) gel electrophoresis. Under menadione stress conditions, the 23 upregulated proteins were clearly identified only in the wild- type strain of KNU5377. Among the proteins, Sodl1p Tsa1p, Ahp1, Cpr1p, Cpr3, Ssb2p, and Hsp12p were identified as components of antioxidant systems or protein-folding related systems. The CPR1 protein could not be completely detected in the $cpr1{\Delta}$ mutant of KNU5377 and the other upregulated proteins in the wild-type strain evidenced a clear correlation with the results of immunoblot analysis. Moreover, a reduction in growth patterns (about 50%) could be observed in the $cpr1{\Delta}$ mutant, as compared with that of the wild-type strain under mild MD stress conditions. These results indicate that the upregulation of CPR1 may contribute to tolerance against MD as an inducer of oxidative stress.

• 방사선산업학회지
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• 제5권1호
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• pp.1-5
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• 2011

Since proteomics can be employed to compare changes in the expression levels of many proteins under particular genetic and environmental conditions, using mass spectrometry to establish radiation stimulon, we performed two-dimensional gel electrophoresis and identified E. coli proteins whose expressions are affected by high dose of ionizing radiation. After exposure to 3 kGy, it was found that 6 proteins involved in carbon and energy metabolism were reduced. Although 4 of 7 protein spots showing a significant increase in expression level were neither identified nor classified, uridine phosphorylase (Udp), superoxide dismutase (SodB), and thioredoxin-dependent thiol peroxidase (Bcp) were proven to be up-regulated after irradiation. This suggests that E. coli subjected to high doses of radiation (3 kGy) may operate a defense system that is able to detoxify reactive oxygen species and stimulate the salvage pathway of nucleotide synthesis to replenish damaged DNA.

• 대한약침학회지
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• 제25권1호
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• pp.52-62
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• 2022

Objectives: Snake venom is a complex mixture of various pharmacologically active substances, such as small proteins, peptides, and organic and mineral components. This paper aims to identify and analyse the proteins in common venomous snakes, such as Gloydius blomhoffii (G. blomhoffii) and Agkistrodon acutus (A. acutus), in Korea. Methods: We used mass spectrometry, electrophoresis, N-terminal sequencing and in-gel digestion to analyse the proteins in these two snake venoms. Results: We identified eight proteins in G. blomhoffii venom and four proteins in A. acutus venom. The proteins detected in G. blomhoffii and A. acutus venoms were phospholipase A₂, snake venom metalloproteinase and cysteine-rich secretory protein. Snake C-type lectin (snaclec) was unique to A. acutus venom. Conclusion: These data will contribute to the current knowledge of proteins present in the venoms of viper snakes and provide useful information for investigating their therapeutic potential.

• 농업과학연구
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• 제38권1호
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• pp.65-70
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• 2011

Development of mouse fetus brains can be defined morphologically and functionally by three developmental stages, embryo day (ED) 16, postnatal stage one week and eight weeks. These defined stages of brain development may be closely associated with differential gene expression rates due to limited cellular resources such as energy, space, and free water. Complex patterns of expressed genes and proteins during brain development suggests the changes in relative concentrations of proteins rather than the increase in numbers of new gene products. This study was designed to evaluate early protein expression pattern in mouse fetus brain. The mouse brain proteome of fetus at ED 15.5, and 19.5 was obtained using 2-dimensional gel electrophoresis (DE). Analysis of the 2-DE gels in pH 3-10 range revealed the presence of 15 differentially expressed spots, of which 11 spots were identified to be known proteins following MALDI-TOF analysis; 3 spots were up-regulated and 8 spots were down-regulated in the mouse fetus brain at ED 15.5. UP-regulated proteins were identified as MCG18238, isoform M2 of pyruvate kinase isozymes M1/M2, isoform 2 of heterogeneous nuclear ribonucleoprotein K, heterogeneous nuclear ribonucleoprotein H2, creatine kinase B-type, 40S ribosomal protein SA and hemoglobin subunit beta-H1. Down-regulated proteins were putative uncharacterized protein, lactoylglutathione lyase and secreted acidic cysteine rich glycoprotein. Our results revealed composite profiles of mouse fetus brain proteins related to mouse fetus development by 2-DE analysis implying possible roles of these proteins in neural differentiation.

• BMB Reports
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• 제40권6호
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• pp.853-860
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• 2007

Resistance to anticancer drugs is a major obstacle in the effective treatment of tumors. To understand the mechanisms responsible for multidrug resistance (MDR), a proteomic approach was used to identify proteins that were expressed in different levels by the adriamycinresistant human gastric cancer cell line, SGC7901/ADR, and its parental cell line, SGC7901. Two-dimensional gel electrophoresis (2-DE) and image analysis was used to determine which protein spots were expressed in different levels by the two cell lines. These spots were then partially identified using ESI-Q-TOF mass spectrometry, and the differential expressional levels of the partially identified proteins were then determined by western blot analysis and real-time RT-PCR. Additionally, the association of Nucleophosmin (NPM1), a protein that was highly expressed by SGC7901/ADR, with MDR was analyzed using siRNA. As a result of this study, well-resolved, reproducible 2-DE patterns of SGC7901/ADR and SGC7901 were established, and 16 proteins that may playa role in the development of thermo resistance were identified. Additionally, suppression of NPMl expression was found to enhance adriamycin chemosensitivity in SGC7901/ADR. These results provide a fundamental basis for the elucidation of the molecular mechanism of MDR, which may assist in the treatment of gastric cancer.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2000년도 International Symposium on Bioinformatics
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• pp.13-16
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• 2000

Microorganisms have been widely employed for the production of useful bioproducts including primary metabolites such as ethanol, succinic acid, acetone and butanol, secondary metabolites represented by antibiotics, proteins, polysaccharides, lipids and many others. Since these products can be obtained in small quantities under natural condition, mutation and selection processes have been employed for the improvement of strains. Recently, metabolic engineering strategies have been employed for more efficient production of these bioproducts. Metabolic engineering can be defined as purposeful modification of cellular metabolic pathways by introducing new pathways, deleting or modifying the existing pathways for the enhanced production of a desired product or modified/new product, degradation of xenobiotics, and utilization of inexpensive raw materials. Metabolic flux analysis and metabolic control analysis along with recombinant DNA techniques are three important components in designing optimized metabolic pathways, This powerful technology is being further improved by the genomics, proteomics, metabolomics and bioinformatics. Complete genome sequences are providing us with the possibility of addressing complex biological questions including metabolic control, regulation and flux. In silico analysis of microbial metabolic pathways is possible from the completed genome sequences. Transcriptome analysis by employing ONA chip allows us to examine the global pattern of gene expression at mRNA level. Two dimensional gel electrophoresis of cellular proteins can be used to examine the global proteome content, which provides us with the information on gene expression at protein level. Bioinformatics can help us to understand the results obtained with these new techniques, and further provides us with a wide range of information contained in the genome sequences. The strategies taken in our lab for the production of pharmaceutical proteins, polyhydroxyalkanoate (a family of completely biodegradable polymer), succinic acid and me chemicals by employing metabolic engineering powered by genomics, proteomics, metabolomics and bioinformatics will be presented.

• Plant Biotechnology Reports
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• 제4권4호
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• pp.311-319
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• 2010

Lettuce is an economically important leafy vegetable that accumulates a milk-like sap called latex in the laticifer. Previously, we conducted a large-scale lettuce latex proteomic analysis. However, the identified proteins were obtained only from lettuce ESTs and proteins deposited in NCBI databases. To extend the number of known latex proteins, we carried out an analysis identifying 302 additional proteins that were matched to the NCBI non-redundant protein database. Interestingly, the newly identified proteins were not recovered from lettuce EST and protein databases, indicating the usefulness of this hetero system in MudPIT analysis. Gene ontology studies revealed that the newly identified latex proteins are involved in many processes, including many metabolic pathways, binding functions, stress responses, developmental processes, protein metabolism, transport and signal transduction. Application of the non-redundant plant protein database led to the identification of an increased number of latex proteins. These newly identified latex proteins provide a rich source of information for laticifer research.

• Journal of Microbiology and Biotechnology
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• 제29권7호
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• pp.1155-1164
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• 2019

Lichens contain diverse bioactive secondary metabolites with various chemical and biological properties, which have been widely studied. However, details of the inhibitory mechanisms of their secondary metabolites against influenza A virus (IAV) have not been documented. Here, we investigated the antiviral effect of lichen extracts, obtained from South Korea, against IAV in MDCK cells. Of the lichens tested, Nipponoparmelia laevior (LC24) exhibited the most potent inhibitory effect against IAV infection. LC24 extract significantly increased cell viability, and reduced apoptosis in IAV-infected cells. The LC24 extract also markedly reduced (~ 3.2 log-fold) IAV mRNA expression after 48 h of infection. To understand the antiviral mechanism of LC24 against IAV, proteomic (UPLC-$HDMS^E$) analysis was performed to compare proteome modulation in IAV-infected (V) vs. mock (M) and LC24+IAV (LCV) vs. V cells. Based on Ingenuity Pathway Analysis (IPA), LC24 inhibited IAV infection by modulating several antiviral-related genes and proteins (HSPA4, HSPA5, HSPA8, ANXA1, ANXA2, $HIF-1{\alpha}$, AKT1, MX1, HNRNPH1, HNRNPDL, PDIA3, and VCP) via different signaling pathways, including $HIF-1{\alpha}$ signaling, unfolded protein response, and interferon signaling. These molecules were identified as the specific biomarkers for controlling IAV in vitro and further confirmation of their potential against IAV in vivo is required. Our findings provide a platform for further studies on the application of lichen extracts against IAV.

• Journal of Plant Biotechnology
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• 제49권2호
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• pp.118-123
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• 2022

고구마의 저온 내성 반응의 분자적 기작에 대한 정보를 얻기 위해 저온 저장 내성이 높은 고구마 품종 Xushu 15-1과 저온 저장 내성이 낮은 Xushu 15-4에서 발현되는 단백질체를 2-D와 MALDI-TOF/TOF를 이용하여 분석하였다. 저온 처리가 되지 않은 대조구 간의 분석 결과, Xushu 15-1에서는 4개의 단백질 spot이 새롭게 발현되었으며, Xushu 15-4에서는 1개 단백질 spot의 발현량이 Xushu 15-1에 비하여 더 높았다. 이들 중 Xushu 15-1에서 새롭게 발현된 spot 2는 sporamin으로 동정되었다. 4℃ 처리된 2개 품종의 저장뿌리에서 8주 동안의 단백질 발현량의 변화를 조사한 결과, Xushu 15-1에서는 별다른 차이가 없었다. 그러나, Xushu 15-4에서는 1개 단백질 spot의 발현량이 증가하였고 4개 spot들의 발현량은 감소하였다. 발현량이 감소된 단백질 중 spot 7 및 8번은 actin, spot 9 및 10번은 fructokinase-like protein으로 동정되었다. 본 연구의 결과는 저장 중 고구마의 저온 내성과 관련된 복잡한 반응성 기작에 대한 이해를 높이고, 향후 저온 저장 능력이 향상된 신품종 고구마의 개발을 위한 후보 유전자를 특정하는 데 이용될 수 있을 것으로 사료된다.