• Journal of the Korean Magnetic Resonance Society
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• v.23 no.4
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• pp.104-107
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• 2019

Many proteins are expressed as an insoluble form during the production using Escherichia coli (E. coli) system. Although various methods are applied to increase their amounts of soluble expression, refolding is the only feasible way to obtain a target protein in some cases. Moreover, protein NMR experiments require ¹³C/¹⁵N-labeled proteins that can only be obtained from E. coli systems in terms of cost and technical difficulty. The finding of appropriate refolding conditions for a target protein is a time-consuming process. In particular, it is very difficult to determine whether the refolded protein has a native structure, when a target protein has no enzymatic activity and its refolding yield is very low. Here, we showed that 1-dimensional ¹H-¹⁵N heteronuclear single quantum correlation (1D ¹H-¹⁵N HSQC) experiment can be efficiently used to screen an optimal condition for the refolding of a target protein by monitoring both the structure and concentration of the refolded protein.

• Korean Journal of Agricultural Science
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• v.37 no.2
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• pp.245-248
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• 2010

This study was conducted to investigate effect of changes in target fat and protein contents in milk on feed cost using a simulation modeling approach based on the 2001 dairy NRC. Two simulations were done; simulation I had a limitation (up to 20%), but simulation II had no limitation for the use of cottonseed hull in a diet. Using commonly used feed ingredients in Korea, we formulated least cost diets that meet nutrient requirement of a lactating dairy cow producing 36 kg of milk with combinations of 0.1% decrease or 0.1% increase in target milk fat or protein, respectively, from the national average milk fat (4.0%) and milk protein (3.1%). The contents of alfalfa and corn in a least-cost diet were decreased and those of tall fescue, whole cottonseed and rapeseed meal were increased with decreasing fat and/or increasing protein in milk. Scenarios that decreased target milk fat percentage from 4.0% to 3.9% reduced feed cost by 2 won per kg. Due to decrease in feed intake, daily feed cost was even more reduced (136 won per head) by decreasing target milk fat percentage. Increase in target milk protein percentage from 3.1% to 3.2% reduced feed cost by 6 won per kg. Among scenarios simulated, the least feed cost was obtained in scenario aimed for 3.9% fat and 3.2% of protein in milk. We conclude that a feeding practice for increasing milk protein percentage does not directly increase feed cost. In addition, feeding practices that increase protein content in milk is expected to improve economic life-span and reproductive performance of dairy cows.

• Journal of Ginseng Research
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• v.41 no.4
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• pp.534-539
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• 2017

Background: Ginsenosides are the main ingredients of ginseng, which, in traditional Eastern medicine, has been claimed to have therapeutic values for many diseases. In order to verify the effects of ginseng that have been empirically observed, we utilized the reverse docking method to screen for target proteins that are linked to specific diseases. Methods: We constructed a target protein database including 1,078 proteins associated with various kinds of diseases, based on the Potential Drug Target Database, with an added list of kinase proteins. We screened 26 kinds of ginsenosides of this target protein database using docking. Results: We found four potential target proteins for ginsenosides, based on docking scores. Implications of these "hit" targets are discussed. From this screening, we also found four targets linked to possible side effects and toxicities, based on docking scores. Conclusion: Our method and results can be helpful for finding new targets and developing new drugs from natural products.

• YAKHAK HOEJI
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• v.46 no.1
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• pp.24-29
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• 2002

Enoyl-Acyl Carrier Protein Reductase (Fabl) of bacteria is hem as an important target for new antibacterial drugs and plays a determinant role in completing cycles of elongation in type-H fatty acid synthase system. In this study, a fabI gene from Staphylococcus aureus 6538p cloned in pET-l4b vector and FabI protein was over-produced in Escherichaia coli BL2l (DE3). $NH_2$-terminal His-tagged FabI protein was purified by nickel-nitrilotriacetic acid (Ni-NTA) metalaffinity chromatography Purified 6xHis-tagged FabI showed a catalytic activity on tram - 2 - octenoyl - N -acethlcysteamine by utilizing NADPH as a cofactor. For the discovery of new FabI inhibitors from chemical libraries, a target-oriented screening system using a 96-well plate was developed. About 10,000 chemical libraries from Korea Chemical Bank wore tested in this screening system, and 26 chemicals (0.25%) among them showed an inhibitory activity against FabI enzyme. This result showed that a new screening system can be used for the discovery of new FabI inhibitors.

• Biotechnology and Bioprocess Engineering:BBE
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• v.10 no.3
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• pp.248-253
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• 2005

AfsR2, originally identified from Streptomyces lividans, is a global regulatory protein which stimulates antibiotic biosynthesis. Through its stable chromosomal integration, the high level of gene expression of afsR2 significantly induced antibiotic production as well as the sporulation of S. lividans, implying the presence of yet-uncharacterized AfsR2-target proteins. To identify and evaluate the putative AfsR2-target proteins involved in antibiotic regulation, the proteomics-driven approach was applied to the wild-type S. lividans and the afsR2-integrated actinorhodin overproducing strain. The 20 gel-electrophoresis gave approximately 340 protein spots showing different protein expression patterns between these two S. lividans strains. Further MALDI-TOF analysis revealed several AfsR2-target proteins, including glyceraldehyde-3-phosphate dehydrogenase, putative phosphate transport system regulator, guanosine penta phosphate synthetase/polyribonucleotide nucleotidyltransferase, and superoxide dismutase, which suggests that the AfsR2 should be a pleiotropic regulatory protein which controls differential expressions of various kinds of genes in Streptomyces species.

• Molecules and Cells
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• v.43 no.12
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• pp.1035-1045
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• 2020

The Drosophila genome contains four low molecular weight-protein tyrosine phosphatase (LMW-PTP) members: Primo-1, Primo-2, CG14297, and CG31469. The lack of intensive biochemical analysis has limited our understanding of these proteins. Primo-1 and CG31469 were previously classified as pseudophosphatases, but CG31469 was also suggested to be a putative protein arginine phosphatase. Herein, we present the crystal structures of CG31469 and Primo-1, which are the first Drosophila LMW-PTP structures. Structural analysis showed that the two proteins adopt the typical LMW-PTP fold and have a canonically arranged P-loop. Intriguingly, while Primo-1 is presumed to be a canonical LMW-PTP, CG31469 is unique as it contains a threonine residue at the fifth position of the P-loop motif instead of highly conserved isoleucine and a characteristically narrow active site pocket, which should facilitate the accommodation of phosphoarginine. Subsequent biochemical analysis revealed that Primo-1 and CG31469 are enzymatically active on phosphotyrosine and phosphoarginine, respectively, refuting their classification as pseudophosphatases. Collectively, we provide structural and biochemical data on two Drosophila proteins: Primo-1, the canonical LMW-PTP protein, and CG31469, the first investigated eukaryotic protein arginine phosphatase. We named CG31469 as DARP, which stands for Drosophila ARginine Phosphatase.

• Journal of Crop Science and Biotechnology
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• v.10 no.1
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• pp.33-38
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• 2007

Nitrogen management at the panicle initiation stage(PI) should be fine-tuned for securing a concurrent high yield and high quality rice production. For calibration and testing of the recommendation models of N topdressing rates at PI for target grain yield and protein content of rice, three split-split-plot design experiments including five rice cultivars and various N rates were conducted at the experimental farm of Seoul National University, Korea from 2003 to 2005. Data from the first two years of experiments were used to calibrate models to predict grain yield and milled-rice protein content using shoot fresh weight(FW), chlorophyll meter value(SPAD), and the N topdressing rate(Npi) at PI by stepwise multiple regression. The calibrated models explained 85 and 87% of the variation in grain yield and protein content, respectively. The calibrated models were used to recommend Npi for the target protein content of 6.8%, with FW and SPAD measured for each plot in 2005. The recommended N rate treatment was characterized by an average protein content of 6.74%(similar to the target protein content), reduced the coefficient of variation in protein content to 2.5%(compared to 4.6% of the fixed rate treatment), and increased grain yield. In the recommended N rate treatments for the target protein content of 6.8%, grain yield was highly dependent on FW and SPAD at PI. In conclusion, the models for N topdressing rate recommendation at PI were successful under present experimental conditions. However, additional testing under more variable environmental conditions should be performed before universal application of such models.

• KIISE Transactions on Computing Practices
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• v.22 no.1
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• pp.56-60
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• 2016

Peptide identification in tandem mass spectrometry is usually done by searching the spectra against target databases consisting of reference protein sequences. To control false discovery rates for high-confidence peptide identification, spectra are also searched against decoy databases constructed by permuting reference protein sequences. In this case, a peptide of the same sequence could be included in both the target and the decoy databases or multiple entries of a same peptide could exist in the decoy database. These phenomena make the protein identification problem complicated. Thus, it is important to minimize the number of such redundant peptides for accurate protein identification. In this regard, we examined two popular methods for decoy database generation: 'pseudo-shuffling' and 'pseudo-reversing'. We experimented with target databases of varying sizes and investigated the effect of the maximum number of missed cleavage sites allowed in a peptide (MC), which is one of the parameters for target and decoy database generation. In our experiments, the level of redundancy in decoy databases was proportional to the target database size and the value of MC, due to the increase in the number of short peptides (7 to 10 AA). Moreover, 'pseudo-reversing' always generated decoy databases with lower levels of redundancy compared to 'pseudo-shuffling'.

• Animal cells and systems
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• v.8 no.2
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• pp.125-133
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• 2004

We have extended our previous work that cross-linking CD4 molecules using specific MAb induced antigen nonspecific, MHC unrestricted killing of virally infected target cells by CD$4^+$We have extended our previous work that cross-linking CD$4^+$ molecules using specific MAb induced antigen nonspecific, MHC unrestricted killing of virally infected target cells by CD$4^+$ T cells. The killing activity of antibody activated CD$4^+$T cells was completely blocked by herbimycin A, a protein tyrosine kinase (PTK) inhibitor, but not by bisindolylamaleimide, a protein kinase C (PKC) inhibitor. Herbimycin A treated human or bovine peripheral blood CD$4^+$T cells lacked PTK activity and failed to kill virally infected target cells even after cross-linking of CD4 molecules. The CD$4^+$cross-linking failed to induce effector cell proliferation or the transcription of TNF${\beta}$ Upregulation of TNF${\beta}$ was induced by incubating the antibody activated effector cells with BHV-1 infected D17 target cells for 10 h. Anti-TNF${\beta}$ antibody partially abolished (13-44%) the direct effector cell-mediated antiviral cytotoxicity. However, this antibody neutralized 70 to 100% of antiviral activity of effector and target cell culture supernatants against BHV-1 infected D17 cells. The inhibition level of the antiviral activity by the antibody was dependent on the effector and target cell ratio. These results support the hypothesis that increased p$56^ICK enzyme activity in effector cells transduces a signal critical for effector cell recognition of viral glycoproteins expressed on the target cells. Following target cell recognition, lytic cytokines known to participate in target cell killing were produced. A better understanding of the killing activity displayed by CD$4^+$T lymphocytes following surface receptor cross-linking will provide insight into the mechanisms of cytotoxic activity directed toward virally-infected cells.T cells. The killing activity of antibody activated CD$4^+$T cells was completely blocked by herbimycin A, a protein tyrosine kinase (PTK) inhibitor, but not by bisindolylamaleimide, a protein kinase C (PKC) inhibitor. Herbimycin A treated human or bovine peripheral blood CD4T cells lacked PTK activity and failed to kill virally infected target cells even after cross-linking of CD4molecules. The CD4 cross-linking failed to induce effector cell proliferation or the transcription of TNF$\beta$. Upregulation of TNF$\beta$ was induced by incubating the antibody activated effector cells with BHV-1 infected D17 target cells for 10 h. Anti-TNF$\beta$ antibody partially abolished (13-44%) the direct effector cell-mediated antiviral cytotoxicity. However, this antibody neutralized 70 to 100% of antiviral activity of effector and target cell culture supernatants against BHV-1 infected D17 cells. The inhibition level of the antiviral activity by the antibody was dependent on the effector and target cell ratio. These results support the hypothesis that increased $56^ICK enzyme activity in effector cells transduces a signal critical for effector cell recognition of viral glycoproteins expressed on the target cells. Following target cell recognition, lytic cytokines known to participate in target cell killing were produced. A better understanding of the killing activity displayed by CD$4^+$T lymphocytes following surface receptor cross-linking will provide insight into the mechanisms of cytotoxic activity directed toward virally-infected cells.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.10
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• pp.4301-4305
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• 2014

Tanshinone IIA is a pharmacologically active ingredient extracted from Danshen, a Chinese traditional medicine. Its molecular mechanisms are still unclear. The present study utilized computational approaches to uncover the potential targets of this compound. In this research, PharmMapper server was used as the inverse docking tool andnd the results were verified by Autodock vina in PyRx 0.8, and by DRAR-CPI, a server for drug repositioning via the chemical-protein interactome. Results showed that the retinoic acid receptor alpha ($RAR{\alpha}$), a target protein in acute promyelocytic leukemia (APL), was in the top rank, with a pharmacophore model matching well the molecular features of Tanshinone IIA. Moreover, molecular docking and drug repurposing results showed that the complex was also matched in terms of structure and chemical-protein interactions. These results indicated that $RAR{\alpha}$ may be a potential target of Tanshinone IIA for APL. The study can provide useful information for further biological and biochemical research on natural compounds.