• Bulletin of the Korean Chemical Society
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• v.31 no.3
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• pp.606-610
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• 2010

Aminoacyl-tRNA synthetases (aaRSs) play vital roles in protein biosynthesis of living organisms and are interesting antibacterial drug targets. In order to find out new inhibitor candidate molecules as antibacterial agent, the binding modes of the candidate molecules were investigated at the active sites of aaRSs by molecular docking study. The docking simulations were performed with 48 compounds from four different scaffolds into the eight different aaRSs. The results show that scaffolds 3 and 4 compounds have consistently better binding capabilities, specifically for HisRS (E. coli) and IleRS (S. aureus). The binding modes of the best compounds with the proteins were well compatible with those of two ligands in crystal structures. Therefore, we expect that the final compounds we present may have reasonable aaRS inhibitory activity.

• ETRI Journal
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• v.37 no.4
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• pp.813-823
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• 2015

Because protein is a primary element responsible for biological or biochemical roles in living bodies, protein function is the core and basis information for biomedical studies. However, recent advances in bio technologies have created an explosive increase in the amount of published literature; therefore, biomedical researchers have a hard time finding needed protein function information. In this paper, a classification system for biomedical literature providing protein function evidence is proposed. Note that, despite our best efforts, we have been unable to find previous studies on the proposed issue. To classify papers based on protein function evidence, we should consider whether the main claim of a paper is to assert a protein function. We, therefore, propose two novel features - protein and assertion. Our experimental results show a classification performance with 71.89% precision, 90.0% recall, and a 79.94% F-measure. In addition, to verify the usefulness of the proposed classification system, two case study applications are investigated - information retrieval for protein function and automatic summarization for protein function text. It is shown that the proposed classification system can be successfully applied to these applications.

• Proceedings of the Korean Society of Life Science Conference
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• 2003.05a
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• pp.144-144
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• 2003

• Proceedings of the Korean Society of Plant Biotechnology Conference
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• 2005.11a
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• pp.136-136
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• 2005

• Journal of Plant Biotechnology
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• v.36 no.1
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• pp.53-58
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• 2009

Calcium signals can be transduced by binding calmodulin (CaM), a $Ca^{2+}$ sensor in eukaryotes, is known to be involved in the regulation of diverse cellular functions. We isolated a CaM-binding protein 63 kD (AtCBP63) from the pathogen-treated Arabidopsis cDNA expression library. Recently, AtCBP63 was identified as a CaM bining protein. The CaM binding domain of AtCBP63 was reported to be located in its N-terminal region, In this study, however, we showed that ACaM2 could specifically bind to second CaM-binding domain (CaMBD) of AtCBP63 at the C-terminal region. The specific binding of CaM to CaM binding domain was confirmed by a gel mobility shift assay, a split ubiquitin assay, site-directed mutagenesis, and a competition assay using a $Ca^{2+}$/CaM-dependent enzyme. The gene expression of AtCBP63 was induced by pathogens and pathogens related second messengers. This result suggests that a CaM binding protein, AtCBP63, may play role in pathogen defense signaling pathway.

• FOCUS: LIFE SCIENCE
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• no.1
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• pp.3.1-3.7
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• 2024

The article discusses the critical role of chromatography in the analysis and purification of proteins in biopharmaceuticals, emphasizing the importance of comprehensive characterization for ensuring their safety and efficacy. It highlights the use of Avantor® ACE® HPLC columns for the separation and purification of proteins, focusing on the analysis of intact proteins using reversed-phase liquid chromatography (RPLC) with fully porous particles. This article also details the application of different mobile phase additives, such as TFA and formic acid, and emphasizes the advantages of using type B ultra-pure silica-based columns for efficiency and peak shape in biomolecule analysis. Additionally, it addresses the challenges of analyzing intact proteins due to slow molecular diffusion and introduces the concept of solid-core (or superficially porous) particles, emphasizing their benefits over traditional porous particles for the analysis of therapeutic proteins. Furthermore, it discusses the development of Avantor® ACE® UltraCore BIO columns, specifically designed for the high-efficiency separation of large biomolecules, such as proteins, and demonstrates their effectiveness in achieving high-resolution separations, even for higher molecular weight proteins like monoclonal antibodies (mAbs). In addition, it underscores the complexity of analyzing and characterizing intact protein biopharmaceuticals, requiring a range of analytical techniques and the use of wide-pore stationary phases, operated at elevated temperatures and with relatively shallow gradients. It highlights the comprehensive range of options offered by Avantor® ACE® wide pore columns, including both fully porous and solid-core particles, bonded with a variety of complementary stationary phase chemistries to optimize selectivity during method development. The use of ultrapure and highly inert base silica is emphasized for enabling the use of lower concentrations of mobile phase modifiers without compromising analyte peak shape, particularly beneficial for LC-MS applications. Then the article concludes by emphasizing the significance of reversed-phase liquid chromatography and its compatibility with mass spectrometry as a valuable tool for the separation and analysis of intact proteins and their closely related variants in biopharmaceuticals.

• Journal of Sensor Science and Technology
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• v.21 no.5
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• pp.339-344
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• 2012

This article describes a novel method for the detection of amyloid-${\beta}$($A{\beta}$) peptide that utilizes a photo-sensitive field-effect transistor (p-FET). According to a recent study, $A{\beta}$ protein has been known to play a central role in the pathogenesis of Alzheimer's disease (AD). Accordingly, we investigated the variation of photo current generated from p-FET with and without intracellular magnetic beads conjugated with $A{\beta}$ peptides, which are placed on the p-FET sensing areas. The decrease of photo current was observed due to the presence of the magnetic beads on the channel region. Moreover, a similar characteristic was shown when the Raw 264 cells take in magnetic beads treated with $A{\beta}$ peptide. This means that it is possible to simply detect a certain protein using magnetic beads and a p-FET device. Therefore, in this paper, we suggest that our method could detect tiny amounts of $A{\beta}$ for early diagnosis of AD using the p-FET devices.

• Molecules and Cells
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• v.42 no.1
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• pp.67-78
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• 2019

Methylation of HBV cccDNA has been detected in vivo and in vitro; however, the mechanism and its effects on HBV replication remain unclear. HBx derived from a 1.2-mer HBV replicon upregulated protein levels and enzyme activities of DNA methyltransferase 1 (DNMT1), 3a, and 3b, resulting in methylation of the negative regulatory region (NRE) in cccDNA, while none of these effects were observed with an HBx-null mutant. The HBx-positive HBV cccDNA expressed higher levels of HBc and produced about 4-fold higher levels of HBV particles than those from the HBx-null counterpart. For these effects, HBx interrupted the action of NRE binding protein via methylation of the C-1619 within NRE, resulting in activation of the core promoter. Treatment with 5-Aza-2′dC or DNMT1 knock-down drastically impaired the ability of HBx to activate the core promoter and stimulate HBV replication in 1.2-mer HBV replicon and in vitro infection systems, indicating the positive role of HBx-mediated cccDNA methylation in HBV replication.

• Molecules and Cells
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• v.23 no.2
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• pp.161-169
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• 2007

We identified two alternatively spliced variants of the peroxisomal targeting signal 1 (PTS1) receptor protein Pex5ps in monocot (rice, wheat, and barley) but not in dicot (Arabidopsis and tobacco) plants. We characterized the molecular and functional differences between the rice (Oryza sativa) Pex5 splicing variants OsPex5pL and OsPex5pS. There is only a single-copy of OsPEX5 in the rice genome and RT-PCR analysis points to alternative splicing of the transcripts. Putative light-responsive cis-elements were identified in the 5' region flanking OsPEX5L and Northern blot analysis demonstrated that this region affected light-dependent expression of OsPEX5 transcription. Using the pex5-deficient yeast mutant Scpex5, we showed that OsPex5pL and OsPex5pS are able to restore translocation of a model PTS1 protein (GFP-SKL) into peroxisomes. OsPex5pL and OsPex5pS formed homo-complexes via specific interaction domains, and interacted with each other and OsPex14p to form hetero-complexes. Although overexpression of OsPex5pL in the Arabidopsis pex5 mutant (Atpex5) rescued the mutant phenotype, overexpression of OsPex5pS only resulted in partial recovery.

• Environmental Sciences Bulletin of The Korean Environmental Sciences Society
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• v.3 no.3
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• pp.177-188
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• 1999

The effect of ABA on the chloroplast disassembly of Zea mays was investigated by measuring the changes in the relative distribution of chlorophyll(Chl) between the Chl-protein complexes in ABA treated and untreated sensecting leaves. The reaction center(RC)-light harvesting complex(LHC) regions were rapidly disassembled in the late stage of dark-induced senescence. Plus, during dark-induced senescence, the disassembly of a reaction center of P700 apoproteins containing mainly Chl a was faster than that of a reaction center of LHCI apoproteins containing both Chl a and Chl b. The increase in the relative distribution of Chl-protein complexes in the RC-Core2 in the late stage of senescence was due to the accumulation of core complexes such as CP47/43 and reaction centers including D1/D2 apoproteins disassembled from the RC-Corel containing the dimer of D1/D2 apoproteins. The LHCII region was more stable than the other Chl-protein complexes throughout leaf senscence. Accordingly, it is suggested that the preferential breakdown of Chl a gives rise to the disassembly of Chl a-binding proteins, particularly reaction centers and core complexes during dark-induced senescence, plus the primary target of the photosynthetic apparatus in sensecing leaves would seem to be Chl a along with the proteins associated with Chl a. The application of ABA promoted the disassembly of the P700 apoproteins in the PSI reaction center and the dimer of D1/D2 apoproteins, and the conversion of the trimeric LHCII apoprotein to the monometirc LHCII apoprotein during the middle stage of leaf senescence, thereby suggesting that ABA accelerates the disassembly of both Chl a-binding and Chl a+b-binding proteins, particularly Chl a-binding proteins during the middle stage of leaf senescence.