• Genomics & Informatics
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• v.1 no.1
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• pp.7-19
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• 2003

The latest measure of the relative evolutionary age of protein structure families was applied (based on taxonomic diversity) using the protein structural interactome map (PSIMAP). It confirms that, in general, protein domains, which are hubs in this interaction network, are older than protein domains with fewer interaction partners. We apply a hypothesis of 'biological network evolution' to explain the positive correlation between interaction and age. It agrees to the previous suggestions that proteins have acquired an increasing number of interaction partners over time via the stepwise addition of new interactions. This hypothesis is shown to be consistent with the scale-free interaction network topologies proposed by other groups. Closely co-evolved structural interaction and the dynamics of network evolution are used to explain the highly conserved core of protein interaction pathways, which exist across all divisions of life.

• Proceedings of the Korean Society of Life Science Conference
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• 2005.04a
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• pp.202-202
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• 2005

• Proceedings of the KSRS Conference
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• v.2
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• pp.812-815
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• 2006

Proteins are essential agents for controlling, effecting and modulating cellular functions, and proteins with similar sequences have diverged from a common ancestral gene, and have similar structures and functions. Function prediction of unknown proteins remains one of the most challenging problems in bioinformatics. Recently, various computational approaches have been developed for identification of short sequences that are conserved within a family of closely related protein sequence. Protein function is often correlated with highly conserved motifs. Motif is the smallest unit of protein structure and function, and intends to make core part among protein structural and functional components. Therefore, prediction methods using data mining or machine learning have been developed. In this paper, we describe an approach for protein function prediction of motif-based models using data mining. Our work consists of three phrases. We make training and test data set and construct classifier using a training set. Also, through experiments, we evaluate our classifier with other classifiers in point of the accuracy of resulting classification.

• Proceedings of the Korean Biophysical Society Conference
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• 1996.07a
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• pp.11-11
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• 1996

The three-dimensional structure of the carboxyl-terminal domain of the E.coli RNA polymerase $\alpha$ subunit, which is regarded as the contact site for transcription activator proteins and the promoter UP element, was determined by NMR spectroscopy. Its compact structure of four helices and two long arms enclosing its hydrophobic core shows a folding topology distinct from those of other DNA-binding proteins. (omitted)

• Applied Microscopy
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• v.29 no.3
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• pp.323-329
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• 1999

Synthesis of inorganic nanophase particles was performed to verify and understand the binding of non-ferrous metal ions including Al and $UO_2$ to the apoferritin molecules. Reconstituted inorganic particles of Al or $UO_2$ were identified by TEM as discrete electron dense cores encapsulated within the protein shell. The corresponding EDXA spectra confirm the presence of metal ions in the reconstituted ferritin. The Al cores of ferritin has been studied by TEM for the first time. Bimetallic cores with Al/Fe and $UO_2/Al$ were also produced and examined under TEM. Mixed metal cores encapsulated in the protein shell are well formed and its corresponding EDXA spectra also confirm the presence of metal ions in the mineral cores. Therefore, the present study proves that ferritin can be used to synthesize inorganic nanophase particles of Al and $UO_2$.

• Journal of the Korean Magnetic Resonance Society
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• v.20 no.1
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• pp.22-26
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• 2016

FANCJ is a DNA helicase which contributes genome stability by resolving G-quadruplex DNA from 5' to 3' direction. In addition to main ATPase helicase core, FANCJ has the protein binding region at its C-terminal part. BRCA1 and BLM are the binding partner of FANCJ and these protein-protein interactions contribute genomic stability and the proper response to replication stress. As the first attempt for studying FANCJ-BLM interaction, we prepared BLM binding region of FANCJ and characterized with CD and NMR spectroscopy. FANCJ (881-941) with N-ter 6xHis was purified as the oligomer. Secondary structure prediction based on CD data revealed that FANCJ (881-941) composed with ${\beta}$ sheet, turn and coils.$^1H-^{15}N$ HSQC spectra showed nonhomogeneous peak intensities with less number of peaks comparing than the number of amino acids in the construct. It indicated that optimization should be necessary for detailed further structural studies.

• Journal of Microbiology and Biotechnology
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• v.18 no.6
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• pp.1090-1094
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• 2008

In this article, we show that the orf slr1471 from Synechocystis sp. PCC 6803 codes for a functional member of the YidC/Alb3/Oxa1 protein family, and the encoded protein has a transmembrane topology with a common core structure. Using specific antibodies raised against the Synechocystis YidC homologous protein, we further show that the Synechocystis YidC protein appears to be predominantly localized in the cyanobacterial cytoplasmic membrane. The impact of the described findings for synthesis of membrane proteins and for protein sorting within cyanobacterial cells is discussed.

• The Plant Pathology Journal
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• v.24 no.4
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• pp.384-391
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• 2008

Rice blast disease, caused by the pathogenic fungus Magnaporthe grisea, is a serious issue in rice (Oryza sativa L.) growing regions of the world. Transcript profiling in rice inoculated with the fungus has been investigated using the transcriptomics technology, serial analysis of gene expression (SAGE). Short sequence tags containing sufficient information which are ten base-pairs representing the unique transcripts were identified by SAGE technology. We identified a total of 910 tag sequences via the GenBank database, and the resulting genes were shown to be up-regulated in all functional categories under the fungal biotic stress. Compared to the compatible interaction, the stress and defense genes in the incompatible interaction appear to be more up-regulated. Particularly, thaumatin-like gene (TLP) was investigated in determining the gene and protein expression level utilizing Northern and Western blotting analyses, resulting in an increase in both the gene and the protein expression level which arose earlier in the incompatible interaction than in the compatible interaction.

• Molecules and Cells
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• v.25 no.3
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• pp.323-331
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• 2008

Plants are continually exposed to a variety of potentially pathogenic microbes, and the interactions between plants and pathogenic invaders determine the outcome, disease or disease resistance. To defend themselves, plants have developed a sophisticated immune system. Unlike animals, however, they do not have specialized immune cells and, thus all plant cells appear to have the innate ability to recognize pathogens and turn on an appropriate defense response. Using genetic, genomic and biochemical methods, tremendous advances have been made in understanding how plants recognize pathogens and mount effective defenses. The primary immune response is induced by microbe-associated molecular patterns (MAMPs). MAMP receptors recognize the presence of probable pathogens and evoke defense. In the co-evolution of plant-microbe interactions, pathogens gained the ability to make and deliver effector proteins to suppress MAMP-induced defense responses. In response to effector proteins, plants acquired R-proteins to directly or indirectly monitor the presence of effector proteins and activate an effective defense response. In this review we will describe and discuss the plant immune responses induced by two types of elicitors, PAMPs and effector proteins.

• Bulletin of the Korean Chemical Society
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• v.28 no.2
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• pp.200-206
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• 2007

Pharmacophore models for lymphocyte-specific protein tyrosine kinase (P56 LCK) were developed using CATALYST HypoGen with a training set comprising of 25 different P56 LCK inhibitors. The best quantitative pharmacophore hypothesis comprises of one hydrogen bond acceptor, one hydrogen bond donor, one hydrophobic aliphatic and one ring aromatic features with correlation coefficient of 0.941, root mean square deviation (RMSD) of 0.933 and cost difference (null cost-total cost) of 66.23. The pharmacophore model was validated by two methods and the validated model was further used to search databases for new compounds with good estimated LCK inhibitory activity. These compounds were evaluated for their binding properties at the active site by molecular docking studies using GOLD software. The compounds with good estimated activity and docking scores were evaluated for physiological properties based on Lipinski's rules. Finally 68 compounds satisfied all the properties required to be a successful inhibitor candidate.