• Proceedings of the Korea Crystallographic Association Conference
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• 2001.11a
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• pp.8-8
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• 2001

• BT NEWS
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• v.18 no.1
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• pp.80-81
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• 2011

• Korean Journal of Microbiology
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• v.38 no.3
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• pp.213-220
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• 2002

Inducible expression system for the three structural proteins, capsid (C), precursor membrane (prM/M), and envelop (E) of Japanese encephalitis virus (JEV) was established in BHK-21 cells. Doxycycline, a tetracycline analog, was utilized as an inducer. Transfectants BHK-21/IV (vector only), BHK-21/IC (for C), BHK-21/IP3 (for prM), and BHK-21/IE1 (for E) were selected and cloned in the presence of G4l8 or hygromycin. Transcribed mRNAs for the corresponding genes were observed after doxycycline induction. Effects by the JEV structural gene expression on the transfectants were monitored via cell growth, chromatin condensation, internucleosomal DNA fragmentation, and DNA contents analyses. Clear cell growth retardation and chromatin condensation were observed in all three transfectants while only BHK-2/IC corresponded to the induction status in the DNA fragmentation and DNA content analyses. Combined results, therefore, suggested that JEV capsid protein should be one of the direct and independent factors in apoptotic cell death induced by IEV infection.

• The Journal of the Korea Contents Association
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• v.8 no.1
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• pp.259-271
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• 2008

We propose a protein function finding algorithm that is able to predict specific molecular function for unannotated proteins through domain analysis from protein-protein network. To do this, we first construct protein-protein interaction(PPI) network in Saccharomyces cerevisiae from MIPS databases. The PPI network(proteins; 3,637, interactions; 10,391) shows the characteristics of a scale-free network and a hierarchical network that proteins with a number of interactions occur in small and the inherent modularity of protein clusters. Protein-protein interaction databases obtained from a Y2H(Yeast Two Hybrid) screen or a composite data set include random false positives. To filter the database, we reconstruct the PPI networks based on the cellular localization. And then we analyze Hub proteins and the network structure in the reconstructed network and define structural modules from the network. We analyze protein domains from the structural modules and derive functional modules from them. From the derived functional modules with high certainty, we find tentative functions for unannotated proteins.

• Proceedings of the Korea Crystallographic Association Conference
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• 2002.11a
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• pp.4-4
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• 2002

PDZ domains bind to short segments within target proteins in a sequence-specific fashion. GRIP/ABP family proteins contain six to seven PDZ domains and interact via its sixth PDZ domain (class Ⅱ) with the C-termini of various proteins, including liprin-α. In addition the PDZ456 domain mediates the formation of homo- and heteromultimers of GRIP proteins. To better understand the structural basis of peptide recognition by a class Ⅱ PDZ domain and DZ-mediated multimerization, we determined the crystal structures of the GRIPI PDZ6 domain, alone and in complex with a synthetic C-terminal octapeptide of human liprin-α, at resolutions of 1.5 Å and 1.8 Å, respectively. Remarkably, unlike other class Ⅱ PDZ domains, Ile736 at αB5 rather than conserved Leu732 at αB1 makes a direct hydrophobic contact with the side chain of the Tyr at the -2 position of the ligand. Moreover, the peptide-bound structure of PDZ6 shows a slight reorientation of helix αB, indicating that the second hydrophobic pocket undergoes a conformational adaptation to accommodate the bulkiness of the Tyr's side chain, and forms an antiparallel dimer through an interface located at a site distal to the peptide-binding groove. This configuration may enable formation of GRIP multimers and efficient clustering of GRIP-binding proteins.

• Preventive Nutrition and Food Science
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• v.1 no.1
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• pp.134-142
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• 1996

Diabetes carries an increased risk of atherosclerotic disease that is not fully explained by known car-diovascular risk factors. There is accumulating evidence that advanced glycation of structural proteins, and oxidation and glycation of circulating lipoproteins, are implicated in the pathogenesis of diabetic ather-osclerosis. Reactions involving glycation and oxidation of proteins and lipids are believed to contribute to atherogenesis. Glycation, the nonenzymatic binding of glucose to protein molecules, can increase the ather-ogenic potential of certain plasma constituents, including low density lipoptotein(LDL). Glycation of LDL is significant increased in diabetic patients compared with normal subjects, even in the presence of good glycemic control. Metabolic abnormalities associated with glycation of LDL include diminished recognition of LDL by the classic LDL receptor; increased covalent binding of LDL in vessel walls ; enhanced uptake of LDL by the macrophages, thus stimulating foam cell formation ; increased platelet aggregation; formation of LDL-immune complexes ; and generation of oxygen free radicals, resulting on oxidative damage to both the lipid and protein components of LDL and to any nearby macromolecules. Oxidized lipoproteins are characterzied by cytotoxicity, potent stimulation of foam cell formation by macrophages, and procoagulant effects. Combined glycation and oxidation, "glycoxidation" occurs when oxidative reactions affect the initial products of glycation, and results in irreversible structural alterations of proteins. Glycoxidation is of greatest significance in long lived proteins such as collagen. In these proteins, glycoxidation products, believed to be atherogenic, accumulate with advancing age : in diabetes, their rate of accumulate is accelerated. Inhibition of glycation, oxidation and glycoxidation may form the basis of future antiaterogenic strategies in both diabetic and nondiabetic individuals.dividuals.

• BMB Reports
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• v.51 no.10
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• pp.486-492
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• 2018

The CCN protein family is composed of six matricellular proteins, which serve regulatory roles rather than structural roles in the extracellular matrix. First identified as secreted proteins which are induced by oncogenes, the acronym CCN came from the names of the first three members: CYR61, CTGF, and NOV. All six members of the CCN family consist of four cysteine-rich modular domains. CCN proteins are known to regulate cell adhesion, proliferation, differentiation, and apoptosis. In addition, CCN proteins are associated with cardiovascular and skeletal development, injury repair, inflammation, and cancer. They function either through binding to integrin receptors or by regulating the expression and activity of growth factors and cytokines. Given their diverse roles related to the pathology of certain diseases such as fibrosis, arthritis, atherosclerosis, diabetic nephropathy, retinopathy, and cancer, there are many emerging studies targeting CCN protein signaling pathways in attempts to elucidate their potentials as therapeutic targets.

• Journal of Mushroom
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• v.15 no.1
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• pp.1-7
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• 2017

Hydrophobins are surface active proteins that are produced by filamentous fungi including mushrooms. Their ability to self-assemble into an amphipathic membrane at any hydrophilic-hydrophobic interface is most intriguing. These small secreted proteins comprise of eight conserved cysteine residues which form four disulfide bridges and an extraordinary hydrophobic patch. Hydrophobins play critical roles in fungal (and/or mushrooms) growth as structural components and in the interaction of fungi and mushrooms with the environment. The biophysical and biochemical properties of the isolated proteins are remarkable, such as strong adhesion, high surface activity and the formation of various self-assembled structures. With the increasing demands of hydrophobins from fungi and mushroom sources, production and purification in large scale is under challenge. Various applications, ranging from food industries, cosmetics, nanotechnology, biosensors and electrodes, to biomaterials and pharmaceuticals are emerging and a bright future is foreseen.

• BMB Reports
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• v.55 no.7
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• pp.316-322
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• 2022

Ubiquitin is relatively modest in size but involves almost entire cellular signaling pathways. The primary role of ubiquitin is maintaining cellular protein homeostasis. Ubiquitination regulates the fate of target proteins using the proteasome- or autophagy-mediated degradation of ubiquitinated substrates, which can be either intracellular or foreign proteins from invading pathogens. Legionella, a gram-negative intracellular pathogen, hinders the host-ubiquitin system by translocating hundreds of effector proteins into the host cell's cytoplasm. In this review, we describe the current understanding of ubiquitin machinery from Legionella. We summarize structural and biochemical differences between the host-ubiquitin system and ubiquitin-related effectors of Legionella. Some of these effectors act much like canonical host-ubiquitin machinery, whereas others have distinctive structures and accomplish non-canonical ubiquitination via novel biochemical mechanisms.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.32-34
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• 2000

Computational chemistry is a discipline using computational methods for the calculation of molecular structure, properties, and reaction or for the simulation of molecular behavior. Relating and turning the complexity of data from genomics, high-throughput screening, combinatorial chemical synthesis, gene-expression investigations, pharmacogenomics, and proteomics into useful information and knowledge is the primary goal of bioinformatics. In particular, the structure-based molecular design is one of essential fields in bioinformatics and it can be called as structural bioinformatics. Therefore, the conformational analysis for proteins and peptides using the techniques of computational chemistry is expected to play a role in structural bioinformatics. There are two major computational methods for conformational analysis of proteins and peptides; one is the molecular orbital (MO) method and the other is the force field (or empirical potential function) method. The MO method can be classified into ab initio and semiempirical methods, which have been applied to relatively small and large molecules, respectively. However, the improvement in computer hardwares and softwares enables us to use the ab initio MO method for relatively larger biomolecules with up to v100 atoms or ∼800 basis functions. In order to show how computational chemistry can be used in structural bioinformatics, 1 will present on (1) cis-trans isomerization of proline dipeptide and its derivatives, (2) positional preference of proline in ${\alpha}$-helices, and (3) conformations and activities of Arg-Gly-Asp-containing tetrapeptides.