• Proceeding of EDISON Challenge
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• 2013.04a
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• pp.13-24
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• 2013

Dopamine agonists and antagonists and its receptor play a critical role in the information transfer in the nervous system, and dopamine receptor-ligands interactions are deeply related to Parkinson's disease, schizophrenia and some other mental diseases. However, the only experimental 3D structure available for dopamine receptors is human D3 dopamine receptor. Therefore, it is important to create model of subtype dopamine receptor-ligands interactions. We report here the 3D structures of the human D1 and D2 dopamine receptor predicted by using GalaxyTBM, and its predicted binding site determined by using GalaxyDock. The highly conserved Asp on TM 3 and Phe on TM 6 have critical role in ligand binding. Also, highly conserved serines on TM 5 are essential for binding agonists and some kinds of antagonists. We identify differences between binding sites of agonists and antagonists of human D1 and D2 dopamine receptor, and find the reasons of selective binding of antagonists.

• Proceedings of the Korean Vacuum Society Conference
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• 2010.02a
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• pp.404-404
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• 2010

Despite much works have been done on the geometric structures of ripples, defects and edge atoms in a graphene device, there has been no report showing the direct correlation between the structures and the transport property. Unlike scanning tunneling microscopy or other electron microscopes, Scanning Gate Microscope (SGM) is a unique microscopic tool with which the local electronic structure and the transport property of a device can be measured simultaneously. We have performed a transport measurement in nanometer scale using a scanning gate microscope (SGM). We have found the nanoscopic pictures of electron and hole puddles and the role of graphene- device edges in the transport measurements. These experimental findings were successfully explained with a theoretical model.

• Journal of the Korean Society of Food Science and Nutrition
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• v.26 no.6
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• pp.1258-1267
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• 1997

Corbon dioxide id effective for extending the shelf-life of perishable foods by retarding microbial growth. The overall effect of carbon dioxide is to increase both the lag phase and generation time of microorganisms. However, the role of carbon dioxide in affecting the growth and metabolism of any given microorganisms is not clear yet, although its inhibitory effect is generally found at moderate to high concentrations. Systematic studies of the effects of carbon dioxide on microorganisms are therefore warranted. It is also necessary to understand the role of carbon dioxide in the preservation of foods as well as the control by carbon dioxide of fermentations of biotechnological importance. In this review, the antimicrobial effect of carbon dioxide on microorganisms is investigated in terms of its gas and solution properties, inhibition of microbial growth and specific metabolic processes, perturbation of membrane structure.

• Journal of Microbiology and Biotechnology
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• v.33 no.7
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• pp.857-863
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• 2023

Pathogenic bacteria that colonize the human intestinal tract have evolved strategies to overcome acidic conditions when they pass through the gastrointestinal tract. Amino acid-mediated acid resistance systems are effective survival strategies in a stomach that is full of amino acid substrate. The amino acid antiporter, amino acid decarboxylase, and ClC chloride antiporter are all engaged in these systems, and each one plays a role in protecting against or adapting to the acidic environment. The ClC chloride antiporter, a member of the ClC channel family, eliminates negatively charged intracellular chloride ions to avoid inner membrane hyperpolarization as an electrical shunt of the acid resistance system. In this review, we will discuss the structure and function of the prokaryotic ClC chloride antiporter of amino acid-mediated acid resistance system.

• Journal of Integrative Natural Science
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• v.16 no.3
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• pp.97-102
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• 2023

The gasdermins are a family of recently identified pore-forming effector proteins that cause membrane permeabilization and pyroptosis, a lytic pro-inflammatory type of cell death. A role in the regulation of cell proliferation and/or differentiation is suggested by the differentiation status-specific expression of gasdermin proteins in epithelial tissues. One of the GSDM protein is Gasdermin A (GSDMA), which decreased in stomach and esophageal cancers, suggesting a tumor suppressor role. GSDMA receptor antagonists have been researched as potential treatments for inflammatory diseases and baldness. GSDMA's significance in a wide range of disorders makes it an important therapeutic target. As a result, homology modelling of the GSDMA receptor was undertaken in the current study using the crystal structures of Mus musculus (GSDMA3), Human gasdermin D (GSDMD), and Murine gasdermin D (murine GSDMD). The best model was chosen based on the validation results after 20 models were developed utilising single template-based approaches. The generated structures can be used for further binding site and docking studies in the future.

• Bulletin of the Korean Chemical Society
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• v.33 no.8
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• pp.2508-2512
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• 2012

Cold shock proteins (CSPs) are a family of proteins induced at low temperatures. CSPs bind to single-stranded nucleic acids through the ribonucleoprotein 1 and 2 (RNP 1 and 2) binding motifs. CSPs play an essential role in cold adaptation by regulating transcription and translation via molecular chaperones. The solution nuclear magnetic resonance (NMR) or X-ray crystal structures of several CSPs from various microorganisms have been determined, but structural characteristics of psychrophilic CSPs have not been studied. Therefore, we optimized the purification process to obtain highly pure Lm-Csp and determined the three-dimensional structure model of Lm-Csp by comparative homology modeling using MODELLER on the basis of the solution NMR structure of Bs-CspB. Lm-Csp consists of a ${\beta}$-barrel structure, which includes antiparallel ${\beta}$ strands (G4-N10, F15-I18, V26-H29, A46-D50, and P58-Q64). The template protein, Bs-CspB, shares a similar ${\beta}$ sheet structure and an identical chain fold to Lm-Csp. However, the sheets in Lm-Csp were much shorter than those of Bs-CspB. The Lm-Csp side chains, E2 and R20 form a salt bridge, thus, stabilizing the Lm-Csp structure. To evaluate the contribution of this ionic interaction as well as that of the hydrophobic patch on protein stability, we investigated the secondary structures of wild type and mutant protein (W8, F15, and R20) of Lm-Csp using circular dichroism (CD) spectroscopy. The results showed that solvent-exposed aromatic side chains as well as residues participating in ionic interactions are very important for structural stability. Further studies on the three-dimensional structure and dynamics of Lm-Csp using NMR spectroscopy are required.

• The Korean Journal of Physiology and Pharmacology
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• v.8 no.5
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• pp.253-257
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• 2004

Schwann cells play an important role in peripheral nerve regeneration. Upon neuronal injury, activated Schwann cells clean up the myelin debris by phagocytosis, and promote neuronal survival and axon outgrowth by secreting various neurotrophic factors. However, it is unclear how the nerve injury induces Schwann cell activation. Recently, it was reported that certain cytoplasmic molecules, which are secreted by cells undergoing necrotic cell death, induce immune cell activation via the toll-like receptors (TLRs). This suggests that the TLRs expressed on Schwann cells may recognize nerve damage by binding to the endogenous ligands secreted by the damaged nerve, thereby inducing Schwann cell activation. Accordingly, this study was undertaken to examine the expression and the function of the TLRs on primary Schwann cells and iSC, a rat Schwann cell line. The transcripts of TLR2, 3, 4, and 9 were detected on the primary Schwann cells as well as on iSC. The stimulation of iSC with poly (I : C), a synthetic ligand for the TLR3, induced the expression of $TNF-{\alpha}$ and RANTES. In addition, poly (I : C) stimulation induced the iNOS expression and nitric oxide secretion in iSC. These results suggest that the TLRs may be involved in the inflammatory activation of Schwann cells, which is observed during Wallerian degeneration after a peripheral nerve injury.

• The KIPS Transactions:PartB
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• v.16B no.5
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• pp.359-366
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• 2009

Analysis of 3-dimensional (3D) protein structure plays an important role of structural bioinformatics. The protein structure alignment is the main subjects of the structural bioinformatics and the most fundamental problem. Protein Structures are flexible and undergo structural changes as part of their function, and most existing protein structure comparison methods treat them as rigid bodies, which may lead to incorrect alignment. We present a new method that carries out the flexible structure alignment by means of finding SSPs(Similar Substructure Pairs) and flexible points of the protein. In order to find SSPs, we encode the coordinates of atoms in the backbone of protein into RDA(Relative Direction Angle) using local similarity of protein structure. We connect the SSPs with Floyd-Warshall algorithm and make compatible SSPs. We compare the two compatible SSPs and find optimal flexible point in the protein. On our well defined performance experiment, 68 benchmark data set is used and our method is better than three widely used methods (DALI, CE, FATCAT) in terms of alignment accuracy.

• Journal of the Korea Institute of Building Construction
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• v.21 no.3
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• pp.241-247
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• 2021

As construction projects become more complex and larger, the role of the organization becomes more important. In order to increase the performance of the construction management(CM) site organization, it is necessary to find an organizational structure suitable for the CM, lead an organizational culture correctly, and increase the job satisfaction of the members. Therefore, the purpose of this study is to study the influence of the organizational structure of the CM site organization on the organizational culture and job satisfaction. As results of the study, the organizational structure of the CM site organization was the highest at 3.51 for formalization and the lowest at 2.71 for centralization(out of 5). In addition, as results of correlation analysis, organizational structure was found to have a correlation with organizational culture and job satisfaction. This study is considered to be helpful in planning an organizational structure suitable for the CM site organization.

• Korean journal of communication and information
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• v.16
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• pp.168-206
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• 2001

This study attempts to examine the relationships between the major market-based media and the government after closing military regime era, 1961-1987. After the military regime was collapsed, while the mass media in Korea obtained independence and autonomy from government, they have been confronted with the terrible competition not so much comparatively as before. The watchdog role in the traditional liberalism, which is regarded as normative relationship between the media and the government would be transformed in accordance with the market condition and the maturity of democracy. Thus, the watchdog metaphor has been variously deviated in rower-centered society; lap dog, guard dog, attack dog. liberalists argue that the primary democratic role of the media is to art as a public watchdog overseeing the state. Social democrats, however, criticize them as simplistic conception which could be only applied to the government. They argue that the media should be seen as a source of redress against the abuse of all forms of power over others; the home, the economy, and the civil society. The lap dog view is that the media is overwhelmingly dependent on the established power structure contrary to the watchdog. While the guard dog perspective is a means to preserve the power structure alarming with playing 'conflict role', the attack do8 aims to the private interest of the media in intruding into the politics. The attack dog perspective by T. Patterson could be composed of the interpretive style of report, the game schema report over the policy schema in the election, and the negativism against politics and government. The market-dominant press has been likely to transform from lap-guard dog into attack-guard dog. In Roh Tae Woo government(1988-1992), while the press was a lessened lap-guard dog before three parties merger in 1990, after merger the press had been transformed as the reinforced lap-guard dog because this merger entailed joint, party-to-party negotiations, and the formation of the new party preceded by dissolution of the ruling blot. In the early stage of Kim Young Sam government(1993-1997), the press has kept in pace with the reform movement drive-forced by the government. However, the press withdrew the support of Kim's reform in reaching the level of threat to ruling bloc. The press coalesced only circumstantially with government and was interested in preserving some margin of independence. The failure of Kim's reform proved the political muscle of the press in post-autho-ritarianism. In the middle stage of Kim Dae Jung government (1998-) that resulted in the shift of power structure as once-opposition party leader, the stress has been a manifested attack-guard dog owing to the anti-cold war policy, the realignment policy of power, and the minority-base of Kim's government. The press has endeavored to hold political communication within limits relatively less threatening to the established order.