• 생물정신의학
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• 제30권1호
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• pp.17-23
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• 2023

Objectives This study aims to develop valid experimental models for depression through chronic reserpine exposure to zebrafish (Danio rerio). Methods The effect of chronic reserpine on zebrafish behavior in the novel tank was examined. Changes of gene expression on telencephalon were also investigated. Results Chronic reserpine (40 mg/L, 7 days) induced overt behavioral effects, but markedly reduced activity, resembling motor retardation in depression. In telencephalon of zebrafish, gene expression associated with monoamine oxidase and norepinephrine transporter was decreased. Expression of serotonin transporter gene was increased. Conclusions Our results show that the pharmacological model of depression in zebrafish can induce not only behavioral changes, but also monoamine changes in the homology of human mood regulation centers.

• 한국식물병리학회:학술대회논문집
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• 한국식물병리학회 2003년도 정기총회 및 추계학술발표회
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• pp.82-83
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• 2003

Plants have evolved differently from animals having mobile activities. Thus, plants should have developed unique defense mechanisms against biotic/abiotic stresses to which plants are differently exposed, according to seasons. Most organisms have an conserved signaling network using mitogen-activated protein kinase (MAPK) cascade(s). The phenomenon implied that they are functionally very important in all organisms. In fact, they constitute one of the major components of signaling pathways involved in regulating a wide range of cellular activities from growth and development to cell death. Recently, complete MAPK cascade was first characterized in Arabidopsis from the receptor kinase (FLS2) through fellowing MEKKI -MKK4/MKK5-MPK3/MPK6-WRKY22/MRKY29 pathway. Whereas, MAPK cascade signaling pathway in monocot plant including rice (0ryza sativa L.), the most important of all food crops and an established monocot plant research model, MAPKinase kinase kinases (MAPKKK) of rice are the first upstream component of the MAPK cascade, but MAPKKK has been first identified and characterized in our lab and designated as, OsEDRl based on its homology with the Arabidopsis EDRI. The Arabidopsis EDRl was regarded as a negative regulator of defense response and the role of rice OsEDRl was analyzed. Transcriptional regulation of OsEDRl was detected under various stresses and immunoblotting analysis is going on to detect the level of OsEDRl protein in the mutants showing unique phenotype. We also introduced the constitutively active and the dominant negative forms of the OsEDRl for characterizing biological function.

• Journal of Plant Biotechnology
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• 제42권2호
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• pp.93-103
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• 2015

The isolation, cloning, and characterization of an R2R3-MYB transcription factor gene (MtMYB70) from the model legume Medicago truncatula is reported. MtMYB70 consists of a 768-bp coding sequence corresponding to 255 amino acids. Sequence alignment revealed that MtMYB70 cDNA contains conserved R2R3-type MYB domains with highly divergent C terminal regions. MtMYB70 was found to have relatively low sequence homology with known R2R3-MYB genes. Phylogenetic analysis placed the R2R3-MYB domain of MtMYB70 closest to PtMYB1, a known activator of lignin biosynthesis. Overexpression of MtMYB70 under the control of the 35S promoter in transgenic poplar did not cause a significant difference in total lignin content relative to the control, but glucan content was significantly increased in transgenic poplar. Therefore, MtMYB70 might have regulatory role in the biosynthesis of cell wall structural carbohydrates.

• BMB Reports
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• 제47권9호
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• pp.488-493
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• 2014

Adaptor protein FADD forms the death inducing signaling complex (DISC) by recruiting the initiating caspases-8 and -10 through homotypic death effector domain (DED) interactions. Cellular FLICE-inhibitory protein (c-FLIP) is an inhibitor of death ligand-induced apoptosis downstream of death receptors, and FADD competes with procaspase-8/10 for recruitment for DISC. However, the mechanism of action of FADD and c-FLIP proteins remain poorly understood at the molecular level. In this study, we provide evidence indicating that the death effector domain (DED) of FADD interacts directly with the death effector domain of human c-FLIP. In addition, we use homology modeling to develop a molecular docking model of FADD and c-FLIP proteins. We also find that four structure-based mutants (E80A, L84A, K169A and Y171A) of c-FLIP DEDs disturb the interaction with FADD DED, and that these mutations lower the stability of the c-FLIP DED.

• Journal of Microbiology and Biotechnology
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• 제22권8호
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• pp.1059-1065
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• 2012

Biocatalytic transfer of oxygen in isolated cytochrome P450 or whole microbial cells is an elegant and efficient way to achieve selective hydroxylation. Cytochrome P450 CYP105P2 was isolated from Streptomyces peucetius that showed a high degree of amino acid identity with hydroxylases. Previously performed homology modeling, and subsequent docking of the model with flavone, displayed a reasonable docked structure. Therefore, in this study, in a pursuit to hydroxylate the flavone ring, CYP105P2 was co-expressed in a two-vector system with putidaredoxin reductase (camA) and putidaredoxin (camB) from Pseudomonas putida for efficient electron transport. HPLC analysis of the isolated product, together with LC-MS analysis, showed a monohydroxylated flavone, which was further established by subsequent ESI/MS-MS. A successful 10.35% yield was achieved with the whole-cell bioconversion reaction in Escherichia coli. We verified that CYP105P2 is a potential bacterial hydroxylase.

• Journal of Microbiology and Biotechnology
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• 제24권10호
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• pp.1382-1388
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• 2014

Proteus vulgaris K80 lipase was expressed in Escherichia coli BL21 (DE3) cells and immobilized on amine-terminated magnetic microparticles (Mag-MPs). The immobilization yield and activity retention were 84.15% and 7.87%, respectively. A homology model of lipase K80 was constructed using P. mirabilis lipase as the template. Many lysine residues were located on the protein surface, remote from active sites. The biochemical characteristics of immobilized lipase K80 were compared with the soluble free form of lipase K80. The optimum temperature of K80-Mag-MPs was $60^{\circ}C$, which was $20^{\circ}C$ higher than that of the soluble form. K80-Mag-MPs also tended to be more stable than the soluble form at elevated temperatures and a broad range of pH. K80-Mag-MP maintained its stable form at up to $40^{\circ}C$ and in a pH range of 5.0-10.0, whereas soluble K80 maintained its activity up to $35^{\circ}C$ and pH 6.0-10.0. K80-Mag-MPs had broader substrate specificity compared with that of soluble K80. K80-Mag-MPs showed about 80% residual relative activity after five recovery trials. These results indicate the potential benefit of K80-Mag-MPs as a biocatalyst in various industries.

• 통합자연과학논문집
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• 제4권3호
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• pp.202-209
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• 2011

Tuberculosis is a major health problem in humans because of its multidrug resistance and discovering new treatments for this disease is urgently required. The synthesis of isoprenoids in Mycobacterium tuberculosis has been reported as an interesting pathway to target. In this context, 2C-methyl-D-erythritol 4-phosphate (MEP) pathway of M. tuberculosis has drawn attention. The MEP pathway begins with the condensation of glyceraldehyde 3-phosphate and pyruvate forming 1-deoxy-D-xylulose 5-phosphate (DXP) which is catalyzed by 1-deoxy-D-xylulose 5-phosphate synthase (DXS). As there is no X-ray structure was reported for this target, comparative modeling was used to generate the three dimensional structure. The structure was further validated by PROCHECK, VERIFY-3D, PROSA, ERRAT and WHATIF. Molecular docking studies was performed with the substrate (Thiamine pyrophosphate) and the reported inhibitor 2-methyl-3-(4-fluorophenyl)-5-(4-methoxy-phenyl)-4H-pyrazolol[1,5-a]pyrimidin-7-one) against the developed model to identify the crucial residues in the active site. This study may further be useful to provide structure based drug design.

• Bulletin of the Korean Chemical Society
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• 제32권7호
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• pp.2325-2331
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• 2011

Human CDX1 and CDX2 genes play important roles in the regulation of cell proliferation and differentiation in the intestine. Hox genes clustered on four chromosomal regions (A-D) specify positional signaling along the anterior-posterior body axis, including intestinal development. Using glutathione S-transferase (GST) pulldown assays, molecular interaction measurements, and fluorescence measurements, we found that the homeodomains (HDs) of CDX1 and CDX2 directly interact with that of HOXD8 in vitro. CDX1 showed significant affinity for HOXD8, but CDX2 showed weak affinity for HOXD8. Thus far, three-dimensional structures of CDX1/2 and HOXD8 have not been determined. In this study, we developed a molecular docking model by homology modeling based on the structures of other HD members. Proteins with mutations in the HD of CDX1 (S185A, N190A, T194A, and V212A) also bound to the HD of HOXD8. Our study suggests that the HDs of CDX1/2 resemble those of HOXD8, and we provide the first insight into the interaction between the HDs of CDX1/2 proteins and those of HOXD8.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2000년도 International Symposium on Bioinformatics
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• pp.17-20
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• 2000

Structural genomics aims to provide a good experimental structure or computational model of every tractable protein in a complete genome. Underlying this goal is the immense value of protein structure, especially in permitting recognition of distant evolutionary relationships for proteins whose sequence analysis has failed to find any significant homolog. A considerable fraction of the genes in all sequenced genomes have no known function, and structure determination provides a direct means of revealing homology that may be used to infer their putative molecular function. The solved structures will be similarly useful for elucidating the biochemical or biophysical role of proteins that have been previously ascribed only phenotypic functions. More generally, knowledge of an increasingly complete repertoire of protein structures will aid structure prediction methods, improve understanding of protein structure, and ultimately lend insight into molecular interactions and pathways. We use computational methods to select families whose structures cannot be predicted and which are likely to be amenable to experimental characterization. Methods to be employed included modern sequence analysis and clustering algorithms. A critical component is consultation of the presage database for structural genomics, which records the community's experimental work underway and computational predictions. The protein families are ranked according to several criteria including taxonomic diversity and known functional information. Individual proteins, often homologs from hyperthermophiles, are selected from these families as targets for structure determination. The solved structures are examined for structural similarity to other proteins of known structure. Homologous proteins in sequence databases are computationally modeled, to provide a resource of protein structure models complementing the experimentally solved protein structures.

• Bulletin of the Korean Chemical Society
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• 제35권1호
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• pp.62-68
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• 2014

Coptis chinensis 3'-hydroxy-N-methylcoclaurine 4'-O-methyltransferase (HOMT), an essential enzyme in the berberine biosynthetic pathway, catalyzes the methylation of 3'-hydroxy-N-methylcoclaurine (HMC) producing reticuline. A 3D model of HOMT was constructed by homology modeling and further subjected to docking with its ligands and molecular dynamics simulations. The 3D structure of HOMT revealed unique structural features which permitted the methylation of HMC. The methylation of HMC was proposed to proceed by deprotonation of the 4'-hydroxyl group via His257 and Asp258 of HOMT, followed by a nucleophilic attack on the SAM-methyl group resulting in reticuline. HOMT showed high substrate specificity for methylation of HMC. The study evidenced that Gly117, Thr312 and Asp258 in HOMT might be the key residues for orienting substrate for specific catalysis.