• Bulletin of the Korean Chemical Society
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• 제35권6호
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• pp.1769-1776
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• 2014

Binding modes of a series of catechol derivatives such as protein tyrosine phosphatase 1B (PTP1B) inhibitors were identified by molecular modeling techniques. Docking, molecular dynamics simulations and free energy calculations were employed to determine the modes of these new inhibitors. Binding free energies were calculated by involving different energy components using the Molecular Mechanics-Poisson-Boltzmann Surface Area and Generalized Born Surface Area methods. Relatively larger binding energies were obtained for the catechol derivatives compared to one of the PTP1B inhibitors already in use. The Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) free energy decomposition analysis indicated that the hydroxyl functional groups and biphenyl ring system had favorable interactions with Met258, Tyr46, Gln262 and Phe182 residues of PTP1B. The results of hydrogen bound analysis indicated that catechol derivatives, in addition to hydrogen bonding interactions, Val49, Ile219, Gln266, Asp181 and amino acid residues of PTP1B are responsible for governing the inhibitor potency of the compounds. The information generated from the present study should be useful for the design of more potent PTP1B inhibitors as anti-diabetic agents.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2004년도 The 3rd Annual Conference for The Korean Society for Bioinformatics Association of Asian Societies for Bioinformatics 2004 Symposium
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• pp.221-233
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• 2004

Molecular docking falls into the general category of global optimization problems since its main purpose is to find the most stable complex consisting of a receptor and its ligand. Conformational space annealing (CSA), a powerful global optimization method, is incorporated with the Tinker molecular modeling package to perform molecular docking simulations of six receptor-ligand complexes (3PTB, 1ULB, 2CPP, 1STP, 3CPA and 1PPH) from the Protein Data Bank. In parallel, Monte Carlo with minimization (MCM) method is also incorporated into the Tinker package for comparison. The energy function, consisting of electrostatic interactions, van der Waals interactions and torsional energy terms, is calculated using the AMBER94 all-atom empirical force field. Rigid docking simulations for all six complexes and flexible docking simulations for three complexes (1STP, 3CPA and 1PPH) are carried out using the CSA and the MCM methods. The simulation results show that the docking procedures using the CSA method generally find the most stable complexes as well as the native -like complexes more efficiently and accurately than those using the MCM, demonstrating that CSA is a promising search method for molecular docking problems.

• BMB Reports
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• 제54권3호
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• pp.164-169
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• 2021

Neuronal growth regulator 1 (NEGR1) is a GPI-anchored membrane protein that is involved in neural cell adhesion and communication. Multiple genome wide association studies have found that NEGR1 is a generic risk factor for multiple human diseases, including obesity, autism, and depression. Recently, we reported that Negr1-/- mice showed a highly increased fat mass and affective behavior. In the present study, we identified Na/K-ATPase, beta1-subunit (ATP1B1) as an NEGR1 binding partner by yeast two-hybrid screening. NEGR1 and ATP1B1 were found to form a relatively stable complex in cells, at least partially co-localizing in membrane lipid rafts. We found that NEGR1 binds with ATP1B1 at its C-terminus, away from the binding site for the alpha subunit, and may contribute to intercellular interactions. Collectively, we report ATP1B1 as a novel NEGR1-interacting protein, which may help deciphering molecular networks underlying NEGR1-associated human diseases.

• BMB Reports
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• 제37권1호
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• pp.45-52
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• 2004

The goal of interaction proteomics that studies the protein-protein interactions of all expressed proteins is to understand biological processes that are strictly regulated by these interactions. The availability of entire genome sequences of many organisms and high-throughput analysis tools has led scientists to study the entire proteome (Pandey and Mann, 2000). There are various high-throughput methods for detecting protein interactions such as yeast two-hybrid approach and mass spectrometry to produce vast amounts of data that can be utilized to decipher protein functions in complicated biological networks. In this review, we discuss recent developments in analytical methods for large-scale protein interactions and the future direction of interaction proteomics.

• BMB Reports
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• 제56권3호
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• pp.133-139
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• 2023

The human intestine is home to a dense community of microbiota that plays a key role in human health and disease. Nutrients are essential regulators of both host and microbial physiology and function as key coordinators of host-microbe interactions. Therefore, understanding the specific roles and underlying mechanisms of each nutrient in regulating the host-microbe interactions will be essential in developing new strategies for improving human health through microbiota and nutrient intervention. This review will give a basic overview of the role of vitamin A, an essential micronutrient, on human health, and highlight recent findings on the mechanisms by which it regulates the host-microbe interactions.

• Biotechnology and Bioprocess Engineering:BBE
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• 제10권3호
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• pp.192-197
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• 2005

The effects of macronutrients $(NO_3^-,\; NH_4^+\;and\;PO_4^{3-})$ on cell growth and triterpenoids production in Centella asiatica cell suspension cultures were analyzed using the Box­Behnken response surface model experimental design. In screening and optimization experiments, $PO_4^{3-}$ as a single factor significantly influenced cell growth where increasing the phosphate level from 0.1 to 2.4 or 2.6 mM, elevated cell growth from 3.9 to $14\~16g/L$. The optimum values predicted from the response surface model are 5.05mM $NH_4^+$, 15.0mM $NO_3^-$ and 2.6mM $PO_4^{3-}$, yielding 16.0g/L cell dry weight with $99\%$ fitness to the experimental data. While the $NH_4^+-NO_3^-$ interaction influenced cell growth positively in the optimization experiment, $NH_4^+$ and $NO_3^-$ as single factors; and interactions of $NO_3^--PO_4^{3-},\;NH_4^+-PO_4^{3-}$ and $NH_4^+-NO_3^-$ were all negative in the screening experiment. Cell growth and the final pH level were positively affected by $PO_4^{3-}$, but negatively affected by $NH_4^+\;and\;NH_4^+-PO_4^{3-}$ interactions. The different effects of factors and their interactions on cell growth and final pH are influenced by a broad or narrow range of macronutrient concentrations. The productions of triterpenoids however were lower than 4mg/g cell dry weight.

• Journal of Photoscience
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• 제7권4호
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• pp.153-154
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• 2000

No Abstract. See full-text

• 한국응용곤충학회:학술대회논문집
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• 한국응용곤충학회 2004년도 춘계 학술발표회
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• pp.33-33
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• 2004

• 한국식물병리학회:학술대회논문집
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• 한국식물병리학회 2004년도 The 2004 KSPP Annual Meeting & International Symposium
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• pp.48-52
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• 2004

We have found the role of rice mitogen-activated protein kinase kinase kinase (MAPKKK), OsEDR1, as controling hypersensitive response (HR) and increased disease resistance to rice blast fungus Magnaporthe grisea. Generation of transgenic rice plants through introduction of the over-expression construct of OsEDR1 using Agrobacterium-mediated transformation results in lesion mimic phenotype. Up-regulation of defense mechanism was detected through detection of increased transcription level of rice PBZ1 and PR1a. Inoculation of rice blast fungus on the lesion mimic transgenic lines displayed significantly increased resistance. The disease symptoms were arrested like HR responses which are commonly detected in the incompatible interactions. High accumulation of phenolic compounds around developing lesions was detected under UV light. There was variation among transgenic lines on the timing of lesion progression as well as the lesion numbers on the rice leaves. Transgenic lines with few lesions also show increased resistance as well as equal amount of grain yields compared to that of wild type rice cultivar Nipponbare. This is the first report of the MAPKKK as a positive regulator molecule on defense mechanism through inducing HR-like cell death lesion mimic phenotype. The application of OsEDR1 is highly expected for the development of resistant cultivars against rice pathogens.

• Molecules and Cells
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• 제23권2호
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• pp.207-214
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• 2007

lant ${\beta}$-1, 3-glucanases are involved in plant defense and in development. Very little data are available on the expression of rice glucanases both in developmental tissues and under various stresses. In this study, we cloned and characterized twenty-seven rice ${\beta}$-1, 3-glucanases (OsGlu) from at total of 71 putative glucanases. The OsGlu genes were obtained by PCR from a cDNA library and were classified into seven groups (Group I to VII) according to their DNA or amino acid sequence homology. Analysis of the expression of the twenty-seven OsGlu genes by Northern blotting revealed that they were differentially expressed in different developmental tissues as well as in response to plant hormones, biotic stress, high salt etc. OsGlu11 and 27 in Group IV were clearly expressed only in stem and leaf and were also induced strongly by SA (5 mM), ABA ($200{\mu}M$), and M. grisea. OsGlu1, 10, 11, and 14 were induced earlier and to higher levels in incompatible M. grisea interaction than in compatible one. Taken together, our findings suggest that the twenty-seven rice OsGlu gene products play diverse roles not only in plant defense but also in hormonal responses and in development.