• Proceedings of the IEEK Conference
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• 2000.06b
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• pp.306-309
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• 2000

In this work, we investigated A1 cluster deposition on Al (100) surface using molecular dynamics simulation. A result of simulations showed that large cluster with low energy was proper for good surfaced-films without craters at the low temperatures. We investigated the maximum substrate temperature and the time taken for substrate temperature to reach its maximum as a function of cluster size in the case of the same total energy and in the case of the same energy Per atom. The correlated collisions play an important role in interaction between energetic cluster and surface, and as cluster size and cluster energy increases, the correlated collisions effect affects interaction between energetic cluster and surface.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.17
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• pp.7663-7670
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• 2015

DNA methyltransferase 1 (DNMT1) is a relatively large protein family responsible for maintenance of normal methylation, cell growth and survival in mammals. Toxic industrial chemical exposure associated methylation misregulation has been shown to have epigenetic influence. Such misregulation could effectively contribute to cancer development and progression. Methyl isocyanate (MIC) is a noxious industrial chemical used extensively in the production of carbamate pesticides. We here applied an in silico molecular docking approach to study the interaction of MIC with diverse domains of DNMT1, to predict cancer risk in the Bhopal population exposed to MIC during 1984. For the first time, we investigated the interaction of MIC and its hydrolytic product (1,3-dimethylurea) with DNMT1 interacting (such as DMAP1, RFTS, and CXXC) and catalytic (SAM, SAH, and Sinefungin) domains using computer simulations. The results of the present study showed a potential interaction of MIC and 1,3-dimethylurea with these domains. Obviously, strong binding of MIC with DNMT1 interrupting normal methylation will lead to epigenetic alterations in the exposed humans. We suggest therefore that the MIC-exposed individuals surviving after 1984 disaster have excess risk of cancer, which can be attributed to alterations in their epigenome. Our findings will help in better understanding the underlying epigenetic mechanisms in humans exposed to MIC.

• Genomics & Informatics
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• v.13 no.2
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• pp.45-52
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• 2015

Acute myeloid leukemia is a well characterized blood cancer in which the unnatural growth of immature white blood cell takes place, where several genes transcription is regulated by the micro RNAs (miRNAs). Argonaute (AGO) protein is a protein family that binds to the miRNAs and mRNA complex where a strong binding affinity is crucial for its RNA silencing function. By understanding pattern recognition between the miRNAs-mRNA complex and its binding affinity with AGO protein, one can decipher the regulation of a particular gene and develop suitable siRNA for the same in disease condition. In the current work, HOXA9 gene has been selected from literature, whose deregulation is well-established in acute myeloid leukemia. Four miRNAs (mir-145, mir-126, let-7a, and mir-196b) have been selected to target mRNA of HOXA9 (NCBI accession No. NM_152739.3). The binding interaction between mRNAs and mRNA of HOXA9 gene was studied computationally. From result, it was observed mir-145 has highest affinity for HOXA9 gene. Furthermore, the interaction between miRNAs-mRNA duplex of all chosen miRNAs are docked with AGO protein (PDB ID: 3F73, chain A) to study their interaction at molecular level through an in silico approach. The residual interaction and hydrogen bonding are inspected in Discovery Studio 3.5 suites. The current investigation throws light on understanding of AGO-assisted miRNA based gene silencing mechanism in HOXA9 gene associated in acute myeloid leukemia computationally.

• The Plant Pathology Journal
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• v.38 no.6
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• pp.603-615
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• 2022

Soybean (Glycine max (L) Merr.) provides plant-derived proteins, soy vegetable oils, and various beneficial metabolites to humans and livestock. The importance of soybean is highly underlined, especially when carbon-negative sustainable agriculture is noticeable. However, many diseases by pests and pathogens threaten sustainable soybean production. Therefore, understanding molecular interaction between diverse cultivated varieties and pathogens is essential to developing disease-resistant soybean plants. Here, we established a pathosystem of the Korean domestic cultivar Kwangan against Pseudomonas syringae pv. syringae B728a. This bacterial strain caused apparent disease symptoms and grew well in trifoliate leaves of soybean plants. To examine the disease susceptibility of the cultivar, we analyzed transcriptional changes in soybean leaves on day 5 after P. syringae pv. syringae B728a infection. About 8,900 and 7,780 differentially expressed genes (DEGs) were identified in this study, and significant proportions of DEGs were engaged in various primary and secondary metabolisms. On the other hand, soybean orthologs to well-known plant immune-related genes, especially in plant hormone signal transduction, mitogen-activated protein kinase signaling, and plant-pathogen interaction, were mainly reduced in transcript levels at 5 days post inoculation. These findings present the feature of the compatible interaction between cultivar Kwangan and P. syringae pv. syringae B728a, as a hemibiotroph, at the late infection phase. Collectively, we propose that P. syringae pv. syringae B728a successfully inhibits plant immune response in susceptible plants and deregulates host metabolic processes for their colonization and proliferation, whereas host plants employ diverse metabolites to protect themselves against infection with the hemibiotrophic pathogen at the late infection phase.

• Macromolecular Research
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• v.9 no.2
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• pp.100-106
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• 2001

Several star-polymers with aliphatic cores were synthesized by ring opening polymerization (ROP) of $\xi$-caprolactone using stannous 2-ethyl-hexanoate as a catalyst. The star-polymers were thoroughly analyzed by MALDI-TOF mass spectrometry, temperature gradient interaction chromatography and $\^$13/C-NMR to obtain detailed information of the molecular structure. The imperfection of the star-polymers seemed to be originated from restricted participation of sterically hindered hydroxyl groups of initiator. The synthesized star-polymers had narrow molecular weight distributions. Various reaction conditions to control the imperfection were studied.

• Interaction and multiscale mechanics
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• v.4 no.3
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• pp.219-237
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• 2011

Recent advances in scientific computing enable the full atomistic simulation of DNA molecules. However, there exists length and time scale limitations in molecular dynamics (MD) simulation for large DNA molecules. In this work, a two-level homogenization of DNA molecules is proposed. A wavelet projection method is first introduced to form a coarse-grained DNA molecule represented with superatoms. The coarsened MD model offers a simplified molecular structure for the continuum description of DNA molecules. The coarsened DNA molecular structure is then homogenized into a three-dimensional beam with embedded molecular properties. The methods to determine the elasticity constants in the continuum model are also presented. The proposed continuum model is adopted for the study of mechanical behavior of DNA loop.

• BMB Reports
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• v.29 no.4
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• pp.294-299
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• 1996

Glyoxalase I (Ee 4.4.1.5, lactoylglutathione lyase) from Chlamydomonas reinhardtii was purified to homogeneity by ammonium sulfate fractionation, anion-exchange chromatography, hydrophobic interaction chromatography, and affinity chromatography on S-hexylglutathione agarose. The purified enzyme was judged to be homogeneous on SDS-PAGE, and consisted of a single polypeptide chain with a relative molecular weight of 24,000. The enzyme was most active at $40^{\circ}C$ and pH 7.5. It was catalytically most active with methylglyoxal as substrate. A number of properties of the Chlamydomonas glyoxalase I enzyme, such as substrate specificity, molecular mass, kinetic parameters, pi, metal ion effect, have been determined and compared with those reported for preparations from other sources. It had somewhat different characteristics from mammalian enzymes.

• KSBB Journal
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• v.6 no.2
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• pp.175-180
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• 1991

The quantitative effects of molecular weight and concentrations of two phase-forming polymers-polyethylene glycol and crude dextran on the two phase extractive ethanol fermentation were investigated using a Box-Wilson central composite protocol. The regression model obtained was used in order to determine optimum compositions of aqueous two phase system. In the aqueous two phase extractive ethanol fermentation of Kluyueromyces fragilis CBS 1555 with Jerusalem artichoke juice, it was found from the regression model that the variables influenlcing on ethanol fermentation were PEG concentration, time, Dx concentration, and PEG molecular weight strongly in order. The interaction of PEG concentration and PEG molecular weight was also found, and the effect of PEG concentration decreased with increase in molecular weight of PEG. The ethanol concentration incresed with increase in molecular weight of PEG, and with decrease in concentration of PEG. In conolusion, maximum concentration of ethanol produced was obtained at the following compositions; PEG MW 20000, Dx concentration ranged from 4% to 5%, and PEG concentration ranged from 3% to 7%.

• Proceedings of the Korean Vacuum Society Conference
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• 2010.02a
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• pp.11-11
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• 2010

Supramolecualr ordering has been actively studied due to it's possible applications to the fabrication processes of nano-electronic devices. Van der Waals interaction and hydrogen bonding are frequently studied mechanisms for various molecular structures based on non-uniform charge distributions. Halogen atoms in molecules can have electrostatic interactions with similar strength. Big halogen atoms have strong non-uniform charge distributions. To study molecular orderings formed by hydrogen and halogen interactions, we chose a molecular system containing oxygen, hydrogen, and bromine atoms, a bromo-quinone. A two-dimensional molecular network was studied on Au(111) using a low-temperature scanning tunneling microscope. Bromo-quinonemolecules form self-assembled square grids having windmill structures. Their molecular orderings, chiral structures, and defects are explained in terms of hydrogen and halogen interactions.

• Proceedings of the Korean Vacuum Society Conference
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• 2010.02a
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• pp.354-354
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• 2010

Supramolecualr ordering has been actively studied due to it's possible applications to the fabrication processes of nano-electronic devices. Van der Waals interaction and hydrogen bonding are frequently studied mechanisms for various molecular structures based on non-uniform charge distributions. Halogen atoms in molecules can have electrostatic interactions with similar strength. Big halogen atoms have strong non-uniform charge distributions. To study molecular orderings formed by hydrogen and halogen interactions, we chose a molecular system containing oxygen, hydrogen, and bromine atoms, a bromo-quinone. A two-dimensional molecular network was studied on Au(111) using a low-temperature scanning tunneling microscope. Bromo-quinone molecules form self-assembled square grids having windmill structures. Their molecular orderings, chiral structures, and defects are explained in terms of hydrogen and halogen interactions.