• Tribology and Lubricants
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• v.36 no.2
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• pp.55-63
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• 2020

Recently, graphene has attracted considerable attention owing to its unique electrical, optical, thermal, and mechanical properties. The broad spectrum of applications from optics, sensors, and electronics to biodevice have been proposed based on these properties. In particular, graphene has been proposed as a protective coating layer and solid lubricant for microdevices and nanodevices because of its high mechanical strength, chemical inertness, and low friction characteristics. During the past decade, extensive efforts have been made to explore the tribological characteristics of graphene under various conditions and to expand its applicability. In addition to the experimental approaches, the molecular simulations performed provide fundamental insights into the friction and wear characteristics of graphene resulting from molecular interactions. This work is a review of the studies conducted over the past decade on the tribological characteristics of graphene using molecular simulation. These studies demonstrate the principal mechanisms of the superlubricity of graphene and help clarify the influences of surface conditions on tribological behavior. In particular, the investigation of the effects of the number of layers, strength of adhesion to the substrate, surface roughness, and commensurability provides deeper insights into the tribological characteristics of graphene. These fundamental understandings can help elucidate the feasibility of graphene as a protective coating layer and solid lubricant for microdevices and nanodevices.

• Molecules and Cells
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• v.43 no.4
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• pp.397-407
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• 2020

DNAJB9 is known to be a member of the molecular chaperone gene family, whose cellular function has not yet been fully characterized. Here, we investigated the cellular function of DNAJB9 under strong mitogenic signals. We found that DNAJB9 inhibits p53-dependent oncogene-induced senescence (OIS) and induces neoplastic transformation under oncogenic RAS activation in mouse primary fibroblasts. In addition, we observed that DNAJB9 interacts physically with p53 under oncogenic RAS activation and that the p53-interacting region of DNAJB9 is critical for the inhibition of p53-dependent OIS and induction of neoplastic transformation by DNAJB9. These results suggest that DNAJB9 induces cell transformation under strong mitogenic signals, which is attributable to the inhibition of p53-dependent OIS by physical interactions with p53. This study might contribute to our understanding of the cellular function of DNAJB9 and the molecular basis of cell transformation.

• Molecules and Cells
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• v.43 no.9
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• pp.804-812
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• 2020

In cells, proteins form macromolecular complexes to execute their own unique roles in biological processes. Conventional structural biology methods adopt a bottom-up approach starting from defined sets of proteins to investigate the structures and interactions of protein complexes. However, this approach does not reflect the diverse and complex landscape of endogenous molecular architectures. Here, we introduce a top-down approach called Electron Microscopy screening for endogenous Protein ArchitectureS (EMPAS) to investigate the diverse and complex landscape of endogenous macromolecular architectures in an unbiased manner. By applying EMPAS, we discovered a spiral architecture and identified it as AdhE. Furthermore, we performed screening to examine endogenous molecular architectures of human embryonic stem cells (hESCs), mouse brains, cyanobacteria and plant leaves, revealing their diverse repertoires of molecular architectures. This study suggests that EMPAS may serve as a tool to investigate the molecular architectures of endogenous macromolecular proteins.

• Proceedings of the Korean Institute of Surface Engineering Conference
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• 2012.11a
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• pp.4-4
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• 2012

Proteins enable biology to be viable through molecular interactions (such as in antigen-antibody, ligand-receptor, and drug-target) with

• Publications of The Korean Astronomical Society
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• v.27 no.4
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• pp.243-248
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• 2012

Nearby spiral galaxies M101 and M81 are considered to have undergone a galaxy-galaxy interaction. M101 has experienced HI gas infall due to the interaction. With AKARI far-infrared (IR) photometric observations, we found regions with enhanced star forming activity, which are spatially close to regions affected by the interaction. In addition, the relation between the star formation rate (SFR) and the gas content for such regions shows a significant difference from typical spiral arm regions. We discuss possible explanations for star formation processes on a kiloparsec scale and the association with interaction-triggered star formation. We also observed the compact group of galaxies Stephan's Quintet (SQ) with the AKARI Far-infrared Surveyor (FIS). The SQ shows diffuse intergalactic medium (IGM) due to multiple collisions between the member galaxies and the IGM. The intruder galaxy NGC 7318b is currently colliding with the IGM and causes a large-scale shock. The 160 micron image clearly shows the structure along the shock ridge as seen in warm molecular hydrogen line emission and X-ray emission. The far-IR emission from the shocked region comes from the luminous [CII]$158{\mu}m$ line and cold dust (~ 20 K) that coexist with molecular hydrogen gas. Survival of dust grains is indispensable to form molecular hydrogen gas within the collision age (~ 5 Myr). At the stage of the dusty IGM environment, [CII] and $H_2$ lines rather than X-ray emission are powerful cooling channels to release the collision energy.

• BMB Reports
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• v.36 no.3
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• pp.299-304
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• 2003

For deciphering the cyclic guanosine monophosphate (cGMP) signaling pathway, we employed chemical proteomics to identify the novel target molecules of cGMP. We used cGMP that was immobilized onto agarose beads with linkers directed at three different positions of cGMP. We performed a pull-down assay using the beads as baits on tissue lysates and identified 9 proteins by MALDI-TOF (Matrix-Assisted Laser Desorption/Ionization Time-of-Flight) mass spectrometry. Some of the identified proteins were previously known cGMP targets, including cGMP-dependent protein kinase and cGMP-stimulated phosphodiesterase. Surprisingly, some of the co-precipitated proteins were never formerly reported to associate with the cGMP signaling pathway. The competition binding assays showed that the interactions are not by nonspecific binding to either the linker or bead itself, but by specific binding to cGMP. Furthermore, we observed that the interactions are highly specific to cGMP against other nucleotides, such as cyclic adenosine monophosphate (cAMP) and 5'-GMP, which are structurally similar to cGMP. As one of the identified targets, MAPK1 was confirmed by immunoblotting with an anti-MAPK1 antibody. For further proof, we observed that the membrane-permeable cGMP (8-bromo cyclic GMP) stimulated mitogen-activated protein kinase 1 signaling in the treated cells. Our present study suggests that chemical proteomics can be a very useful and powerful technique for identifying the target proteins of small bioactive molecules.

• Molecules and Cells
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• v.40 no.9
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• pp.621-631
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• 2017

Vaccinia-related kinase 1 (VRK1) and VRK3 are members of the VRK family of serine/threonine kinases and are principally localized in the nucleus. Despite the crucial roles of VRK1/VRK3 in physiology and disease, the molecular and functional interactions of VRK1/VRK3 are poorly understood. Here, we identified over 200 unreported VRK1/VRK3-interacting candidate proteins by affinity purification and LC-MS/MS. The networks of VRK1 and VRK3 interactomes were found to be associated with important biological processes such as the cell cycle, DNA repair, chromatin assembly, and RNA processing. Interactions of interacting proteins with VRK1/VRK3 were confirmed by biochemical assays. We also found that phosphorylations of XRCC5 were regulated by both VRK1/VRK3, and that of CCNB1 was regulated by VRK3. In liver cancer cells and tissues, VRK1/VRK3 were highly upregulated and its depletion affected cell cycle progression in the different phases. VRK3 seemed to affect S phase progression and G2 or M phase entry and exit, whereas VRK1 affects G1/S transition in the liver cancer, which could be explained by different interacting candidate proteins. Thus, this study not only provides a resource for investigating the unidentified functions of VRK1/VRK3, but also an insight into the regulatory roles of VRK1/VRK3 in biological processes.

• Journal of the Korean Chemical Society
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• v.24 no.4
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• pp.280-287
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• 1980

The interactions of chemical carcinogens, such as polycyclic aromatic hydrocarbons, dimethylaminoazobenzene (DAB) and its derivatives and heterocyclic compounds with tissue components, especially with deoxyribonucleic acid (DNA), were examined by means of simple Huckel method. Assuming that the formations of a loose molecular complex between the carcinogens and the tissue components are the first step of chemical carcinogenesis, the most proble orientation between the chemical carcinogens and adenine-thymine (A=T) pair or guanine-cytosine $(G\equivC)$ pair is determined. It has been found that, in the case of the formation of molecular complex between chemical carcinogens and A=T pair, the two atoms of K-region of the carcinogens and the atom of L-region in the proximity of their K-region are combined correspondingly with C-l' carbon atom in the sugar that is attached to thymine, N-1 nitrogen atom and C-5 carbon atom in the thymine part of A=T pair, while, in the case of that between the carcinogens and $G\equivC$ pair, the above three atoms of the carcinogens are combined correspondingly with C-8 carbon atom, N-9 nitrogen atom and N-3 nitrogen atom in the guanine part of $G\equivC$ pair.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.13
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• pp.5445-5451
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• 2015

Fascin-1 (FSCN1) is an actin-bundling protein that induces cell membrane protrusions, increases cell motility, and is overexpressed in various human epithelial cancers, including esophageal squamous cell carcinoma (ESCC). We analyzed various protein-protein interactions (PPI) of differentially-expressed genes (DEGs), in fascin knockdown ESCC cells, to explore the role of fascin overexpression. The node-degree distributions indicated these PPI sub-networks to be characterized as scale-free. Subcellular localization analysis revealed DEGs to interact with other proteins directly or indirectly, distributed in multiple layers of extracellular membrane-cytoskeleton/ cytoplasm-nucleus. The functional annotation map revealed hundreds of significant gene ontology (GO) terms, especially those associated with cytoskeleton organization of FSCN1. The Random Walk with Restart algorithm was applied to identify the prioritizations of these DEGs when considering their relationship with FSCN1. These analyses based on PPI network have greatly expanded our comprehension of the mRNA expression profile following fascin knockdown to future examine the roles and mechanisms of fascin action.

• Korean Journal of Ecology and Environment
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• v.51 no.1
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• pp.16-28
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• 2018

Although physiological and ecological characteristics of cyanobacteria have been studied extensively for decades, unknown areas still remain greater than the already known. Recently, the development of omics techniques based on molecular biology has made it possible to view the ecosystem from a new and holistic perspective. The molecular mechanism of toxin production is being widely investigated, by comparative genomics and the transcriptomic studies. Biological interaction between bacteria and cyanobacteria is also explored: how their interactions and genetic biodiversity change depending on seasons and environmental factors, and how these interactions finally affect each component of ecosystem. Bioinformatics techniques have combined with ecoinformatics and omics data, enabling us to understand the underlying complex mechanisms of ecosystems. Particularly omics started to provide a whole picture of biological responses, occurring from all layers of hierarchical processes from DNA to metabolites. The expectation is growing further that algal blooms could be controlled more effectively in the near future. And an important insight for the successful bloom control would come from a novel blueprint drawn by omics studies.