• Macromolecular Research
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• v.14 no.1
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• pp.34-37
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• 2006

Attaching the organosilyl groups to macromolecular chains of 2-hydroxyethyl methacrylate (HEMA) should lead to important modifications of polymer properties. t-$BuMe_{2}Si$ and cubane-l, 4-dicarboxylic acid (CDA) were covalently linked with 2-hydroxyethyl methacrylate (HEMA). The silyl-linked HEMA is abbreviated as TSMA, while cubane-l ,4-dicarboxylic acid (CDA) linked to two HEMA groups is the cross-linking agent (CA). Free radical cross-linking copolymerization of TSMA and HEMA with various ratios of CA as the cross-linking agent was carried out at 60-70$^{circ}C$. The compositions of the cross-linked, three-dimensional polymers were determined by FTIR spectroscopy. The glass transition temperature ($T_{g}$) of the network polymers was determined calorimetrically. The $T_{g}$ of the network polymer increased with increasing cross-linking degree.

• Current Optics and Photonics
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• v.4 no.4
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• pp.336-344
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• 2020

Exact optical characterization of virtual and augmented reality devices using conventional luminance measuring methods is a time-consuming process. A new measurement method is proposed to estimate in a relatively short time the boundary of ray trajectories emitting from a specific position on a virtual images. It is assumed that the virtual image can be modeled to be formed in front of one's eyes and seen through some optical aperture (field stop) that limits the field of view. Circular and rectangular shaped virtual images were investigated. From the estimated ray boundary, optical characteristics, such as the viewing direction and three dimensional range inside which a eye can observe the specified positions of the virtual image, were derived. The proposed method can provide useful data for avoiding the unnecessary measurements required for the previously reported method. Therefore, this method can be complementary to the previously reported method for reducing the whole measurement time of optical characteristics.

• Investigative Magnetic Resonance Imaging
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• v.23 no.1
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• pp.1-16
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• 2019

Dynamic contrast enhanced (DCE) magnetic resonance (MR) imaging plays an important role in non-invasive detection and characterization of primary and metastatic lesions in the liver. Recently, efforts have been made to improve spatial and temporal resolution of DCE liver MRI for arterial phase imaging. Review of recent publications related to arterial phase imaging of the liver indicates that there exist primarily two approaches: breath-hold and free-breathing. For breath-hold imaging, acquiring multiple arterial phase images in a breath-hold is the preferred approach over conventional single-phase imaging. For free-breathing imaging, a combination of three-dimensional (3D) stack-of-stars golden-angle sampling and compressed sensing parallel imaging reconstruction is one of emerging techniques. Self-gating can be used to decrease respiratory motion artifact. This article introduces recent MRI technologies relevant to hepatic arterial phase imaging, including differential subsampling with Cartesian ordering (DISCO), golden-angle radial sparse parallel (GRASP), and X-D GRASP. This article also describes techniques related to dynamic 3D image reconstruction of the liver from golden-angle stack-of-stars data.

• Molecules and Cells
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• v.42 no.7
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• pp.512-522
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• 2019

Chromosomes located in the nucleus form discrete units of genetic material composed of DNA and protein complexes. The genetic information is encoded in linear DNA sequences, but its interpretation requires an understanding of three-dimensional (3D) structure of the chromosome, in which distant DNA sequences can be juxtaposed by highly condensed chromatin packing in the space of nucleus to precisely control gene expression. Recent technological innovations in exploring higher-order chromatin structure have uncovered organizational principles of the 3D genome and its various biological implications. Very recently, it has been reported that large-scale genomic variations may disrupt higher-order chromatin organization and as a consequence, greatly contribute to disease-specific gene regulation for a range of human diseases. Here, we review recent developments in studying the effect of structural variation in gene regulation, and the detection and the interpretation of structural variations in the context of 3D chromatin structure.

• 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.

• Transactions of the Korean Society of Mechanical Engineers B
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• v.39 no.6
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• pp.541-548
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• 2015

We study the structural and functional characteristics of zinc oxide (ZnO) nanostructures that are grown on carbon nanotube (CNT) constructs via step-wise chemical vapor deposition (CVD). First, we optimize the CVD process to directly grow ZnO nanostructures on CNTs by controlling the growth temperature below $600^{\circ}C$, where CNTs can be sustained in a ZnO-growing oxidative atmosphere. We then investigate how the morphology and areal density of ZnO nanostructures evolve depending on process parameters, such as pressure, temperature, and gas feeding composition, while focusing on the effect of underlying CNT topology on ZnO nucleation and growth. Because various types of ZnO nanostructures, including nanowires, nanorods, nanoplates, and polycrystalline nanocrystals, can be conformally formed on highly conductive CNT platforms, this electrically addressable three-dimensional hybrid nanoarchitecture may better meet a wide range of nanoelectronic application-specific needs.

• Genomics & Informatics
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• v.21 no.1
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• pp.7.1-7.11
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• 2023

The gram-positive bacterium Listeria monocytogenes is an important foodborne intracellular pathogen that is widespread in the environment. The functions of hypothetical proteins (HP) from various pathogenic bacteria have been successfully annotated using a variety of bioinformatics strategies. In this study, a HP Imo0888 (NP_464414.1) from the Listeria monocytogenes EGD-e strain was annotated using several bioinformatics tools. Various techniques, including CELLO, PSORTb, and SOSUIGramN, identified the candidate protein as cytoplasmic. Domain and motif analysis revealed that the target protein is a PemK/MazF-like toxin protein of the type II toxin-antitoxin system (TAS) which was consistent with BLASTp analysis. Through secondary structure analysis, we found the random coil to be the most frequent. The Alpha Fold 2 Protein Structure Prediction Database was used to determine the three-dimensional (3D) structure of the HP using the template structure of a type II TAS PemK/MazF family toxin protein (DB ID_AFDB: A0A4B9HQB9) with 99.1% sequence identity. Various quality evaluation tools, such as PROCHECK, ERRAT, Verify 3D, and QMEAN were used to validate the 3D structure. Following the YASARA energy minimization method, the target protein's 3D structure became more stable. The active site of the developed 3D structure was determined by the CASTp server. Most pathogens that harbor TAS create a crucial risk to human health. Our aim to annotate the HP Imo088 found in Listeria could offer a chance to understand bacterial pathogenicity and identify a number of potential targets for drug development.

• Molecules and Cells
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• v.22 no.1
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• pp.13-20
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• 2006

Hepatitis C virus (HCV) non-structural protein 5A protein (NS5A), which consists of three functional domains, is involved in regulating viral replication, interferon resistance, and apoptosis. Recently, the three-dimensional structure of the domain 1 was determined. However, currently the molecular basis for the domains 2 and 3 of HCV NS5A is yet to be defined. Toward this end, we expressed, purified the domain 2 of the NS5A (NS5A-D2), and then performed biochemical and structural studies. The purified domain 2 was active and was able to bind NS5B and PKR, biological partners of NS5A. The results from gel filtration, CD analysis, 1D $^1H$ NMR and 2D $^1H-^{15}N$ heteronuclear single quantum correlation (HSQC) spectroscopy indicate that the domain 2 of NS5A appears to be flexible and disordered.

• Proceedings of the Korean Society of Propulsion Engineers Conference
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• 2010.05a
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• pp.437-440
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• 2010

This paper represents a simple and effective calculation method to predict the orthotropic engineering constants for C/SiC woven fabric composite. The method, a quasi-analytical method using the modified equivalent laminated model, idealizes the woven fabric structure as a symmetric three-ply laminate to utilize a classical laminated plate theory. The required initial parameters are in-plane modulus from experiments and crimp ratio of the woven fabric. This study shows its feasibility by demonstrating example to calculate the engineering constants to thickness direction needed for three dimensional thermo-mechanical stress calculations.

• Genomics & Informatics
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• v.20 no.4
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• pp.41.1-41.9
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• 2022

The pathogen Gallibacterium anatis has caused heavy economic losses for commercial poultry farms around the world. However, despite its importance, the functions of its hypothetical proteins (HPs) have been poorly characterized. The present study analyzed the functions and structures of HPs obtained from Gallibacterium anatis (NCTC11413) using various bioinformatics tools. Initially, all the functions of HPs were predicted using the VICMpred tool, and the physicochemical properties of the identified virulence proteins were then analyzed using Expasy's ProtParam server. A virulence protein (WP_013745346.1) that can act as a potential drug target was further analyzed for its secondary structure, followed by homology modeling and three-dimensional (3D) structure determination using the Swiss-Model and Phyre2 servers. The quality assessment and validation of the 3D model were conducted using ERRAT, Verify3D, and PROCHECK programs. The functional and phylogenetic analysis was conducted using ProFunc, STRING, KEGG servers, and MEGA software. The bioinformatics analysis revealed 201 HPs related to cellular processes (n = 119), metabolism (n = 61), virulence (n = 11), and information/storage molecules (n = 10). Among the virulence proteins, three were detected as drug targets and six as vaccine targets. The characterized virulence protein WP_013745346.1 is proven to be stable, a drug target, and an enzyme related to the citrate cycle in the present pathogen. This enzyme was also found to facilitate other metabolic pathways, the biosynthesis of secondary metabolites, and the biosynthesis of amino acids.