• Bulletin of the Korean Chemical Society
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• v.33 no.11
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• pp.3719-3726
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• 2012

Formation of Z-DNA, a left-handed double helix, from B-DNA, the canonical right-handed double helix, occurs during important biological processes such as gene expression and DNA transcription. Such B-Z transitions can also be induced by high salt concentration in vitro, but the changes in the relative stability of B-DNA and Z-DNA with salt concentration have not been fully explained despite numerous attempts. For example, electrostatic effects alone could not account for salt-induced B-Z transitions in previous studies. In this paper, we propose that the B-Z transition can be explained if counterion entropy is considered along with the electrostatic interactions. This can be achieved by conducting all-atom, explicit-solvent MD simulations followed by MM-PBSA and molecular DFT calculations. Our MD simulations show that counterions tend to bind at specific sites in B-DNA and Z-DNA, and that more ions cluster near Z-DNA than near B-DNA. Moreover, the difference in counterion ordering near B-DNA and Z-DNA is larger at a low salt concentration than at a high concentration. The results imply that the exclusion of counterions by Z-DNA-binding proteins may facilitate Z-DNA formation under physiological conditions.

• Transactions of the Korean Society of Mechanical Engineers A
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• v.28 no.11
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• pp.1752-1759
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• 2004

Reinforced braid layer (RBL) in automobile power steering hose plays an important role in power steering system. When the working oil is applied to the power steering hose, RBL suppresses rubber hose deformation from internal pressure and heat expansion. RBL is woven textile composites having a double-row structure of nylon cords twisted with the specific helix angle. In this paper, effective material properties of RBL are estimated using a detailed 3-D finite element model considering its complicated geometry. Numerical experiments based on a superposition method are carried out to simulate uniaxial tensile loading condition.

• Journal of the Korea Convergence Society
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• v.7 no.4
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• pp.181-190
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• 2016

The objective of this study is to find the effective stiffness and compressive strengths of a unit-cell pinwheel truss and double pinwheel truss model designed following a double helical geometry similar to that of the DNA (deoxyribonucleic acid) structure in biology. The ideal solution for their derived relative density is correlated with a ratio of the truss thickness and length. To validate the relative stiffness or relative strength, ABAQUS software is used for the computational model analysis on five models having a different size of truss diameter from 1mm to 5mm. Applied material properties are stainless steel type 304. The boundary conditions applied were fixed bottom and 5 mm downward displacement. It was assumed that the width, length, and height are all equal. Consequently, it is found that the truss model has a lower effective stiffness and a lower effective yielding strength.

• BMB Reports
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• v.40 no.2
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• pp.163-171
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• 2007

Functional elements of the conserved helix 7 in the poreforming domain of the Bacillus thuringiensis Cry $\delta$- endotoxins have not yet been clearly identified. Here, we initially performed alanine substitutions of four highly conserved aromatic residues, $Trp^{243}$, $Phe^{246}$, $Tyr^{249}$ and $Phe^{264}$, in helix 7 of the Cry4Ba mosquito-larvicidal protein. All mutant toxins were overexpressed in Escherichia coli as 130-kDa protoxins at levels comparable to the wild-type. Bioassays against Stegomyia aegypti mosquito larvae revealed that only W243A, Y249A or F264A mutant toxins displayed a dramatic decrease in toxicity. Further mutagenic analysis showed that replacements with an aromatic residue particularly at $Tyr^{249}$ and $Phe^{264}$ still retained the high-level toxin activity. In addition, a nearly complete loss in larvicidal activity was found for Y249L/F264L or F264A/ Y249A double mutants, confirming the involvement in toxicity of both aromatic residues which face towards the same direction. Furthermore, the Y249L/F264L mutant was found to be structurally stable upon toxin solubilisation and trypsin digestion, albeit a small change in the circular dichroism spectrum. Altogether, the present study provides for the first time an insight into the highly conserved aromaticity of $Tyr^{249}$ and $Phe^{264}$ within helix 7 playing an important role in larvicidal activity of the Cry4Ba toxin.

• 한국정보디스플레이학회:학술대회논문집
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• 2008.10a
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• pp.1381-1382
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• 2008

Cholesteric Blue phase (ChBP) is constructed by the regular arrangement of the double helix, whereas the Smectic Blue phase (SmBP) has the inter-connected multi-lamellar structure. Orientation fluctuations of polymer stabilized ChBP and spontaneously super-cooled SmBP are discussed. Spatial topology of the defects play key role on the dynamic properties.

• Proceedings of the Korean Society of Machine Tool Engineers Conference
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• 2001.10a
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• pp.292-297
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• 2001

Twin screw extruders are the heart of the polymer processing industry. They are used at some stage in nearly all polymer processing operations. This paper is concerned with the basic elements of the extruder design. The proper design of the geometry of the extruder screw is of crucial importance to the proper functioning of the extruder. If the material transport instabilities occur as a result of improper screw geometry, even the most sophisticated computerized control system cannot solve the problem. For this purpose, a characteristic design on flights shape of the extruder screw. This paper presents cross section designs of a closely intermeshing twin screw extruder with double-flighted screw elements, and channel depth characteristics for a double flighted corotating self-wiping twin screw extruder.

• Journal of Life Science
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• v.6 no.4
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• pp.234-240
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• 1996

A double-stranded RNA binding factor (RBF), characterized as an inhibitor of PKR kinase in our previous study, was evaluated for its RNA binding specificities by RNA gel electrophoretic mobility shift analysis and membrane filter binding assay, RBF displayed affinities for a broad range of RNAs including viral RNAs and synthetic RNAs consiting of stem and loop structures. GC-rich RNA stem helices as short as 11 bp are suggested to represent the minimal binding motif for RBF. RBF binding to all the natural RNAs tested was reversible by poly(I): poly(C) addition, but E. coli 5S RNA was inefficient.

• Journal of Life Science
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• v.12 no.4
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• pp.464-468
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• 2002

Enzymatic activities and fluorescence spectroscopic properties of the double mutant proteins P96L/F139W, P96L/F258W and a triple mutant protein P96L/F139W/F258W of tryptophan synthase $\alpha$ subunit from Escherichia coli was examined to study tertiary and local structure changes around the tryptophan residues. The enzymatic activities of P96l./F139W and P96L/F258W were similar, but P96L/F139W/F258W had lower activity, as compared to wild type. The fluorescence intensities of double mutant, P96L/F139W and P96L/F258W, were decreased but that of a triple mutant, P96L/F139W/F258W, was increased when compared to wild type. The sum of the maximum fluorescence intensity (fluorescence intensity at the λ$_{max}$) for the double mutant proteins was not equal to the intensity seen in the triple mutant protein. The enzymatic activity and fluorescence data indicate that the replacement of Pro$^{96}$ longrightarrowLeu might affect on the stability of helix 8 and the loop located between strand 4 and helix4. The result suggests that the tertiary structure of triple mutant (P96L/F139W/F258W), being different from wild type, might have more compact residual structure at the vicinity of 139 and 258.8.

• Journal of the Korean Association of Oral and Maxillofacial Surgeons
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• v.34 no.5
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• pp.509-517
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• 2008

DNA damage accumulates in cells as a result of exposure to exogenous agents such as benzopyrene, cigarette smoke, ultraviolet light, X-ray, and endogenous chemicals including reactive oxygen species produced from normal metabolic byproducts. DNA damage can also occur during aberrant DNA processing reactions such as DNA replication, recombination, and repair. The major of DNA damage affects the primary structure of the double helix; that is, the bases are chemically modified. These modification can disrupt the molecules'regular helical structure by introducing non-native chemical bonds or bulky adducts that do not fit in the standard double helix. DNA repair genes and proteins scan the global genome to detect and remove DNA damage and damage to single nucleotides. Direct reversal of DNA damage, base excision repair, double strand break. DNA repair are known relevant DNA repair mechanisms. Four different mechanisms are distinguished within excision repair: direct reversal, base excision repair, nucleotide excision repair, and mismatch repair. Genetic variation in DNA repair genes can modulate DNA repair capacity and alter cancer risk. The instability of a cell to properly regulate its proliferation in the presence of DNA damage increase risk of gene mutation and carcinogenesis. This article aimed to review mechanism of excision repair and to understand the relationship between genetic variation of excision repair genes and head and neck cancer.

• BMB Reports
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• v.34 no.1
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• pp.73-79
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• 2001

Transcriptional activation domains are known to be inherently "unstructured" with no tertiary structure. A recent NMR study, however, has shown that the transactivation domain in human p53 is populated with an amphipathic helix and two nascent turns. This suggests that the presence of such local secondary structures within the overall "unstructured" structural framework is a general feature of acidic transactivation domains. These pre-existing local structures in p53, formed selectively by positional conserved hydrophobic residues that are known to be critical for transcriptional activity, thus appear to constitute the specific structural motifs that regulate recognition of the p53 transactivation domain by target proteins. Here, we report the results of a NMR structural comparison between the native human p53 transactivation domain and an inactive mutant (22L,23W$\rightarrow$22R,23S). Results show that the mutant has an identical overall structural topology as the native protein, to the extent that the amphipathic helix formed by the residues 18T 26L within the native p53 transactivating domain is preserved in the double mutant. Therefore, the lack of transcriptional activity in the double mutant should be ascribed to the disruption of the essential hydrophobic contacts between the p53 transactivation domain and target proteins due to the (22L,23W$\rightarrow$22R,23S) mutation.