• Bulletin of the Korean Chemical Society
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• 제33권11호
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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.

• 대한기계학회논문집A
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• 제28권11호
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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.

• 한국융합학회논문지
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• 제7권4호
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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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• 제40권2호
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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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• 한국정보디스플레이학회 2008년도 International Meeting on Information Display
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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.

• 한국공작기계학회:학술대회논문집
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• 한국공작기계학회 2001년도 추계학술대회(한국공작기계학회)
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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.

• 생명과학회지
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• 제6권4호
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• pp.234-240
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• 1996

PKR인산화효소의 억제인자로서 밝혀진 이중선RNA결합단백질 (RBF)의 RNA결합특이성을 정기영도에 의한 RNA 이동변화실험과 여과막결합도실험에 의해 측정하였다. RBF는 바이러스RNA나 stem/loop구조를 지니는 합성 RNA들에 대한 다양한 친화력을 지니는 것으로 나타났으며 충분한 GC가 포함된 11염기쌍으로 이루어진 RNA stem helix RBF가 결합하기 위한 최소한의 RNA구조로 제시되고 있다. 자연적 RNA구조에 대한 RBF의 결합은 poly(I) : poly(C)의 첨가에 의해 반전되었으며 E. coli 5S RNA경우는 효과를 거의 나타내지 않았다.

• 생명과학회지
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• 제12권4호
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• pp.464-468
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• 2002

대장균 트립토판 중합효소(tryptophan synthase) $\alpha$ 소단 위체의 96번, 139번 과 258번 자리를 돌연변이 시킨 이중 돌연변이체 P96L/F139W, P6L/F258W와 삼중 돌연변이체 P96L/F139W/F258W의 효소 활성도와 형광 분광계를 이용한 분광학적 성질을 조사하였다. 이중 돌연변이체의 효소 활성도는 야생형과 유사하나 삼중 돌연변이체는 40% 감소된 활성도를 가진다. P96L/F139W 와 P96L/F258W의 형광세기는 야생형에 비해 감소하였으나 P96L/F139W/F258W는 야생형에 비해 증가하였다. 효소 활성도와 형광 결과는 96번의 치환이 8번 알파구조와 4번 베타 구조와 4번 알파구조 사이의 loop의 안정성에 영향을 준 것을 나타낸다. 이 결과로부터 P96L/F139W/F258W는 야생형과 다른 3차 구조를 가지나 139번과 258면 주위는 더 조밀한 구조를 가지고 있다는 것을 보여준다.

• Journal of the Korean Association of Oral and Maxillofacial Surgeons
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• 제34권5호
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• pp.509-517
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• 2008

DNA 손상 치유 유전자 연구를 기초로 한 임상적 접근이 새로운 치료방법으로 떠오르고 있다. 많은 연구들이 중요한 DNA 수복유전자의 다형성을 찾아내어 각각의 단백질의 활동성에 대한 영향을 알아내고 특정한 치료법을 찾아내고 임상적 적용을 시도하고 결과를 평가하였다. 그 결과 암 치료에서 정상 세포와 암세포에서 DNA 수복 유전자의 발현 분석은 화학요법이나 방사선 치료에서 개인맞춤형 치료법을 가능하게 하고 있다. 예를 들어, NER이 결핍된 종양은 cisplatin 치료에 민감성을 나타내고, MMR 결핍세포는 알킬화 화학요법 약제에 높은 내성을 나타낸다. 선천성 비폴립성 결장암과 같은 MMR 결손종양 또한 알킬화 화학요법 약제에 의한 치료에 내성을 가진다. 신경교종(glioma)에서 MGMT 유전자 프로모터가 흔히 메틸화되는데 이것은 유전자 발현이 억제되고 알킬화 화학요법제에 대한 반응성을 증가시킨다. 향후 구강악안면외과 영역에서도 구강암의 발생의 위험성을 증가시킬 수 있는 더 많은 DNA 수복 유전자의 다형성을 발굴하고 임상적으로 개인맞춤형 치료법을 개발하고 적용할 수 있는 많은 연구가 필요할 것으로 사료된다.

• BMB Reports
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• 제34권1호
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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.