• Weed & Turfgrass Science
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• 제6권1호
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• pp.28-31
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• 2017

The mutation rate of proline in the position 197 (Pro197) in acetohydroxy acid synthase (AHAS) is highest among sulfonylurea (SU) herbicide-resistance mutants. Therefore, it is significant to investigate the resistance mechanism for the mutation and to develop the herbicides specific to the mutants. SU herbicide resistance mechanism of the mutants, 197Ser, 197Thr and 197Ala, in AHAS were targeted for designing new SU-herbicide. We did molecular dynamics (MD) simulation for understanding SU herbicide-resistance mechanisms of AHAS mutants and designed new herbicides with docking and MD evaluations. We have found that mutation to 197Ala and 197Ser enlarged the entrance of the active site, while 197Thr contracted. Map of the root mean square derivation (RMSD) and radius gyrations (Rg) revealed the domain indicating the conformations for herbicide resistant. Based on the enlarging-contracting mechanism of active site entrance, we designed new herbicides with substitution at the heterocyclic moiety of a SU herbicide for the complementary binding to the changed active site entrances of mutants, and designed new herbicides. We confirmed that our screened new herbicides bonded to both AHAS wild type and mutants with higher affinity, showing more stable binding conformation than the existing herbicides.

• 전자공학회논문지D
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• 제36D권7호
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• pp.9-16
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• 1999

본 논문은 극 저 에너지 이온 주입의 원자단위 연구를 위하여 국부 셀 격자결함 축적 모델(local cell damage accumulation model)을 제안하고, 분자 역학 방법(molecular dynamics method)을 사용한 이온 주입 시뮬레이션 결과를 보여주고 있다. 국부 격자 결함 확률 축적 함수는 각 단위 셀에 축적된 에너지, 이온빔 전류, 기판 물질, 주입 이온과 이온 발생 순서 등으로 구성되어 있다. 시뮬레이션 결과는 SIMS 측정치 및 다른 분자 역학 시뮬레이션과 잘 일치한다. 격자결함을 고려하지 않는 MDRANGE는 격자결함으로 인한 채널링 억제 효과가 나타나지 않기 때문에 불순물 분포의 꼬리 부분에서 많은 차이를 보였다. 또한 국부 격자결함 축적 모델을 사용한 경우와 이를 고려하지 않는 경우의 불순물과 격자결함에 관한 2차원 분포를 계산하여 국부적으로 축적된 격자결함이 이온의 진행에 큰 영향을 미치는 것으로 나타났다.

• Bulletin of the Korean Chemical Society
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• 제35권6호
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• pp.1713-1719
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• 2014

1FSD is a 28-residue designed protein with a ${\beta}{\beta}{\alpha}$ motif. Since this protein displays most essential features of protein structures in such a small size, this model protein can be an outstanding system for evaluating the balance in the propensity of the secondary structures and the quality of all-atom protein force fields. Particularly, this protein would be difficult to fold to its correct native structure without establishing proper balances between the secondary structure elements in all-atom energy functions. In this work, a series of the recently optimized five amber protein force fields [$ff03^*$, $f99sb^*$-ildn, ff99sb-${\phi}^{\prime}$-ildn, ff99sb-nmr1-ildn, ff99sb-${\Phi}{\Psi}$(G24, CS)-ildn] were investigated for the simulations of 1FSD using a conventional molecular dynamics (MD) and a biased-exchange meta-dynamics (BEMD) methods. Among those tested force fields, we found that ff99sb-nmr1-ildn and ff99sb-${\Phi}{\Psi}$(G24, CS)-ildn are promising in that both force fields can locate the native state of 1FSD with a high accuracy (backbone rmsd ${\leq}1.7{\AA}$) in the global free energy minimum basin with a reasonable energetics conforming to a previous circular dichroism (CD) experiment. Furthermore, both force fields led to a common set of two distinct folding pathways with a heterogeneous nature of the transition state to the folding. We anticipate that these force fields are reasonably well balanced, thereby transferable to many other protein folds.

• 대한기계학회논문집B
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• 제40권10호
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• pp.659-666
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• 2016

본 연구는 길이에 따른 사각 기둥 타입을 변수로 선정하여 각각의 길이 패턴을 지닌 고체 표면에서의 물 액적 젖음 특성을 분자 동역학을 이용하여 규명하였다. 기둥의 표면 형상을 정사각형과 직사각형의 형태로 가정하였고, 정해진 형상에서의 표면 면적을 증가시켰다. 정사각형 형상의 경우 각 변의 길이가 $4.24{\AA}$, $8.48{\AA}$, $12.72{\AA}$로 증가하였으며, 직사각형 형상의 경우 고정된 한 변은 $8.48{\AA}$의 길이를 가지며 다른 한 변의 길이는 $4.24{\AA}$, $8.48{\AA}$, $12.72{\AA}$로 증가하였다. 이러한 길이 변화를 통해 사각기둥 표면형상의 변화 및 전체 고체표면의 면적 대비 기둥이 차지하는 면적의 비율에 따른 물 액적의 변화를 살펴보고, 표면과 물 액적과의 접촉각을 측정하여 비교 분석하였다.

• Bulletin of the Korean Chemical Society
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• 제35권8호
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• pp.2494-2504
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• 2014

P38 mitogen activated protein (MAP) kinase is an important anti-inflammatory drug target, which can be activated by responding to various stimuli such as stress and immune response. Based on the conformation of the conserved DFG loop (in or out), binding inhibitors are termed as type-I and II. Type-I inhibitors are ATP competitive, whereas type-II inhibitors bind in DFG-out conformation of allosteric pocket. It remains unclear that how these allosteric inhibitors stabilize the DFG-out conformation and interact. Organosilicon compounds provide unusual opportunity to enhance potency and diversity of drug molecules due to their low toxicity. However, very few examples have been reported to utilize this property. In this regard, we performed docking of an inhibitor (BIRB) and its silicon analog (Si-BIRB) in an allosteric binding pocket of p38. Further, molecular dynamics (MD) simulations were performed to study the dynamic behavior of the simulated complexes. The difference in the biological activity and mechanism of action of the simulated inhibitors could be explained based on the molecular mechanics/generalized Born surface area (MM/GBSA) binding free energy per residue decomposition. MM/GBSA showed that biological activities were related with calculated binding free energy of inhibitors. Analyses of the per-residue decomposed energy indicated that van der Waals and non-polar interactions were predominant in the ligand-protein interactions. Further, crucial residues identified for hydrogen bond, salt bridge and hydrophobic interactions were Tyr35, Lys53, Glu71, Leu74, Leu75, Ile84, Met109, Leu167, Asp168 and Phe169. Our results indicate that stronger hydrophobic interaction of Si-BIRB with the binding site residues could be responsible for its greater binding affinity compared with BIRB.

• Journal of Ginseng Research
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• 제39권2호
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• pp.141-147
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• 2015

Background: Adipocytes, which are the main cellular component of adipose tissue, are the building blocks of obesity. The nuclear hormone receptor $PPAR{\gamma}$ is a major regulator of adipocyte differentiation and development. Obesity, which is one of the most dangerous yet silent diseases of all time, is fast becoming a critical area of research focus. Methods: In this study, we initially aimed to investigate whether the ginsenoside Rf, a compound that is only present in Panax ginseng Meyer, interacts with $PPAR{\gamma}$ by molecular docking simulations. After we performed the docking simulation the result has been analyzed with several different software programs, including Discovery Studio, Pymol, Chimera, Ligplus, and Pose View. All of the programs identified the same mechanism of interaction between $PPAR{\gamma}$ and Rf, at the same active site. To determine the drug-like and biological activities of Rf, we calculate its absorption, distribution, metabolism, excretion, and toxic (ADMET) and prediction of activity spectra for substances (PASS) properties. Considering the results obtained from the computational investigations, the focus was on the in vitro experiments. Results: Because the docking simulations predicted the formation of structural bonds between Rf and $PPAR{\gamma}$, we also investigated whether any evidence for these bonds could be observed at the cellular level. These experiments revealed that Rf treatment of 3T3-L1 adipocytes downregulated the expression levels of $PPAR{\gamma}$ and perilipin, and also decreased the amount of lipid accumulated at different doses. Conclusion: The ginsenoside Rf appears to be promising compound that could prove useful in antiobesity treatments.

• Bulletin of the Korean Chemical Society
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• 제33권11호
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• pp.3601-3606
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• 2012

Structural properties of a small hexapeptide molecule modeled after metal-binding siderochrome immersed in a room-temperature ionic liquid (RTIL) are studied via molecular dynamics simulations. We consider two different RTILs, each of which is made up of the same cationic species, 1-butyl-3-methylimidazolium ($BMI^+$), but different anions, hexafluorophosphate ($PF_6{^-}$) and chloride ($Cl^-$). We investigate how anionic properties such as hydrophobicity/hydrophilicity or hydrogen bonding capability affect the stabilization of the peptide in RTILs. To examine the effect of peptide-RTIL electrostatic interactions on solvation, we also consider a hypothetical solvent $BMI^0Cl^0$, a non-ionic counter-part of $BMI^+Cl^-$. For reference, we investigate solvation structures in common polar solvents, water and dimethylsulfoxide (DMSO). Comparison of $BMI^+Cl^-$ and $BMI^0Cl^0$ shows that electrostatic interactions of the peptide and RTIL play a significant role in the conformational fluctuation of the peptide. For example, strong electrostatic interactions between the two favor an extended conformation of the peptide by reducing its structural fluctuations. The hydrophobicity/hydrophilicity of RTIL anions also exerts a notable influence; specifically, structural fluctuations of the peptide become reduced in more hydrophilic $BMI^+Cl^-$, compared with those in more hydrophobic $BMI^+PF_6{^-}$. This is ascribed to the good hydrogen-bond accepting power of chloride anions, which enables them to bind strongly to hydroxyl groups of the peptide and to stabilize its structure. Transport properties of the peptide are examined briefly. Translations of the peptide significantly slow down in highly viscous RTILs.

• Composites Research
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• 제33권4호
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• pp.198-204
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• 2020

본 연구에서는 탄소나노튜브 다발을 포함하는 나노복합재료의 열-기계적 특성을 정량적으로 예측하기 위하여 분자동역학 전산모사와 유한요소 기반 균질화 기법을 적용하였다. 응집된 탄소나노튜브의 수가 증가함에 따라 동일한 탄소나노튜브의 체적분율에도 불구하고, 면내 영률 및 면내 전단계수는 감소하였고, 면내 열팽창계수는 증가함을 확인할 수 있었다. 계면의 두께를 조사하기 위하여 밀도의 반경 방향 분포(Radial density distribution)을 조사하였으며, 계면의 두께는 탄소나노튜브의 수와는 거의 무관함을 확인할 수 있었다. 기지와 계면은 등방성 재료로 가정하였으며, 예측한 계면의 열-기계적 특성에 따르면, 응집된 탄소나노튜브의 수가 증가함에 따라 계면의 영률 및 전단계수는 감소하였으며, 열팽창계수는 반대로 증가하였다. 이를 토대로, 탄소나노튜브 다발을 포함하는 PLA 나노복합재료의 열-기계적 특성 예측을 위한 멀티스케일 균질화 모델을 개발하였다.

• 대한기계학회논문집A
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• 제38권2호
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• pp.105-113
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• 2014

중앙에 균열을 갖는 단층 그래핀시트(single layer graphene sheet, SLGS)의 모드 II 파괴 거동을 원자 시뮬레이션과 해석 모델에 기초하여 고찰하였다. 지그재그 그래핀 모델의 파괴를 분자동역학(molecular dynamics, MD)에 의해 해석한 결과 모드 II 파괴인성은 $2.04MPa{\sqrt{m}}$인 것으로 밝혀졌다. 또한 SLGS의 이론적인 $K_{IIc}$를 유도하기 위해 면내전단하중을 받는 다공체에 대한 파괴역학적 해석도 진행하였고 유한요소해석도 병행하였다. 모드 I과 모드 II의 비를 다양하게 변화시켜가면서 SLGS 의 혼합모드 파괴를 검토한 결과 혼합모드 파괴조건식이 얻어졌고 다른 문헌의 결과와 비슷함을 알 수 있었다.

• 멤브레인
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• 제29권1호
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• pp.11-17
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• 2019

수처리 분리막 분야에서 고분자는 세라믹과 함께 가장 중요한 소재로 이용되고 있다. 본 총설에서는 이러한 고분자 분리막 소재의 기술동향을 상용화 제품을 중심으로 분석하고자 하였으며, 이를 위하여 수처리 분리막의 종류에 따라 MF (Microfiltration), UF (Ultrafiltration), NF (Nanofiltration)/RO (Reverse Osmosis) 분리막으로 구분하여, 국가별, 소재별, 회사별 고분자 분리막 제품 동향을 살펴보았다. 이를 통하여, 각 분리막 종류별로 주로 사용되고 있는 소재의 종류를 파악할 수 있었으며, 동시에 시장 지배적인 위치에 있는 업체들을 파악하고 이들 업체들이 어떤 소재들로 제품 포트폴리오를 구성하고 있는지 분석할 수 있었다. 이러한 결과들을 바탕으로 각각의 분리막 종류에 따른 소재 시장의 특징을 제시하였으며, 이런 특징을 바탕으로 각 시장에 신규로 진입하기 위한 기술 개발 전략을 제안하였다.