• Applied Biological Chemistry
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• 제41권8호
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• pp.568-571
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• 1998

The conformations of human insulin precursors, proinsulin and preproinsulin, are described in terms of molecular dynamics simulations. Despite the presence of the C-peptide and/or the signal peptide, molecular dynamics calculations utilizing the hydration shell model over a period of 500 ps indicate that the native conformations of the A and B chains are well conserved in both cases. These results further support the NMR spectroscopy results that the C-peptide is relatively disordered and does not influence the overall conformation of the native structure. The robustness of the native structure as demonstrated by experiment and simulation will permit future protein engineering applications, whereby the expression or purification yields can be improved upon sequence modification of the C-peptide and/or the signal peptide.

• Bulletin of the Korean Chemical Society
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• 제18권4호
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• pp.415-424
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• 1997

Conformational flexibilities of the GlcNAc(β1,3)Gal(β)OMe are investigated through NMR spectroscopy and molecular modeling. Adiabatic energy map generated with a dielectric constant of 50 contains three local minima. All of the molecular dynamics simulations on three local minimum energy structures show fluctuations between two low energy structures, N2 at φ=80° and ψ=60° and N3 at φ=60° and ψ=-40°. We have presented adequate evidences to state that GlcNAc(β1,3)Gal(β)OMe exists in two conformationally discrete forms. Two state model of N2 and N3 conformers with a population ratio of 40:60 is used to calculate the effective cross relaxation rate and reproduces the experimental NOEs very well. Molecular dynamics simulation in conjunction with two state model proves successfully the dynamic equilibrium existed in GlcNAc(β1,3)Gal(β)OMe and can be considered as a powerful method to analyze the motional properties in the structure of carbohydrate. This observation also cautions against the indiscriminate use of a rigid model to analyze NMR data.

• Bulletin of the Korean Chemical Society
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• 제29권3호
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• pp.641-646
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• 2008

Equilibrium molecular dynamics simulations in a canonical ensemble are performed to evaluate the transport coefficients of several Lennard-Jones (LJ) mixtures at a liquid argon states of 94.4 K and 1 atm via modified Green-Kubo formulas. Two component mixture of A and B is built by considering the interaction between A and A as the attractive (A) potential, that between A and B as the attractive potential (A), and that between B and B as the repulsive potential (R), labelled as AAR mixture. Three more mixtures - ARA, ARR, and RAR are created in the same way. The behavior of the LJ energy and the transport properties for all the mixtures is easily understood in terms of the portion of attractive potential (A %). The behavior of the thermal conductivities by the translational energy transport due to molecular motion exactly coincides with that of diffusion constant while that of the thermal conductivities by the potential energy transport due to molecular motion is easily understood from the fact that the LJ energy of AAR, ARR, and RAR mixtures increases negatively with the increase of A % from that of the pure repulsive system while that of ARA changes rarely.

• Bulletin of the Korean Chemical Society
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• 제29권4호
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• pp.741-748
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• 2008

We have studied the folding mechanism of $\beta$ -hairpins in the proteins 1GB1, 3AIT and 1A2P by conducting unfolding simulations at moderately high temperatures. The analysis of trajectories obtained from molecular dynamics simulations in explicit aqueous solution suggests that the positions of the hydrophobic core residues lead to subtle differences in the details of folding dynamics. However, the folding of three different hairpins can be explained by a unified mechanism that is a blend of the hydrogen-bond-centric and the hydrophobiccentric models. The initial stage of $\beta$-hairpin folding involves various partially folded intermediate structures which are stabilized by both the van der Waals interactions of hydrophobic core residues and the electrostatic interactions of non-native hydrogen bonds. The native structure is obtained by forming native contacts in the final tune-up process. Depending on the relative positions of the hydrophobic residues, the actual mechanism of hairpi n folding may or may not exhibit well-defined intermediates.

• 대한기계학회논문집B
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• 제36권8호
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• pp.873-876
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• 2012

Ionic Liquids (ILs) 는 표준상태에서 액체이온으로 존재하는 물질로 여러 가지 방법으로 다양한 특성을 띄게 할 수 있다. 이런 성질을 적절하게 이용하여 계면활성제 등 다양한 분야로의 응용이 가능하다. ILs의 한 종류인 1-10-alkyl-3-methylimidazolium bromide([C10mim][Br]) 은 특정한 환경에서 양친매성을 가진다. 이번 논문에서 우리는 분자동역학을 이용하여 수용액에서의 [C10mim][Br]의 응집 거동에 대한 연구를 진행하였다. 정준모듬(canonical ensemble)을 이용하여 모사 간 시스템의 부피와 온도를 일정하게 유지시키고 5ns 동안의 전산모사를 통하여 얻은 radial distribution function(RDF)을 이용하여 [C10mim][Br]과 물 분자간의 상호작용 및 그 분포의 특성에 대하여 논의하였다. 분자동역학적 계산을 위하여 LAMMPS 코드를 사용하였고, VMD 코드를 이용하여 후처리(post processing)을 진행하였다.

• Genomics & Informatics
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• 제19권4호
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• pp.48.1-48.10
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• 2021

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) encodes small envelope protein (E) that plays a major role in viral assembly, release, pathogenesis, and host inflammation. Previous studies demonstrated that pyrazine ring containing amiloride analogs inhibit this protein in different types of coronavirus including SARS-CoV-1 small envelope protein E (SARS-CoV-1 E). SARS-CoV-1 E has 93.42% sequence identity with SARS-CoV-2 E and shared a conserved domain NS3/small envelope protein (NS3_envE). Amiloride analog hexamethylene amiloride (HMA) can inhibit SARS-CoV-1 E. Therefore, we performed molecular docking and dynamics simulations to explore whether amiloride analogs are effective in inhibiting SARS-CoV-2 E. To do so, SARS-CoV-1 E and SARS-CoV-2 E proteins were taken as receptors while HMA and 3-amino-5-(azepan-1-yl)-N-(diaminomethylidene)-6-pyrimidin-5-ylpyrazine-2-carboxamide (3A5NP2C) were selected as ligands. Molecular docking simulation showed higher binding affinity scores of HMA and 3A5NP2C for SARS-CoV-2 E than SARS-CoV-1 E. Moreover, HMA and 3A5NP2C engaged more amino acids in SARS-CoV-2 E. Molecular dynamics simulation for 1 ㎲ (1,000 ns) revealed that these ligands could alter the native structure of the proteins and their flexibility. Our study suggests that suitable amiloride analogs might yield a prospective drug against coronavirus disease 2019.

• 멤브레인
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• 제25권2호
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• pp.162-170
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• 2015

본 연구에서는 다양한 아민기를 가지는 폴리이미드 소재 및 분리막을 제조하여 그들의 구조의 변화에 따른 기체 투과도를 측정하였으며 동력학(Molecular dynamics; MD) 기술을 이용하여 해당 기체의 시간의 변화에 따른 위치와 속도를 계산하여, 기체분자의 동적 특성을 분석하는데 활용하였다. 투과도 측정결과 합성된 고분자 소재의 경우 고분자 내의 free volume을 증가시키는 치환기를 도입시켰을 경우 기체투과도가 증가되었으나 rigid한 구조가 도입된 폴리이미드는 투과도가 감소되는 경향을 확인하였다. 또한 분자동력학 시뮬레이션을 이용하여 기체투과거동 변화를 분석한 결과 실제 기체투과도 측정결과와 유사한 결과를 나타냄을 확인할 수 있었다.

• Bulletin of the Korean Chemical Society
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• 제19권10호
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• pp.1047-1054
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• 1998

We present the results of molecular dynamics simulations for three different systems of bilayers of long-chain alkyl thiol [S(CH2)15CH3] molecules on an solid-solid interface using the extended collapsed atom model for the chain-molecule. It is found that there exist two possible transitions: a continuous transition characterized by a change in molecular interaction between sites of different chain molecules with increasing area per molecule and a sudden transition from an ordered lattice-like state to a liquid-like state due to the lack of interactions between sites of chain molecules on different surfaces with increasing distance between two solid surfaces. The third system displays a smooth change in probability distribution characterized by the increment of gauche structure in the near-tail part of the chain with increasing area per molecule. The analyses of energetic results and chain conformation results demonstrate the characteristic change of chain structure of each system.

• Nuclear Engineering and Technology
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• 제54권8호
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• pp.2783-2791
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• 2022

Molecular dynamics simulations were performed to predict the behavior of graphite atoms under neutron irradiation using large-scale atomic/molecular massively parallel simulator (LAMMPS) package with adaptive intermolecular reactive empirical bond order (AIREBOM) potential. Defect structures of graphite were compared with results from previous studies by means of density functional theory (DFT) calculations. The quantitative relation between primary knock-on atom (PKA) energy and irradiation damage on graphite was calculated. and the effect of PKA direction on the amount of defects is estimated by counting displaced atoms. Defects are classified into four groups: structural defects, energy defects, vacancies, and near-defect structures, where a structural defect is further subdivided into six types by decision tree method which is one of the supervised machine learning techniques.

• 한국수소및신에너지학회논문집
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• 제11권3호
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• pp.127-136
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• 2000

Molecular dynamics simulations have been carried out to investigate the scattering and penetration properties of hydrogen ions with the normal incident angle to Ni (100) surface. The initial kinetic energies of hydrogen ions range from 100 to 1,600 eV. The simulation results are used to assess the applicabilities of theoretical predictions based on the binary collision approximation, and, in the high kinetic regime, theoretical results for scattering energies were shown to he a good agreement with molecular simulations. The angle dependencies on both scattering and penetration distributions were found in the longitudinal direction, but not in the azimuthal direction except for the high kinetic energy of 1,600 eV.