• Bulletin of the Korean Chemical Society
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• 제33권3호
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• pp.828-832
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• 2012

We performed replica exchange molecular dynamics (REMD) simulations of the tripzip2 peptide (betahairpin) using the GB implicit and TI3P explicit solvation models. By comparing the resulting free energy surfaces of these two solvation model, we found that the GB solvation model produced a distorted free energy map, but the explicit solvation model yielded a reasonable free energy landscape with a precise location of the native structure in its global free energy minimum state. Our result showed that in particular, the GB solvation model failed to describe the tryptophan packing of trpzip2, leading to a distorted free energy landscape. When the GB solvation model is replaced with the explicit solvation model, the distortion of free energy shape disappears with the native-like structure in the lowest free energy minimum state and the experimentally observed tryptophan packing is precisely recovered. This finding indicates that the main source of this problem is due to artifact of the GB solvation model. Therefore, further efforts to refine this model are needed for better predictions of various aromatic side chain packing forms in proteins.

• 대한화학회지
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• 제57권5호
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• pp.554-559
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• 2013

본 연구에서는 ${\beta}$-D-glucopyranose 분자의 hydroxymethyl group의 두 torsion angle의 변화에 따른 포텐셜 에너지의 변화를 진공 상태와 implicit water 상태에서 연구하였으며 이를 통해 Solvation Energy가 구조에 미치는 영향에 대해서 알아보았다. 계산에 사용한 프로그램은 AMBER package였으며, force field는 GLYCAM_06을 사용하였다. Solvation model은 Hawkins, Cramer, Truhlar 등이 제안한 generalized Born model을 사용하였다. 계산 결과, methyl hydroxyl group 내의 hydroxyl group이 고리구조의 hydroxyl group과 강한 수소결합이 가능한 영역에서 많은 변화가 일어났다. 이를 통해 solvation effect로 인해서 수소 결합의 중요성이 감소했다는 결론을 내렸다.

• Bulletin of the Korean Chemical Society
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• 제24권12호
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• pp.1742-1750
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• 2003

In order to characterize the hydrophobic parameters of N-acetyl amino acid amides in 1-octanol/water, a theoretical calculation was carried out using a solvation free energy density model. The hydrophobicity parameters of the molecules are obtained with the consideration of the solvation free energy over the solvent volume surrounding the solute, using a grid model. Our method can account for the solvent accessible surface area of the molecules according to conformational variations. Through a comparison of the hydrophobicity of our calculation and that of other experimental/theoretical works, the solvation free energy density model is proven to be a useful tool for the evaluation of the hydrophobicity of amino acids and peptides. In order to evaluate the solvation free energy density model as a method of calculating the activity of drugs using the hydrophobicity of its building blocks, the contracture of Bradykinin potentiating pentapeptide was also predicted from the hydrophobicity of each residue. The solvation free energy density model can be used to employ descriptors for the prediction of peptide activities in drug discovery, as well as to calculate the hydrophobicity of amino acids.

• Bulletin of the Korean Chemical Society
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• 제26권2호
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• pp.238-240
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• 2005

The enthalpies of transfer, ${\Delta}H_t{\Theta}$, of NaI from water to aqueous methanol, ethanol and isopropanol, iPrOH, systems are reported. These data have been analysed in terms of the new solvation theory. These data are considered in terms of the new developed solvation theory including variable ($\alpha$n + $\beta$N), the net effect of the solute on the solvent-solvent bonding, is positive if there is a net breaking or weakening of solvent-solvent bonds. The solvation parameters recovered from the analyses indicate that the net affect of NaI on solvent structure is a breaking of solvent-solvent bonds and that NaI is preferentially solvated by water in all aqueous alcohol systems considered. ($\alpha$n + $\beta$N) values increase with increasing in the size of the alcohol alkyl residue from methanol to iPrOH.

• 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.

• BMB Reports
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• 제36권3호
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• pp.243-250
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• 2003

In this paper we investigate (using AM1 semi-empirical as well as HF methods at the STO-3G, 3-21G, 6-31G, 6-$31G^*$ and 6-31+$G^{**}$ level) the conformations, geometrical parameters, Mulliken charges, and solvation effects of the triphosphate form of AZT (AZTTP), as well as the thymidine nucleotide (dTTP) structure. Our calculated geometrical parameters and Mulliken charges, with and without solvation effects, are correlated with recent experimental results.

• Bulletin of the Korean Chemical Society
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• 제31권12호
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• pp.3785-3787
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• 2010

• 한국수소및신에너지학회논문집
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• 제24권2호
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• pp.172-178
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• 2013

This study examined the electrochemical deposition and dissolution of lithium on nickel electrodes in 1 mol $dm^{-3}$ (M) $LiPF_6$ dissolved in propylene carbonate (PC) containing different 1,2-dimethoxyethane (DME) concentrations as a co-solvent. The DME concentration was found to have a significant effect on the reactions occurring at the electrode. The poor cycleability of the electrodes in the pure PC solution was improved considerably by adding small amounts of DME. This results suggested that the dendritic lithium growth could be suppressed by using co-solvents. After hundredth cycling in the 1 M $LiPF_6$/PC:DME (67:33) solution, almost no dead lithium has been found from the disassembled cell, resulting from suppression of dendritic lithium growth. Scanning electron microscopy revealed that dendritic lithium formation was greatly affected by the ratio of DME. Raman spectroscopy results suggested that the structure of solvated lithium ions is a crucial important factor in suppressing dendritic lithium formation.

• 한국생물공학회:학술대회논문집
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• 한국생물공학회 2001년도 추계학술발표대회
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• pp.886-889
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• 2001

C-terminus specific immobilization often results in a increased structural stability resistant to various denaturation factors. In order to elucidate the immobilization effect on the c-terminus in molecular level, we made over 200 protein data set from Protein Data Bank(PDB), analyzed c-terminus structure of each protein, and investigated the structural relationship with the stabilizing factors such as hydrogen bond, ion pairs, cation pi, disulfide bond, solvation free energy, surface area, flexibility and so on.

• EDISON SW 활용 경진대회 논문집
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• 제3회(2014년)
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• pp.237-249
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• 2014

Deposition of amyloid-${\beta}$ ($A{\beta}$) proteins is the conventional pathological hallmark of Alzheimer's disease (AD). The $A{\beta}$ protein formed from the amyloid precursor protein is predominated by the 40 residue protein ($A{\beta}40$) and by the 42 residue protein ($A{\beta}42$). While $A{\beta}40$ and $A{\beta}42$ differ in only two amino acid residues at the C-terminal end, $A{\beta}42$ is much more prone to aggregate and exhibits more neurotoxicity than $A{\beta}40$. Here, we investigate the molecular origin of the difference in the aggregation propensity of these two proteins by performing fully atomistic, explicit-water molecular dynamics simulations. Then, it is followed by the solvation thermodynamic analysis based on the integral-equation theory of liquids. We find that $A{\beta}42$ displays higher tendency to adopt ${\beta}$-sheet conformations than $A{\beta}40$, which would consequently facilitate the conversion to the ${\beta}$-sheet rich fibril structure. Furthermore, the solvation thermodynamic analysis on the simulated protein conformations indicates that $A{\beta}42$ is more hydrophobic than $A{\beta}40$, implying that the surrounding water imparts a larger thermodynamic driving force for the self-assembly of $A{\beta}42$. Taken together, our results provide structural and thermodynamic grounds on why $A{\beta}42$ is more aggregation-prone than $A{\beta}40$ in aqueous environments.