• Bulletin of the Korean Chemical Society
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• v.24 no.3
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• pp.377-383
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• 2003

Physicochemical properties of a series of PC monolayers with different alkyl chains (C24, C20, C16, and C8), at the air/water interface were investigated. The surface pressure is influenced mainly by the hydrophobicity of the PCs, which is confirmed by the curve shape and the on-set value of π-A isotherms at the air/water interface by increasing the number of alkyl chain. The on-set values of surface pressure were 125 Ų/molecule for DOPC(C8), 87 Ų/molecule for DPPC(C16), 75 Ų/molecule for DAPC(C20), and 55 Ų/molecule for DLPC(C24), respectively. The orientations of alkyl chains at the air/water interface are closely connected with the rigidity of the monolayers, and it was confirmed by the tendency of monolayer thickness in ellipsometry data. The temperature dependence of a series of PCs shows that the surface pressure decreases by increasing temperature, because the longer the alkyl chain length, the larger the hydrophobic interaction in surface pressure. The temperature effects and the conformational changes of unsaturated and saturated PCs were confirmed by the computer simulation study of the cis-trans transition with POPC and DPPC(C16). The cistrans conformational energy difference of POPC is 62.06 kcal/mol and that of DPPC(C16) is 6.75 kcal/mol. Due to the high conformational energy barrier of POPC, phase transition of POPC is limited in comparison with DPPC(C16).

• Bulletin of the Korean Chemical Society
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• v.32 no.3
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• pp.988-992
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• 2011

$CO_2$ adsorption on mineral sorbents has a potential to sequester $CO_2$. This study used a density functional theory (DFT) study of $CO_2$ adsorption on barium oxide (BaO) in the presence of $H_2O$ to determine the role of $H_2O$ on the $CO_2$ adsorption properties on the ($2{\times}2$; $11.05\;{\AA}{\times}11.05\;{\AA}$) BaO (100) surface because BaO shows a high reactivity for $CO_2$ adsorption and the gas mixture of power plants generally contains $CO_2$ and $H_2O$. We investigated the adsorption properties (e.g., adsorption energies and geometries) of a single $CO_2$ molecule, a single $H_2O$ molecule on the surface to achieve molecular structures and molecular reaction mechanisms. In order to evaluate the coordinative effect of $H_2O$ molecules, this study also carried out the adsorption of a pair of $H_2O$ molecules, which was strongly bounded to neighboring (-1.91 eV) oxygen sites and distant sites (-1.86 eV), and two molecules ($CO_2$ and $H_2O$), which were also firmly bounded to neighboring sites (-2.32 eV) and distant sites (-2.23 eV). The quantum mechanical calculations show that $H_2O$ molecule does not influence on the chemisorption of $CO_2$ on the BaO surface, producing a stable carbonate due to the strong interaction between the $CO_2$ molecule and the BaO surface, resulting from the high charge transfer (-0.76 e).

• Molecules and Cells
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• v.44 no.2
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• pp.79-87
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• 2021

Chromatin dynamics is essential for maintaining genomic integrity and regulating gene expression. Conserved bromodomain-containing AAA+ ATPases play important roles in nucleosome organization as histone chaperones. Recently, the high-resolution cryo-electron microscopy structures of Schizosaccharomyces pombe Abo1 revealed that it forms a hexameric ring and undergoes a conformational change upon ATP hydrolysis. In addition, single-molecule imaging demonstrated that Abo1 loads H3-H4 histones onto DNA in an ATP hydrolysis-dependent manner. However, the molecular mechanism by which Abo1 loads histones remains unknown. Here, we investigated the details concerning Abo1-mediated histone loading onto DNA and the Abo1-DNA interaction using single-molecule imaging techniques and biochemical assays. We show that Abo1 does not load H2A-H2B histones. Interestingly, Abo1 deposits multiple copies of H3-H4 histones as the DNA length increases and requires at least 80 bp DNA. Unexpectedly, Abo1 weakly binds DNA regardless of ATP, and neither histone nor DNA stimulates the ATP hydrolysis activity of Abo1. Based on our results, we propose an allosteric communication model in which the ATP hydrolysis of Abo1 changes the configuration of histones to facilitate their deposition onto DNA.

• Journal of Microbiology and Biotechnology
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• v.17 no.11
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• pp.1789-1796
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• 2007

A ${\beta}$-glucosidase with the molecular mass of 160,000 Da was purified to homogeneity from cell extract of a cellulolytic bacterium, Cellulomonas uda CS1-1. The kinetic parameters ($K_m$ and $V_{max}$) of the enzyme were determined with pNP-cellooligosccharides (DP 1-5) and cellobiose. The molecular orbital theoretical studies on the cellulolytic reactivity between the pNP-cellooligosaccharides as substrate (S) molecules and the purified ${\beta}$-glucosidase (E) were conducted by applying the frontier molecular orbital (FMO) interaction theory. The results of the FMO interaction between E and S molecules verified that the first stage of the reaction was induced by exocyclic cleavage, which occurred in an electrophilic reaction based on a strong charge-controlled reaction between the highest occupied molecular orbital (HOMO) energy of the S molecule and the lowest occupied molecular orbital (LUMO) energy of the hydronium ion ($H_3O^+$), more than endocyclic cleavage, whereas a nucleophilic substitution reaction was induced by an orbital-controlled reaction between the LUMO energy of the oxonium ion ($SH^+$) protonated to the S molecule and the HOMO energy of the $H_2O_2$ molecule. A hypothetic reaction route was proposed with the experimental results in which the enzymatic acid-catalyst hydrolysis reaction of E and S molecules would be progressed via $SN_1$ and $SN_2$ reactions. In addition, the quantitative structure-activity relationships (QSARs) between these kinetic parameters showed that $K_m$ has a significant correlation with hydrophobicity (logP), and specific activity has with dipole moment, respectively.

• Analytical Science and Technology
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• v.20 no.4
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• pp.339-346
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• 2007

To search the ninhydrin derivatives that have high chromogenic and fluorogenic properties, molecular holographic quantitative structure property relationship (HQSPR) models on the reactivity between glycine and ninhydrin analogues as latent fingerprint detector were derived and investigated quantitatively. The ${\varepsilon}LUMO$ (e.v.) energy of ninhydrin molecule was an important factor to reactivity of ninhydrin. And, it is suggested that the nucleophilic reaction by orbital-controlled reaction from the frontier molecular orbital (FMO) interaction between glycine and ninhydrin derivatives was more superior than that of electrophilic reaction by charged controlled reaction. The analytical results in atomic contribution maps also shows that the reactivity of ninhydrin was increased by meta-substituents as strong electron withdrawing groups on the benzo ring. Therefore, it is sugested by HQSPR and QSPR model that the 5,6-dinitroninhydrin molecule would increase the reactivity as much as three times as compared to none substituted ninhydrin molecule.

• Journal of the Korean Chemical Society
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• v.8 no.2
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• pp.43-46
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• 1964

Quenching constants, q, determined for N,N-dimethylanilines by liquid scintillation counting indicate that the quenching involves an energy transfer process to these compounds causing strong n-${\pi}$ interaction within the quencher molecule, which is then followed by an non-radiative degradation of the excitation energy to ground state.

• Journal of Neurogastroenterology and Motility
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• v.24 no.4
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• pp.678-680
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• 2018

• International Journal of Oral Biology
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• v.37 no.3
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• pp.130-136
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• 2012

The GroEL heat-shock protein from Fusobacterium nucleatum, a periodontopathogen, activates risk factors for atherosclerosis in human microvascular endothelial cells (HMEC-1) and ApoE-/- mice. In this study, we analyzed the signaling pathways by which F. nucleatum GroEL induces the proinflammatory factors in HMEC-1 cells known to be risk factors associated with the development of atherosclerosis and identified the cellular receptor used by GroEL. The MAPK and NF-${\kappa}B$ signaling pathways were found to be activated by GroEL to induce the expression of interleukin-8 (IL-8), monocyte chemoattractant protein 1 (MCP-1), intercellular adhesion molecule 1 (ICAM-1), vascular cell adhesion molecule 1 (VCAM-1), E-selectin, and tissue factor (TF). These effects were inhibited by a TLR4 knockdown. Our results thus indicate that TLR4 is a key receptor that mediates the interaction of F. nucleatum GroEL with HMEC-1 cells and subsequently induces an inflammatory response via the MAPK and NF-${\kappa}B$ pathways.

• Journal of the Korean Magnetic Resonance Society
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• v.16 no.1
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• pp.67-77
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• 2012

The small molecule binding to the c-Jun N-terminal kinase 3 (JNK3) was examined by the measurements of saturation transfer difference (STD) NMR experiments. The STD NMR experiment of ATP added to JNK3 clearly showed the binding of the nucleotide to the kinase. The STD NMR spectrum of dNTPs added to JNK3 discriminated the kinase-bound nucleotide from the unbound ones. After the five-fold addition of ATP to the dNTPs and JNK3 mixture, only signals of the cognate substrate of JNK3, ATP, were observed from the STD NMR experiment. These results signify that by the STD NMR the small molecules bound to JNK3 can be discriminated from the pool of the unbound molecules. Furthermore the binding mode of the small molecule to JNK3 can be determined by the competition experiments with ATP.

• Proceedings of the Optical Society of Korea Conference
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• 2001.02a
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• pp.272-273
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• 2001

We demonstrate the first separation of neutral molecules using optical forces. Unlike laser atomic cooling or optical tweezers, optical separation technique requires the manipulation of only one component of the molecular motion. Thus the mixtures can be separated, in principle, with less complex schemes. When an Intense nonresonant laser beam is focused onto a beam of molecules, the interaction between the laser electric field and the induced dipole moment of a molecule invokes a mechanical force on the molecule proportional to the field gradient and the molecular polarizability ($\alpha$) to mass (m) ratio $\alpha$/m. (omitted)