• Molecules and Cells
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• v.45 no.1
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• pp.33-40
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• 2022

The various DNA-protein interactions associated with the expression of genetic information involve double-stranded DNA (dsDNA) bending. Due to the importance of the formation of the dsDNA bending structure, dsDNA bending properties have long been investigated in the biophysics field. Conventionally, DNA bendability is characterized by innate averaging data from bulk experiments. The advent of single-molecule methods, such as atomic force microscopy, optical and magnetic tweezers, tethered particle motion, and single-molecule fluorescence resonance energy transfer measurement, has provided valuable tools to investigate not only the static structures but also the dynamic properties of bent dsDNA. Here, we reviewed the single-molecule methods that have been used for investigating dsDNA bendability and new findings related to dsDNA bending. Single-molecule approaches are promising tools for revealing the unknown properties of dsDNA related to its bending, particularly in cells.

• Tunnel and Underground Space
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• v.10 no.1
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• pp.70-79
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• 2000

We carried out NPT-ensemble (constant-number of particles, pressure, and temperature) Molecular Dynamics (MD) simulations for measuring strength anisotropy under uniaxial compressive stress rotated to the crystallographic axes in $\alpha$-quartz. Uniaxial compressive strengths of a single quartz crystal were measured in directions of the a- and c-axis. Measured uniaxial strength of a single quartz crystal was higher in the direction parallel to the c-axis than that measured in the direction normal to the c-axis. However the reverse was found in calculated uniaxial strengths by MD simulation. The contradictive result of strengths was observed in both cases but was found to be different in origin. Strength anisotropy of defectless $\alpha$-quartz crystal in MD simulation is basically caused by structural difference of quartz. By contrast, anisotropy of measured strength in the uniaxial compression test is related to oriented micro-defects developed during crystal growth.

• Bulletin of the Korean Chemical Society
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• v.32 no.8
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• pp.2537-2543
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• 2011

A self-assembled Al-bridged diiminopyridine-based ligand (3) was synthesized and characterized by FT-IR, ESI-MS and NMR spectroscopy. Electron spectral titrations were performed to confirm the formation of a novel trinuclear bis(imino)pyridyl iron(II) complex (4) upon addition of $FeCl_2$ into Al-bridged ligand 3 in methanol solution. Simultaneously, a typical bis(imino)pyridine-iron(II) complex (2) was synthesized and fully characterized. The X-ray crystal study of the iron(II) complex 2 disclosed a five-coordinate, distorted square-pyramidal structure with the tridentate N^N^N ligand and chlorides. The optimal molecular structure of 4 was obtained by means of molecular mechanics, which showed that each iron atom in the complex 4 is surrounded by two chlorides, a tridentate N^N^N ligand and one oxygen atom, supporting considerations about the possibility of six-coordinate geometry from MMAO or the ethylene access. A comparison of 4 with the reference 2 revealed a remarkable decrease of the catalytic activity and MMAO consumption (activity up to $0.41{\times}10^3\;kg\;{mol_{Fe}}^{-1}h^{-1}bar^{-1}$, Al/Fe = 650 for 4 and $7.02{\times}10^3\;kg\;{mol_{Fe}}^{-1}h^{-1}bar^{-1}$, Al/Fe = 1600 for 2).

• BMB Reports
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• v.31 no.5
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• pp.459-467
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• 1998

A new set of functional group interaction energy descriptors relevant to the ACE (Angiotensin-Converting Enzyme) inhibitory peptide, QSAR (Quantitative Structure Activity Relationships), is presented. The functional group interaction energies approximate the charged interactions and distances between functional groups in molecules. The effective energies of the computationally derived geometries are useful parameters for deriving 3D-QSAR models, especially in the absence of experimentally known active site conformation. ACE is a regulatory zinc protease in the renin-angiotensin system. Therapeutic inhibition of this enzyme has proven to be a very effective treatment for the management of hypertension. The non bond interaction energy values among functional groups of six-feature of ACE inhibitory peptides were used as descriptor terms and analyzed for multivariate correlation with ACE inhibition activity. The functional group interaction energy descriptors used in the regression analysis were obtained by a series of inhibitor structures derived from molecular mechanics and semi-empirical calculations. The descriptors calculated using electrostatic and steric fields from the precisely defined functional group were sufficient to explain the biological activity of inhibitor. Application of the descriptors to the inhibition of ACE indicates that the derived QSAR has good predicting ability and provides insight into the mechanism of enzyme inhibition. The method, functional group interaction energy analysis, is expected to be applicable to predict enzyme inhibitory activity of the rationally designed inhibitors.

• Bulletin of the Korean Chemical Society
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• v.35 no.8
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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 for History of Mathematics
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• v.21 no.3
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• pp.1-30
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• 2008

The success of Newton's Gravitational Theory has influenced the theory of capillarity, beginning in the early nineteenth century, by providing a major model of molecular attraction. He used the equation of the attraction of spheroids, which is expressed by second order partial differential equations, to utilize this analogy as the same kind of a particle's force, between gravitational, refractive force of light, and capillarity. The solution of the differential equation corresponds to the geometrical figure of the vessel and the contact angle which is made by the fluid. Unknown abstract functions $\varphi(f)$ represent interaction forces between molecules, giving their potential functions. By conducting several kinds of experimental conditions, it was found that the height of the ascending fluid in the tube is inversely proportional to the rayon of the tube or the distance of the plate. This model is an essential element in the theory of capillarity. Laplace has brought Newtonian mechanics to completion, which relates to the standard model of gravitational theory. Laplace-Young's equation of capillarity is applicable to minimal surfaces in mathematics, to surface tensional phenomena in physics, and to soap bubble experiments.

• Journal of the Korean Chemical Society
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• v.37 no.10
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• pp.903-909
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• 1993

Reaction mechanism of palladium(0, II)-phosphines complexes catalyzed cyclocarbonylation for unsaturated carboxylic acid such as crotonic acid, methacrylic acid and 3-butenoic acid has been investigated by product analysis, molecular mechanics and extended Huckel molecular orbital method. Reaction of 3-butenoic acid with palladium(0, II)-phosphines catalyst gives palladium containing cycloester through intermediate palladium-olefin ${\pi}$ -complex in the catalytic carbonylation. Palladium(0, II)-phosphines complexes catalyze the cyclocarbonylation of 3-butenoic acid to give 3-methylsuccinic anhydride and glutaric anhydride. But ${\pi}$ -complexes with palladium(0, II)-phosphines and unsaturated carboxylic acids such as crotonic acid and methacrylic acid are not effective the catalytic cyclocarbonylation.

• Journal of the Korean Chemical Society
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• v.37 no.4
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• pp.431-441
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• 1993

The structure and reactivity of ${\pi}$-and metallacycle form in the bis(trimethylphosphine) palladium(0) complexes with acrylic acid, methacrylic acid, crotonic acid(A group) and 3-butenoic acid, 4-pentenoic acid(B group) have been investigated by Molecular Mechanics and Extended Huckel Molecular Orbital method. The calculation shows that A groups with large value of frontier electron density of HOMO and LUMO produce $\pi-complexes$ instead of metallacycle. But B groups with small value of frontier electron density of LUMO, especially 3-butenoic acid, form stable metallacycle. Moreover the methyl-substituted five-membered compared with the six-membered metallacycle is energetically stable conformation.

• Bulletin of the Korean Chemical Society
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• v.27 no.1
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• pp.77-81
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• 2006

The commercially available Amberlite XAD-2 and XAD-4 resins were modified with macrocyclic protoporphyrin IX (PPIX) or tetrakis(p-carboxyphenyl) porphyrin (TCPP) to enhance the adsorption capacity for phenol and chlorophenols. The chemically modified polymeric adsorbents (XAD-2+PPIX, XAD-2+TCPP, XAD-4+PPIX, and XAD-4+TCPP) were applied to the solid phase extraction as an adsorbent material for the preconcentration of phenol and chlorophenols in environmental waters. Generally, the synthesized adsorbents showed higher recoveries than underivatized adsorbents, XAD-2 and XAD-4, without matrix interferences. Especially, XAD-4+PPIX showed more than 90% recoveries for all compounds used in this study including hydrophilic phenol. The major factor for the increase of the adsorption capacity was the increase of $\pi$-$\pi$ interaction between adsorbents and samples due to the introduction of the porphyrin molecule. However, the breakthrough volumes and recovery values of the XADs+TCPP columns were slightly decreased for the bulky chlorophenols such as TCP and PCP. Using molecular mechanics methods, the structures of TCPP and PPIX were compared with that of porphine, the parent molecule of porphyrin. Four bulky p-carboxyphenyl groups of TCPP were torsional each other, thus the molecular plane of TCPP were not on the same level. In conclusion, the decrease of breakthrough volumes and recovery values of XADs+TCPP columns for bulky phenols can be explained by the steric hindrance of the $\pi$-$\pi$ interaction between porphyrin plane and the phenols.

• Molecules and Cells
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• v.40 no.2
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• pp.117-122
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• 2017

Despite the fact that porcine embryonic stem cells (ESCs) are a practical study tool, in vitro long-term maintenance of these cells is difficult in a two-dimensional (2D) microenvironment using cellular niche or extracellular matrix proteins. However, a three-dimensional (3D) microenvironment, similar to that enclosing the inner cell mass of the blastocyst, may improve in vitro maintenance of self-renewal. Accordingly, as a first step toward constructing a 3D microenvironment optimized to maintain porcine ESC self-renewal, we investigated different culture dimensions for porcine ICM-derived cells to enhance the maintenance of self-renewal. Porcine ICM-derived cells were cultured in agarose-based 3D hydrogel with self-renewal-friendly mechanics and in 2D culture plates with or without feeder cells. Subsequently, the effects of the 3D microenvironment on maintenance of self-renewal were identified by analyzing colony formation and morphology, alkaline phosphatase (AP) activity, and transcriptional and translational regulation of self-renewal-related genes. The 3D microenvironment using a 1.5% (w/v) agarose-based 3D hydrogel resulted in significantly more colonies with stereoscopic morphology, significantly improved AP activity, and increased protein expression of self-renewal-related genes compared to those in the 2D microenvironment. These results demonstrate that self-renewal of porcine ICM-derived cells can be maintained more effectively in a 3D microenvironment than in a 2D microenvironment. These results will help develop novel culture systems for ICM-derived cells derived from diverse species, which will contribute to stimulating basic and applicable studies related to ESCs.