• YAKHAK HOEJI
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• v.26 no.2
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• pp.85-90
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• 1982

The binding of the 1-anilinonaphthalene-8-sulfonate(ANS) to bovine serum albumin was studied by fluorescence spectroscopy. The effect of pH, ionic strength, and protein concentration on the binding of ANS to protein were compared. The binding between ANS and protein was dependent on pH and ionic strength. It seems that both hydrophobic binding and some electrostatic forces are involved in the binding of ANS to protein. The binding constants for ANS increased with increasing protein concentration. This suggests the possibility of a sharing of one ANS molecule by more than one protein molecule at relatively high protein concentration.

• Bulletin of the Korean Chemical Society
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• v.11 no.2
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• pp.144-149
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• 1990

Conformational free energy calculations using an empirical potential function (ECEPP/2) and the hydration shell model were carried out on the sulfonylurea herbicides of bensulfuron methyl (Londax) and metsulfuron methyl (Ally). The conformational energy was minimized from starting conformations which included possible combinations of torsion angles in the molecule. The conformational entropy of each conformation was computed using a harmonic approximation. To understand the hydration effect on the conformation of the molecule in aqueous solution, the hydration free energy of each group was calculated and compared each other. It was found that the low-free-energy conformations of two molecules in aqueous solution prefer the overall folded structure, in which an interaction between the carbonyl group of ester in aryl ring and the first amido group of urea bridge plays an important role. From the analysis of total free energy, the hydration and conformational entropy are known to be essential in stabilizing low-free-energy conformations of Londax, whereas the conformational energy is proved to be a major contribution to the total free energy of low-free-energy conformations of Ally.

• YAKHAK HOEJI
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• v.50 no.4
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• pp.263-267
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• 2006

CD1d is an unique antigen presenting molecule which provides antigenic repertoires to NKT cells. To examine molecules required for CD1d antigen presentation, we determined an interaction between CD1d and several endoplasmic reticulum (ER) resident molecular chaperones by co-immunoprecipitation. Results indicated that calnexin and calreticulin seem to be bound to mouse CD1d, but TAP and tapasin do not bind. Further, we screened an yeat two hybrid system to identify proteins that help mouse CD1d transportation in the cytosol. We found that two proteins, heat shock protein a sub-unit $(Hsp90{\alpha})$ and protein kinase C and casein kinase substrate in neurons 3 (PACSIN-3), interact with CD1d. Future study will be focus on the role of these molecules during the CD1d antigen presentation.

• BMB Reports
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• v.47 no.8
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• pp.424-432
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• 2014

The defining feature of Parkinson's disease is a progressive and selective demise of dopaminergic neurons. A recent report on Parkinson's disease animal model demonstrates that poly (ADP-ribose) (PAR) dependent cell death, also named parthanatos, is accountable for selective dopaminergic neuronal loss. Parthanatos is a programmed necrotic cell death, characterized by PARP1 activation, apoptosis inducing factor (AIF) nuclear translocation, and large scale DNA fragmentation. Besides cell death regulation via interaction with AIF, PAR molecule mediates diverse cellular processes including genomic stability, cell division, transcription, epigenetic regulation, and stress granule formation. In this review, we will discuss the roles of PARP1 activation and PAR molecules in the pathological processes of Parkinson's disease. Potential interaction between PAR molecule and Parkinson's disease protein interactome are briefly introduced. Finally, we suggest promising points of therapeutic intervention in the pathological PAR signaling cascade to halt progression in Parkinson's disease.

• Journal of the Korean Magnetics Society
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• v.26 no.4
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• pp.119-123
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• 2016

We have studied electronic and magnetic structure of cubane-type Cu magnetic molecule using density functional method. The calculated density of states show that Cu has 3d $x^2-y^2$ hole orbital because of short distances between Cu atom and in-plane 4 ligand atoms. The calculated total energy with in-plane antiferromagnetic spin configuration is lower than those of ferromagnetic configurations. The calculated exchange interaction J between in-plane Cu atoms is much larger than those between out-plane Cu atoms, since the $x^2-y^2$ hole orbital ordering of Cu 3d orbitals induces strong super-exchange interaction between in-plane Cu atoms.

• Journal of the Korean Magnetics Society
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• v.27 no.4
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• pp.140-144
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• 2017

We have studied electronic and magnetic structure of cubane-type Co magnetic molecule using density functional method. The calculated density of states show $Co^{+2}$ ionic state and high-spin state because of large exchange interaction between inside Co 3d electrons. The exchange interaction J between Co atoms depends Co-O-Co angle. The calculated J is ferromagnetic with right angles. On the other hand J is antiferromagnetic with large angles since super-exchange interactions between $Co^{+2}$ atoms. It induces that Co cubane has a antiferromagnetic spin structure of AFM1 = [${\uparrow}{\uparrow}{\downarrow}{\downarrow}$]

• Bulletin of the Korean Chemical Society
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• v.14 no.2
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• pp.244-250
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• 1993

The interaction of 1,3,5-trithian molecule with Ag(111) surface is studied employing Extended Huckel method. The Ag(111) surface is modeled by the three layer metal clusters composed of 43 Ag atoms. We assume that the 1,3,5-trithian is lying flat on Ag(111) surface in the chair conformation. The geometry of 1,3,5-trithian itself is assumed to be the same as in the gas phase, which is obtained through the AM1 SCF-MO calculation with full geometry optimization. The calculation for 3-fold site adsorption leads to the weakening of C-S bond, which is compatible with the observed 5 cm$^{-1}$ decrease of the C-S stretching frequency upon surface adsorption, while the on-top site adsorption leads to strengthening of C-S bond. The major component of the C-S bond of trithian is S $3p_{pi}\;(S\;3p_x+S\;3p_y)$ and therefore only the 3-fold site adsorption causes the weakening of this bond. In addition, it is found that the trithian molecule binds to the 3-fold site more strongly.

• Genomics & Informatics
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• v.1 no.1
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• pp.1-6
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• 2003

In conclusion, the seemingly fuzzy and disorganized data of biology with thousands of different layers ranging from molecule to the Internet have refused so far to be mapped precisely and predicted successfully by mathematicians, physicists or computer scientists. Genomics and bioinformatics are the fields that process such complex data. The insights on the nature of biological entities as complex interaction networks are opening a door toward a generalization of the representation of biological entities. The main challenge of genomics and bioinformatics now lies in 1) how to data mine the networks of the domains of bioinformatics, namely, the literature, metabolic pathways, and proteome and structures, in terms of interaction; and 2) how to generalize the networks in order to integrate the information into computable genomic data for computers regardless of the levels of layer. Once bioinformatists succeed to find a general principle on the way components interact each other to form any organic interaction network at genomic scale, true simulation and prediction of life in silico will be possible.

• Bulletin of the Korean Chemical Society
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• v.26 no.9
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• pp.1369-1380
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• 2005

The reaction of methyl radical with iodine molecule on an attractive potential energy surface is studied by classical trajectory procedures. The reaction occurs over a wide range of impact parameters with the majority of reactive events occurring in the backward rebound region on a subpicosecond scale. A small fraction of reactive events take place in the forward hemisphere on a longer time scale. The ensemble average of reaction times is 0.36 ps. The occurrence of reactive events is strongly favored when the incident radical and the target molecule align in the neighborhood of collinear geometry. Since the rotational velocity of I2 is slow, the preferential occurrence of reactive events at the collinear configuration of $CH_3{\ldots}I{\ldots}$I leads to the reaction exhibiting an anisotropic dependence on the orientation of $I_2$. During the collision, there is a rapid flow of energy from the $H_3C{\ldots}$I interaction to the I-I bond. The $CH_3I$ translation and $H_3C$-I vibration share nearly all the energy released in the reaction, and the distribution of the vibrational energy is statistical. The reaction probability is $\cong$0.4 at the $CH_3$ and I2 temperatures maintained at 1000 K and 300 K, respectively. The probability is weakly dependent on the $CH_3\;and\;I_2$ temperatures between 300 K and 1500 K.

• Bulletin of the Korean Chemical Society
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• v.35 no.3
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• pp.875-880
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• 2014

Adsorption of 4,4'-bis(mercaptomethyl)biphenyl (44BMBP) on silver nanoparticles has been investigated by surface-enhanced Raman scattering (SERS) spectroscopy. In addition, the Raman spectra of 44BMBP in solid state and in basic condition have been obtained for comparative study to elicit the characteristics of adsorption. The observed Raman and SERS spectra were analyzed comparing with the normal modes and vibrational frequencies from density functional theory (DFT) calculations performed for the feasible structures of 44BMBP molecule. On the basis of excellent agreement between the calculated and the experimental results, the molecule is found to have both the cis- and trans-forms for the mercaptomethyl groups in the solid state as well as in the basic condition. In contrast, the molecule is found to be chemisorbed on the silver surface by forming two Ag-S linkages only in the cis-form but not in the trans-form due to the steric interruption, which indicates the parallel orientation of molecules on the surface. Particularly, the spectral features in the SERS spectra such as the absence of the C-H stretching band and enhancement for the out-of-plane skeletal modes are confirmatory for the parallel geometry through ${\pi}$ interaction between the phenyl rings and the metal surface, based on the electromagnetic surface selection rule.