• 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.

• Bulletin of the Korean Chemical Society
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• v.35 no.8
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• pp.2299-2303
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• 2014

Two diastereoisomers of cyclo(Pro-Tyr) have been synthesized simultaneously. The crystal structures and conformations of both cyclo($\small{L}$-Pro-$\small{L}$-Tyr) and a racemic mixture of cyclo($\small{D}$-Pro-$\small{L}$-Tyr) and cyclo($\small{L}$-Pro-$\small{D}$-Tyr), abbreviated as rac-cyclo($\small{D}$-Pro-$\small{L}$-Tyr/$\small{L}$-Pro-$\small{D}$-Tyr), have been determined by a single-crystal X-ray diffraction study at low temperature. The crystals of rac-cyclo($\small{D}$-Pro-$\small{L}$-Tyr/$\small{L}$-Pro-$\small{D}$-Tyr) belong to orthorhombic space group $Pna2_1$ with a = 10.755 (1), b = 12.699 (1), c = 9.600 (1) ${\AA}$ and Z = 4. The tyrosine side chain is folded towards the diketopiperazine (DKP) ring. The DKP ring adopts a twist boat conformation with pseudo symmetry $C_{2v}$. The pyrrolidine ring has an envelope conformation with the N5, C4, C7 and C8 atoms in a plane. The crystal of rac-cyclo($\small{D}$-Pro-$\small{L}$-Tyr/$\small{L}$-Pro-$\small{D}$-Tyr) is stabilized by hydrogen bonds between amide N2-H2 and carbonyl oxygen O2 in the neighbor. The hydroxyl group of tyrosine residue is also hydrogen bonded to the oxygen of the carbonyl group of the DKP ring in the next molecule. The spectroscopic properties of both isomers are also described.

• Journal of the Korean Chemical Society
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• v.43 no.5
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• pp.540-546
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• 1999

Solution conformation of cyclo-($Gln^1-Trp^2-Phe^3-{\beta}Ala^4-Leu^5-Met^6$), new NK-2 antagonist in dimethyl sulfoxide solution, has been determined by the use of two-dimensional nuclear magnetic resonance spectroscopy combined with simulated annealing calculations. The peptide exhibited converged structures with the atomic root-mean-square difference for the backbone atoms ($N,\;C^{\alpha},\;C'$) of all residues being 0.02${\AA}$ in the 25 annealed structures. The analysis of the structures indicated that the cyclic peptide has three intramolecular hydrogen bonds between $Met^6NH$ and ${\beta}Ala^4CO$, ${\beta}Ala^4NH$ and $Met^6CO$, $Phe^3NH$ and $Met^6CO$, and contain a type-I ${\beta}$-turn with Gln and Trp and ${\gamma}$-turn with Leu. The addition of an extra methylene group to Gly, i.e. P-Ala residue, may relax some unfavorable restraints in the cyclic backbone structure, hence enabling an additional hydrogen bond, which results in stabilizing one conformation.

• Korean Journal of Community Nutrition
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• v.16 no.3
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• pp.307-314
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• 2011

The purpose of this study is finding the easy way of 4 categories activity level confirmation for estimated energy requirement calculation. Total of 386, 5th and 6th grade primary school students participated. The time spent on 7 kinds of activity were collected for 1 day by the internet program developed. Judged by the activity coefficient, sedentary were 6.7% and 5.1%, low active 33.2% and 40.4%, active 43.8%, and45.5%, and very active 16.3% and 9.0% for boy and girl, respectively. The highest and significant correlation coefficient between activity coefficient and time spent on activities shown were 0.339 in commute activity for boys, and 0.466 in leisure for girls. The sensitivity of the sedentary conformation by commute hour for boys was 0.79, and that of very active was 0.56. The sensitivity of the sedentary conformation by leisure hour for girls was 0.67, and that of very active was 0.63. The sensitivity of low active and active by 7 different types of activity was quite low, 0.04~0.37. The exact agreement of activity level conformed by easy way developed was 30.8% and 33.7%, for boys and girls, respectively. More accurate way to identify 4 categories activity level needs to be developed, especially sensitive to conformation of low active and active levels.

• Journal of the Korean Chemical Society
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• v.50 no.4
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• pp.291-297
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• 2006

The equilibrium structures, relative energies and NBO analyses for the possible conformations and transition states which can exist on the internal rotation of CPDFB and CPCFB molecules have been investigated using DFT and ab initio methods with various basis sets. The interaction between bonding orbital ((C1-C3, C2-C3)) and antibonding orbital (n*(B9) and *(B9-Cl11)) was the main characteristic hyperconjugation in both molecules. In addition, the stabilization energy of CPDFB was 6.63kcal/mol and that of CPCFB was 6.97(E-form)/6.79(Z-form) kcal/mol for each conformation. The rotational barriers by internal rotation of BF2- and BFCl- functional groups were evaluated to be 5.3~6.7kcal/mol and 5.7~6.5kcal/mol respectively, which showed good agreement with the experimental values reported by previous dynamic NMR study. Finally, Z-form was more stable than E-form by 0.2 kcal/mol in CPCFB molecule and therefore Z-form was confirmed as global minimum.

• Bulletin of the Korean Chemical Society
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• v.25 no.6
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• pp.838-842
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• 2004

Amyloid peptide (A${\beta}$) is the major component of senile plaques found in the brain of patient of Alzheimer's disease. ${\beta}$-amyloid peptide (25-35) (A${\beta}$25-35) is biologically active fragment of A${\beta}$. The three-dimensional structure of A${\beta}$25-35 in aqueous solution with 50% (vol/vol) TFE determined by NMR spectroscopy previously adopts an ${\alpha}$-helical conformation from $Ala^{30}$ to $Met^{35}$. It has been proposed that A${\beta}$(25-35) exhibits pH- and concentration-dependent ${\alpha}-helix{\leftrightarrow}{\beta}$sheet transition. This conformational transition with concomitant peptide aggregation is a possible mechanism of plaque formation. Here, in order to gain more insight into the mechanism of ${\alpha}$-helix formation of A${\beta}$25-35 peptide by TFE, which particularly stabilizes ${\alpha}$-helical conformation, we studied the secondary-structural elements of A${\beta}$25-35 peptide by molecular dynamics simulations. Secondary structural elements determined from NMR spectroscopy in aqueous TFE solution are preserved during the MD simulation. TFE/water mixed solvent has reduced capacity for forming hydrogen bond to the peptide compared to pure water solvent. TFE allows A${\beta}$25-35 to form bifurcated hydrogen bonds to TFE as well as to residues in peptide itself. MD simulation in this study supports the notion that TFE can act as an ${\alpha}$-helical structure forming solvent.

• Korean Journal of Food Science and Technology
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• v.21 no.5
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• pp.714-720
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• 1989

Effects of acetylation on conformational changes of glycinin was studied using solvent perturbation, second derivative spectroscopy, near uv circular dichroism spectra and viscosity. Glycinin with purity of more than 93% was used for the experiment. Modification was carried out with acetic anhydride and glycinin with lysine residue modification of 0%, 28%, 65%, 85%, and 95% were used for the experiment. The result of solvent perturbation using some selected perturbants, such as glycerol, ethylene glycol, and dimethyl sulfoxide revealed that acetylation has caused increase In solvent accessibility of tyrosine residues from less than 40% in native protein to more than 70% for 95% acetylated glycinin. This was confirmed by second derivative spectroscopy. Near ultraviolet circular dichroism revealed that the spectra of native and acetylated glycinin were almost identical differing only in intensity and no other useful information could be derived from it. However, in the case of 95% acetylated glycinin the influence of tryptophan on the spectrum was more pronounced Specific viscosity of glycinin also increased by modification, the extent of which depended upon the degree of acetylation. These results supported that acetylation had caused globular conformation of glycinin to be expanded and denatured.

• Analytical Science and Technology
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• v.17 no.1
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• pp.53-59
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• 2004

Up to now, methods for the detection of genetic alterations as single strand conformation polymorphism (SSCP) or denaturing gradient gel electrophoresis (DGGE) have been used. It is too labor-intensive and expensive to serve for routine analysis. Moreover, lower in its sensitivity and specificity being also strongly dependent on the experience of the investigater. To improve these problems, we analysed mutation of ${\beta}_2$-adrenergic receptor gene that controls bronchial asthma by denaturing high performance liquid chromatography (DHPLC) according to ion-pair reversed phase chromatography (IP-RPC). We extracted genomic DNA from 80 asthma patients and then amplified DNA using PCR and analysed PCR product by SSCP and DHPLC. As a result, we analysed mutation frequency is 19 (23.75%) on SSCP and 25 (31.25%) on DHPLC in ${\beta}_2$-adrenergic receptor gene. We conclude that DHPLC is a fast and simple screening method rather than SSCP analysis.

• Journal of Life Science
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• v.18 no.4
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• pp.585-589
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• 2008

Chronophin is a phosphatase responsible for the dephosphorylation of cofilin, which regulates the rearrangement of actin cytoskeleton. It is also known as a phosphatase for pyrodoxal 5'-phosphate (PLP), an active form of vitamin $B_6$, and maintains the level of PLP in the cytoplasm. Since this phosphatase belongs to a HAD subfamily containing a cap domain, it is expected to undergo a conformational change for the binding of a substrate. However, the crystal structure of chronophin has a disulfide bridge between the cap and core domains preventing a movement of the cap domain against the core domain. It is possible that the disulfide bond between C91 and C221 was formed by an oxidation during the crystallization. Here, we obtained chronophin crystals under a reduced condition and determined the crystal structure. This reduced chronophin does not contain a disulfide bridge and shows a closed conformation like the oxidized form. It implies that an active chronophin binds its substrate under the closed conformation without the disulfide bond and shows a high substrate specificity in the cell.

• Applied Chemistry for Engineering
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• v.31 no.2
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• pp.187-192
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• 2020

(2S,3R)-3-hydroxyhomoserine lactone (HSL) has been used as a key intermediate for the synthesis of various biologically active compounds. In this study, we demonstrated an efficient synthesis of HSL via anti selective dihydroxylation of a protected vinyl glycine analog with an oxabicyclo[2.2.2]octyl orthoester (OBO) ester group. Because the acyclic conformation of the substrate was efficiently controlled by the bulky OBO ester group, a diastereoselectivity of > 10 : 1 was obtained in the dihydroxylation reaction without the use of a chiral reagent. By using this result, the target compound 1 can be obtained from commercially available N-Cbz-L-serine 2 in seven steps with an overall yeid of 34%. This result could be applied to the stereoselective synthesis of biologically active molecules containing a vicinal amino diol moiety.