• Bulletin of the Korean Chemical Society
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• v.31 no.6
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• pp.1519-1526
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• 2010

The behavior of peptide or protein solutes in saline aqueous solution is a fundamental topic in physical chemistry. Addition of ions can strongly alter the thermodynamic and physical properties of peptide molecules in solution. In order to study the effects of added ionic salts on protein conformation and dynamics, we have used the molecular dynamics (MD) simulations to investigate the behavior of Staphylococcus aureus Hfq protein under two different ionic concentrations: 0.1 M NaCl and 1.0 M NaCl in presence and absence of RNA (a hepta-oligoribonucleotide AU5G). Hfq, a global regulator of gene expression is highly conserved and abundant RNA-binding protein. It is already reported that in vivo the increase of ionic strength results in a drastic reduction of Hfq affinity for $Q{\beta}$ RNA and reduces the tendency of aggregation of Escherichia coli host factor hexamers. Our results revealed the crucial role of 0.1 M NaCl Hfq system on the bases with strong hydrogen bonding interactions and by stabilizing the aromatic stacking of Tyr42 residue of the adjacent subunits/monomers with the adenine and uridine nucleobases. An increase in RNA pore diameter and weakened compactness of the Hfq-RNA complex was clearly observed in 1.0 M NaCl Hfq system with bound RNA. Aggregation of monomers in Hfq and the interaction of Hfq with RNA are greatly affected due to the presence of high ionic strength. Higher the ionic concentration, weaker is the aggregation and interaction. Our results were compatible with the experimental data and this is the first theoretical report for the experimental study done in 1980 by Uhlenbeck group for the present system.

• Journal of the Korean Chemical Society
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• v.38 no.10
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• pp.710-718
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• 1994

We suggest a statistical thermodynamic theory for the conformational transition of a synthetic alanine (Ala), ${\alpha}$-aminoisobutyric acid (Aib) alternative oligopeptide, Buo-(Ala-Aib)$_n$-oMe, where the terminal groups Buo and oMe stand for t-butoxy and methoxy, respectively. Pure Aib homo-oligomers have always been found to adopt $3_{10}$ helical conformations, while polyalanine has always $\alpha$ helical conformation. In an organic solvent (e.g. $CD_3$CN) it shows that the length for the $3_{10}$/${\alpha}$ helix transitions of Buo-(Ala-Aib)$_n$-oMe, is 8 at room temperature. In an aqueous solution oligopeptide has always coil conformation at room temperature. In an organic solution, helical structures of the oligopeptide are more stable than coil structure, so we studied the $$3_{10}/\alpha$ helix transitions, considering coiled-conformations, coiled and $3_{10}$ helical conformations, and coiled and $\alpha$ helical conformations by using the zipper model. We determined the values of parameters ($\sigma_A$, $\sigma_T$, $\xi_A$, $\xi_T$) from the relating published data; $\sigma_A$ = 0.00011, $\sigma_T$ = 0.0060, $\xi_A$ = 10.1, $\xi_T$ = 3.90. The distributions of $\alpha$ helical length can be N-2, N-3, N-4, ${\cdots}$, 3, 2, 1 (N = 2n) while those of $3_{10}$ helical length, N-1, N-2, N-3, N-4, ${\cdots}$, 3, 2, 1.

• Journal of Conservation Science
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• v.31 no.4
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• pp.341-350
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• 2015

The preservation has been conducted for wooden ship timber excavated from Bonghwang-Dong, Gimhae, Korea. The species were analyzed for conservation as pre-treatment. Outer panel was analyzed as Cinnamomum spp. and trapezoid wooden material, wooden wedge was Cryptomeria japonica D. Don.. Wooden ship timber have been treated by vacuum-freeze drying after impregnation with aqueous PEG#3,350 solution(almost 45%). The timber of Bonghwang-Dong ship is considered as Japanese ship that many data such as conformation of ship, location of site, japanese artifact of around site were confirmed. In addition, The ship timber give us the important information about the international trade with Japan.

• Journal of Soil and Groundwater Environment
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• v.10 no.5
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• pp.61-69
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• 2005

Changes in pyrene binding by dissolved and kaolinite-associated humic substances (HS) due to HS adsorptive fractionation processes were examined using purified Aldrich humic acid (PAHA) at different pH (4, 7 and 9). Irrespective of solution pH, molecular weight (MW) fractionation occurred upon adsorption of PAHA onto kaolinite, resulting in the deviation of residual PAHA MW from the original MW prior to sorption. Variation in $K_{OC}$ by bulk PAHA was observed at different pH due to relative contributions of partitioning and size exclusion effects (i.e., specific interactions). For all pH conditions investigated, carbon-normalized pyrene binding coefficients for nonadsorbed, residual fractions $(K_{OC}(res))$ were different from the original dissolved PAHA $K_{OC}$ value $(K_{OC}(orig))$ prior to contact with the kaolinite suspensions. Positive correlations between pyrene $(K_{OC}(res))$ and weight-average molecular weight $(MW_W)$ for residual PAHA fractions were observed for pH 7 and 9. However, such a positive correlation was not found at pH 4 due to the absence of the dramatic fractionation observed for high pH conditions (i.e., exclusive fractionation with respect to higher MW), suggesting that actual MW distribution pattern is more important for sorption-fractionated HS than the composite MW value. For adsorbed PAHA, conformational changes of PAHA upon adsorption seem to be important for the extent of pyrene binding. At relatively high pH (7 and 9), lower extent of pyrene binding was observed for adsorbed PAHA versus nonadsorbed PAHA. The conformation effects were more pronounced at higher pH.

• BMB Reports
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• v.38 no.2
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• pp.198-205
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• 2005

Resveratrol (RES) and genistein (GEN) are the dietary natural products known to possess chemopreventive property and also the ability to repair DNA damage induced by mutagens/carcinogens. It is believed that the therapeutic activity of these compounds could be primarily due to their interaction with nucleic acids but detailed reports are not available. We here explore the interaction of these drugs with nucleic acids considering DNA and RNA as a potential therapeutic target. The interaction of RES and GEN has been analysed in buffered solution with DNA [saline sodium citrate (SSC)] and RNA [tris ethylene diammine tetra acetic acid (TE)] using UV-absorption and Fourier transform infrared (FTIR) spectroscopy. The UV analysis revealed lesser binding affinity with nucleic acids at lower concentration of RES (P/D = 5.00 and 10.00), while at higher drug concentration (P/D = 0.75, 1.00 and 2.50) hyperchromic effect with shift in the ${\lambda}_{max}$ is noted for DNA and RNA. A major RES-nucleic acids complexes was observed through base pairs and phosphate backbone groups with K = $35.782\;M^{-1}$ and K = $34.25\;M^{-1}$ for DNA-RES and RNA-RES complexes respectively. At various concentrations of GEN (P/D = 0.25, 0.50, 0.75, 1.00 and 2.50) hyperchromicity with shift in the ${\lambda}_{max}$ from 260 $\rightarrow$ 263 om and 260 $\rightarrow$ 270 nm is observed for DNA-GEN and RNA-GEN complexes respectively. The binding constant (from UV analysis) for GEN-nucleic acids complexes could not be obtained due to GEN absorbance overlap with that of nucleic acids at 260 nm. Nevertheless a detailed analysis with regard to the interaction of these drugs (RES/GEN) with DNA and RNA could feasibly be understood by FTIR spectroscopy. The NH band of free DNA and RNA which appeared at $3550-3100\;cm^{-1}$ and $3650-2700\;cm^{-1}$ shifted to $3450-2950\;cm^{-1}$ and $3550-3000\;cm^{-1}$ in DNA-RES and RNA-RES complexes respectively. Similarly shifts corresponding to $3650-3100\;cm^{-1}$ and $3420-3000\;cm^{-1}$ have been observed in DNA-GEN and RNA-GEN complexes respectively. The observed reduction in NH band of free nucleic acids upon complexation of these drugs is an indication of the involvement of the hydroxyl (OH) and imino (NH) group during the interaction of the drugs and nucleic acids (DNA/RNA) through H-bonded formation. The interaction of RES and GEN with bases appears in the order of G $\geq$ T > C > A and A > C $\geq$ T > G. Further interaction of these natural compounds with DNA and RNA is also supported by changes in the vibrational frequency (shift/intensity) in symmetrical and asymmetrical stretching of aromatic rings of drugs in the complex spectra. No appreciable shift is observed in the DNA and RNA marker bands, indicating that the B-DNA form and A-family conformation of RNA are not altered during their interaction with RES and GEN.

• Journal of Life Science
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• v.27 no.1
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• pp.44-49
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• 2017

Natural anti-oxidative compounds have important disease prevention and food preservation properties, in addition to anti-bacterial, anti-inflammation, anti-cancer, and skin whitening effects. High-performance liquid chromatography (HPLC), with an ultra vilolet (UV) detector coupled to a reverse phase C18 column and an online measurement system for 1, 1-diphenyl-2-picryl hydrazyl (DPPH) radicals, was used to search for potent antioxidative compounds in crude extracts. The online HPLC-DPPH assay was then applied to confirm antioxidative compounds in water extracts from Radix of Pueraria lobata, Rhizoma of Zingiber officinale, Fructus of Chaenomeles sinensis, Cortex of Ulmus pumila, and Radix of Astragalus membranaceus. To determine the yields of the extracts, the Brix% of each extract solution was measured using a refractometer. When the relative DPPH radical scavenging ability values of the water extracts were compared with those of a positive control (ascorbic acid), the water extracts of P. lobata, C. sinensis, and U. pumila were 7.77%, 4.71%, and 4.19%, respectively. The results suggest that this method provides a useful assay for rapid measurement of DPPH radical scavenging abilities and conformation of antioxidative compounds in natural products. Moreover, it can reduce the time spent on the separation of active compounds from natural materials, such as medicinal plants, in addition to the use of reagents for separation.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.30 no.2
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• pp.244-251
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• 1997

The relationship between structure and biological activity was studied on the three neuropeptides (mammalian, trout- and goldfish-neuropeptide $\gamma$) that were syntheized by the solid-phase method. Circular dichroism spectra showed that mammalian, trout- and goldfish-neuropeptide $\gamma$ adopted an unordered structure in buffer solution. In the-presence of neutral and acidic liposomes, mammalian and trout-neuropeptioe $\gamma$ also took a random structure. However, goldfish-neuropeptide $\gamma$ took an $\alpha-helical$ structure in acidic liposomes. The intestinal motility response was investigated with carp intestines, guinea-pig ileums and rat duodenums. In case of carp intestine, contractile activity was as follows : goldfish-neuropeptide $\gamma\simeq$ trout-neuropeptide $\gamma>$ mammalian-neuropeptide $\gamma$, On the other hand, the contractile activity of mammalian-neuropeptide $\gamma$ was more potent than trout- and goldfish-neuropeptide $\gamma$ in the guinea-pig ileums and rat duodenums. These results suggest that neuropeptide $\gamma$ show the species-specific activity.

• The Korean Journal of Physiology
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• v.17 no.2
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• pp.135-142
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• 1983

$PGE_2$ and $PGF_{2{\alpha}}$ are known to act similarly in a number of animal tissues. They both facilitate regression of corpus luteum(Poyser, 1972; Fuch et al, 1974; Coudert et at, 1974) and stimulate contraction of uterine muscle (Laudanski et al, 1977; Porter et al, 1979; Hollingsworth et al, 1980). It is, however, not known whether these two prostaglandins exert similar actions in osmotic fragility of erythrocytes (Rasmussen et al, 1975) and $PGF_{2{\alpha}}$ alters conformation of membrane proteins (Meyers aud Swislocki, 1974). The former effect may not be mediated through changes in c- AMP concentration in the cell, since the adenylate cyclase activity in human erythrocyte is extremely low (Rodan et al, 1976; Sutherland et al, 1962) and the latter effect implies that physical state (or fluidity) of the membrane is altered by $PGF_{2{\alpha}}$. The present study was undertaken to elucidate mechanisms of action of $PGE_2$ and $PGF_{2{\alpha}}$ on the human erythocyte membrane by examining their effects on osmotic fragility and $Ca^{++}$ binding to the membrane fragments. The results are summarized as follows: 1) $PGE_2$ and $PGF_{2{\alpha}}$ increased osmotic fragility at concentrations above $10^{11}\;M$, the effect being similar for both hormones. The concentration of NaCl for 100% hemolysis was $1/16{\sim}1/17\;M$ in the presence of $10^{11}\;M\;PGE_2$ or $PGF_{2{\alpha}}$ and 1/18 M in the absence of the hormone (control). 2) When erythrocytes were suspended in 1/15 M NaCl solution, $44.2{\pm}4.3%$ of cells were hemolyzed. Addition of $10^{12}\;M\;PGE_2$ or $PGF_{2{\alpha}}$ did not increase hemolysis. When the concentration of the hormones was increased to $10^{11}\;M$, however the degree of hemolysis increased markealy to about 80%. No further increase in hemolysis was observed at concentration of the hormones above $10^{11}\;M$. 3) The additional hemolysis due to $10^{11}\;M\;PGE_2$ and $PGF_{2{\alpha}}$ appeared to he identical regardless of absence or presence of $Ca^{++}\;(0.5{\sim}10\;mM)$ in the suspending medium. 4) In the absence of prostaglandin, the binding of $Ca^{++}$ to the erythrocyte membrane increased curvilinearly as the $Ca^{++}$ concentration increased up to 5 mM above which it leveled off. A similar dependence of $Ca^{++}$ binding on the $Ca^{++}$ concentration was observed in the presence of $10^{11}\;M\;PGE_2$ or $PGF_{2{\alpha}}$, however, the amount of $Ca^{++}$ bound at a given $Ca^{++}$ concentration was significantly higher than in the absence of the hormones. 5) As in the hemolysis, $PGE_2$ and $PGF_{2{\alpha}}$ did not affect the $Ca^{++}$ binding at a concentration of $10^{12}\;M$, but increased it by about 100% at concentration above $10^{11}\;M$. These result indicate that both tile osmotic fragility of erythrocyte and the $Ca^{++}$ binding to the erythrocyte membrane are similarly enhanced by $PGE_2$ and $PGF_{2{\alpha}}$, but these two effects are not causally related. It is, therefore, concluded that the prostaglandin-induced hemolysis is not directly associated with alterations of the $Ca^{++}$ content in the membrane.

• Analytical Science and Technology
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• v.13 no.4
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• pp.494-503
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• 2000

A 21-residue peptide corresponding to amino acids 84-104 of $p16^{INK4A}$, the tumor suppressor, has been synthesized and its structure was studied by Circular Dichroism, $^1H$ NMR spectroscopy and molecular modeling. A p16-derived peptide (84-104 amino acids) forming stable complex with CDK4 and CDK6 inhibits the ability of CDK4/6 to phosphorylate pRb in vitro, and blocks cell-cycle progression through G1/S phase as shown in the function of the full-length p16. Its NMR spectral data including NOEs, $^3J_{NH-H{\alpha}}$ coupling constants, $C_{\alpha}H$ chemical shift, the average amplitude of amide chemical shift oscillation and temperature coefficients indicate that the secondary structure of a p16-derived peptide is similar to that of the same region of full-length p16, which consists of helix-turn-helix structure. The 3-D distance geometry structure based on NOE-hased distance and torsion angle restraints is characterized by ${\gamma}$-turn conformation between residues $Gly^{89}-Leu^{91}$(${\varphi}_{i+1}=-79.8^{\circ}$, ${\varphi}_{i+1}=60.2^{\circ}$) as evidenced in a single crystal structure for the corresponding region of p18 or p19, but is undefined at both the N and C termini. This compact and rigid ${\gamma}$-turn region is considered to stabilize the structure of p16-derived peptide and serve as a site recognizing cyelin dependent kinase, and this well-defined ${\gamma}$-turn structure could be utilized for the design of anti-cancer drug candidates.

• Korean Journal of Agricultural Science
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• v.10 no.2
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• pp.354-364
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• 1983

Confonmation of (Z)-cinnamonitrile have been studied by molecular orbital theoretically using extended Huckel theory(EHT) and CNDO/2 molecular orbital calculation methods. The results indicate that the stability of conformation is(Z)-gauch>(Z)-planar. The rate constants for alkalie hydrolysis of cinnamonitrile at pH 7.0-14.0 range have been determined by ultra-violet spectrophotometry in 50% methanol at $25^{\circ}C$ and the following rate equation which can be applied over wide pH range was obtained; $${\therefore}k=({\frac{1.41{\times}10^{-14}+1.21{\times}10^7/[H_3O^+]}{2.65{\times}10^{-7}+1.64/[H_3O^+]})+9.14{\times}10^9/[H_3O^+]$$ The rate equation reveals that, at pH 7.0-10.0, the reaction is initiated by the addition of water molecule to unsaturated cabon-carhon double bond of cinnamonitrile and ${\alpha}C-{\beta}C$ bond scission follow subsequently in neutral and alkalie media. At pH 12.0-14.0, in strong alkalie solution, that so-called Michael type nucleophilic addition that the over-all rate constants is only dependent upon the concentration of hydroxide ion occurs competitively and are very complicated. Hence, the reaction mechanism of alkalie hydrolysis of cinnamonitrile which did not carefully before can be fully explained.