• Korean Journal of Microbiology
• /
• v.54 no.4
• /
• pp.420-427
• /
• 2018

The orthogonal pair of Saccharomyces cerevisiae tyrosyl-tRNA synthetase (Sc YRS) and a variant of E. coli initiator tRNA, fMam $tRNA_{CUA}$ which recognizes the amber stop codon is an effective tool for site-specific incorporation of unnatural amino acids into the protein in E. coli. To evolve the amber suppression activity of the orthogonal pair, we generated a mutant library of Sc YRS by randomizing two amino acids at 320 and 321 which involve recognition of the first base of anticodon in fMam $tRNA_{CUA}$. Two positive clones are selected from the library screening with chloramphenicol resistance mediated by amber suppression. They showed growth resistance against high concentration of chloramphenicol and their $IC_{50}$ values were approximately 1.7~2.3 fold higher than the wild type YRS. In vivo amber suppression assay reveals that mutant YRS-3 (mYRS-3) clone containing amino acid substitutions of P320A and D321A showed 6.5-fold higher activity of amber suppression compared with the wild type. In addition, in vitro aminoacylation kinetics of mYRS-3 also showed approximately 7-fold higher activity than the wild type, and the enhancement was mainly due to the increase of tRNA binding affinity. These results demonstrate that optimization of anticodon recognition by engineered aminoacyl tRNA synthetase improves the efficiency of unnatural amino acid incorporation in response to nonsense codon.

• Journal of Ginseng Research
• /
• v.44 no.3
• /
• pp.461-474
• /
• 2020

Background: Ginseng effectively reduces fatigue in both animal models and clinical trials. However, the mechanism of action is not completely understood, and its molecular targets remain largely unknown. Methods: By screening for proteins that interact with the primary components of ginseng (ginsenosides) in an affinity chromatography assay, we have identified muscle-type creatine kinase (CK-MM) as a potential target in skeletal muscle tissues. Results: Biolayer interferometry analysis showed that ginsenoside metabolites, instead of parent ginsenosides, had direct interaction with recombinant human CK-MM. Subsequently, 20(S)-protopanaxadiol (PPD), which is a ginsenoside metabolite and displayed the strongest interaction with CK-MM in the study, was selected as a representative to confirm direct binding and its biological importance. Biolayer interferometry kinetics analysis and isothermal titration calorimetry assay demonstrated that PPD specifically bound to human CK-MM. Moreover, the mutation of key amino acids predicted by molecular docking decreased the affinity between PPD and CK-MM. The direct binding activated CK-MM activity in vitro and in vivo, which increased the levels of tissue phosphocreatine and strengthened the function of the creatine kinase/phosphocreatine system in skeletal muscle, thus buffering cellular ATP, delaying exercise-induced lactate accumulation, and improving exercise performance in mice. Conclusion: Our results suggest a cellular target and an initiating molecular event by which ginseng reduces fatigue. All these findings indicate PPD as a small molecular activator of CK-MM, which can help in further developing better CK-MM activators based on the dammarane-type triterpenoid structure.

• The Journal of the Korean Society for Microbiology
• /
• v.34 no.6
• /
• pp.533-542
• /
• 1999

H. pylori produces urease abundantly amounting to 6% of total protein of bacterial mass. Urease genes are composed of a cluster of 9 genes of ureC, ureD, ureA, ureB, ureI, ureE, ureF, ureG, ureH. Production of H. pylori urease in E. coli was studied with genetic cotransformation. Structural genes ureA and ureB produce urease apoprotein in E. coli but the apoprotein has no enzymatic activity. ureC and ureD do not affect urease production nor enzyme activity ureF, ureG, and ureH are essential to produce the catalytically active H. pylori urease of structural genes (ureA and ureB) in E.coli. The kinetics of activation of H. pylori urease apoprotein were examined to understand the production of active H. pylori urease. Activation of H. pylori urease apoprotein, pH dependency, reversibility of $CO_2$ binding, irreversibility of $CO_2$ and $Ni^{2+}$ incorporation, and $CO_2$ dependency of initial rate of urease activity have been observed in vitro. The intrinsic reactivity (ko) for carbamylation of urease apoprotein co expressed with accessory genes was 17-fold greater than that of urease apoprotein expressed without accessory genes. It is concluded that accessory genes function in maximizing the carbamylating deprotonated ${\varepsilon}$-amino group of Lys 219 of urease B subunit and metallocenter of urease apoprotein is supposed to be assembled by reaction of a deprotonated protein side chain with an activating $CO_2$ molecule to generate ligands that facilitate productive nickel binding.

• The Korean Journal of Nuclear Medicine
• /
• v.31 no.4
• /
• pp.421-426
• /
• 1997

We evaluated the in vivo kinetics, distribution, and pharmacology of N-(4-[$^{18}F$]fluoromethylbenzyl)spiperone ([$^{18}F$]FMBS), a newly developed derivative of spiperone, as a potentially more selective radiotracer for the dopamine (DA) $D_2$ receptors. Mice received 1.9-3.7 MBq (1.8-3.6 nmol/kg) of [$^{18}F$]FMBS by tail vein injection. The time course and regional distribution of the tracer in brain were assessed. Blocking studies were carried out by intravenously preinjecting DA $D_2$ receptor blockers (spiperone, butaclamol) as well as drugs with high affinity for DA $D_1$ (SCH 23390), DA transporter (GBR 12909), and serotonin $S_2$ ($5-HT_2$) (ketanserin) sites. After injection of the tracer, the radioactivity in striatum increased steadily over time, resulting in a striatal-to-cerebellar ratio of 4.8 at 120 min postinjection. By contrast, the radioactivity in cerebellum, frontal cortex, and remaining cortex washed out rapidly. Preinjection of unlabeled FMBS (1 mg/kg) and spiperone (1 mg/kg) reduced [$^{18}F$]FMBS striatal-to-cerebellar ratio by 41% and 80%, respectively. (+)-Butaclamol (1 mg/kg) blocked 80% of the striatal [$^{18}F$]FMBS binding, while (-)-butaclamol (1 mg/kg) did not. Preinjection of SCH 23390 (1 mg/kg) and GBR 12909 (5 mg/kg) had no significant effect on [$^{18}F$]FMBS binding. Ketanserin (1 mg/kg), a ligand for the $5-HT_2$ receptors, did not cause significant inhibition either in striatum, in frontal cortex, or the remaining cortex. The results demonstrate that [$^{18}F$]FMBS labels DA $D_2$ receptors selectively in vivo in the mouse brain. It may hold promise as a selective radiotracer for studying DA $D_2$ receptors in vivo by PET.

• Journal of the Korean Chemical Society
• /
• v.55 no.2
• /
• pp.177-182
• /
• 2011

A diketo-type ligand was synthesized by the Knoevenagel condensation reaction of thiophene-2-aldehyde with acetylacetone, subsequently its transition metal complexes with Cu(II), Ni(II), and Co(II) chlorides were also prepared. All the complexes were characterized by various physico-chemical methods. The molar conductivity data reveals ionic nature for the complexes. The electronic spectrum and the EPR values suggest square planar geometry for the Cu(II) ion. Interaction of the Cu(II) complex with CTDNA (calf thymus DNA) was studied by absorption spectral method and cyclic voltammetry. The $k_{obs}$ values versus [DNA] gave a linear plot suggesting psuedo-first order reaction kinetics. The cyclic voltammogram of the Cu(II) complex reveals a quasi-reversible wave attributed to Cu(II)/Cu(I) redox couple for one electron transfer with $E_{1/2}$ values -0.240 V and -0.194 V. respectively. On addition of CTDNA, there is a shift in the $E_{1/2}$ values 168 mV and 18 mV respectively and decrease in Ep values. The shift in $E_{1/2}$ values in the presence of CTDNA suggests strong binding of Cu(II) complex to the CTDNA.

• Bulletin of the Korean Chemical Society
• /
• v.27 no.5
• /
• pp.657-662
• /
• 2006

Identification of accessible sites in targeted RNAs is a major limitation to the effectiveness of antisense oligonucleotides. A class of antisense oligodeoxynucleotides, known as the “10-23” DNA enzyme or DNAzyme, which is a small catalytic DNA, has been shown to efficiently cleave target RNA at purine-pyrimidine junctions in vitro. We have designed a strategy to identify accessible cleavage sites in the target RNA, which is hepatitis C virus nonstructural gene 3 (HCV NS3) RNA that encodes viral helicase and protease, from a pool of random DNAzyme library. A pool of DNAzymes of 58 nucleotides-length that possess randomized annealing arms, catalytic core sequence, and fixed 5'/3'-end flanking sequences was designed and screened for their ability to cleave the target RNA. The screening procedure, which includes binding of DNAzyme pool to the target RNA under inactive condition, selection and amplification of active DNAzymes, incubation of the selected DNAzymes with the target RNA, and target site identification on sequencing gels, identified 16 potential cleavage sites in the target RNA. Corresponding DNAzymes were constructed for the selected target sites and were tested for RNA-cleavage in terms of kinetics and accessibility. These selected DNAzymes were effective in cleaving the target RNA in the presence of $Mg^{2+}$. This strategy can be applicable to identify accessible sites in any target RNA for antisense oligonucleotides-based gene inactivation methods.

• BMB Reports
• /
• v.33 no.2
• /
• pp.172-178
• /
• 2000

The lipoxygenase was purified 35 fold to homogeneity from the Korean red potato by an ammonium sulfate precipitation and DEAE-cellulose column chromatography. The simple purification method is useful for the preparation of pure lipoxygenase. The molecular weight of the enzyme was estimated to be 38,000 by SDS-polyacrylamide gel electrophoreses and Sepharose 6B column chromatography. The purified enzyme with 2 M $(NH_4)_2SO_4$ in a potassium phosphate buffer, pH 7.0, was very stable for 5 months at $-20^{\circ}C$. Because the purified lipoxygenase is very stable, it could be useful for the screening of a lipoxygenase inhibitor. The optimal pH and temperature for lipoxygenase purified from the red potato were found to be pH 9.0. and $30^{\circ}C$, respectively. The Km and Vmax values for linoleic acid of the lipoxygenase purified from the red potato were $48\;{\mu}M$ and $0.03\;{\mu}M$ per minute per milligram of protein, respectively. The enzyme was insensitive to the metal chelating agents tested (2 mM KCN, 1 and 10mM EDTA, and 1 mM $NaN_3$), but was inhibited by several divalent cations, such as $Cu^{++}$, $Co^{++}$ and $Ni^{++}$. The essential amino acids that were involved in the catalytic mechanism of the 5-lipoxygenase from the Korean red potato were determined by chemical modification studies. The catalytic activity of lipoxygenase from the red potato was seriously reduced after treatment with a diethylpyrocarbonate (DEPC) modifying histidine residue and Woodward's reagent (WRK) modifying aspartic/glutamic acid. The inactivation reaction of DEPC (WRK) processed in the form of pseudo-first-order kinetics. The double-logarithmic plot of the observed pseudo-first-order rate constant against the modifier concentration yielded a reaction order 2, indicating that two histidine residues (carboxylic acids) were essential for the lipoxygenase activity from the red potato. The linoleic acid protected the enzyme against inactivation by DEPC(WRK), revealing that histidine and carboxylic amino acids residues were present at the substrate binding site of the enzyme molecules.

• BMB Reports
• /
• v.28 no.2
• /
• pp.112-117
• /
• 1995

Succinic semialdehyde reductase was inactivated by o-phthalaldehyde. The inactivation followed pseudo-first order kinetics, and the second-order rate constant for the inactivation process was 28 $M^{-1}s^{-1}$ at pH 7.4 and $25^{\circ}C$. The absorption spectrum ($\lambda_{max}$ 337 nm) and fluorescence excitation ($\lambda_{max}$ 340 nm) and fluorescence emission spectra ($\lambda_{max}$ 409 nm) were consistent with the formation of an isoindole derivative in the catalytic site between a cysteine and a lysine residue approximately about 3 $\AA$ apart. The substrate, succinic semialdehyde, did not protect enzymatic activity against inactivation, whereas the coenzyme NADPH protected against o-phthaladehyde induced inactivation of the enzyme. About 1 isoindole group per mol of the enzyme was formed following complete loss of enzymatic activity. These results suggest that the amino acid residues of the enzyme participating in a reaction with o-phthalaldehyde are cysteinyl and lysyl residues at or near the NADPH binding site.

• Microbiology and Biotechnology Letters
• /
• v.34 no.4
• /
• pp.368-372
• /
• 2006

Quercetin is a flavonoid molecule that is known to tie in various sources of natural products such as vegetables and fruits. It has been proven that quercetin plays a crucial role in the prevention of colon cancer as well as homeostasis as radical scavenger in human body. It is also well-known that glycosidases, including $\alpha$-glucosidase, are involved in a variety of degenerative metabolic disorders. In the course of screening useful $\alpha$-glucosidase inhibitors, we screened out quercetin as a $\alpha$-glucosidase inhibitor from chemical libraries. Quercetin was shown to be a reversible, slow-binding, and noncompetitive inhibitor of yeast a-glucosidase with a K$_i$ value of $6.3\times10^{-8}$ M when it was included with an enzyme mixture. Together, these results show that quercetin has potential in treating disorders including diabetes, although the further mechanistic study is needed.

• Journal of Microbiology and Biotechnology
• /
• v.19 no.7
• /
• pp.713-717
• /
• 2009

The dependence of the catalytic properties of horseradish peroxidase on the structural changes of ionic liquids was investigated with two water-miscible ionic liquids, N-butyl-3methypyridinium tetraftuoroborate ([$BMP_y$][$BF_4$]) and 1-butyl-3-methylimidazolium methylsulfate ([BMIM][$MeSO_4$]), each of which shares an anion ($BF_4^-$) or a cation ($BMIM^+$) with 1-butyl-3-methylimidazolium tetraftuoroborate ([BMIM][$BF_4$]), respectively. The oxidation of guaiacol (2-methoxyphenol) with $H_2O_2$was used as a model reaction. In order to minimize the effect of solution viscosity on the kinetic constants of the enzymatic catalysis, the enzymatic reactions for the kinetic study were performed in water-ionic liquid mixtures containing 25% (v/v) ionic liquid at maximum. Similarly to the previously reported results for [BMIM][$BF_4$], as the concentration of [$BMP_y$][$BF_4$] increased, the $K_m$value increased with a decrease in the $k_{cat}$value: the $K_m$value increased markedly from 2.8 mM in 100% water to 12.6 mM in 25% (v/v) ionic liquid, indicating that ionic liquid significantly weakens the binding affinity of guaiacol to the enzyme. On the contrary, [BMIM][$MeSO_4$] decreased the Km value to 1.4 mM in 25% (v/v) ionic liquid. [BMIM][$MeSO_4$] also decreased $k_{cat}$more than 3-folds [from 13.8 $s^{-1}$in 100% water to 4.1 $s^{-1}$in 25% (v/v) ionic liquid]. These results indicate that the ionic liquids interact with the enzyme at the molecular level as well as at a macroscopic thermodynamic scale. Specifically, the anionic component of the ionic liquids influenced the catalysis of horseradish peroxidase in different ways.