• Journal of Microbiology and Biotechnology
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• v.15 no.5
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• pp.1022-1027
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• 2005

Based on plasmid display technology by the complexes of fusion protein and the encoding plasmid DNA, an in vitro selection method for high affinity DNA-binding protein was developed and experimentally demonstrated. The GAL4 DNA-binding domain (GAL4 DBD) was selected as a model DNA-binding protein, and enhanced green fluorescent protein (EGFP) was used as an expression reporter for the selection of target proteins. Error prone PCR was conducted to construct a mutant library of the model. Based on the affinity decrease with increased salt concentration, mutants of GAL4 DBD having high affinity were selected from the mutant protein library of protein-encoding plasmid complex by this method. Two mutants of (Lys33Glu, Arg123Lys, Ile127Lys) and (Ser47Pro, Ser85Pro) having high affinity were obtained from the first generation mutants. This method can be used for rapid in vitro selection of high affinity DNA-binding proteins, and has high potential for the screening of high affinity DNA-binding proteins in a sequence-specific manner.

• Bulletin of the Korean Chemical Society
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• v.28 no.12
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• pp.2248-2252
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• 2007

SOMT-9 is an O-methyltransferase that utilizes quercetin to produce 3'-methoxy quercetin. In order to determine which amino acids of SOMT-9 are important for this reaction and its regioselectivity, molecular docking experiments followed by site directed mutagenesis were performed. Molecular modeling and molecular docking experiments identified several amino acid residues involved in metal binding, AdoMet binding, and substrate binding. Site-directed mutagenesis showed that Asp188 is critical for metal binding and that Lys165 assists other metal binding residues in maintaining quercetin in the proper position during the reaction. In addition, Tyr207 was shown to play an important role in the determination of the regioselectivity and Met60 was shown to be involved in formation of the hydrophobic pocket necessary for substrate binding. The molecular modeling and docking experiments discussed in this study could be applicable to future research including prediction of substrate binding and regioselectivity of an enzyme.

• Bulletin of the Korean Chemical Society
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• v.32 no.12
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• pp.4199-4204
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• 2011

Using models simulating the environment of two distinct adsorption sites of $H_2$ in metal-organic framework-5 (MOF-5), binding energies of $H_2$ to MOF-5 were evaluated at the MP2 and CCSD(T) level. For organic linker section modeled as dilithium 1,4-benzenedicarboxylate ($C_6H_4(COO)_2Li_2$), the MP2 and CCSD(T) basis set limit binding energies are estimated to be 5.1 and 4.4 kJ/mol, respectively. For metal oxide cluster section modeled as $Zn_4O(CO_2H)_6$, while the MP2 basis set limit binding energy estimate amounts to 5.4 kJ/mol, CCSD(T) correction to the MP2 results is shown to be insignificant with basis sets of small size. Substitution of benzene ring with pyrazine ring in the model for the organic linker section in MOF-5 is shown to decrease the $H_2$ binding energy noticeably at both the MP2 and CCSD(T) level, in contrast to the previous study based on DFT calculation results which manifested substantial increase of $H_2$ binding energies upon substitution of benzene ring with pyrazine ring in the similar model.

• Bulletin of the Korean Chemical Society
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• v.25 no.11
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• pp.1635-1640
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• 2004

The cyclophanes 1a-d containing two benzo[b]furan rings connected by various bridges have been prepared and their binding behaviors with N-benzylphenethylammonium cation 2 were examined by NMR titration method. The successive alkylation reactions of 4-hydroxyl groups and then 2-hydroxyl groups of 2,4-dihydroxybenzophenonse gave macrocycles 5a-c. Photoirradiation of the macrocycles 5a-c with 350 nm mercury lamp followed by dehydration afforded the cyclophanes 1a-c. Hydrolysis of two ester groups pendant on a bridge of 1b produced the carboxyl group-containing cyclophane 1d. The cyclophane 1a having a p-xylene bridge showed 1 : 1 binding with 2 with the binding constant of $36{\pm}6M^{-1}$ in 3 : 1 $CDCl_3$/methanol-$d_4$ solvent, while 1b and 1c which have neutral flexible bridges exhibited no appreciable binding with 2. The disodium salt of 1d showed much higher binding affinity for 2 forming 1 : 1 and 1 : 2 complexes.

• Bulletin of the Korean Chemical Society
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• v.10 no.4
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• pp.339-343
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• 1989

The interaction of cationic surfactants, n-alkyltrimethylammonium bromide ($C_nTAB$; n = 12, 14, 16) with anionic polyelectrolyte, poly(styrenesulfonate) (PSS) has been studied by surface tension measurement. In the absence of added salt, the cationic surfactants bind to PSS quantitatively up to ca. 60% coverage of anionic sites of the polyanion and the complexes were surface inactive. Further binding of the surfactant cations on PSS caused a sharp conformational transition of the surfactant/ PSS complexes to surface active complexes and accompanied precipitation. The binding showed a biphasic behavior in the presence of NaCl and cooperativity of the binding became less as the concentration of NaCl increased. Binding of the cationic surfactants on poly(vinylsulfonate) also showed the biphasic behavior and the cooperativity of the binding was much less even in the absence of NaCl. The binding of surfactant to PSS provided hydrophobic environment to solubilized pyrene and reduced the viscosity of the solution greatly even at surfactant concentrations well below cmc. This study indicated that the surfactant bound to PSS up to $60{\%}$ coverage of PSS sites are present as surfactant aggregates which are wrapped up with PSS chains, and hydrophobic interaction is an important factor in the binding of the surfactants to PSS.

• Bulletin of the Korean Chemical Society
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• v.19 no.2
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• pp.252-254
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• 1998

• Bulletin of the Korean Chemical Society
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• v.19 no.2
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• pp.254-257
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• 1998

• Journal of Microbiology and Biotechnology
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• v.26 no.6
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• pp.1077-1086
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• 2016

Glycerol dehydrogenases (GlyDHs) are essential for glycerol metabolism in vivo, catalyzing its reversible reduction to 1,3-dihydroxypropranone (DHA). The gldA gene encoding a putative GlyDH was cloned from Thermoanaerobacterium thermosaccharolyticum DSM 571 (TtGlyDH) and expressed in Escherichia coli. The presence of Mn²⁺ enhanced its enzymatic activity by 79.5%. Three highly conserved residues (Asp¹⁷¹, His²⁵⁴, and His²⁷¹) in TtGlyDH were associated with metal ion binding. Based on an investigation of glycerol oxidation and DHA reduction, TtGlyDH showed maximum activity towards glycerol at 60℃ and pH 8.0 and towards DHA at 60℃ and pH 6.0. DHA reduction was the dominant reaction, with a lower K_m(DHA) of 1.08 ± 0.13 mM and V_max of 0.0053 ± 0.0001 mM/s, compared with glycerol oxidation, with a K_m(glycerol) of 30.29 ± 3.42 mM and V_max of 0.042 ± 0.002 mM/s. TtGlyDH had an apparent activation energy of 312.94 kJ/mol. The recombinant TtGlyDH was thermostable, maintaining 65% of its activity after a 2-h incubation at 60℃. Molecular modeling and site-directed mutagenesis analyses demonstrated that TtGlyDH had an atypical dinucleotide binding motif (GGG motif) and a basic residue Arg⁴³, both related to dinucleotide binding.

• Bulletin of the Korean Chemical Society
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• v.29 no.2
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• pp.431-437
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• 2008

The solvent effects on the relative free energies of binding of K+ and Na+ ions to 12-crown-4 and Dlog Ks (the difference of stability constant of binding) have been investigated by a Monte Carlo simulation of statistical perturbation theory (SPT) in several solvents. Comparing the relative free energies of binding of K+ and Na+ ions to 12-crown-4, in CH3OH of this study with experimental works, there is a good agreement among the studies. We have reported here the quantitative solvent-polarity relationships (QSPR) studied on the solvent effects the relative free energies of binding of K+ and Na+ ions to 12-crown-4. We noted that DN(donor number) dominates the differences in relative solvation Gibbs free energies of K+ and Na+ ions and DN dominates the negative values in differences in the stability constant (Dlog Ks) as well as the relative free energies of binding of K+ and Na+ ions to 12-crown-4 and p* (Kamlet-Tafts solvatochromic parameters) dominates the positive values in differences in the stability constant (Dlog Ks) as well as the relative free energies of binding of K+ and Na+ ions to 12-crown-4.

• Bulletin of the Korean Chemical Society
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• v.29 no.9
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• pp.1765-1768
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• 2008

Functionalized benzoxazole derivatives were designed and synthesized based on the structural features of PIB and FDDNP, which show excellent binding affinities to aggregated A$\beta$ 42 fibrils. All the synthesized compounds were evaluated by competitive binding assay against aggregated A$\beta$ 42 fibrils using [$^{125}$I]TZDM and displayed good in vitro binding affinities with Ki values (0.47-15.3 nM) from subnanomolar to nanomolar range. Among them, benzoxazoles 1f and 1a having malononitrile and ester moieties at C-6 exhibited superior binding affinities ($K_i$ = 0.47 and 0.61 nM, respectively) to PIB ($K_i$ = 0.77 nM).