• Bulletin of the Korean Chemical Society
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• v.34 no.2
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• pp.545-548
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• 2013

It has been shown that calculating atomic charges using quantum mechanical level theory greatly improves the accuracy of docking. A protocol was developed and shown to be effective. That this protocol works is just a manifestation of the fact that electrostatic interactions are important in protein-ligand binding. In order to investigate how the same protocol helps in prediction of binding affinities, we took a series of known cocrystal structures of influenza neuraminidase inhibitors with the receptor and performed docking with Glide SP, Glide XP, and QPLD, the last being a workflow that incorporates QM/MM calculations to replace the fixed atomic charges of force fields with quantum mechanically recalculated ones at a given docking pose, and predicted the binding affinities of each cocrystal. The correlation with experimental binding affinities considerably improved with QPLD compared to Glide SP/XP yielding $r^2$ = 0.83. The results suggest that for binding sites, such as that of neuraminidase, which are laden with hydrophilic residues, protocols such as QPLD which utilizes QM-based atomic charges can better predict the binding affinities.

• Archives of Pharmacal Research
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• v.21 no.4
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• pp.429-435
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• 1998

Lectins and its A- and B-chains from Korean mistletoe (Viscum album var. coloratum) were isolated by affinity chromatography on the Sepharose 4B modified by lactose-BSA conjugate synthesized by reductive amination of ligand (lactose) to .epsilon.-amino groups of lysine residues of spacer (BSA) after reduction by $NaCNBH_3$. The lactose-BSA conjugate was coupled to Sepharose 4B activated by cyanogen bromide. The molecular weight determined by SDS-PAGE were a 31 kD of A-chain and a 35kD of B-chain. Amino acid analysis and N-terminal sequencing were performed. The effects of pH, temperature and guanidine chloride on the conformation of the lectin were investigated by measuring its intrinsic fluorescence and compared with its hemagglutinating activities. Blue shift was detected on the acidic pH and there was a close relationship between activities and conformation of the lectin. Under denaturing conditions, the tryptophan emission profile of lectin showed typical denaturaiional red shift which also correspond to the conformations and activity of lectin.

• The Korean Journal of Nuclear Medicine
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• v.31 no.4
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• pp.440-451
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• 1997

This study was designed to prospect the $^{111}In$-labelled paclitaxel as tumor imaging agent. In order to provide a taxol molecule with a functional group which is able to chelate In-111, taxol-DTPA conjugate and 2'-hemisuccinyltaxol were synthesized by esterification of taxol at C-2'on C-13 carbon with DTPA anhydride and succinic anhydride, respectively. Synthesis yield of the taxol derivatives was 34% for taxol-DTPA and 80% for 2'-hemisuccinyltaxol. Cytotoxicity of the taxol derivatives were measured by MTT method toward cell lines HT29, B16, P388, and CT26. The cytotoxic activities of the taxol derivatives were maintained, although less active than taxol. Radiolabelling of the taxol derivatives were proceeded directly with $^{111}InCl_3$ or indirectly with $^{111}In$-citrate(ligand-exchange method). The ligand-exchange method was not suitable because some precipitates appeared during the reaction. On the contrary, by direct radiolabelling method, we were able to obtain taxol-DTPA-$^{111}In$ in 100% radiochemical yield. However, 2'-hemisuccinyltaxol was not labelled by both methods. Yield and radiochemical purity of the radiolabelled com-pound were determined by HPLC, paper chromatography and instant thin layer chromatography. Taxol-DTPA-$^{111}In$ was characterized to be hydrophilic by lipophilicity test, and nearly non-adhesive to HT29, B16, P388, and CT26 by cell binding affinity test. Binding affinity of the taxol-DTPA-$^{111}In$ complex to serum proteins was also examined by protein precipitation with 30% trichloroacetic acid. The results showed that 30% of the taxol-DTPA-$^{111}In$ complex binds with serum proteins.

• Bulletin of the Korean Chemical Society
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• v.12 no.2
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• pp.130-137
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• 1991

The following new cryptand 221 complexes of lanthanides(Ⅲ) and dioxouranium(Ⅵ) nitrate have been synthesized: $(Ln(C_{16}H_{32}N_2O_5)(H_2O)_2(NO_3)_3\ and \((UO_2)_2(C_{16}H_{32}N_2O_5)(H_2O)_4(NO_3)_4$. These complexes have been identified by elemental analysis, moisture titration, conductivity measurements and various spectroscopic techniques. The proton and carbon-13 NMR as well as calorimetric measurements were used to study the interaction of cryptand 221 with La(Ⅲ), Pr(Ⅲ ), Ho(Ⅲ) and $UO_2(Ⅱ)$ ions in nonaqueous solvents. The bands of metal-oxygen atoms, metal-nitrogen atoms and O-U-O in the IR spectra shift upon complexation to lower frequencies, and the vibrational spectra ({\delta}NMN$) of metal-amide complexes in the crystalline state exhibit lattice vibrations below 300 $cm^{-1}$. The NMR spectra of the lanthanides(Ⅲ) and dioxouranium(Ⅵ) nitrate complexes in nonaqueous solvents are quite different, indicating that the ligand exists in different conformation, and also the $^1H$ and $^{13}C-NMR$ studies indicated that the nitrogen atom of the ring has greater affinity to metal ions than does the oxygen atom, and the planalities of the ring are lost by complexation with metal ions. Calorimetric measurements show that cryptand 221 forms more stable complexes with $La^{3+}$ and $Pr^{3+}$ ions than with $UO^{22+}$ ion, and $La^{3+}/Pr^{3+}$ and $UO^{22+}/Pr^{3+}$ selectivity depends on the solvents. These changes on the stabilities are dependent on the basicity of the ligand and the size of the metal ions. The absorption band (230-260 nm) of the complex which arises from the direct interaction of macrocyclic donor atoms with the metal ion is due to n-{\delta}*$ transition and also that (640-675 nm) of $UO^{22+}$-cryptand 221 complex, which arises from interaction between two-dioxouranium(Ⅵ) ions in being out of cavity of the ligand ring is due to d-d* transition.

• Parasites, Hosts and Diseases
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• v.29 no.1
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• pp.1-8
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• 1991

Out of many component proteins in crude saline extract of Spirometra mansoni plerocercoid (sparganum) , 36 kDa and 29 kDa proteins were found to be the most antigenic and were already purified by immunoaffinity chromatography using monoclonal antibody as a ligand. In this study, a single step purification of these potent antigenic proteins of sparganum extract was investigated. When the crude saline extract was charged to gelatin-Sepharose 4B affinity column, 36 kDa and 29 kDa protein fractions were bound. SDS-polyacrylamide gel electrophoresis (PAGE) and SDS-PAGE/immunoblot confirmed that the bound protein to gelatin was serologically pure. When evaluated by ELISA with patients sera, the purified protein of 36 and 29 kDa also showed improved antigenicity.

• The Korean Journal of Mycology
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• v.17 no.3
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• pp.105-113
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• 1989

For selective purification of proteins in Pleurotus cornucopiae, affinity chromatography was performed by p-aminoanilinylsuccinyl-AH-Sepharose 4B gel synthesized by treating p-phenylene diamine with succinyl-AH-Sepharose 4B, which was prepared by treating AH-Sepharose 4B with succinic anhydride. The capacity of p-aminoanilinyl ligand group was 6.1 micromole per milliliter of gel. Total apparent molecular weight of the affinity proteins eluted from the synthesized gel was 167 KD, which were a protein complex of 130 KD and 37 KD. The contents of the nonpolar, polar, positively and/or negatively charged amino acids in the affinity protein were 44.57%, 24.75%, 21.25%, and 9.43%, respectively. Total apparent molecular weight of the affinity proteins eluted from the AH-Sepharose 4B gel was 95.2 KD, which were a protein complex of 61 KD, 31 KD and 3.2 KD. The contents of the nonpolar, positively and/or negatively charged amino acids in the affinity protein by AH-Sepharose 4B gel were 44.05%, 29.13%, and 12.91% respectively.

• The Korean Journal of Nuclear Medicine
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• v.32 no.4
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• pp.305-313
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• 1998

The reduction in the amount of asialoglycoprotein (ASGP) receptor, which resides exclusively on the plasma membrane of functioning mammalian hepatocytes, as a consequence of hepato-cellular damage has been demonstrated in various pathologic conditions of the liver. Galac-tosylated human serum albumin (GSA) is a newly developed receptor-binding agent, specific for the ASGP receptor. Tc-99m GSA binds quantitatively to liver ASGP receptors and the rate of accumulation in the liver is dependent on hepatic function represented as the amount of receptor, as well as the amount of ligand injected, its affinity to the receptor and the hepatic blood flow. The findings of Tc-99m GSA scintigraphy were reported to reflect the hepatic function of the patients with large hepatic tumors, obstructive jaundice, acute and chronic liver disease. Tc-99m GSA scintigraphy is an easy and reliable test and has the clinical potentials to evaluate the liver function in the patients with hepatic disorders.

• Journal of the Korean Society of Food Science and Nutrition
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• v.24 no.3
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• pp.389-395
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• 1995

The neutral sugar sidechains of apple pectins were hydrolyzed by commercial hemicellulase produced from Aspergillus niger, and the corresponding changes in solution viscosity were investigated in dilute(cc*) pectin solutions. Pectinase activity included in hemicellulases was removed by Epoxy-activated Sepharose 6B affinity chromatography using polygalacturonic acid as a ligand. Enzymatic hydrolysis of sidechains did not affect the specifc viscosity of dilute(0.5%) pectin solutions, while viscosity significantly decreased in concentrated(2.0∼6.0%) region. These results strongly suggest that the sidechains of pectins exists as an entangled state in concentrated solutions. It was also found that in the concentrated region the extent of viscosity reduction was dependent on pectin concentrations.

• KSBB Journal
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• v.17 no.1
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• pp.1-13
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• 2002

Label-free optical methods for the monitoring of interactions between biological molecules have become increasingly popular within the last decade. A rising number of publications have demonstrated the benefits of direct biomolecular interaction analysis(BIA) for biology and biochemistry, such as antigen-antibody Interactions, receptor-ligand interactions, protein-DNA, DNA- intercalator, and DNA-DNA interactions. This article gives an overview of the historical development, principle and application of label-free optical biosensor to examine the functional characteristics of biospecific interaction, such as kinetics, affinity, and binding position of biomolecular between an immobilized species at the transducer surface and its dissolved binding partner.

• BMB Reports
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• v.28 no.6
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• pp.552-555
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• 1995

Treatment of microsomal vesicles isolated from etiolated Pisum sativum L cv. Alaska epicotyl tissue with agents inhibiting protein dephosphorylation, namely NaF and/or ATP, resulted in increased binding of the phytotropin NPA to the putative auxin efflux carriers localized on the plasma membrane. The phytotropin effect was especially conspicuous if the vesicles were simultaneously treated with Triton X-100. Kinetic analysis of the binding indicated the existance of two distinct sites for NPA, each having different affinities. Increased binding of the phytotropin to the membrane where protein dephosphorylation was inhibited was attributable to the increased ligand affinity of both sites. Treatment of tissue segments with flubride was found to enhance in vivo auxin transport. Implications of covalent modification of the auxin efflux carrier complex for the regulation of membrane transport of auxin molecules are discussed.