• Bulletin of the Korean Chemical Society
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• v.24 no.6
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• pp.859-863
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• 2003

We report on the theoretical positron affinities of closed-shell atomic anions. The second-order many-body perturbation theory is applied taking the positron-electron interaction as a perturbation. The corrections for the complete basis set effects to the second order affinity are calculated based on the variational and nonvariational energy functionals of explicitly correlated geminals. It is shown that the explicitly correlated methods accelerate the convergence of the expansion significantly giving the account of the cusp behavior outside the orbital space.

• Journal of Microbiology and Biotechnology
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• v.16 no.1
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• pp.109-117
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• 2006

The Rev binding to Rev Responsive Element (RRE) of HIV-1 mRNA plays an important role in the HIV-I viral replication cycle. The disruption of the Rev-RRE interaction has been studied extensively in order to develop a potential antiviral drug. In order to provide the basis for a more promising approach to develop a Rev-RRE binding inhibitor against HIV-I infection, it is necessary to understand the binding modes of the aminoglycoside antibiotics to RRE. In the present study, the binding mode of a modified antibiotic, a neamine conjugated with pyrene and arginine (NCPA), to RRE has been studied by the methods of $T_m$ measurement and spectroscopic analysis of RRE with or without antibiotics. The results confirmed that NCPA competes with Rev in binding to RRE.

• Mass Spectrometry Letters
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• v.9 no.2
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• pp.51-55
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• 2018

Capture of non-glycoproteins during lectin affinity chromatography is frequently observed, although it would seem to be anomalous. In actuality, lectin affinity chromatography works at post-translational modification (PTM) sites on a glycoprotein which is not involved in protein-protein interactions (PPIs). In this study, serial affinity column set (SACS) using lectins followed by proteomics methods was used to identify PPI mechanisms of captured proteins in human plasma. MetaCore, STRING, Ingenuity Pathway Analysis (IPA), and IntAct were individually used to elucidate the interactions of the identified abundant proteins and to obtain the corresponding interaction maps. The abundant non-glycoproteins were captured with the binding to the selected glycoproteins. Therefore, depletion process in sample pretreatment for abundant protein removal should be considered with more caution because it may lose precious disease-related low abundant proteins through PPIs of the removed abundant proteins in human plasma during the depletion process in biomarker discovery. Glycoproteins bearing specific glycans are frequently associated with cancer and can be specifically isolated by lectin affinity chromatography. Therefore, SACS using Lycopersicon esculentum lectin (LEL) can also be used to study disease interactomes.

• BMB Reports
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• v.33 no.6
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• pp.531-536
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• 2000

Tropomyosin (TM) is an important actin binding protein involved in regulation of muscle contraction. Unacetylated striated tropomyosin failed to bind to actin whereas unacetylated smooth tropomyosin bound well to actin. It has been demonstrated that high actin affinity of unacetylated ${\alpha}-tropomyosin$ was ascribed to the carboxyl terminal amino acid residues. In order to define the role of the carboxyl terminal residues of tropomyosin molecule on actin binding, two mutant tropomyosins were constructed. TM11 is identical to the striated tropomyosin except that the carboxyl terminal last three amino acids was replaced with $^{282}NNM^{284}$ whereas in TM14 $^{276}HA^{277}$ was substituted with smooth specific $^{276}QT^{277}$. TM11 and TM14 were overproduced in Escherichia coli and analyzed for actin affinity. The apparent binding constants (Kapp) of unacetylated tropomyosins were $2.2{\times}10^6M^{-1}$ for sm9, $1.03{\times}10^6M^{-1}$ for TM14, $0.19{\times}10^6M^{-1}$ for TM11, $>0.1{\times}10^6M^{-1}$ for striated, respectively. This result indicated that higher actin affinity of the unacetylated smooth tropomyosin was primarily attributed to the presence of QT residues in the smooth sequence. In case of the Ala-Ser (AS) dipeptide extension of the amino terminus of tropomyosin, Kapp were $21.1{\times}10^6M^{-1}$ for AS-sm9, $8.0{\times}10^6M^{-1}$ for AS-11, $4.7{\times}10^6M^{-1}$ for AS-14, $3.8{\times}10^6M^{-1}$ for AS-striated. AS-TM11 showed considerably higher actin affinity than AS-TM14, implying that interaction of Ala-Ser of the amino terminus with the carboxyl terminal residues. Since Kapp of AS-TM11 was significantly lower than that of AS-sm9, the presence of QT might be required for restoration of high actin affinity of the smooth ${\alpha}-tropomyosin$. These results suggested that the carboxyl terminal amino acid residues Glutamine275-Threonine276 are important for actin affinity of the recombinant smooth ${\alpha}-tropomyosin$, particularly of unacetylated smooth ${\alpha}-tropomyosin$.

• 한국생물공학회:학술대회논문집
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• 2005.10a
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• pp.749-750
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• 2005

• Journal of Pharmaceutical Investigation
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• v.19 no.3
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• pp.163-171
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• 1989

To investigate the protein binding characteristics of cephalothin, the effects of ionic strength, pH and temperature on the binding of cephalothin to bovine serum albumin (BSA) were studied by UV difference spectrophotometric method. With increasing ionic strength at constant PH and temperature, association constant decreased, but the number of binding sites sites was about 2 constantly. It may be deduced that the binding process is not only due to electrostatic forces. And the increased association constant at high ionic strength is explained by conformational changes of BSA from complex to subunits. The pH effect on the affinity of interaction indicated that the binding affinity of drug is higher in the neutral region than in the alkaline region. And, at high pH value, the number of binding sites decreased from 2 to 1 because of the conformational changes of BSA in alkaline region. The decrease in binding affinity of BSA to drug with increasing temperature was characteristic of an exothermic reaction. And the negative sign of ${\Delta}G^{\circ}$ meant that the binding process occurs spontaneously under the experimental conditions. In cephalothin-BSA complex formation, since the net enthalpy change value and entropy change value are positive, it is assumed that hydrophobic bindings are predominant in this binding process.

• Bulletin of the Korean Chemical Society
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• v.28 no.5
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• pp.758-762
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• 2007

A new alkyldithiocarbonate (xanthate), as sodium salts, C2H5OCS2Na, was synthesized by the reaction between CS2 with ethyl alcohol in the presence of NaOH. The new xanthate was characterized by 1H NMR, IR and elemental analysis. Then, the new synthesized compound was examined for functional study of cresolase activity of Mushroom Tyrosinase (MT) from a commercial source of Agricus bisporus in 10 mM phosphate buffer pH 6.8, at three temperatures of 10, 20 and 33℃ using UV spectrophotemetry. 4-[(4-methylphenyl)- azo]-phenol (MePAPh) was used as a synthetic substrate for the enzyme for cresolase reaction. The results show that ethyl xanthate can activate or inhibit the cresolase activity of mushroom tyrosinase depending to the concentration of ethyl xanthate. It was concluded that the enzyme has two distinct sites for ethyl xanthate. The first one is a high-affinity activation site and the other is a low-affinity inhibition site. Activation of the enzyme in the low concentration of ethyl xanthate arises from increasing the affinity of binding for the substrate as well as increasing the enzyme catalytic constant. The affinity of ligand binding in the activation site is decreased by increasing of the temperature, which is the opposite result for the inhibition site. Hence, the nature of the interaction of ethyl xanthate is different in two distinct sites. The binding process for cresolase inhibition is only entropy driven, meanwhile the binding process for cresolase activation is not only entropy driven but also enthalpy driven means that hydrophobic interaction is more important in the inhibition site.

• BMB Reports
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• v.45 no.6
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• pp.360-364
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• 2012

Uptake of circulating glucose into the cells happens via the insulin-mediated signalling pathway, which translocates the glucose transporter 4 (GLUT4) vesicles from the intracellular compartment to the plasma membrane. Rab GTPases are involved in this vesicle trafficking, where Rab GTPases-activating proteins (RabGAP) enhance the GTP to GDP hydrolysis. TBC1D4 (AS160) and TBC1D1 are functional RabGAPs in the adipocytes and the skeletonal myocytes, respectively. These proteins contain two phosphotyrosine-binding domains (PTBs) at the amino-terminus of the catalytic RabGAP domain. The second PTB has been shown to interact with the cytoplasmic region of the insulin-regulated aminopeptidase (IRAP) of the GLUT4 vesicle. In this study, we quantitatively measured the ${\sim}{\mu}M$ affinity ($K_D$) between TBC1D4 PTB and IRAP using isothermal titration calorimetry, and further showed that IRAP residues 1-49 are the major region mediating this interaction. We also demonstrated that the IRAP residues 1-15 are necessary but not sufficient for the PTB interaction.

• Journal of Korea Technical Association of The Pulp and Paper Industry
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• v.42 no.4
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• pp.71-77
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• 2010

To utilize modified pulp fibers in papermaking system, it is necessary to evaluate the interaction between modified fibers and papermaking additives. Fluorescent whitening agent (FWA) is an important additive which has been widely used for production of writing and printing paper. We modified pulp fiber surface by Layer-by-Layer multilayering of polyelectrolytes, and investigated the interaction between these fibers and FWA used in internal addition or surface treatment. Pulp fiber with cationic surface charge showed a good affinity to internal FWA. For FWA in surface sizing agent, whiteness and brightness of paper was dependent on pickup weight and polyelectrolyte type. Pulp fibers with C-starch/PSS multilayer showed better optical properties than poly-DADMAC/PSS treatment. It indicated that polyelectrolyte type in Layer-by-Layer multilayering as well as a good affinity to FWA is important to get better whiteness and brightness.

• Bulletin of the Korean Chemical Society
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• v.32 no.7
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• pp.2325-2331
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• 2011

Human CDX1 and CDX2 genes play important roles in the regulation of cell proliferation and differentiation in the intestine. Hox genes clustered on four chromosomal regions (A-D) specify positional signaling along the anterior-posterior body axis, including intestinal development. Using glutathione S-transferase (GST) pulldown assays, molecular interaction measurements, and fluorescence measurements, we found that the homeodomains (HDs) of CDX1 and CDX2 directly interact with that of HOXD8 in vitro. CDX1 showed significant affinity for HOXD8, but CDX2 showed weak affinity for HOXD8. Thus far, three-dimensional structures of CDX1/2 and HOXD8 have not been determined. In this study, we developed a molecular docking model by homology modeling based on the structures of other HD members. Proteins with mutations in the HD of CDX1 (S185A, N190A, T194A, and V212A) also bound to the HD of HOXD8. Our study suggests that the HDs of CDX1/2 resemble those of HOXD8, and we provide the first insight into the interaction between the HDs of CDX1/2 proteins and those of HOXD8.