• BMB Reports
• /
• v.43 no.6
• /
• pp.407-412
• /
• 2010

Homeodomain (HD) is a highly conserved DNA-binding domain composed of helix-turn-helix motif. Drosophila Vnd (Ventral nervous system defective) containing HD acts as a regulator to either enhance or suppress gene expression upon binding to its target sequence. In this study, kinetic analysis of Vnd binding to DNA was performed. The result demonstrates that DNA-binding affinity of the recombinant protein containing HD and NK2-specific domain (NK2-SD) was higher than that of the full-length Vnd. To access whether phosphorylation sites within HD and NK2-SD affect the interaction of the protein with the target sequence, alanine substitutions were introduced. The result shows that S631A mutation within NK2-SD does not contribute significantly to the DNA-binding affinity. However, S571A and T600A mutations within HD showed lower affinity for DNA binding. In addition, DNA-binding analysis using embryonic nuclear protein also demonstrates that Vnd interacts with other nuclear proteins, suggesting the existence of Vnd as a complex.

• BMB Reports
• /
• v.36 no.3
• /
• pp.305-311
• /
• 2003

A modified actinomycin D was prepared with a hydroxyl group that replaced the amino group at the chromophore 2-position, a substitution known to strongly reduce affinity for double-stranded DNA. Interactions of the modified drug on single-stranded DNAs of the defined sequence were investigated. Competition assays showed that 2-hydroxyactinomycin D has low affinity for two oligonucleotides that have high affinities ($K_a\;=\;5-10{\times}10^6\;M^{-1}$ oligomer) for 7-aminoactinomycin D and actinomycin D. Primer extension inhibition assays performed on several single-stranded DNA templates totaling around 1000 nt in length detected a single high affinity site for 2-hydroxyactinomycin D, while many high affinity binding sites of unmodified actinomycin D were found on the same templates. The sequence selectivity of 2-hydroxyactinomycin D binding is unusually high and approximates the selectivity of restriction endonucleases. Binding appears to require a complex structure, including residues well removed from the polymerase pause site.

• KSBB Journal
• /
• v.13 no.2
• /
• pp.125-132
• /
• 1998

Protein affinity membrane was prepared via the coating of chitosan gel on the porous flat polysulfone membrane surface, followed by the immobilization f the reactive dye (Cibacron Blue 3GA) to the chitonsan gel. The maximum protein binding capacity of affinity membrane was about 70${\mu}g/cm^2$ determined by the batch adsorption experiments of human serum albumin (HSA). Using module of this membrane, the characteristics of protein chromatography were investigated through the experiments of elution and frontal chromatography of HSA. This membrane module promises as a chromatography column, since it represented a lower pressure drop and a greater reproducibility. The protein separation ratio was significantly influenced by the flow rate of mobile phase and the injection quantity of HSA. The dynamic protein binding capacity of module decreased from the equilibrium binding capacity with increasing flow rate and approached the value of 15 - 20 ${\mu}g/cm^2$ for flow rates above 6 mL/min.

• KSBB Journal
• /
• v.14 no.4
• /
• pp.396-402
• /
• 1999

To verify enchancing effect of polycation of polycation on the retroviral infecivity, we directly measured the binding affinity of retroviruses to the target cells in the presence or in the absence of polybrene with R18 fluorescence assay and examined the effect of the polymers on the relationship between the host cell and the retroviral infecity. There was no difference in the effect of the types of charge of the polymer on the binding affinity. However, polycations, in general, show effect on the retrovirus infecity. This results suggest that the enhancing effect of polybrene and other polycations on the infecity is not due to the binding step but due to the post-binding steps, especially the internalization step. With the result of the internalization of FITC-labeled poly-L-lysine into the host cells, it is suggested that the uptake of polycations into the host cells would play a crucial role in the intermalization of retroviruses.

• Journal of Microbiology
• /
• v.45 no.6
• /
• pp.528-533
• /
• 2007

In a previous study we generated an anti-Hepatitis B Virus (HBV) preS1 humanized antibody (HzKR127) that showed in vivo HBV-neutralizing activity in chimpanzees. However, the antigen-binding affinity of the humanized antibody may not be sufficient for clinical use and thus affinity maturation is required for better therapeutic efficacy. In this study, phage display technique was employed to increase the affinity of HzKR127. All six amino acid residues (Glu95-Tyr96-Asp97-Glu98-Ala99-Tyr100) in the heavy (H) chain complementary-determining region 3 (HCDR3) of HzKR127 were randomized and phage-displayed single chain Fv (scFv) library was constructed. After three rounds of panning, 12 different clones exhibiting higher antigen-binding activity than the wild type ScFv were selected and their antigen-binding specificity for the preS1 confirmed. Subsequently, five ScFv clones were converted to whole IgG and subjected to affinity determination. The results showed that two clones (B3 and A19) exhibited an approximately 6 fold higher affinities than that of HzKR127. The affinity-matured humanized antibodies may be useful in anti-HBV immunotherapy.

• The Korean Journal of Pharmacology
• /
• v.30 no.1
• /
• pp.49-57
• /
• 1994

The binding properties of oxomemazine to muscarinic receptors using the ability of oxomemazine to inhibit $[^3H]QNB$ binding in membrane fractions of rat cerebrum and guinea pig ventricle and ileum were investigated. $[^3H]QNB$ bound to a single class of muscarinic receptors with a dissociation constant of approximately 60 pM in three tissue preparations. Pirenzepine and oxomemazine inhibited $[^3H]QNB$ binding in cerebrum with a Hill coefficient lower than unity, and the inhibition data were best described by a two-site model. The relative densities of the high $(M_1)\;and\;low\;(M_2)$ affinity sites for pirenzepine were 60 and 40%, with corresponding Ki values of 16 and 431 nM, and those $(O_H\;and\;O_L)$ for oxomemazine 40 and 60%, with corresponding Ki values of 80 and 1350 nM. However, the inhibition data of both drugs vs $[^3H]QNB$ in ventricle and ileum appeared to obey the law of mass-action (Hill coefficient close to 1). The apparent Ki values of pirenzepine were 850 and 250 nM, and those of oxomemazine 1460 and 570 nM in ventricle and ileum, respectively. Thus, oxomemazine like pirenzepine has high affinity for cerebrum, moderate affinity for ileum and low affinity for ventricle. These results suggest that oxomemazine could recognize the muscarinic receptor subtypes with a high affinity for the $M_1$ sites.

• YAKHAK HOEJI
• /
• v.28 no.3
• /
• pp.129-138
• /
• 1984

Specific [$^{3}H$] ouabain binding and $Ca^{2+}$ -uptake were measured to elucidate the role of high affinity [$^{3}H$] ouabain binding site in rat cardiac myocytes which contain 65% of rod cells. High affinity [$^{3}$H] ouabain binding site, which is about 3% of total pump sites, with apparent dissociation constant ($K_{D}$) of $1.1{\times}10^{-7}M$ and maximum binding site concentration (Bmax) of 1.2 pmol/mg protein ($1.754{\times}10^{5}cells$) were identified. At the concentration of $10^{-7}M$ to $10^{-4}M$, ouabain produced concentration dependent increase in $Ca^{2+}$-uptake of myocytes. The effect of ouabain on $Ca^{2+}$-uptake was not effected by membrane depolarization (elevated K+ in incubation medium) or verapamil. These results suggest that in rat ventricular myocytes the ouabain receptor complex to high affinity site may increase Na+ - $Ca^{2+}$ exchange across the sarcolemmal membrane by inhibition of Na+, K+ - ATPase.

• Membrane Journal
• /
• v.19 no.2
• /
• pp.113-121
• /
• 2009

Porous affinity chitosan and chitin membranes with good mechanical strength and high protein binding capacity were prepared by using silica particles as porogen. The maximum binding capacity of affinity chitosan membrane for BSA protein is 21.8mg/mL, and that of affinity chitin membrane for lysozyme enzyme is 26.1mg/mL. Chromatographic separations of BSA and lysozyme proteins using the porous affinity chitosan and chitin membranes were performed with change of the flow rate, loading amount and concentration of protein loading solutions. Protein eluted amount and binding yield were calculated from the filtration chromatograms consisted of loading/washing/elution sequences. Protein binding amount and yield were increased with decreasing of flow rate, increasing of loading amount and concentration of protein loading solutions. Those results suggest that the porous chitosan and chitin membranes prepared by using silica particles as porogen are suitable in affinity filtration chromatography for large scale separation of proteins.

• Korean Journal of Pharmacognosy
• /
• v.32 no.3 s.126
• /
• pp.212-218
• /
• 2001

The water extracts of 82 Korean medicinal herbs were prepared and were examined for the binding affinity on the glycine binding site of NMDA (N-methyl-D-aspartate) receptor prepared by the synaptic membranes from the forebrains of male Sprague-Dawley rats. Among the tested, the extracts of Dioscoreae Rhizoma, Hoveniae Semen cum Fructus, Astragali Radix, Armeniacae Semen, Huttuynia cordata Herba, Acanthopanacis Cortex, Aurantii nobilis Pericarpium, Phellinus linteus, Amomi Fructus, Artemisiae capillaris Herba, Polyporus, Agastachis Herba and of Galli Stomachichum Corium were found to exhibit significant competitions with $[^3H]-MDL$ 105,519 for the glycine specific binding site of NMDA receptor in a dose dependent manner, respectively.

• Journal of the Korean Magnetic Resonance Society
• /
• v.20 no.3
• /
• pp.71-75
• /
• 2016

The replication protein A (RPA) plays a crucial role in DNA replication, recombination, and repair. RPA consists of 70, 32 and 14 kDa subunits and has high single-stranded DNA (ssDNA) binding affinity. The largest subunit, RPA70, mainly contributes to bind to ssDNA as well as interact with many cellular and viral proteins. In this study, we performed nuclear magnetic resonance experiments on the complex of the DNA binding domain A of human RPA70 (RPA70A) with ssDNA, d(CCCCC), at various pH, to understand the effect of pH on the ssDNA binding of RPA70A. The chemical shift perturbations of binding residues were most significant at pH 6.5 and they reduced with pH increment. This study provides valuable insights into the molecular mechanism of the ssDNA binding of human RPA.