• Mass Spectrometry Letters
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• v.2 no.2
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• pp.49-52
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• 2011

Competitive binding of $C_{60}$ and $C_{70}$ to meso-substituted porphyrins was studied by mass spectrometry (MS). Electrospray ionization MS was employed to acquire the mass spectra of 1 : 1 porphyrin-fullerene complexes formed in a mixture of mesosubstituted porphyrin and fullerite to determine the ratio of complexes between $C_{60}$ and $C_{70}$. Matrix-free laser desorption ionization MS was used to obtain the mass spectra of fullerite to measure the mole fraction of $C_{60}$ and $C_{70}$. The binding constant ratio ($K_{70}$/$K_{60}$) was determined from the mass spectral data. The difference in standard Gibbs free energy change, ${\Delta}({\Delta}G^o)_{70-60}$, for the competitive binding of $C_{60}$ and $C_{70}$ was calculated from $K_{70}$/$K_{60}$. Of the five porphyrins, tetraphenyl, tetra(4-pyridyl), tetra(4-carboxyphenyl), tetra(3,5-di-tert-butylphenyl), and tetra(pentafluorophenyl) porphyrins, the first three non-bulky porphyrins yield negative values of ${\Delta}({\Delta}G^o)_{70-60}$, whereas the other two bulky porphyrins result in positive values of ${\Delta}({\Delta}G^o)_{70-60}$. This result indicates that $C_{70}$ binding to porphyrin is thermodynamically favored over $C_{60}$ binding in non-bulky porphyrins, but disfavored in bulky ones. It also suggests that the binding mode of $C_{70}$is different between non-bulky and bulky porphyrins, which is in line with previous experimental findings of the "side-on" binding to non-bulky porphyrins and the $C_{60}$-like "end-on" binding to bulky porphyrins.

• Restorative Dentistry and Endodontics
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• v.22 no.1
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• pp.170-180
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• 1997

Cariogenicity of the bacteria is attributed to their binding capacity to the teeth. Bacterial attachment to oral surfaces is an essential step for colonization and subsequently infection. Therefore, it is conceivable that caries prevention can be achieved fundamentally by inhibition of bacterial attachment. The rationale for caries prevention through the use of sugar substitutes or limited use of sugar has been revealed. Among many sugar substitutes, xylitol has been shown to exhibit the most profound cariostatic effect, inhibiting glucose metabolism and possibly binding of mutans streptococci. The purpose of this study was to examine the effect of xylitol on binding of different species of oral bacteria. The effect of xylitol on binding of [$^3H$]-labeled oral bacteria to hydroxyapatite coated with human saliva(SHA) as a model for the pellicle-coated tooth surfaces was investigated. The strains of oral bacteria used in this study were A. viscosus T14V, A. viscosus WVU627, P. gingivaiis 2561, P. gingivalis A7Al-28, S. gordonii G9B, S. gordonii Challis, S. sobrinus 6715, S. mutans UA101, S. mutans KPSK -2, S. mutans T8, and S. mutans UA130. The obtained results were as follows: 1. P. gingivalis A7 Al-28, S. mutans UA130, S. mutans T8 grown with xylitol showed greater binding to SHA than the organism grown without xylitol. Among these, S. mutans T8 showed the greatest rate of increase in its binding to SHA ; 8-fold increase in its binding with xylitol. 2. S. mutans KPSK -2 grown with xylitol showed 2 times lesser binding to SHA than the organism grown without xylitol. 3. Binding ability of the remaining strains grown with xylitol to SHA was almost same as that of the organisms grown without xylitol. The overall results suggest that use of xylitol in the oral cavity may affect the complex oral bacterial ecosystem.

• Animal cells and systems
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• v.2 no.1
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• pp.117-122
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• 1998

D-raf, a Drosophila homolog of the human c-raf-1, is known as a signal transducer in cell proliferation and differentiation. A previous study found that the D-raf gene expression is regulated by the DNA replication-related element (DRE)/DRE-binding factor (DREF) system. In this study, we found the sequences homologous to transcription factor C/EBP, MyoD, STAT and Myc recognition sites in the D-raf promoter. We have generated various base substitutional mutations in these recognition sites and subsequently examined their effects on D-raf promoter activity through transient CAT assays in Kc cells with reporter plasmids p5'-878DrafCAT carrying the mutations in these binding sites. Through gel mobility shift assay using nuclear extracts of Kc cells, we detected factors binding to these recognition sites. Our results show that transcription factor C/EBP, STAT and Myc binding sites in D-raf promoter region play a positive role in transcriptional regulation of the D-raf gene and the Myo D binding site plays a negative role.

• BMB Reports
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• v.29 no.3
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• pp.205-209
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• 1996

To investigate the role of heparin in keratinocyte growth factor (KGF) and acidic fibroblast growth factor (aFGF) high affinity binding to the KGF receptor (KGFR), a cell free system was established which utilized a secreted chimeric molecule between the KGFR extracellular domain and the immunoglobulin heavy chain Fc domain (KGFR-HFc). KGFR-HFc was purified from NIH 3T3 cells and demonstrated the binding of $[^3H]-heparin$ as well as heparin Sepharose. Scatchard analysis showed that the dissociation constant for heparin binding to KGFR-HFc was 140 nM. High affinity KGF and aFGF binding to KGFR-HFc remained unchanged after treatment with 0.6 M NaCl, which is the concentration sufficient to release any bound heparin to the KGFR-HFc. These results strongly suggest that although the KGFR interacts with heparin, the presence of heparin is not absolutely required for high affinity binding of either KGF or aFGF to the KGFR.

• Textile Coloration and Finishing
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• v.9 no.3
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• pp.27-32
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• 1997

Two poly(4-vinylpyridines) having different degree of crosslinking were prepared by radical copolymerization of 4-vinylpyridine with N, N'-tetramethylenebis-acrylamide as a crosslinker. The abilities of these crosslinked polymers to bind acid dyes (methyl orange, ethyl orange, and propyl orange) were investigated at various temperatures in ethylene glycol as the binding medium. From the equilibrium amounts, the first binding constants and thermodynamic parameters for the bindings were evaluated. The first binding constants and thermodynamic parameters were not varied with these dyes. This result indicates that there is no hydrophobic interaction between the crosslinked polymers and the dyes in ethylene glycol. However, the first binding constants showed bell-shaped curves againtst the binding temperatures. This result could be explained in terms of the crosslinked hole size with temperature variation.

• Interdisciplinary Bio Central
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• v.2 no.2
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• pp.6.1-6.5
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• 2010

Fragment molecular orbital (FMO) method provides a novel tool for ab initio calculations of large biomolecules. This method overcomes the size limitation difficulties in conventional molecular orbital methods and has several advantages compared to classical force field approaches. While there are many features in this method, we here focus on explaining the issues related to protein-ligand binding: FMO method provides useful interaction-analysis tools such as IFIE, CAFI and FILM. FMO calculations can provide not only binding energies, which are well correlated with experimental binding affinity, but also QSAR descriptors. In addition, FMO-derived charges improve the descriptions of electrostatic properties and the correlations between docking scores and experimental binding affinities. These calculations can be performed by the ABINIT-MPX program and the calculation results can be visualized by its proper BioStation Viewer. The acceleration of FMO calculations on various computer facilities is ongoing, and we are also developing methods to deal with cytochrome P450, which belongs to the family of drug metabolic enzymes.

• BMB Reports
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• v.47 no.9
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• pp.518-523
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• 2014

The maternal transcription factor Dorsal (Dl) functions as both an activator and a repressor in a context-dependent manner to control dorsal-ventral patterning in the Drosophila embryo. Previous studies have suggested that Dl is an intrinsic activator and its repressive activity requires additional corepressors that bind corepressor-binding sites near Dl-binding sites. However, the molecular identities of the corepressors have yet to be identified. Here, we present evidence that Capicua (Cic) is involved in Dl-mediated repression in the zerkn$\ddot{u}$llt (zen) ventral repression element (VRE). Computational and genetic analyses indicate that a DNA-binding consensus sequence of Cic is highly analogous with previously identified corepressor-binding sequences and that Dl failed to repress zen expression in lateral regions of cic mutant embryos. Furthermore, electrophoretic mobility shift assay (EMSA) shows that Cic directly interacts with several corepressor-binding sites in the zen VRE. These results suggest that Cic may function as a corepressor by binding the VRE.

• Journal of Microbiology and Biotechnology
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• v.9 no.3
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• pp.361-364
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• 1999

The binding characteristics of Anagrapha falcifera nuclear polyhedrosis virus (AtNPV) to Spodoptera frugiperda 21 (Sf21) cells were investigated. The cells displayed an affinity of 4.7×10/sup 10/M/sup -1/ with about 3,300 binding sites per cell. The biochemical nature of the AfNPV-binding sites on the cell surface was also partially identified. Our findings suggest that the binding-site moiety has a glycoprotein component, but that the direct involvement of oligosacccharides containing N-acetylglucosamine or sialic acid residues in binding is unlikely, and that AfNPV entry into Sf21 cells may be via receptor-mediated endocytosis.

• Mass Spectrometry Letters
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• v.6 no.3
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• pp.80-84
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• 2015

Here, we demonstrate the use of MALDI-TOF as a fast and simple analytical approach to evaluate the DNA-binding capability of various peptides. Specifically, by varying the amino acid sequence of the peptides consisting of lysine (K) and tryptophan (W), we identified peptides with strong DNA-binding capabilities using MALDI-TOF. Mass spectrometric analysis reveals an interesting novel finding that lysine residues show sequence selective preference, which used to be considered as mediator of electrostatic interactions with DNA phosphate backbones. Moreover, tryptophan residues show higher affinity to DNA than lysine residues. Since there are numerous possible combinations to make peptide oligomers, it is valuable to introduce a simple and reliable analytical approach in order to quickly identify DNA-binding peptides.

• Molecules and Cells
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• v.20 no.2
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• pp.297-302
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• 2005

The integrity and proper functioning of telomeres require association of telomeric DNA sequences with specific binding proteins. We have characterized PLP-1, a $PUR{\alpha}$ homolog encoded by F45E4.2, which we previously identified as a candidate double stranded telomere binding protein, by affinity chromatography followed by mass spectrometry. PLP-1 bound double-stranded telomeric DNA in vitro as shown by competition assays. Core binding was provided by the third and fourth nucleotides of the TTAGGC telomeric repeat. This is quite different from the binding sequence of CEH-37, another C. elegans telomere binding protein, suggesting that multiple proteins may bind nematode telomeric DNA simultaneously in vivo.