Phylogenetic analysis and homology modelling of <Emphasis Type=Italic>Paracentrotus lividus</Emphasis> nectin

The extracellular matrix protein Pl-nectin, a 210-kDa homodimer originally purified from sea urchin eggs, plays a crucial role in cell adhesion and embryonic morphogenesis. The compiled cDNA sequence, obtained by RT-PCR primer walking and 3′ RACE, identified a 984aa product containing a 23aa signal peptide and including all six internal peptides identified by protein microsequencing. The protein is a new member of the galactose-binding protein superfamily as it consists of six 151–156aa-long tandemly repeated domains (D1–D6), homologous to the discoidin-like domains, also known as F5/8-type C domains. Based on homology modelling, we present a three-dimensional structure (3D) for D5, identified as the prototype domain. The molecular modelling of the assembled Pl-nectin homodimer accounts for a Pl-nectin quaternary structure composed of two 105-kDa C-shaped monomers linked by a S–S bridge. The presence of an LDT motif between the first and the second exposed loops of the D2 domain suggests the binding of Pl-nectin to an integrin receptor. Altogether, the in silico analysis described here is consistent with previous biochemical reports and offers a basis for predictions to be experimentally tested.     

Adsorption of thiolates to singly coordinated sites on Au111 evidenced by photoelectron diffraction

The adsorption structure of methylthiolate (CH3S) adsorbed on Au(111), a long-standing controversial issue, has been unambiguously determined by scanned-energy and scanned-angle S 2p photoelectron diffraction. The methylthiolate molecules are found to occupy atop sites with a S-Au distance of 2.42 +/- 0.03 A. The angular distribution of the S 2p photoelectrons due to forward scattering reveals that the S-C bond is inclined by approximately 50 degrees from the surface normal towards both the [211] and [121] (nearest-neighbor thiolate) directions.     

Excimer Fluorescence as a Tool for Monitoring Protein Domain Dynamics Applied to Actin Conformation Changes Based on Circulary Polarized Fluorescence Spectroscopy

Fluorescence-detected circular dichroism (FDCD) was introduced into the study of protein conformation changes. Actin was used as a model protein which undergoes dynamic conformation changes as it polymerizes. Actin labeled with N-(1-pyrene)iodoacetamide (PIA) showed monomer fluorescence peak at 386 and 410 nm, and excimer fluorescence peak at around 480 nm. Excimer was formed by PIA-dimers labeled to different sites of amino acid residues. New information concerned with actin structural changes were monitored by fluorescence emission spectra excited with left- and right-circulary polarized light at 355 nm. FDCD intensities were shown as the difference in the fluorescence emission ΔF, where ΔF=(F _L−F _R)/(F _L+F _R) denoting F _L and F _R as emissions obtained by excitation with left- and right-circulary polarized light. When solvent conditions of PIA-actin were changed by addition of NaCl, TFE, or ATP, ΔF showed sensitive responses to these compounds. From the analysis of ΔF _M and ΔF _E which represent the peaks of ΔF at the monomer- and excimer-emission band, the information concerned with the actin intrastructural changes were obtained. This method based on monitoring the excimer fluorescence with FDCD could be used for other proteins to extract finer structural changes that cannot be detected by the normal fluorescence spectroscopy.     

Stability of all-trans-β-carotene under ultrasound treatment in a model system: Effects of different factors,kinetics and newly formed compounds

The effects of factors and kinetics of all-trans-β-carotene degradation under ultrasound treatment in a model system were investigated. The compounds of degradation were also tentatively identified by HPLC-DAD, Raman and FT-IR spectroscopy. The type of solvents and temperature were important factors in determining the degradation reaction. Liquid height, ultrasonic intensity and duty cycle of ultrasound exposure only affected the rate of degradation but did not change the nature of degradation. Degradation rate of β-carotene in dichloromethane was the highest. Degradation rate of β-carotene decreased with increasing of temperature. Degradation kinetics of all-trans-β-carotene under ultrasound fitted first-order reaction at ?5 to 15 °C, and fitted second-order reaction at 25 °C. Degradation products included isomers: 15-cis-β-carotene, di-cis-β-carotene and other compounds with function group of C–O.     

Design of sugar–oligonucleotide conjugates installed gold nanoparticle for effective delivery to hepatic parenchymal cells

A novel oligonucleotide delivery system that is based on oligonucleotide–nanoparticle conjugates has been described. Installed oligonucleotides were modified with the carbohydrate at the 3′ terminus, accordingly, constructed nanoparticles display clustered carbohydrates on their outer layer for the targeted delivery of oligonucleotides. The method for the construction of ligand-functionalized nanoparticle was simple and reproducible. The stability of the nanoparticles displaying clustered carbohydrates greatly increased in serum compared to nanoparticles without carbohydrates. In order to investigate the targetability of oligonucleotide–nanoparticle conjugates into primary hepatic parenchymal cells, freshly isolated rat hepatocytes were incubated with nanoparticles and the amount of internalized gold nanoparticles was evaluated by an inductively coupled plasma mass spectroscopy analysis. Nanoparticles displaying clustered carbohydrates internalized more efficiently than nanoparticles without carbohydrate modifications. In particular, the cellular uptakes of oligonucleotide-conjugated gold nanoparticle increased 1.7 ～2.0-fold by galactose modification. Competition assay revealed that clustered galactose enhanced the internalization of the nanoparticle into primary hepatic parenchymal cells by a receptor-mediated process.

The number of labeled graphs placeable by a given permutation

Let S be a finite set and σ a permutation on S. The permutation σ* on the set of 2-subsets of S is naturally induced by σ. Suppose G is a graph and V(G), E(G) are the vertex set, the edge set, respectively. Let V(G) = S. If E(G) and σ*(E(G)), the image of E(G) by σ*, have no common element, then G is said to be placeable by σ. This notion is generalized as follows. If any two sets of {E(G), (σ¹)*(E(G)),…,(σ^l−1)* (E(G))} have no common element, then G is said to be I-placeable by σ. In this paper, we count the number of labeled graphs which are I-placeable by a given permutation. At first, we introduce the interspaced Ith Fibonacci and Lucas numbers. When I = 2 these numbers are the ordinary Fibonacci and Lucas numbers. It is known that the Fibonacci and Lucas numbers are rounded powers. We show that the interspaced Ith Fibonacci and Lucas numbers are also rounded powers when I = 3. Next, we show the number of labeled graphs which are I-placeable by a given permutation is a product of the interspaced Ith Lucas numbers. Finally, using a property of the generalized binomial series, we count the number of labeled graphs of size k which are I-placeable by σ. © 1996 John Wiley & Sons, Inc.     

Study of the thermal degradability of poly(α-methylstyrene) with modified end groups

To induce degradabilities in polymers in response to environmental conditions, endm odification reactions of poly(α-methylstyrene) (PMS) derivatives were carried out. 2-Phenylallyl halide derivatives such as 2-phenylallyl bromide, 2-(p-tolyl)allyl bromide, and α-trifluoromethylstyrene were found to be suitable end-modification agents. For example, the ω-2-phenylallyl-PMS derivative was prepared with almost quantitative functionality by the reaction of the living PMS derivative with 2-phenylallyl bromide. In a similar way, ω-3,3-difluoro-2-phenylallyl- and ω-2-(4-toly)allyl-PMS derivatives were synthesized. Based on thermogravimetric analysis, the onset of the degradation temperature of the endmodified PMS derivatives decreased in the following order: ω-hydrogen- > ω-3,3-difluoro-2-phenylallyl- > ω-2-phenylallyl- > ω-2-(p-tolyl)allyl-PMS. Actually, the onset temperature of ω-2-(p-tolyl)allyl-PMS derivatives was 50°C lower than that of ω-H-PMS derivatives. These results indicate that the active species is produced effectively at the endunsaturated bond, which initiates depolymerization of the polymer at rather low temperatures. Therefore, it is concluded that a 2-phenylallyl substituent at the end of the PMS chain induces effective degradation through a radical mechanism.     

Relaxation spectrometry in solid polymers based on NMR and EPR measurements

Wide distribution of relaxation times is taken into consideration in determination of the activation energy of the molecular motion associated with the motional narrowings of line widths of magnetic resonance spectra. The molecular motion of rotational vibration around the chain axis of polyethylene in urea-polyethylene inclusion complex is examined. Relaxation spectra can be obtained from the data of the motional narrowings of EPR and NMR by assuming the activation energy as a parameter. Also, the representative relaxation times corresponding to EPR and NMR observations can be estimated. These relaxation times give us an activation energy since EPR and NMR observations correspond to different time constants of observations. The activation energy estimated from the data of the representative correlation times is identical with the activation energy obtained as a parameter in determination of the identical relaxation spectrum from the data of motional narrowings of EPR and NMR observations.     

Ni-catalyzed hydroboration and hydrosilylation of olefins with diboron and silylborane

Herein we report a Ni-catalyzed formal hydroboration of olefins, which afforded anti-Markovnikov-type alkylboranes with B₂pin₂ and a stoichiometric amount of water. Formal hydrosilylation using air- and moisture-sensitive silylboranes also proceeded under optimized conditions. The reaction with trans-stilbene and D₂O resulted in 1,2-H migration, which suggested that the reaction proceeded via β-hydride elimination and reinsertion mechanisms.