Lanthanide labeling offers fast NMR approach to 3D structure determinations of protein-protein complexes

A novel nuclear magnetic resonance (NMR) strategy based on labeling with lanthanides achieves rapid determinations of accurate three-dimensional (3D) structures of protein-protein complexes. The method employs pseudocontact shifts (PCS) induced by a site-specifically bound lanthanide ion to anchor the coordinate system of the magnetic susceptibility tensor in the molecular frames of the two molecules. Simple superposition of the tensors detected in the two protein molecules brings them together in a 3D model of the protein-protein complex. The method is demonstrated with the 30 kDa complex between two subunits of Escherichia coli polymerase III, comprising the N-terminal domain of the exonuclease subunit epsilon and the subunit theta. The 3D structures of the individual molecules were docked based on a limited number of PCS observed in 2D 15N-heteronuclear single quantum coherence spectra. Degeneracies in the mutual orientation of the protein structures were resolved by the use of two different lanthanide ions, Dy3+ and Er3+.     

Gradient symplectic algorithms for solving the radial Schrodinger equation

The radial Schrodinger equation for a spherically symmetric potential can be regarded as a one-dimensional classical harmonic oscillator with a time-dependent spring constant. For solving classical dynamics problems, symplectic integrators are well known for their excellent conservation properties. The class of gradient symplectic algorithms is particularly suited for solving harmonic-oscillator dynamics. By use of Suzuki's rule [Proc. Jpn. Acad., Ser. B: Phys. Biol. Sci. 69, 161 (1993)] for decomposing time-ordered operators, these algorithms can be easily applied to the Schrodinger equation. We demonstrate the power of this class of gradient algorithms by solving the spectrum of highly singular radial potentials using Killingbeck's method [J. Phys. A 18, 245 (1985)] of backward Newton-Ralphson iterations.     

Photoluminescence from C60-coupled porous structures formed on Fe+-implanted silicon

111-oriented p-type Si wafer with a resistivity of 1-5 Omega cm was implanted with Fe+ and then annealed at 1100 degrees C in N2 for 60 min, followed by anodization in a solution of HF to form porous structure with beta-FeSi2 nanocrystallites. Photoluminescence (PL) spectral measurements show that a strong PL peak appears in the range of 610-670 nm. The position of the PL peak remains unchanged, but its intensity increases with the storage time in air until about three months and then saturates. C60 molecules were chemically coupled on the porous structure through a kind of silane coupling agent to form a nanocomposite. It is revealed that the stable PL peak monotonically shifts to a pinning wavelength at 570 nm. Experimental results from PL, PL excitation, Raman scattering, and x-ray diffraction measurements clearly show that the pinned PL originates from optical transition in C60-related defect states, whereas the photoexcited carriers occur in the beta-FeSi2 nanocrystallites formed during anodization. This work opens a new way to tailor nanometer environment for seeking optimal luminescent properties.     

Analysis of cold denaturation mechanism of β‐lactoglobulin and comparison with thermal denaturation from Raman spectroscopy investigations

Cold‐ and heat‐induced β‐lactoglobulin (BLG) transformations have been analyzed in the presence of 4 M urea, from Raman spectroscopy investigations carried out simultaneously in the low wavenumber range (10–400 cm⁻¹) and in the amide I region (1500–1800 cm⁻¹). These investigations show common features between the denaturation processes at low and high temperatures. The denatured states are reached via an intermediate state characterized by a soft tertiary structure without detectable conformational changes. This intermediate is intimately connected with a tetrahedral hydrogen‐bond structure of water which extends over a limited range. It is shown that the disruption of the hydrogen‐bond network of D₂O has an important consequence on the solvent dynamics, which controls protein dynamics and is characterized by an anharmonic behavior. By monitoring the amide I mode, conformational changes are detected at low temperature (below 5 °C) and determined to be similar to those detected at high temperature in the presence of urea near 65 °C, and in the absence of urea near 80 °C. The conformational changes are described as a loss of α‐helix structures and a concomitant formation of β‐sheets. The temperature dependence of the amide I wavenumber in BLG dissolved in the 4 M urea aqueous solution was interpreted on the basis of a two‐state model, leading to the protein stability curve related to its molecular conformation. Copyright © 2011 John Wiley & Sons, Ltd.     

Riesz basis property of the generalized eigenvector system of a Timoshenko beam

The Riesz basis property of the generalized eigenvector system of a Timoshenko beam with boundary feedback controls appliedto two ends is studied in this paper. The spectral property of the operator A determined by the closed loop system is investigated.It is shown that operator A has compact resolvent and generatesa C₀ semigroup, and its spectrum consistsof two branches and has two asymptotes under some conditions.Furthermore it is proved that the sequence of all generalizedeigenvectors of the system principal operator forms a Rieszbasis for the state Hilbert space.     

Identification of p-Coumaric Acid and Ethyl p-Coumarate as the Main Phenolic Components of Hemp (Cannabis sativa L.) Roots

Hemp (Cannabis sativa L.) contains a variety of secondary metabolites, including cannabinoids, such as psychoactive (−)-trans-Δ⁹-tetrahydrocannabinol. The present study was conducted to identify the major phenolic components contained in hemp root, which has been relatively under-researched compared to other parts of hemp. The aqueous ethanol extract of hemp roots was fractionated into methylene chloride (MC), ethyl acetate (EA), and water (WT) fractions, and high-performance liquid chromatography with photodiode array detection (HPLC-DAD) analysis was performed. The main ultraviolet (UV)-absorbing phenolic compound contained in the EA fraction was identified as p-coumaric acid by comparing the retention time and UV absorption spectrum with a standard. Silica gel column chromatography was performed to isolate a hydrophobic derivative of p-coumaric acid contained in the MC fraction. Nuclear magnetic resonance (NMR) analysis identified the isolated compound as ethyl p-coumarate. For comparative purposes, ethyl p-coumarate was also chemically synthesized by the esterification reaction of p-coumaric acid. The content of p-coumaric acid and ethyl p-coumarate in the total extract of hemp root was estimated to be 2.61 mg g⁻¹ and 6.47 mg g⁻¹, respectively, by HPLC-DAD analysis. These values correspond to 84 mg Kg⁻¹ dry root and 216 mg Kg⁻¹ dry root, respectively. In conclusion, this study identified p-coumaric acid and ethyl p-coumarate as the main phenolic compounds contained in the hemp roots.     

Inhibition of Ampicillin-resistance in Bacteria by Modified DNAzymes

To overcome ampicillin-resistance of bacteria which is believed to attribute their endogenous B-lactamase, we designed three 10-23 DNAzymes（Dz1, Dz2. Dz3） targeting the coding region of B-lactamase mRNA and examined their inhibitory capabilities of the ampicillin-resistance of TEM-1 and TEM-3 bacteria. Dz1 was a traditional 10-23 DNAzyme, Dz2 was the mutant of Dz1 by addition of the protected nucleotide to each ann of the enzyme, and Dz3 was a mutant of Dz1 at antisense arms of which phosphorothioate modifications were made. Kinetic analysis, bacterial growth, and β-lactamase activity measurement showed that all the three DNAzymes worked efficiently in vitro and in vivo. A 9 hours bacterial growth inhibition test showed that the inhibition rates of TEM-1 bacteria by Dz1, Dz2, and Dz3 were 27%, 50%, and 29%, respectively. In addition, the inhibition rates of TEM-3 bacteria by those three DNAzymes were found io be 49%, 58%, and 45%, respectively. The current findings suggest that DNAzymes may become potential candidates of alternative inhibitors for bacteria drug-resistance.     

The Anti-Inflammatory Activities of Fermented Curcuma That Contains Butyrate Mitigate DSS-Induced Colitis in Mice

Inflammatory bowel disease is characterized by a radical imbalance of inflammatory signaling pathways in the gastrointestinal tract, and it is categorized into two diseases, such as Crohn’s disease and ulcerative colitis. In this study, we investigated anti-inflammatory activities using fermented Curcuma that contains butyrate (FB). Nitric oxide production in RAW 264.7 cells and the expression of inducible nitric oxide synthase in the intestinal mucosa appears to be enhanced in active ulcerative colitis. Here, the cytotoxicity, physiological activity, and anti-inflammatory efficacy of FB in colitis animals were investigated. To verify the anti-inflammatory effect, this study was conducted using the dextran sulfate sodium (DSS)-induced colitis mice model. As a result, non-toxicity was confirmed, and anti-inflammatory effects were revealed by inducing a reduction of LPS-induced NO production. In the DSS-induced colitis, reduced weight was recovered and a decrease in inflammatory factors Ig-E and TNF-α in the mesenteric lymph node (MLN) and spleen was induced, and it was confirmed to help with the morphological remodeling of the intestine. In conclusion, this paper suggests that FB can help to alleviate intestinal inflammation and to improve the intestinal environment, with the help of morphological remodeling.     

Hesperidin Exhibits Protective Effects against PM2.5-Mediated Mitochondrial Damage,Cell Cycle Arrest,and Cellular Senescence in Human HaCaT Keratinocytes

Particulate matter 2.5 (PM_2.5) exposure can trigger adverse health outcomes in the human skin, such as skin aging, wrinkles, pigment spots, and atopic dermatitis. PM_2.5 is associated with mitochondrial damage and the generation of reactive oxygen species (ROS). Hesperidin is a bioflavonoid that exhibits antioxidant and anti-inflammatory properties. This study aimed to determine the mechanism underlying the protective effect of hesperidin on human HaCaT keratinocytes against PM_2.5-induced mitochondrial damage, cell cycle arrest, and cellular senescence. Human HaCaT keratinocytes were pre-treated with hesperidin and then treated with PM_2.5. Hesperidin attenuated PM_2.5-induced mitochondrial and DNA damage, G₀/G₁ cell cycle arrest, and SA-βGal activity, the protein levels of cell cycle regulators, and matrix metalloproteinases (MMPs). Moreover, treatment with a specific c-Jun N-terminal kinase (JNK) inhibitor, SP600125, along with hesperidin markedly restored PM_2.5-induced cell cycle arrest and cellular senescence. In addition, hesperidin significantly reduced the activation of MMPs, including MMP-1, MMP-2, and MMP-9, by inhibiting the activation of activator protein 1. In conclusion, hesperidin ameliorates PM_2.5-induced mitochondrial damage, cell cycle arrest, and cellular senescence in human HaCaT keratinocytes via the ROS/JNK pathway.