Protein family classification and functional annotation

With the accelerated accumulation of genomic sequence data, there is a pressing need to develop computational methods and advanced bioinformatics infrastructure for reliable and large-scale protein annotation and biological knowledge discovery. The Protein Information Resource (PIR) provides an integrated public resource of protein informatics to support genomic and proteomic research. PIR produces the Protein Sequence Database of functionally annotated protein sequences. The annotation problems are addressed by a classification-driven and rule-based method with evidence attribution, coupled with an integrated knowledge base system being developed. The approach allows sensitive identification, consistent and rich annotation, and systematic detection of annotation errors, as well as distinction of experimentally verified and computationally predicted features. The knowledge base consists of two new databases, sequence analysis tools, and graphical interfaces. PIR-NREF, a non-redundant reference database, provides a timely and comprehensive collection of all protein sequences, totaling more than 1,000,000 entries. iProClass, an integrated database of protein family, function, and structure information, provides extensive value-added features for about 830,000 proteins with rich links to over 50 molecular databases. This paper describes our approach to protein functional annotation with case studies and examines common identification errors. It also illustrates that data integration in PIR supports exploration of protein relationships and may reveal protein functional associations beyond sequence homology.     

Entropic barriers in nanoscale adhesion studied by variable temperature chemical force microscopy

Intermolecular interactions drive the vast majority of condensed phase phenomena from molecular recognition to protein folding to particle adhesion. Complex energy barriers encountered in these interactions include contributions from van der Waals forces, hydrogen bonding, and solvent medium. With the spectacular exception of hydrophobic interactions, contributions from the medium are usually considered secondary. We report a variable temperature force microscopy study of the interactions between several hydrogen bonds in different solvents that challenges this point of view. Surprisingly, we observed an increase in the strength of the interaction between carboxylic acid groups in ethanol as the temperature increased. Moreover, when we switched to a nonpolar solvent we observed the opposite behavior: The binding force decreased as the temperature increased. Kinetic model of bond dissociation provided quantitative interpretation of our measurements. We attributed the observed phenomena to a large entropic contribution from the ordered solvent layers that are forming on the probe and sample surfaces upon detachment. The observed reversal in the force vs temperature trend is a manifestation of a transition between thermodynamic and kinetic regimes of unbinding predicted by the model. Our results indicate that entropic barriers dominated by the interactions of solvent molecules with the surface exist in a much wider variety of systems than previously thought.     

Synthesis, stereochemistry confirmation and biological activity evaluation of a constituent from Isodon excisus

A synthesis and stereochemistry confirmation of a constituent recently isolated from the whole plant Isodon excisus is reported. An enantioselective catalytic boron-mediated reduction of an α-bromoketone was utilized in the key synthetic transformation. The methodology described herein was also used for the synthesis of the natural product's enantiomer and several derivatives. In addition, the compounds were evaluated for inhibitory activity in a caspase induction assay. The natural product was found to be devoid of activity, but several derivatives had moderate inhibitory activity (EC₅₀<1 μM).     

Synthesis and Cytotoxicity Evaluation of Metal‐Chelator‐Bearing Flavone,Carbazole, Dibenzofuran,Xanthone, and Anthraquinone

2‐(Aryloxymethyl)‐5‐benzyloxy‐1‐methyl‐1H‐pyridin‐4‐ones 8a – 8g , 2‐(aryloxymethyl)‐5‐hydroxy‐4H‐pyran‐4‐ones 9a – 9g , and 2‐(aryloxymethyl)‐5‐hydroxy‐1‐methyl‐1H‐pyridin‐4‐ones 10a – 10g were prepared from the known 5‐benzyloxy‐2‐(hydroxymethyl)pyran‐4‐one ( 3 ) in a good overall yield. These compounds were evaluated in vitro against a three‐cell lines panel consisting of MCF7 (breast), NCI‐H460 (lung), and SF‐268 (CNS), and the active compounds passed on for evaluation in the full panel of 60 human tumor cell lines derived from nine cancer cell types. The results indicated that 5‐hydroxy derivatives are more favorable than their corresponding 5‐benzyloxy precursors ( 10a – 10g vs. 8a – 8g ), and 1‐methyl‐1H‐pyridin‐4‐ones are more favorable than their corresponding pyran‐4(1H)‐ones ( 10a – 10g vs. 9a – 9g ). Among these three types of compounds, 2‐(aryloxymethyl)‐5‐hydroxy‐1‐methyl‐1H‐pyridin‐4‐ones 10a – 10g were the most cytotoxic; they inhibited the growth of almost all the cancer cells tested. On the contrary, compound 8a (a mean GI₅₀=27.8 μM ), 8b (38.5), 8d (11.0), and 8e (30.5) are especially active against the growth of SK‐MEL‐5 (a melanoma cancer cell) with a GI₅₀ of <0.01, 5.65, 0.55, and 0.03 μM , respectively (cf. Table 2).     

A new ruthenium-catalyzed hydrogen-transfer reaction: transformation of 3-benzyl but-1-ynyl ethers into 1,3-dienes and benzaldehyde

We report a ruthenium-catalyzed reaction for various 3-benzyl but-1-ynyl ethers with suitable functionalities. Treatment of these substrates with TpRu(PPh3)(CH3CN)2PF6 (8.0 mol %) catalyst in 1,2-dichloroethane (80 degrees C, 12 h) afforded functionalized 1,3-dienes and benzyl aldehyde in good yields. This process is considered to be a tandem dealkoxylation and transfer hydrogenation. Deuterium-labeling experiments reveal that the migration of different hydrogen atoms proceeds regiospecifically. A plausible mechanism is proposed on the basis of the results of isotope experiment.     

Effect of Surface‐Hydroxylated CdS Nanoparticles on the Morphological Transformation of Polystyrene‐block‐Poly(ethylene oxide) Thin Films

Summary: Polystyrene‐block‐poly(ethylene oxide) (SEO) block copolymer thin films, in which CdS clusters have been sequestered into the PEO domains of the SEO block copolymers, are found to induce the morphological transformation of PEO from cylinders to spheres, as shown by using atomic force microscopy (AFM), transmission electron microscopy (TEM), and scanning electron microscopy (SEM). This transformation is caused by the presence of hydrogen‐bonding interactions between surface‐hydroxylated CdS and PEO, as confirmed by nuclear magnetic resonance (NMR) studies.

Morphological transformation of PEO cylinders into CdS/PEO spheres by hydrogen‐bonding interactions between surface‐hydroxylated CdS and PEO.     

Origin of Thermal Degradation of Sr(2-x)Si(5)N(8):Eu(x) Phosphors in Air for Light-Emitting Diodes

The orange-red emitting phosphors based on M(2)Si(5)N(8):Eu (M = Sr, Ba) are widely utilized in white light-emitting diodes (WLEDs) because of their improvement of the color rendering index (CRI), which is brilliant for warm white light emission. Nitride-based phosphors are adopted in high-performance applications because of their excellent thermal and chemical stabilities. A series of nitridosilicate phosphor compounds, M(2-x)Si(5)N(8):Eu(x) (M = Sr, Ba), were prepared by solid-state reaction. The thermal degradation in air was only observed in Sr(2-x)Si(5)N(8):Eu(x) with x = 0.10, but it did not appear in Sr(2-x)Si(5)N(8):Eu(x) with x = 0.02 and Ba analogue with x = 0.10. This is an unprecedented investigation to study this phenomenon in the stable nitrides. The crystal structural variation upon heating treatment of these compounds was carried out using the in situ XRD measurements. The valence of Eu ions in these compounds was determined by electron spectroscopy for chemical analysis (ESCA) and X-ray absorption near-edge structure (XANES) spectroscopy. The morphology of these materials was examined by transmission electron microscopy (TEM). Combining all results, it is concluded that the origin of the thermal degradation in Sr(2-x)Si(5)N(8):Eu(x) with x = 0.10 is due to the formation of an amorphous layer on the surface of the nitride phosphor grain during oxidative heating treatment, which results in the oxidation of Eu ions from divalent to trivalent. This study provides a new perspective for the impact of the degradation problem as a consequence of heating processes in luminescent materials.     

Importance of electroosmotic flow and multiple ionic species on the electrophoresis of a rigid sphere in a charge-regulated zwitterionic cylindrical pore

The influence of electroosmotic flow (EOF) on the electrophoretic behavior of a particle is investigated by considering a rigid sphere in a charge-regulated, zwitterionic cylindrical pore filled with an aqueous solution containing multiple ionic species. This extends conventional analyses to a more general and realistic case. Taking a pore with pK(a) = 7 and pK(b) = 2 (point of zero charge is pH = 2.5) filled with an aqueous NaCl solution as an example, several interesting results are observed. For instance, if pH < 5.5, the particle mobility is influenced mainly by boundary effect, and is influenced by both EOF and boundary effects if pH ≥ 5.5. If pH is sufficiently high, the particle behavior is dominated by EOF, which might alter the direction of electrophoresis. The ratio of (pore radius/particle radius) influences not only the boundary effect, but also the strength of EOF. If the boundary effect is insignificant, the mobility varies roughly linearly with log(bulk salt concentration). These findings are of practical significance to both the interpretation of experimental data and the design of electrophoresis devices.     

Antiproliferation and Induction of Apoptosis in Ca9-22 Oral Cancer Cells by Ethanolic Extract of <em>Gracilaria tenuistipitata</em>

The water extract of Gracilaria tenuistipitata have been found to be protective against oxidative stress-induced cellular DNA damage, but the biological function of the ethanolic extracts of G. tenuistipitata (EEGT) is still unknown. In this study, the effect of EEGT on oral squamous cell cancer (OSCC) Ca9-22 cell line was examined in terms of the cell proliferation and oxidative stress responses. The cell viability of EEGT-treated OSCC cells was significantly reduced in a dose-response manner (p < 0.0001). The annexin V intensity and pan-caspase activity of EEGT-treated OSCC cells were significantly increased in a dose-response manner (p < 0.05 to 0.0001). EEGT significantly increased the reactive oxygen species (ROS) level (p < 0.0001) and decreased the glutathione (GSH) level (p < 0.01) in a dose-response manner. The mitochondrial membrane potential (MMP) of EEGT-treated OSCC cells was significantly decreased in a dose-response manner (p < 0.005). In conclusion, we have demonstrated that EEGT induced the growth inhibition and apoptosis of OSCC cells, which was accompanied by ROS increase, GSH depletion, caspase activation, and mitochondrial depolarization. Therefore, EEGT may have potent antitumor effect against oral cancer cells.     

Insight into the dinuclear {Fe(NO)2}10{Fe(NO)2}10 and mononuclear {Fe(NO)2}10 dinitrosyliron complexes

The reversible redox transformations [(NO)(2)Fe(S(t)Bu)(2)](-) ? [Fe(μ-S(t)Bu)(NO)(2)](2)(2-) ? [Fe(μ-S(t)Bu)(NO)(2)](2)(-) ? [Fe(μ-S(t)Bu)(NO)(2)](2) and [cation][(NO)(2)Fe(SEt)(2)] ? [cation](2)[(NO)(2)Fe(SEt)(2)] (cation = K(+)-18-crown-6 ether) are demonstrated. The countercation of the {Fe(NO)(2)}(9) dinitrosyliron complexes (DNICs) functions to control the formation of the {Fe(NO)(2)}(10){Fe(NO)(2)}(10) dianionic reduced Roussin's red ester (RRE) [PPN](2)[Fe(μ-SR)(NO)(2)](2) or the {Fe(NO)(2)}(10) dianionic reduced monomeric DNIC [K(+)-18-crown-6 ether](2)[(NO)(2)Fe(SR)(2)] upon reduction of the {Fe(NO)(2)}(9) DNICs [cation][(NO)(2)Fe(SR)(2)] (cation = PPN(+), K(+)-18-crown-6 ether; R = alkyl). The binding preference of ligands [OPh](-)/[SR](-) toward the {Fe(NO)(2)}(10){Fe(NO)(2)}(10) motif of dianionic reduced RRE follows the ligand-displacement series [SR](-) > [OPh](-). Compared to the Fe K-edge preedge energy falling within the range of 7113.6-7113.8 eV for the dinuclear {Fe(NO)(2)}(9){Fe(NO)(2)}(9) DNICs and 7113.4-7113.8 eV for the mononuclear {Fe(NO)(2)}(9) DNICs, the {Fe(NO)(2)}(10) dianionic reduced monomeric DNICs and the {Fe(NO)(2)}(10){Fe(NO)(2)}(10) dianionic reduced RREs containing S/O/N-ligation modes display the characteristic preedge energy 7113.1-7113.3 eV, which may be adopted to probe the formation of the EPR-silent {Fe(NO)(2)}(10)-{Fe(NO)(2)}(10) dianionic reduced RREs and {Fe(NO)(2)}(10) dianionic reduced monomeric DNICs in biology. In addition to the characteristic Fe/S K-edge preedge energy, the IR ν(NO) spectra may also be adopted to characterize and discriminate [(NO)(2)Fe(μ-S(t)Bu)](2) [IR ν(NO) 1809 vw, 1778 s, 1753 s cm(-1) (KBr)], [Fe(μ-S(t)Bu)(NO)(2)](2)(-) [IR ν(NO) 1674 s, 1651 s cm(-1) (KBr)], [Fe(μ-S(t)Bu)(NO)(2)](2)(2-) [IR ν(NO) 1637 m, 1613 s, 1578 s, 1567 s cm(-1) (KBr)], and [K-18-crown-6 ether](2)[(NO)(2)Fe(SEt)(2)] [IR ν(NO) 1604 s, 1560 s cm(-1) (KBr)].