Protein folds recognized by an intelligent predictor based‐on evolutionary and structural information

Protein fold recognition is an important and essential step in determining tertiary structure of a protein in biological science. In this study, a model termed NiRecor is developed for recognizing protein folds based on artificial neural networks incorporated in an adaptive heterogeneous particle swarm optimizer. The main contribution of NiRecor is that it is a data‐driven and highly‐performing predictor without manually tuning control parameters for different data sets. In biological science, since evolutionary‐ and structure‐based information of amino acid sequences is greatly important in determination of tertiary structure of a protein, accordingly, in NiRecor we employ two different feature sets, which involve position specific scoring matrix and secondary structure prediction matrix, to predict the structural classes of protein folds. The experimental results demonstrate the proposed method is powerful in predicting protein folds with higher precisions by improvements of 1.1 ∼7.8 percentages on three benchmark datasets by comparing with several existing predictors. © 2015 Wiley Periodicals, Inc.     

A Reversible DNA Logic Gate Platform Operated by One‐ and Two‐Photon Excitations

We demonstrate the use of two different wavelength ranges of excitation light as inputs to remotely trigger the responses of the self‐assembled DNA devices (D‐OR). As an important feature of this device, the dependence of the readout fluorescent signals on the two external inputs, UV excitation for 1 min and/or near infrared irradiation (NIR) at 800 nm fs laser pulses, can mimic function of signal communication in OR logic gates. Their operations could be reset easily to its initial state. Furthermore, these DNA devices exhibit efficient cellular uptake, low cytotoxicity, and high bio‐stability in different cell lines. They are considered as the first example of a photo‐responsive DNA logic gate system, as well as a biocompatible, multi‐wavelength excited system in response to UV and NIR. This is an important step to explore the concept of photo‐responsive DNA‐based systems as versatile tools in DNA computing, display devices, optical communication, and biology.     

Novel intramolecular cyclopropanation reaction of unsaturated beta-keto esters

[reaction: see text] Fused cyclopropane beta-keto esters are versatile intermediates for the synthesis of many biologically active natural products. Here we report a new intramolecular cyclopropanation reaction of unsaturated beta-keto esters. In the presence of I(2), Et(3)N, and Lewis acids such as Mg(ClO(4))(2) and Yb(OTf)(3), beta-keto esters 1 bearing various olefin substituents were transformed to fused cyclopropanes 2 in a highly stereospecific manner with moderate to good yields. The mechanism of the reaction was also investigated.     

Determination of surfactant concentration using micellar enhanced fluorescence and flow injection titration

Flow injection titration was used for the determination of anionic, cationic, nonionic and zwitterionic surfactants. The procedure was based on the micellar-enhanced fluorescence of 1,8-anilino-naphthalene sulfonate (ANS). Samples were injected into a carrier stream of phosphate buffer and 1.0 mol l⁻¹ NaCl. The sample then passed through a mixing chamber which generated the exponential peak shape needed for the titration as well as diluted the sample in the carrier stream to control the pH and ionic strength of the sample. The peak width was linearly related to the logarithm of the surfactant concentration. The minimum detectable concentration was governed by the critical micelle concentration for anionic, zwitterionic and nonionic surfactants, but below the critical micelle concentration for cationic surfactants. The linear range extended for 1.5 orders of magnitude. Reproducibility ranged from 12% at the lower end of the calibration range to 1.1% at higher concentrations. For SDS recoveries of 82–108% were achieved in matrices as concentrated as 1 mol l⁻¹ in NaCl or Na₂SO₄.     

STRUCTURE, MOLECULAR WEIGHT AND BIOACTIVITIES OF （1→3）-β-D-GLUCANS AND ITS SULFATED DERIVATIVES FROM FOUR KINDS OF LENTINUS EDODES

Abstract Lentinan samples, (1→3)-β-D-glucans containing 4.6-15.2 wt% proteins, coded as L-I1. L-I2. L-I3 and L-I4 (L-I)were isolated from four kinds of Lentinus edodes. These glucans were treated with acetone to remove the protein in order to obtain free protein glucans coded as LNP-I1. LNP-I2, LNP-I3 and LNP-I4 (LNP-I). The free-protein polysaccharides were sulfated to give derivatives (S-LNP-I) with degree of substitution (DS) from 0.4-0.8. The structural features and weight- average molecular weight (Mw) of the samples were investigated by using infrared spectroscopy, elemental analysis,^13C-NMR, size exclusion chromatography combined with laser light scattering (SEC-LLS) and viscometry. The effects of structure and conformation of the polysaccharides on antitumor activities were assayed in vivo (Sarcoma 180 solid tumors)and in vitro (Sarcoma 180, HL-60, MCF-7 and Vero tumors). The results indicated that the predominant species of the samples L-I and LNP-I in 0.2 mol/L NaCl aqueous solution existed as triple-helical chains with high rigidity and in dimethyl sulfoxide (DMSO) as single-flexible chains. Interestingly, the antitumor activities of LNP-I are lower than those of the native glucans (L-I), whereas their sulfated derivatives have higher inhibition ratio against Sarcoma 180 than LNP-I. The results reveal that the binding of protein, sulfated modification and the triple helix conformation are important factors in the enhancement of the antitumor activities of polysaccharides on the whole.     

A stereospecific synthesis of vitamin A from 2,2,6-trimethyl-cyclohexanone.

An efficient synthesis of all-(E) vitamin A acetate from 2,2,6-trimethyl-cyclohexanone has been achieved via the intermediacy of 1-(9-acetoxy-3, 7-dimethyl-nona-3,5,7-trien-1-ynyl)-2,2,6-trimethyl-cyclohexanol ( 25 ), readily prepared in high yield by allylic rearrangement of tertiary propenols with glacial acetic acid. The key step in the synthesis is the transformation of 25 to the unsaturated ketone 27 (9-acetoxy-3,7-dimethyl-1-(2,6,6-trimethyl-cyclohex-1-enyl)-nona-3,5,7-trien- 2-one) using a novel vanadium(V)-catalysed rearrangement reaction. The carbonyl in 27 affords the means for the essential isomerization of the adjacent double bond to the (E) isomer and the product is readily transformed into the polyene by reduction and elimination. An overall yield of 18–31% of vitamin A acetate from 2,2,6-trimethyl-cyclohexanone has been realized.     

Ruthenium complexes with a terminal hydrazido ligand. Synthesis, spectroscopy, and X-ray crystal structure

Bis(1,1-diphenylhydrazido(1-))ruthenium(IV) porphyrins, [Ru(IV)(Por)(NHNPh2)2] (Por = TPP, TTP, 4-Cl-TPP, 4-MeO-TPP), were prepared in approximately 60% yields through the reaction of dioxoruthenium(VI) porphyrins, [Ru(VI)(Por)O2], with 1,1-diphenylhydrazine in ethanol. This new type of ruthenium complex has been characterized by 1H NMR, IR, UV-vis, and FABMS with elemental analysis. The crystal structure of [Ru(IV)(TTP)(NHNPh2)2], which reveals an eta1-coordination mode for both hydrazido axial ligands, has been determined. The average Ru-NHNPh2 distance and Ru-N-N angle were found to be 1.911(3) A and 141.1(3) degrees, respectively. The porphyrin ring exhibits a ruffling distortion that is unprecedentedly large for ruthenium complexes with simple porphyrinato ligands (such as TTP). This is probably due to the steric effect of the axial hydrazido(1-) ligands.     

Variegated micelle surfaces: correlating the microstructure of mixed surfactant micelles with bulk solution properties

Electron paramagnetic resonance, viscosity, and small-angle neutron scattering (SANS) measurements have been used to study the interaction of mixed anionic/nonionic surfactant micelles with the polyampholytic protein gelatin. Sodium dodecyl sulfate (SDS) and the nonionic surfactant dodecylmalono-bis-N-methylglucamide (C12BNMG) were chosen as "interacting" and "noninteracting" surfactants, respectively; SDS micelles bind strongly to gelatin but C12BNMG micelles do not. Further, the two surfactants interact synergistically in the absence of the gelatin. The effects of total surfactant concentration and surfactant mole fraction have been investigated. Previous work (Griffiths et al. Langmuir 2000, 16 (26), 9983-9990) has shown that above a critical solution mole fraction, mixed micelles bind to gelatin. This critical mole fraction corresponds to a micelle surface that has no displaceable water (Griffiths et al. J. Phys. Chem. B 2001, 105 (31), 7465). On binding of the mixed micelle, the bulk solution viscosity increases, with the viscosity-surfactant concentration behavior being strongly dependent on the solution surfactant mole fraction. The viscosity at a stoichiometry of approximately one micelle per gelatin molecule observed in SDS-rich mixtures scales with the surface area of the micelle occupied by the interacting surfactant, SDS. Below the critical solution mole fraction, there is no significant increase in viscosity with increasing surfactant concentration. Further, the SANS behavior of the gelatin/mixed surfactant systems below the critical micelle mole fraction can be described as a simple summation of those arising from the separate gelatin and binary mixed surfactant micelles. By contrast, for systems above the critical micelle mole fraction, the SANS data cannot be described by such a simple approach. No signature from any unperturbed gelatin could be detected in the gelatin/mixed surfactant system. The gelatin scattering is very similar in form to the surfactant scattering, confirming the widely accepted picture that the polymer "wraps" around the micelle surface. The gelatin scattering in the presence of deuterated surfactants is insensitive to the micelle composition provided the composition is above the critical value, suggesting that the viscosity enhancement observed arises from the number and strength of the micelle-polymer contact points rather than the gelatin conformation per se.