TLR4 signaling is coupled to SRC family kinase activation, tyrosine phosphorylation of zonula adherens proteins, and opening of the paracellular pathway in human lung microvascular endothelia

Bacterial lipopolysaccharide (LPS) is a key mediator in the vascular leak syndromes associated with Gram-negative bacterial infections. LPS opens the paracellular pathway in pulmonary vascular endothelia through protein tyrosine phosphorylation. We now have identified the protein-tyrosine kinases (PTKs) and their substrates required for LPS-induced protein tyrosine phosphorylation and opening of the paracellular pathway in human lung microvascular endothelial cells (HMVEC-Ls). LPS disrupted barrier integrity in a dose- and time-dependent manner, and prior broad spectrum PTK inhibition was protective. LPS increased tyrosine phosphorylation of zonula adherens proteins, VE-cadherin, gamma-catenin, and p120(ctn). Two SRC family PTK (SFK)-selective inhibitors, PP2 and SU6656, blocked LPS-induced increments in tyrosine phosphorylation of VE-cadherin and p120(ctn) and paracellular permeability. In HMVEC-Ls, c-SRC, YES, FYN, and LYN were expressed at both mRNA and protein levels. Selective small interfering RNA-induced knockdown of c-SRC, FYN, or YES diminished LPS-induced SRC Tyr(416) phosphorylation, tyrosine phosphorylation of VE-cadherin and p120(ctn), and barrier disruption, whereas knockdown of LYN did not. For VE-cadherin phosphorylation, knockdown of either c-SRC or FYN provided total protection, whereas YES knockdown was only partially protective. For p120(ctn) phosphorylation, knockdown of FYN, c-SRC, or YES each provided comparable but partial protection. Toll-like receptor 4 (TLR4) was expressed both on the surface and intracellular compartment of HMVEC-Ls. Prior knockdown of TLR4 blocked both LPS-induced SFK activation and barrier disruption. These data indicate that LPS recognition by TLR4 activates the SFKs, c-SRC, FYN, and YES, which, in turn, contribute to tyrosine phosphorylation of zonula adherens proteins to open the endothelial paracellular pathway.     

Cadmium sulfide-modified GCE for direct signal-amplified sensing of DNA hybridization

A novel DNA hybridization sensor based on nanoparticle CdS modified glass carbon electrode (GCE) was constructed and characterized coupled with Cyclic Voltammogram (CV) and Differential Pulse Voltammogram (DPV) techniques. The mercapto group-linked probe DNA was covalently immobilized onto the CdS layer and exposed to oligonucleotide (ODN) target for hybridization. The structure of DNA sensor was characterized by X-ray diffraction (XRD), field-emission microscopy (FESEM) and X-ray photoelectron spectra (XPS). Sensitive electrical readout achieved by CV and DPV techniques shown that when the target DNA hybridized with probe CdS-ODN conjugates and the double helix formed on the modified electrode, a significant increased response was observed comparing with the bare electrodes. The selectivity of the sensor was tested using a series of matched and certain-point mismatched sequences with concentration grads ranging from 10(-6) microM to 10(1) microM. The signal was in good linear with the minus logarithm of target oligonucleotide concentration with detection limit <1 pM and the optimized target DNA concentration was 10(-6) microM for the signal amplification. Due to great surface properties, the additional negative charges and space resistance of as-prepared CdS nanoparticles, the sensor was able to robustly discriminate the DNA hybridization responses with good sensitivity and stability.     

A tool for the prediction of structures of complex sugars

In two recent back to back articles(Xia et al., J Chem Theory Comput 3:1620–1628 and 1629–1643, 2007a, b) we have started to address the problem of complex oligosaccharide conformation and folding. The scheme previously presented was based on exhaustive searches in configuration space in conjunction with Nuclear Overhauser Effect (NOE) calculations and the use of a complex rotameric library that takes branching into account. NOEs are extremely useful for structural determination but only provide information about short range interactions and ordering. Instead, the measurement of residual dipolar couplings (RDC), yields information about molecular ordering or folding that is long range in nature. In this article we show the results obtained by incorporation RDC calculations into our prediction scheme. Using this new approach we are able to accurately predict the structure of six human milk sugars: LNF-1, LND-1, LNF-2, LNF-3, LNnT and LNT. Our exhaustive search in dihedral configuration space combined with RDC and NOE calculations allows for highly accurate structural predictions that, because of the non-ergodic nature of these molecules on a time scale compatible with molecular dynamics simulations, are extremely hard to obtain otherwise (Almond et al., Biochemistry 43:5853–5863, 2004). Molecular dynamics simulations in explicit solvent using as initial configurations the structures predicted by our algorithm show that the histo-blood group epitopes in these sugars are relatively rigid and that the whole family of oligosaccharides derives its conformational variability almost exclusively from their common linkage (β-d-GlcNAc-(1→3)-β-d-Gal) which can exist in two distinct conformational states. A population analysis based on the conformational variability of this flexible glycosidic link indicates that the relative population of the two distinct states varies for different human milk oligosaccharides. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Efficient ensemble schemes for protein secondary structure prediction

This paper proposes an efficient ensemble system to tackle the protein secondary structure prediction problem with neural networks as base classifiers. The experimental results show that the multi-layer system can lead to better results. When deploying more accurate classifiers, the higher accuracy of the ensemble system can be obtained.     

New antibiotic with typical plant anthraquinone structure obtained studying terrestrial and marine Streptomycetes

In our screening for new antibiotics from bacteria, the streptomycete isolate M097 from Jiaozhou Bay in China was found to produce aloesaponarin II (1a) and 1,6-dihydroxy-8-hydroxymethyl-anthraquinone (2). Similarly, a terrestrial streptomycete GW24/1694 produced 1a and its methyl ether, the new compound 1-hydroxy-6-methoxy-8-methyl-anthraquinone (1b). All structures were derived by spectrochemical analysis and by comparison with reference data. The results showed that the marine streptomycete isolate M097 and the terrestrial streptomycete GW24/1694 could be a promising material for studying the biosynthetic pathway of polyketides.     

Domain conformational switch of the iron-sulfur protein in cytochrome bc1 complex is induced by the electron transfer from cytochrome bL to bH

Intensive biochemical, biophysical and structural studies of the cytochrome (cyt) bc(1) complex in the past have led to the formulation of the "protonmotive Q-cycle" mechanism for electron and proton transfer in this vitally important complex. The key step of this mechanism is the separation of electrons during the oxidation of a substrate quinol at the Q(P) site with both electrons transferred simultaneously to ISP and cyt b(L) when the extrinsic domain of ISP (ISP-ED) is located at the b-position. Pre-steady state fast kinetic analysis of bc(1) demonstrates that the reduced ISP-ED moves to the c(1)-position to reduce cyt c(1) only after the reduced cyt b(L) is oxidized by cyt b(H). However, the question of how the conformational switch of ISP-ED is initiated remains unanswered. The results obtained from analysis of inhibitory efficacy and binding affinity of two types of Q(P) site inhibitors, Pm and Pf, under various redox states of the bc(1) complex, suggest that the electron transfer from heme b(L) to b(H) is the driving force for the releasing of the reduced ISP-ED from the b-position to c(1)-position to reduce cyt c(1).     

Sensitive quantitation of isoglobotriaosylceramide in the presence of isobaric components using electrospray ionization-ion trap mass spectrometry

Isoglobotriaosylceramide (iGb3) is a stimulatory antigen for a unique type of T cell, Natural Killer T cells. Produced in the lysosomal compartment by mammalian antigen-presenting cells, iGb3 is one of the few clearly identified carbohydrate ligands for biological receptors. A major source of glycoconjugate structural diversity arises from the possibility of forming different linkages between the same monosaccharide units. Globotriaosylceramide (Gb3) exists as a natural isomer for iGb3, and both isomers are frequently found together in mixtures of glycosphingolipids extracted from mammalian cell membranes. Discriminating these isomers has been feasible using monoclonal antibodies raised against specific carbohydrate epitopes, or by unambiguous structural characterization, which requires relatively large amounts of pure compounds isolated from grams, or tens of grams, of biological samples. However, the precise detection of iGb3 from small amounts of biological samples, where it may be mixed with Gb3 present in much higher abundance, is a prerequisite for answering further important biological questions such as stimulation of NKT cells. Here we describe a specific and sensitive method based on ion trap mass spectrometry to discriminate iGb3 from Gb3. We also demonstrate its application to quantifying the amount of iGb3 in a prototype antigen-presenting cell, rat RBL-CD1d cells, using a chemically synthesized short N-acyl chain iGb3 as internal standard. This methodology may have wide implications for functional glycosphingolipidomics of immune cells and glycosphingolipid biomarker analysis.     

Purification, structure and immunobiological activity of a new water-soluble polysaccharide from the mycelium of Polyporus albicans (Imaz.) Teng

A new water-soluble intracellular polysaccharide named as PTP, with a molecular mass of 3.7x10(4) Da, was obtained from the mycelium of Polyporus albicans (Imaz.) Teng. Structure features of the purified polysaccharide were investigated by a combination of chemical and instrumental analysis. The results indicated that PTP consisted of a backbone composed of (1-->3)-linked-beta-d-mannopyranosyl, (1-->3,6)-linked-beta-d-mannopyranosyl and (1-->6)-linked-alpha-d-galactopyranosyl residues in the ratio of 3:1:1, and terminated with a single non-reducing terminal (1-->)-beta-d-mannopyranosyl residues at the C-6 position of (1-->3,6)-linked-beta-d-mannopyranosyl, along the main chain. This is the first report describing the isolation and structure elucidation of a new intracellular polysaccharide produced from the mycelium of P. albicans (Imaz.) Teng. Preliminary tests in vitro showed PTP have potent stimulating effects on murine lymphocyte proliferation induced by concanavalin A or lipopolysaccharide and its branches are extremely important for the expression of the enhancement of the immunological activity.     

Substituted dipiperidine alcohols as potent CCR2 antagonists

The synthesis and biological evaluation of a series of substituted dipiperidine alcohols are described. Structure-activity relationship studies led to the discovery of potent CCR2 antagonists displaying IC(50) values in the nanomolar or subnanomolar range. The cinnamoyl compounds had higher binding affinities than the corresponding urea analogs.