Interaction of heparin and heparin-derived oligosaccharides with synthetic peptide analogues of the heparin-binding domain of heparin/heparan sulfate-interacting protein

Background

Although protamine is effective as an antidote of heparin, there is a need to replace protamine due to its side effects. HIP peptide has been reported to neutralize the anticoagulant activity of heparin. The interaction of HIP analog peptides with heparin and heparin-derived oligosaccharides is investigated in this paper.

Methods

Seven analogues of the heparin-binding domain of heparin/heparan sulfate-interacting protein (HIP) were synthesized, and their interaction with heparin was characterized by heparin affinity chromatography, isothermal titration calorimetry, and NMR.

Results

NMR results indicate the imidazolium groups of the His side chains of histidine-containing Hip analog peptide interact site-specifically with heparin at pH 5.5. Heparin has identical affinities for HIP analog peptides of opposite chirality. Analysis by counterion condensation theory indicates the peptide AC-SRPKAKAKAKAKDQTK-NH₂ makes on average ∼ 3 ionic interactions with heparin that result in displacement of ∼ 2 Na⁺ ions, and ionic interactions account for ∼ 46% of the binding free energy at a Na⁺ concentration of 0.15 M.

Conclusions

The affinity of heparin for the peptides is strongly dependent on the nature of the cationic side chains and pH. The thermodynamic parameters measured for the interaction of HIP peptide analogs with heparin are strongly dependent on the peptide sequence and pH.

General significance

The information obtained in this research will be of use in the design of new agents for neutralization of the anticoagulant activity of heparin. The site-specific binding of protonated histidine side chains to heparin provides a molecular-level explanation for the pH-dependent binding of β-amyloid peptides by heparin and heparan sulfate proteoglycan and may have implications for amyloid formation.     

Three new multidimensional organic-inorganic hybrids based on polyoxometalates and copper coordination polymers with 4,4′-bipyridine ligands

Three new organic-inorganic hybrid materials with 4,4′-bipy ligands and copper cations as linkers, [Cu^II(H₂O)(4,4′-bipy)₂][Cu^II(H₂O)(4,4′-bpy)₂]₂H[Cu^IIP₈Mo₁₂O₆₂H₁₂] · 5H₂O (1), [Cu^I(4,4′-bipy)][Cu^II(4,4′-bipy)]₂ (BW₁₂O₄₀) · (4,4′-bipy) · 2H₂O (2) and [Cu^I (4,4′-bipy)]₃ (PMo₁₂O₄₀) · (pip) · 2H₂O (3) (pip = piperazine; 4,4′-bipy = 4,4′-bipyridine), have been hydrothermally synthesized. The single X-ray structural analysis reveals that the structure of 1 is constructed from [Cu(H₂O)(4,4′-bipy)₂] complexes into a novel, three-dimensional supermolecular network with 1-D channels in which Cu[P₄Mo₆]₂ dimer clusters reside. To the best of our knowledge, compound 1 is the first complex in which the [P₄Mo₆] clusters have been used as a non-coordinating anionic template for the construction of a novel, three-dimensional supermolecular network. Compound 2 is constructed from the six-supported [BW₁₂O₄₀]⁵⁻ polyoxoanions and [Cu^I(4,4′-bipy)] and [Cu^II(4,4′-bipy)] groups into a novel, 3-D network. Compound 3 exhibits unusual 3-D supramolecular frameworks, which are constructed from tetrasupporting [PMo₁₂O₄₀]³⁻ clusters and [Cu^I (4,4′-bipy)_n] coordination polymer chains. The electrochemical properties of 2 and 3 have been investigated in detail.     

Rapid changes of microsatellite flanking sequence in the allopolyploidization of new synthesized hexaploid wheat

Polyploidy has been found to be very common inplants. Comparative genome studies have revealed thateven species that were considered as typical diploidsincluding maize[1], soybean[2], Arabidopsis[3] have un-dergone polyploidization during their evolution. Ge-nome polyploidization is a major force of evolutionthat affects genome size and gene copy number[4,5]. Polyploids can be formed via the duplication ofgenomes, either of the same genomes (autopolyploid)or of diverged genomes with homoe…     

Anti-Tumor Activity of an Enzymatically Synthesized α-1,6 Branched α-1,4-Glucan,Glycogen

Oral administration of an enzymatically synthesized α-1,4:1,6-glycogen (ESG) at a dose of 50 μg/ml significantly prolonged the survival time of Meth A tumor-bearing mice. ESG also significantly stimulated macrophage-like cells (J774.1), leading to augmented production of nitric oxide (NO) and tumor necrosis factor-α (TNF-α). The weight-average degree of polymerization (DPw) and the ratio of branch linkage (BL) of ESG were 149,000 and 8.1% respectively. β-Amylase-treated ESG, however, lost J774.1-activating activity although inhibited subcutaneous growth of Meth A tumor cells admixed with it. Its DPw and BL changed to 126,000 and 20% respectively. Partially degraded amylopectin [(AP), DPw: 110,000, BL; 5.1] was also effective at stimulating J774.1, but its activity was lower than that of ESG. Other α-glucans [cycloamylose (CA), enzymatically synthesized amylose (ESA), highly branched cyclic dextrin (HBCD), and β-amylase-treated HBCD], of which DPw was lower than that of ESG, showed no J774.1-activating activity and weaker anti-tumor activity.     

A family of small cyclic amphipathic peptides (SCAmpPs) genes in citrus

Background

Citrus represents a crop of global importance both in economic impact and significance to nutrition. Citrus production worldwide is threatened by the disease Huanglongbing (HLB), caused by the phloem-limited pathogen Candidatus Liberibacter spp.. As a source of stable HLB-resistance has yet to be identified, there is considerable interest in characterization of novel disease-associated citrus genes.

Results

A gene family of Small Cyclic Amphipathic Peptides (SCAmpPs) in citrus is described. The citrus genomes contain 100–150 SCAmpPs genes, approximately 50 of which are represented in the citrus EST database. These genes encode small ~50 residue precursor proteins that are post-translationally processed, releasing 5–10 residue cyclic peptides. The structures of the SCAmpPs genes are highly conserved, with the small coding domains interrupted by a single intron and relatively extended untranslated regions. Some family members are very highly transcribed in specific citrus tissues, as determined by representation in tissue-specific cDNA libraries. Comparison of the ESTs of related SCAmpPs revealed an unexpected evolutionary profile, consistent with targeted mutagenesis of the predicted cyclic peptide domain. The SCAmpPs genes are displayed in clusters on the citrus chromosomes, with apparent association with receptor leucine-rich repeat protein arrays. This study focused on three SCAmpPs family members with high constitutive expression in citrus phloem. Unexpectedly high sequence conservation was observed in the promoter region of two phloem-expressed SCAmpPs that encode very distinct predicted cyclic products. The processed cyclic product of one of these phloem SCAmpPs was characterized by LC-MS-MS analysis of phloem tissue, revealing properties consistent with a K⁺ ionophore.

Conclusions

The SCAmpPs amino acid composition, protein structure, expression patterns, evolutionary profile and chromosomal distribution are consistent with designation as ribosomally synthesized defense-related peptides.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1486-4) contains supplementary material, which is available to authorized users.     

我国植物食用色素资源开发利用评价

古代人们使用的着色剂都是天然产品,除少数矿物颜料外,主要是植物源色素。我国古代就有以红曲米作为着色剂利用的习惯;在高等植物方面,生产蓝色、黄色、绿色的颜料的高等植物种类不少,大多沿用至今。自19世纪中叶以后,人工合成色素以着色牢固、鲜艳、成本低廉等特点,迅速占领了印染、食品等许多行业,但20世纪60年代以后,许多研究表明,一般合成色素都有程度不等的毒性,特别是化学结构含偶氮型的色素有可能在人体内成为致癌物。同时,在色素合成的过程中,还有可能污染有重金属及其他有害物质。因此,合成色素越来越使人们感到不安全。从20世纪50年代的100多种人工合成色素用于食品着色,到20世纪末,已有60~70余种被禁用了,而植物食用色素在食品行业中成为主要着色剂。近年来又涌现出多种有价值的高等植物源色素,我们选择其主要一些植物种类做些介绍,供有关方面参考。     

Identification of a poly-cyclopropylglycine–containing peptide via bioinformatic mapping of radical S-adenosylmethionine enzymes

Peptide-derived natural products are a large class of bioactive molecules that often contain chemically challenging modifications. In the biosynthesis of ribosomally synthesized and posttranslationally modified peptides (RiPPs), radical-SAM (rSAM) enzymes have been shown to catalyze the formation of ether, thioether, and carbon-carbon bonds on the precursor peptide. The installation of these bonds typically establishes the skeleton of the mature RiPP. To facilitate the search for unexplored rSAM-dependent RiPPs for the community, we employed a bioinformatic strategy to screen a subfamily of peptide-modifying rSAM enzymes which are known to bind up to three [4Fe-4S] clusters. A sequence similarity network was used to partition related families of rSAM enzymes into >250 clusters. Using representative sequences, genome neighborhood diagrams were generated using the Genome Neighborhood Tool. Manual inspection of bacterial genomes yielded numerous putative rSAM-dependent RiPP pathways with unique features. From this analysis, we identified and experimentally characterized the rSAM enzyme, TvgB, from the tvg gene cluster from Halomonas anticariensis. In the tvg gene cluster, the precursor peptide, TvgA, is comprised of a repeating TVGG motif. Structural characterization of the TvgB product revealed the repeated formation of cyclopropylglycine, where a new bond is formed between the γ-carbons on the precursor valine. This novel RiPP modification broadens the functional potential of rSAM enzymes and validates the proposed bioinformatic approach as a practical broad search tool for the discovery of new RiPP topologies.     

Microbial production of small medicinal molecules and biologics: From nature to synthetic pathways

Natural products are promising chemicals due to their structural diversity and bioactivities. Over the decades, a vast variety of gene clusters encoding natural products have been identified and overexpressed in microbes. Recently, the development of metabolic engineering, synthetic biology and bioinformatics strategies have facilitated target discovery and design. Microbial cells have been therefore constantly engineered for product accumulation. This review summarizes approaches of domesticating microbial hosts in producing major classes of natural products, with an emphasis on recent advances.     

Investigation of the apparent inefficiency of the coupling between Photosystem II electron transfer and ATP formation

The maximum phosphorylation efficiency achieved with synchronous turnovers of Photosystem II (PS II) in spinach chloroplast lamellae is 0.3 molecules of ATP per pair of electrons transferred. This is the same as the efficiency observed for PS II operating alone in continuous light and would seem to indicate less than 50% coupling efficiency. Flash-induced ATP synthesis associated with both photosystems acting in unison closely approaches twice the flash-induced ATP synthesis associated with the Photosystem-I-dependent oxidation of duroquinol (itself 0.6) and comes close to equalling the highest efficiency observed in steady-state PS I + PS II electron transport. The anomalously low coupling efficiency seen when PS II is operating alone can be overcome by a ΔpH of two units imposed before flash illumination, or by a prior flash series involving the entire electron transfer chain. In contrast, prior electron transport through PS II alone is only slightly effective in enhancing the coupling efficiency of subsequent PS II turnovers. (It should be noted that in all cases where supplementary energy was provided, either by a proton gradient or by prior illumination, this supplementary energy was always below the energetic threshold for phosphorylation. Furthermore, the enhancement of PS II coupling efficiency by supplementary energy persisted even after a large number of subsequent PS II-inducing flashes). The efficiency of flash-induced ATP synthesis associated with whole-chain electron transfer or with PS-I-dependent duroquinol oxidation is also enhanced by the supplementary energy, but only during the first few inefficient flashes, suggesting that in this case the supplementary energy may simply be contributing to the initial build-up of an energetic threshold for ATP synthesis. This cannot be the case when the same supplementary energy contributes to the efficiency of the PS II reaction, since the enhancement then persists for a long time and contributes to an essentially constant flash yield of ATP. Our results imply that during electron transfer involving both photosystems, PS II participates in generating about half of the total ATP, whereas it operates inefficiently only when operating alone. Since hydrogen ions produced by PS I are able to raise the efficiency of subsequent PS-II-dependent phosphorylation, at least some cooperation between the two photosystems takes place and this suggests some donation of protons from PS I to PS II. However, the inability of PS II alone to achieve high efficiency, even with prolonged pre-illumination, would seem to indicate some functional distinction of protons from the two photosystems.