Forming a Double-Helix Phase of Single Polymer Chains by the Cooperation between Local Structure and Nonlocal Attraction.

Double-helix structures, such as DNA, are formed in nature to realize many unique functions. Inspired by this, researchers are pursuing strategies to design such structures from polymers. A key question is whether the double helix can be formed from the self-folding of a single polymer chain without specific interactions. Here, using Langevin dynamics simulation and theoretical analysis, we find that a stable double-helix phase can be achieved by the self-folding of single semiflexible polymers as a result of the cooperation between local structure and nonlocal attraction. The critical temperature of double-helix formation approximately follows T^{cri}∼ln(k_{θ}) and T^{cri}∼ln(k_{τ}), where k_{θ} and k_{τ} are the polymer bending and torsion stiffness, respectively. Furthermore, the double helix can exhibit major and minor grooves due to symmetric break for better packing. Our results provide a novel guide to the experimental design of the double helix.

Phycobiliproteins-A Family of Algae-Derived Biliproteins: Productions, Characterization and Pharmaceutical Potentials.

Phycobiliproteins (PBPs) are colored and water-soluble biliproteins found in cyanobacteria, rhodophytes, cryptomonads and cyanelles. They are divided into three main types: allophycocyanin, phycocyanin and phycoerythrin, according to their spectral properties. There are two methods for PBPs preparation. One is the extraction and purification of native PBPs from Cyanobacteria, Cryptophyta and Rhodophyta, and the other way is the production of recombinant PBPs by heterologous hosts. Apart from their function as light-harvesting antenna in photosynthesis, PBPs can be used as food colorants, nutraceuticals and fluorescent probes in immunofluorescence analysis. An increasing number of reports have revealed their pharmaceutical potentials such as antioxidant, anti-tumor, anti-inflammatory and antidiabetic effects. The advances in PBP biogenesis make it feasible to construct novel PBPs with various activities and produce recombinant PBPs by heterologous hosts at low cost. In this review, we present a critical overview on the productions, characterization and pharmaceutical potentials of PBPs, and discuss the key issues and future perspectives on the exploration of these valuable proteins.

Transcriptomic analysis of Bursaphelenchus xylophilus treated by a potential phytonematicide, punicalagin.

Punicalagin showed significant nematotoxic activity against pine wood nematode (PWN), Bursaphelenchus xylophilus, in the authors' previous research. The authors performed high-throughput transcriptomic sequencing of punicalagin-treated nematodes to generate clues for its nematotoxic mechanism of action. The authors identified 2,575 differentially expressed genes, 1,428 of which were up-regulated and 1,147 down-regulated. Based on a comprehensive functional in silico analysis, the authors speculate that PWN may respond to the stimulus of punicalagin through phagosome, endocytosis, peroxisome and MAPK signaling pathways. In addition, punicalagin could greatly affect PWN energy metabolism including oxidative phosphorylation. The genes encoding twitchin and a nematode cuticular collagen could be crucial regulation targets of punicalagin, which might contribute to its nematotoxic activity against PWN.Punicalagin showed significant nematotoxic activity against pine wood nematode (PWN), Bursaphelenchus xylophilus, in the authors' previous research. The authors performed high-throughput transcriptomic sequencing of punicalagin-treated nematodes to generate clues for its nematotoxic mechanism of action. The authors identified 2,575 differentially expressed genes, 1,428 of which were up-regulated and 1,147 down-regulated. Based on a comprehensive functional in silico analysis, the authors speculate that PWN may respond to the stimulus of punicalagin through phagosome, endocytosis, peroxisome and MAPK signaling pathways. In addition, punicalagin could greatly affect PWN energy metabolism including oxidative phosphorylation. The genes encoding twitchin and a nematode cuticular collagen could be crucial regulation targets of punicalagin, which might contribute to its nematotoxic activity against PWN.

Dietary Recombinant Phycoerythrin Modulates the Gut Microbiota of H22 Tumor-Bearing Mice.

Normal intestinal flora is widely involved in many functions of the host: nutritional metabolism; maintenance of intestinal microecological balance; regulation of intestinal endocrine function and nerve signal transduction; promotion of intestinal immune system development and maturation; inhibition of pathogenic bacteria growth and colonization, reduction of its invasion to intestinal mucosa, and so on. In recent years, more and more studies have shown that intestinal flora is closely related to the occurrence, development, and treatment of various tumors. It is indicated that recombinant phycoerythrin (RPE) has significant anti-tumor and immunomodulatory effects. However, little is known about the mechanism of the effect of oral (or intragastric) administration of RPE on gut microbiota in tumor-bearing animals. In this study, using high-throughput 16S rDNA sequencing, we examined the response of gut microbiota in H22-bearing mice to dietary RPE supplementation. The results showed that the abundance of beneficial bacteria in the mice intestinal flora decreased and that of the detrimental flora increased after inoculation with tumor cells (H22); following treatment with dietary RPE, the abundance of beneficial bacteria in the intestinal flora significantly increased and that of detrimental bacteria decreased. In this study, for the first time, it was demonstrated that dietary RPE could modulate the gut microbiota of the H22 bearing mice by increasing the abundance of beneficial bacteria and decreasing that of detrimental bacteria among intestinal bacteria, providing evidence for the mechanism by which bioactive proteins affect intestinal nutrition and disease resistance in animals.

A nematicidal tannin from Punica granatum L. rind and its physiological effect on pine wood nematode (Bursaphelenchus xylophilus).

The ethanol extract of Punica granatum L. rind was tested to show significant nematicidal activity against pine wood nematode. Three nematicidal compounds were obtained from the ethanol extract by bioassay-guided fractionation and identified as punicalagin 1, punicalin 2, and corilagin 3 by mass and nuclear magnetic resonance spectral data analysis. Punicalagin 1 was most active against PWN among the purified compounds with the LC50 value of 307.08µM in 72h. According to the enzyme assays in vitro, punicalagin 1 could inhibit the activity of acetylcholinesterase, amylase and cellulase from PWN with IC50 value of 0.60mM, 0.96mM and 1.24mM, respectively. The morphological structures of PWNs treated by punicalagin 1 were greatly changed. These physiological effects of punicalagin 1 on PWN may helpful to elucidate its nematicidal mechanism.

Contribution of active site residues to substrate hydrolysis by USP2: insights into catalysis by ubiquitin specific proteases.

The ubiquitin-specific protease (USP) structural class represents the largest and most diverse family of deubiquitinating enzymes (DUBs). Many USPs assume important biological roles and emerge as potential targets for therapeutic intervention. A clear understanding of USP catalytic mechanism requires a functional evaluation of the proposed key active site residues. Crystallographic data of ubiquitin aldehyde adducts of USP catalytic cores provided structural details on the catalytic triad residues, namely the conserved Cys and His, and a variable putative third residue, and inferred indirect structural roles for two other conserved residues (Asn and Asp), in stabilizing via a bridging water molecule the oxyanion of the tetrahedral intermediate (TI). We have expressed the catalytic domain of USP2 and probed by site-directed mutagenesis the role of these active site residues in the hydrolysis of peptide and isopeptide substrates, including a synthetic K48-linked diubiquitin substrate for which a label-free, mass spectrometry based assay has been developed to monitor cleavage. Hydrolysis of ubiquitin-AMC, a model substrate, was not affected by the mutations. Molecular dynamics simulations of USP2, free and complexed with the TI of a bona fide isopeptide substrate, were carried out. We found that Asn271 is structurally poised to directly stabilize the oxyanion developed in the acylation step, while being structurally supported by the adjacent absolutely conserved Asp575. Mutagenesis data functionally confirmed this structural role independent of the nature (isopeptide vs peptide) of the bond being cleaved. We also found that Asn574, structurally located as the third member of the catalytic triad, does not fulfill this role functionally. A dual supporting role is inferred from double-point mutation and structural data for the absolutely conserved residue Asp575, in oxyanion hole formation, and in maintaining the correct alignment and protonation of His557 for catalytic competency.

Design of noncovalent inhibitors of human cathepsin L. From the 96-residue proregion to optimized tripeptides.

A novel series of noncovalent inhibitors of cathepsin L have been designed to mimic the mode of autoinhibition of procathepsin L. Just like the propeptide, these peptide-based inhibitors have a reverse-binding mode relative to a substrate and span both the S' and S subsites of the enzyme active site. In contrast to previous studies in which even moderate truncation of the full-length propeptide led to rapid reduction in potency, these blocked tripeptide-sized inhibitors maintain nanomolar potency. Moreover, these short peptides show higher selectivity (up to 310-fold) for inhibiting cathepsin L over K versus only 2-fold selectivity of the 96-residue propeptide of cathepsin L. A 1.9 A X-ray crystallographic structure of the complex of cathepsin L with one of the inhibitors confirms the designed reverse-binding mode of the inhibitor as well as its noncovalent nature. Enzymatic analysis also shows the inhibitors to be resistant to hydrolysis at elevated concentrations of the enzyme. The mode of inhibition of these molecules provides a general strategy for inhibiting other cathepsins as well as other proteases.

Effects of spraying rare earths on contents of rare Earth elements and effective components in tea.

Rare earth (RE) fertilizer is widely applied in China to increase the yield and the quality of crops including tea. However, the effects of spraying RE fertilizer on the contents of rare earth elements (REE) and effective components in tea are unknown. The results from basin and field experiments show that the values of the REE concentrations in new shoots of tea plants and the concentration of REE in the soil (REE/REEs) either from control basins or from treatment basins were smaller than those in other parts of tea plant and similar between control and treatment. The longer the interval between spraying RE fertilizer and picking the shoots of tea plants, the less the effects from spraying. About 80% summation operator REE (the sum of the concentrations of 15 REE) in tea, whether it came from spraying or not, was insoluble in the infusion. About 10% the soluble REE of summation operator REE in tea infusion was bound to polysaccharide, and the amount of REE bound polysaccharide decreased over time. At least a 25 day safety interval is needed between spraying and picking if the microelement fertilizer is used, in order to enhance tea output and to ensure tea safety.

[Nutrient contents and heavy metal pollutions in composted sewage sludge from different municipal wastewater treatment plants in Beijing region].

Changes of nutrient contents and heavy metal pollutions in composted sewage sludge from different municipal wastewater treatment plants (as represented by CSS-A and CSS-B, respectively) in Beijing region were investigated. The results showed that the pH values, nutrient contents, trace elements and heavy metals in CSS-A and CSS-B depended on the sludge resources and particular years. The average of organic matter content in different years (203 338.0 mg x kg(-1)) from CSS-A met both the requirement of sludge quality standard for agricultural use (CJ/T 309-2009) and land improvement (GB/T 24600-2009) in China except the permitted limit of sludge quality standards for garden or park use (GB/T 23486-2009) in China. Moreover, the average of organic matter in different years (298531.5 mg x kg(-1)) from CSS-B and the averages of pH values (7.1 and 7.2, respectively) and NPK concentrations (41 111.7 mg x kg(-1) and 65 901.5 mg x kg(-1), respectively) in different years from CSS-A and CSS-B all met the requirements of sludge quality standards for the above-mentioned disposal types of sewage sludge from municipal wastewater treatment plants. The contents of heavy metals in CSS-A and CSS-B except Hg and Ni were below the permitted limits of the A-class sludge quality standard for agricultural use (CJ/T 309-2009) , being the most stringent standards in China. It was suggested that composted sewage sludge from different municipal wastewater treatment plants in Beijing region use as a fertilizer in agriculture, land improvement, and garden or park, but the top concern about potential environmental pollution of Hg and Ni should be considered.

Simvastatin activates the PPARγ-dependent pathway to prevent left ventricular hypertrophy associated with inhibition of RhoA signaling.

Left ventricular hypertrophy is an independent risk factor for major adverse cardiovascular events. Statins have positive effects on this condition; however, the mechanisms are incompletely understood. In this study, we examined whether the effect of simvastatin on left ventricular hypertrophy can be mediated with the peroxisome proliferator-activated receptor (PPAR)γ-dependent pathway in rabbits with nonischemic heart failure (HF). We induced aortic insufficiency and constriction in 48 rabbits and divided them equally into control, HF, and HF with simvastatin therapy (HF-SIM) groups. The HF-SIM group was given 10 mg/kg/d of simvastatin. We echocardiographically measured baseline and 8-week cardiac structure and function, and we used Western blot, polymerase chain reaction, and electrophoretic analytic techniques to evaluate messenger RNA expression and protein expression and activity. In comparison with the HF group, the HF-SIM rabbits had an increased ejection fraction and decreased left ventricular mass index, interventricular septal thickness, ventricular posterior-wall thickness, and collagen volume fraction. Moreover, the messenger RNA and protein expression of PPARγ in the HF-SIM rabbits were significantly higher than those in the HF rabbits; and the activity and expression of nuclear factor-κB subunit p65, RhoA, and Rho GTPase were significantly lower. Our results indicate that simvastatin therapy attenuates the PPARγ-dependent pathway in association with the inhibition of RhoA and Rho GTPase signaling to inhibit nuclear factor-κB activation, thus preventing the development of left ventricular hypertrophy and fibrosis in rabbits with nonischemic heart failure.

Selectivity in ISG15 and ubiquitin recognition by the SARS coronavirus papain-like protease.

The severe acute respiratory syndrome coronavirus papain-like protease (SARS-CoV PLpro) carries out N-terminal processing of the viral replicase polyprotein, and also exhibits Lys48-linked polyubiquitin chain debranching and ISG15 precursor processing activities in vitro. Here, we used SDS-PAGE and fluorescence-based assays to demonstrate that ISG15 derivatives are the preferred substrates for the deubiquitinating activity of the PLpro. With k(cat)/K(M) of 602,000 M(-1)s(-1), PLpro hydrolyzes ISG15-AMC 30- and 60-fold more efficiently than Ub-AMC and Nedd8-AMC, respectively. Data obtained with truncated ISG15 and hybrid Ub/ISG15 substrates indicate that both the N- and C-terminal Ub-like domains of ISG15 contribute to this preference. The enzyme also displays a preference for debranching Lys48- over Lys63-linked polyubiquitin chains. Our results demonstrate that SARS-CoV PLpro can differentiate between ubiquitin-like modifiers sharing a common C-terminal sequence, and that the debranching activity of the PLpro is linkage type selective. The potential structural basis for the demonstrated specificity of SARS-CoV PLpro is discussed.