Potentiating effect of distant sites in non-phosphorylated cyclic peptide antagonists of the Grb2-SH2 domain

Without the presence of a phosphotyrosyl group, a phage library derived non-phosphorylated cyclic peptide ligand of Grb2-SH2 domain attributed its high affinity and specificity to well-defined and highly favored interactions of its structural elements with the binding pocket of the protein. We have disclosed a significant compensatory role of the Glu(2-) sidechain for the absence of the phosphate functionality on Tyr(0) in the peptide ligand, cyclo(CH(2)CO-Glu(2-)-Leu-Tyr(0)-Glu-Asn-Val-Gly-Met(5+)-Tyr-Cys)-amide (termed G1TE). In this study, we report the importance of hydrophobic residue at the Tyr+5 site in G1TE. Both acidic and basic amino acid substitutes are disfavored at this position, and replacement of Met with beta-tert-butyl-Ala was found to improve the antagonist properties. Besides, the polarity of the cyclization linkage was implicated as important in stabilizing the favored binding conformation. Oxidation of the thioether linkage into sulfoxide facilitated the binding to Grb2-SH2 markedly. Simultaneous modification of the three distant sites within G1TE provided the best agent with an IC(50) of 220 nM, which is among the most potent non-phosphorous- and non-phosphotyrosine-mimic containing Grb2-SH2 domain inhibitors yet reported. This potent peptidomimetic provides a novel template for the development of chemotherapeutic agents for the treatment of erbB2-related cancer. Biological assays on G1TE(Gla(2-)) in which the original residue of Glu(2-) was substituted by gamma-carboxyglutamic acid (Gla) indicated that it could inhibit the interaction between activated GF receptor and Grb2 protein in cell homogenates of MDA-MB-453 breast cancer cells at the 2 microM level. More significantly, both G1TE(Gla(2-)) alone and the conjugate of G1TE(Gla(2-)) with a peptide carrier can effectively inhibit intracellular association of erbB2 and Grb2 in the same cell lines with IC(50) of 50 and 2 microM, respectively.     

Characterization of bacterial strains able to grow on high molecular mass residues from crude oil processing

Oil residues containing high molecular mass hydrocarbons, rich in polyaromatic compounds, are frequent end-products of crude oil processing and are poorly biodegradable. Their disposal poses an environmental problem. Through batch-enrichments from contaminated soils we have isolated and characterized seven bacterial strains that can use a residue from crude oil processing as a source of carbon and energy. The residue was a complex mixture of high molecular mass compounds, including saturated, aromatic and polycyclic aromatic hydrocarbons (PAHs). Analysis of the metabolic profiles of the strains isolated showed that they could all metabolize long-chain-length alkanes efficiently, but not PAHs. Strains degrading naphthalene, a simple PAH, did exist in the soil inocula used, but could be isolated only when enrichments were performed using pure naphthalene as the sole carbon source. All strains tested emulsified the oil residue and their ability to produce surfactants was studied.     

Involvement of lysine residues in the binding of ovine chorionic somatomammotropin to lactogenic and somatotropic receptors

The biological activities of several ovine chorionic somatomammotropin (oCS) derivatives obtained by chemical modification of the lysine residues were studied by radioreceptor assays using rabbit mammary homogenates (lactogenic activity, L.A.) and liver homogenates (somatotropic activity, S.A.). Even if the control treatment with BH-4 markedly decreased the L.A., it was clear that methylation mainly affected the S.A. and that ethylation reduced both activities. Guanidination inactivated almost completely both activities and acetimidination at a very low degree (3 of 14 lysines) led to less than 50% of both activities. These results show the involvement of lysine residues in the interaction of oCS with lactogenic and somatotropic receptors.     

农田生态条件下玉米秸杆腐解过程腐解物的热解变化特征

用热分析法研究了农田生态条件下玉米秸杆腐解过程腐解物的热解变化特征 ,并探讨了腐解物中不同组分对腐解物热解特征的影响。结果表明 ,腐解物 DTA曲线的 2 80℃、3 3 0℃、4 50℃放热峰 ,DTG曲线的第二失重峰和 h330℃ /h4 50℃ 值可作为表征腐解进程的特征峰和特征值。由腐解物 DTA、DTG所得能量各参数 ( ΔH,E)与文献 [3 ]所述腐解物能态 ( Qv)呈现波动起伏 ,趋于稳定 2个阶段相符 ,二者相互印证 ,显示热分析方法用于植物残体腐解进程研究的可行性。 DTA的2 80℃放热峰主要由苯 -醇溶性物、水溶性物引起。苯 -醇溶性物、水溶性物和纤维素、半纤维素是影响腐解物热解及其能态变化特征的主要物质组分。木质素组分对腐解后期腐解物的热解及其能态特征趋于稳定具有重要作用     

Position-specific residue preference features around the ends of helices and strands and a novel strategy for the prediction of secondary structures

It has been many years since position-specific residue preference around the ends of a helix was revealed. However, all the existing secondary structure prediction methods did not exploit this preference feature, resulting in low accuracy in predicting the ends of secondary structures. In this study, we collected a relatively large data set consisting of 1860 high-resolution, non-homology proteins from the PDB, and further analyzed the residue distributions around the ends of regular secondary structures. It was found that there exist position-specific residue preferences (PSRP) around the ends of not only helices but also strands. Based on the unique features, we proposed a novel strategy and developed a tool named E-SSpred that treats the secondary structure as a whole and builds models to predict entire secondary structure segments directly by integrating relevant features. In E-SSpred, the support vector machine (SVM) method is adopted to model and predict the ends of helices and strands according to the unique residue distributions around them. A simple linear discriminate analysis method is applied to model and predict entire secondary structure segments by integrating end-prediction results, tri-peptide composition, and length distribution features of secondary structures, as well as the prediction results of the most famous program PSIPRED. The results of fivefold cross-validation on a widely used data set demonstrate that the accuracy of E-SSpred in predicting ends of secondary structures is about 10% higher than PSIPRED, and the overall prediction accuracy (Q(3) value) of E-SSpred (82.2%) is also better than PSIPRED (80.3%). The E-SSpred web server is available at http://bioinfo.hust.edu.cn/bio/tools/E-SSpred/index.html.     

Importance of Dietary Cholesterol for the Maturation of Mouse Brain Myelin

The effect of nil (control), 1% (CH-l) and 5% (CH-5) dietary cholesterol on the myelination of mouse brain, and its deposition in the heart and liver were investigated during infancy. Swiss Webstar female mice were given formulated diets from early gestation, and their pups were weaned on the same diet as that of the individual mothers up to 60 days after birth. The test diets increased the liver weight and cholesterol content compared to the control even in suckling pups (20 days), but did not significantly influence the heart weight until 60 days. The cholesterol content of the heart was not increased by the CH-l diet throughout the feeding period, but it did increase the mole ratio of major myelin lipids and hastened its maturation. Myelin cholesterol was 10% higher in 20-day-old suckling pups in the CH-5 group compared to the control. Data indicate that dietary cholesterol altered the brain myelination rate of weaning mice, and that the mother’s dietary cholesterol influenced myelination of the suckling pups.     

Indirect carbon dioxide emissions from producing bioenergy from forest harvest residues

Forest harvest residues are important raw materials for bioenergy in regions practicing forestry. Removing these residues from a harvest site reduces the carbon stock of the forest compared with conventional stem‐only harvest because less litter in left on the site. The indirect carbon dioxide (CO₂) emission from producing bioenergy occur when carbon in the logging residues is emitted into the atmosphere at once through combustion, instead of being released little by little as a result of decomposition at the harvest sites. In this study (1) we introduce an approach to calculate this indirect emission from using logging residues for bioenergy production, and (2) estimate this emission at a typical target of harvest residue removal, i.e. boreal Norway spruce forest in Finland. The removal of stumps caused a larger indirect emission per unit of energy produced than the removal of branches because of a lower decomposition rate of the stumps. The indirect emission per unit of energy produced decreased with time since starting to collect the harvest residues as a result of decomposition at older harvest sites. During the 100 years of conducting this practice, the indirect emission from average‐sized branches (diameter 2 cm) decreased from 340 to 70 kg CO₂ eq. MWh^?1 and that from stumps (diameter 26 cm) from 340 to 160 kg CO₂ eq. MWh^?1. These emissions are an order of magnitude larger than the other emissions (collecting, transporting, etc.) from the bioenergy production chain. When the bioenergy production was started, the total emissions were comparable to fossil fuels. The practice had to be carried out for 22 (stumps) or four (branches) years until the total emissions dropped below the emissions of natural gas. Our results emphasize the importance of accounting for land‐use‐related indirect emissions to correctly estimate the efficiency of bioenergy in reducing CO₂ emission into the atmosphere.     

色氨酸残基在磷酸烯醇式丙酮酸羧化酶催化功能中的作用

在pH7.5条件下,用NBS对PEP羧化酶中色氨酸残基进行共价修饰表明,PEP羧化酶中48个色氨酸残基均能被NBS修饰。用邹承鲁图解法求得,其中4个残基为酶表现催化活性所必需的。 PEP羧化酶的变构效应剂G6P、Gly及Mal分别与酶预保温后,再经NBS修饰,前两种处理中,同样浓度的NBS所用修饰的色氨酸残基数和处理后的残存酶活与对照相比有很大的差异,而用Mal处理的,两者与对照相差无几。     

Wild bee diversity is enhanced by experimental removal of timber harvest residue within intensively managed conifer forest

The use of timber harvest residue as an energy source is thought to have environmental benefits relative to food‐based crops, yet the ecological impact of this practice remains largely unknown. We assessed whether the abundance and diversity of wild bees (Apoidea) were influenced by the removal of harvest residue and associated soil compaction within managed conifer forest in western Oregon, USA. We sampled bees over two years (2014–2015) on study plots that were subjected to five treatments representing gradients in removal of harvest residue and soil compaction. We collected >7,500 bee specimens from 92 distinct species/morphospecies that represented five of the seven bee families. We trapped 3x more individuals in the second year of the study despite identical sampling effort in both years, with most trapped bees classified as ground‐nesting species. Members of the sweat bee family (Halictidae) comprised more than half of all specimens, and the most abundant genus was composed of metallic green bees (Agapostemon, 33.6%), followed by long‐horned bees (Melissodes, 16.5%), sweat bees (Halictus, 15.9%), and bumble bees (Bombus, 13.6%). In both years, abundance and observed species richness were greatest in the most intensive harvest residue treatment, with other treatments having similar values for both measures. Our study indicates that early successional managed conifer forest that has experienced removal of harvest residue can harbor a surprising diversity of wild bees, which are likely to have important contributions to the broader ecological community through the pollination services they provide.     

RBRDetector: Improved prediction of binding residues on RNA‐binding protein structures using complementary feature‐ and template‐based strategies

Computational prediction of RNA‐binding residues is helpful in uncovering the mechanisms underlying protein‐RNA interactions. Traditional algorithms individually applied feature‐ or template‐based prediction strategy to recognize these crucial residues, which could restrict their predictive power. To improve RNA‐binding residue prediction, herein we propose the first integrative algorithm termed RBRDetector (RNA‐Binding Residue Detector) by combining these two strategies. We developed a feature‐based approach that is an ensemble learning predictor comprising multiple structure‐based classifiers, in which well‐defined evolutionary and structural features in conjunction with sequential or structural microenvironment were used as the inputs of support vector machines. Meanwhile, we constructed a template‐based predictor to recognize the putative RNA‐binding regions by structurally aligning the query protein to the RNA‐binding proteins with known structures. The final RBRDetector algorithm is an ingenious fusion of our feature‐ and template‐based approaches based on a piecewise function. By validating our predictors with diverse types of structural data, including bound and unbound structures, native and simulated structures, and protein structures binding to different RNA functional groups, we consistently demonstrated that RBRDetector not only had clear advantages over its component methods, but also significantly outperformed the current state‐of‐the‐art algorithms. Nevertheless, the major limitation of our algorithm is that it performed relatively well on DNA‐binding proteins and thus incorrectly predicted the DNA‐binding regions as RNA‐binding interfaces. Finally, we implemented the RBRDetector algorithm as a user‐friendly web server, which is freely accessible at http://ibi.hzau.edu.cn/rbrdetector . Proteins 2014; 82:2455–2471. © 2014 Wiley Periodicals, Inc.