Synergic approach to XAFS analysis for the identification of most probable binding motifs for mononuclear zinc sites in metalloproteins

In the present work a data analysis approach, based on XAFS data, is proposed for the identification of most probable binding motifs of unknown mononuclear zinc sites in metalloproteins. This approach combines multiple‐scattering EXAFS analysis performed within the rigid‐body refinement scheme, non‐muffin‐tin ab initio XANES simulations, average structural information on amino acids and metal binding clusters provided by the Protein Data Bank, and Debye–Waller factor calculations based on density functional theory. The efficiency of the method is tested by using three reference zinc proteins for which the local structure around the metal is already known from protein crystallography. To show the applicability of the present analysis to structures not deposited in the Protein Data Bank, the XAFS spectra of six mononuclear zinc binding sites present in diverse membrane proteins, for which we have previously proposed the coordinating amino acids by applying a similar approach, is also reported. By comparing the Zn K‐edge XAFS features exhibited by these proteins with those pertaining to the reference structures, key spectral characteristics, related to specific binding motifs, are observed. These case studies exemplify the combined data analysis proposed and further support its validity.     

A degradable atom transfer radical polymerization inimer: Synthesis,polymerization, and cleavage of the resulting polymer products

A novel degradable inimer for atom transfer radical polymerization (ATRP), 2‐(6‐(2‐((2‐bromo‐2‐methylpropanoyl)oxy)ethyl)pyridin‐2‐yl)ethyl methacrylate (PyDEBrMΑ), was synthesized by the two‐step esterification of 2,6‐pyridinediethanol, first with α‐bromoisobutyryl bromide in order to introduce the initiator moiety, and then with methacryloyl chloride in order to introduce the monomer moiety. PyDEBrMA was subsequently used to initiate the self‐condensing ATRP of methyl methacrylate (MMA) to obtain a hyperbranched MMA homopolymer which could be cleaved at the PyDEBrMA residue either by treatment under mildly alkaline hydrolysis conditions (sodium deuteroxide in d₆‐DMSO at room temperature) or thermolysis at 150 °C. The lability of the PyDEBrMA residue arises from the presence in its structure of two 2‐(pyridin‐2‐yl)ethyl ester moieties. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2017 , 55, 2831–2839     

Competitive solvent extraction of alkaline earth metals by ionizable nano-baskets of calixarene

The competitive solvent extraction of alkaline earth metals using different nano-baskets was investigated. The novelty of this work is to study the correlations between the isomer structure of calixarenes and their extraction properties. The objective was to quantify the effects of aryl groups in the ionisable pendant moieties, calixarene conformation, steric orientations (cis- and trans-) and relative positions (ortho- and para-) of pendant moieties upon the extraction efficiency, pH_1/2 and the selectivity of calix[4]arene complexes. Alkaline earth metals were extracted from aqueous solutions into chloroform by di-ionisable calix[4]arenes and were measured using ion chromatography. The results revealed that alternation of aryl group in the pendant moieties, changing their orientation from cis- to trans-analogues as well as from ortho- to para- analogues, showed no changes in the selectivity, the extraction efficiency and the pH_1/2 of calix[4]arene complexes. Changing the scaffold of calixarene's ring to the cone, 1,2-alternate and partial-cone conformers altered their complexation ability towards alkaline earth metals and their extraction efficiency.     

十二烷基二甲基苄基氯化铵从碱性氰化液中固相萃取金的研究

建立了一种用十二烷基二甲基苄基氯化铵(BDMDAC)从碱性氰化液中固相萃取金的新方法：在碱性介质中,十二烷基二甲基苄基氯化铵溶液(BDMDAC)与Au(CN)2-络阴离子生成离子缔合物,该离子缔合物可被反相键合硅胶固相萃取柱萃取、富集,用乙醇洗脱,反相键合硅胶固相萃取柱可重复使用。该方法用于从碱性氰化液中固相萃取痕量金,萃取回收率可超过98%。     

从分子碎片到活性位：分子筛催化材料的原位、共振紫外拉曼光谱研究

在过去的近十年中,各种新型原位表征技术和反应器设计被应用于多相催化过程和催化材料的合成研究中,并获得了许多新认识．特别是最近几年,利用原位、共振拉曼光谱技术对分子筛合成关键物种检测、杂原子分子筛催化活性位的研究取得了一系列进展．这些技术的应用使得从分子水平认识复杂的多孔材料成为可能：从合成初期碎片基元检测、碎片相互连接的关键化学键到预组装类微孔结构;从高度隔离过渡金属中心到配位化学键断裂生成活性中间物种,再到完成催化反应循环．这为设计特定功能和结构的催化材料及高选择性的活性中心奠定了坚实的基础．     

Dephosphorylation of intact glycoprotein to greatly improve digestion efficiency coupled with matrix-assisted laser desorption/ionization–Fourier transform ion cyclotron resonance mass spectrometric analysis

Sialylation is essential for a variety of cellular functions. Herein, we used bovine fetuin with three potential N-linked glycosylation sites containing complex-type glycan structures, four potential O-linked glycosylation sites and six potential phosphorylation sites as a model compound to develop a highly-efficient digestion strategy for sialylated glycoproteins and efficient enrichment strategy for sialylated glycopeptides using titanium dioxide. The former according to the process of alkaline phosphatase digestion followed by tryptic digestion and then proteinase K digestion could greatly improve the enzymatic efficiency on fetuin, and the latter could obviously enhance the enrichment efficiency for multisialylated glycopeptides using phosphoric acid solution as elution buffer. The mass spectra of the enriched glycopeptides derived from fetuin reveal that several series of the ion clusters with mass difference of 291 Da correspond to the presence of multisialylated glycopeptides. In addition, the approach was applied to characterize the sialylated status of α2-macroglobulin and transferrin, respectively, from the sera of healthy subjects and sex- and age-matched patients with thyroid cancer, and their spectra indicate that the change in the amount of the glycoforms containing different number of sialic acid (SA) residues from one glycosylation site may be used to differentiate between healthy subjects and cancer cases.     

Resonant-Mie-scattering of aggregates of phosphomolybdate and papaverine for measuring activities and screening inhibitors of cyclic nucleotide phosphodiesterase isozymes

A resonant-light-scattering (RLS) method was proposed to quantify phosphate for screening inhibitors of isozymes of cyclic nucleotide phosphodiesterase (PDE). In acidified mixtures of phosphate, papaverine and molybdate, there were aggregates exhibiting micrometre sizes, no absorbance peaks over 360 nm but strong RLS peaks at 392 nm; Mie scattering thus accounted for the RLS signals. When papaverine was added before molybdate to acidified samples of phosphate, RLS signals at 392 nm were stable from 5 to 25 min since the addition of molybdate; after optimization, phosphate from 0.40 to 3.60 μM was quantifiable. This RLS method tolerated 60 mg L⁻¹ proteins besides common PDE inhibitors and dimethyl sulfoxide in acidified samples of phosphate; the integration of this RLS method with the coupled action of a phosphomonoesterase on PDE product was thus rational to measure PDE activities without the removal of proteins in samples. By quantifying activities of a truncated mutant of human PDE4B2 via this RLS method, Michaelis–Menten constant, inhibition constants of rolipram, papaverine and theophylline varied over three magnitudes and were consistent with those estimated by an improved malachite green assay of phosphate, respectively. Hence, this novel RLS method was promising for screening inhibitors of PDE isozymes.     

Regular arrays of triangular‐microstructure formed on silicon (111) surface via ultrafast laser irradiation in KOH solution

The regular micrometer‐scale triangular arrays were formed using ultrafast femtosecond laser irradiation on (111) surface of silicon wafer immersed in KOH solution (0.1 g/ml). At low laser fluence, the resulting surface is covered by triangular pits microstructures, whereas at high laser fluence, the structures are transformed to multilayer‐triangular stacks‐microstructures. The number of triangular stacks layer increased as the laser fluence increased. The formation of triangle microstructure arrays depends on both silicon surface crystallographic orientation and the concentration of KOH solution. Either for lower KOH solution concentration (0.02 g/ml) or other silicon crystallographic orientation, triangle arrays cannot be obtained. We attribute the formation of triangular microstructure arrays to the laser‐assisted chemical etching process. Copyright © 2013 John Wiley & Sons, Ltd.