在不同激发波长下的单壁碳纳米管的拉曼光谱研究

采用直流电弧法制备单壁碳纳米管样品,用457.5和632.8nm两种不同的激发光分别测得单壁碳纳米管的正常拉曼光谱和共振拉曼光谱.通过理论分析得到了单壁碳纳米管的直径分布,进一步推测了其类型及结构参数;对单壁碳纳米管的正切拉伸模的成分进行了归属.在632.8nm激发波长下得到了IG/ID值随激光功率变化的曲线,认为在2.5mW时,单壁碳纳米管缺陷的结构可能发生了改变.在用457.5nm波长激发的单壁碳纳米管的拉曼光谱中,首次发现了1421cm-1的拉曼谱峰.     

不同液化条件下生物质残渣的燃烧特性研究

对锯屑在不同液化条件（溶剂、气氛、温度、催化剂）下所得液化残渣在热天平上进行了燃烧特性研究,通过比较液化残渣燃烧的三个特征温度,着火点ti、燃烧峰温tp和燃烬温度tb,分析了液化条件对残渣燃烧特性的影响。同时通过热重曲线所得数据探讨了液化残渣燃烧过程的动力学,并计算了活化能和频率因子 。结果表明,不同溶剂下所得液化残渣的燃烧特性显著不同,以四氢萘为溶剂所得液化残渣具有较好的燃烧特性;不同气氛下所得残渣的燃烧特性没有明显的不同;350℃下所得液化残渣的燃烧特性要好于300℃下所得液化残渣的燃烧特性;由于催化剂的影响,加入1%Mo后降低了所得液化残渣的燃烧特性;液化残渣的燃烧反应符合两段一级反应动力学。     

透明质酸酶的色氨酸残基修饰与荧光光谱研究

北五味子[Schisandra chinensis（Turcz．）Baill．]属广义木兰科植物,主产于我国东北,故又称“辽五味”,中药五味子的主要药材为北五味子的干燥果实,作为一种传统中药,五味子具有收敛固涩,益气生津,补肾宁心的功效,用于肺喘虚咳,心悸失眠诸病。     

菊粉酶中色氨酸残基的化学修饰及其荧光光谱

用N-溴代琥珀酰亚胺为修饰剂, 研究菊粉酶中的Trp残基的分布及其对酶生物学功能的影响, 为进一步研究菊粉酶结构与其功能之间的关系提供了新的信息.     

自由基引发剂用于渣油减黏裂化的研究

基于热裂化按照自由基反应机理进行的特点,在高压釜式反应器中分别添加四种自由基引发剂偶氮二异丁腈(AIBN)、过氧化特二丁基(DTBP)、单质硫(S)和单质碘(I2),考察引发剂在390℃～410℃,引发剂添加量0～3000×10-6条件下对三种减压渣油减黏裂化的影响。通过测定减黏前后渣油的运动黏度和四组分的变化,对引发剂的作用机理进行了初步研究。结果表明,自由基引发剂对不同基属的减压渣油减黏裂化反应均有明显的促进作用,大小依次为:LHVR≥GDVRDQVR,并且这种促进作用在较低的反应温度下更加明显,促进效果由渣油本身的物理化学性质所决定。在同等条件下,I2和S促进渣油减黏的效果是AIBN和DTBP降黏率的两倍,这与S和I2形成氢化物的"活性原子"可以多次循环发生作用有关。与S相比,单质I2减黏促进作用更为明显。     

Tryptophan Modification and Fluorescence Spectrum of Hyaluronidase

Tryptophan residues in hyaluronidase （HAase） were modified by N-bromosuccinimide （NBS）, the results indicated that there were eleven tryptophan residues in HAase, one of which was exposed and essential for the activity of the enzyme. The study on fluorescence quenching showed that KI could not quench all of the fluorescence from Trp residues in HAase, while acrylamide （Acr） could quench almost all of the fluorescence from Trp residues in HAase. The collisional quenching constants （KD） of HAase at different concentrations of Acr were calculated in terms of Stern-Volmer equation. The results implied that some of the Trp residues were buried in the interior of HAase and the Trp residue on the surface of HAase was not located in the hydrophobic pocket.     

Novel Concepts for the Immunological Detection of Bound Residues

Abstract

Immunoassays could be applied successfully to the determination of bound residues in soil and other complex matrices. Nevertheless, there was some doubt whether these assays could be regarded as quantitative and selective. We present some results, which imply that several approaches are quite promising. One approach is based on a non-competitive saturation immunoassay, which evens out the different cross-reactivities of the bound species. This may lead to a true molar sum value, which is not an equivalent concentration. For competitive assays, a method for the determination of the affinity constant(s) of the bound species is discussed. This would enable a correction for the cross-reactivity. The selectivity problem could be diminished very much, too. The application of special blocking reagents and the use of inhibition tests essentially solved the problem of non-specific binding (NSB). In addition, it could be proven experimentally that adsorbed analytes do not disturb the non-competitive assays, which have been suspected to be highly selective for covalently bound residues.     

Synthesis and hybridization properties of oligonucleotides containing polyamines at the C-2 position of purines: a pre-synthetic approach for the incorporation of spermine into oligodeoxynucleotides containing 2-(4,9,13-triazatridecyl)-2'-deoxyguanosine

We have developed a synthesis of spermine-containing oligonucleotides (ODN-sper) which allows incorporation of multiple polyamine residues. This approach was based on the pertrifluoroacetylated 5'DMT-dGsper phosphoramidite synthon. Its coupling yield with resin-bound ODN decreased dramatically when close to the 3'-end. Optimization of the coupling conditions allowed 22-mer ODNs containing up to six spermine residues to be synthesized. Several ODNs of different sequences with 1-4 pendent spermines could be purified and their hybridization properties were evaluated. Duplex melting temperatures increased linearly with the number of polyamine residues (deltaTm/sper = 3.0 +/- 0.2 degrees C in 100mM NaCl). This compares very favorably with values reported for duplexes of similar initial stability containing other cation-substituted bases. Moreover, the stability increase was neither sequence nor position-dependent, and even contiguous spermine residues did not cross-talk. Extrapolation based on these findings leads to the conclusion that a duplex formed with a 22-mer oligonucleotide containing seven spermine residues would be as stable as genomic DNA, which highlights its potential for DNA strand invasion.     

Molecular Modeling and Docking of Mannose-binding Lectin from Lycoris radiata

Lycoris radiata mannose-binding lectin（LRL） is a protein which binds mannose residues specifically. The maturation peptide and three mannose-binding domains（residues 49-57, 80-88 and 113--121） of LRL were identified by sequence analysis. The 3D structure of LRL constructed by homology modeling shaped a flstular triangular prism. Three flanks of the prism are mainly composed of β-sheets and each flank has a mannose-binding domain. According to the docking and dynamics simulation, the bindings of residues 49--57 and 80--88 with mannose are more stable than that of residues 113--121 with it. The key residues for binding mannose are Gin80, Asp82, Ash84 and Tyr88. The study preliminarily analyzed the interaction sites and mechanism of LRL with mannoses, which could be useful for the study on insect-resistance and related drug discovery of LRL.     

Quantitative proteomics reveals the kinetics of trypsin-catalyzed protein digestion

Trypsin is the popular protease to digest proteins into peptides in shotgun proteomics, but few studies have attempted to systematically investigate the kinetics of trypsin-catalyzed protein digestion in proteome samples. In this study, we applied quantitative proteomics via triplex stable isotope dimethyl labeling to investigate the kinetics of trypsin-catalyzed cleavage. It was found that trypsin cleaves the C-terminal to lysine (K) and arginine (R) residues with higher rates for R. And the cleavage sites surrounded by neutral residues could be quickly cut, while those with neighboring charged residues (D/E/K/R) or proline residue (P) could be slowly cut. In a proteome sample, a huge number of proteins with different physical chemical properties coexists. If any type of protein could be preferably digested, then limited digestion could be applied to reduce the sample complexity. However, we found that protein abundance and other physicochemical properties, such as molecular weight (Mw), grand average of hydropathicity (GRAVY), aliphatic index, and isoelectric point (pI) have no notable correlation with digestion priority of proteins. Graphical Abstract

Sequence logos of four cleavage site types with different kinetics (very fast, fast, slow, and very slow sites)     

The substrate specificity of a glucoamylase with steroidal saponin-rhamnosidase activity from Curvularia lunata

In previous work, we studied and reported that an enzyme from Curvularia lunata 3.4381 had the novel specificity to hydrolyze the terminal rhamnosyl at C-3 position of steroidal saponin and obtained four transformed products; the enzyme was purified and ascertained as glucoamylase (EC 3.2.1.3 GA). In this work, the enzyme exhibiting steroidal saponin-rhamnosidase activity was systematically studied on 21 steroidal saponins and 6 ginsenosides. The results showed that the α-1,2-linked end-rhamnosyl residues at C-3 position of steroidal saponins could be hydrolyzed to corresponding secondary steroidal saponins, among which 18 compounds were isolated and identified, including 3 new secondary compounds. For the furostanosides having glucosyl residues at the C-26 position, hydrolysis occurred first at end-rhamnosyl at C-3 position to produce secondary furostanosides. The reaction of hydrolyzing glucosyl at C-26 position depended considerably on longer reaction times yielding the corresponding secondary spirostanosides (without rhamnosyl and glucosyl residues). The enzyme had the strict specificity for the terminal α-1,2-linked rhamnosyl residues of linear chain, or the terminal α-1,2-linked rhamnosyl residues with branched chain of 1,4-linked glycosyl residues of sugar chain at C-3 position of steroidal saponins, it was not specific for different aglycones, different glycons, and the number of glycon of sugar chain of steroidal saponin. The end-rhamnosyl of ginsenosides and p-nitrophenyl-α-l-rhamnopyranoside (pNPR) could not be hydrolyzed by the enzyme from C. lunata.     

A molecular docking model of SARS-CoV S1 protein in complex with its receptor, human ACE2

The exact residues within severe acute respiratory syndrome coronavirus (SARS-CoV) S1 protein and its receptor, human ACE2, involved in their interaction still remain largely undetermined. Identification of exact amino acid residues that are crucial for the interaction of S1 with ACE2 could provide working hypotheses for experimental studies and might be helpful for the development of antiviral inhibitor. In this paper, a molecular docking model of SARS-CoV S1 protein in complex with human ACE2 was constructed. The interacting residue pairs within this complex model and their contact types were also identified. Our model, supported by significant biochemical evidence, suggested receptor-binding residues were concentrated in two segments of S1 protein. In contrast, the interfacial residues in ACE2, though close to each other in tertiary structure, were found to be widely scattered in the primary sequence. In particular, the S1 residue ARG453 and ACE2 residue LYS341 might be the key residues in the complex formation.     

A highly ordered hydrogen-bonded network

Self-assembled, hydrogen bonded, supramolecular complexes based on the interaction of pyridine with carboxylic acids have been synthesized. These contain different proportions of a compound with two terminal benzoic acid residues and a pentaerythritol-based tetra-pyridyl. They have been investigated for possible mesomorphic properties. Surprisingly for a tetrahedral pentaerythritol-based complex, a mesophase was observed with a grainy microscopic texture, which was fluid and could be sheared. The mesogenic unit is formed on hydrogen bonding complexation between the pyridyl residues and the carboxylic acid residues. Infrared spectra, as a function of the temperature, were recorded for the 1:1 complex; these show pyridyl complexation and changes on isotropisation. These changes are discussed in terms of the hydrogen bonding. Fibres could be drawn from the (mesophase) melt, supporting a polymeric, extended-chain structure for the complexes.     

XPS investigation of the composition of the external surface of concrete after demoulding,cleaning and carbonation

X‐ray photoelectron spectroscopy (XPS) coupled with ion beam etching allows the measurements of concentrations gradients at the external surface of concrete. The chemical modifications, caused by the moulding and cleaning operations and due to carbonation, are efficiently investigated. Based on the detection of specific elements (such as chlorine, carbon and silicon), the presence of formworks residues is established on the concrete surface. Similarly, aliphatic (C –(C,H) and carbonaceous (C –O) residues of the demoulding agent can be detected. The concentration gradients show the presence of moulding residues is mainly superficial and decreases rapidly according to the depth. However, certain of these contaminants (and especially polydimethylsiloxane residues) could alter the wetting of aqueous‐based coatings. The sandblasting process can partially remove the moulding residues, but the decontamination remains incomplete in spite of the high increase of the roughness of the samples. On the contrary, the concentrations in aliphatic and carbonaceous residues increase after cleaning with solvents, which can be trapped in the pores of concrete to contaminate the surface. The carbonation process is also investigated by XPS. The concentration gradient of the carbonate component of the C 1 s peak shows a front of carbonation progressing as a function of the time after demoulding. Copyright © 2012 John Wiley & Sons, Ltd.     

Observation of highly flexible residues in amyloid fibrils of the HET-s prion

We report the observation of undetected (until now) residues of the prion protein fragment HET-s(218-289) which give rise to well-resolved (13)C, (15)N, and (1)H NMR resonances under high-resolution magic-angle spinning (HRMAS) conditions. The observed signals belong to large polymeric units as shown by measuring the lateral diffusion constants. The amino acids identified in the spectra are compatible with their localization in the segments of the protein which could not be detected in earlier solid-state NMR experiments. The observed chemical shifts indicate that these residues are in a random-coil conformation. Complementary experiments which detect only dynamic or static residues, respectively, strongly suggest that they belong to different parts of the same molecule.     

Preparation and flammability of a novel intumescent flame-retardant poly(ethylene-co-vinyl acetate) system

A phosphorus-containing flame retardant, 4-(5,5-dimethyl-2-oxo-1,3,2-dioxaphosphorinan-2-yloxymethyl)-2,6,7-trioxa-1-phospha-bicyclo[2.2.2]octane-1-oxide (MOPO), was synthesized successfully and characterized. The flame retardancy and thermal behavior of a new intumescent flame-retardant (IFR) system for EVA, which was made of MOPO and ammonium polyphosphate (APP), were investigated by limiting oxygen index (LOI) test, vertical burning test (UL-94), cone calorimeter, and thermogravimetric analysis (TGA). An LOI value of 28.4 and UL-94 V-0 rating can be achieved when the total loading of MOPO and APP was 30 wt.%. The results from cone calorimeter indicate that both the heat release rate (HRR) and the total heat release (THR) of IFR-EVA decreased significantly compared with those of neat EVA. TG curves showed that the amount of residues increased significantly when intumescent additives were added; it also could be found that the LOI values increased with the increase in char residues. Meanwhile, morphology of the residues obtained from burning IFR-EVA in LOI test was studied through the SEM observations and rich compact char layers could explain the excellent flame retardance.     

Nitrite-Mediated Inactivation of Human Plasma Paraoxonase-1: Possible Beneficial Effect of Aromatic Amino Acids

Paraoxonase-1 (PON-1) is a high-density-lipoprotein-bound enzyme, and its major function is to prevent oxidation of low-density lipoprotein. Atherogenesis could be related to decreased activity of this enzyme. Nitrites (), either present as a contaminant and/or the main metabolic end product of nitric oxide (NO) degradation, may trigger nitrative damage to PON-1 enzyme. Minimal information is available concerning the effect of nitrite on the enzyme activity and the mechanism which it exerts its effect. The aim of this study was to analyze whether nitrites could play a role in modifying human PON-1 activity. Our results revealed that PON-1 activity was inhibited by nitrite in dose- and time-dependent manner. Site-specific nitration focused on phenolic residues, particularly tyrosine residues of the enzyme, may result in modification of its biological functions. Nitration of phenolic residues occurs via peroxynitrite (ONOO⁻) formation, which requires peroxides and nitrite. Thus, we tested the presence of peroxides, which are found in all plasma samples regardless of nitrite concentration. The inhibition of PON-1 activity by nitrite was significantly reduced by tryptophan, reduced glutathione (GSH), and catalase additions. Therefore, we concluded that nitrites may have a role in the inactivation of PON-1, probably through nitration of enzyme phenyl residues, and additions of individual aromatic amino acids, with highlighting on tryptophan, could be of important value in minimizing the nitrite-induced inhibition of PON-1 enzyme.     

A molecular dynamics investigation on the interaction properties of AzrC and its cofactor

In this report, the main contributions of FMN were employed in the reductive cleavage reaction of AzrC protein (as a member of azoreductase family). Molecular dynamics simulations of three models in the presence and absence of FMN and ligand were performed to gather information about the dynamic nature of active site residues of AzrC. Combination of pairwise decomposition and alanine scanning calculations provides critical information about the FMN binding sites. The MD results analyzed by alanine scanning method revealed the high negative scores for N 10 (A) A, N 12 (A) A, S 17 (A) A and Y 151 (A) A mutations, which were in agreement with pairwise decomposition analyses. Hydrogen bond analyses indicated that these residues play critical roles in establishing appropriate hydrogen bonds between AzrC and FMN. Negative energy results for nonpolar residues such as W 103 (A), M 102 (A) and F 105 (A) and binding free energy analyses of three complexes indicate that the VDW interactions could be regarded as some favorable contribution in FMN and AzrC protein and confirmed the critical role of FMN in ligand binding (35.84 %), in addition to its catalytic function. This information could be used for future experimental investigations.     

Design of radical-resistant amino acid residues: a combined theoretical and experimental investigation

Ab initio calculations have been used to design radical-resistant amino acid residues. Optimized structures of free and protected amino acids and their corresponding alpha-carbon-centered radicals were determined with B3-LYP/6-31G(d). Single-point RMP2/6-31G(d) calculations on these structures were then used to obtain radical stabilization energies, to examine the effect of steric repulsion between the side chains and amide carbonyl groups on the stability of alpha-carbon-centered peptide radicals. Relative to glycine, the destabilization for alanine and valine residues was found to be approximately 9 and 18 kJ mol(-1), respectively, which correlates with the reactivity of analogous amino acid residues in peptides toward hydrogen atom abstraction in conventional free radical reactions. To design amino acid residues that would resist radical reactions, strategies by which the steric effects could be magnified were considered. This resulted in the identification of tert-leucine and 3,3,3-trifluoroalanine as suitable molecules. With these amino acid residues, the destabilization of the alpha-carbon-centered radicals relative to that of glycine is increased substantially to approximately 36 and 41 kJ mol(-1), respectively. The theoretical predictions have been supported by experimental observations: a tert-leucine derivative was shown to be very slow to react with N-bromosuccinimide, while the corresponding trifluoroalanine derivative was found to be inert.     

Spectrochemical study for the in situ detection of oil spill residues using laser-induced breakdown spectroscopy

Laser-induced breakdown spectroscopy (LIBS) has been used to identify the differences or similarities between crude oil and fuel residues. Firstly, a man portable LIBS analyzer was used for the on-site environmental control and analysis of the oil spill from The Prestige. An exhaustive analysis of crude oil and oil spill residues (collected during the field campaign in the Galician Coast) was performed in the laboratory. Characteristics elements in petroleum such as C, H, N, O, Mg, Na, Fe and V were detected. In addition, contributions from Ca, Si and Al in the composition of residues have been found. The use of intensity ratios of line and band emissions in the original fuel (crude oil) and in the aged residues allowed a better characterization of the samples than the simple use of peak intensities. The chemical composition between the crude oil and the fuel residues was found completely different. As well, a statistical method was employed in order to discriminate residues. Although significant differences were observed, no conclusions in terms of age and provenance could be reached due to the unknowledgment in the origin of the samples.