TargetATPsite: A template‐free method for ATP‐binding sites prediction with residue evolution image sparse representation and classifier ensemble

Understanding the interactions between proteins and ligands is critical for protein function annotations and drug discovery. We report a new sequence‐based template‐free predictor (TargetATPsite) to identify the Adenosine‐5′‐triphosphate (ATP) binding sites with machine‐learning approaches. Two steps are implemented in TargetATPsite: binding residues and pockets predictions, respectively. To predict the binding residues, a novel image sparse representation technique is proposed to encode residue evolution information treated as the input features. An ensemble classifier constructed based on support vector machines (SVM) from multiple random under‐samplings is used as the prediction model, which is effective for dealing with imbalance phenomenon between the positive and negative training samples. Compared with the existing ATP‐specific sequence‐based predictors, TargetATPsite is featured by the second step of possessing the capability of further identifying the binding pockets from the predicted binding residues through a spatial clustering algorithm. Experimental results on three benchmark datasets demonstrate the efficacy of TargetATPsite. © 2013 Wiley Periodicals, Inc.     

Surfactant-Free Multiple Pickering Emulsions Stabilized by Combining Hydrophobic and Hydrophilic Nanoparticles

A series of W/O/W or O/W/O emulsion stabilized solely by two different types of solid nanoparticles were prepared by a two-step method. We explored the option of particular emulsifiers for the multiple Pickering emulsions, and a variety of nanoparticles (silica, iron oxide, and clay) only differing in their wettability was used. The primary W/O emulsion was obtained by the hydrophobic nanoparticles, and then the hydrophilic nanoparticles were used as emulsifier in the secondary emulsification to prepare the W/O/W emulsion. In a similar way, the primary O/W emulsion of the O/W/O emulsion was stabilized by the hydrophilic nanoparticles, while the secondary emulsification to prepare the O/W/O emulsion was effected with the hydrophobic nanoparticles. The resultant multiple Pickering emulsion was stable to coalescence for more than 3 months, except the W/O/W emulsions of which the secondary emulsion stabilized by clay nanoparticles became a simple O/W emulsion in a day after preparation. Moreover, the temperature and pH sensitive poly(N-isopropylacrylamide-co-methacrylic acid) (P(NIPAm-co-MAA)) microgels were introduced as an emulsifier for the secondary emulsification to obtain the stimulus-responsive multiple W/O/W emulsion. Such microgel-stabilized multiple emulsions could realize the efficient controlled release of water-soluble dye, Rhodamine B (RB) on demand in a multiple-emulsion delivery system.      

Synthesis and Properties of Aromatic Side Chained N‐Acyltaurate Surfactants

A series of anionic N‐acyltaurate surfactants, side chain containing aromatic nucleus (abbreviated as SAATT), were synthesized via Williamson reaction, hydrolyzation, and acylation. Krafft temperatures and surface properties of these surfactants at 30°C, that is, critical micelle concentration, cmc, surface excess concentration, Γ_max, surface area demand per molecule, A _min, efficiency in surface tension reduction, pC₂₀, effectiveness in surface tension reduction, π_cmc, and cmc/C₂₀ parameter were determined. It was shown that these surfactants exhibit good solubility which was confirmed by measuring Krafft temperature. The cmc of SAATT was much smaller than that of conventional surfactants with similar effective carbon numbers, and shifted to lower concentration with increasing hydrocarbon chain length. In addition, the γ_cmc decreased with decrease in Γ_max. The pC₂₀ and the cmc/C₂₀ got larger with the increase in hydrocarbon chain length. From the fluorescence intensity ratios of I ₁ (373 nm) and I ₃ (384 nm) using pyrene as a probe, it was indicated that the molecules of SAATT formed loose micelles with a broad size distribution.     

Synthesis of Two Schiff Base Transition Metal Complexes Bearing Morpholine Side Chains and Kinetics of PNPP Catalytic Hydrolysis in Brij35 Micelle

Two Schiff base transitional metal complexes bearing morpholine side chains were synthesized and characterized, and were used as a simulative hydrolase in the catalytic hydrolysis of p‐nitrophenyl picolinate (PNPP) in this article. A mechanism of PNPP catalytic hydrolysis in the Brij35 micellar solution was proposed and supported by the results of the spectral analysis and the kinetic calculation. The kinetic model of PNPP catalytic hydrolysis was studied. The some kinetic and the thermodynamic constants on the catalytic reaction were calculated. The results of the study show that the metallomicelle made up of the Schiff base transitional metal complexes and Brij35 micelle revealed a good catalytic activity in PNPP catalytic hydrolysis; the rate of the PNPP catalytic hydrolysis is increased following the increase of the pH values in the buffer solution and affected by the polarization action of metal ion of complex.     

Studies on the Effects of Additional Components on Micellization of CTAB via Surface Tension Measurements

The effects of Tris-HCl buffer solution on the cmc of cetyltrimethylammonium bromide (CTAB) were studied by surface tension measurement. The result shows that the effect of the buffer solution depends on the interaction between CTAB and NaCl and the structure accelerants of water, Tris. A series of parameters, including the critical micelle concentration (cmc), the surface tension at cmc (γ_cmc), the adsorption efficiency (pC₂₀), and the effectiveness of surface tension reduction (∏_cmc) were obtained from the surface tension measurements in the presence of glycine with different concentration in the Tris-HCl buffer solution at 27°C. In addition, maximum surface excess concentration (Γ _max) and minimum surface area per molecule (A_min) at the air-water interface were estimated according to the Gibbs adsorption isotherm. The thermodynamic parameters (Δ C _p,m , Δ H _m,tr , Δ C _p,m,tr ) of micellization for CTAB in the absence and presence of glycine at different temperature were also been obtained.     

Synthesis and Characterization of Mesoporous Silica Templated by Amphiphilic RTILs

This article reports a novel preparation of mesoporous silica with series of 1-alky-3-methylimidazolium bromide (C_nMIM)Br (n = 12, 14, 16), a kind of amphiphilic room-temperature ionic liquids (RTILs), as a template via a sol-gel nanocasting technique. The pore morphology and structures of these mesoporous silica were characterized by Transmission electron microscopy (TEM). The results show that the RTIL bearing longer alkyl chain is preferred to form the mesoporous silica material with bigger pores. (C₁₆MIM)Br has been chosen to study how the various influencing factors affect the synthesis and structure of the mesoporous silica material, such as the acid concentration, the solling time, the gelling time and the calcination time. N₂ adsorption-desorption isotherms measurement was used to characterize the pore size distribution and BET surface area. The results indicate that all of the factors can make an influence on the preparation of the mesoporous silica, which is more sensitive to the concentration of the acid.     

在线质谱仪检测植物排放的挥发性有机物

利用在线检测质谱仪(SPIMS-1000)分别对高温烘烤、长时间密封保存、机械损伤等处理过的松科松属马尾松(Pinus Massoniana L.)样品排放的挥发性有机物(VOCs)与新鲜样品进行对比检测。SPIMS-1000在线检测质谱仪能够检测出植物排放的异戊二烯(m/z 68)和单萜(m/z 136),及其它一些特异性组分,如(Z)-3-己烯醛(m/z 98)等。利用在线检测质谱仪实现敞开环境中原位植物排放气体的检测。实验表明,在线检测质谱仪被广泛应用于环境中VOCs的实时、在线、定性快速检测。     

气相色谱法测定海洋沉积物中十氯酮残留

研究了提取溶剂效率、毛细管柱极性、净化条件及共溶出干扰物等因素对十氯酮测定的影响;对比了加速溶剂提取及超声波提取方式,考察了DB-17、DB-1701与DB-5毛细管柱分离度,及不同比例甲醇/正己烷混合溶液作为定容溶液的分析结果。建立了加速溶剂萃取,H2SO4净化分离,DB-5毛细管柱电子捕获检测器(ECD)-气相色谱法(GC)测定海洋沉积物介质中有机氯农药类持久性有机污染物十氯酮残留分析方法。将5 g沉积物干样与3 g活化铜粉及3 g无水Na2SO4混匀后,采用二氯甲烷-丙酮(1∶1,V/V)进行加速溶剂萃取;萃取液浓缩后,用H2SO4净化,以1%甲醇-正己烷混合溶液定容后,采用DB-5非极性毛细管柱,及配备电子捕获检测器气相色谱测定十氯酮含量。本方法采用外标法进行定量分析,在0.005～0.1 mg/L浓度范围内,线性相关系数为0.9989;加标回收率为75%～98%;相对标准偏差为3.7%～9.6%(n=6);检出限为0.12 ng/g。     

宽离子能量检测范围垂直引入反射式飞行时间质谱仪的研制

本实验室研制了国内首台宽离子能量检测范围飞行时间质谱仪。仪器采用紧凑式电子轰击源设计,配合离子透镜系统有效的调制离子流,飞行时间质量分析器采用了离子垂直引入式,双场加速和双场反射以及大尺寸MCP检测装置设计。仪器单离子信号半峰宽约2 ns,仪器分辨率优于1600FWHM,检测实际样品质量范围为1~127 amu(仪器理论质量检测上限优于800 amu),可检测离子能量范围优于2个数量级(3~140 eV)。若该TOF质量分析器与短瞬高压脉冲放电离子源耦合联用,可广泛应用于高能离子束的快速检测,如真空阴极放电对制备薄膜、离子注入材料的表征,导电材料的离子电荷态分布以及离子扩散速度的测定等。     

Synthesis, Structure and Properties of a Novel Cobalt(Ⅱ) Bromide Complex Supported by Phosphine Ligands

<正>The C-Br bond of 2-bromothiophene was successfully cleavaged by tetrakis(trimethylphosphine)cobalt(0). Penta-coordinate cobalt(II) bromide complex 1 (α-C_4H_3S)CoBr(PMe_3)_3 as C-Br bond activation product was obtained. The molecular and crystal structures of complex 1 were determined by single-crystal X-ray diffraction. Complex 1 belongs to the orthorhombic crystal system, space group Pnma with a = 20.428(4) , b =11.036(2) , c = 9.201(2), V = 2074.3(7)~3, Z = 4, D_c = 1.442 g/cm~3, μ = 0.401 mm~(-1), F(000) = 924 and T = 273 K. Complex 1 was also characterized by elemental analysis, IR, UV-Vis, photoluminescence (PL) spectroscopy and TGA.