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.     

The Effects of Alcohol with Different Chain Length on the Phase Equilibria of Nonionic Surfactant System

Addition of alcohol with longer chain length (C₆H₁₃OH, C₈H₁₇OH, and C₁₂H₂₁OH) caused a reduction the cloud point of a commercial nonionic surfactant, Tesgitol (T_15-s-9). The formation of lamellar liquid crystal (LLC) was favored so that isotropic liquid (L₁)-LLC two-phase region became wider with increasing temperature at an appropriate weight ratio of surfactant to alcohol. The isotropic liquid phase/liquid two phase transformation was replaced by a two-phase transformation to isotropic liquid/lamellar liquid crystal at the cloud point for the system without alcohol.     

Core/Shell Structured PCM Nanocapsules Obtained by Resin Fortified Emulsion Process

Phase change material (PCM, octadecane) nanocapsules were successfully prepared by resin fortified emulsion (RFE) polymerization using the alkali soluble resin (ASR) of poly(ethylene‐co‐acrylic acid) (EAA) and poly(styrene‐co‐acrylic acid) (SAA). Stable PCM nanocapsules were obtained by resin fortified emulsion polymerization, which could be attributed to the prevention of Ostwald ripening due to PCM being hydrophobic. Analysis of online FTIR measurements throughout the reaction confirmed that the nanocapsules contained octadecane as a PCM. TEM imaging of the PCM nanocapsules showed spherical and core/shell morphology. The characteristics of PCM nanocapsules can be controlled by process parameters. As a result, the particle size and particle size distribution (i.e., polydispersity index (Dw/Dn)) of the PCM nanocapsules were created by adjusting manufacturing conditions. The PCM nanocapsules exhibited thermal energy storage (～49.8 J/g) and release (～47.9 J/g) behavior.     

超临界水中钾对甲醛降解过程影响的研究

为掌握生物质中钾对生物质超临界水降解过程的影响,选择生物质气化转化过程中生成的重要小分子中间产物甲醛作为研究对象,研究不同工艺条件下(反应温度400～650℃、压力23～29 MPa、停留时间4～12 s),单一钾成分(KHCO₃/K₂CO₃/KCl)或混合钾成分(KHCO₃、K₂CO₃、KCl)对甲醛超临界水降解气体产物的影响。结果表明,KHCO₃、K₂CO₃、KCl、混合钾均降低了气体产物中CO的体积分数,提高了CO₂的体积分数,但KCl的影响程度弱于其他三种钾成分。此外,由于不同钾成分均不利于气体产物中CO和H₂体积分数的提高,从而使得气体产物的热值降低。KHCO₃、K₂CO₃、KCl、混合钾均降低了H₂、CO、CO₂的产率以及气化率,其对H₂产率以及气化率的抑制程度从大到小依次为:混合钾、KHCO₃、K₂CO₃、KCl,且提高反应温度、延长反应停留时间时抑制气体生成的作用相对越明显。而当反应压力改变时,钾成分对H₂产率及气化率的影响程度变化较小。较高反应温度、较高反应压力、较长停留时间时,混合钾中各成分出现协同作用,明显抑制了气体产物的生成。     

奎宁-杂多酸杂化催化剂催化H2O2为氧源的苯羟基化反应

将奎宁与Keggin结构磷钼钒杂多酸结合制备出一种新颖的多相苯羟基化杂化催化剂, 采用傅里叶变换红外光谱、紫外-可见光谱、X射线衍射、扫描电镜、热重、N₂吸附-脱附和CHN元素分析等表征手段对催化剂进行了分析. 结果表明, 该催化剂是一种具有较高比表面积和孔体积的半无定形有机杂多酸盐. 在H₂O₂为氧源的苯羟基化反应中, 杂化催化剂引导了液-固两相催化体系, 表现出较高催化活性和重复使用稳定性. 催化剂中奎宁与杂多阴离子间的氢键和电子相互作用赋予了其高熔点和难溶性, 而高比表面积和因奎宁而改善的杂多阴离子的氧化还原性是其获得优异催化性能的主要原因. 这为多相苯羟基化反应提供了一种新的且制备便捷的基于多金属氧酸盐的高效催化剂.     

超临界流体中制备微孔和介孔结构金属有机框架负载Ru及其催化性能

以柠檬酸为螯合剂,十六烷基三甲基溴化胺为表面活性剂,通过ZrOCl2·8H2O 与对苯二甲酸 (H2BDC) 反应制备了同时具有微孔和介孔结构的Zr基金属有机骨架材料(Zr-MOF),并在超临界CO2-甲醇流体中将 Ru 负载于 Zr-MOF 上, 制备了 Ru@Zr-MOF催化剂,采用傅里叶变换红外光谱、X射线粉末衍射、透射电子显微镜、热重分析、N2吸附-脱附、X射线光电子能谱和电感耦合等离子体发射光谱对催化剂进行了表征,研究了该催化剂在苯及其同系物加氢反应中的催化性能. 结果表明,Ru纳米金属颗粒均匀地分散在Zr-MOF载体上,平均粒径约为2.3nm,在苯及其同系物的加氢反应中表现出很高的催化活性和稳定性.     

Synthesis,Characterization, and Crystal Structure of One Novel Indolo[3,2-b]carbazole Derivative

Indolocarbazole derivatives have been reported to be promising organic semicon- ductor candidates and electroluminescent （EL） materials. One novel indolocarbazole derivative, 2,8-acetyl-5,11-dihexyl-6,12-（di-p-tolyl）-5,11-indolo[3,2-b]carbazole （YK4）, has been synthesized, and its crystal structure has also been carefully studied. YK4 is triclinic, space groups Pi with a = 9.409（5）, b = 13.974（5）, c = 15.488（5） A, α = 90.281（5）, β = 105.456（5）, Z= 93.728（5）°, M,. = 688.94, V= 1958.1（14） A3, Z = 2, Dc.= 1.168 g/cm-3,μ = 0.070 mm-1, F（000） = 740, Rint = 0.0475, R （I〉 20（/）） = 0.1146, wR （I〉 20（/）） = 0.2186, R（all data） = 0.2192 and wR （all data） = 0.2701. Like other indolo[3, 2-b]carbazole derivatives which were introduced in the 5- and 11-positions, the intermolecular short contacts are localized between the pendant groups and acetyl groups of the neighboring indolocarbazole molecules. The molecule of YK4 possesses poor face-to-face π-π stacking between two adjacent molecules in the crystal. The calculated bond lengths and bond angles of YK4 also proved the result of crystallography.     

Self-assembled discotic nematic liquid crystals formed by simple hydrogen bonding between phenol and pyridine moieties

New discotic nematic liquid crystals have been prepared through intermolecular hydrogen bonding between the core of 1,3,5-trihydroxybenzene (phloroglucinol, PG) or 1,3,5-tris(4-hydroxyphenyl)benzene (THPB) and the peripheral molecules of stilbazole derivatives. The various nematic phases formed by new hydrogen bonding building blocks were investigated by differential scanning calorimetry, polarising optical microscopy and X-ray diffraction. The first discotic complexes of PG and trans-4-alkoxy-4′-stilbazoles exhibited nematic columnar (N_C) and hexagonal columnar phases depending on the length of alkyl chains, which were considered as the basic discotic structure. Several structural variations on the building blocks were attempted to examine their effects on the liquid crystalline properties of discotic complexes. The nematic lateral phase (N_L) with enhanced intercolumnar order was observed for the complexes of PG and trans-4-cyanoalkoxy-4′ stilbazoles due probably to the strong dipole interactions between cyano groups at the end of alkoxy chains. By introducing the nonlinear structure in three arms of supramolecular discotic mesogen, a discotic nematic phase (N_D) was observed for the complex of THPB and trans-4-octyloxy-4 -stilbazole. The single hydrogen bonding between phenol and pyridine moieties in this study provides a simple and effective method for preparing the rarely found discotic nematic liquid crystals.     

Effect of introducing thioether linkages on the molecular organization of chiral twin liquid crystals

Novel symmetric and non-symmetric chiral twin compounds possessing one or two thioether groups in a central spacer were prepared, and the effect of substituting oxygen for sulphur on the liquid crystalline properties investigated. Chiral twin compounds possessing an alkylsulphanyl spacer showed an antiferroelectric phase exclusively. However, replacing the alkyloxy chain of the analogous monomer by the alkylsulphanyl chain has no significant effect on the phase transition behaviour, i.e. both of the monomers showed the ferro- and ferri-electric phases as well as the antiferroelectric phase. Thus, different effects of introducing the thioether linkage were for the first time observed between twin and monomeric systems. The introduction of oxygen or sulphur atoms into the central alkyl spacer of the chiral twin was also investigated, and these modifications were found to stabilize the SmA phase. Furthermore, the twin compound possessing a thiaalkyl spacer showed two different molecular assemblies in the smectic A phase.     

The Effect of Albumin Fusion Patterns on the Production and Bioactivity of the Somatostatin-14 Fusion Protein in Pichia pastoris

Somatostatin is a natural inhibitor of growth hormone, and its analogues are clinically used for the therapy of acromegaly, gigantism, thyrotropinoma, and other carcinoid syndrome. However, natural somatostatin is limited for clinical usage because of its short half-life in vivo. Albumin fusion technology was used to construct long-acting fusion proteins, and Pichia pastoris was used as an expression system. Three fusion proteins, (somatostatin (SS)14)₂-human serum albumin (HSA), (SS14)₃-HSA, and HSA-(SS14)₃, were constructed with different fusion copies of somatostatin-14 and fusion orientations. The expression level of (SS14)₃-HSA and HSA-(SS14)₃ was much lower than (SS14)₂-HSA due to the additional fusion of the somatostatin-14 molecule. Matrix-assisted laser desorption ionization-time-of-flight mass spectrometry revealed that severe degradation occurred in the fermentation process. Similar to the standard of somatostatin-14, all three fusion proteins were able to inhibit growth hormone secretion in the blood, with (SS14)₂-HSA being the most effective one. On the whole, (SS14)₂-HSA was the most effective protein in both production level and bioactivity, and increasing the number of small protein copies fused to HSA may not be a suitable method to improve the protein bioactivity.