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.     

Influence of Emulsifiers on Acrylate Latex Blends

The poly(methyl methacrylate/butyl acrylate/acrylic acid) [P(MMA/BA/AA)] and poly (styrene/butyl acrylate/acrylic acid) [P(St/BA/AA)] latexes were synthesized using the emulsifier octylphenol polyoxyethylene(10) ether (OP-10) and ammonium sulfate allyloxy nonylphenoxy poly(ethyleneoxy)(10) ether(DNS-86). The optimum amount of OP-10 and DNS-86 was 1.5% and 2.5% respectively. The P(MMA/BA/AA) and P(St/BA/AA) latex containing 1.5% OP-10 or 2.5% DNS-86 were blended pairwise. The performances of latex blends and parent latexes as a function of emulsifiers content in parent latexes were determined. The results indicated that the stability of latex blends is favorable, and particle size distribution was more uniform and thermal stability was improved after blending.     

The State of NaOH in NaOH/Poly(Sodium Acrylate) Composite

NaOH/poly(sodium acrylate) composites were prepared by in situ polymerization of acrylic acid with an overneutralization level by adding excess NaOH. The composites were studied by XRD, IR and ²³Na MAS NMR spectroscopy. The results showed that the high neutralization degree (>100%) may lead to a complete polymerization. Both XRD and ²³Na MAS NMR spectra did not show any peaks of phase-separated NaOH or Na₂CO₃ until the neutralization degree was up to 217.5%. It can be presumed that the aggregates of Na⁺ ions can contain approximately two Na⁺ units for every carboxyl group before the phase separation.     

Relationship Between the Polymer Structures and Destabilization of Polymer‐Containing Water‐in‐Oil Emulsions

The viscous properties, scanning electronic microscopy (SEM), and water/oil interfacial tension (IFT) of partially hydrolyzed polyacryamide (HPAM) and hydrophobically associating hydrolyzed polyacryamides modified with N‐dodecylacrylamide were studied with the objective of investigating the influence on destabilization of emulsions. As expected, the copolymers exhibit significant viscosity enhancing capacity and three‐dimensional network structures due to intermolecular hydrophobic associations, and also present high interfacial activities as the IFT decrease with increasing polymer concentration. As a result, the existences of copolymers increased both the viscosity of emulsions and the intensity of interfacial film, in which case slow down the diffusion of demulsifier molecules and enhance the stability of emulsions, finally, the separation of water from oil becomes more difficult.     

Pt/Au/Fe3O4的制备及其电化学性能

以制得的纳米Fe₃O₄颗粒作为载体,用还原法将还原出的Au与Pt分别负载到Fe₃O₄颗粒表面,制得纳米Pt/Au/Fe₃O₄复合材料。对Pt/Au/Fe₃O₄进行紫外可见光吸收光谱、透射电子显微镜、X射线衍射及光电子能谱等物理表征,结果表明,Au与Pt均匀地沉积到了Fe₃O₄纳米颗粒表面。对纳米Pt/Au/Fe₃O₄复合材料进行循环伏安扫描,当H₂PtCl₆的加入量达到8 mL时,Pt/Au/Fe₃O₄催化性能最佳;正扫电流峰i_p与扫描速率的平方根v^1/2线性相关,Pt/Au/Fe₃O₄催化氧化甲醇的过程受扩散控制;对催化剂进行201次循环伏安扫描,催化剂仍然能保持较好的催化性能且稳定性良好。因此,所合成催化剂Pt/Au/Fe₃O₄是一种具有良好化学稳定性的阳极催化剂材料。     

Influence of clay on the morphology and phase separation behavior of poly(methyl methacrylate)/poly(styrene-co-acrylonitrile) blends

The effect of clay on the morphology and phase-separation behavior of poly(methyl methacrylate)/poly(styreneco-acrylonitrile)(PMMA/SAN) blends and the variation of clay dispersion have been investigated. With the evolution of phase separation in PMMA/SAN, most of the clays are first located at the boundaries between PMMA and SAN, and then gradually move to the PMMA-rich domain, owing to the affinity of clay to PMMA. The introduction of clay causes the increase of binodal and spinodal temperatures of PMMA/SAN and enlarges their metastable region, indicating the phase stabilizing effect of clay on the matrix. But the influence of clay on the cloud points obviously depends on the composition of PMMA/SAN. The selective adsorption of PMMA on the clay results in the difference between the composition of surface layer and that of polymer matrix. Hence, the clay plays the role of an agent changing the conditions of phase structure formation.     

Crystal orientation and melting behavior of poly(ɛ-Caprolactone) under one-dimensionally “hard” confined microenvironment

Crystal orientation and melting behavior of poly(ε-caprolactone) in a diblock copolymer of poly(ε-caprolactone)-block-poly(2,5-bis[4-methoxyphenyl]oxycarbonyl)styrene) (PCL-b-PMPCS) was investigated. The degrees of polymerization of the PCL and PMPCS block are 200 and 98, respectively. With the PMPCS in a columnar liquid crystalline phase, the diblock is rod-coil one, which exhibits a lamellar phase morphology with the PCL layer thickness of 15.2 nm. Since the glass transition temperature of PMPCS block is much higher than the melting temperature of PCL, the crystallization of PCL is in a one-dimensionally "hard" confinement environment. Mainly on the basis of two-dimensional wide-angle X-ray diffraction experiments, we identified the orientation of PCL isothermally crystallized at various crystallization temperatures (Tcs). At high Tcs (Tc≥10℃), the c-axis of the PCL crystal is along the layer normal of the microphase-separated sturcture. Decreasing Tc can result in the tilting of PCL c-axis with respect to the layer normal. The lower the Tc is, the more the c-axis inclines. Meanwhile, the b-axis of PCL remains perpendicular to the layer normal. At a very low Tc of -78℃, the orientation of the PCL crystals is completely random. For the samples isothermally crystallized at Tc≤10℃, double melting behavior can be observed. While the low temperature endotherm reflects the melting of the crystals originally formed at the Tc applied, the high temperature one is associated with the crystals subjected to the process of recrystallization/reorganization upon heating due to the annealing effect.     

Crystallization of calcium carbonate controlled by Pluronic P123 in room-temperature ionic liquid

The crystallization of calcium carbonate (CaCO₃) controlled by Pluronic P123 in a room-temperature ionic liquid, ethylamine nitrate (EAN), was investigated. The CaCO₃ aggregates were obtained by rapid mixing of ammonium carbonate ((NH₄)₂CO₃) and calcium chloride (CaCl₂). Cubic calcite, spherical vaterite, and bagel-like vaterite were obtained easily by changing P123 concentration and reaction temperature. The morphologies of the as-prepared CaCO₃ aggregates were investigated by transmission electron microscopy and scanning electronic microscopy. The phase change of the obtained crystals was confirmed by X-ray diffraction and Fourier transform infrared spectroscopy. It was shown that higher P123 concentration and higher reaction temperature favor the formation of vaterite in EAN. Unusual bagel-like vaterite was first obtained at 60 °C in the presence of 5 g/L P123 in EAN. Mineralization of CaCO₃ regulated by P123 in EAN is a simple, novel, and environment-friendly strategy for vaterite synthesis.     

Curcumin Inhibits the Sortase A Activity of the Streptococcus mutans UA159

Streptococcus mutans (S. mutans) forms part of the commensal microflora and is deemed to be the major pathogen responsible for the generation of dental caries. The enzyme, sortase A enzyme, modulates the surface properties and cariogenicity of S. mutans. Curcumin has been reported to be an inhibitor of Staphylococcus aureus sortase A. In this study, inhibition of a purified S. mutans UA159 sortase A by curcumin was evaluated. Curcumin exerted strong inhibitory activity with a half maximal inhibitory concentration (IC₅₀) of 10.2?±?0.7 μM which was lower than the minimum inhibitory concentration of 175 μM and the minimum bactericidal concentration of 350 μM. These results indicated that curcumin is a S. mutans UA159 sortase A inhibitor and therefore represents as a promising anticaries agent.     

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.