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.     

Improvement in Uranium Adsorption Properties of Amidoxime-Based Adsorbent Through Cografting of Amine Group

Amidoxime (AO)/amine co-functionalized polypropylene fiber adsorbents were prepared. The all-polymeric structures were characterized by using Fourier transform infrared spectroscopy (FTIR), optical microscope, contact angle meter and electron spin resonance (ESR) analysis methods, confirming the grafting, modification, and amidoximation stages gravimetrically, spectroscopically, and visually. The properties for the removal of uranyl(VI) from aqueous solutions were investigated. For amidoxime (AO) fiber, high adsorption rate was observed within the first 30 minutes and the plateau value of 40.6% uranium loading (0.0812 mg/g) was reached at around 30 minutes. The adsorption equilibrium for AO/amine fiber was attained within 20 minutes, resulting in the adsorption of 92.6% uranium loading (0.185 mg/g). The percentage of adsorption increases with increasing pH value (2–6), reaches a maximum at pH 6.0 and then remains almost constant for AO/amine fiber, whereas reduces slightly for AO fiber.     

Studies on the Phenol Oxidation with H2O2 Catalyzed by Metallomicelle Made from Crowned Schiff Base Mn(III) Complexes

Metallomicelles made from two Schiff base manganese(III) complexes (MnL¹ and MnL²) and surfactants (CTAB and Brij35) were used as mimetic peroxidase in the catalytic oxidation of phenol by H₂O₂. The catalytic activity of the complexes (MnL¹ and MnL²) were investigated. The mechanism and a kinetic mathematic model of the phenol catalytic oxidation were also studied. The results show the optimum acidity of the enzyme-like system in the paper is ca. pH 7.0, the optimum temperature which is ca. 35°C and the optimum molar ratio of H₂O₂ to the complex is ca. 30 in the complexes-H₂O₂-buffered solution; the Schiff base manganese(III) complexes and their metallomicelles as peroxidase mimics exhibit good catalytic activity and similar catalytic character to natural enzyme.     

Polyvinyl alcohol fibers with functional phosphonic acid group: synthesis and adsorption of uranyl (VI) ions in aqueous solutions

PVA functionalized with vinylphosphonic acid was prepared as a new adsorbent for uranyl (VI) adsorption from aqueous solutions. The vinylphosphonic acid was cografted onto PVA fibers by preirradiation grafting technique. The adsorbent were characterized by Fourier transform infrared spectroscopy and scanning electron microscopy. The adsorbent was observed to possess a fibrous structure and was bonded with phosphonic acid groups successfully. The adsorbent was used for the adsorption of low levels uranyl (VI) ions from aqueous solutions. The influence of analytical parameters including pH, adsorption time, amount of adsorbent, metal ion concentration, and temperature were investigated on the recovery of uranyl (VI) ion in aqueous solution. The maximum adsorption capacity (32.1 mg g^?1) and fast equilibrium time (30 min) were achieved at pH of 4.5 at room temperature. Thermodynamic parameters (ΔH° = 2.695 kJ mol^?1; ΔS° = 31.15 J mol^?1 K^?1; ΔG° = ?6.748 kJ mol^?1) show the adsorption of an exothermic process and spontaneous nature, respectively. The possible coordination mechanism was illustrated. Adsorption and desorption coexist in aqueous solutions and then the system becomes equilibrium.     

氢分离与CO催化甲烷化双功能型钯复合膜

以多孔Al₂O₃陶瓷为基体材料, 采用浸渍法担载NiO后用2B铅笔修饰NiO/Al₂O₃表面, 通过化学镀法沉积约5 μm厚的金属钯, 还原后成功制得Pd/Pencil/Ni/Al₂O₃膜. 为进行对比, 还制备了未担载镍的Pd/Pencil/Al₂O₃膜. 膜的表面和断面形貌分别采用扫描电镜和金相显微镜观测, 膜的透氢动力学通过H₂/N₂单气体法测试, 并以成分为H₂ 77.8%, CO 5.2%, CO₂ 13.5%和CH₄ 3.5%的原料氢测定了膜的氢分离效果. 结果表明, 未载镍的Pd/Pencil/Al₂O₃膜只具有氢分离作用, 而Pd/Pencil/Ni/Al₂O₃膜还可以有效地将钯膜泄漏的CO和CO₂转化为甲烷, 因而成为双功能型钯膜. 这种双功能膜尤其适用于面向质子交换膜燃料电池(PEMFC)的氢气分离, 既有效解决了PEMFC对氢燃料中CO格外敏感的难题, 又提高了对钯膜缺陷的容忍度, 因而延长了钯膜的使用寿命.     

New chiral liquid crystal monomers and cholesteric polyacrylates: synthesis and characterisation

The synthesis of new chiral monomers (M₁ ?M₃ ) based on menthol and the corresponding polyacrylates (P₁ ?P₃ ) is described. The chemical structures, formula and phase behaviour of the obtained monomers and polymers were characterised with FT-IR, ¹H-NMR, elemental analyses, differential scanning calorimetry (DSC), polarising optical microscopy (POM) and X-ray diffraction (XRD). The effect of the mesogenic core rigidity, spacer length and menthyl steric effect on the phase behaviour of M₁ ?M₃ and P₁ ?P₃ is discussed. The expected mesophase of the compounds based on menthol can be obtained by inserting a flexible spacer between the mesogenic core and the terminal groups. For the chiral monomers and polyacrylates, their corresponding melting temperature (T _m), glass transition temperature (T _g) and clearing temperature (T _i) increased with an increase of the mesogenic core rigidity; while the T _m, T _g and T _i decreased with increasing the spacer length. M₁ and P₁ showed no mesophase, while M₂ and M₃ all revealed a SmC* and cholesteric phases. P₂ and P₃ only showed a cholesteric phase.     

Effect of the twisted alignment on the liquid crystal wave‐front corrector

The effect of twisted alignment on the phase modulation of a liquid crystal wave‐front corrector was investigated. First, the effect of twisted alignment is discussed in terms of the modulation principle of the liquid crystal molecule. Only partial incident light can be modulated because of the effect of the twisted alignment. Other unmodulated light will affect the correction accuracy and the resolution of the image. The blazed grating method is proposed to solve this problem. Adaptive correction was performed without the blazed grating method and the correction results are poor. A similar adaptive correction experiment was performed with the blazed grating method and a better correction result is obtained. The residual averaged wave‐front errors are PV = 0.101λ and RMS = 0.015λ and a resolvable image is obtained.     

The optimal cell gap determination of a liquid crystal wavefront corrector from a single photoelectric measurement

It has been a crucial technique to improve the dynamic response characteristics of a liquid crystal wavefront corrector (LCWFC) with optimal cell gap since the LCWFC needs at least 2π (or π) phase modulation in adaptive optics systems (AOSs). We have given a complete process for obtaining the optimal cell gap accurately from a single photoelectric measurement, which can be conducted with a liquid crystal (LC) cell of any known thickness. This method has been analysed theoretically and confirmed experimentally by using a wedge-shaped cell; the experimental results match very well with the theoretical analysis. The response time of an optimal gap cell can be a novel evaluation method of response performance of LC materials.     

The effect of mesogenic and non-mesogenic crosslinking units on the phase behaviour of side-chain smectic and cholesteric elastomers

Chiral monomer (M₁ ), mesogenic and non-mesogenic crosslinking agents (C₁ and C₂ ), and the corresponding liquid crystalline elastomers (P₁ and P₂ series), have been synthesised. Their chemical structures have been characterised by Fourier transform infrared or ¹H nuclear magnetic resonance and their phase behaviour investigated by differential scanning calorimetry, polarising optical miscoscopy, thermo-gravimetric analysis (TGA) and X-ray diffraction. The effect of the crosslinking unit on the phase behaviour of the elastomers has been studied. M₁ showed a cholesteric oily streak and focal conic texture. C₂ exhibited a nematic enantiotropic thread-like and schlieren texture, and a monotropic fan-shaped texture in the S_A phase. Due to the introduction of the mesogenic crosslinking unit, elastomers, P_2-1 ?P_2-5 , exhibited a cholesteric phase, while elastomers, P_1-1 ?P_1-4 , derived from a non-mesogenic crosslinking unit, exhibit a S_A phase. As the content of the crosslinking unit increased, the T _g of the P₁ series initially decreased and then increased, and the T _i of the series decreased. In the P₂ series the T _g increased, but the T _i initially increased and then decreased. TGA confirmed that all the elastomers had improved thermal stability.     

Synthesis and characterization of side chain cholesteric liquid crystalline elastomers derived from chiral bisolefinic crosslinking units

In this work we prepared a nematic monomer (4′‐allyloxybiphenyl 4′‐ethoxybenzoate, M₁ ), a chiral crosslinking agent (isosorbide 4‐allyloxybenzoyl bisate, M₂ ) and a series of new side chain cholesteric liquid crystalline elastomers derived from M₁ and M₂ . The chemical structures of the monomers and polymers were confirmed by FTIR and ¹H NMR spectroscopy. The mesomorphic properties were investigated by differential scanning calorimetry, thermogravimetric analysis, polarizing optical microscopy and X‐ray diffraction. The effect of the content of the crosslinking unit on phase behaviour of the elastomers is discussed. Polymer P₁ showed a nematic phase, P₂ –P₇ showed a cholesteric phase; P₆ formed a blue Grandjean texture over a broad temperature range 145–209.6°C, with no changed on the cooling. Polymers P₄ –P₇ , with more than 6?mol?% of chiral crosslinking agent, gave rise to selective reflection. Elastomers containing less than 15?mol?% of the crosslinking units displayed elasticity, reversible phase transition with wide mesophase temperature ranges, and high thermal stability. Experimental results demonstrated that, with increasing content of crosslinking agent, the glass transition temperatures first fell and then increased; the isotropization temperatures and mesophase temperature ranges decreased.