Fluorescent staining of protein in SDS polyacrylamide gels by salicylaldehyde azine

As a noncovalent fluorescence probe, in this study, salicylaldehyde azine (SA) was introduced as a sensitive fluorescence‐based dye for detecting proteins both in 1D and 2D polyacrylamide electrophoresis gels. Down to 0.2 ng of single protein band could be detected within 1 h, which is similar to that of glutaraldehyde‐silver stain, but approximately four times higher than that of SYPRO Ruby fluorescent stain. Furthermore, comparative analysis of the MS compatibility of SA stain with SYPRO Ruby stain indicated that SA stain is compatible with the downstream of protein identification by LC‐MS/MS. Additionally, the probable mechanism of the SA stain was investigated by molecular docking. The results demonstrated that the interaction between SA and protein was mainly contributed by hydrogen bonding and hydrophobic forces.     

FIPSDock: A new molecular docking technique driven by fully informed swarm optimization algorithm

The accurate prediction of protein–ligand binding is of great importance for rational drug design. We present herein a novel docking algorithm called as FIPSDock, which implements a variant of the Fully Informed Particle Swarm (FIPS) optimization method and adopts the newly developed energy function of AutoDock 4.20 suite for solving flexible protein–ligand docking problems. The search ability and docking accuracy of FIPSDock were first evaluated by multiple cognate docking experiments. In a benchmarking test for 77 protein/ligand complex structures derived from GOLD benchmark set, FIPSDock has obtained a successful predicting rate of 93.5% and outperformed a few docking programs including particle swarm optimization (PSO)@AutoDock, SODOCK, AutoDock, DOCK, Glide, GOLD, FlexX, Surflex, and MolDock. More importantly, FIPSDock was evaluated against PSO@AutoDock, SODOCK, and AutoDock 4.20 suite by cross‐docking experiments of 74 protein–ligand complexes among eight protein targets (CDK2, ESR1, F2, MAPK14, MMP8, MMP13, PDE4B, and PDE5A) derived from Sutherland‐crossdock‐set. Remarkably, FIPSDock is superior to PSO@AutoDock, SODOCK, and AutoDock in seven out of eight cross‐docking experiments. The results reveal that FIPS algorithm might be more suitable than the conventional genetic algorithm‐based algorithms in dealing with highly flexible docking problems. © 2012 Wiley Periodicals, Inc.     

A fast parallel clustering algorithm for molecular simulation trajectories

We implemented a GPU‐powered parallel k‐centers algorithm to perform clustering on the conformations of molecular dynamics (MD) simulations. The algorithm is up to two orders of magnitude faster than the CPU implementation. We tested our algorithm on four protein MD simulation datasets ranging from the small Alanine Dipeptide to a 370‐residue Maltose Binding Protein (MBP). It is capable of grouping 250,000 conformations of the MBP into 4000 clusters within 40 seconds. To achieve this, we effectively parallelized the code on the GPU and utilize the triangle inequality of metric spaces. Furthermore, the algorithm's running time is linear with respect to the number of cluster centers. In addition, we found the triangle inequality to be less effective in higher dimensions and provide a mathematical rationale. Finally, using Alanine Dipeptide as an example, we show a strong correlation between cluster populations resulting from the k‐centers algorithm and the underlying density. © 2012 Wiley Periodicals, Inc.     

Investigation on the Stability of the Dispersion System of Cross-Linked Polyacrylamide Microspheres

The salt resistance, temperature resistance, and shear stability of a cross-linked polyacrylamide microsphere system are studied by microfiltration, light diffraction analysis, and optical microscopy. The results show that other conditions being equal, the particle diameter of cross-linked polyacrylamide microspheres decreases with increased NaCl concentration. When NaCl concentration is lower than 10,000 mg/L, its effect on the plugging performance of a cross-linked polyacrylamide microsphere system in regard to the nuclear pore membrane is weak in comparison with a linked polymer solution, but the former system has better salt tolerance. Particle diameter decreases with increased swelling temperature. When the swelling temperature is below 90°C, its effect on the plugging performance of the cross-linked polyacrylamide microsphere system in regard to nuclear pore membrane is weak in comparison with the linked polymer solution, but has better temperature tolerance. Particle size shows little change, with shearing rate being increased, while the shape remains about the same and the effect of shearing on the plugging performance of the cross-linked polyacrylamide microsphere dispersion system in regard to the nuclear pore membrane is weak in comparison with the linked polymer solution, but has better shear stability. The salt tolerance, temperature tolerance, and shear stability of microspheres are associated with a particular cross-linked structure.     

Kinetics for the Reaction between Potassium Ferricyanide and Cobalt Chloride in Aqueous Solution and Microemulsion

The kinetics for the reaction between potassium ferricyanide (K₃Fe(CN)₆) and cobalt chloride (CoCl₂) in aqueous solution and water/bis(2-ethylhexyl) sodium sulfosuccianate (AOT)/isooctane microemulsions were studied by three-wavelength spectrophotometry at 298.2 K. The second-order rate constants (k₂) were calculated from the time dependence of the concentration of reactant K₃Fe(CN)₆. The result showed that the reaction rates in water/AOT/isooctane microemulsions were slower than that in the aqueous solution, and k₂ decreased with molar ratio (ω) of water to AOT in microemulsions, which was interpreted by the transition state theory and confirmed that the reaction took place at the interfaces of the microemulsion water pools.     

Heat-Induced Formation of Monodisperse Gold Nanoparticles in Different Conditions

We investigate the preparation of nearly monodisperse gold nanoparticles by heat treatment in different conditions. The effects of various solvents, heating temperature, and heating time length on the monodispersity of gold nanoparticles were studied systematically and a general route to generate gold nanoparticles with uniform size was determined. The first step was to prepare gold nanoparticles with less than 3 nm and the following operation was to heat the gold nanoparticles in the present of thiolated solvents where monodispersed gold nanoparticles could be obtained easily. Our approach has enriched synthesis of monodisperse gold nanoparticles, and may provide some valuable experimental data about how the heating process affects the size evolution of gold nanoparticles.     

Effect of the Spherical Silica Surface on the Photoluminescence of the Loaded CdS Nanoparticles

CdS nanoparticles were formed on the surface of silica microspheres by the improved layer‐by‐layer self‐assembled technique. High‐resolution electron microscope (HRTEM) image and energy dispersive x‐ray analysis (EDX) confirmed formation of a quasi‐continuous CdS nanoparticles film on the silica microspheres. The results of UV‐vis and fluorescence spectra display that the spherical silica surface has a great effect on the photoluminescence of the loaded CdS nanoparticles. In contrast to the CdS nanoparticles powder, the composite can exhibit the emission ascribed to the band gap transition when the CdS nanoparticles film is relatively thick. This phenomenon is probably due to an enhancement of the crystallinity of CdS nanoparticles induced by the silica spheres.     

仿生制备有机-无机复合微囊固定化葡萄糖氧化酶

将层层自组装技术与仿生矿化技术相结合,由聚苯乙烯磺酸钠、聚二甲基二烯丙基氯化铵和二氧化硅成功制备(聚苯乙烯磺酸钠-聚二甲基二烯丙基氯化铵)₂-二氧化硅复合微囊.采用扫描电子显微镜、红外光谱和热重对微囊的形貌和化学结构进行了表征.以该复合微囊作为理想载体固定化葡萄糖氧化酶.结果表明,固定于复合微囊中的葡萄糖氧化酶的热稳定性、pH稳定性、操作稳定性得到了提高;在最适条件下,复合微囊固定化葡萄糖氧化酶的酶活回收率为72.85%,米氏常数是游离葡萄糖氧化酶的2.21倍.复合微囊在化学/生物催化、药物/基因传递系统和生物传感器应用方面具有一定的潜能.     

电喷雾电离源测定印刷线路板阵列离子阱的分析性能

电喷雾电离源(ESI)测定了印刷线路板材料制成的四通道PCB矩形离子阱中一个通道的的分析性能。结果表明,质谱峰检测到的离子信号的种类和强度明显受到离子动能的影响。当离子动能低于18 eV,则得到的质谱峰主要为精氨酸Arg离子(m/z 175.2),增加其离子动能则Arg离子(m/z 175.2)易碎裂,发生脱胍基、脱水等反应。在正弦波的射频模式下测定了离子质量隔离和离子质量选择激发,以SWIFT缺口频率为50～60 kHz,75～85 kHz和130～145 kHz分别隔离了m/z 175.2,117.3和71.8的离子;用频率为55、80和135 kHz的正弦波(振幅为1.0 V)选择激发弹出了m/z 175.2,117.3和71.8的离子。在氦气气氛下,频率为102 kHz正弦波可以使得Arg离子(m/z 175.2)发生碎裂,得到m/z 157.2,130.3和117.3碎片离子。电流积分法的测定结果表明,在256 kHz共振激发时离子测定效率为46.3%,在边界弹出时,离子测定效率约为9.7%。     

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.