NeuDATool：支持GPU硬件加速和计算机集群跨节点并行的开源中子散射数据分析软件

实验势精修是20世纪80年代英国散裂中子源无定型材料组开发的用于分析中子散射实验数据的软件. 实验势精修的目标是根据中子散射数据重建样品的三维原子结构. 在过去的几十年,实验势精修被广泛用于中子散射实验数据分析,为实验用户提供了可靠的分析结果. 但是实验势精修是基于共享内存并行计算(OpenMP)的Fortran程序,不支持计算机服务器集群跨节点并行加速和GPU加速;这限制了它的分析速度. 随着计算机服务器集群的广泛建设和GPU加速技术的普遍使用,有必要重新编写EPSR程序以提高运算速度. 本文使用面向对象的C++语言,开发了一套实现EPSR算法的开源软件包NeuDATool;软件通过MPI和CUDA C实现了计算机集群跨节点并行和GPU加速. 使用液态水和玻璃态二氧化硅的中子散射实验数据对软件进行了测试. 测试显示软件可以正确重建出样品的三维原子结构;并且模拟体系达到10万原子以上时,使用GPU加速可以比串行的CPU算法提高400倍以上的模拟速度. NeuDATool为中子实验用户尤其是对熟悉C++编程并希望定义特殊分析算法的实验科学家提供了一种新的选择.     

Molecular beacons with oxidized bases report on substrate specificity of DNA oxoguanine glycosylases

DNA glycosylase enzymes recognize and remove structurally distinct modified forms of DNA bases, thereby repairing genomic DNA from chemically induced damage or erasing epigenetic marks. However, these enzymes are often promiscuous, and advanced tools are needed to evaluate and engineer their substrate specificity. Thus, in the present study, we developed a new strategy to rapidly profile the substrate specificity of 8-oxoguanine glycosylases, which cleave biologically relevant oxidized forms of guanine. We monitored the enzymatic excision of fluorophore-labeled oligonucleotides containing synthetic modifications 8-oxoG and FapyG, or G. Using this molecular beacon approach, we identified several hOGG1 mutants with higher specificity for FapyG than 8-oxoG. This approach and the newly synthesized probes will be useful for the characterization of glycosylase substrate specificity and damage excision mechanisms, as well as for evaluating engineered enzymes with altered reactivities.

A three-color fluorescent molecular beacon assay for rapid profiling of substrate specificity of hOGG1 variants, and for engineering proteins to map genomic modifications.     

蛋白质的电化学分析研究进展

对蛋白质的电化学分析的进展及应用进行综述。从蛋白质的极谱行为、在固体电极上的电化学行为、催化氢波、与小分子物质的配合作用等多角度介绍了近期的研究热点,分析了蛋白质化学研究的意义与现状,并对今后的发展方向作了展望,引用相关文献28篇。     

Identification of clusters from reactions of ruthenium arene anticancer complex with glutathione using nanoscale liquid chromatography fourier transform ion cyclotron mass spectrometry combined with <Superscript>18</Superscript>O-labeling

Reactions of the anticancer complex [(eta(6)-bip)Ru(en)Cl](+) (where bip is biphenyl and en is ethylenediamine) with the tripeptide glutathione (gamma-L-Glu-L-Cys-Gly; GSH), the abundant intracellular thiol, in aqueous solution give rise to two ruthenium cluster complexes, which could not be identified by electrospray mass spectrometry (ESI-MS) using a quadrupole mass analyzer. Here we use Fourier transform ion cyclotron mass spectrometry (nanoLC-FT-ICR MS) to identify the clusters separated by nanoscale liquid chromatography as the tetranuclear complex [{(eta(6)-bip)Ru(GSO(2))}(4)](2-) (2) and dinuclear complex [{(eta(6)-bip)Ru(GSO(2))(2)}(2)](8-) (3) containing glutathione sulfinate (GSO(2)) ligands. Use of (18)OH(2) showed that oxygen from water can readily be incorporated into the oxidized glutathione ligands. These data illustrate the power of high-resolution MS for identifying highly charged multinuclear complexes and elucidating novel reaction pathways for metallodrugs, including ligand-based redox reactions.     

Protein surface recognition of the novel tetra-carboxylphenyl calix[4]arene to cytochrome c

The interaction of the novel tetra-carboxylphenyl calix[4]arene （TCPC） with the bovine heart cytochrome c （Cc） was first investigated by fluorescence spectroscopy and molecular modeling methods. The formation of a stable 1：1 complex was monitored by fluorescence titration, and its binding constant is 1.916 ×10^7 L mol^-1. Molecular modeling reveals the recognition mechanism of TCPC to the Cc surface, that is, the electrostatic interaction drives TCPC to the Cc surface, and the van der Waals interaction orientates TCPC parallel to the cleft of Cc.     

一例新型桥联吡啶化合物的合成和结构研究

利用改进的Sonogashira反应一锅法合成了一例未见报道的叁键桥联的联吡啶类化合物L[2,6-二(3'-吡啶乙炔基)-4-甲基苯胺],与常规的分步合成方法相比,新方法不需脱除保护,从而简化了反应步骤,提高了产率.对所合成的化合物利用红外、核磁、元素分析等确定了其结构,并进一步利用X射线单晶衍射法测得了该化合物的单晶结构.单晶分析显示该化合物结晶于正交晶系、Pca21空间群中,a=10.178A,b=10.972A,c=28.949 A;a=β=γ=90°,Z=8.该化合物在配位化学方面具有潜在的应用前景.我们测定了其固态下的荧光性质,显示其能够发出较强的蓝色光.     

纳米四氧化三锰温和水相合成及其电容性能

采用温和水相合成法制备出纳米Mn3O4,采用X射线衍射（XRD）、电子能谱（XPS）及透射电子显微镜（TEM）等技术手段对其结构、组成与形貌进行了研究分析;并利用循环伏安（CV）及充放电等电化学测试研究了纳米Mn3O4的电容性能。 结果表明,本实验所制备的纳米Mn3O4为四方相γ-Mn3O4,其粒径大小为40~60 nm;该材料具有良好的电容性能,其比电容值可达270 F/g,且经1000次循环后,其比电容值可达原来的85%。     

加速溶剂萃取–液相色谱法测定五灵脂药材中原儿茶酸的含量

建立了五灵脂中原儿茶酸含量的测定方法。利用加速溶剂萃取仪(ASE),以75%乙醇水溶液提取样品中的待测物,用Diamosil C18(4.6 mm×250 mm,5.0μm)色谱柱在梯度洗脱条件下分离待测物,外标法定量。原儿茶酸的线性范围为0.1~10.0 mg/L,相关系数r=0.9998。方法的回收率为83%~107%,测定结果的相对标准偏差为4.6%~10.5%,方法的定量限为1.0 mg/kg。该方法操作简便、快速,提取效率高,适用于检测和分析五灵脂中原儿茶酸的含量。     

Unsymmetrical N and/or O-bridged calixarene derivatives: synthesis,structure and encapsulation of solvent molecules in the solid state

Eight unsymmetrical N and/or O-bridged calixarene derivatives were obtained by 1 (naphthalene-2,7-diol), 2 (bis(4-hydroxyphenyl)methanone), 3 (4,4′-methylenedianiline), 4 (3,3′-methylenedianiline), 5 (4,4′-oxydianiline) and 6 (4,4′-(perfluoropropane-2,2-diyl)dianiline) reacting with fragment a (4,4′-bis(dichloro-s-triazinyloxy)propane-2,2-diyldibenzene) and b (N,N′-bis(dichloro-s-triazinyl)-4,4′-methylenedianiline) under very mild reaction conditions via efficient fragment coupling strategy. We also obtained the crystal structure of 1a (tetraoxocalix[2](propane-2,2-diyldibenzene,naphthalene)[2]triazine) which can form a molecular capsule by two dimers with C–H?N and C–H?O quadruple hydrogen bonds, and it has the encapsulation ability toward solvent molecules.