Precise and global identification of phospholipid molecular species by an Orbitrap mass spectrometer and automated search engine Lipid Search

In the present research, we have established a new lipidomics approach for the comprehensive and precise identification of molecular species in a crude lipid mixture using a LTQ Orbitrap mass spectrometer (MS) and reverse-phase liquid chromatography (RPLC) combination with our newly developed lipid search engine “Lipid Search”. LTQ Orbitrap provides high mass accuracy MS spectra by Fourier-transform (FT) mass spectrometer mode and can perform rapid MSⁿ by ion trap (IT) mass spectrometer mode. In this study, the negative ion mode was selected to detect fragment ions from phospholipids, such as fatty acid anions, by MS2 or MS3. We selected the specific detection approach by neutral loss survey-dependent MS3, for the identification of molecular species of phosphatidylcholine, sphingomyelin and phosphatidylserine. Identification of molecular species was performed by using both the high mass accuracy of the mass spectrometric data obtained from FT mode and structural data obtained from fragments in IT mode. Some alkylacyl and alkenylacyl species have the same m/z value as molecular-related ions and fragment ions, thus, direct acid hydrolysis analysis was performed to identify alkylacyl and alkenylacyl species, and then the RPLC–LTQ Orbitrap method was applied. As a result, 290 species from mouse liver and 248 species from mouse brain were identified within six different classes of phospholipid, only those in manually detected and confirmed. Most of all manually detected mass peaks were also automatically detected by “Lipid Search”. Adding to differences in molecular species in different classes of phospholipids, many characteristic differences in molecular species were detected in mouse liver and brain. More variable number of saturated and monounsaturated fatty acid-containing molecular species were detected in mouse brain than liver.     

天然无序蛋白质:序列-结构-功能的新关系

天然无序蛋白质是一类新发现的蛋白质,它们在天然条件下没有确定的三维结构,却具有正常的生物学功能,广泛参与信号传递、DNA转录、细胞分裂和蛋白质聚集等重要的生理与病理过程.无序蛋白质的发现是对传统的蛋白质"序列-结构-功能"范式的挑战.在这篇综述里,我们首先回顾了蛋白质的传统范式以及无序蛋白质的发现过程,然后介绍无序蛋白质在结构、序列、功能等方面的特征与相互作用,并以分子识别过程为例,进一步阐述目前国际上对无序蛋白质所具有优势的一些认识与观点.我们还分析了无序蛋白质研究在生命科学和医学等领域的应用前景,并介绍了国内在无序蛋白质领域的研究现状.     

PdO0,±1, PdH0,±1及PdOH分子结构和电子性质的从头计算

利用多种从头计算方法对PdO0,±1, PdH0,±1以及PdOH的结构和电子性质进行了理论研究. 优化了PdO分子两个能量相近的态(3∏和3∑-), 结果表明PdO 的3∏态较3∑-态更为稳定, 在单双激发耦合簇理论(CCSD)水平下3∑-态的总能量比3∏态的高出0.286 eV. 在结构优化的基础上计算了PdO以及PdH的绝热电离能(AIE)和电子亲和能(AEA), 计算结果与实验值符合得很好. PdOH的基态为Cs对称性的角型结构Pd—OH(2A'态), 另外还优化得到两个2A'态的亚稳结构, 分别对应于Pd—OH和O—Pd—H, CCSD水平下两个亚稳态的总能量较基态分别高0.405和2.284 eV, 优化得到了连接这两个2A'态的过渡态, 并计算了相应的反应能垒.     

同源模建和分子对接研究HDAC1/HDAC8的选择性

组蛋白去乙酰化酶(HDACs)是近年来治疗肿瘤的重要靶标之一.由于HDACs包含多种亚型,且各亚型的生理功能存在一定的差异,其选择性抑制剂的开发已成为当前的研发热点.我们通过同源模建的HDAC1结构,与已有的HDAC8晶体结构的活性位点进行比较分析,探讨了对两者选择性有重要影响的残基,为基于受体的选择性抑制剂研究提供重要信息.同时选择了52个HDAC抑制剂,分别建立了HDAC1、HDAC8的活性值与对接打分值的线性回归模型.所建的HDAC1和HDAC8的线性构效关系模型的非交叉验证系数R2分别为0.82和0.80,表明具有一定的统计学意义.利用所建模型对已设计合成的化合物进行了预测,预测结果对HDAC1、HDAC8选择性抑制剂的优化改造提供了一定的指导意义.     

海藻糖抑制淀粉质多肽42构象转变的分子动力学模拟

应用分子动力学模拟方法研究了海藻糖抑制淀粉质多肽42(Aβ42)构象转变的分子机理.结果表明,海藻糖溶液浓度对Aβ42构象转变具有非常重要的影响.在水和低浓度海藻糖溶液(0.18mol·L-1)中,Aβ42可由初始的α-螺旋结构转变成β-折叠的二级结构;但海藻糖浓度为0.37mol·L-1时即可有效抑制Aβ42的构象转变.这是因为海藻糖利用其优先排阻作用使水分子在多肽周围0.2nm内富集,而其自身却在距离多肽0.4nm的位置附近团聚.另外,海藻糖还可通过降低多肽间的疏水相互作用,减少多肽分子内远距离的接触,有效抑制多肽的疏水塌缩和构象转变.上述分子模拟的结果对于进一步合理设计阿尔茨海默病的高效抑制剂具有非常重要的理论指导意义.     

拉曼光谱与拉曼效应的量子模型结构分析

散射光谱这种新谱线对应于散射分子中能级的跃迁,为研究分子结构提供了一种重要手段,引起学术界极大兴趣,拉曼也因此荣获1930年诺贝尔物理学奖。并称这种谱线为拉曼光谱。介绍了拉曼光谱的基本原理、拉曼光谱的应用以及其发展,由于拉曼光谱非常弱,实验要求比较高,最后介绍了实验仪器及利用拉曼光谱研究分子的结构。     

A discontinuous Galerkin finite-element method for a 1D prototype of the Boltzmann equation

To develop and analyze new computational techniques for the Boltzmann equation based on model or approximation adaptivity, it is imperative to have disposal of a compliant model problem that displays the essential characteristics of the Boltzmann equation and that admits the extraction of highly accurate reference solutions. For standard collision processes, the Boltzmann equation itself fails to meet the second requirement for d = 2, 3 spatial dimensions, on account of its setting in 2d, while for d = 1 the first requirement is violated because the Boltzmann equation then lacks the convergence-to-equilibrium property that forms the substructure of simplified models. In this article we present a numerical investigation of a new one-dimensional prototype of the Boltzmann equation. The underlying molecular model is endowed with random collisions, which have been fabricated such that the corresponding Boltzmann equation exhibits convergence to Maxwell–Boltzmann equilibrium solutions. The new Boltzmann model is approximated by means of a discontinuous Galerkin (DG) finite-element method. To validate the one-dimensional Boltzmann model, we conduct numerical experiments and compare the results with Monte-Carlo simulations of equivalent molecular-dynamics models.     

Interaction of diethyl aniline methylphosphonate with DNA: Spectroscopic and isothermal titration calorimetry

In this study the diethyl aniline methylphosphonate (DAM) was synthesized, the interaction of DAM with ct-DNA has been investigated by fluorescence spectra, UV spectra, molecular modeling and isothermal titration calorimetry (ITC). The binding constant of DAM to ct-DNA calculated from both isothermal titration calorimetry and fluorescence spectra were found to be in the 10⁴ M⁻¹ range. According to the ethidium bromide displacement studies, UV spectra and isothermal titration calorimetry experimental results, it can be concluded that DAM is an intercalator that can slide into the G-C rich region of ct-DNA. Furthermore, the results obtained from molecular modeling corroborated the experimental results obtanied from spectroscopic and ITC investigations. At the same time, fluorescence spectra suggested that the mechanism of the interaction of DAM to ct-DNA was a static enhancing type. ITC data showed that ct-DNA/DAM binding is enthalpy controlled.     

Measurements of self-broadening and self-pressure-induced shift parameters of the methane spectral lines in the 5556-6166 cm range

The absorption spectra of methane at different path lengths and different pressures for three temperatures 180, 240 and 296 K have been recorded in the 5556-6166 cm⁻¹ region using the Bruker IFS 120 HR and 125 HR high-resolution Fourier transform spectrometers. The multispectrum fitting procedure has been applied to these spectra to recover the spectral line parameters. The main goal of this procedure was the determination of self-broadening and self-pressure-induced shift coefficients and the exponents of their temperature dependences. These parameters have been derived for 406 assigned lines with good values of the signal to noise ratio. The rotational dependence of these parameters is discussed.     

Molecular dynamics simulations on local structure and diffusion in liquid TixAl1−x alloys

The microscopic structure and dynamics of liquid Ti_xAl_1-x alloys together with pure liquid Ti and Al metals were investigated by means of molecular dynamics simulations. This work gives the structural properties, including pair-correlation function, bond-angle distribution function, HA and Voronoi indices, and their composition dependence. The dynamical properties have also been studied. The calculated pair-correlation function, bond-angle distribution function, and HA and Voronoi indices suggest that the stoichiometric composition Ti_0.75Al_0.25 exhibits a different local structure order compared with other concentrations, which help us understand the appearance of the minimum diffusion coefficient at this composition. These results indicate that the mobility of atoms strongly depends on their atomic local structure.