Identification of isomeric 5‐hydroxytryptophan‐ and oxindolylalanine‐containing peptides by mass spectrometry

Cells continuously produce reactive oxidative species that can modify all cellular components. In proteins, for example, cysteine, methionine, tryptophan (Trp), and tyrosine residues are particularly prone to oxidation. Here, we report two new approaches to distinguish two isomeric oxidation products of Trp residues, i.e. 5‐hydroxytryptophan (5‐HTP) and oxindolylalanine (Oia) residues, in peptides. First, 2‐nitrobenzenesulfenyl chloride, known to derivatize Trp residues in position 2 of the indole ring, was used to label 5‐HTP residues. The mass shift of 152.98 m/z units allowed identifying 5‐HTP‐ besides Trp‐containing peptides by mass spectrometry, whereas Oia residues were not labeled. Second, fragmentation of the Oia‐ and 5‐HTP‐derived immonium ions at m/z 175.08 produced ions characteristic for each residue that allowed their identification even in the presence of y₁ ions at m/z 175.12 derived from peptides with C‐terminal arginine residues. The pseudo MS³ spectra acquired on a quadrupole time‐of‐flight hybrid mass spectrometer displayed two signals at m/z 130.05 and m/z 132.05 characteristic for Oia‐containing peptides and a group of six signals (m/z 103.04, 120.04, 130.04, 133.03, 146.04, and 148.04) for 5‐HTP‐cointaining peptides. In both cases, the relative signal intensities appeared to be independent of the sequence providing a specific fingerprint of each oxidative modification. Copyright © 2012 John Wiley & Sons, Ltd.     

The use of mass defect in modern mass spectrometry

Mass defect is defined as the difference between a compound's exact mass and its nominal mass. This concept has been increasingly used in mass spectrometry over the years, mainly due to the growing use of high resolution mass spectrometers capable of exact mass measurements in many application areas in analytical and bioanalytical chemistry. This article is meant as an introduction to the different uses of mass defect in applications using modern MS instrumentation. Visualizing complex mass spectra may be simplified with the concept of Kendrick mass by plotting nominal mass as a function of Kendrick mass defect, based on hydrocarbons subunits, as well as slight variations on this theme. Mass defect filtering of complex MS data has been used for selectively detecting compounds of interest, including drugs and their metabolites or endogenous compounds such as peptides and small molecule metabolites. Several strategies have been applied for labeling analytes with reagents containing unique mass defect features, thus shifting molecules into a less noisy area in the mass spectrum, thus increasing their detectability, especially in the area of proteomics. All these concepts will be covered to introduce the interested reader to the plethora of possibilities of mass defect analysis of high resolution mass spectra. Copyright © 2012 John Wiley & Sons, Ltd.     

Plectoneme formation in twisted fluctuating rods

The mechanics of DNA supercoiling is a subject of crucial importance to uncover the mechanism and kinetics of several enzymes. It is therefore being investigated using several biochemical and biophysical methods including single molecule experimental techniques. An interesting problem within this realm is that of torsional buckling and plectoneme formation in DNA as it is simultaneously put under tensile and torsional stress. Analytical solutions to this problem are difficult to find since it involves nonlinear kinematics and thermal fluctuations. In this paper we use ideas from the Kirchhoff theory of filaments to find semi-analytical solutions for the average shape of the fluctuating DNA under the assumption that there is no self-contact. The basic step in our method consists of combining a helical solution of the rod with a non-planar localizing solution in such a way that the force, moment, position and slope remain continuous everywhere along the rod. Our solutions allow us to predict the extension vs. linking number behavior of long pieces of DNA for various values of the tension and temperature. An interesting outcome of our calculations is the prediction of a sudden change in extension at buckling which does not seem to have been emphasized in earlier theoretical models or experiments. Our predictions are amenable to falsification by recently developed single molecule techniques which can simultaneously track the force-extension as well as the torque-rotation behavior of DNA.     

Modeling the growth and branching of plants: A simple rod-based model

A rod-based model for plant growth and branching is developed in this paper. Specifically, Euler's theory of the elastica is modified to accommodate growth and remodeling. In addition, branching is characterized using a configuration force and evolution equations are postulated for the flexural stiffness and intrinsic curvature. The theory is illustrated with examples of multiple static equilibria of a branched plant and the remodeling and tip growth of a plant stem under gravitational loading.     

温度和pH双重敏感荧光复合微凝胶制备和表征

通过反相悬浮聚合法制备N-异丙基丙烯酰胺(NIPAM)和甲基丙烯酸(MAA)的共聚微凝胶P(NIPAM-co-MAA), 以其为模板, 利用3-氨丙基三乙氧基硅烷(APTES)在碱性条件下的水解缩合反应, 制备得到了由氨基修饰的P(NIPAM-co- MAA)/SiO₂高分子/无机复合微凝胶, 再通过异硫氰酸荧光素(FITC)与氨基的键和作用, 得到了具有核-壳结构的温度和pH双重敏感荧光复合微凝胶. 通过扫描电子显微镜(SEM)、傅立叶变换红外光谱(FT-IR)、热台偏光显微镜(POM)和共聚焦激光扫描显微镜(CLSM)等手段对复合微凝胶进行了结构和性质表征, 结果表明, 该复合微凝胶对温度和pH均具有良好的响应特性, 并在可见光激发下发出荧光.     

双光子荧光探针

双光子吸收是指在强光激发下,介质分子同时吸收两个光子,从基态跃迁到两倍光子能量的激发态的过程。荧光显微成像是研究活体生物的重要工具,而最通常的细胞成像方法则是使用单光子激发荧光团的单光子显微成像。近红外光源激发的双光子荧光探针克服了单光子荧光探针的光漂白与光致毒而更适于生物检测与成像,为生命科学研究提供了更为锐利的工具。双光子荧光探针的作用机理包括分子内电荷迁移(ICT)、荧光共振能量迁移(FRET)、光诱导电子迁移(PET)与基团转换(GC) 4种方式。该文综述了双光子阳离子探针(Mg²⁺, Ca²⁺, Pb²⁺, Hg²⁺, Ag⁺, Fe³⁺, Zn²⁺, Na⁺, Cr³⁺)、双光子阴离子探针(F^-)、pH探针、双光子葡萄糖示踪器、双光子脂筏探针、双光子巯基探针、双光子半胱氨酸探针和双光子生物标记探针,以及双光子荧光探针在生物成像方面的应用,展望了双光子荧光探针的发展趋势与应用前景。     

基于荧光共轭聚合物的金属离子检测

以聚乙炔、聚芴、聚噻吩、聚苯撑为代表的荧光共轭聚合物,由于具有独特的光学性能、自组装性能和结构与性能的可调控性,可作为优异的光学传感材料。利用其具有较高摩尔消光系数和荧光量子产率的特点,可设计具有较高灵敏度和选择性的传感器,这已成为生物传感领域的研究热点。以荧光共轭聚合物为基础的金属离子检测,最初是以非水溶性的共轭聚合物为主,通过金属离子与聚合物链上特定基团(如吡啶、冠醚)的结合引起的聚合物荧光性质的变化可实现对某些离子的检测。在共轭聚合物主链上引入亲水性侧链,可大大增强共轭聚合物的水溶性,为金属离子的生物传感检测提供了新的思路,例如可引入能与金属离子结合的生物分子(如DNA、糖基等)来设计传感策略,进一步提高检测的特异性和灵敏度。本文综述了近年来以非水溶性和水溶性荧光共轭聚合物为传感材料,对具有重要生物学意义的重金属离子(Hg²⁺、Pb²⁺)、过渡金属离子(Cu²⁺、Eu³⁺、Ni²⁺、Fe³⁺、Fe²⁺、Ru³⁺、Ag⁺)和碱金属离子(K⁺、Na⁺、Li⁺)进行高灵敏度检测方面的研究进展,并对该领域的发展前景进行了展望。     

CdSe/ZnSe量子点在油水两相体系下的聚合物包覆相转移及其光谱表征

采用油水两相溶液体系,借助于双亲聚合物包覆实现了CdSe/ZnSe核壳结构量子点自油相到水相的相转移。油水两相中的聚合物包覆与已经报道的均相溶液中聚合物包覆量子点的方法不同,包覆过程在油水两相界面处完成,有效地减少了聚合物缠绕引起的量子点团聚,实现了聚合物对量子点的无团聚单分散包覆。透射电镜和激光粒度分析仪对聚合物包覆量子点的表征结果表明获得的水溶性量子点具有良好的分散性,均一的水力尺寸。吸收和发射光谱表明聚合物包覆过程对量子点的发射峰位和峰型没有引起明显的改变,维持了较高的量子产率。通过荧光微区成像技术成功实现了对人IgG蛋白的特异性检测,证实这种方法获得的聚合物包覆量子点具有较好的与生物分子偶联的功能化基团,适合于生物学标记应用。     

生物样品的散射和吸收特性对双光子激发和共焦成象深度的影响

本文研究了生物样品的散射和吸收特性对双光子激发和共焦成象深度的影响.生物组织内30μm的成象结果表明,双光子激发具有比共焦成象更深的成象深度.来自生物组织的模型实验和蒙特卡罗模拟均表明,散射和吸收的影响是导致这一特点的重要原因.     

边界条件对生物组织漫射光时域模拟计算的影响

采用蒙特卡洛方法与漫射近似相结合的杂合算法,在不同的边界条件下(零边界条件、外延边界条件、部分流边界条件),对板状生物组织模型的漫射光的时域分布进行了计算,计算结果表明:采用外延边界条件,在保证计算精度的基础上,和单纯的蒙特卡洛方法相比,较大地提高了运算速度.