Differentiation of isomeric amino acid residues in proteins and peptides using mass spectrometry

Characterization and differentiation of isomers in biological macromolecules using mass spectrometry is one of the most significant challenges facing scientists in the field. The capability of high-resolution MS instruments along with the development of new fragmentation methods now provides the ability to indirectly differentiate between some isomers. This ability has enabled mass spectrometry to evolve into a multidisciplinary technique incorporating areas such as pharmaceutical research, proteomics, polymer science, medicine, environmental chemistry, and recently archeology. This article aims to review recent developments in mass spectrometry methodologies in the identification of structural and spatial isomers in biological macromolecules, such as aspartic acid and isoaspartic acid (Asp/IsoAsp), leucine and isoleucine (Leu/Ile), glutamic acid and γ-glutamic acid, and D/L enantiomers. ? 2012 Wiley Periodicals, Inc. Mass Spec Rev 31:609-625, 2012.     

Calibration of broadband active acoustic systems using a single standard spherical target

When calibrating a broadband active acoustic system with a single standard target such as a sphere, the inherent resonances associated with the scattering by the sphere pose a significant challenge. In this paper, a method is developed which completely eliminates the source of resonances through isolating and exploiting the echo from the front interface of a sphere. This echo is relatively insensitive to frequency over a wide range of frequencies, lacking resonances, and is relatively insensitive to small changes in material properties and, in the case of spherical shells, shell thickness. The research builds upon the concept of using this echo for calibration in the work of Dragonette et al. [J. Acoust. Soc. Am. 69, 1186-1189 (1981)]. This current work generalizes that of Dragonette by (1) incorporating a pulse compression technique to significantly improve the ability to resolve the echo, and (2) rigorously accounting for the scattering physics of the echo so that the technique is applicable over a wide range of frequencies and material properties of the sphere. The utility of the new approach is illustrated through application to data collected at sea with an air-filled aluminum spherical shell and long broadband chirp signals (30-105 kHz).     

Evaluation of the cross correlation method by using PIV standard images

Effects of various parameters for PIV image acquiring and processing on the final velocity field is studied by using PIV standard images (Okamoto et al., 1997) to evaluate the cross correlation method. The studied parameters include the size of interrogation window, the size of search window, the number of tracer particles, the diameter of tracer particles, out-of-plane velocity and average image velocity or the time interval between two images. In order to improve the PIV sub-pixel accuracy, the validity of the “sub-pixel interpolation” process also is discussed in the paper. Some useful conclusions are suggested for the optimal parameter selection for a final PIV result with high accuracy.     

棉籽17种氨基酸含量的NIRS定标模型构建与测定方法研究

选用氨基酸含量差异较大的多年份、多品种、多地点种植的445份棉花种子为材料,分别对其进行近红外光谱扫描。用一阶导数的数学处理(1,4,4,1)、标准正态变换和去趋势(SNV+D)最佳组合的预处理方法,结合改良的偏最小二乘法(MPLS)构建棉籽17种氨基酸成分的近红外定标模型。定标结果表明,天冬氨酸、苏氨酸、谷氨酸、甘氨酸、丙氨酸、缬氨酸、异亮氨酸、亮氨酸、苯丙氨酸、赖氨酸、组氨酸和精氨酸等12种氨基酸含量的定标模型较好,其RPDc为3.735~7.132,外部检验r2为0.910~0.979,近红外光谱分析完全可以替代化学测定;而丝氨酸、蛋氨酸、酪氨酸和脯氨酸等四种氨基酸的定标模型次之,其RP-Dc为2.205~2.814,外部检验r2为0.800~0.830,近红外分析技术虽不能完全替代化学测定的结果,但仍可用于大量样品的筛选。半胱氨酸定标方程的RPDc较小(RPDc=1.358),因此,棉籽中半胱氨酸含量不能用近红外分析方法进行检测。     

Identification and quantification of amyloid beta-related peptides in human plasma using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Proteolytic processing of the amyloid precursor protein (APP) by β-secretase and γ-secretase leads to the generation and deposition of amyloid β (Aβ) in Alzheimer’s disease (AD). N-terminally or C-terminally truncated Aβ variants have been found in human cerebrospinal fluid and cultured cell media using immunoprecipitation and mass spectrometry. Unfortunately, the profile of plasma Aβ variants has not been revealed due to the difficulty of isolating Aβ from plasma. We present here for the first time studies of Aβ and related peptides in human plasma. Twenty-two Aβ-related peptides including novel peptides truncated before the β-secretase site were detected in human plasma and 20 of the peptides were identified by tandem mass spectrometry. Using an internal standard, we developed a quantitative assay for the Aβ-related peptides and demonstrated plasma dilution linearity and the precision required for their quantitation. The present method should enhance the understanding of APP processing and clearance in AD progression.     

单自由度非线性保守系统作大振幅振动时周期的计算方法

简要介绍了单自由度非线性保守系统作大振幅振动时周期的计算方法,并给出了几个常见典型振动问题的周期公式．     

Simultaneous detection of dopamine and ascorbic acid in urine using the H-point standard addition method

A highly sensitive H-point standard addition method (HPSAM) was investigated for identification of dopamine and ascorbic acid in some synthetic and pharmaceutical samples in an aqueous medium at pH 9.2 using a universal buffer. The most suitable wavelengths for dopamine and ascorbic acid detection are 260:271 nm and 248:270 nm respectively. Recovery values are between 99.0–101 %. Also, the effect of most common interferents was studied. Detection ranges for dopamine and ascorbic acid are 2·10^–6–5·10^–5 M and 6·10^–6–3·10^–5 M respectively with an RSD range between 1.3 and 2.0 %. The method was used to determine both reagents in real and synthesized samples.     

Synthesis and photophysical behavior of a novel zinc phthalocyanine containing a single carboxylic acid and three phenylthio substituents

Zinc 2, (3)-tri-(phenylthio)-2, (3)-carboxy phthalocyanine (ZnPc(COOH)(SPh)₃), zinc 2, (3)-tetra-(phenylthio) phthalocyanine (ZnPc(SPh)₄) and 2, (3)-tetra-(phenylthio) phthalocyanine (H₂Pc(SPh)₄) were synthesized and their photophysical behavior were compared with those of a number of zinc phthalocyanine (ZnPc) derivatives. ZnPc(COOH)(SPh)₃ and ZnPc(SPh)₄ had similar fluorescence (Φ_F=0.14) and triplet state (Φ_T=0.65) quantum yields in dimethylsulfoxide, hence showing no effects of the replacement of one of the phenylthio groups with a carboxylic acid group. ZnPc(COOH)(SPh)₃ displayed a slightly shorter triplet lifetime (τ_T=331 μs) than ZnPc (τ_T=350 μs) in DMSO, but within the range of ZnPc derivatives. The triplet lifetime for ZnPc(COOH)(SPh)₃ is much longer than for the symmetrical derivative (ZnPc(SPh)₄) with τ_T=149 μs in DMSO.     

In vivo quantification of the metabolites in normal brain and brain tumors by proton MR spectroscopy using water as an internal standard

Metabolite concentrations in normal adult brains and in gliomas were quantitatively analyzed by in vivo proton magnetic resonance spectroscopy (MRS) using the fully relaxed water signal as an internal standard. Between January 1998 and October 2001, 28 healthy volunteers and 18 patients with gliomas were examined by in vivo proton MRS. Single-voxel spectra were acquired using the point-resolved spectroscopic (PRESS) pulse sequence with a 1.5 T scanner (TR/TE/Ave = 3000 ms/30 ms/64). The calculated concentrations of N-acetyl-aspartate (NAA), creatine (Cre), choline (Cho), and water(H(2)O) in the normal hemispheric white matter were 23.59 +/- 2.62 mM (mean +/- SD), 13.06 +/- 1.8 mM, 4.28 +/- 0.8 mM, and 47280.96 +/- 5414.85 mM, respectively. The metabolite concentrations were not necessarily uniform in different parts of the brain. The concentrations of NAA and Cre decreased in all gliomas (p < 0.001). The NAA/Cho and NAA/H(2)O ratios can distinguish the normal brain from gliomas and low-grade from high-grade astrocytoma (p < 0.001). The concentration of taurine (Tau) in medulloblastomas was 29.64 +/- 5.76 mM. This is the first quantitative analysis of Tau in medulloblastoma in vivo and confirms earlier in vitro findings.     

In vivo quantification of the metabolites in normal brain and brain tumors by proton MR spectroscopy using water as an internal standard

Metabolite concentrations in normal adult brains and in gliomas were quantitatively analyzed by in vivo proton magnetic resonance spectroscopy (MRS) using the fully relaxed water signal as an internal standard. Between January 1998 and October 2001, 28 healthy volunteers and 18 patients with gliomas were examined by in vivo proton MRS. Single voxel spectra were acquired using the point-resolved spectroscopic pulse sequence with a 1.5-T scanner (TR/TE/Ave = 3000 ms/30 ms/64). The calculated concentrations of N-acetyl-aspartate (NAA), creatine (Cre), choline (Cho), and water (H2O) in the normal hemispheric white matter were 23.59 +/- 2.62 mM (mean +/- SD), 13.06 +/- 1.8 mM, 4.28 +/- 0.8 mM, and 47280.96 +/- 5414.85 mM, respectively. The metabolite concentrations were not necessarily uniform in different parts of the brain. The concentrations of NAA and Cre decreased in all gliomas (p < 0.001). The NAA/Cho and NAA/H2O ratios can distinguish the normal brain from gliomas, and low-grade astrocytoma from high-grade group (p < 0.001). The concentration of taurine (Tau) in medulloblastomas was 29.64 +/- 5.76 mM. This is the first quantitative analysis of Tau in medulloblastoma in vivo and confirms earlier in vitro findings.     

Robustness of fat quantification using chemical shift imaging

The purpose of this study was to investigate the effect of parameter changes that can potentially lead to unreliable measurements in fat quantification. Chemical shift imaging was performed using spoiled gradient echo sequences with systematic variations in the following: two-dimensional/three-dimensional sequence, number of echoes, delta echo time, fractional echo factor, slice thickness, repetition time, flip angle, bandwidth, matrix size, flow compensation and field strength. Results indicated no significant (or significant but small) changes in fat fraction with parameter. The significant changes can be attributed to the known effects of T1 bias and two forms of noise bias.     

Interaction of single viruslike particles with vesicles containing glycosphingolipids

Glycosphingolipids are involved in the first steps of virus-cell interaction, where they mediate specific recognition of the host cell membrane. We have employed total-internal-reflection fluorescence microscopy to explore the interaction kinetics between individual unlabeled noroviruslike particles, which are attached to a glycosphingolipid-containing lipid bilayer, and fluorescent vesicles containing different types and concentrations of glycosphingolipids. Under association equilibrium, the vesicle-binding rate is found to be kinetically limited, yielding information on the corresponding activation energy. The dissociation kinetics are logarithmic over a wide range of time. The latter is explained by the vesicle-size-related distribution of the dissociation activation energy. The biological, pharmaceutical, and diagnostic relevance of the study is briefly discussed.     

Unidirectional growth of l-alanine single crystal: NLO material from the amino acid family

Single crystal of l-alanine (LALA) has been grown by using the Sankaranarayanan and Ramasamy (SR) method. The identity of the crystal was confirmed using single crystal X-ray diffraction. The crystalline perfection was evaluated using high-resolution X-ray diffractometry (HRXRD). Infrared (IR) spectroscopic, UV–vis–NIR spectral and second harmonic generation (SHG) conversion efficiency studies were carried out. Microhardness measurements and thermal studies of the compound were made and reported.     

Reducing the NMR sample volume using a single organic liquid: Increased sensitivity for mass-limited samples with standard NMR probes

A simple inexpensive protocol for confining an aqueous sample to the active region of a standard NMR probe is examined for high-resolution NMR. The aqueous sample is sandwiched between an inert perfluorinated organic liquid that has been exploited in the design of micro-coil NMR probes. The procedure is demonstrated with 3 mm NMR tubes at ambient and elevated temperatures but should be equally applicable to smaller diameter tubes. It is shown that confinement has minimal effects on line shape and provides at least a two fold increase in sensitivity over a conventional sample, for the same mass of solute.     

Incorporation of peptides in phospholipid aggregates using ultrasound

This study presents the highlights of ultrasonic effects on peptides incorporated on phospholipid aggregates (liposomes). These liposomes or vesicles are known as transport agents in skin drug delivery and for hair treatment. They might be a good model to deliver larger peptides into hair to restore fibre strength after hair coloration, modelling, permanent wave and/or straightening. The preparation of liposomes 1,2-dipalmitoyl-sn-glycerol-3-phosphocholine (DPPC) with peptides (LLLLK LLLLK LLLLK LLLLK; LLLLL LCLCL LLKAK AK) was made by the thin film hydration method. The LUVs (uni-lamellar vesicles) were obtained by sonication, applying different experimental conditions, such as depth (mm) and power intensity (%). Photon-correlation spectroscopy (PCS) and electronic microscopy (EM) results confirmed that the incorporation of these peptides, with different sequence of amino acids, presented differences on the diameter, zeta-potential of membrane surface and shape of liposomes. The liposomes that included peptide LLLLK LLLLK LLLLK LLLLK present an increased in zeta-potential values after using ultrasound and an "amorphous" aspect. Conversely, the liposomes that incorporated the peptide LLLLL LCLCL LLKAK AK presented a define shape (rod shape) and the potential surface of liposome did not change significantly by the use of ultrasound.     

Folding/unfolding kinetics of lattice proteins studied using a simple statistical mechanical model for protein folding, I: Dependence on native structures and amino acid sequences

The folding/unfolding kinetics of a three-dimensional lattice protein was studied using a simple statistical mechanical model for protein folding that we developed earlier. We calculated a characteristic relaxation rate for the free energy profile starting from a completely unfolded structure (or native structure) that is assumed to be associated with a folding rate (or an unfolding rate). The chevron plot of these rates as a function of the inverse temperature was obtained for four lattice proteins, namely, proteins a1, a2, b1, and b2, in order to investigate the dependency of the folding and unfolding rates on their native structures and amino acid sequences. Proteins a1 and a2 fold to the same native conformation, but their amino acid sequences differ. The same is the case for proteins b1 and b2, but their native conformation is different from that of proteins a1 and a2. However, the chevron plots of proteins a1 and a2 are very similar to each other, and those of proteins b1 and b2 differ considerably. Since the contact orders of proteins b1 and b2 are identical, the differences in their kinetics should be attributed to the amino acid sequences and consequently to the interactions between the amino acid residues. A detailed analysis revealed that long-range interactions play an important role in causing the difference in the folding rates. The chevron plots for the four proteins exhibit a chevron rollover under both strongly folding and strongly unfolding conditions. The slower relaxation time on the broad and flat free energy surfaces of the unfolding conformations is considered to be the main origin of the chevron rollover, although the free energy surfaces have features that are rather complicated to be described in detail here. Finally, in order to concretely examine the relationship between changes in the free energy profiles and the chevron plots, we illustrate some examples of single amino acid substitutions that increase the folding rate.     

Phase transitions in crystals of protein amino acids

The temperature dependence of the piezoelectric response of many protein amino acids and their compounds exhibits a sharp increase in the piezoelectric response signals at a certain temperature. It has been shown using the example of the known ferroelectrics without a piezoelectric effect in the paraphase (triglycine sulfate, glycine phosphite, trisarcosine calcium chloride) that such an increase in the piezoelectric response is associated with the structural phase transition to the low-symmetry piezoelectric phase with a large number of piezoelectric coefficients. The specific features of the phase transitions with the symmetry change D ₂-C ₂ have been discussed.