Quantifying amino acid and protein substitution using Raman spectroscopy

Raman spectroscopy can be a powerful tool for the characterization of modified amino acids and proteins. In addition to the potential for quantitative results, it offers the advantage of not requiring any sample preparation. Modification of amines and thiols on amino acids and proteins are common reactions used for medical, biological, food, and agricultural purposes. We hypothesized that the Raman spectrum could be used to quantify the reactions and would be more informative than typical characterization techniques such as the ninhydrin test. To prove the hypothesis, the amino acids alanine, cysteine, and lysine were modified with ethyl vinyl sulfone (EVS) using a nucleophilic addition reaction known as the Michael addition and the product was characterized using Raman spectroscopy. The Raman spectroscopy results were compared with ultraviolet‐visible spectroscopy results based on ninhydrin analysis of the modified amino acids. The Raman spectroscopy analysis was able to discern site‐specific reactions on the amino acids and suggested that more amino acid moieties were substituted than predicted using the ninhydrin test alone. Substitution of the full protein ovalbumin with EVS showed similar results. The ninhydrin test showed the substitution of primary amines and thiols but could not detect substitution of secondary amines remaining after loss of the primary amine. Copyright © 2010 John Wiley & Sons, Ltd.     

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.     

Preferential mode of cyclization of tetrahydrofuran amino acids containing peptides: some theoretical insights

Theoretical insights have been provided for the observed preference of cyclodimerization over intramolecular cyclization reactions in linear tripeptides containing “2,5‐cis” (2S,5R)‐tetrahydrofuran amino acid as well as in those containing “2,5‐trans” (2S,5S)‐tetrahydrofuran amino acid, using quantum chemical methods. The geometries of species involved as well as the feasibility of cyclization reactions are studied at the B3LYP/6‐31G(d,p) level of theory in gas phase as well as in solvent phase. Thermodynamic data from Hessian calculations favor the intermolecular cyclization. Analysis of optimized geometries reveals the existence of additional stabilizing hydrogen bonding interactions in intermolecularly cyclized products. The existence of these second‐order interactions is substantiated by topological (atoms in molecules (AIM)) and natural bond orbital (NBO) analyses. Such interactions are absent in the intramolecular cyclization products. Further justification for the presence of stabilizing interactions in intermolecularly cyclized products comes from the molecular electrostatic potentials and electron density surfaces. Kinetic control favoring the intermolecularly cyclized products due to additional entropy of activation in the intramolecular case is surmised. Copyright © 2009 John Wiley & Sons, Ltd.     

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.     

Probabilistic analysis of the frequencies of amino acid pairs within characterized protein sequences

Here, we describe a unique probabilistic evaluation of the 20, naturally occurring, amino acids and their distributions within the Swiss-Prot and Complete Human Genebank databases. We have developed a computational technique that imparts both directionality and length constraints into searches for unique combinations of amino acids within protein sequences. Using statistical approaches, we have carried out searches of all possible two- and three-residue motifs contained within these databases. This technique is based on the unusually high occurrence of a small number of these motifs when compared to the expected probability of finding a specific residue grouping within a given database. Subsequent filtering of this search to identify such unique combinations has provided several examples that can be used as markers to identify particular proteins within or across databases. We focus on three of these motifs, which were found to be of greatest interest to us. The CC, CM and a combination of the two, CCM motifs all occur either more or less frequently than would be predicted based on standard amino acid distributions within the entire human proteome.     

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。     

TXRF quantification of interfering heavy metals using deconvolution,cross‐correlation,and external standard calibration

We developed a general procedure that includes external standard calibration and a deconvolution of spectral signals, which determined with high accuracy the relative proportion and absolute quantification of elements that habitually overlap in total reflection X‐ray fluorescence spectroscopy. The deconvolution proposed takes advantage of the well‐known method of a cross‐correlation technique, offering improvements in identification of simultaneous signals and in the determination of the relative elemental proportions. The external standard calibration was studied determining its range of application for the elements of interest and implemented in certified standard samples producing excellent results for the quantification of the mentioned elements. In this paper, we show the quality of the results obtained for specific heavy metals of currently health and industrial interest in the range of linear response of 0.2–200 ng. Copyright © 2013 John Wiley & Sons, Ltd.     

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.     

Production of biologically active peptides by hydrolysis of whey protein isolates using hydrodynamic cavitation

Whey protein isolate (WPI) hydrolysates have higher solubility in aqueous phase and enhanced biological properties. Hydrolysis of WPI was optimized using operating pressure (ΔP, bar), number of passes (N), and WPI concentration (C, %) as deciding parameters in hydrodynamic cavitation treatment. The optimum conditions for generation of WPI hydrolysate with full factorial design were 8 bar, 28 passes, and 4.5% WPI concentration yielding 32.69 ± 1.22 mg/mL soluble proteins. WPI hydrolysate showed alterations in binding capacity over WPI. SDS-PAGE and particle size analysis confirmed the hydrolysis of WPI. Spectroscopic, thermal and crystallinity analyses showed typical properties of proteins with slight variations after hydrodynamic cavitation treatment. ABTS, DPPH and FRAP assays of WPI hydrolysate showed 7–66, 9–149, and 0.038–0.272 µmol/mL GAE at 1–10, 0.25–4, and 3–30 mg/mL concentration, respectively. Further, a considerable enhancement in fresh weight, chlorophyll, carotenoids, reducing sugars, total soluble sugars, soluble proteins content and total phenolics content was noticed during in vitro growth of sugarcane in WPI hydrolysate supplemented medium at 50–200 mg/L concentration over the control. The process cost (INR/kg) to hydrolyze WPI was also calculated.     

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.     

芳香族氨基酸的太赫兹光谱研究

利用太赫兹时域光谱研究了三种芳香族氨基酸，即酪氨酸、色氨酸和苯丙氨酸，在02—1 6THz波段的光学特性，得到了对应的吸收谱.对比各自的吸收谱发现，酪氨酸和色氨酸分 别在0976THz和1465THz有明显的吸收峰，而苯丙氨酸则没有明显的吸收峰.利用密度泛 函(DFT)理论初步计算表明，氨基酸在THz波段的吸收是由分子转动或扭动造成的，氨基酸的 不同结构造成了它们在THz波段不同的吸收峰位.另外，还得到了三种氨基酸在该波段的折射 率谱并首次定量给出了三种氨基酸在02—16THz波段的平均折射率.酪氨酸、色氨酸和苯 丙氨酸的平均折射率分别为1507，1526和1686.这项研究不仅为研究生物分子结构和 动力学提供了新的理论和实验方法，而且对进一步利用THz时域光谱研究其他生物大分子具 有借鉴意义. 关键词： 太赫兹(THz)时域光谱 芳香族氨基酸 吸收谱 分子动力学     

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.     

Sources of primary production to Arctic bivalves identified using amino acid stable carbon isotope fingerprinting*

ABSTRACT

Benthic invertebrates are a crucial trophic link in Arctic marine food webs. However, estimates of the contribution of different primary production sources sustaining these organisms are not well characterised. We measured the stable carbon isotope values (δ¹³C) of essential amino acids (EAAs) in muscle tissue from two common bivalve genera (Macoma spp. and Astarte spp.) collected in Hanna Shoal in the northeastern Chukchi Sea. Mixing models comparing the δ¹³C_EAA fingerprints of the bivalves to a suite of primary production endmembers revealed relatively high contributions of EAAs from phytoplankton and bacteria in both species. We also examined whether δ¹³C_EAA fingerprints could be produced from the EAAs preserved in bivalve shells, which could allow primary production sources to be estimated from ancient bivalve shells. The δ¹³C_EAA fingerprints from a suite of paired modern bivalve shells and muscle from Macoma calcarea from across the Chukchi Sea revealed a correspondence between the estimates of the dominant primary production source of EAAs derived from analyses of these two tissue types. Our findings indicate that δ¹³C_EAA fingerprinting of marine bivalves can be used to examine dominant organic matter sources in the Arctic marine benthos in recent years as well as in deeper time.