Silver Cluster Interactions with Tyrosine: Towards Amino Acid Detection

Tyrosine (Tyr) is involved in the synthesis of neurotransmitters, catecholamines, thyroid hormones, etc. Multiple pathologies are associated with impaired Tyr metabolism. Silver nanoclusters (Ag NCs) can be applied for colorimetric, fluorescent, and surface-enhanced Raman spectroscopy (SERS) detection of Tyr. However, one should understand the theoretical basics of interactions between Tyr and Ag NCs. Thereby, we calculated the binding energy (E_b) between Tyr and Ag_n^q (n = 1–8; q = 0–2) NCs using the density functional theory (DFT) to find the most stable complexes. Since Ag NCs are synthesized on Tyr in an aqueous solution at pH 12.5, we studied Tyr⁻¹, semiquinone (SemiQ⁻¹), and Tyr⁻². Ag₃²⁺ and Ag₅⁺ had the highest E_b. The absorption spectrum of Tyr⁻² significantly red-shifts with the attachment of Ag₃²⁺, which is prospective for colorimetric Tyr detection. Ag₃²⁺ interacts with all functional groups of SemiQ⁻¹ (phenolate, amino group, and carboxylate), which makes detection of Tyr possible due to band emergence at 1324 cm⁻¹ in the vibrational spectrum. The ground state charge transfer between Ag and carboxylate determines the band emergence at 1661 cm⁻¹ in the Raman spectrum of the SemiQ⁻¹–Ag₃²⁺ complex. Thus, the prospects of Tyr detection using silver nanoclusters were demonstrated.     

Analyzing Variability in Nectar Amino Acids: Composition Is Less Variable Than Concentration

Thirty species of flowering plants were analyzed for floral nectar amino acid composition. High-performance liquid chromatography (HPLC) was used in conjunction with AccQtag derivatization to produce accurate and precise data. For any one species, the total concentration of amino acids varies greatly (average coefficient of variation 0.65), but composition is much less variable (average correlation among samples from a single species 0.85). Absolute concentration of individual amino acids is much more variable than the relative abundance (coefficients of variation 0.98 and 0.77, respectively; N = 544, t = 16.98, P < 0.001). When amino acids that occur in only small relative abundance (<1%) are removed from the analysis, the difference is even more marked (0.78 and 0.51, respectively; N = 344, t = 15.13, P < 0.001). The results highlight the need for large sample sizes when making observations concerning the absolute amounts of amino acids in nectar and for sensitive analyses of the composition, as even small changes may be biologically significant.     

Amino Acid Composition,Molecular Weight Distribution and Gel Electrophoresis of Walnut (Juglans regia L.) Proteins and Protein Fractionations

As a by-product of oil production, walnut proteins are considered as an additional source of plant protein for human food. To make full use of the protein resource, a comprehensive understanding of composition and characteristics of walnut proteins are required. Walnut proteins have been fractionated and characterized in this study. Amino acid composition, molecular weight distribution and gel electrophoresis of walnut proteins and protein fractionations were analyzed. The proteins were sequentially separated into four fractions according to their solubility. Glutelin was the main component of the protein extract. The content of glutelin, albumin, globulin and prolamin was about 72.06%, 7.54%, 15.67% and 4.73% respectively. Glutelin, albumin and globulin have a balanced content of essential amino acids, except for methionine, with respect to the FAO pattern recommended for adults. SDS-PAGE patterns of albumin, globulin and glutelin showed several polypeptides with molecular weights 14.4 to 66.2 kDa. The pattern of walnut proteins in two-dimension electrophoresis (2-DE) showed that the isoelectric point was mainly in the range of 4.8–6.8. The results of size exclusion chromatogram indicated molecular weight of the major components of walnut proteins were between 3.54 and 81.76 kDa.     

高效液相色谱法测定发酵酱油中的氨基酸含量及分析

采用高效液相色谱法分析了两种发酵酱油中的氨基酸。结果表明,低盐固态发酵酱油与高盐稀态发酵酱油中均含有丰富的氨基酸,8种必需氨基酸含量比例分别达到46.05%与41.45%。虽然低盐固态发酵酱油的总氨基酸与必须氨基酸的含量高于高盐稀态发酵酱油,但高盐稀态发酵酱油中呈味氨基酸特别是甜味和鲜味氨基酸的含量较高,从而使高盐稀态发酵酱油滋味更加鲜美。     

甘草酸氨基酸复盐的制备及性质

按改进文献方法提取甘草酸,用甘草酸和氨基酸在70%乙醇水溶液中,pH≈5和60°C的水浴上反应制备复盐。通过元素分析、热重、红外、紫外光谱分析对复盐进行表征,确定复盐的组成,分别为:C6H15N2O2)2.HG、(C6H10N3O2)2.HG、(C6H15N4O2)2.HG,为进一步研究甘草在中药复方中的功效提供参考。     

新型氨基酸肥料的研究与肥效试验

分析了我国现阶段市场上供应的氨基酸肥料的作用机理及应用效果,提出了开发新型氨基酸肥料的创新理念。通过大量的盆栽肥效试验,肯定了中浓度、多功能、高效益的新型氨基酸肥料研发方向,为肥料企业转型升级提供了新的思路。     

复合氨基酸微量元素螯合肥的制备及应用研究

以动物蛋白废弃物水解而成的复合氨基酸为原料,研究其与微量元素锰、锌、铜螯合的最佳工艺条件。结果表明:制备复合氨基酸微量元素螯合肥的最佳pH值范围为6.0~7.0;反应温度为80℃;反应时间为60 min。在此条件下,产品螯合率可达95%以上,且产品质量稳定。田间试验表明:在同等使用剂量下,复合氨基酸微量元素螯合肥对作物的增产效果明显优于无机微量元素肥料,差异达到显著水平。     

微生物资源与氨基酸的生产和应用

微生物资源具有多样性、易变性、生长快等特征，与动、植物资源相比存在许多未知数。对微生物生产氨基酸进行了概述．提出了应积极研究、开发和利用产氨基酸的微生物资源，拓展氨基酸产品，重组具特殊优良性能的氨基酸的生产菌种，大力发展有特色的氨基酸试剂。     

iHyd-PseAAC: Predicting Hydroxyproline and Hydroxylysine in Proteins by Incorporating Dipeptide Position-Specific Propensity into Pseudo Amino Acid Composition

Post-translational modifications (PTMs) play crucial roles in various cell functions and biological processes. Protein hydroxylation is one type of PTM that usually occurs at the sites of proline and lysine. Given an uncharacterized protein sequence, which site of its Pro (or Lys) can be hydroxylated and which site cannot? This is a challenging problem, not only for in-depth understanding of the hydroxylation mechanism, but also for drug development, because protein hydroxylation is closely relevant to major diseases, such as stomach and lung cancers. With the avalanche of protein sequences generated in the post-genomic age, it is highly desired to develop computational methods to address this problem. In view of this, a new predictor called “iHyd-PseAAC” (identify hydroxylation by pseudo amino acid composition) was proposed by incorporating the dipeptide position-specific propensity into the general form of pseudo amino acid composition. It was demonstrated by rigorous cross-validation tests on stringent benchmark datasets that the new predictor is quite promising and may become a useful high throughput tool in this area. A user-friendly web-server for iHyd-PseAAC is accessible at http://app.aporc.org/iHyd-PseAAC/. Furthermore, for the convenience of the majority of experimental scientists, a step-by-step guide on how to use the web-server is given. Users can easily obtain their desired results by following these steps without the need of understanding the complicated mathematical equations presented in this paper just for its integrity.     

三烷基胺萃取氨基磺酸及其废水的特性研究

p-Amino benzene sulfonic acid (PABSA) is selected as the solute with amphoteric functional group, Lewis acid and Lewis base, to be separated from its dilute solutions. An aliphatic, straight chain amine, Alamine 336, is used as the extractant, and kerosene, 1-octanol, chloroform, butyl acetate and benzene as the diluent. The effects of pH value of solution, extractant concentration, salt and types of diluent on the distribution coefficient, D, are studied. There is a peak of D value with pH value of solution, the polar diluents are favorable for extracting PABSA, and the salt in aqueous phase reduces values of D apparently. The extraction equilibrium is described using the mass action law, and the calculated data according to the proposed model agree with the experimental data well. Further, the extraction behavior for other amino benzene sulfonic acids, 1-amino-8-naphtol-3,6-disulfonic acid (H acid) and 4,4′-diaminostilbene-2,2′-disulfonic acid (DSD acid), is investigated in a wide pH value region. Finally. H acid and DSD acid are successfully removed from wastewater by the extraction with Alamine 336.     

4种鸡汤中游离氨基酸的组成及呈味贡献对比分析

将鸡肉煮汤,经离心、冷冻干燥后,利用氨基酸自动分析仪进行游离氨基酸的测定及呈味分析,研究了北京油鸡、三黄鸡、奔跑鸡、散养鸡的鸡汤中游离氨基酸的种类及对呈味的贡献。4种鸡汤中均鉴定出17种游离氨基酸,其中必需氨基酸7种,含量最高的是组氨酸。总氨基酸含量最高的是散养鸡汤(46.47 g/L),最低的是三黄鸡汤(16.86 g/L)。必需氨基酸总含量最高的是散养鸡汤(10.02 g/L),最少的是三黄鸡汤(3.88 g/L)。4种鸡汤中苦味氨基酸各为9种,鲜味2种,甜味5种,鲜味氨基酸质量分数最高的为三黄鸡汤(18.42%),甜味氨基酸质量分数最高的为奔跑鸡汤(30.41%)。根据氨基酸滋味活性值(TAV)得出,北京油鸡汤中对滋味有贡献的氨基酸为11种,三黄鸡汤6种,奔跑鸡汤10种,散养鸡汤11种。通过电子舌主成分分析(PCA)和判别指数,表明差异最小的是奔跑鸡汤和三黄鸡汤,最大的是散养鸡汤和北京油鸡汤。     

Cold Atmospheric Plasma Changes the Amino Acid Composition of Solutions and Influences the Anti-Tumor Effect on Melanoma Cells

Cold Atmospheric Plasma (CAP) is an ionized gas near room temperature. Its anti-tumor effect can be transmitted either by direct treatment or mediated by a plasma-treated solution (PTS), such as treated standard cell culture medium, which contains different amino acids, inorganic salts, vitamins and other substances. Despite extensive research, the active components in PTS and its molecular or cellular mechanisms are not yet fully understood. The purpose of this study was the measurement of the reactive species in PTS and their effect on tumor cells using different plasma modes and treatment durations. The PTS analysis yielded mode- and dose-dependent differences in the production of reactive oxygen and nitrogen species (RONS), and in the decomposition and modification of the amino acids Tyrosine (Tyr) and Tryptophan (Trp). The Trp metabolites Formylkynurenine (FKyn) and Kynurenine (Kyn) were produced in PTS with the 4 kHz (oxygen) mode, inducing apoptosis in Mel Im melanoma cells. Nitrated derivatives of Trp and Tyr were formed in the 8 kHz (nitrogen) mode, elevating the p16 mRNA expression and senescence-associated ß-Galactosidase staining. In conclusion, the plasma mode has a strong impact on the composition of the active components in PTS and affects its anti-tumor mechanism. These findings are of decisive importance for the development of plasma devices and the effectiveness of tumor treatment.     

iNR-Drug: Predicting the Interaction of Drugs with Nuclear Receptors in Cellular Networking

Nuclear receptors (NRs) are closely associated with various major diseases such as cancer, diabetes, inflammatory disease, and osteoporosis. Therefore, NRs have become a frequent target for drug development. During the process of developing drugs against these diseases by targeting NRs, we are often facing a problem: Given a NR and chemical compound, can we identify whether they are really in interaction with each other in a cell? To address this problem, a predictor called “iNR-Drug” was developed. In the predictor, the drug compound concerned was formulated by a 256-D (dimensional) vector derived from its molecular fingerprint, and the NR by a 500-D vector formed by incorporating its sequential evolution information and physicochemical features into the general form of pseudo amino acid composition, and the prediction engine was operated by the SVM (support vector machine) algorithm. Compared with the existing prediction methods in this area, iNR-Drug not only can yield a higher success rate, but is also featured by a user-friendly web-server established at http://www.jci-bioinfo.cn/iNR-Drug/, which is particularly useful for most experimental scientists to obtain their desired data in a timely manner. It is anticipated that the iNR-Drug server may become a useful high throughput tool for both basic research and drug development, and that the current approach may be easily extended to study the interactions of drug with other targets as well.     

Eggshell Composition of Squamate Reptiles: Relationship between Eggshell Permeability and Amino Acid Distribution

Most snakes and lizards produce eggs with flexible shells that interact with the environment to maintain water balance. Geckos produce rigid eggshells that are independent of an external source of water and can be oviposited in more open, dryer locations. In this study, we analyzed and compared the amino acid composition of 24 lizard species, six snake species, and four outgroups (including avian and reptilian elastin and chicken eggshell). Rigid Gecko eggshells had significantly lower levels of seven of the 17 amino acids evaluated. Multivariate analysis showed that proline was the most important amino acid in distinguishing between these two groups of eggshells, occurring at significantly higher levels in flexible eggshells. High levels of proline have also been observed in the eggshells of other species. Proline and other amino acids are associated with the alleviation of water and salt stress in plants.     

复合氨基酸微量元素螯合物饲料添加剂的应用与开发

介绍了复合氨基酸微量元素螯合物代替无机盐作为饲料添加剂在饲料行业应用研究的情况和生产工艺改进所取得的成果。分析了推广该产品的关键在于改进生产工艺,选择最佳工艺路线,合理开发利用废弃的蛋白资源,获取廉价的复合氨基酸微量元素螯合物。     

RNA Aminoacylation Mediated by Sequential Action of Two Ribozymes and a Nonactivated Amino Acid

In the transition from the RNA world to the modern DNA/protein world, RNA‐catalyzed aminoacylation might have been a key step towards early translation. A number of ribozymes capable of aminoacylating their own 3′ termini have been developed by in vitro selection. However, all of those catalysts require a previously activated amino acid—typically an aminoacyl‐AMP—as substrate. Here we present two ribozymes connected by intermolecular base pairing and carrying out the two steps of aminoacylation: ribozyme 1 loads nonactivated phenylalanine onto its phosphorylated 5′ terminus, thereby forming a high‐energy mixed anhydride. Thereafter, a complex of ribozymes 1 and 2 is formed by intermolecular base pairing, and the “activated” phenylalanine is transferred from the 5′ terminus of ribozyme 1 to the 3′ terminus of ribozyme 2. This kind of simple RNA aminoacylase complex was engineered from previously selected ribozymes possessing the two required activities. RNA aminoacylation with a nonactivated amino acid as described here is advantageous to RNA world scenarios because initial amino acid activation by an additional reagent (in most cases, ATP) and an additional ribozyme would not be necessary.     

Aromatic Amino Acid Decarboxylase Deficiency: The Added Value of Biochemistry

Aromatic amino acid decarboxylase (AADC) deficiency is a rare, autosomal recessive neurometabolic disorder caused by mutations in the DDC gene, leading to a deficit of AADC, a pyridoxal 5′-phosphate requiring enzyme that catalyzes the decarboxylation of L-Dopa and L-5-hydroxytryptophan in dopamine and serotonin, respectively. Although clinical and genetic studies have given the major contribution to the diagnosis and therapy of AADC deficiency, biochemical investigations have also helped the comprehension of this disorder at a molecular level. Here, we reported the steps leading to the elucidation of the functional and structural features of the enzyme that were useful to identify the different molecular defects caused by the mutations, either in homozygosis or in heterozygosis, associated with AADC deficiency. By revisiting the biochemical data available on the characterization of the pathogenic variants in the purified recombinant form, and interpreting them on the basis of the structure-function relationship of AADC, it was possible: (i) to define the enzymatic phenotype of patients harboring pathogenic mutations and at the same time to propose specific therapeutic managements, and (ii) to identify residues and/or regions of the enzyme relevant for catalysis and/or folding of AADC.     

Generating Cyan Fluorescence with De Novo Tripeptides: An In Vitro Mutation Study on the Role of Single Amino Acid Residues and Their Sequence

Amino acids are natural choices as building blocks when developing biofunctional entities owing to their superior diversity and versatile physicochemical properties compared to nucleotide bases. A simple permutation of the amino acids creates a broad palette of proteins and these have been successfully engineered into useful biofunctional agents. For example, the intrinsic ultraviolet fluorescence of phenylalanine and tryptophan has been engineered to emit in the visible spectrum, which has broad applications for imaging/sensing probes, photothermal therapy agents, optogenetic switches, etc. Nature produces more colorful coats/furs, feathers/hairs, and eyes through various biochemical modifications of tyrosine-based pigmentation. However, it is challenging to modulate the fluorescence wavelength from the UV to the visible region through oligopeptides. Herein, we report an innovative approach to obtain cyan fluorescence by using de novo tripeptides containing glycine, tyrosine, and lysine, which form robust dimer structures under moderate oxidizing conditions. Through an in vitro mutation approach, we deduce that both the amino acids and their sequence play significant roles in modulating the fluorescence. We believe this work holds great promise for developing novel cell imaging and resonance energy-transfer-based fluorescent probes.     

Mass Spectrometry Analysis Coupled with de novo Sequencing Reveals Amino Acid Substitutions in Nucleocapsid Protein from Influenza A Virus

Amino acid substitutions in influenza A virus are the main reasons for both antigenic shift and virulence change, which result from non-synonymous mutations in the viral genome. Nucleocapsid protein (NP), one of the major structural proteins of influenza virus, is responsible for regulation of viral RNA synthesis and replication. In this report we used LC-MS/MS to analyze tryptic digestion of nucleocapsid protein of influenza virus (A/Puerto Rico/8/1934 H1N1), which was isolated and purified by SDS poly-acrylamide gel electrophoresis. Thus, LC-MS/MS analyses, coupled with manual de novo sequencing, allowed the determination of three substituted amino acid residues R452K, T423A and N430T in two tryptic peptides. The obtained results provided experimental evidence that amino acid substitutions resulted from non-synonymous gene mutations could be directly characterized by mass spectrometry in proteins of RNA viruses such as influenza A virus.     

棉籽酸化油的理化性质及脂肪酸组成分析

采用气相色谱法分析了棉籽酸化油的脂肪酸组成,并对其理化性质进行了研究。分析结果表明,棉籽酸化油的含油率为91.33%,酸值为144.35mgKOH/g,碘值为116.58gI2/100g,皂化值为199.80mgKOH/g;其主要脂肪酸为棕榈酸(21.29%)、硬脂酸(2.29%)、油酸(23.72%)、亚油酸(50.23%)和亚麻酸(0.39%),其中不饱和脂肪酸的含量高达74%,具有很高的工业利用价值。