Grouping of amino acid types and extraction of amino acid properties from multiple sequence alignments using variance maximization

Understanding of amino acid type co-occurrence in trusted multiple sequence alignments is a prerequisite for improved sequence alignment and remote homology detection algorithms. Two objective approaches were used to investigate co-occurrence, both based on variance maximization of the weighted residue frequencies in columns taken from a large alignment database. The first approach discretely grouped amino acid types, and the second approach extracted orthogonal properties of amino acids using principal components analysis. The grouping results corresponded to amino acid physical properties such as side chain hydrophobicity, size, or backbone flexibility, and an optimal arrangement of approximately eight groups was observed. However, interpretation of the orthogonal properties was more complex. Although the principal components accounting for the largest variances exhibited modest correlations with hydrophobicity and conservation of glycine, in general principal components did not correspond to physical properties of amino acids. Although not intuitive, these amino acid mathematical properties were demonstrated to be robust and to improve local pairwise alignment accuracy, relative to 20 amino acid frequencies alone, for a simple test case.     

YddG from Escherichia coli promotes export of aromatic amino acids

The inner membrane protein YddG of Escherichia coli is a homologue of the known amino acid exporters RhtA and YdeD. It was found that the yddG gene overexpression conferred resistance upon E. coli cells to the inhibiting concentrations of l-phenylalanine and aromatic amino acid analogues, dl-p-fluorophenylalanine, dl-o-fluorophenylalanine and dl-5-fluorotryptophan. In addition, yddG overexpression enhanced the production of l-phenylalanine, l-tyrosine or l-tryptophan by the respective E. coli-producing strains. On the other hand, the inactivation of yddG decreased the aromatic amino acid accumulation by these strains. The cells of the E. colil-phenylalanine-producing strain containing overexpressed yddG accumulated less l-phenylalanine inside and exported the amino acid at a higher rate than the cells of the isogenic strain containing wild-type yddG. Taken together, these results indicate that YddG functions as an aromatic amino acid exporter.     

Free amino acids in some sponges

Most invertebrates, particularly those of marine origin, have relatively high concentrations of free amino acids which are considered an important constituent of their osmoregulatory mechanisms [1]. Very little information is available on the free amino acid distribution in Porifera [2,3]. Common amino acids in some sponges were recognised by paper chromatography by Inskip and Cassidy [4] and Ackermann et al. [5,6] included a few sponges in their survey of the occurence of nitrogen compounds in marine invertebrates. More recently Bergquist and Hartman [7] surveyed semiquantitatively the distribution of free amino acids in several sponges. In the present paper we report on the amino acid composition of 12 species of sponges belonging to the class Demospongiae as a part of a study on the metabolites of Porifera [8]. Fresh sponges were extracted with aqueous ethanol. The organic solvent was removed and the aqueous solution, after removal of the ether soluble compounds, was separated into cationic, anionic and neutral fractions by ion-exchange chromatography. The cation fraction was analysed for amino acids using an automatic amino acid analyser. The results, which are presented in Table 1, show that all species of sponges examined have a similar composition in common amino acids. Glycine almost always appears as the dominant protein amino acid, followed by high concentrations of alanine and glutamic acid, whereas relatively lower concentrations of basic amino acids are present. In Axinella cannabina, Chondrosia reniformis, Chondrilla nucula, Cliona viridis and Hymeniacidon sanguinea, glycine represents more than 77% of the total amino acids. The high percentage of free glycine (90.4%) in Chondrosia reniformis is noteworthy. The anionic and the neutral fractions were examined for sulfur-containing amino acids using PC. Taurine (Table 2) was detected in all the Porifera examined; this is in agreement with previous observations [5–7]. N-Methyltaurine was identified in some of the species examined, whereas neither N,N-dimethyltaurine nor N,N,N-trimethyltaurine were found.     

4种野生蔬菜的氨基酸含量及其营养价值评价

野生蔬菜具有独特的口味,丰富的营养,有些还具有防病治病的功能,对人体有良好的保健作用.白子菜[Gynura divaricata (L.) DC.]茎叶有消热、舒筋及止血祛瘀的作用,用于镇咳、风湿性关节痛、骨折、创伤止血,痈肿疮疥等症,在民间还作抗癌草使用[1].红凤菜(Gynura bicolor DC.)茎叶有活血止血,解毒消肿的功效,治痛经,血崩,咳血,创伤出血,溃疡久不收口[2].诸葛菜[Orychophragmus violaceus (L.) Schulz]作为野生蔬菜在江苏、安徽民间有很长的食用历史,测定结果表明,该种含有黄酮类化合物[3].马齿苋(Portulaca oleracea L.)具有清热解毒、消炎、利尿、消肿的功效,民间还用于白发症、糖尿病、心血管疾病的治疗[4],中国卫生部将它列为药食同用的植物.     

Analysis of energetic amino acid metabolism in Acyrthosiphon pisum: A multidimensional approach to amino acid metabolism in aphids

Aphids are highly specialized insects that feed on the phloem-sap of plants, the amino acid composition of which is very unbalanced. Amino acid metabolism is thus crucial in aphids, and we describe a novel investigation method based on the use of ¹⁴C-labeled amino acids added in an artificial diet. A metabolism cage for aphids was constructed, allowing for the collection and analysis of the radioactivity incorporated into the aphid body, expired as CO₂, and rejected in the honeydew and exuviae. This method was applied to the study of the metabolism of eight energetic amino acids (aspartate, glutamate, glutamine, glycine, serine, alanine, proline, and threonine) in the pea aphid, Acyrthosiphon pisum. All these amino acids except threonine were subject to substantial catabolism as measured by high ¹⁴CO₂ production. The highest turnover was displayed by aspartate, with 60% of its carbons expired as CO₂. For the first time in an aphid, we directly demonstrated the synthesis of three essential amino acids (threonine, isoleucine, and lysine) from carbons of common amino acids. The synthesis of these three compounds was only observed from amino acids that were previously converted into glutamate. This conversion was important for aspartate, and lower for alanine and proline. To explain the quantitative results of interconversion between amino acids, we propose a compartmentation model with the intervention of bacterial endosymbiotes for the synthesis of essential amino acids and with glutamate as the only amino acid supplied by the insect to the symbiotes. Moreover, proline exhibited partial conversion into arginine, and it is suggested that proline is probably indirectly involved in excretory nitrogen metabolism. © 1995 Wiley-Liss, Inc.     

Lipophilicity of amino acids

Summary The lipophilicity (or hydrophobicity) of amino acids is an important property relevant for protein folding and therefore of great interest in protein engineering. For peptides or peptidomimetics of potential therapeutic interest, lipophilicity is related to absorption and distribution, and thus indirectly relates to their bioactivity. A rationalization of peptide lipophilicity requires basic knowledge of the lipophilicity of the constituting amino acids. In the present contribution we will review methods to measure or calculate the lipophilicities of amino acids, including unusual amino acids, and we will make a comparison between various lipophilicity scales.     

Conversion of cysteinyl residues to unnatural amino acid analogs. Examination in a model system

Improved and efficient techniques have led to an explosive growth in the application of site-directed mutagenesis to the study of enzymes. However, the limited availability of only those 20 amino acids that are translated by the genetic code has prevented the systematic variation of an amino acid's properties in order to define more precisely its role in the catalytic mechanism of an enzyme. An approach is being examined that combines the high specificity of site-directed mutagenesis with the flexibility of chemical modification to overcome these limitations. A set of reagents has been synthesized and reacted with a cysteine model to produce a series of amino acid structural analogs at appreciable rates and in good overall yields. The selective incorporation of these analogs in place of important functional amino acids in a protein will allow a more detailed examination of the role of that amino acid.     

Regulation of the plasma amino acid profile by leucine via the system L amino acid transporter

Plasma concentrations of amino acids reflect the intracellular amino acid pool in mammals. However, the regulatory mechanism requires clarification. In this study, we examined the effect of leucine administration on plasma amino acid profiles in mice with and without the treatment of 2-aminobicyclo-(2,2,1)-heptane-2-carboxylic acid (BCH) or rapamycin as an inhibitor of system L or mammalian target of rapamycin complex 1, respectively. The elevation of plasma leucine concentration after leucine administration was associated with a significant decrease in the plasma concentrations of isoleucine, valine, methionine, phenylalanine, and tyrosine; BCH treatment almost completely blocked the leucine-induced decrease in plasma amino acid concentrations. Rapamycin treatment had much less effects on the actions of leucine than BCH treatment. These results suggest that leucine regulates the plasma concentrations of branched-chain amino acids, methionine, phenylalanine, and tyrosine, and that system L amino acid transporters are involved in the leucine action.     

The amino acid composition of gum exudates from Prosopis species

The amino acid compositions of the proteinaceous components of the gum exudates from Prosopis alba, P. chilensis, P. glandulosa, P. laevigata, P. torreyana and P. velutina, and for a sample of commercial gum mesquite, are presented. In agreement with data published previously for the polysaccharide components of their gums, only minor differences in composition are shown by these species. The amino acid compositions are characterized by very high proportions of hydroxyproline and by high proportions of proline and serine; these three amino acids account for 62.5% of those present in the gum from Prosopis velutina. The amino acid compositions of these Prosopis gums are remarkably similar to that established recently for the gum from Acacia senegal (gum arabic).     

氨基酸转运载体LAT1研究进展

哺乳动物氨基酸的跨膜运输由多种氨基酸转运载体蛋白介导,其中L型氨基酸转运载体1（LAT1）属于L系统,主要转运大分子支链氨基酸和芳香族中性氨基酸。研究表明,LAT1广泛存在于哺乳动物肝脏、骨髓、大脑、胎盘、心脏和睾丸组织中,LAT1在恶性肿瘤中大量表达,对其不断的增殖起着重要的作用。目前国内对氨基酸转运载体LAT1的研究仍是空白,鉴于LAT1的研究在医学、营养等生命科学领域的研究意义,本文就氨基酸转运载体蛋白LAT1的表达、调节及其相关研究进展作一综述。     

Induction of amino acid transporters expression by endurance exercise in rat skeletal muscle

We here investigated whether an acute bout of endurance exercise would induce the expression of amino acid transporters that regulate leucine transport across plasma and lysosomal membranes in rat skeletal muscle. Rats ran on a motor-driven treadmill at a speed of 28 m/min for 90 min. Immediately after the exercise, we observed that expression of mRNAs encoding l-type amino acid transporter 1 (LAT1) and CD98 was induced in the gastrocnemius, soleus, and extensor digitorum longus (EDL) muscles. Sodium-coupled neutral amino acid transporter 2 (SNAT2) mRNA was also induced by the exercise in those three muscles. Expression of proton-assisted amino acid transporter 1 (PAT1) mRNA was slightly but not significantly induced by a single bout of exercise in soleus and EDL muscles. Exercise-induced mRNA expression of these amino acid transporters appeared to be attenuated by repeated bouts of the exercise. These results suggested that the expression of amino acid transporters for leucine may be induced in response to an increase in the requirement for this amino acid in the cells of working skeletal muscles.     

湖南道地白芷氨基酸含量与组成分析

白芷是我国常用中药材的一种,关于白芷镇痛的有效成分,主要认为是异欧前胡素、欧前胡素等香豆素类具有解痉、镇痛等作用的挥发油类化学成分,但白芷镇痛的成分及其机理尚不十分清楚,是否有其他物质也具有一定的药理作用也不得而知,比如说某些药效性氨基酸。该研究采用自动氨基酸分析仪测定了湖南道地茶陵白芷的蛋白质类氨基酸和游离氨基酸的含量,并分析其氨基酸组成。结果表明:总氨基酸检出除Asn以外的其他16种蛋白质氨基酸,含量最高的Arg占总氨基酸的31.21%,接近1/3;必需氨基酸总量达27.01%,其中含量最高的是Leu,占总必需氨基酸的24.14%;药效氨基酸比例较高,在酸水解产物总氨基酸和游离氨基酸中分别达到73.89%和85.78%,其中Arg的含量最高,达1.383g·100g-1,占比为42.24%,游离氨基酸中γ-氨基丁酸、鸟氨酸含量也较高。此外,还含有少量的高半胱氨酸和鹅肌肽等游离非蛋白质氨基酸和短肽;必需氨基酸的组成接近WHO/FAO的建议摄入值,但Met+Cys的RC值最小,为第一限制性氨基酸。这些药效性氨基酸和游离氨基酸可能是茶陵白芷具有良好药效的一个因素,而且茶陵白芷的氨基酸组成和配比较合理、符合人体需要,在强化含硫氨基酸的基础上具有开发成为新型药食同源保健性食品的潜力。研究结果可为进一步研究白芷的药理作用提供依据。     

Sugar amino acids in designing new molecules

Emulating the basic principles followed by Nature to build its vast repertoire of biomolecules, organic chemists are developing many novel multifunctional building blocks and using them to create ‘nature-like’ and yet unnatural organic molecules. Sugar amino acids constitute an important class of such polyfunctional scaffolds where the carboxyl, amino and hydroxyl termini provide an excellent opportunity to organic chemists to create structural diversities akin to Nature’s molecular arsenal. This article describes some of our works on various sugar amino acids and many other related building blocks, like furan amino acids, pyrrole amino acids etc. used in wide-ranging peptidomimetic studies. Published in 2005.Based on the invited lecture presented at the XVII International Symposium on Glycoconjugates held in January 12–16, 2003 at Bangalore, India.     

The kinetics of diastereomeric amino acids with o-phthaldialdehyde.

The kinetics of the reaction of the amino acid epimers L-isoleucine, D-allo-isoleucine, L-threonine, and D-allo-threonine with o-phthaldialdehyde and mercaptoethanol were determined at 25 degrees C. L-Isoleucine reacts faster than its D-epimer whereas L-threonine reacts slightly slower than its D-epimer. In the case of isoleucine, the consequence can be an allo/iso ratio which in the worst case is 25% too low if these amino acids are quantified by liquid chromatography and o-phthaldialdehyde fluorescence detection. The effect on dating of fossils by amino acid racemization is discussed.     

AAP1 transports uncharged amino acids into roots of Arabidopsis

Amino acids are available to plants in some soils in significant amounts, and plants frequently make use of these nitrogen sources. The goal of this study was to identify transporters involved in the uptake of amino acids into root cells. Based on the fact that high concentrations of amino acids inhibit plant growth, we hypothesized that mutants tolerating toxic levels of amino acids might be deficient in the uptake of amino acids from the environment. To test this hypothesis, we employed a forward genetic screen for Arabidopsis thaliana mutants tolerating toxic concentrations of amino acids in the media. We identified an Arabidopsis mutant that is deficient in the amino acid permease 1 (AAP1, At1g58360) and resistant to 10 mm phenylalanine and a range of other amino acids. The transporter was localized to the plasma membrane of root epidermal cells, root hairs, and throughout the root tip of Arabidopsis. Feeding experiments with [(14)C]-labeled neutral, acidic and basic amino acids showed significantly reduced uptake of amino acids in the mutant, underscoring that increased tolerance of aap1 to high levels of amino acids is coupled with reduced uptake by the root. The growth and uptake studies identified glutamate, histidine and neutral amino acids, including phenylalanine, as physiological substrates for AAP1, whereas aspartate, lysine and arginine are not. We also demonstrate that AAP1 imports amino acids into root cells when these are supplied at ecologically relevant concentrations. Together, our data indicate an important role of AAP1 for efficient use of nitrogen sources present in the rhizosphere.     

Changes with aging in the levels of amino acids in rat CNS structural elements II. Taurine and small neutral amino acids

Taurine (Tau) and the small neutral amino acids glycine (Gly), serine (Ser), threonine (Thr), and alanine (Ala) were measured in 53 brain areas of 3- and 29-month-old male Fisher 344 rats. The ratio of highest to lowest level was 34 for Tau, 9.1 for Thr, 7.6 for Gly and Ser, and 6.5 for Ala. The heterogeneity was found in numerous areas; for example, Tau levels were more than 90 nmol/mg protein in 6 areas, and less than 20 nmol/mg protein in 10 areas. Similar heterogeneity was found with the other amino acids. The relative distribution of the small neutral amino acids showed several similarities; Tau distribution was different. With age, four amino acids decreased in 10–18 areas, and increased in only 1–3, while Thr increased in more areas than it decreased. The five amino acids of this paper, and the four of the previous paper, are among the amino acids at highest level in the brain; the sequence in their levels shows considerable regional heterogeneity.     

Peptidases and amino acid catabolism in lactic acid bacteria

The conversion of peptides to free amino acids and their subsequent utilization is a central metabolic activity in prokaryotes. At least 16 peptidases from lactic acid bacteria (LAB) have been characterized biochemically and/or genetically. Among LAB, the peptidase systems of Lactobacillus helveticus and Lactococcus lactis have been examined in greatest detail. While there are homologous enzymes common to both systems, significant differences exist in the peptidase complement of these organisms. The characterization of single and multiple peptidase mutants indicate that these strains generally exhibit reduced specific growth rates in milk compared to the parental strains. LAB can also catabolize amino acids produced by peptide hydrolysis. While the catabolism of amino acids such as Arg, Thr, and His is well understood, few other amino acid catabolic pathways from lactic acid bacteria have been characterized in significant detail. Increasing research attention is being directed toward elucidating these pathways as well as characterizing their physiological and industrial significance.     

Simple and efficient synthesis of chiral amino alcohols with an amino acid-based skeleton

Sodium bis(2-methoxyethoxy)aluminum hydride, NaAlH₂(OCH₂CH₂OCH₃)₂, commercially known as Vitride® or Red-Al®, enables rapid synthesis of pure optically active N-protected amino alcohols and peptide alcohols in very high yields. The method is very simple and attractive, as it does not require an additional step of N-protected amino acid derivatization and proceeds without the loss of enantiomeric homogeneity.     

Nonaqueous titration of amino groups in polymeric matrix of plant cell walls

Nonaqueous titration was used for detection of free amino groups in the polymeric matrix of plant cell walls. The content of amino groups varied in the range 0.54–0.91 and total nitrogen in the range 1.0–4.2 mmol per gram dry mass of cell walls depending on the plant species. However, these data on the high content of free amino groups do not correlate with the present day concept that the nitrogen fraction in charged amino groups in plant cell wall proteins, which are assumed to be mainly amino groups of lysine and arginine residues, is about 10%. It is supposed that most detected free amino groups belong to the hydroxy-amino acids hydroxyproline and tyrosine that can be bound at the hydroxyl group with the carbohydrate part of glycoprotein or another structural cell wall polymer.     

A universal evolutionary index for amino acid changes

Different nonsynonymous changes may be under different selective pressure during evolution. Of the 190 possible interchanges among the 20 amino acids, only 75 can be attained by a single-base substitution. An evolutionary index (EI) can be empirically computed for each of the 75 elementary changes as the likelihood of substitutions, relative to that of synonymous changes. We used 280, 1,306, 2,488, and 309 orthologous genes from primates (human versus Old World monkey), rodents (mouse versus rat), yeast (S. cerevisiae versus S. paradoxus), and Drosophila (D. melanogaster versus D. simulans), respectively, to estimate the EIs. In each data set, EI varies more than 10-fold, and the correlation coefficients of EIs from the pairwise comparisons are high (e.g., r = 0.91 between rodent and yeast). The high correlations suggest that the amino acid properties are strong determinants of protein evolution, irrespective of the identities of the proteins or the taxa of interest. However, these properties are not well captured in conventional measures of amino acid exchangeability. We, therefore, propose a universal index of exchange (U): for any large data set, its EI can be expressed as U*R, where R is the average Ka/Ks for that data set. The codon-based, empirically determined EI (i.e., U*R) makes much better predictions on protein evolution than do previous methods.