AAindex: amino acid index database

AAindex is a database of amino acid indices and amino acid mutation matrices. An amino acid index is a set of 20 numerical values representing various physico-chemical and biochemical properties of amino acids. An amino acid mutation matrix is generally 20 × 20 numerical values representing similarity of amino acids. AAindex consists of two sections: AAindex1 for the collection of published amino acid indices and AAindex2 for the collection of published amino acid mutation matrices. Each entry of either AAindex1 or AAindex2 consists of the definition, the reference information, a list of related entries in terms of the correlation coefficient and the actual data. The database may be accessed through the DBGET/LinkDB system at GenomeNet (http://www.genome.ad.jp/aaindex/ ) or may be downloaded by anonymous FTP (ftp://ftp.genome.ad.jp/db/genomenet/aaindex/ ).     

Identification of specific residues involved in substrate discrimination in two plant O-methyltransferases.

Among the large number of plant O-methyltransferases that are involved in secondary metabolism, only a few have been enzymatically characterized, and little information is available on the structure of their substrate binding site and the mechanism which determines their substrate specificity and methylation regiospecificity. We have previously reported the isolation of two O-methyltransferases, S-adenosyl-l-methionine:(iso)eugenol O-methyltransferase (IEMT) and S-adenosyl-l-methionine:caffeic acid O-methyltransferase (COMT) from Clarkia breweri, an annual plant from California. While IEMT and COMT (which methylate eugenol/isoeugenol and caffeic acid/5-hydroxyferulic acid, respectively) share 83% identity at the amino acid level, they have distinct substrate specificity and methylation regiospecificity. We report here that seven amino acids play a critical role in discriminating between eugenol/isoeugenol and caffeic acid/5-hydroxyferulic acid. When these amino acids in IEMT were replaced by the corresponding residues of COMT, the hybrid protein showed activity only with caffeic acid/5-hydroxyferulic acid. Conversely, when these amino acids in COMT were replaced by corresponding IEMT residues, the hybrid protein had activity only with eugenol/isoeugenol. These results provide strong evidence that O-methyltransferase substrate preference could be determined by a few amino acid residues and that new OMTs with different substrate specificity could begin to evolve from an existing OMT by mutation of a few amino acids. Phylogenetic analysis confirms that C. breweri IEMT evolved recently from COMT.     

Release of Neurotransmitter Amino Acids from Synaptosomes: Enhancement of Calcium-Independent Efflux by Oleic and Arachidonic Acids

Abstract: The release of preloaded [¹⁴C]neuroactive amino acids (glutamic acid, proline, γ-aminobutyric acid) from rat brain synaptosomes can occur via a time-dependent, Ca²⁺ -independent process. This Ca²⁺-independent efflux is increased by compounds that activate Na⁺ channels (veratridine, scorpion venoms), by the ionophore gramicidin D, and by low concentrations of unsaturated fatty acids (oleic acid and arachidonic acid). Saturated fatty acids have no effect on the efflux process. Neither saturated nor unsaturated fatty acids have an effect on the release of [¹⁴C]leucine, an amino acid not known to possess neurotransmitter properties. The increase in the efflux of neuroactive amino acids by oleic and arachidonic acids can also be demonstrated using synaptosomal membrane vesicles. Under conditions in which unsaturated free fatty acids enhance amino acid efflux, no effect on ²²Na⁺ permeability is observed. Since Na⁺ permeability is not altered by fatty acids, the synaptosomes are not depolarized in their presence and, thus, the Na⁺ gradient can be assumed to be undisturbed. We conclude that unsaturated fatty acids represent a potentially important class of endogenous modulators of neuroactive amino acid transport in nerve endings and further postulate that their action is the result of an uncoupling of amino acid transport from the synaptosomal Na⁺ gradient.     

Amino acid exchange mechanism in the basolateral membrane of the midgut epithelium from the larva ofHyalophora cecropia

Summary It is concluded that the amino acid, -aminoisobutyric acid, is taken up from the blood into the midgut epithelium by an exchange mechanism for the following reasons: 1. The amino acid uptake becomes saturated with increasing amino acid concentration on the blood side; 2. The amino acid in the tissue cannot be washed out again to the blood side unless an amino acid is present in the blood side bathing solution; 3. The uptake mechanism is independent of metabolism. This amino acid exchange mechanism is independent of the active transport of potassium from blood side to lumen side, the exchange of potassium between blood and midgut tissue, and the transport of the amino acid, -aminoisobutyric acid, across the midgut epithelium from lumen to blood.     

Molecular cloning and nucleotide sequence of cDNA for murine senile amyloid protein: nucleotide substitutions found in apolipoprotein A-II cDNA of senescence accelerated mouse (SAM).

cDNA clones encoding the murine senile amyloid protein (ASSAM) have been isolated from animal models of accelerated senescence (SAM-P/1) and from normal aging (SAM-R/1). Immunochemical and protein sequence studies revealed that apolipoprotein (apo) A-II is a serum precursor of ASSAM. A 17-base synthetic oligonucleotide based on residues 39-44 of ASSAM was used as a hybridization probe for screening newly constructed SAM-P/1 and SAM-R/1 liver cDNA libraries. The structure of murine apo A-II cDNA is of interest because of the amino acid substitution found in ASSAM and serum apo A-II of SAM-P; in SAM-R or other random bred slc:ICR mice, amino acid residue 5 of mature apo A-II is proline but, in SAM-P, this amino acid is changed to glutamine. This amino acid replacement is caused by two nucleotide substitutions (CCA for proline codon to CAG for glutamine codon). The third base mutation may not be relevant to the substitution of amino acid. Attention is directed to the relation of this amino acid substitution to the specific deposition of apo A-II, as a tissue amyloid fibril.     

TSSub: eukaryotic protein subcellular localization by extracting features from profiles

This paper introduces a new subcellular localization system (TSSub) for eukaryotic proteins. This system extracts features from both profiles and amino acid sequences. Four different features are extracted from profiles by four probabilistic neural network (PNN) classifiers, respectively (the amino acid composition from whole profiles; the amino acid composition from the N-terminus of profiles; the dipeptide composition from whole profiles and the amino acid composition from fragments of profiles). In addition, a support vector machine (SVM) classifier is added to implement the residue-couple feature extracted from amino acid sequences. The results from the five classifiers are fused by an additional SVM classifier. The overall accuracies of this TSSub reach 93.0 and 77.4% on Reinhardt and Hubbard's eukaryotic protein dataset and Huang and Li's eukaryotic protein dataset, respectively. The comparison with existing methods results shows TSSub provides better prediction performance than existing methods. AVAILABILITY: The web server is available from http://166.111.24.5/webtools/TSSub/index.html.     

Induction of cat-86 by chloramphenicol and amino acid starvation in relaxed mutants of Bacillus subtilis

The chloramphenicol acetyltransferase gene cat-86 is induced through a mechanism that is a variation of classical attenuation. Induction results from the destabilization of an RNA stem-loop that normally sequesters the cat-86 ribosome-binding site. Destabilization of the stem-loop is due to the stalling of a ribosome in the leader region of cat-86 mRNA at a position that places the A site of the stalled ribosome at leader codon 6. Two events can stall ribosomes at the correct location to induce cat-86 translation: addition of chloramphenicol to cells and starvation of cells for the amino acid specified by leader codon 6. Induction by amino acid starvation is an anomaly because translation of the cat-86 coding sequence requires all 20 amino acids. To explain this apparent contradiction we postulated that amino acid starvation triggers intracellular proteolysis, thereby providing levels of the deprived amino acid sufficient for cat-86 translation. Here we show that a mutation in relA, the structural gene for stringent factor, blocks intracellular proteolysis that is normally triggered by amino acid starvation. The relA mutation also blocks induction of cat-86 by amino acid starvation, but the mutation does not interfere with chloramphenicol induction. Induction by amino acid starvation can be demonstrated in relA mutant cells if the depleted amino acid is restored at very low levels (e.g., 2 micrograms/ml). A mutation in relC, which may be the gene for ribosomal protein L11, blocks induction of cat-86 by either chloramphenicol or amino acid starvation. We believe this effect is due to a structural alteration of the ribosome resulting from the relC mutation and not to the relaxed phenotype of the cells.     

Model of amino acid substitution in proteins encoded by mitochondrial DNA

Mitochondrial DNA (mtDNA) sequences are widely used for inferring the phylogenetic relationships among species. Clearly, the assumed model of nucleotide or amino acid substitution used should be as realistic as possible. Dependence among neighboring nucleotides in a codon complicates modeling of nucleotide substitutions in protein-encoding genes. It seems preferable to model amino acid substitution rather than nucleotide substitution. Therefore, we present a transition probability matrix of the general reversible Markov model of amino acid substitution for mtDNA-encoded proteins. The matrix is estimated by the maximum likelihood (ML) method from the complete sequence data of mtDNA from 20 vertebrate species. This matrix represents the substitution pattern of the mtDNA-encoded proteins and shows some differences from the matrix estimated from the nuclear-encoded proteins. The use of this matrix would be recommended in inferring trees from mtDNA-encoded protein sequences by the ML method. Received: 3 May 1995 / Accepted: 31 October 1995     

Functional characterization of two novel mammalian electrogenic proton-dependent amino acid cotransporters

We cloned two cDNAs encoding proton/amino acid cotransporters, designated as mPAT1 and mPAT2, from murine tissues. They were identified by sequence similarity to the amino acid/auxin permease family member of lower eukaryotes. We functionally characterized both transporters by flux studies and electrophysiology after expression in Xenopus laevis oocytes. Both mPAT1 and mPAT2 induced a pH-dependent electrogenic transport activity for small amino acids (glycine, alanine, and proline) that is altered by membrane potential. Direct evidence for amino acid/H(+)-symport was shown by intracellular acidification, and a flux coupling stoichiometry for proline/H(+)-symport of 1:1 was determined for both transporters. Besides small apolar L-amino acids, the transporters also recognize their D-enantiomers and selected amino acid derivatives such as gamma-aminobutyric acid. The mPAT1 transporter, the murine orthologue of the recently cloned rat LYAAT-1 transporter, can be considered as a low affinity system when compared with mPAT2. The mRNA of mPAT1 is highly expressed in small intestine, colon, kidney, and brain; the mPAT2-mRNA is mainly found in heart and lung. Phenotypically, the PAT1 transporter possesses the same functional characteristics as the previously described proton-dependent amino acid transport process in apical membranes of intestinal and renal epithelial cells.     

Kinetic and Thermodynamic Aspects of Sodium-Coupled Amino Acid Transport by Marine Invertebrates

SYNOPSIS. Marine invertebrates absorb amino acids directly acrosstheir external body surfaces. This absorption process occursvia carrier-mediated transport systems which, recent evidencesuggests, may be sodium-dependent. Steady-state amino acid gradientsare maintained at levels exceeding 10³–10⁶ times thatof the external environment. Examination of the standing gradientsof total free amino acids, Na, and K in seven invertebratessuggests that an Na/amino acid cotransport model, or an Na/K/aminoacid cotransport model can account for amino acid gradientsof this magnitude. However, the Na : amino acid coupling coefficientsmust be 2 or 3 depending on factors such as membrane potentialand the intracellular Na activities. Evidence from studies ofL-alanine transport in the integument of the polychaete Glyceradibranchiata is presented showing that, for this case, the Na: alanine coupling coefficient is 3. It is concluded that themodels presented are plausible and readily testable explanationsfor the observed amino acid gradients in marine invertebrates.     

Stable-isotope and amino acid profiles of the New Zealand giant Pliocene oyster Crussostreu ingens

Mitchell, L., Curry, G.B. & Fallick, A.E. 1995 11 30: Stable-isotope and amino acid profiles of the New Zealand giant Pliocene oyster Crassostrea ingens .
Oxygen and carbon stable-isotope profiles and intracrystalline amino acid profiles (free and total) were determined for the New Zealand giant Pliocene oyster Crassostrea ingens by sampling annual growth increments along a sagittal section. These profiles reflect both ontogenetic and environmental change over the life-time of the oyster (approximately 20 years). There is a gradual increase in δ¹⁸O from the umbo towards the shell margin and a subsequent levelling-off about halfway along the shell. This pattern probably reflects a decrease in the growth rate of the oyster rather than a temperature effect. The δ¹³C profile initially increases sharply at the umbo and then gradually decreases towards the shell margin. This may be due to kinetic or metabolic effects associated with the development of a fast-growing juvenile into a slower-growing, sexually mature adult, or it may be due to the influence of ¹³C-depleted carbon derived from the oxidation of organic matter in the surrounding sediment. The amino acid profile reveals a gradual decrease in abundance from the umbo to the shell margin, indicative of a progressive increase in the relative amounts of inorganic carbonate to protein over the life of the oyster, that may also be a consequence of decreasing growth rate. Glycine and alanine are the two most common amino acids in both the free and total amino acid profiles: free (i.e. naturally hydrolysed) amino acids account for about three quarters of the total amino acids present. □ Biogeochemistiy, stable isotopes, amino acids, environment, ontogeny .     

AAindex: Amino Acid Index Database.

AAindex is a database of numerical indices representing various physicochemical and biochemical properties of amino acids and pairs of amino acids. It consists of two sections: AAindex1 for the amino acid index of 20 numerical values and AAindex2 for the amino acid mutation matrix of 210 numerical values. Each entry of either AAindex1 or AAindex2 consists of the definition, the reference information, a list of related entries in terms of the correlation coefficient, and the actual data. The database may be accessed through the DBGET/LinkDB system at GenomeNet (http://www.genome.ad. jp/dbget/) or may be downloaded by anonymous FTP (ftp://ftp.genome. ad.jp/db/genomenet/aaindex/).     

Occurrence of motifs with six amino acid residues in three eukaryotic proteomes

Now it is known that 18 neurological inherited diseases connected with mutations of multiple insertion of one amino acid residue in protein sequence. Therefore, studying the functional role of such simple motifs is an important task in biology. In this work we have investigated how often homorepeats, i.e. runs of a single amino acid residue, of 6 amino acid residues long as well as simple motifs consisting from two amino acid residues of 6 residues long situated in any position occur in three eukaryotic well studied proteomes: Homo sapiens, Drosophila melanogaster, Caenorhabditis elegans. It turns out that many simple motifs occur very often. The occurrence for each motif can be found at our site: http://antares.protres.ru/motifs_six_residues.html. One can suggest that such short similar motifs are responsible for the common functions for nongomologous, unrelated proteins from different organisms.     

Changes in the Levels of Free Amino Acids in Various Regions of Cuscuta during Growth

The angiospermous plant parasite Cuscuta derives reduced carbonand nitrogen compounds primarily from its host. Free amino acidsalong Cuscuta vines in three zones, viz., 0 to 5 cm, 5 to 15cm, and 15 to 30 cm, which in a broad sense represent the regionof cell division, cell elongation and differentiation and vasculartissue differentiation respectively, were quantitatively estimated.The free amino acid content was the highest in the 0 to 5 cmregion and progressively decreased along the posterior regionsof the vine. The haustorial region showed the lowest contentof free amino acids. In general, the free amino acid contentin samples collected at 7 p.m. was found to be higher than thatin the samples collected at 7 a.m. Three basic amino acids,histidine, the uncommon amino acid -hydroxyarginine, and arginineconstituted more than 50% of the total free amino acids in allthe zones studied except the haustorial region. Aspartic acidand glutamic acid constituted the major portion in the acidicand neutral fraction of amino acids. Glutamine, asparagine,threonine, and serine were eluted together and occurred in substantialamounts. -Hydroxyarginine constituted the largest fraction inthe cut end exudate of Cuscuta and presumably appeared to bethe major form of transport amino acid. -Hydroxyarginine wasalso a major constituent of the basic amino acids in Cuscutavines parasitizing host plants from widely separated families,suggesting that this amino acid is a biosynthetic product ofthe parasite rather than that of the hosts. Also, U-¹⁴C argininewas converted to -hydroxyarginine by cut Cuscuta vines, suggestingthat -hydroxyarginine is synthesized de novo from arginine byCuscuta. (Received March 30, 1987; Accepted June 7, 1988)     

Chemical Properties of Syringomycin and Syringotoxin: Toxigenic Peptides Produced by Pseudomonas syringae

Syringomycin (SR) and syringotoxin (ST), wide spectrum antibiotics and phytotoxins isolated from ecotypic strains of Pseudomonas syringa , were purified to homogeneity and compared for their physicochemical properties. Acid hydrolysates of SR and ST were analysed for ninhydrin-reactive components by paper chromatography and the Durrum single-column method of amino acid analysis. Both active and base inactivated preparations of SR yielded substances tentatively identified as serine, phenylalanine, an unidentified basic amino acid, and arginine in a 2:1:2:1 mole ratio, respectively. Preparations of SR from ecotypic strains of P. syringae from pear, peach and millet hosts, had an identical amino acid composition which appeared to exclude a potential role of SR in the plant host specificity of P. syringae . ST isolated from a strain of P. syringae from a citrus host, contained substances tentatively identified as threonine, serine, glycine, ornithine, and the same unidentified basic amino acid found in SR in a 1:1:1:1:1 mole ratio. Although autoradiographs of paper chromatograms of acid hydrolysates of ¹⁴C-SR and various chromogenic reagents did not indicate the presence of substances other than amino acids, the nitrogen content of SR by combustion analyses was lower than expected which suggested the possible presence of another component.     

Utilization of amino acids and dipeptides by Lactobacillus plantarum from orange in nutritionally stressed conditions

Aims:  To investigate amino acid and dipeptide utilization by Lactobacillus plantarum N4 isolated from orange peel, in a nutritionally depleted medium based on MRS (Mann, Rogosa, Sharpe).
Methods and Results:  In MRS with 0·1 g l⁻¹ of meat extract and without peptone and yeast extract, growth increased when essential and stimulatory amino acids and nonessential amino acid were added to the medium. Replacement of the essential amino acid, leucine, and the nonessential amino acid, glycine, by leucyl-leucine (Leu-Leu) and/or glycyl-glycine (Gly-Gly) significantly enhanced growth. Essential amino acids were mainly consumed and the dipeptides were almost completely used at the end of growth. Leucine and glycine accumulated internally from the peptides were higher than from the free amino acids. Glucose utilization increased in the media containing dipeptides compared with the medium containing free amino acids.
Conclusions:  In a N-depleted medium, Leu-Leu and/or Gly-Gly were more effective than the respective amino acids in supporting growth of the micro-organism. The more efficient internal accumulation of glycine and especially leucine from dipeptides confirmed the ability of the strain to assimilate mainly complex nitrogen molecules rather than simple ones.
Significance and Impact of the Study:  The ability of Lact. plantarum N4 to efficiently use dipeptides could contribute to spoilage development in the natural medium of the organism, orange juice.     

Kinetic analysis of blood-brain barrier transport of amino acids.

The Michaelis-Menten kinetics of blood-brain barrier transport of fourteen amino acids was investigated with a tissue-sampling, single-injection technique in the anesthetized rat. Tracer quantities of 14C-labelled amino acids and 3H2O, used as a freely diffusible internal reference, were mixed in 0.2 ml of buffered Ringer's solution and injected rapidly into a common carotid artery. Circulation was terminated by decapitation at 15s following injection. A brain uptake index (Ib) was determined from the ratio of 14C dpm in the brain tissue and the injection mixture divided by the same ratio for the 3H2O reference. Brain clearance of tracer concentration of amino acid was saturable when various concentrations of unlabeled amino acid were added to the injection solution. Double reciprocal plots of the saturation data yielded Km (mM) values that ranged from a low of 0.09 mM for arginine to a high of 0.75 mM for cycloleucine. Transport V values were determined from the relationship P = V/Km where P is the blood-brain barrier permeability constant (ml/g per min): P was calculated from the Ib for each amino acid based on a cerebral blood flow of 0.56 ml/g per min and a fractional extraction of 0.75 for the 3H2O reference 15s following carotid injection. The V values ranged from a low of 6.2 nmol/g per min for lysine to a high of 64 nmol/g per min for l-DOPA. Efflux of the tracer amino acid during the 15-s period after injection was assumed to be slow, since the rate constant of cycloleucine from brain to blood was low, 0.11 min-1.     

Restriction of amino acid change in influenza A virus H3HA: comparison of amino acid changes observed in nature and in vitro

We introduced 248 single-point amino acid changes into hemagglutinin (HA) protein of the A/Aichi/2/68 (H3N2) strain by a PCR random mutation method. These changes were classified as positive or negative according to their effect on hemadsorption activity. We observed following results. (i) The percentage of surviving amino acid changes on the HA1 domain that did not abrogate hemadsorption activity was calculated to be ca. 44%. In nature, it is estimated to be ca. 39.6%. This difference in surviving amino acid changes on the HA protein between natural isolates and in vitro mutants might be due to the immune pressure against the former. (ii) A total of 26 amino acid changes in the in vitro mutants matched those at which mainstream amino acid changes had occurred in the H3HA1 polypeptide from 1968 to 2000. Of these, 25 were positive. We suggest that the majority of amino acid changes on the HA protein during evolution might be restricted to those that were positive on the HA of A/Aichi/2/68. (iii) We constructed two-point amino acid changes on the HA protein by using positive mutants. These two-point amino acid changes with a random combination did not inhibit hemadsorption activity. It is possible that an accumulation of amino acid change might occur without order. (iv) From the analysis of amino acids participating in mainstream amino acid change, each antigenic site could be further divided into smaller sites. The amino acid substitutions in the gaps between these smaller sites resulted in mostly hemadsorption-negative changes. These gap positions may play an important role in maintaining the function of the HA protein, and therefore amino acid changes are restricted at these locations.     

Effect of coordinated addition of specific amino acids on the synthesis of recombinant glucose isomerase

The amplified expression of a recombinant protein is known to lead to an intracellular depletion of specific amino acid pools which in turn may affect the production of the desired protein. In order to counteract and overcome such a situation during the fermentation of the recombinant Escherichia coli (PMSG27) containing the glucose isomerase (GI) gene from Streptomyces sp. NCIM 2730, the effect of addition of different amino acids on the specific activity of GI was studied. The amino acid composition of GI from Streptomyces sp. NCIM 2730 reveals predominantly aspartic acid, glutamic acid, and glycine; therefore, in the present paper, the effect of coordinated addition of the assorted combinations of these three amino acids on the synthesis of recombinant GI was studied. The results were analyzed using a 2³ factorial design. The following conclusions were derived from the analysis of two-factor interactions of the three amino acids: (i) The interaction between the aspartic and glutamic acid is independent of aspartic acid concentration but is affected by the increasing concentrations of glutamic acid, (ii) The effect of aspartic acid concentration is more than that of glycine, and (iii) During the interaction of glutamic acid and glycine, the effect of glutamic acid is more prominent than that of glycine. The three-factor interaction analyses reveal that the effect of the three amino acids is in the order aspartic acid > glutamic acid > glycine.