Analysis of free amino acids in mammalian brain extracts

An optimized method for analysis of free amino acids using a modified lithium-citrate buffer system with a Hitachi L-8800 amino acid analyzer is described. It demonstrates clear advantages over the sodium-citrate buffer system commonly used for the analysis of protein hydrolysates. A sample pretreatment technique for amino acid analysis of brain extracts is also discussed. The focus has been placed on the possibility of quantitative determination of the reduced form of glutathione (GSH) with simultaneous analysis of all other amino acids in brain extracts. The method was validated and calibration coefficient (K _GSH) was determined. Examples of chromatographic separation of free amino acids in extracts derived from different parts of the brain are presented.     

Synthesis of biological molecules on molecular sieves

Catalytic properties of aluminosilicates may play a role in the synthesis of biological molecules from simple gaseous molecules commonly found in planetary atmospheres. Urea, amino acids and UV absorbing substances have been obtained by heating CO and NH₃ with Linde molecular sieves saturated with Ca⁺², NH₄ ⁺ or Fe⁺³. The yields of amino acids produced have been determined by an amino acid analyzer. The quantity of urea produced largely depends on the nature of the saturating cation. Experiments using¹⁴CO confirm that the amino acids are not due to contaminants adsorbed on the surface of the molecular sieves.     

Inclusion of nonproteinous amino acids in thermally prepared models for prebiotic protein

Sixteen nonproteinous amino acids (those not coded for in contemporary protein biosynthesis) were incorporated during the thermal formation of polyamino acids under postulated prebiotic conditions, although not all into a single polyamino acid. The copresence of proteinous or even α-amino acids was not required. (Norleucine color equivalents and elution times on a Beckman model 120C amino acid analyzer were determined for these nonproteinous amino acids). The results suggest that prebiotically available nonproteinous amino acids would have been constituents of prebiotic protein if the latter were formed thermally. Some differences in properties of the polyamino acids could be attributed to particular nonproteinous amino acid residues; however, the tested properties did not suggest a means for evolutionary selection against nonproteinous amino acids as a group. Selection against this class of amino acids in toto was likely a later, biotic, event.     

Synthesis of biological molecules on molecular sieves.

Catalytic properties of aluminosilicates may play a role in the synthesis of biological molecules from simple gaseous molecules commonly found in planetary atmospheres. Urea, amino acids and UV absorbing substances have been obtained by heating CO and NH3 with Linde molecular sieves saturated with Ca+2, NH4+ or Fe+3. The yields of amino acids produced have been determined by an amino acid analyzer. The quantity of urea produced largely depends on the nature of the saturating cation. Experiments using 14CO confirm that the amino acids are not due to contaminants adsorbed on the surface of the molecular sieves.     

The Use of Ascorbate as an Oxidation Inhibitor in Prebiotic Amino Acid Synthesis: A Cautionary Note

It is generally thought that the terrestrial atmosphere at the time of the origin of life was CO₂-rich and that organic compounds such as amino acids would not have been efficiently formed abiotically under such conditions. It has been pointed out, however, that the previously reported low yields of amino acids may have been partially due to oxidation by nitrite/nitrate during acid hydrolysis. Specifically, the yield of amino acids was found to have increased significantly (by a factor of several hundred) after acid hydrolysis with ascorbic acid as an oxidation inhibitor. However, it has not been shown that CO₂ was the carbon source for the formation of the amino acids detected after acid hydrolysis with ascorbic acid. We therefore reinvestigated the prebiotic synthesis of amino acids in a CO₂-rich atmosphere using an isotope labeling experiment. Herein, we report that ascorbic acid does not behave as an appropriate oxidation inhibitor, because it contributes amino acid contaminants as a consequence of its reactions with the nitrogen containing species and formic acid produced during the spark discharge experiment. Thus, amino acids are not efficiently formed from a CO₂-rich atmosphere under the conditions studied.     

Discarding functional residues from the substitution table improves predictions of active sites within three-dimensional structures

Substitutions of individual amino acids in proteins may be under very different evolutionary restraints depending on their structural and functional roles. The Environment Specific Substitution Table (ESST) describes the pattern of substitutions in terms of amino acid location within elements of secondary structure, solvent accessibility, and the existence of hydrogen bonds between side chains and neighbouring amino acid residues. Clearly amino acids that have very different local environments in their functional state compared to those in the protein analysed will give rise to inconsistencies in the calculation of amino acid substitution tables. Here, we describe how the calculation of ESSTs can be improved by discarding the functional residues from the calculation of substitution tables. Four categories of functions are examined in this study: protein–protein interactions, protein–nucleic acid interactions, protein–ligand interactions, and catalytic activity of enzymes. Their contributions to residue conservation are measured and investigated. We test our new ESSTs using the program CRESCENDO, designed to predict functional residues by exploiting knowledge of amino acid substitutions, and compare the benchmark results with proteins whose functions have been defined experimentally. The new methodology increases the Z-score by 98% at the active site residues and finds 16% more active sites compared with the old ESST. We also find that discarding amino acids responsible for protein–protein interactions helps in the prediction of those residues although they are not as conserved as the residues of active sites. Our methodology can make the substitution tables better reflect and describe the substitution patterns of amino acids that are under structural restraints only.     

Single column analysis of amino acids in protein hydrolysates utilizing the fluorescamine reaction

A system is described for the separation of the amino acids commonly found in protein hydrolysates at the picomole level using a single ion exchange column and for their quantitation by the fluorescamine (4-phenylspiro[furan-2 (3H),1′-phthalan]-3,3′-dione) reaction. Three sodium citrate buffers were required for the separation of the amino acids with an analysis time of approximately 3 hr. The amino acids in 1 μg of hydrolyzed bovine serum albumin were separated using a single ion exchange column and were detected in the effluent from the column by the fluorescamine assay. The results were compared with those obtained using a commercial amino acid analyzer and 150 μg of hydrolyzed bovine serum albumin. The chromatogram produced by the more sensitive analyzer utilizing the fluorescamine reaction to detect the amino acids compared favorably with the chromatogram produced by the commercial analyzer utilizing the ninhydrin reaction with the exception that the proline peak was missing. Proline and hydroxyproline fail to yield fluorescence on reaction with fluorescamine unless converted from imines to primary amines.     

Ribonucleotide reductase activity during the cell cycle of Saccharomyces cerevisiae

A fluorometric amino acid analyzer using fluorescamine for the assay of the full array of natural amino acids including proline on a single column is reported. The proline determination was carried out by specific introduction of a solution of N-chlorosuccinimide into the flow system. Single column fluorometric amino acid analysis was carried out in a significantly shorter time and with a sensitivity almost two orders of magnitude greater than that obtained with a commerical colorimetric ninhydrin amino acid analyzer.     

Analysis of free amino acids during fermentation by Bacillus subtilis using capillary electrophoresis

A high performance capillary electrophoresis (HPCE) method was presented to identify and quantitate free amino acids during fermentation by Bacillus subtilis. Amino acids, pre-column derivatized with phenylisothicyanate, were separated and characterized by HPCE. In order to optimize separation conditions, the assay was developed by varying the β-cyclodextrin concentration and pH of the background electrolyte. A buffer system comprising 30 mM phosphate and 3 mM β-cyclodextrin at pH 7.0, voltage of 20 kV and detection wavelength of 254 nm showed the best results, with 17 out of 20 phenylthioncarbamyl amino acids in a solution adequately separated. For quantification, p-aminobenzoic acid was added as an internal standard. Analysis of free amino acids in Bacillus subtilis culture medium using this method revealed good consistency with the values obtained using conventional ninhydrin-based amino acid analyzer. Four free amino acids (aspartic acid, glutamic acid, proline, and tyrosine) concentration in an extracellular matrix during fermentation by Bacillus subtilis were mainly monitored using this method.     

High-sensitivity amino acid analysis: methodology for the determination of amino acid compositions with less than 100 picomoles of peptides

Highly sensitive methodology is described for the determination of amino acid compositions of picomole quantities of peptides using an automated fluorescence amino acid analyzer with o-phthalaldehyde as the detection agent. All commonly occurring amino acids, including cystine, proline, and tryptophan, can be quantitated. High sensitivity is primarily achieved by using simple procedures which effectively and reliably reduce the level of interfering contamination present in buffers and reagents or introduced during sample handling. Accurate and reproducible amino acid compositions are obtained with 50 pmol or less peptide.     

Selectivity in vitamin B-6 model reactions: Selective α or β deuteration of amino acids under transamination or racemization conditions

Al(III)-catalyzed reactions of vitamin B-6 (pyridoxal)-amino acid schiff bases have been studied in ²H₂O. By using excess of the amino acid and varying conditions, amino acids selectively deuterated in the α-position, the β-position, or in both α- and β-positions are isolated. Reaction conditions are those of model systems in which amino acids are known to be reversibly transaminated and racemized by pyridoxal and Al(III). The racemization reaction leads to α-deuteration of the amino acid while transamination followed by its reverse leads to both α- and β-deuteration. The two reactions are viewed as passing through a common dihydropyridine intermediate. The Al(III) serves as an interesting model for the enzyme in that it not only catalyzes transamination and racemization but also can be made to select which of these reactions predominates. This selective catalysis of these reactions is attributed to strong and different pH dependence of the reactivity of various sites of the dihydropyridine intermediate for vitamin B-6 catalysis when incorporated in an Al(III) complex. The biochemical importance of this selectivity and the practical extension of the method of deuteration to other amino acids is discussed.     

A precise method for the quantitation of proteins taking into account their amino acid composition.

A method for the quantitation of protein in biological material is described which gives the same response for all proteins irrespective of their amino acid composition. The method is based on the ninhydrin reaction of amino acids released after total acid hydrolysis of 5- to 20-μl solutions containing 1 to 100 μg of protein. The ammonia is released from the hydrolysate by diffusion and the amino acids are quantitated without fractionation using the continuous-flow system of an amino acid analyzer. Calibration is obtained with solutions of known amino acid content. The protein of a sample is calculated by multiplying the nanomoles of total amino acids found by a conversion factor F. F is the weight in micrograms of 1 nmol of the specific mixture of amino acid residues that the protein of the sample is composed of F has to be determined once for all further quantitations of the same material by quantitative amino acid analysis following standard procedures. By this method as little as 30 ng of protein per aliquot of hydrolysate analyzed can be determined.     

Precise ultraviolet absorbance study of the interactions of amino acids and mononucleosides in aqueous solution

The association constants of various amino acids or their derivatives (methyl esters, amides, etc.) with mononucleosides in aqueous solutions have been measured by using precise ultraviolet difference absorbance photometry. Some of the results are in agreement with those of the previous solubility experiments. The superiority of this ultraviolet absorbance method over the solubility experiments is that it can discriminate between stacking and hydrogen-bonding interactions. New types of specific interactions of some amino acids with nucleic acid bases by using a peptidyl carboxylate ion and another donor or acceptor in their side chains have been found using this technique.     

Partial molar volumes of proteins: amino acid side-chain contributions derived from the partial molar volumes of some tripeptides over the temperature range 10-90 degrees C

The partial molar volumes of tripeptides of sequence glycyl-X-glycine, where X is one of the amino acids alanine, leucine, threonine, glutamine, phenylalanine, histidine, cysteine, proline, glutamic acid, and arginine, have been determined in aqueous solution over the temperature range 10-90 degrees C using differential scanning densitometry . These data, together with those reported previously, have been used to derive the partial molar volumes of the side-chains of all 20 amino acids. The side-chain volumes are critically compared with literature values derived using partial molar volumes for alternative model compounds. The new amino acid side-chain volumes, along with that for the backbone glycyl group, were used to calculate the partial specific volumes of several proteins in aqueous solution. The results obtained are compared with those observed experimentally. The new side-chain volumes have also been used to re-determine residue volume changes upon protein folding.     

Free amino acids and nucleic acid content of cell nuclei isolated by a modification of Behrens' technique

1. Nuclei were prepared from frozen rat liver by a modification of the technique of Behrens, and were studied with regard to the content of free amino acids and nucleic acid. 2. Under rigorously controlled conditions, preparations of nuclei are obtained by the Behrens' method which form a gel in the presence of 5 or 10 per cent NaCl or of water plus a small amount of dilute alkali; whereas when conditions are less rigorously controlled, nuclei are obtained which form no such gel. The property of forming gels with alkali is probably characteristic of all cell nuclei which have not undergone autolysis. 3. Nuclei prepared by the Behrens' technique contain the enzymes arginase, catalase, and esterase in very appreciable concentrations. 4. The free amino acids of the isolated cell nuclei, as well as of other liver cell fractions, have been investigated using the technique of paper chromatography. 5. The chromatographic patterns of the free amino acids of whole cells, ground cytoplasm, and isolated cell nuclei were very similar or identical. A feature of interest in these chromatograms was the faintness or absence of the spots due to a number of the essential amino acids, as compared to the intensities of the spots due to glycine, alanine, and glutamic acid. Glutathione was present in the isolated nuclei as well as in the whole cells. 6. Chromatograms made from hydrolysates of nuclei showed high concentrations of the essential amino acids and were similar to chromatograms of hydrolysates of typical proteins.     

Free amino acid contents of the gametophytic blades from the green mutant conchocelis and the heterozygous conchocelis in Porphyra yezoensis Ueda (Bangiales, Rhodophyta)

Free amino acid contents in green mutant(G-1) blades and sectored F₁gametophytic blades with green andwild-type portions, which were developedfrom heterozygous conchocelis obtained by across between the wild type (0110) and thegreen mutant (G-1) of Porphyrayezoensis, were compared with those of thewild-type blades in laboratory culture. The contents of the major four free aminoacids (aspartic acid, glutamic acid,alanine and taurine) as well as those ofthe total free amino acids were highest inthe green mutant blades, intermediate inthe F₁ gametophytic blades, and lowestin the wild-type blades. A similar trendwas obtained in the blades developed frommonospores of the F₁ gametophyticblades. In addition, the green-typesectors also had a higher content of thefour major free amino acids and total freeamino acids compared with the wild-typesectors in the F₁ blades cultivated ata nori farm. The green mutant ischaracterized by higher contents of thefour major free amino acids compared withthe wild type, which has a higher growthrate. Hence, it is considered that thesectored F₁ gametophytic bladesproduced from the heterozygous conchocelishave both parental advantages (high freeamino acid contents and high growth rate)and compensate for both parentaldisadvantages. This seems to be one of thepossible ways of genetic improvement inregards to the taste of nori and stableproduction in Porphyra cultivation.     

Determination of amino acids in fodders and raw materials using capillary zone electrophoresis

Two schemes were offered for analysis of amino acid contents in fodders and raw materials for mixed fodders by capillary zone electrophoresis (CZE). The first variant provides express analysis of four technologically important amino acids (lysine, methionine, threonine, cystine) in borate buffer on characteristic absorption of aminogroup (190 nm), with limits of quantitation being on average 0.2%. The second scheme includes pre-capillary derivatization of amino acids using phenylisothiocyanate (PITC) and separation of phenylthiocarbamyl (PTC)-derivatives obtained by CZE with a detection on 254 nm, which allows to widen a list of detectable components up to 19 (without tryptophan) and significantly improve detection limits down to 0.01%. Acid hydrolysis was used for a sample preparation. The results of analysis of fodders were compared using such methods, as CZE, ion exchange chromatography (amino acid analyzer) and reversed-phase (RP)-HPLC (with gradient technique of elution).     

Amino Acid Homochirality may be Linked to the Origin of Phosphate-Based Life

Phosphorylation has to have been one of the key events in prebiotic evolution on earth. In this article, the emergence of phosphoryl amino acid 5′-nucleosides having a P–N bond is described as a model of the origin of amino acid homochirality and Genetic Code. It is proposed that the intramolecular interaction between the nucleotide base and the amino acid side-chain influences the stability of particular amino acid 5′-nucleotides, and the interaction also selects for the chirality of amino acids. The differences between l- and d-conformation energies (ΔE _conf) are evaluated by DFT methods at the B3LYP/6-31G(d) level. Although, as expected, these ΔE _conf values are not large, they do give differences in energy that can distinguish the chirality of amino acids. Based on our calculations, the chiral selection of the earliest amino acids for l-enantiomers seems to be determined by a clear stereochemical/physicochemical relationship. As later amino acids developed from the earliest amino acids, we deduce that the chirality of these late amino acids was inherited from that of the early amino acids. This idea reaches far back into evolution, and we hope that it will guide further experiments in this area.     

Mouse macrophage β subunit (CD11b) cDNA for the CR3 complement receptor/Mac-1 antigen

The cDNA for the common \_Mac-1 subunit (CD11b) of the mouse LFA-1/Mac-1/p150,95 group of leukocyte cell adhesion receptors, formally designated integrin \₂, has been cloned and sequenced. Clones were isolated from cDNA libraries made from J774 macrophage and WEHI-3B myelomonocytic tumor cells which express this subunit as a component of the macrophage activation antigen 1 (Mac-1), also known as complement receptor type 3 (CR3). This subunit is expressed as a single, abundant mRNA species approximately 2.7 kilobase (kb) in size. The 2422 base pair (bp) cDNA sequence obtained codes for a 771 amino acid protein organized with leader, extracellular, transmembrane, and cytoplamic domains of 23, 680, 23, and 46 amino acids, respectively, yielding an 82700 mature protein of 747 amino acids. The mouse \_Mac-1 subunit is highly similar to its human counterpart with an overall sequence identity of 81% and identical positioning of 5 out of 6 potential N-linked glycosylation sites, as well as 56 Cys residues that are organized in repeating motifs characteristic of integrin \ subunits. The most highly conserved regions are the transmembrane and cytoplasmic domains where only 4 out of 69 amino acids differ, indicating that the functions associated with this domain in Mac-1-mediated processes, such as iC3b-triggered phagocytosis, have been evolutionarily conserved.The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned the accession number M31039. Offprint requests to: P. M. Hogarth.     

The establishment of essential and metabolically derived amino acid profiles in developing chick embryo organs

The accumulation of certain essential and metabolically derived amino acids in the free amino acid pools of three excitable tissues has been studied in the chick embryo. Valine together with leucine are at the onset present in the yolk at higher concentrations than any of the other essential amino acids. By 15 days all the amino acids studied have accumulated in the embryonic pools at a higher rate than valine, although certain amino acids, such as phenylalanine or methionine, always remain at lower relative concentrations than valine. This reflects their low supply in the yolk, rather than a more rapid rate of disappearance (utilization). During early embryogenesis (E₂–E₄), tissues preferentially concentrate glutamic acid, besides taurine and phosphoethanolamine (6). The next distinct stage of development (E₄–E₇) is marked in the brain by a gradual rise in glutamic acid, glutamine and aspartic acid; the same three amino, acids do not demonstrate a further increase in the pool of the heart, while in the whole eye the amino acid profile begins to resemble the blood. Leucine in all three tissues declines rapidly, to reach isoleucine levels by day 7 of development; tyrosine increases slowly in apparent reciprocity to an equally gradual phenylalanine decrease. Into the second week of embryo growth (E₇–E₁₅), GABA appears in the mesencephalon (E₇) and the eye (E₉–E₁₀). In the mesencephalon, the free amino acid pool composition exhibits a rather sudden increase of most metabolically derived amino acids. Glutamic acid and glutamine in the brain increase in parallel; the rate of GABA and aspartic acid accumulation is slower, and for GABA stabilizes on day 14, as does glutamine. In the eye, by day 15, GABA levels are more closely aligned with the aspartic acid content. Finally, throughout embryogenesis serine fluctuations in blood and tissues are in parallel with those of threonine, and different from glycine or alanine which also change in tandem.