Condensation of oligoglycines with trimeta- and tetrametaphosphate in aqueous solutions

The dehydration condensation of glycine with trimetaphosphate in aqueous solution has been reinvestigated. Although it has been reported that the condensation of glycine under the alkaline conditions was brought about through the formation of cyclic acylphosphoramidate and hence the condensation of polyglycines could not occur, we found that the condensation of oligoglycines with trimeta- and tetrametaphosphate in aqueous solution are possible through the formation of their acylphosphates under the neutral or weak acidic conditions.Aqueous solutions of 1.0 M glycylglycine and 1.0 M trimetaphosphate in the various pH from 4.0 to 9.0 were incubated at 38 °C. The solutions were analyzed by HPLC with ninhydrin reaction system. Tetraglycine and hexaglycine were detected and their maximum yields were given in the reaction carried out around pH 7. They are approximately 15% and 4% after 30 days, respectively. Analogous experiments were performed with tetrametaphosphate. The results showed a similar pH dependence for the condensation, but the yields were about one-tenth of those of corresponding experiments with trimetaphosphate.Relative rates of dimerization of glycine, diglycine and triglycine in the equimolar concentration were also investigated at pH 6.0 at 38 °C. The rates for digylcine and triglycine were approximately twice and four times as large as that for glycine.Relevance of the experiments to chemical evolution is discussed.     

Quantitative polyphosphate-induced "prebiotic" peptide formation in H2O by addition of certain azoles and ions

Aqueous solutions of 0.1 M amino acid and 0.1 M trimetaphosphate maintained at chosen pH values between 8.0 and 10.5 and at room temperature in the presence of imidazole or 1,2,4-triazole give rise after a few days to the corresponding peptides. Yields are highest when the pH is adjusted with concentrated NaOH or KOH instead of ammonia; in some cases glycine is quantitatively transformed within 10-15 days into peptides, mainly di-and tripeptides.     

Quantitative polyphosphate-induced “prebiotic” peptide formation in H2O by addition of certain azoles and ions

Summary Aqueous solutions of 0.1 M amino acid and 0.1 M trimetaphosphate maintained at chosen pH values between 8.0 and 10.5 and at room temperature in the presence of imidazole or 1,2,4-triazole give rise after a few days to the corresponding peptides. Yields are highest when the pH is adjusted with concentrated NaOH or KOH instead of ammonia; in some cases glycine is quantitatively transformed within 10–15 days into peptides, mainly diand tripeptides.     

α-Amino acid behaves differently from β- or γ-amino acids as treated by trimetaphosphate

Summary. The condensation reactions of sodium trimetaphosphate with single amino acids, namely glycine, L-alanine, β-alanine and γ-aminobutyric acid or pairs of these amino acids were reinvestigated by electrospray ion-trap mass spectrometry and high performance liquid chromatography. It was found when mixtures were treated by sodium trimetaphosphate only in the presence of α-amino acid dipeptides were formed. Without addition of α-amino acids, the β-amino acid or γ-aminobutyric acid could not form peptide either by themselves or with their mixtures under the same conditions. From the data it is concluded that phosphate might select α-amino acids to produce the peptides being important precursors for the origin of life. Authors’ address: Dr. Pengxiang Xu, The Key Laboratory for Chemical Biology of Fujian Province, Department of Chemistry, Xiamen University, Xiamen 361005, China     

Inhibition of glycine synthase by branched-chain α-keto acids: A possible mechanism for abnormal glycine metabolism in ketotic hyperglycinemia

The effect of various amino acid metabolites on glycine oxidation by rat liver homogenate was investigated. Three compounds, α-ketoisovaleric acid, α-ketoisocaproic acid, and α-keto-β-methylvaleric acid, were found to inhibit glycine oxidation by 40–60%. In addition, these compounds also inhibited the glycine-CO₂ exchange reaction, a partial reaction of glycine synthase. The reverse reaction, glycine synthesis, was stimulated 4-fold by these α-keto acids. Pyruvate and α-ketoglutarate had no effect on any of these reactions. The parent amino acids, valine, isoleucine, and leucine, also had no effect on the reactions nor did any of their other metabolites with the exception of the branched-chain α-keto acids. The concentration dependence of the inhibition of glycine oxidation and stimulation of glycine synthesis by these branched-chain α-keto acids suggested that the inhibition of glycine oxidation by these compounds was the result of their further oxidation by branched-chain α-keto acid dehydrogenase. However, the products of the branched-chain α-keto acid dehydrogenase, isobutyryl CoA, isovaleryl CoA, or α-methylbutyryl CoA had no effect on glycine oxidation. Thus, it appeared that either the branched-chain α-keto acids altered glycine oxidation by direct binding to glycine synthase or that electrons derived from the oxidation of branched-chain α-keto acids were transferred to the glycine synthase system. It is proposed that glycine synthase and branched-chain α-keto acid dehydrogenase either share a common subunit, possibly lipoamide dehydrogenase, or are so arranged on the mitochondrial membrane that electron transfer between these two enzymes occurs.     

CONDENSATION OF GLYCYLGLYCINE TO OLIGOGLYCINES WITH TRIMETAPHOSPHATE IN AQUEOUS SOLUTION. II: Catalytic Effect of Magnesium Ion

The previously reported condensation reaction of glycylglycine with trimetaphosphate (Yamanaka et al., 1988) was reinvestigated and shown to be catalyzed by magnesium ion. Aqueous solutions containing glycylglycine (0.5 M), trimetaphosphate (0.5 M) and magnesium chloride (0.5 M) were incubated at 38 °C at pH 4, 5, 6, 7 and 8. After incubation for ten days at pH 5, the maximum yields of tetraglycine and hexaglycine as condensation products were found to be about 12 and 1.4%, respectively. This result indicated the presence of a considerable catalytic effect of magnesium ion compared with the maximum yield of about 2% for tetraglycine and 0% for hexaglycine in the absence of magnesium ion.     

Mineral Induced Phosphorylation of Glycolate Ion – a Metaphor in Chemical Evolution

Bilateral surface-active minerals with excess positive charge concentrate glycolate and trimetaphosphate ion from 10^–3 m aqueous solution to half-saturation of the internal surface sites, and induce phosphorylation of glycolate ion in the mineral with trimetaphosphate, sorbed from 10^–2 m solution. By utilizing reactants from dilute solution at near-neutral pH, and eliminating the need for participating organic nitrogen compounds, the reaction comprises several elements considered necessary for geochemical realism in models for molecular evolution.     

Phosphorylation of glyceric acid in aqueous solution using trimetaphosphate

The phosphorylation of glyceric acid is an interesting prebiotic reaction because it converts a simple, potentially prebiotic organic molecule into phosphate derivatives that are central to carbohydrate metabolism. We find that 0.05 M glyceric acid in the presence of 0.5 M trimetaphosphate in alkaline solution gives a mixture of 2- and 3-phosphoglyceric acids in combined yields of up to 40%.Abbreviations P3! trimetaphosphate - 2-P 2-Phosphoglycerate - 3-P 3-Phosphoglycerate - TSPS 3-trimethylsilyl propionic acid, sodium salt - NMR nuclear magnetic resonance     

Substrate specificity and pH dependence of homogeneous wheat germ acid phosphatase.

The broad substrate specificity of a homogeneous isoenzyme of wheat germ acid phosphatase (WGAP) was extensively investigated by chromatographic, electrophoretic, NMR, and kinetic procedures. WGAP exhibited no divalent metal ion requirement and was unaffected upon incubation with EDTA or o-phenanthroline. A comparison of two catalytically homogeneous isoenzymes revealed little difference in substrate specificity. The specificity of WGAP was established by determining the Michaelis constants for a wide variety of substrates. p-Nitrophenyl phosphate, pyrophosphate, tripolyphosphate, and ATP were preferred substrates while lesser activities were seen toward sugar phosphates, trimetaphosphate, phosphoproteins, and (much less) phosphodiesters. An extensive table of Km and Vmax values is given. The pathway for the hydrolysis of trimetaphosphate was examined by colorimetric and 31P NMR methods and it was found that linear tripolyphosphate is not a free intermediate in the enzymatic reaction. In contrast to literature reports, homogeneous wheat germ acid phosphatase exhibits no measurable carboxylesterase activity, nor does it hydrolyze phenyl phosphonothioate esters or phytic acid at significant rates.     

Glycine fermentation by Clostridium histolyticum

Clostridium histolyticum grew on glycine, arginine, or threonine as sole substrate. Arginine degradation preceded that of glycine and partially inhibited that of threonine when two amino acids were present. Each amino acid seemed to be individually catabolized, not by a Stickland type of reaction. Glycine fermentation required the presence of complex ingredients. Therefore, an effect of selenite on glycine catabolism could only be demonstrated after scavenging selenium contamination by preculturing Peptostreptococcus glycinophilus in that medium. C. acidiurici was not suited as selenium accumulating organism as C. histolyticum was inhibited by the residual uric acid. Arginine catabolism was unaffected by seleniuum depriviation. The labelling pattern obtained in acetate after incubation of C. histolyticum with [1-¹⁴C]- or [2-¹⁴C]glycine strongly indicated the metabolism of glycine via the glycine reductase pathway.     

Brilliant skyblue pigment formation from gardenia fruits

It is well known that blue pigment is formed by the reaction of amino acids with genipin, the hydrolyzate of geniposide from gardenia fruits. We studied the effect of the amino acid on blue pigment formation and found a linear relationship between the molecular weight of the neutral amino acid and the λ_max of the blue pigment formed. Thin layer chromatographic analysis revealed brilliant skyblue components of the blue pigments formed from glycine, alanine, leucine, phenylalanine and tyrosine. Furthermore, a brilliant skyblue color was obtained by a reverse phase column chromatography (HP-20) of blue pigments formed from glycine, leucine and phenylalanine. The λ_max of these purified pigments lay above 600 nm, and the peaks were sharper than those of crude pigments. After standing for two weeks at 40°C in 40% ethanol solution, the brilliant skyblue pigment formed from genipin and glycine remained stable, losing none of its initial absorbance.     

Kinetic modelling of Amadori N-(1-deoxy-D-fructos-1-yl)-glycine degradation pathways. Part I--reaction mechanism

The fate of the Amadori compound N-(1-deoxy-D-fructos-1-yl)-glycine (DFG) was studied in aqueous model systems as a function of pH and temperature. The samples were heated at 100 and 120 degrees C with initial reaction pH of 5.5 and 6.8. Special attention was paid to the formation of the free amino acid, glycine; parent sugars, glucose and mannose; organic acids, formic and acetic acid and alpha-dicarbonyls, 1- and 3-deoxyosone together with methylglyoxal. For the studied conditions decreasing the initial reaction pH with 1.3 units or increasing the temperature with 20 degrees C has the same effect on the DFG degradation as well as on glycine formation. An increase in pH seems to favour the formation of 1-deoxyosone. The lower amount found comparatively to 3-deoxyosone, in all studied systems, seems to be related with the higher reactivity of 1-deoxyosone. Independently of the taken pathway, enolization or retro-aldolization, DFG degradation is accompanied by amino acid release. Together with glycine, acetic acid was the main end product formed. Values of 83 and 55 mol% were obtained, respectively. The rate of parent sugars formation increased with pH, but the type of sugar formed also changed with pH. Mannose was preferably formed at pH 5.5 whereas at pH 6.8 the opposite was observed, that is, glucose was formed in higher amounts than mannose. Also, independently of the temperature, at higher pH fructose was also detected. pH, more than temperature, had an influence on the reaction products formed. The initial steps for a complete multiresponse kinetic analysis have been discussed. Based on the established reaction network a kinetic model will be proposed and evaluated by multiresponse kinetic modelling in a subsequent paper.     

The Role of GlycineB Binding Site and Glycine Transporter (GlyT1) in the Regulation of [3H]GABA and [3H]Glycine Release in the Rat Brain

The effect of N-methyl-D-aspartic acid (NMDA), a selective glutamate receptor agonist, on the release of previously incorporated [³H]-aminobutyric acid(GABA) was examined in superfused striatal slices of the rat. NMDA (0.01 to 1.0 mM) increased [³H]GABA overflow with an EC₅₀ value of 0.09 mM. The [³H]GABA releasing effect of NMDA was an external Ca²⁺-dependent process and the GABA uptake inhibitor nipecotic acid (0.1 mM) potentiated this effect. These findings support the view that NMDA evokes GABA release from vesicular pool in striatal GABAergic neurons. Addition of glycine (1 mM), a cotransmitter for NMDA receptor, did not influence the NMDA-induced [³H]GABA overflow. Kynurenic acid (1 mM), an antagonist of glycine_B site, decreased the [³H]GABA-releasing effect of NMDA and this reduction was suspended by addition of 1 mM glycine. Neither glycine nor kynurenic acid exerted effects on resting [³H]GABA outflow. These data suggest that glycine_B binding site at NMDA receptor may be saturated by glycine released from neighboring cells. Glycyldodecylamide (GDA) and N-dodecylsarcosine, inhibitors of glycineT1 transporter, inhibited the uptake of [³H]glycine (IC₅₀ 33 and 16 M) in synaptosomes prepared from rat hippocampus. When hippocampal slices were loaded with [³H]glycine, resting efflux was detected whereas electrical stimulation failed to evoke [³H]glycine overflow. Neither GDA (0.1 mM) nor N-dodecylsarcosine (0.3 mM) influenced [³H]glycine efflux. Using Krebs-bicarbonate buffer with reduced Na⁺ for superfusion of hippocampal slices produced an increased [³H]glycine outflow and electrical stimulation further enhanced this release. These experiments speak for glial and neuronal [³H]glycine release in hippocampus with a dominant role of the former one. GDA, however, did not influence resting or stimulated [³H]glycine efflux even when buffer with low Na⁺ concentration was applied.     

Mechanism of decarboxylation of glycine and glycolate by isolated soybean cells

Isolated soybean leaf mesophyll cells decarboxylated exogenously added [1-¹⁴C]glycolate and [1-¹⁴C]glycine in the dark. The rate of CO₂ release from glycine was inhibited over 90% by isonicotinic acid hydrazide and about 80% by KCN, two inhibitors of the glycine to serine plus CO₂ reaction. The release of CO₂ from glycolate was inhibited by less than 50% under the same conditions. This indicates that about 50% of the CO₂ released from glycolate occurred at a site other than the glycine to serine reaction. The sensitivity of this alternative site of CO₂ release to an inhibitor of glycolate oxidase (methyl-2-hydroxy-3-butynoate) but not an inhibitor of the glutamate:glyoxylate aminotransferase (2,3-epoxypropionate) indicates that this alternative (isonicotinic acid hydrazide insensitive) site of CO₂ release involved glyoxylate. Catalase inhibited this CO₂ release. Under the conditions used it is suggested that about half of the CO₂ released from glycolate occurred at the conversion of glycine to serine plus CO₂ while the remaining half of the CO₂ loss resulted from the direct oxidation of glyoxylate by H₂O₂.     

Inhibitory Effect of Glycine on the Production of Amylase and Proteinase by Bacillus subtilis

It was found that the production of amylase and proteinase by washed cells of Bacillus subtilis var. amyloliquefaciens was inhibited by glycine and its peptides but not by glycine derivatives, in which the free amino group was protected with various groups. Incorporation experiments of glycine-C¹⁴ revealed that about 60 per cent of the radioactivity which had been incorporated into the cells was found in the free amino acid fraction of the bacteria. The inhibitory effect of glycine was easily reversed by the addition of amino acid such as alanine, methionine and glutamic acid. Spermine also caused the reversal of inhibition of the enzyme production by glycine.     

An inquiry into the selective protection of glycine during the radiolysis of glycine-alanine mixtures in aqueous solutions and its implications to the preservation of optically active amino acids in the early earth

Akaboshi et al. (1990) has found an unexpected protection of the achiral amino acid, glycine, towards ionizing radiation at the expense of the selective destruction of the chiral amino acids, alanine and aspartic acid. The present work examines the mechanism of this protection for the case of alanine. We have developed a computer model for the radiolysis of glycine, alanine and glycine-alanine mixtures in aqueous solution. It is established that this protection is due in part to the reaction of the α-radical of glycine with alanine to regenerate a more stable α-radical, according to the following reaction, $$ \cdot CH(NH_3^ + )CO_2^ - + CH_3 CH(NH_3^ + )CO_2^ - \to CH_2 (NH_3^ + )CO_2^ - + CH_3 \dot C(NH_3^ + )CO_2^ -$$ The rate constant of this reaction was estimated to be ≤10⁴M^-1s^-1. The implications for this selective protection of glycine are considered for a hypothetical case in which there would be an enrichment of about 10% ofL-alanine in the primitive ocean and taking the glycine/alanine ratios obtained in CH₄-and CO₂- dominated atmospheres using electric discharge experiments. It is predicted that alanine would be rapidly destroyed and radioracemized in spite of the fact that the concentration of alanine is equal or significantly lower than that of glycine. Assuming that chiral amino acids were a prerequisite for the origin of life, it can be deduced that life could have appeared in a relatively short period of time unless there was a constant supply of optical amino acids from extraterrestrial sources.     

Effect of temperature and pressure on the protonation of glycine

Flow calorimetry has been used to study the interaction of glycine with protons in water at temperatures of 298.15, 323.15, and 348.15 K and pressures up to 12.50 MPa. By combining the measured heat for glycine solutions titrated with NaOH with the heat of ionization for water, the enthalpy of protonation of glycine is obtained. The reaction is exothermic at all temperatures and pressures studied. The effect of pressure on the enthalpy of reaction is very small. The experimental heat data are analyzed to yield equilibrium constant (K), enthalpy change (ΔH), and entropy change (ΔS) values for the protonation reaction as a function of temperature. These values are compared with those reported previously at 298.15 K. The ΔH and ΔS values increase (become more positive), whereas log K values decrease, as temperature increases. The trends for ΔH and ΔS with temperature are opposite to those reported previously for the protonation of several alkanolamines. However, log K values for proton interaction with both glycine and the alkanolamines decrease with increasing temperature. The effect of the nitrogen atom substituent on log K for protonation of glycine and alkanolamines is discussed in terms of changes in long-range and short-range solvent effects. These effects are used to explain the difference in ΔH and ΔS trends between glycine protonation and those found earlier for alkanolamine protonation.     

A ribozyme that triphosphorylates RNA 5′-hydroxyl groups

The RNA world hypothesis describes a stage in the early evolution of life in which RNA served as genome and as the only genome-encoded catalyst. To test whether RNA world organisms could have used cyclic trimetaphosphate as an energy source, we developed an in vitro selection strategy for isolating ribozymes that catalyze the triphosphorylation of RNA 5′-hydroxyl groups with trimetaphosphate. Several active sequences were isolated, and one ribozyme was analyzed in more detail. The ribozyme was truncated to 96 nt, while retaining full activity. It was converted to a trans-format and reacted with rates of 0.16 min⁻¹ under optimal conditions. The secondary structure appears to contain a four-helical junction motif. This study showed that ribozymes can use trimetaphosphate to triphosphorylate RNA 5′-hydroxyl groups and suggested that RNA world organisms could have used trimetaphosphate as their energy source.     

Gene cloning and characterization of glycine oxidase from newly isolated <Emphasis Type="Italic">Bacillus subtilis</Emphasis> strain R5

The gene encoding the glycine oxidase from Bacillus subtilis strain R5 (goxR) was cloned and expressed in Escherichia coli. The gene consisted of 1,110 nucleotides that encoded a protein (GoxR) of 369 amino acid residues with a molecular mass of 40,761 Da. The GoxR exhibited 98.6% identity with glycine oxidase from B. subtilis strain 168. Gene expression and purification of the recombinant GoxR were performed. The recombinant GoxR existed in a homotetramer form. The recombinant protein effectively catalyzed the oxidation of glycine and d-alanine. The specific activity of the purified recombinant GoxR was 0.96 U/mg when glycine was used as a substrate and 1.0 U/mg when d-alanine was substrate. The enzyme displayed its highest activity at pH 8.0 and at a temperature of 50°C. The activation energy of the reaction catalyzed by the enzyme was calculated to be 26 kJ/mol. The enzyme activity was significantly inhibited in the presence of organic solvents. No enhancement of enzyme activity was observed in the presence of metal cations. The experimental results presented in this study demonstrate that the enzyme was a bonafide glycine oxidase.     

The mechanism of action of serine transhydroxymethylase

1. The preparation of stereospecifically tritiated glycines and the determination of their absolute configurations by the use of d-amino acid oxidase are described. 2. The reaction catalysed by serine transhydroxymethylase, which results in the conversion of glycine into serine, has been separated into at least four partial reactions. It is suggested that the first event in this conversion is the formation of a Schiff base intermediate of glycine and pyridoxal phosphate. The next important step involves the removal of the 2S-hydrogen atom of glycine to give a carbanion intermediate. Experiments pertinent to the mechanism of conversion of this carbanion intermediate into serine are described. 3. The enzyme preparation catalysing the conversion of glycine into serine also participates in the conversion of glycine into threonine and allothreonine. In both these conversions, glycine → serine and glycine → threonine, the 2S-hydrogen atom of glycine is eliminated and the 2R-hydrogen atom of glycine is retained. 4. In the light of these experiments the mechanism of action of serine transhydroxymethylase is discussed. It is suggested that methylenetetrahydrofolate is the carrier of formaldehyde, from which formaldehyde may be liberated at the active site of the enzyme, thus allowing the overall reaction to take place.