Diketopiperazine-mediated peptide formation in aqueous solution

Though diketopiperazines (DKP) are formed in most experiments concerning the prebiotic peptide formation, the molecules have not been paid attention in the studies of chemical evolution. We have found that triglycine, tetraglycine or pentaglycine are formed in aqueous solution of glycine anhydride (DKP) and glycine, diglycine or triglycine, respectively. A reaction of alanine with DKP resulted in the formation of glycylglycylalanine under the same conditions. These results indicate that the formation of the peptide bonds proceeds through the nucleophilic attack of an amino group of the amino acids or the oligoglycines on the DKP accompanied by the ring-opening.The formation of glycine anhydride, di-, tri- and tetraglycine was also observed in a mixed aqueous solution of urea and glycine in an open system to allow the evaporation of ammonia. A probable pathway is proposed for prebiotic peptide formation through diketopiperazine on the primitive Earth.     

Neutral salt effects on the velocity and activation volume of the lactate dehydrogenase reaction: Evidence for enzyme hydration changes during catalysis

The effects of different neutral salts on the maximal velocity (V) and activation volume ($\text{Δ}\text{V3}$) of the M₄-lactate dehydrogenase reaction were studied to determine the mechanistic basis of the inhibitory effects of these salts. For salting-in salts (which increase protein group solubility), increasing salt concentrations led to reductions in V and increases in $\text{Δ}\text{V3}$, with the order of salt effectiveness following the Hofmeister (lyotropic) series: KSCN > KI > KBr. A 50% reduction in V was associated with an approximately 17 cm³ mol^?1 increase in $\text{Δ}\text{V3}$ for different concentrations of the same salt and for equal concentrations of different salting-in salts. Salting-out salts were also inhibitory, but no uniform correlation between changes in V and $\text{Δ}\text{V3}$ was observed. The strongly salting-out salt KF decreased $\text{Δ}\text{V3}$ at all concentrations. The weaker salting-out salt K₂SO₄ increased $\text{Δ}\text{V3}$ at concentrations below 0.1 m and decreased $\text{Δ}\text{V3}$ at higher concentrations. KCl increased $\text{Δ}\text{V3}$ as the salt concentration was raised to approximately 0.2 m; further increases in KCl concentration were without effect on $\text{Δ}\text{V3}$. The rate and volume effects of these neutral salts, especially the highly regular covariation in V and $\text{Δ}\text{V3}$ found for salting-in salts, seem difficult to explain in terms of salt-induced changes in the geometry of the active site. We propose instead that these salt effects can all be explained in terms of the energy and volume changes which accompany transfers of protein groups (amino acid side chains and peptide backbone linkages) between the hydrophobic interior of the enzyme and the enzyme-water interface during catalytic conformational changes.     

The formation of peptides from glycine thioesters

Summary The condensation products obtained from 0.01M S-glycyl-N-acetyl-cysteamine at different pH's were investigated. The highest yields of diketo-piperazine (approx. 50%) were observed in phosphate buffers between pH 7.5 and 8.5. The highest yields of diglycine (46%), triglycine (10%) and tetraglycine (2%) were observed in carbonate buffers at pH 9.5. At pH 8.0, over 90% of the glycyl residues of 0.15M S-glycyl-N-acetylcysteamine were incorporated into condensation products, mainly DKP (60–70%). The yields of products from the condensation of S-glycyl-ethanethiol under similar conditions closely re-sembled those obtained with S-glycyl-N-acetylcysteamine.Abbreviations Boc-gly N-tert-butyloxycarbonylglycine - Ac-cys N-acetylcysteine - csa cysteamine - Ac-csa N-acetylcysteamine - DKP diketopiperazine - (gly) ₂ diglycine - (gly) ₃ triglycine - (gly) ₄ tetraglycine - glySEt S-glycyl-ethanethiol - glyS-(Ac-cys) S-glycyl-N-acetylcysteine - glyS-(Ac-csa) S-glycyl-N-acetylcysteamine - Boc-glyS-(Ac-cys) S-(Boc-glycyl)-N-acetylcysteine - Boc-glyS-(Ac-csa) S-(Boc-glycyl)-N-acetylcysteamine - Boc-glySEt S-(Boc-glycyl)-ethanethiol - gly-bydrox glycine hydroxamate     

Better conditions for mammalian in vitro splicing provided by acetate and glutamate as potassium counterions

We demonstrate here that replacing potassium chloride (KCl) with potassium acetate (KAc) or potassium glutamate (KGlu) routinely enhances the yield of RNA intermediates and products obtained from in vitro splicing reactions performed in HeLa cell nuclear extract. This effect was reproducibly observed with multiple splicing substrates. The enhanced yields are at least partially due to stabilization of splicing precursors and products in the KAc and KGlu reactions. This stabilization relative to KCl reactions was greatest with KGlu and was observed over an extended potassium concentration range. The RNA stability differences could not be attributed to heavy metal contamination of the KCl, since ultrapure preparations of this salt yielded similar results. After testing various methods for altering the salts, we found that substitution of KAc or KGlu for KCl and MgAc₂ for MgCl₂ in splicing reactions is the simplest and most effective. Since the conditions defined here more closely mimic in vivo ionic concentrations, they may permit the study of more weakly spliced substrates, as well as facilitate more detailed analyses of spliceosome structure and function.     

Physical chemical studies of short-chain lecithin homologues. 3. Phase separation and light scattering studies on aqueous dioctanoyllecithin solutions

Some phase separation phenomena in aqueous dioctanoyllecithin solutions including the effects of NaCl and Lil on the phase diagram are reported. At low electrolyte concentrations (below 0.2 M) both salts cause the upper consolute temperatures (u.c.t) to decrease, probably due to a decrease of electrostatic attraction between the lipid molecules. At higher salt concentrations the effect of Lil continues in the same direction (salting-in) but NaCl leads to an increase of the u.c.t. (salting-out).Micellar weight determinations could be performed at room temperature in homogeneous lecithin solutions containing 0.2 M Lil. An attempt was made to interpret the light scattering data with the help of the open association model (equal association constants for aggregation steps beyond a certain step) and the Flory-Huegins type of thermodynamic nonideality. The angular dependence of the light scattering points to very large and extended micelles. The radii of gyration are approximately proportional to the square root of the micellar weights.     

Partial molar volumes,expansibilities, and compressibilities of oligoglycines in aqueous solutions at 18–55°C

We have determined the partial molar volumes, expansibilities, and adiabatic compressibilities of glycine, diglycine, triglycine, tetraglycine, and pentaglycine over the temperature range 18–55°C. These data were analyzed and interpreted in terms of the hydration of these short oligoglycines and their constituent groups. From our results, we have estimated the contributions of the peptide group to the partial molar volume and the partial molar adiabatic compressibility of these oligoglycines. Based on these data, we propose that each of the polar atomic groups of the peptide bond forms approximately two hydrogen bonds with adjacent water molecules. Furthermore, the temperature dependence of the partial molar volume suggests that water that solvates the polar groups of a peptide linkage behaves more like a “normal” liquid than does bulk water, which exhibits its well-known anomalous liquid properties. © 1994 John Wiley & Sons, Inc.     

Thermodynamic interaction between urea and the peptide group in aqueous solutions at 25°C

Isopiestic vapor pressure measurements of the ternary systems water + triglycine + urea and water + glycine-L-alanine + urea were made and used to calculate the Gibbs free energy of these systems. Together with recently published analogous results on systems, in which the first solute was glycine or alanine or diglycine, and measurements of the excess enthalpy of all these solutions, it is possible to calculate the Gibbs free energy of transfer and the enthalpy of transfer of the peptide group from water to aqueous urea solutions. The transfer can be described as a binding of urea to the peptide group with ΔG = ?1.85 kJ mol^?1 and ΔH = ?18.7 kJ mol^?1 at 298.1 K.     

Bimodal response in a chemotactic behaviour of Drosophila larvae to monovalent salts

A chemotactic behaviour in Drosophila larvae to monovalent salts was investigated. Larvae showed clear-cut bimodal responses; they preferred low concentration of salts and rejected high. For example, they were attracted to solutions over the range of concentrations of NaCl from 10^?4 M to 10^?1 M but avoided concentrations above 2 × 10^?1 M.The responses to KCl, KBr and Kl showed differences in attraction whereas avoidance thresholds were similar. On the other hand, when the responses to ChCl and ChBr were compared with those to KCl and KBr respectively, only the avoidance responses were depressed. Furthermore, from choice experiments between KCl, NaCl and ChCl, it was shown that cations did not affect the attraction responses.The results observed strongly suggest the existence of two salt receptors (or receptor sites) which act antagonistically on the chemotaxis.     

Determination of Gibbs free energy of transfer for some univalent ions from water to methanol,acetonitrile, dimethylsulfoxide,pyridine, tetrahydrothiophene and liquid ammonia; standard electrode potentials of some couples in these solvents

The free energy of transfer, ΔG°_tr, for 21 univalent ions are determined from water to methanol, acetonitrile, dimethylsulfoxide (DMSO), pyridine, tetrahydrothiophene and liquid ammonia. These solvents show a wide range of donor properties, whereby water and methanol are regarded as hard donors, dimethylsulfoxide and acetonitrile are on the borderline between hard and soft, and the remaining solvents are regarded as typical soft donors. The ΔG°_tr values of ionic compounds are calculated from solubility product measurements of 1:1 salts. The extrathermodynamic tetraphenylarsonium tetraphenylborate (TATB) assumption has been applied in order to calculate the contributions from the single ions. The TATB assumption implies that the two large ions Ph₄As⁺ and BPh₄⁻ are equally solvated, thus ΔG°_tr(AsPh₄⁺)=ΔG°_tr(BPh₄⁻), for all solvent pairs. Standard electrode potentials in non-aqueous solvents can be calculated from the standard electrode potentials in water and the ΔG°_tr values. The standard electrode potentials calculated from the solubility product measurements, and the potentiometrically determined ones were found to be in excellent agreement. The extrathermodynamic assumption has thereby been experimentally shown to be close to the truth.     

Purification, properties and mechanism of action of a staphylolytic enzyme produced by Aeromonas hydrophila

1. An enzyme produced by Aeromonas hydrophila and capable of lysing Staphylococcus aureus cells was purified 180-fold by gel filtration and chromatography on columns of AG-50 W resin. 2. Physical measurements on the purified enzyme suggest that it is a small basic protein with an isoelectric point between pH9·0 and pH9·5. 3. Maximum lytic activity was obtained in 20mm-tris–glycine buffer, pH8·5, at 45°, with no detectable activity in the absence of a nitrogenous base. 4. The enzyme is active in the above buffer containing 1·5m-sucrose, and is useful for the preparation of protoplasts of Staphylococcus aureus. 5. Purified cell wall peptidoglycans of two strains of Staphylococcus aureus, differing in amino acid composition, were hydrolysed by the enzyme with the liberation of glycine oligopeptides, principally diglycine and triglycine. 6. Synthetic glycine oligopeptides larger than triglycine, but not polyglycine, were hydrolysed, as were a number of leucine-containing dipeptides and tripeptides, but no proteolytic activity could be demonstrated. 7. It is concluded that the enzyme is lytic towards Staphylococcus aureus because it splits the pentaglycine cross-links of the cell-wall peptidoglycan.     

Reaction of lysyl oxidase with soluble protein substrates: effect of neutral salts.

Soluble proteins released into the medium of aortic tissues in culture behave as substrates for the enzyme lysyl oxidase. The reaction shows an unusual dependence on the concentration of neutral salts in the assay medium. Practically no enzyme activity was observed in Tris-HCl, 0.005 m, pH 7.6 buffer. However, supplementing the buffer with high concentrations of KCl, KBr, NaCl, and (NH₄)₂SO₄ (in decreasing order of effectiveness) accelerated velocities as much as 10-fold. CaCl₂, KSCN, and KI at increasing concentrations became strongly inhibitory. β-Aminopropionitrile, a specific inhibitor of lysyl oxidase, effectively blocked the catalysis in low and high KCl. The salt-stimulated effects on lysyl oxidase activity were not as noticeable when insoluble proteins were used as substrates. Kinetic studies employing double reciprocal plots revealed that high KCl concentrations (2.0 m) raised the maximum velocity of the reaction but did not alter the apparent K_m. Thus high salt concentrations did not affect the binding of the soluble substrate to the enzyme. In high salts, however, more radioactive substrate proteins appeared to bind to the enzyme, suggesting that the high salt environment increases the fraction of the total enzyme potentially capable of binding to and catalyzing a reaction with the substrate.     

Energetic performance is improved by specific activation of K fluxes through KCa channels in heart mitochondria

Mitochondrial volume regulation depends on K⁺ movement across the inner membrane and a mitochondrial Ca²⁺-dependent K⁺ channel (mitoK_Ca) reportedly contributes to mitochondrial K⁺ uniporter activity. Here we utilize a novel K_Ca channel activator, NS11021, to examine the role of mitoK_Ca in regulating mitochondrial function by measuring K⁺ flux, membrane potential (ΔΨ_m), light scattering, and respiration in guinea pig heart mitochondria. K⁺ uptake and the influence of anions were assessed in mitochondria loaded with the K⁺ sensor PBFI by adding either the chloride (KCl), acetate (KAc), or phosphate (KH₂PO₄) salts of K⁺ to energized mitochondria in a sucrose-based medium. K⁺ fluxes saturated at ∼ 10 mM for each salt, attaining maximal rates of 172 ± 17, 54 ± 2.4, and 33 ± 3.8 nmol K⁺/min/mg in KCl, KAc, or KH₂PO₄, respectively. NS11021 (50 nM) increased the maximal K⁺ uptake rate by 2.5-fold in the presence of KH₂PO₄ or KAc and increased mitochondrial volume, with little effect on ΔΨ_m. In KCl, NS11021 increased K⁺ uptake by only 30% and did not increase volume. The effects of NS11021 on K⁺ uptake were inhibited by the K_Ca toxins charybdotoxin (200 nM) or paxilline (1 μM). Fifty nanomolar of NS11021 increased the mitochondrial respiratory control ratio (RCR) in KH₂PO₄, but not in KCl; however, above 1 μM, NS11021 decreased RCR and depolarized ΔΨ_m. A control compound lacking K_Ca activator properties did not increase K⁺ uptake or volume but had similar nonspecific (toxin-insensitive) effects at high concentrations. The results indicate that activating K⁺ flux through mitoK_Ca mediates a beneficial effect on energetics that depends on mitochondrial swelling with maintained ΔΨ_m.     

Involvement of glycine transfer ribonucleic acids in development of the posterior silk gland of Bombyx mori

Glycine transfer RNAs from the two physiological phases, V-2, the stage of maximum growth, and V-5, the stage of maximum fibroin production, during the development of the posterior silk gland of Bombyx mori were examined. The tRNAs from both phases could be fractionated into two major isoaccepting species on a benzoylated DEAE-cellulose column. No significant qualitative differences were observed among the tRNAs, but the total amount of the isoaccepting species of tRNA^Gly in each gland of V-5 stage was 6-fold higher than the amount of tRNA^Gly in the V-2 gland. The codon recognition properties of the tRNA^Gly species were examined. It was found that tRNA^Gly₁ responded to the copolymer (G:U) preferentially while tRNA^Gly_II recognized the copolymer (A:G). The ratio between the extent of incorporation of labeled glycine from glycyl-tRNA^Gly₁ and glycyl-tRNA^Gly_II into protein in a cell-free system utilizing polysomes from the V-5 glands was similar to the relative abundance of the isoaccepting species present in the glands at that time. It also reflected the ratio between the corresponding codons assigned for glycine based on the sequence analysis of fibroin-mRNA [Suzuki, Y., and Brown, D. D. (1972) J. Mol. Biol.63: 409]. These results suggest that the abundance of tRNA^Gly in the posterior silk gland and the changes in the relative amounts of the isoaccepting species are quite specific for the development of the gland.     

Duplication of the structural gene for glycyl-transfer RNA synthetase in Escherichia coli

Earlier, Folk &; Berg (1970a,b) described a class of mutants affecting the structural gene for glycyl-transfer RNA synthetase (glyS); their Gly⁻ phenotype (requirement for added glycine to minimal medium) was thought to result from a lowered affinity of the enzyme for glycine and consequently a reduced rate of esterification of glycine to tRNA^Gly at normal intracellular levels of glycine. Such mutants revert to a Gly⁺ phenotype at a high frequency (> 10⁻⁵) although the glyS mutant allele remains unchanged.     

Conductance behavior of symmetrical tetraalkylammonium halides in aqueous sucrose solutions

The conductance behavior of some tetraalkylammonium halides (R₄NX) in saturated, aqueous solutions of sucrose has been investigated, and data on the conductance of these salts in water saturated by sucrose at 50° are reported at several temperatures within the range 25 to 70°. In these homogeneous, ternary systems, plots of —log K versus 1/T show a break at the saturation temperature, where two straight lines intersect one another. Divergence of the pair of straight lines has been found to decrease with increasing chain-length of the R₄N⁺ ions, in contrast to the structural behavior of common, alkali-metal ions. The results are interpreted in terms of the hydrophobic nature of the tetraalkylammonium halides, as well as the salting-in behavior of these salts towards sucrose molecules.     

Mean activity coefficients for the simple electrolyte in aqueous mixtures of polyelectrolyte and simple electrolyte. V. common counterion mixtures of alkali-metal dextransulfates with alkali metal chlorides

Mean molal activity coefficients of simple electrolyte in aqueous solutions of Li, Na, K or Cs salts of dextransulfate (DS) with added LjCl, NaCl, KCl or CsCl are reported. The measurements were carried out by means of an electrochemical cell method using a cation exchange membrane as cation selective electrode and Ag/AgCl electrodes. For LiDS-LiCl, NaDS-NaCl and CsDS-CsCl systems the polymer concentration, m_p, was varied from 0.0088 to 0.113 m and at a given m_p the ratio X of the polymer to salt concentration was varied from 0.5 to 16. Due to the insolubility of KDS in high concentration of KCl, the measurements on KDS-KCl system were performed in the m_p range of 0.0088–0.089 m and some of the smaller X values were omitted. The activity coefficient results are compared to Manning's limiting laws, the additivity rule, and to new limiting laws. The additivity rule can give an excellent representation of the data for all m_p values when γ_p is used as an adjustable parameter.     

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.     

Activity coefficients of the peptide and the electrolyte in ternary systems water+glycylglycine+NaCl, +NaBr, +KCl and +KBr at 298.2 K

The activity coefficients of glycylglycine in four aqueous electrolyte solutions (+NaCl, +NaBr, +KCl and +KBr) were obtained at 298.2 K. The mean ionic activity coefficient of the electrolyte in aqueous solutions containing the peptide was determined from measurements of the potential differences of a cation and an anion ion-selective-electrode, each vs. a double junction reference electrode. The results show that the nature of the anion has a major effect on the activity coefficients of glycylglycine. Comparison of activity coefficient data for glycylglycine with literature data for glycine, both in aqueous NaCl solutions, indicates that the effect of the electrolyte is larger for the peptide than for the amino acid. For the peptide, in all cases, the effect of the electrolyte is more important at low molalities of the electrolyte. The Wilson equation was used to correlate the activity coefficient data obtained. The correlation results were satisfactory for the region of concentrated electrolyte.     

Diketopiperazine-mediated peptide formation in aqueous solution II. Catalytic effect of phosphate

The previous paper (I) reported that DKP (glycine anhydride) spontaneously reacts with glycine (Gly) or oligoglycines (Gly _n ) to produce longer oligoglycines (Gly _n+2). This paper presents that phosphate catalyzes the condensation reaction quite effectively.Formation of Gly₄ from DKP (0.1 M) and Gly₂ (0.1 M) in phosphate solution of various concentrations was investigated at a neutral pH at 41 °C. The yields of Gly₄ increased almost linearly with the concentration of phosphate from 0.06 M to 0.24 M. The yield in 0.24 M phosphate solution was approximately one hundred times as high as that in the absence of the phosphate, whereas in the case of Gly₃ formation from DKP and Gly the effect of the phosphate was of ten times lower than in the former case. Orthophosphate was the most effective catalyst among the various kind of chemicals tried in the present investigation including polyphosphates.     

Normal and Mutant Glycine Transfer RNAs

THE glycine-specific tRNAs of E. coli can be grouped into three subspecies which are separated by chromatography on benzoylated DEAE cellulose (BDC): tRNA^Gly₁ (GGG), tRNA^Gly₂ (GGA/G) and tRNA^Gly₃ (GGU/C)^1,2. The tRNA^Gly₁ and tRNA^Gly₂ are specified by the genes, glyU and glyT, respectively, which have been located at 55 and 77 minutes on the E. coli chromosome. Suppressors of tryptophan A gene (trpA) missense mutations and partial diploid strains have been used extensively to characterize the glycine tRNA structural genes (Table 1)^1–3. A common property of these suppressor mutations is that the altered tRNA^Gly is no longer aminoacylated at the normal rate by the glycyl tRNA synthetase (GRS). When ordinary loading conditions are used virtually none of the suppressor tRNA species are amino-acylated. These studies have shown that single gene copies are normally present at the glyT and glyU loci.