Determination of binding constants of cyclodextrin inclusion complexes with amino acids and dipeptides by potentiometric titration

Cyclodextrins are well known for their ability to separate enantiomers of drugs, natural products, and other chiral substances using HPLC, GC, or CE. The resolution of the enantiomers is due to the formation of diastereomeric complexes between the cyclodextrin and the pairs of enantiomers. The aim of this study was to determine the binding constants of the complexes between alpha- and beta-cyclodextrin and the enantiomers of a series of aliphatic and aromatic amino acids, and dipeptides, using a potentiometric titration method. The results of this method are compared to other methods, and correlated to findings in cyclodextrin-modified capillary electrophoresis and possible complex structures. Potentiometric titration was found to be an appropriate tool to determine the binding constants of cyclodextrin inclusion complexes.     

Enzymatic digestibility of peptides cross-linked by ionizing radiation

p6gestibility by proteolytic enzymes of peptides cross-linked by ionizing radiation was investigated. Small peptides of alanine and phenylalanine were chosen as model compounds and aminopeptidases and carboxypeptidases were used as proteolytic enzymes. Peptides exposed to gamma-radiation in aqueous solution were analysed by high-performance liquid chromatography before and after hydrolysis by aminopeptidase M, leucine aminopeptidase, carboxypeptidase A and carboxypeptidase Y. The results obtained clearly demonstrate the different actions of these enzymes on cross-linked aliphatic and aromatic peptides. Peptide bonds of cross-linked dipeptides of alanine were completely resistant to enzymatic hydrolysis whereas the enzymes, except for carboxypeptidase Y, cleaved all peptide bonds of cross-linked peptides of phenylalanine. The actions of the enzymes on these particular compounds are discussed in detail.     

Specificity of the wound-induced leucine aminopeptidase (LAP-A) of tomato activity on dipeptide and tripeptide substrates.

Wounding of tomato leaves results in the accumulation of an exoprotease called leucine aminopeptidase (LAP-A) that preferentially hydrolyzes amino acid-p-nitroanilide and -beta-naphthylamide substrates with N-terminal Leu, Met and Arg residues. To determine the substrate specificity of LAP-A on more natural substrates, the rates of hydrolysis of 60 dipeptide and seven tripeptide substrates were determined. For comparison, the specificities of the porcine and Escherichia coli LAPs were evaluated in parallel. Several marked differences in substrate specificities for the animal, plant and prokaryotic LAP enzymes were observed. Substrates with variable N-terminal (P1) residues (Xaa) were evaluated; these substrates had Leu or Gly in the penultimate (P1') position. The plant, animal, and prokaryotic LAPs hydrolyzed dipeptides with N-terminal nonpolar aliphatic (Leu, Val, Ile, and Ala), basic (Arg), and sulfur-containing (Met) residues rapidly, while P1 Asp or Gly were cleaved inefficiently from peptides. Significant differences in the cleavage of dipeptides with P1 aromatic residues (Phe, Tyr, and Trp) were noted. To systematically evaluate the impact of the P1' residue on cleavage of dipeptides, three series of dipeptides (Leu-Xaa, Gly-Xaa, and Arg-Xaa) were evaluated. The P1' residue strongly influenced hydrolysis of dipeptides and the magnitude of its effect was dependent on the P1 residue. P1' Pro, Asp, Lys and Gly slowed the hydrolysis rates of the tomato LAP-A, porcine LAP, and E. coli PepA markedly. Analysis six Arg-Gly-Xaa tripeptides showed that more diversity was tolerated in the P2' position. P2' Arg inhibited tripeptide cleavage by all three enzymes, while P2' Asp enhanced hydrolysis rates for the porcine and prokaryotic LAPs.     

Porphyromonas gingivalis DPP-7 represents a novel type of dipeptidylpeptidase

A novel dipeptidylpeptidase (DPP-7) was purified from the membrane fraction of Porphyromonas gingivalis. This enzyme, with an apparent molecular mass of 76 kDa, has the specificity for both aliphatic and aromatic residues in the P1 position. Although it belongs to the serine class of peptidases, it does not resemble other known dipeptidylpeptidases. Interestingly, the amino acid sequence around the putative active site serine residue shows significant similarity to the C-terminal region of the Staphylococcus aureus V-8 endopeptidase. The genes encoding homologues of DPP-7 were found in genomes of Xylella fastidiosa, Shewanella putrefaciens, and P. gingivalis. It is likely that at least in P. gingivalis, DPP-7 and its homologue, in concert with other di- and tripeptidases, serve nutritional functions by providing dipeptides to this asaccharolytic bacterium.     

Pepsin-catalyzed peptide synthesis

The use of pepsin as a catalyst for the synthesis of peptide bonds was investigated. It is shown that the enzyme enables the preparation of several protected dipeptides and tripeptides containing two adjacent aromatic residues of the type P-Al-Phe-Y, P-PHe-Ar-Y, or P-AR-Phe-Y where P and Y are amino and carboxyl protecting groups, AL is an aliphatic amino acid residue, and Ar is an aromatic, amino acid residue. They yields are in the rang 25–97%. The high yields, combined with the enzyme's stereospecificity, permit the isolation of optically pure enantiomers from racemic mixtures. For example, when Z-DL -Ph-OH is allowed to react with an excess of H-L -Phe-NH₂, the stereoisomer Z-L -Phe-L -Phe-NH₂ is obtained in practically quantitative yield. At the same time, the unreacted, optically pure Z-D -Phe-OH can be recovered (Z = carbobenzyloxy, Phe = phenylalanine). The advantages and disadvantages of the enzymatic coupling procedure as a possible routine method for peptide synthesis are discussed.     

Hydrolytic and enzymatic degradation of liquid-crystalline aromatic/aliphatic copolyesters

Aromatic/aliphatic copolyesters containing hydrophilic moieties in the main chain or side chain were synthesized by bulk polycondensation of aromatic monomers without or with solubilizing substituents and aliphatic monomers. Hydrolytic and enzymatic degradation studies were carried out in vitro at 37 degrees C in pH 7.4 phosphate buffer and in Tris-HCl buffer containing proteinase K. The results indicate that liquid-crystalline aromatic/aliphatic copolyesters are degradable hydrolytically as well as enzymatically. The change in composition and morphology of the polyester films were monitored by nuclear magnetic resonance and scanning electron microscopy. The results suggested that aromatic species and aliphatic moieties could be released into aqueous solution during hydrolytic degradation of aromatic/aliphatic copolyesters with ethyleneoxy groups on the side chain. Modifying aromatic species with hydrophilic groups in aromatic/aliphatic copolyesters was an efficient method to improve degradability and biocompatibility due to improved solubility of degradation products in aqueous solution. Mechanical tests indicated that the copolyesters exhibited good mechanical properties prior to degradation, which can be of relevance for bone tissue engineering.     

Mechanism of interaction of the antileukemic drug cytosine arabinoside with aromatic peptides: role of sugar conformation and peptide backbone

Interaction of the antileukemic drugs, cytosine-arabinoside (Ara-C) and adenosine-arabinoside (Ara-A) and a structural analogue, cytidine, with aromatic dipeptides has been studied by fluorescence and NMR spectroscopy. Ara-C and cytidine bind tryptophanyl and histidyl dipeptides but not tyrosyl dipeptides, while Ara-A does not bind to any of them. Both studies indicate association involving stacking of aromatic moieties. NMR spectra also indicate a protonation of the histidine moiety by Ara-C. In case of cytidine, the chemical shifts observed on binding to His-Phe imply that the backbone protons of the dipeptide participate in the binding. The conformation of the sugar and the base seem to play a very important role in the binding phenomenon as three similar molecules, Ara-C, Ara-A and cytidine bind in totally different ways.     

Pulsefluorimetry of tyrosyl peptides

The fluorescence quantum yield and the fluorescence decay of aqueous solutions of derivatives containina a single tyrosine residue have been measured at different pH. In these derivatives tyrosine was substituted on its amino end (series I) or/and, on its carboxyl end (series II), by acyl, amino or amino acyl groups. The fluorescence decays of series I derivatives are monoexponential regardless to the ionization state of their amino group. Upon deprotonation of the α-amino group, the quantum yields and the lifetimes increase in the case of dipeptides, and slightly decrease, for the tripeptides. The quantum yield and the lifetime increase with the side chain length of the aliphatic residue adjacent to the tyrosine residue, (the fluorescence of Val Tyr anion being identical to that of free Tyrosine). Quite different is the behavior of series II derivatives: their decays at pH 5.5 must be described by two exponential terms, one of them decaying with a short time constant (about 0.5 ns) and little side chain effect is observed. The fluorescence intensity increases upon deprolonalion of the α-amino proup (though to a lesser extent than for series I derivatives); a nearly monoexponential decay is observed at basic pH for dipeptides. but not for tyrosine amide, amide or dipeptides, or tripeptides. The following interpretation of our results is proposed: fluorescence quenching occurs in molecular conformations in which a peptide carbonyl can come in contact with the phenolic chromophore. This condition depends mainly on the value of the angle x₁ which determines the conformation of the tyrosyl residue around its C_α-C_β bond. It appears that the rotamer in which quenching occurs are not the same for series I and series II derivatives, which can explain the different behavior of these two kinds of compounds. The interpretation of the fluorescence properties is developed taking into account on one side the relative population of the rotamers in the ground state, which is given by studies of crystals and of solutions, and on the other side the possibility of an exchange between these rotamers during the excited state time. In this scheme the protonated α-amino groups would act to reinforce the quenching efficiency of the carbonyl. At last it is found that the radiative lifetime of the phenolic chromophore is the same for all the compounds studies.     

Thermodynamics of aliphatic and aromatic hydrocarbons in water

Makhatadze and Privalov have analyzed the thermodynamics of transfer of aliphatic and aromatic hydrocarbons from the gas phase into water. Finding that the hydration free energy of aliphatic and aromatic hydrocarbons have different signs, they conclude that the mechanism causing hydrophobicity of these solutes is of a different nature. Here, we offer an alternative analysis of the dissolution of these non-polar compounds into water based on a recently published interpretation scheme for thermodynamic transfer functions. Our analysis shows that the hydrophobicity of aromatic and aliphatic hydrocarbons is qualitatively the same, i.e. its causes are the same namely the extremely high cohesive energy of water which overcomes the favorable solute-solute and solute-water interactions. However, both analyses conclude that the experimentally observed quantitative difference between the interactions of water with aliphatic and aromatic hydrocarbons, can be assigned to the formation of aromatic ring-water H-bonds.     

Homoserine-derived cyclic sulfamidate as chiral educt for the diversity-oriented synthesis of lactam-bridged dipeptides

Introduction of structural constraint into peptides is an effective way for studying their conformation-activity relationships. Conformationally restrained dipeptidyl lactams, important building blocks for the synthesis of peptidomimetics, have now been synthesized from N-[9-(9-phenylfluorenyl)]-L-aspartic acid alpha-cumyl beta-methyl diester as an inexpensive chiral educt. After selective reduction of the beta-methyl ester with diisobutylaluminum hydride (DIBAL-H), homoserine was treated with thionyl chloride, imidazole, and triethylamine to give sulfamidites. Diastereoisomers were separated by chromatography and oxidation of the major sulfamidite (2R,4S)- with catalytic ruthenium trichloride afforded sulfamidate. A series of gamma-lactam-bridged dipeptides was then obtained by ring opening of sulfamidate cumyl ester with a series of amino esters, selective cumyl ester removal, and lactam formation. The resulting dipeptidyl lactams possessed aliphatic, aromatic, amino, thioether, and carboxylate side chains. A gamma-lactam analog of Pro-Leu-Gly-NH2 (PLG), was synthesized to illustrate the potential for using this approach in the synthesis of biologically active peptide mimics.     

Emulsifier of Arthrobacter RAG-1: specificity of hydrocarbon substrate.

The purified extracellular emulsifying factor produced by Arthrobacter RAG-1 (EF-RAG) emulsified light petroleum oil, diesel oil, and a variety of crude oils and gas oils. Although kerosine and gasoline were emulsified poorly by EF-RAG, they were converted into good substrates for emulsification by addition of aromatic compounds, such as 2-methylnaphthalene. Neither aromatic nor aliphatic fractions of crude oil were emulsified by EF-RAG; however, mixtures containing both fractions were emulsified. Pure aliphatic or aromatic hydrocarbons were emulsified poorly by EF-RAG. Binary mixtures containing an aliphatic and an aromatic hydrocarbon, however, were excellent substrates for EF-RAG-induced emulsification. Of a variety of alkylcyclohexane and alkylbenzene derivatives tested, only hexyl- or heptylbenzene and octyl- or decylcyclohexane were effectively emulsified by EF-RAG. These data indicate that for EF-RAG to induce emulsification of hydrocarbons in water, the hydrocarbon substrate must contain both aliphatic and cyclic components. With binary mixtures of methylnaphthalene and hexadecane, maximum emulsion was obtained with 25% hexadecane.     

Evidence for a dipeptide porter in the lysosome membrane

Small neutral dipeptides such as Gly-Gly are known to cross the lysosome membrane rapidly. The mode of dipeptide translocation was studied, using an osmotic-protection method. Results with dipeptide analogues, such as omega-amino aliphatic acids and taurine, indicated that dipeptides do not cross the rat liver lysosome membrane by unassisted diffusion. Using seven pairs of dipeptide stereoisomers, the penetration of the L-isomer was always found to be much more rapid than that of the D-analogue. It is concluded that the lysosome membrane contains a porter that recognizes and transports L-dipeptides.     

Emulsifier of Arthrobacter RAG-1: specificity of hydrocarbon substrate.

The purified extracellular emulsifying factor produced by Arthrobacter RAG-1 (EF-RAG) emulsified light petroleum oil, diesel oil, and a variety of crude oils and gas oils. Although kerosine and gasoline were emulsified poorly by EF-RAG, they were converted into good substrates for emulsification by addition of aromatic compounds, such as 2-methylnaphthalene. Neither aromatic nor aliphatic fractions of crude oil were emulsified by EF-RAG; however, mixtures containing both fractions were emulsified. Pure aliphatic or aromatic hydrocarbons were emulsified poorly by EF-RAG. Binary mixtures containing an aliphatic and an aromatic hydrocarbon, however, were excellent substrates for EF-RAG-induced emulsification. Of a variety of alkylcyclohexane and alkylbenzene derivatives tested, only hexyl- or heptylbenzene and octyl- or decylcyclohexane were effectively emulsified by EF-RAG. These data indicate that for EF-RAG to induce emulsification of hydrocarbons in water, the hydrocarbon substrate must contain both aliphatic and cyclic components. With binary mixtures of methylnaphthalene and hexadecane, maximum emulsion was obtained with 25% hexadecane.     

Detection of side-chain proton resonances of fully protonated biosolids in nano-litre volumes by magic angle spinning solid-state NMR

We present a new solid-state NMR proton-detected three-dimensional experiment dedicated to the observation of protein proton side chain resonances in nano-liter volumes. The experiment takes advantage of very fast magic angle spinning and double quantum 13C–13C transfer to establish efficient (H)CCH correlations detected on side chain protons. Our approach is demonstrated on the HET-s prion domain in its functional amyloid fibrillar form, fully protonated, with a sample amount of less than 500 µg using a MAS frequency of 70 kHz. The majority of aliphatic and aromatic side chain protons (70%) are observable, in addition to Hα resonances, in a single experiment providing a complementary approach to the established proton-detected amide-based multidimensional solid-state NMR experiments for the study and resonance assignment of biosolid samples, in particular for aromatic side chain resonances.     

Chromatographic properties of human leukocyte alpha-interferon A on sorbents with sepharose and silochrome matrices

Chromatography on immobilized monoclonal antibodies NK-2 from a bacterial strain-producer resulted in a pure human leukocyte alpha-interferon A (alpha-INF-A) homogeneous upon polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate and reverse phase high performance liquid chromatography. The chromatographic properties of partially purified alpha-INF-A on synthetic and commercial sorbents containing immobilized dyes, aromatic dipeptides, chelating and hydrophobic ligands as well as on porous glass have been investigated. In most cases, [125I]alpha-INF-A was used as an inner standard. The chromatographic behaviour of native and [125I]-labeled alpha-INF-A was practically the same. alpha-INF-A was most effectively chromatographed on porous glass, L-Trp-L-Trp-Sepharose 4B and Cu2+-chelate sorbents. In the latter case, the feasibility of substitution of the Sepharose matrix for the silochrome one has been demonstrated. It has been proposed that alpha-INF-A has a hydrophobic "pocket" with exposed aromatic amino acid residues which are capable of selective binding to aromatic dipeptides.     

Energetics of interactions of aromatic hydrocarbons with water

The thermodynamics of transfer of aromatic (benzene, toluene) and aliphatic (ethane, propane, butane) hydrocarbons from the gas phase into water in the temperature range 5–125°C have been analyzed in order to determine the net hydration effect of these compounds. In the case of the aromatic hydrocarbons the enthalpic contribution predominates over the entropic contribution to the Gibbs energy of hydration. This results in a negative value of the hydration Gibbs energy of aromatic hydrocarbons, in contrast to the positive Gibbs energy of hydration of aliphatic hydrocarbons. The different sign of the hydration Gibbs energies indicates that the mechanism causing hydrophobicity of aromatic hydrocarbons has different nature than that causing the hydrophobicity of aliphatic hydrocarbons. The comparison of hydration of aliphatic and aromatic hydrocarbons leads to the following thermodynamic parameters for these additional interactions between the benzene ring and water at 25°C: enthalpy −5.4 kJ/mol, entropy 26.8 J/K mol and Gibbs energy −13.4 kJ/mol. The large enthalpic contribution to the Gibbs energy of hydration of aromatic hydrocarbons probably comes from the ability of the aromatic ring to accept hydrogens from water, forming hydrogen bonds.     

Fate of organic carbon during decomposition of different litter types in Japan

Carbon dynamics during litter decomposition have been described in a variety of forest ecosystems and provided insights into carbon flow in soils. To quantitatively assess how decomposition processes vary between litter types, solid-state ¹³C cross-polarization and magic-angle spinning nuclear magnetic resonance (CPMAS NMR) technique was applied to analyze conifer (cedar, cypress) and hardwood (chinquapin, beech, oak, birch) litter which had degraded during a 3 year litterbag experiment throughout Japan. The results were used to identify compositional changes and estimate decomposition constants (k values) in exponential equations. Total litter and carbon type mass losses during decomposition varied significantly between litter types, being affected by the initial physicochemical litter quality. Concomitant increases and decreases in carbonyl and O/N-alkyl C compositions, respectively, were observed for all litter types, but aromatic and aliphatic C dynamics were less consistent. In hardwoods, [aromatic/aliphatic C ratio] was generally stable during decomposition, suggesting that, in hardwoods, the decomposabilities of aromatic and aliphatic C were similar. In the conifers, an increasing [aromatic/aliphatic C ratio] during decomposition suggested that aromatic C was more recalcitrant than aliphatic C. These results suggest that different decomposition processes between litter types might be related to different aromatic and aliphatic C behaviors, as affected by lignin stability and lipid leachability and biosynthesis. Variations in the k values for total litter and carbon types were not obvious between litter types, although the mass loss patterns differed significantly. The k values estimated in this study may contribute to predictions of soil carbon dynamics and the validation of carbon compartment models in forest ecosystems.     

Conformational study of Ac-Xaa-Pro-NHMe dipeptides: proline puckering and trans/cis imide bond.

The conformational study on 20 Ac-Xaa-Pro-NHMe dipeptides has been carried out using an empirical potential function ECEPP/3 in order to investigate the factors responsible for the preference of proline puckering of the peptides with the trans or cis imide bond preceding the proline. The general conformational preference for down- and up-puckered dipeptides is calculated as trans-down > trans-up > cis-down > cis-up, which is reasonably in accord with that estimated by analyzing X-ray structures of proteins and the result for the single proline residue. The overestimated occurrence of trans-down conformations of proline seems to be caused by excluding long-range interactions that short dipeptides cannot have. The average computed occurrence of dipeptides with cis imide bonds is about 3%, somewhat lower than the value calculated for Ac-Pro-NHMe, which is close to experimental estimates obtained from X-ray structures of proteins. In particular, the interaction of the aromatic side chain of Xaa residue with the proline ring appears not to be strong enough to stabilize the stacked conformations of small dipeptides with cis imide bonds. The propensity to adopt trans or cis imide bond and to form secondary structures of Xaa-Pro sequences is discussed and compared with results obtained from X-ray structures of proteins.     

Nucleolipids as potential organogelators

Four different series of nucleolipids or bola-nucleolipids were synthesized or re-synthesized. Most of the compounds were studied with respect to their gelation properties toward either water or aromatic, hetero-aromatic, and aliphatic hydrocarbons. Bola-nucleolipids 6 and 7 do not gelate any solvent tested, neither as sole additive nor by adding up to 10 wt% of a 1:1 mixture. The nucleolipid 22 carrying the antiviral acyclovir as a head group proved to be a potent organogelator for aromatic hydrocarbons such as toluene, but not for hetarenes, aliphatic hydrocarbons or water. The mono-tailed nucleolipid 24 exhibits excellent organogelator properties for both aromatic and aliphatic hydrocarbons. These were studied as a function of concentration and temperature.     

Properties of the major carboxypeptidase in the larvae of the webbing clothes moth, Tineola bisselliella.

The larvae of the webbing clothes moth, Tineola bisselliella contain two carboxypeptidases (EC 3.4.12-) and one of these has been purified by preparative polyacrylamide gel electrophoresis. Its pH optimum for the hydrolysis of N-benzyloxycarbonyl-glycyl-leucine was pH 7.5-7.7 and its molecular weight as judged by gel filtration was 72 000. It is strongly inhibited by disopropylfluorophosphate, thiol reagents and some metal cations and also by 1:10 phenanthroline but not EDTA. Km and V values for the hydrolysis of 13 N-acyl dipeptides were determined. The enzyme has a strong preference for neutral aliphatic amino acid residues and does not hydrolyse C-terminal proline, arginine or lysine. It is a true carboxypeptidase, requiring an L-amino acid in the C-terminal position, with a free carboxyl group and hydrolysing peptide substrates consecutively from the C-terminal end. Dipeptides are cleaved much more slosly than tripeptides or N-acyl dipeptides.