Pepsin as a catalyst of peptide synthesis. Enzyme co-precipitation with emerging peptide products.

Pepsin successfully catalyzed the synthesis of several peptide derivatives from N-protected di- or tripeptides and amino acid or peptide esters or p-nitroanilides in dimethylformamide-water solutions at pH 4.6. An optimal substrates:pepsin ratio depended on the structure of starting peptides, especially their fit to the substrate binding sites of the enzyme. For hexapeptide Z-Ala-Ala-Phe-Leu-Ala-Ala-OCH3 formation, an equilibrium yield was attained at 1:3.10(5) enzyme-substrates ratio that indicated high efficiency of pepsin in synthesis reactions. In the course of the equilibrium peptide synthesis, pepsin gradually disappeared from the liquid phase due to its entrapment within a gel, formed by the hexapeptide product, while retaining its activity. The inclusion into the precipitate was not specific for pepsin, so far as inert proteins, lysozyme, ribonuclease A and carbonic anhydrase, when added to the reaction mixture, became also co-precipitated with the hexapeptide formed. It appears that co-precipitation of pepsin, an important factor limiting the enzyme efficiency, might be operative as well for other proteinases used to catalyze peptide synthesis.     

Course of pH during the formation of amoxicillin by a suspension-to-suspension reaction

Amoxicillin can be produced in an enzymatic suspension-to-suspension reaction in which the substrate(s) and product(s) are mainly present as solid particles, while the reaction takes place in the liquid phase. During these suspension-to-suspension reactions different subprocesses take place, such as dissolution/crystallization of substrates and products, enzymatic synthesis of the product(s), and undesired enzymatic hydrolysis of substrates and/or products. All these subprocesses are influenced by pH and also influence the pH because the reactants are weak electrolytes. This paper describes a quantitative model for predicting pH and concentrations of reactants during suspension-to-suspension reactions. The model is based on mass and charge balances, pH-dependent solubilities of the reactants, and enzyme kinetics. For the validation of this model, the kinetically controlled synthesis of amoxicillin from 6-aminopenicillanic acid and D-(p)hydroxyphenylglycine methyl ester was studied. The pH and the dissolved concentrations took a very different course at different initial substrate amounts. This was described quite reasonably by the model. Therefore, the model can be used as a tool to optimize suspension-to-suspension reactions of weak electrolytes.     

Protease-catalyzed synthesis of oligopeptides in heterogenous substrate mixtures

A systematic study of enzymatic peptide synthesis in heterogeneous substrate mixtures was carried out, with the aim of establishing the preparative scope of this methodology. Semiliquid eutectics were obtained with various combinations of neutral, acidic, and basic amino acid derivatives, in the presence or absence of adjuvants. A range of serine cysteine, and metalloproteases readily catalyzed the formation of the required dipeptides under these conditions. The synthetic usefulness of the approach was demonstrated by the sequential and convergent synthesis of derivatives of a number of bioactive di-, tri-, and pentapeptides, including aspartame, sweet lysine peptide, kyotorphin amide, ACE-inhibiting and -immunoactive tripeptides, and Leu-enkephalin amide, with overallyields of 21% to 84% and productivities of 0.13 to 0.75 g/g being obtained. (c) 1994 John Wiley & Sons, Inc.     

The control of lipase-catalysed transesterification and esterification reaction rates. Effects of substrate polarity, water activity and water molecules on enzyme activity

The reaction rate of two lipase-catalysed reactions, esterification and transesterification, were studied in a liquid/solid two-phase system in order to investigate the effect of water partition between the enzyme preparation and the liquid phase composed of only the reactants, i.e. without the conventional solvents. Lipase from Candida cylindracea was used for these studies. The enzyme was inactive in dehydrated systems. In the case of monoester synthesis, the reaction rate increased with increasing water activity. The reaction rates of the non-specific C. cylindracea lipase-catalysed reactions were very sensitive to the nature of the substrates in this unusual system. For instance, the transesterification reaction rate of ethyl propionate was 48 times higher with nonanol than heptanol in the case of dehydrated substrates, but only 2.2 times higher in the case of water-saturated substrates. The results presented here demonstrate the absolute necessity to consider the polarity of every substrate, because of its ability to modify the water partition between the solid phase (enzyme preparation) and the liquid phase (substrate and product), which results in drastic changes in enzyme activity. Contrary to esterification, which is known to be activated by the water produced, the rate of transesterification remained constant at the beginning of the reaction. However, when transesterification and esterification were carried out in the same liquid phase, the transesterification reaction rate was controlled by the water produced by the concomitant esterification. Activation effects of the water molecules produced during the enzymatic reaction were of exactly the same order of magnitude for both reactions.     

DNA liquid crystals as a possible system of testing the interactions between DNA and biologically active compounds of platinum (II) and various antibiotics

DNA liquid crystals forming in water-salt solutions containing polyethylene glycol were used as a system for testing consequences of reactions of antitumor compounds belonging to two different groups with molecules of nucleic acids. It was found that with due account of the level of DNA molecule filling with daunorubicin it was possible to form two cholester phases characterized by the textures of "finger prints" and CD spectra with intensive bands of unlike signs, as well as the nematic phase characterized by the texture of the "black twisted fiber" system and the absence of the CD spectrum intensive band. Modification of the DNA molecules resulting from the reaction with cysdichlorodiamine platinum (II) led to formation of a new liquid crystalline phase with properties differing from those of the liquid crystalline phases of the cholester or nematic type.     

Kinetics of enzymatic solid-to-solid peptide synthesis: intersubstrate compound, substrate ratio, and mixing effects

A systematic study of thermolysin-catalyzed solid-to-solid peptide synthesis using Z-Gln and Leu-NH2 as model substrates was carried out. The aim was to extend the kinetic knowledge of this new reaction system involving highly concentrated substrate mixtures with little water (10% to 20% w/w). Preheating of the substrates, and ultrasonic treatment, as described in the literature, had no significant effect on our system. The formation of a third compound, the salt of the two substrates, was discovered during melting point experiments. This was associated with a very strong dependence of kinetics on the exact substrate ratio (e.g., twofold higher initial rate with 60% Leu-NH2 and 40% Z-Gln than with the equimolar substrate ratio). A model was developed to show how the composition and pH of the liquid phase depends on the substrate ratio, and seemed to explain the experimental rates. In addition, the influences of different mixing and water distribution methods are described. Finally, we can now summarize the major effects of the reaction system as a starting point for further research and scale-up studies.     

Ionic liquids for aqueous two-phase extraction and stabilization of enzymes

The ionic liquid (IL) Ammoeng110 contains cations with oligoethyleneglycol units and was found to be highly effective for the formation of aqueous two-phase systems (ATPS) that can be used for the biocompatible purification of active enzymes. Above critical concentrations of the IL and an inorganic salt in aqueous solution, phase separation takes place resulting in the formation of an IL-enriched upper and a salt-enriched lower phase. For the optimization of the composition of IL-based ATPS with regard to the extraction of catalytically active enzymes, the Box-Wilson method of experimental design was successfully applied; IL-based ATPS proved to be suitable for the purification and stabilization of two different alcohol dehydrogenases (from Lactobacillus brevis and a thermophilic bacterium). Both enzymes were enriched in the IL-containing upper phase resulting in an increase of specific activity by a factor of 2 and 4 respectively. Furthermore, the presence of IL within the system provided the opportunity to combine the extraction process with the performance of enzyme-catalyzed reactions. The IL was found to exhibit a stability improving effect on both enzymes and a solubility enhancing effect on hydrophobic substrates. Thus the conversion and volumetric productivity of ADH catalyzed reduction of acetophenone could be increased significantly.     

Biomimetic nanosystems and novel composite nanobiomaterials

Biophysicochemical approaches to the solution of nanotechnology problems associated with the design of functional biomimetic nanosystems, hybrid and composite nanobiomaterials and study of their structure-function relationships. The results of studies concerned with physicochemical mechanisms of the formation of organized biomimetic nanostructures and bioinorganic nanomaterials in systems involving a bulky liquid phase and the interface (gas-liquid, solid-liquid, liquid-liquid)during the synthesis and structure formation with the participation of the components of colloid systems, inorganic nanoparticles of various composition and clusters of metals, surfactants, polyelectrolytes and their complexes are discussed. In the development of the methods for the formation of composite bioinorganic nanosystems containing inorganic nanocomponents, two major approaches were used: adsorption and incorporation into the biomolecular matrix or colloid system of presynthesized inorganic nanoparticles, as well as the synthesis of the inorganic nanophase immediately in the biomolecular system. The methods of obtaining biomaterials and nanosystems are based on the principles of biomimetics, biomineralization, self-assembly and self-organization, combination and integration of a number of synthetic and physicochemical methods (physical and chemical adsorption, Langmuir technique, the formation of polycomplexes, chemical linking, competitive interactions, and substitution of ligands in supramolecular and coordination complexes) and nanocomponents of different nature. In particular, a novel approach to the preparation of highly organized nanofilm materials was developed, which is based on the effect of self-assembly and self-organization of colloid nanoparticles during the formation of their complexes with polyfunctional biogenic ligands in the volume of the liquid phase in the absence of any surfaces and interfaces. The physical and chemical factors responsible for the formation of structurally ordered biomolecular and composite nanosystems including nano-sized components of different nature and the possibilities to control the composition, structure, and properties of resulting nanomaterials and nanosystems are discussed. The experimental methods and approaches developed may be useful in studies of structure-property relationships and basic mechanisms of structural organization and transformation at the nanoscales level in biological, artificial, and hybrid nanosystems. The problems of practical application of the synthetic methods and the corresponding nanomaterials are discussed.     

Induction of T4 DNA ligase in a recombinant strain of Escherichia coli

The kinetics of cell growth and foreign protein production, as well as factors affecting protein stability, were studied and optimized in batch and fed-batch fermentations of a recombinant strain of Escherichia coli. The pL promoter from bacteriophage lambda under the control of a temperature-sensitive cl represser, with the entire construct integrated into the E. coli chromosome through the use of a defective bacteriophage lambda lysogen, was used to direct the synthesis of T4 DNA ligase. The biphasic fermentations consisted of a primary growth phase at 30 degrees C followed by an induction phase which was initiated by shifting the temperature to 42 degrees C. In the fed-batch fermentations, additional nutrients were added at the time of initiating induction. Maintenance of sufficiently high concentrations of the organic substrates (glucose and casamino acids) during the induction phase was required for continued cell growth at 42 degrees C. Such growth was essential for T4 DNA ligase formation and in vivo stability. Hence, fed-batch fermentations produced the highest yield of the foreign protein Commensurate with providing lower total amounts of substrates. In such cases, high cell densities (6 g dry wt/L) with substantial intracellular levels of T4 DNA ligase (4.6% total cellular protein, or 2.7% of the dry biomass) were achieved.     

Inhibition of lipid-linked mannose and mannoprotein synthesis in yeast by diumycin in vitro

Diumycin, a phosphoglycolipid antibiotic, inhibits different mannosyl transfer reactions in yeast. Using membrane preparations, the drug effectively inhibited the formation of dolichyl phosphate mannose (DolP-Man); 50% inhibition was observed at approximately 10 microgram/ml. To a lesser extent also mannosyl transfer from DolP-Man to protein decreased in presence of diumycin. Both mannosyl transfer to protein-serine/threonine acceptor sites as well as into positions within the asparagine-linked polymannose part of the yeast mannoprotein are inhibited to about 60% under conditions where DolP-Man formation is blocked. DolP-Man synthesis as well as mannosyl transfer from DolP-Man to protein are also inhibited by diumycin using solubilized enzymes and exogenous acceptor substrates. Glycosyltransfer reactions from GDP-mannose either to protein-serine/threonine-linked mannose (formation of short manno-oligosaccharides) or to dolichyl-diphosphate-linked chitobiose (formation of lipid-linked trisaccharide) are not inhibited by diumycin under conditions where DolP-Man synthesis is blocked by the antibiotic. The inhibitory action of diumycin on DolP-Man formation does not seem to be competitive with respect to dolichyl phosphate, since it cannot be overcome by higher concentrations of dolichyl phosphate.     

Enzyme-assisted synthesis and structure characterization of glucuronide conjugates of eleven anabolic steroid metabolites

Enzyme-assisted in vitro synthesis of eleven glucuronide-conjugated anabolic androgenic steroid (AAS) metabolites was performed using biphenyl-induced rat liver microsomal enzymes. The substrates within the study were the main compounds and metabolites detected in human urine after dosing of, e.g. metandienone, metenolone, methyltestosterone, nandrolone, and testosterone. Yields of glucuronidation reactions were 13-28% for most compounds, but significantly higher (77-78%) for the substrates with 4-ene-3-one double bond system of the steroid A-ring. Characterization of glucuronide-conjugated AAS structures was based on nuclear magnetic resonance spectroscopy ((1)H NMR) and on liquid chromatographic-mass spectrometric (LC-MS) and tandem mass spectrometric (LC-MS/MS) analyses in positive and negative ion mode electrospray ionization (ESI). Only minor differences were observed in optimal synthesis conditions between various substrates, which offer a potential to apply this in vitro assay as a default method for glucuronidation of new AAS substrates. The method allowed for a rapid production pathway of stereochemically pure AAS glucuronides in milligram amount, such as needed, e.g. in the development of analytical methods in forensic or pharmaceutical sciences, as well as in doping control.     

Thermodynamically based solvent design for enzymatic saccharide acylation with hydroxycinnamic acids in non-conventional media

Enzyme-catalyzed synthesis has been widely studied with lipases (EC 3.1.1.3), but feruloyl esterases (FAEs; EC 3.1.1.73) may provide advantages such as higher substrate affinity and regioselectivity in the synthesis of hydroxycinnamate saccharide esters. These compounds are interesting because of their amphiphilicity and antioxidative potential. Synthetic reactions using mono- or disaccharides as one of the substrates may moreover direct new routes for biomass upgrading in the biorefinery. The paper reviews the available data for enzymatic hydroxycinnamate saccharide ester synthesis in organic solvent systems as well as other enzymatic hydroxycinnamate acylations in ionic liquid systems. The choice of solvent system is highly decisive for enzyme stability, selectivity, and reaction yields in these synthesis reactions. To increase the understanding of the reaction environment and to facilitate solvent screening as a crucial part of the reaction design, the review explores the use of activity coefficient models for describing these systems and - more importantly - the use of group contribution model UNIFAC and quantum chemistry based COSMO-RS for thermodynamic predictions and preliminary solvent screening. Surfactant-free microemulsions of a hydrocarbon, a polar alcohol, and water are interesting solvent systems because they accommodate different substrate and product solubilities and maintain enzyme stability. Ionic liquids may provide advantages as solvents in terms of increased substrate and product solubility, higher reactivity and selectivity, as well as tunable physicochemical properties, but their design should be carefully considered in relation to enzyme stability. The treatise shows that thermodynamic modeling tools for solvent design provide a new toolbox to design enzyme-catalyzed synthetic reactions from biomass sources.     

Lipase-catalyzed syntheses of sugar esters in non-aqueous media

The lipase-catalyzed reaction is useful to obtain sugar esters with chemically defined structures and will contribute to the synthesis of sugar-based compounds by a chemo-enzymatic pathway. The synthesis of sugar esters in nonaqueous media has been attempted for a quarter century. To facilitate the reactions, they have been performed either in an organic solvent with/without a polar adjuvant or in an ionic liquid, or by using a hydrophobic sugar derivative. In this review, the following points are discussed: (1) various synthetic methods of sugar esters; (2) role of the solvents or adjuvants; and (3) improvement in the productivity.     

Comparative Analysis of the Biological Activity and Chromatographic Profiles of the Extracts of <Emphasis Type="Italic">Beauveria bassiana</Emphasis> and <Emphasis Type="Italic">B. pseudobassiana</Emphasis> Cultures Grown on Different Nutrient Substrates

Soil, enodphytic, and insect-pathogenic micromycetes of the genus Beauveria are widespread in nature and are important producers on mycoinsecticides, enzymes, and pharmacologically usable and toxic compounds. The goal of the work was to determine chemodiagnostic approaches to differentiation of Beauveria cryptic species using the strains B. bassiana BBL and B. pseudobassiana BCu22 by comparing their toxicological properties (insecticidal, antimicrobial, phytotoxic, cytotoxic, and esterase-inhibition activity) and metabolite profiles (TLC and HPLC/DAD patterns) of the extracts from the cultures of these fungi growing on different loose substrates, on solid and liquid media. It was shown that when the strains were cultured in liquid media (SDAY and Adámek medium) and on solid substrates (millet and Czapek agar medium), they could be differentiated by the extract yield and chromatographic profiles, as well as by their insecticidal, antifungal, and cytotoxic activity. Thus, antifungal properties were more pronounced in B. pseudobassiana BCu22 grown in liquid Adámek and SDAY media, while cytotoxic properties were more notable in B. bassiana BBL grown in Adámek medium and on millet. Insecticidal properties of the extracts from these cultures varied depending on the substrate composition. Since the extracts of the studied fungi exhibited a broad spectrum of biological activity, the toxic properties of Beauveria spp. should be considered in the course of assessment of safety of these fungi as bioinsecticides.     

Problems in the estimation of mutation rates and in the detection of induced mutations in man

The contribution of nuclear-directed protein synthesis in the repair of lethal and mitochondrial genetic damage after UV-irradiation of exponential and stiationary phase haploid yeast cells was examined. This was carried out using cycloheximide (CH), a specific inhibitor of nuclear protein synthesis. It appears that nuclear protein synthesis required for the increase in survival seen after the liquid holding of cells at both stages, as well as for the “petite” recovery seen after the liquid holding of exponential phase cells. The characteristic negative liquid holding effect observed for the UV induction of “petites” in stationary phase cells (increase of the frequency of “petites” during storage) remained following all the treatments which inhibited nuclear protein synthesis. However, the application of photoreactivating light following dark holding with cycloheximide indicates that some steps of the repair of both nuclear and mitochondrial damage are performed in the absence of a synthesis of proteins.     

Dynamic properties of concentrated suspensions of charged polystyrene spheres

Ordered structure formation of charged polystyrene spheres was studied by measuring the order-disorder phase diagrams as well as the mechanical properties. The phase diagrams indicate that the ordering of polystyrene spheres obeys Lindemann's law of crystal melting, in which the Lindemann's parameter is about 5%. The rigidity of about 10(3) dyn/cm(2) was observed in the ordered suspension of polystyrene spheres as measured by a torsional quartz crystal method. The steady flow properties of suspensions of polystyrene spheres showed a remarkable change from a Bingham body to a Newtonian liquid at the transition point. The limit of elasticity in the ordered phase was about 1 dyn/cm(2). The viscosity in the disordered phase was well explained by the free volume theory of liquids. It is concluded from these facts that the ordered phase of polystyrene spheres is a real "crystal" whereas the disordered phase is a "liquid". Properties of ordered structures in biological systems are also discussed.     

Isolation and properties of a testicular ribonucleic acid polymerase

A procedure is described for isolation in a soluble form of a ribonucleic acid polymerase from rat testes. Evidence is presented that this enzyme catalyzes three distinct reactions: (a) deoxyribonucleic acid-directed synthesis of RNA in the presence of all four major ribonucleoside triphosphates; (b) DNA-primed formation of polyadenylic acid and other ribohomopolymers in the presence of single ribonucleoside triphosphate substrates; (c) synthesis of complementary polyribonucleotides in the presence of various ribohomopolymer primers. The properties of these reactions are discussed with respect to metal ion requirements, affinities for ribonucleoside triphosphates and primer polynucleotides, heat denaturation of DNA primers, and the effects of ionic strength, beta-mercaptoethanol, polyamines, temperature, and inhibitors on the rates and extent of the reactions. The testicular ribonucleic acid polymerase is a very unstable enzyme that can be stabilized by high concentrations of glycerol.     

Three different examples of enzymatic bioconversion in liquid membrane reactors

Three different examples of enzyme emulsions are presented. The enzymes are immobilized in liquid surfactant membranes. The effect of the organic membrane phase is discussed as well as the influence of the membrane composition on the transport of substrates and products through the membrane. An enzyme emulsion system for the production of l-leucine with continuous co-factor regeneration is described. It is not necessary to increase the molecular weight of the co-factor by linking it to a soluble high molecular weight compound (e.g., PEG), since the coenzyme cannot pass the liquid membrane without a suitable carrier. Also, a product (6-APA) can be enriched in the internal phase of the liquid membrane. The separation effect is not based on differences in molecular weight, but on the chemical behavior of the substances to be separated.     

Kinetics and specificity of serine proteases in peptide synthesis catalyzed in organic solvents

Initial rates of peptide-bond synthesis catalyzed by poly(ethylene glycol)-modified chymotrypsin in benzene were determined using high-performance liquid chromatography. Enzymatic synthesis of N-benzoyl-L-tyrosyl-L-phenylalanine amide from N-benzoyl-L-tyrosine ethyl ester and L-phenylalanine amide was found to obey Michaelis-Menten kinetics an to be consistent with a ping-pong mechanism modified by a hydrolytic branch. The catalytic activity of modified chymotrypsin was dependent on both water concentration and type of organic solvent, the highest synthesis rate being obtained in toluene. Since the chymotrypsin specificity in the organic phase was actually altered, the enzyme's apparent kinetic parameters were determined for different substrates and compared to those obtained with other serine proteases in benzene. Both N-benzoyl-L-tyrosine ethyl ester and N-alpha-benzoyl-L-lysine methyl ester were comparable acyl donors in benzene and the (kcat/Km)app value of modified chymotrypsin was only 10-fold smaller than that obtained with poly(ethylene glycol)-modified trypsin in the synthesis of N-alpha-benzoyl-L-lysyl-L-phenylalanine amide. The change in chymotrypsin specificity was also confirmed through the binding of trypsin inhibitors in benzene. The overall results suggest that hydrophobic bonding between the enzyme and its substrate should not be taken into account during catalysis in the organic phase. In general, if hydrophobic interactions are involved in the binding of substrates to the active site in aqueous media, the replacement of water by hydrophobic solvents will induce some change in enzyme specificity. Moreover, secondary residues of enzyme-binding sites may also exert a significant influence on specificity since, as observed in this study, chymotrypsin exhibited high affinity for cationic substrates and cationic inhibitors as well in apolar solvents.     

Chemical synthesis of lipids and the origin of life

Keeping in mind the importance of amphiphilic lipids for the formation of semipermeable membranes, a review summary of the sources of appropriate precursors, and chemical reactions for the abiotic synthesis of lipids is presented here within the framework of the theory of chemical evolution. It covers the presence in different cosmic environments of precursors for the formation of the biochemical molecules necessary for the emergence of life on Earth. It starts (1) with a short introduction. Then the following matters are briefly reviewed: (2) The circumstellar and interstellar molecules, some of which, could generate straight chain fatty acids through C₉. (3) The possible reactions of hydrogenation and hydrolysis of cyanopolyynes which in the presence first of hydrogen and then liquid water could lead to the formation of aliphatic acids. (4) The composition of comets, where the preliminary analysis by mass spectrometry indicate straight chain hydrocarbons through only C₅. (5) The organic compounds in carbonaceous chondrites where aliphatic acids through C₁₂ have been identified, although the branched chain isomers are abundant. (6) The synthesis of some biochemical compounds, such as amino acids present in carbonaceous chondrites, which were probably formed by condensation of presolar precursors, aldehydes and ketones, with HCN in the presence of ammonia and liquid water in the meteorite parent body. The isotopic evidence seems to support this interpretation. (7) The formation of the Earth-Moon system by the catastrophic impact of a Mars-size body with the proto-Earth. (8) The subsequent capture of cometary water, organic and inorganic compounds, which must have led to a very reactive primitive Earth's atmospheric environment. The cometary iron-nickel grains could have catalyzed the formation of fatty acids by Fischer-Tropsch reactions. (9) The laboratory synthesis of straight chain fatty acids from C₅ through C₂₀ by Fischer-Tropsch processes. The amounts are usually in excess of the yields of aliphatic hydrocarbons. The chemical synthesis of glycerophospholipids including phosphatidylcholine. (10) The formation of liposomes, primarily, from phosphatidylcholine and the encapsulation within them of biopolymers. (11) Speculations on protocellular models of increasing complexity based on liposomes enclosing catalytic biomolecules. (12) Finally, some of the important problems remaining to be solved concerning the experimental approach to the study of the origin of life are briefly considered. It is hoped that in the next century, significant advances will be made in our understanding of the origin of life on Earth.