pH Feedback control of enzyme membranes

pH feedback on immobilized enzymes is theoretically examined with respect to substrate and pH levels, strength of acids produced by the reaction, buffering and asymmetry of the system. All the productions of proton by the different reactions are taken into account by using a ‘symbolic species’ H^*. The system of differential diffusion-reaction equations is then integrated using numerical methods. The local ‘effective enzyme activity’ modulated by an acidity factor enables us to predict and quantify evolutions of the systems: NonMichacIian behavior of an immobilized MichaeIis-Mentcn-type enzyme is shown, even when pH back-actions are excluded: the analysis of intramembranc pH profiles shows that the shift of the optimal pH is a complex function of the substrate and pH levels, the intrinsic pH dependence of the enzyme, and the membrane characteristics. This study may easily be transposed to other types of effector such as divalent cations and used in examining self-regulations of multienzyme systems where pH-active reactions are involved.     

Peroxidase and polyphenol oxidase activity in malformed mango inflorescence caused byFusarium moniliforme var.subglutinans

Peroxidase and polyphenol oxidase activities in malformed mango inflorescences of ‘Himsagar’ and ‘Bombay green’ oultivars wore found to be increased considerably following infection byFusarium moniliforme var.subglutinans. Whether such increased activities were due to their synthesis by the pathogen or the host, or both, was not studied although it was found that the pathogen was incapable of producing the enzymesin vitro. The activities of both the enzymes in infected tissues were found to increase considerably during the experimental period. It was found that activities of polyphenol oxidase were inhibited in the presence of sodium diethyldithiocarbamate and phenylthiourea; the former acted as chelating agent of Cu of the enzymes and the latter as a competitive inhibitor. Similarly, peroxidase activity was found to be inhibited by cycloheximide which acted as inhibitor of enzyme protein synthesis. The fact that the ‘Himsagar’ cultivar showed greater enzyme activity than the ‘Bombay green’ cultivar possibly suggests its higher resistance to the pathogen.     

A large scale enzyme screen in the search for new methods of silicon-oxygen bond formation

Biotransformations make use of biological systems to catalyze or promote specific chemical reactions. Transformations that utilize enzymes as “greener” and milder catalysts compared to traditional reaction conditions are of particular interest. Recently, organosilicon compounds have begun to be explored as non-natural enzymatic substrates for biotransformations. The aims of this study were to screen readily available (approximately eighty) enzymes for their ability to catalyze in vitro siloxane bond formation under mild reaction conditions using a model monoalkoxysilane as the substrate and to make a preliminary evaluation of potential factors that might lead to activity or inactivity of a particular enzyme. Several new hydrolase enzymes were observed to catalyze the formation of the condensation product when compared to peptide controls, or buffer solutions at the same pH, as judged from quantitative analyses by gas chromatography. Aspergillus ficuum phytase, Aspergillus niger phytase, chicken egg white lysozyme, porcine gastric mucosa pepsin, and Rhizopus oryzae lipase all catalyzed the condensation of silanols in aqueous media. Factors involved in determining the activity of an enzyme towards silanol condensation appear to include: the presence of imidazole and hydroxyl functions in the active site; solvent; the presence of water; the surface properties of the enzyme; possible covalent inhibition; and steric factors in the substrate.     

Control of the rate of photosynthetic carbon dioxide fixation

A simplified model of the reductive pentose phosphate pathway of photosynthesis is analysed in order to quantify the degree to which each of the constituent reactions controls the rate of CO₂ fixation (given by the control coefficient). The analysis focuses on the four largely irreversible reactions of the cycle together with the first irreversible reaction in the sucrose and starch synthetic pathways. The model assumes that the other reactions are at equilibrium. The photorespiratory and electron transport systems are not included in the model. The analysis demonstrates that: (1) an analytical approach can be used to investigate the distribution of flux control in autocatalytic and moiety-conserved cycles; (2) measurements of enzyme kinetic parameters and certain fluxes and substrate concentrations can be used to solve the equations defining the enzyme control coefficients; (3) the conservation of total stromal phosphate and the intricate regulatory mechanisms of the photosynthetic system result in a relationship between the control coefficients that is complex and may defy any intuitive assessment of ‘rate limitation’; (4) ribulose-1,5-bisphosphate carboxylase / oxygenase may, under certain conditions, be a major controller of the rate of CO₂ fixation and, by regulating the concentration of ribulose 1,5-bisphosphate, may be important in governing the ratio of organic to inorganic phosphate in the stroma; (5) the other enzymes may also serve an important role in determining the distribution of phosphate between organic and inorganic species because they catalyze reactions at the branch points between starch and sucrose synthesis and ribulose 1,5-bisphosphate regeneration; (6) these enzymes that catalyze ‘branch-pint’ reactions may have negative control coefficients because of their ability to reduce the total concentration of cycle intermediates; (7) an approach combining the use of the equations presented in this paper and flux and substrate concentration measurements may be adequate for determining the control coefficients of several enzymes of the reductive pentose phosphate pathway.     

Fermentative glycolysis with purified Escherichia coli enzymes for in vitro ATP production and evaluating an engineered enzyme

Each of the twelve enzymes for glycolytic fermentation, eleven from Escherichia coli and one from Saccharomyces cerevisiae, have been over-expressed in E. coli and purified with His-tags. Simple assays have been developed for each enzyme and they have been assembled for fermentation of glucose to ethanol. Phosphorus-31 NMR revealed that this in vitro reaction accumulates fructose 1,6-bisphosphate while recycling the cofactors NAD⁺ and ATP. This reaction represents a defined ATP-regeneration system that can be tailored to suit in vitro biochemical reactions such as cell-free protein synthesis. The enzyme from S. cerevisiae, pyruvate decarboxylase 1 (Pdc1; EC 4.1.1.1), was identified as one of the major ‘flux controlling’ enzymes for the reaction and was replaced with an evolved version of Pdc1 that has over 20-fold greater activity under glycolysis reaction conditions. This substitution was only beneficial when the ratio of glycolytic enzymes was adjusted to suit greater Pdc1 activity.     

Changes in the forms of invertase during germination of mung bean seeds

High levels of ‘alkaline’ invertase activity occur in dormant mung bean seeds. During germination this activity decreases rapidly and is replaced by high ‘acid’ invertase activity. Cycloheximide prevented the formation of the latter activity and also inhibited germination. It is suggested that de novo synthesis of ‘acid’ invertase occurs during germination. Both enzymes bind to concanavalin A and, hence, are presumed to be glycoproteins. Affinity-purified enzyme samples show similar ratios of ‘acid’ and ‘alkaline’ invertase activities to the crude preparations indicating that specific enzyme inhibitors or activators are probably not involved in controlling the activities in vivo.     

Monitoring of artificial enzyme membrane systems by electric currents: I. Analytical treatment with direct current and buffered conductivity

Continuous electric fields (E) modify the transport flows and the intramembrane concentration profiles of protons or of ionic substrates or cofactors (inhibitors). These ‘mediators’ induce variations in enzyme activity, quantifiable by a generalized Damköhler group II Ψ distinguishing electrotransport reactions from diffusion reactions. For three typical reaction schemas, using only one mediator, the steady-state equations have been established. Depending on boundary conditions, the direction of electric current (for asymmetrical systems) and the value of Ψ. activations, inhibitions or activations followed by inactivations have been found. With buffered conductivity (supporting electrolyte), the limiting concentration profiles (E → ∞) are uniformly equal to the boundary values; i.e., diffusion constraints are suppressed and the regime is controlled by the reaction. The calculations give the relative activity variations for partially suppressed transport controls.     

Cardiolipin synthases of Escherichia coli have phospholipid class specific phospholipase D activity dependent on endogenous and foreign phospholipids

E. coli has three Cls-isoenzymes for cardiolipin (CL) synthesis but the differences between these three enzymes remain unresolved. All three Cls enzymes contain the phospholipase D (PLD) characteristic HKD motive and synthesize CL using PLD activity. Here, using LC-MS we show the effect of overexpressing or deletion of the three individual Cls enzymes on the lipidome, which included changes in lipid class distribution and CL species profiles. We demonstrate, for the first time, that overexpression of only ClsB resulted in the appreciable synthesis of a variety of phosphatidylalcohols, thereby establishing a ‘classic’ PLD activity for this enzyme: phospholipid headgroup exchange. Endogenous E. coli lipids and primary alcohols were substrates for this trans-phosphatidylation reaction. Furthermore, we show that endogenous levels of ClsA mediated a similar trans-phosphatidylation reaction to form phosphatidylalcohols, however this reaction was dependent on the presence of the foreign phospholipid class phosphatidylcholine (PC). This allows us to clarify the different specificities of the cardiolipin synthases.     

Interaction mechanisms of imipramine and desipramine with enkephalin-degrading aminopeptidases in vitro

In the last few years, considerable evidence has appeared concerning the importance of the opioid systems in the action mechanism of some antidepressant drugs. This action mechanism could be mediated through the inhibition of the enzymes reponsible for enkephalin degradation. In this sense, imipramine treatment in vivo increases the enkephalin levels, and this effect is enhanced by inhibitors of enkephalin-degrading enzymes. The present work shows the effects in vitro of imipramine and its active metabolite desipramine on the activities of two membrane-bound enkephalin-degrading aminopeptidases present in rat brain. Imipramine and desipramine in vitro do not affect the aminopeptidase M activity, but they reversibly inhibits the aminoeptidase MII. The enzyme kinetic analysis shows that this enzyme molecule has two different binding sites for each drug, which exert a mixed type enzyme inhibition.     

Kinetically guided,ratiometric tuning of fatty acid biosynthesis

Cellular metabolism is a nonlinear reaction network in which dynamic shifts in enzyme concentration help regulate the flux of carbon to different products. Despite the apparent simplicity of these biochemical adjustments, their influence on metabolite biosynthesis tends to be context-dependent, difficult to predict, and challenging to exploit in metabolic engineering. This study combines a detailed kinetic model with a systematic set of in vitro and in vivo analyses to explore the use of enzyme concentration as a control parameter in fatty acid synthesis, an essential metabolic process with important applications in oleochemical production. Compositional analyses of a modeled and experimentally reconstituted fatty acid synthase (FAS) from Escherichia coli indicate that the concentration ratio of two native enzymes—a promiscuous thioesterase and a ketoacyl synthase—can tune the average length of fatty acids, an important design objective of engineered pathways. The influence of this ratio is sensitive to the concentrations of other FAS components, which can narrow or expand the range of accessible chain lengths. Inside the cell, simple changes in enzyme concentration can enhance product-specific titers by as much as 125-fold and elicit shifts in overall product profiles that rival those of thioesterase mutants. This work develops a kinetically guided approach for using ratiometric adjustments in enzyme concentration to control the product profiles of FAS systems and, broadly, provides a detailed framework for understanding how coordinated shifts in enzyme concentration can afford tight control over the outputs of nonlinear metabolic pathways.     

Protein expression patterns in two Spiraea species in response to cold treatment

We analyzed the different cold-resistance species Spiraea trichocarpa Nakai and Spiraea bumalda ‘Goldmound’ for low-temperature protein expression, protein types identification, and investigated the cold resistance mechanisms under different levels of low temperature by two-dimensional gel electrophoresis (2-DE) and mass spectrometry. An average of 668 and 559 protein spots were detected by 2-DE of S. bumalda ‘Goldmound’ and S. trichocarpa Nakai, respectively, under different low-temperature treatments. Matrix-assisted laser desorption/ionization time-of-flight mass spectroscopy identified 48 proteins, with varying expression, related to metabolism, amino acid synthesis, transportation, stress responses and oxidation–reduction reactions. The results showed that the photosynthesis of S. bumalda ‘Goldmound’ had been affected, enzymes (RuBisCO large and small subunits) involved in the Calvin cycle were up- and down-regulated, and ATP synthase in photophosphorylation was down-regulated. Cytosolic malate dehydrogenase expression weakened in the TCA cycle, while amino acid synthesis strengthened. The activity of four antioxidant enzymes (superoxide dismutase [Cu–Zn], L-ascorbate peroxidase, glutathione peroxidase and peroxidase) was reduced under varying low temperatures. Enzymes (ribulose-bisphosphate carboxylase and RuBisCO small chain precursor) involved in the photosynthesis of S. trichocarpa Nakai showed obvious up- and down-regulation under low temperatures. Cold treatment influenced the photosynthesis of S. trichocarpa Nakai and S. bumalda ‘Goldmound’, but the results showed significant differences between the two species, which were supposed to the fact that low temperature modified the metabolic mechanisms and led to the weaker cold resistance in S. bumalda ‘Goldmound’ than in S. trichocarpa Nakai.     

Tuning chitosan’s chemical structure for enhanced biological functions

Chitosan, an amino polysaccharide mostly derived from crustaceans, has been recently highlighted for its biological activities that depend on its molecular weight (MW), degree of deacetylation (DD), and acetylation pattern (AP). More importantly, for some advanced biomaterials, the homogeneity of the chitosan structure is an important factor in determining its biological activity. Here we review emerging enzymes and cell factories, respectively, for in vitro and in vivo preparation of chitosan oligosaccharides (COSs), focusing on advances in the analysis of the AP and structural modification of chitosan to tune its functions. By ‘mapping’ current knowledge on chitosan’s in vitro and in vivo activity with its MW and AP, this work could pave the way for future studies in the field.     

Mutations to the histone H3 αN region selectively alter the outcome of ATP-dependent nucleosome-remodelling reactions

Mutational analysis of the histone H3 N-terminal region has shown it to play an important role both in chromatin function in vivo and nucleosome dynamics in vitro. Here we use a library of mutations in the H3 N-terminal region to investigate the contribution of this region to the action of the ATP-dependent remodelling enzymes Chd1, RSC and SWI/SNF. All of the enzymes were affected differently by the mutations with Chd1 being affected the least and RSC being most sensitive. In addition to affecting the rate of remodelling by RSC, some mutations prevented RSC from moving nucleosomes to locations in which DNA was unravelled. These observations illustrate that the mechanisms by which different ATP-dependent remodelling enzymes act are sensitive to different features of nucleosome structure. They also show how alterations to histones can affect the products generated as a result of ATP-dependent remodelling reactions.     

Evolution in bioids: Hypercompetitivity as a source of bistability and a possible role of metal complexes as prenucleoprotic mediators of molecular asymmetry

Spontaneous production of optically active compounds can occur through kinetic instability of an asymmetric steady state in open systems, in which two enantiomeric autocatalysts compete for a common prochiral substrate in a stereoselective reaction of ordern>2. For the case ofn=3, a proof of instability of a symmetric reacting state in the general case, and functions of reaction parameters (‘Chemical Reynolds Numbers’) governing the existence and stability of 7 different steady states are derived. The ‘extinct state’ (without autocatalyst) is stable; a finite amount of products is required to shift it into one of the reacting steady states. A mutation from one state into another in such systems (‘bioids’) involves an amplification of different ‘kinds of information’, as ‘stochastic’ (noise into dissipative structures), ‘molecular’ (autocatalysts), and ‘stoichiometric’ information. Stereospecific third order kinetics are believed to be realizable on octahedral metal complexes with two-dentated ligands and to have played a role in the prebiological evolution of optically active compounds.     

Biochemical and random mutagenesis analysis of the region carrying the catalytic E152 amino acid of HIV-1 integrase

HIV-1 integrase (IN) catalyzes the integration of the proviral DNA into the cellular genome. The catalytic triad D₆₄, D₁₁₆ and E₁₅₂ of HIV-1 IN is involved in the reaction mechanism and the DNA binding. Since the integration and substrate binding processes are not yet exactly known, we studied the role of amino acids localized in the catalytic site. We focused our interest on the V₁₅₁E₁₅₂S₁₅₃ region. We generated random mutations inside this domain and selected mutated active INs by using the IN-induced yeast lethality assay. In vitro analysis of the selected enzymes showed that the IN nuclease activities (specific 3′-processing and non-sequence-specific endonuclease), the integration and disintegration reactions and the binding of the various DNA substrates were affected differently. Our results support the hypothesis that the three reactions may involve different DNA binding sites, enzyme conformations or mechanisms. We also show that the V₁₅₁E₁₅₂S₁₅₃ region involvement in the integration reaction is more important than for the 3′-processing activity and can be involved in the recognition of DNA. The IN mutants may lead to the development of new tools for studying the integration reaction, and could serve as the basis for the discovery of integration-specific inhibitors.     

High specific activity chemiluminescent and fluorescent markers: Their potential application to high sensitivity and ‘multi-analyte’ immunoassays

The sensitivities of immunoassays relying on conventional radioisotopic labels (i.e. radioimmunoassay (RIA) and immunoradiometric assay (IRMA)) permit the measurement of analyte concentrations above ca 10⁷ molecules/ml. This limitation primarily derives, in the case of ‘competitive’ or ‘limited reagent’ assays, from the manipulation errors arising in the system combined with the physicochemical characteristics of the particular antibody used; however, in the case of ‘non-competitive’ systems, the specific activity of the label may play a more important constraining role. It is theoretically demonstrable that the development of assay techniques yielding detection limits significantly lower than 10⁷ molecules/ml depends on:

• 1 the adoption of ‘non-competitive’ assays designs;
• 2 the use of labels of higher specific activity than radioisotopes;
• 3 highly efficient discrimination between the products of the immunological reactions involved.

Chemiluminescent and fluorescent substances are capable of yielding higher specific activities than commonly used radioisotopes when used as direct reagent labels in this context, and both thus provide a basis for the development of ‘ultra-sensitive’, non-competitive, immunoassay methodologies. Enzymes catalysing chemiluminescent reactions or yielding fluorescent reaction products can likewise be used as labels yielding high effective specific activities and hence enhanced assay sensitivities. A particular advantage of fluorescent labels (albeit one not necessarily confined to them) lies in the possibility they offer of revealing immunological reactions localized in ‘microspots’ distributed on an inert solid support. This opens the way to the development of an entirely new generatio of ‘ambient analyte’ microspot immunoassays perrnitting the simultaneous measurement of tens or even hundreds of different analytes in the same small sample, using (for example) laser scanning techniques. Early experience suggests that microspot assays with sensitivities surpassing that of isotopically based methodologies can readily be developed.     

The induction of an injury reaction in cultured haemocytes from saturniid pupae

The plasmatocytes of diapausing saturniid pupae are round or spindle-shaped cells floating free in the haemolymph. Upon injury to the pupa, these haemocytes become amoeboid and adhesive. A technique is described for the isolation and short-term culture of pupal haemocytes in their inactive state and for their conversion in vitro into the active, ‘injured’ form. The activation of ‘uninjured’ haemocytes was stimulated by fragments of epidermal tissue or by plasma from previously activated blood samples. A fraction capable of stimulating the activation of haemocytes was partially purified from both plasma and epidermal tissue and has been called haemokinin. Haemokinin from either source has a molecular weight in the range of 50,000. The intensity of the haemocyte injury reaction in vitro changes systematically during diapause; the nature and significance of the changes are discussed.