Ion channels as enzymes: analogy or homology?

Ion channels render nerve and muscle excitable. A typical channel protein can mediate the passive transfer of millions of ions per second across the membrane. Thus, channels catalyse the transmembrane flux of ions, fulfilling criteria traditionally associated with enzymes. Is this a semantic coincidence, or do channels and enzymes in fact rely upon similar structural principles? A general answer remains elusive given the paucity of crystallographic data on channels. Nevertheless, emerging evidence points to fundamental similarities between the pores of channels and the active sites of enzymes of resolved structure. Shared features include narrow clefts lined by protein loops, and specific binding of transition intermediates during catalysis. The often cited analogies between channels and enzymes might therefore reflect basic design homologies.

Distribution and pathophysiologic role of molybdenum-containing enzymes

The importance of molybdenum-containing enzymes in the pathophysiology of a number of clinical disorders necessitates a comprehensive understanding of their histological localization and expression. The objectives of this review are to cover such enzymes so far reported and their enzyme- and immunohistochemical localization in various tissues and species, and to discuss their possible pathophysiological effects. The molybdenum cofactor is essential for the activity of the three molybdenum-containing enzymes, sulfite oxidase, xanthine oxidase and aldehyde oxidase. Sulfite oxidase serves as the terminal enzyme in the pathway of the oxidative degradation of sulfur amino acids, and is also involved in preventing the toxic effects of sulfur dioxide. Biochemical study has revealed a high activity of sulfite oxidase mainly in the liver, heart and kidney with lesser activity observed in other tissues. Subcellular observations have shown that this enzyme is present in the mitochondrial intermembraneous spaces. Xanthine oxidase is the final enzyme in the conversion of hypoxanthine to xanthine, and subsequently, to uric acid. Unlike sulfite and aldehyde oxidases, xanthine oxidase can be converted to xanthine dehydrogenase, and vice versa. Xanthine oxidase has been widely investigated for its role in post-ischemic reperfusion tissue injury. Enzyme- and immunohistochemical studies of its localization in various animal species and tissues have shown its ubiquitous distribution in the liver, small and large intestine, lung and kidney, and other tissues. Aldehyde oxidase shares a similar substrate specificity with xanthine oxidase. Although the tissue localization of this enzyme has not been studied as thoroughly as that of xanthine oxidase, aldehyde oxidase is reportedly found in the digestive gland of terrestrial gastropods, the antennae of certain moths as well as the mammalian liver. Recently, the ubiquitous distribution of aldehyde oxidase has been demonstrated in rat tissues. The aldehyde oxidase activity of herbivores exceeds that of carnivores, suggesting a possible role of this enzyme as a protection against the effects of toxic plants. The relationship between the tissue localization of these enzymes and their pathophysiological roles is reviewed.

A simple mechanism decreasing free metabolite pool size in static spatial channelling

We propose a simple mechanism which enables decrease of the free pool of channelled metabolite in static spatial channelling, when the concentration of the enzyme consuming the channelled metabolite is greater than the concentration of the enzyme producing this metabolite. Spatial channelling occurs between two enzymes when the common metabolite is released to a small space between these enzymes and does not from a ternary covalent complex with them, as is the case in covalent (dynamic or static) channelling. The mechanism proposed is qualitatively independent of rate constants, metabolite concentrations as well as other kinetic properties and is quantitatively significant for all physiologically relevant conditions. Calculations show that the free metabolite pool must decrease, when the concentration of the enzyme consuming the channelled metabolite is greater than the enzyme producing it. This mechanism is much more effective than increase in the concentration (or rate constant) of the enzyme consuming the metabolite in the absence of spatial channelling.

The search for the uremic toxin: the case for metabolic acidosis

Much effort has been expended on determining which compound, hormone or metabolic condition causes the uremic syndrome. Byproducts of protein metabolism that can cause uremic symptoms, including loss of lean body mass, have been a focus of research but specific toxins have been difficult to identify. Evidence is provided that implicates metabolic acidosis as the prime signal initiating muscle wasting in uremia since it activates branched-chain ketoacid dehydrogenase and the ubiquitin proteasome pathway. These responses degrade the essential branched chain amino acids and protein in muscle, leading to loss of muscle mass. Correction of the metabolic acidosis with sodium bicarbonate supplements has significant therapeutic implications for uremic patients with even mild degrees of metabolic acidosis.

Predicting enzyme function from sequence: a systematic appraisal

Gapped and ungapped sequence alignment were tested as possible methods to classify proteins into the functional classes defined by the International Enzyme Commission (EC). We exhaustively tested all 15,208 proteins labeled with any EC class in a recent release of the SwissProt database, evaluating all 1,327 relevant EC classes. We effectively tested all possible similarity thresholds that could be used for this assignment through the use of the ROC statistic. Approximately 60% of Enzyme Commission classes containing two or more proteins could not be perfectly discriminated by sequence similarity at any threshold. An analysis of the errors indicates that false positive matches dominate, and that various error mechanisms can be identified, including the multidomain nature of many proteins and polyproteins, convergent evolution, variation in enzyme specificity, and other factors. Many of the putatively false positives are in fact biologically relevant. This work strongly suggests that functional assignment of enzymes should attempt to delimit functionally significant subregions, or domains, before matching to EC classes.

Force effects on biochemical kinetics

Force is an important component in the proper functioning of tissues and cells. In processes ranging from the contraction of muscles to the alignment of chromosomes at the metaphase plate, forces must be adjusted to the proper levels by cells. At the molecular level, it is clear that the motor molecules and other enzymes must respond to changes in mechanical forces by altering enzymatic function. Recent technical advances, primarily the atomic force microscope and laser tweezers, enable us to measure forces at the single molecule level to test how force is transduced into a change in enzyme activity. A priori, four basic mechanisms of coupling enzyme rate and force are considered. The mechanisms extend from the cellular to the molecular level. For example, polymer assembly rates and cytoskeletal matrix concentration are potentially modified by force in ways that feed back on critical enzyme rates. In studies of the known mechanosensitive enzymes, myosin and other motors, the bacterial flagellar rotor, and the F0F1 ATPase, the molecular mechanisms used to transduce force changes into activity changes have not been clearly defined, although it is reasonable to speculate about the nature of these mechanisms from the atomic structures and nanometer measurements of movement.

Peptidergic modulation of synaptic transmission in the parabrachial nucleus in vitro: importance of degradative enzymes in regulating synaptic efficacy

This study examined the effects of substance P (SP) and calcitonin gene-related peptide (CGRP) on synaptic transmission in a pontine slice containing the parabrachial nucleus (PBN). Stimulation of the ventral, external lateral portion of the PBN elicited glutamate-mediated EPSCs in cells recorded using the nystatin perforated-patch recording technique in the external lateral, external medial, and central lateral subnuclei of the PBN. Bath application of SP or CGRP dose-dependently and reversibly attenuated the evoked EPSC. The attenuation of the EPSC induced by both of these peptides was not accompanied by changes in input resistance of PBN cells over a wide voltage range, nor did these peptides alter the inward current induced by a brief bath application of AMPA. The combined application of subthreshold concentrations of these peptides revealed a synergistic interaction in reducing the evoked EPSC. The substance P neurokinin-1 receptor antagonist CGP49823 completely and reversibly blocked both the SP- and the CGRP-induced attenuation of the EPSC. However, the rat CGRP receptor antagonist human-CGRP8-37 did not block the actions of CGRP or SP on the EPSC. Using a metabolically stable analog of SP, SP (5-11), or an endopeptidase inhibitor, phosphoramidon, we were able to demonstrate that CGRP enhances the SP effect by inhibiting an SP endopeptidase. Application of phosphoramidon also revealed an endogenous SP "tone" apparently made effective by blockade of the endopeptidase. These results suggest that SP (and CGRP indirectly through an inhibition of the SP endopeptidase) acts on presynaptic NK-1 receptors to cause an inhibition of excitatory transmission in the PBN. These results indicate an important role of endopeptidases in regulating synaptic modulation by peptides.

Threading your way to protein function

It is still very difficult to determine the function of a protein from its sequence. One potential solution to the problem combines the concept of enzyme superfamilies with modern methods of protein structure prediction. Active-site templates can be used as search tools to identify new members of the superfamilies.

Relationship between phase variation in colony morphology, intrastrain variation in cell wall physiology, and nasopharyngeal colonization by Streptococcus pneumoniae

Streptococcus pneumoniae undergoes phase variation in colony morphology, which has been implicated as a factor in the pathogenesis of pneumococcal disease. Phenotypic differences between opaque and transparent colony forms correlate with differences in rates of autolysis. This study examined whether differences in autolysis are caused by differences in expression of the major amidase, LytA, or the structure of its peptidoglycan substrate. No significant difference was detected by high-pressure liquid chromatography analysis of stem peptides released after treatment of purified peptidoglycan with amidase. Differences in the rate of digestion of purified cell walls, furthermore, did not correlate with susceptibility to autolysis. Lower levels of autolysis in opaque variants, however, was associated with decreased levels of immunodetectable LytA on colony immunoblots and Western blots (immunoblots). Diminished cell-surface-associated LytA in opaque variants was also demonstrated by whole-cell inhibition enzyme-linked immunosorbent assay. Since transparent variants have been shown both to colonize the nasopharynx more efficiently in an animal model and to express more surface-exposed LytA, it was determined whether LytA contributes to colonization in a neonatal rat model of pneumococcal carriage. Defined mutants in the lytA gene were used to show that there was no significant contribution by LytA to nasopharyngeal colonization in this model. Although the expression of LytA was shown to undergo phase variation in association with colony morphology, lytA mutants are still capable of phenotypic variation in colony morphology, which suggests that other factors are responsible for intrastrain differences which affect colonization.

Application of enzymes in food processing

Enzymes offer potential for many exciting applications for the improvement of foods. There is still, however, a long way to go in realizing this potential. Economic factors such as achievement of optimum yields and efficient recovery of desired protein are the main deterrents in the use of enzymes. Changing values in society with respect to recombinant DNA and protein engineering technologies and the growing need to explore all alternative food sources may in time make enzyme applications more attractive to the food industry. Research is continuing on the commercially viable enzymes in use today to improve various properties such as thermostabilities, specificities, and catalytic efficiencies. New and unique enzymes continue to be developed for use in enzymatic reactions to produce food ingredients by hydrolysis, synthesis, or biocatalysis. An aggressive approach is needed to open new opportunities for enzyme applications that can benefit the food industry.

The thiol enzyme from rat spleen that produces bradykinin potentiating peptide from rat plasma

We have focused our studies on a thiol-dependent enzyme of 37 kilodaltons (kDa) that produces a bradykinin (BK) potentiating peptide. The molecular mass of the peptide was estimated to be around 750 Da and its amino acid composition was Pro4 Gly2 Leu1 Ser1 with a proline and a serine at the N- and C-terminals, respectively. Biological activity was assayed by means of uterus contraction. The enzyme differs from Cathepsin L or B by virtue of its immunological reactivity and enzyme kinetics. The inhibitors used were leupeptin, antipain, E-64 and chymostatin in order of effectiveness. The low molecular SH reagents also diminished the enzyme activity. Among the metal ions tested, Cu2+ and Zn2+ inhibited the reaction.

Antidepressants and drug-metabolizing enzymes--expert group report

Antidepressant drugs are extensively metabolized. Consequently, the biotransformation pattern of antidepressants has an important influence on their clinical properties, i.e., pharmacokinetics, toxicity, drug-drug interactions, side-effect profile and last but not least therapeutic efficacy. It was against this background that a multidisciplinary group of experts discussed the clinical relevance of the rapidly increasing body of knowledge of antidepressant-metabolizing enzymes. The variability of the response of a given individual to an antidepressant is determined genetically and by the environment. Genetic polymorphism of drug-metabolizing enzymes and inhibition by other substrates may affect the enzymatic biotransformation of antidepressants. In vitro assay techniques allow an estimation of the potential variability in clinical response to antidepressants and a reasonable prediction of the drug-drug interaction patterns. The results of in vitro tests should therefore be considered early in the development of an antidepressant as a background for designing clinical studies (treatment schedules and dosing). Physicians should have an understanding of the relevance of genetic polymorphism for clinical practice. Education is needed in order to fill the existing gaps in knowledge about antidepressant-enzyme interactions and their application in daily treatment practice. The information on potential drug interactions determined by genetic polymorphism and based on studies with enzymes should be increasingly contained in drug compendia.

Activation-dependent and biphasic electromagnetic field effects: model based on cooperative enzyme kinetics in cellular signaling

Experiments on filed exposure effects of extremely-low-frequency electric and magnetic fields (EMFs) on biological systems have shown that, in many cases, the biological-functional status is of fundamental importance for an effective interaction. For example, studies of calcium uptake regulation in cells of the immune system, particularly in T lymphocytes, have revealed that, depending on the degree of cellular activation, either stimulatory, inhibitory, or no field exposure effects are observed for identical field parameters. A brief summary of the experimental findings is given, and a theoretical approach is presented that accounts in a qualitative manner for EMF exposure effects 1) that depend on the degree of cellular activation and 2) that exhibit a biphasic response behavior (stimulation/ inhibition). In the model, biochemical stimulation of the cell results in activation of specific signaling pathways that regulate calcium dynamics in the cell (calcium release from intracellular calcium stores and capacitative calcium entry). We assume that, controlled by these pathways, a specific EMF-sensitive enzyme system becomes activated. The activated enzyme, in turn, exhibits a feedback control on the signal processes, thus leading to a modulation of calcium entry. This modulation may affect other cellular processes that are calcium dependent (e.g., DNA synthesis). Magnetic field exposure is assumed to alter the kinetics of a specific step within the enzyme-reaction cycle in accord with the radical-pair mechanism, although the formulism is not restricted to this specific example. Results show that inclusion of cooperative steps within the enzyme-reaction cycle provides a theoretical basis that enables a simple description of a biphasic response behavior to EMF exposure.

[The structural and functional characteristics of the dolichol cycle enzymes]

The literature and the authors' our data on the biosynthesis of a dolichol derivative Dol-PP-GlcNAc2Man9Glc3, involved in protein N-glycosylation in the endoplasmic reticulum (ER) of the eukaryotic cells, have been summarized and analysed. The structural and functional characteristics of dolichol-coupled enzymes, catalyzing biosynthesis of Dol-PP-GlcNAc2Man9Glc3, are considered. It is shown that the dolichol cycle enzymes, in conformity with their structural peculiarities and ER membrane topology, can be divided into three groups having the common evolutionary origin. Possible mechanisms of the dolichol derivative translocation through membrane is discussed. A conclusion is made about formation of multicomponent complexes by dolichol-coupled enzymes. These complexes secure functional co-ordination of the enzymes.

Perspectives for biophysicochemical modifications of enzymes

This article reviews the strategies and successes of modifying enzymes by means of biophysicochemical transformations. By judicious choice of methods, it has been possible to modify enzymes through physical interactions, chemical reactions and/or mutagenesis to alter a very wide range of properties ranging from stability and solubility on the one hand to catalytic activity and selectivity on the other.

Control of threonine pathway in E. coli. Application to biotechnologies

Threonine is an essential amino acid for mammals and birds and an adequate supply is necessary for growth and maintenance. Its production has become the aim of metabolic bioengineering and genetic manipulations. We propose in this paper a rational approach for increasing threonine production in an E. coli strain based on metabolic control theory. We have derived a way to measure the control coefficients of threonine pathway in vivo. The method consists in modelling the results of presteady-state experiments. The in vivo concentrations and activities of the enzymes can then be measured and introduced into the model, so that the in vivo steady-state of the pathway can be evaluated. With such a model it is possible to calculate the theoretical values of the control coefficients of the threonine synthesis flux in vivo.

Analysis of thermal injury process based on enzyme deactivation mechanisms

Based upon the analysis of enzyme-catalyzed reactions occurring in living tissue, a model of thermal injury process is presented in which the fraction of denatured enzyme protein was taken as the indicator of thermal damage degrees. The results from this model describe the dependence of thermal damage on exposure time and temperature elevation.

Interactive modelling and simulation of biochemical networks

The analysis of biochemical processes can be supported using methods of modelling and simulation. New methods of computer science are discussed in this field of research. This paper presents a new method which allows the modelling and analysis of complex metabolic networks. Moreover, our simulation shell is based on this formalization and represents the first tool for the interactive simulation of metabolic processes.

Egg chorion tanning in Aedes aegypti mosquito

The biochemical pathway of egg chorion tanning in the mosquito, Aedes aegypti, is described and compared with chorion protein crosslinking in Drosophila and silkmoths and the biochemical pathways of cuticular tanning in insects. Phenol oxidase, dopa decarboxylase and tyrosine are critical components involved in egg chorion tanning in A. aegypti. Tanning of the mosquito egg chorion is initiated following activation of phenol oxidase, which then catalyzes the hydroxylation of tyrosine to dopa and further oxidizes dopa and dopamine to their respective o-quinones. Because intramolecular cyclization is much slower in dopaminequinone than dopaquinone, the chance to react with external nucleophiles to participate in protein crosslinking reactions also is much greater in dopaminequinone than dopaquinone. This might partly explain the necessity for the involvement of dopa decarboxylase in mosquito chorion tanning. Intramolecular cyclization of dopaquinone and dopaminequinone to form dopachrome and dopaminechrome, respectively, the structural rearrangement of these aminochromes to produce 5,6-dihydroxyindole, and the subsequent oxidation of 5,6-dihydroxyindole by phenol oxidase also lead to melanin formation during egg chorion tanning.

On the synergistic effects of enzymes in food with enzymes in the human body. A literature survey and analytical report

Recently, a theory has been postulated that suggests that vital enzymes in ingested food interact synergistically with enzymes within the human body and more specifically with enzymes in the digestive tract. Alterations in food enzymes induced by bulk processing including heating and irradiation and also the addition of chemical additives have been proposed to create a decrease in metabolic availability of nutrients, with the long-term consequence being disease. This review of the medical literature provides evidence that enzymes in food do in fact survive during digestion and can indeed, add significantly to the nutritive value of ingested foodstuffs. Examples of enzyme synergy in human nutrition are provided in whole grains, milk and dairy products, beans and seeds, and meat products. A bibliography on this interesting finding is included as well as concluding remarks on enzyme synergy and its putative interaction with cell metabolism. Finally, the interaction of enzyme synergy with disease is discussed.

Familial adrenal insufficiency, achalasia, alacrima, peripheral neuropathy, microcephaly, normal plasma very long chain fatty acids, and normal muscle mitochondrial respiratory chain enzymes

Adrenal insufficiency has been associated with adrenoleukodystrophy and adrenomyeloneuropathy. In these diseases, plasma very long chain fatty acids are elevated. Peripheral neuropathy is frequently seen in adults with adrenomyeloneuropathy. We encountered two first cousins with adrenal insufficiency, who also developed peripheral neuropathy, achalasia, alacrima, and microcephaly. However, plasma very long chain fatty acids, pipecolic acid, phytanic acid, and cranial computed tomographic scan were normal. Muscle mitochondrial respiratory chain enzymes were also normal. This syndrome of adrenal insufficiency, achalasia, alacrima, microcephaly, and peripheral neuropathy is different from either adrenomyeloneuropathy or adrenoleukodystrophy.

Energy metabolism of developing brain

Recent publications concerning developmental changes in energy metabolism of brain have concentrated on three areas: 1) substrate priority for energy production; 2) balance between glycolytic and respiratory energy production; 3) variation in energy economy by cell type and stage of cellular differentiation; and 4) regional variation in energy reserves and energy demand. These studies have demonstrated a number of significant differences in the energy metabolism of developing brain. Some of these differences appear to derive from the low energy demands of developing brain, some appear to provide neuroprotective advantages (eg, adaptability in carbon sources, high glycogen stores), and some are of uncertain significance (eg, glycogen accumulation in radial glia).

The heat-shock response and the molecular basis of genetic dominance

Wild-type alleles are usually dominant over deleterious mutant alleles. For a particular pair of such alleles possible populations include a wild-type homozygote population, a heterozygote population, and a mutant homozygote population. Fisher's theory that dominance would evolve by selection acting on the heterozygote subpopulation has lost ground in favour of the "dose-response" theory under which dominance is an incidental consequence of selection acting on the wild-type homozygote population. This postulates a "margin of safety" in the quantity of wild-type gene product so that heterozygotes with only one copy of a wild-type allele still have sufficient product for normal function. The selective force postulated to lead to the evolution of this margin of safety is some unspecified "extreme environment disturbance". The author has proposed elsewhere that the heat-shock response evolved very early as part of an intracellular system for self/not-self discrimination. This paper proposes that the rapid decrease in quantity of most normal proteins occurring in the heat-shock response would have provided a sufficient selective force for the margin of safety to have evolved.

Drug-metabolizing enzymes in ligand-modulated transcription

Genes encoding many of the so-called drug-metabolizing enzymes (DMEs) are present in both prokaryotes and eukaryotes, suggesting that these genes arose on this planet more than 3.5 billion years ago--long before animal-plant divergence (estimated to be about 1.2 billion years ago) and long before the use and commercial development of drugs. What, therefore, are the real functions of DMEs? Several years ago I proposed that DMEs are upstream in the regulatory cascade of numerous signal transduction pathways, i.e. necessary for maintaining physiologically "safe", or "acceptable", steady-state levels of all small non-protein endogenous ligands (M(r) = 250 +/- 200) in each cell. Innumerable foreign chemicals and drugs mimic these small endogenous ligands, thus binding to a particular receptor and acting either as an agonist or antagonist in activating or inhibiting genes effecting growth, differentiation, apoptosis, homeostasis and neuroendocrine functions. Discussed in this review are additional examples consistent with this theory and not described in previous reviews, including: (i) insect-plant symbiosis; (ii) "cross-talk" amongst genes in the aromatic hydrocarbon-responsive [Ah] battery; (iii) signal transduction pathways involving the arachidonic acid cascade; and (iv) the explanation in carcinogen-screening studies as to why a maximum, or half maximum, tolerated dose (MTD, MTD50) of many test compounds might cause cell division and tumorigenesis in experimental animals.

Pharmacogenetic phenotyping and genotyping. Present status and future potential

Enzymes that metabolise foreign compounds exhibit a large degree of interindividual variability in their levels of expression. In a number of instances this variability can be accounted for by null or variant alleles resulting from mutations in genes encoding these enzymes. Human variability in drug metabolism can be determined by biochemical and pharmacological assays. In cases where a genetic change has been characterised, polymerase chain reaction techniques have been developed to diagnose metabolism deficiencies. Genetic differences in certain foreign compound metabolising enzymes such as glutathione S-transferase M1, N-acetyltransferase 2 and CYP2D6 have been shown to be associated with risk for developing environmentally and occupationally based diseases such as cancer. Drug therapy can also be compromised by the existence of genetic deficiencies in a number of enzymes, including CYP2D6. It is anticipated that determination of an individual's drug metabolism capabilities by use of phenotyping and genotyping tests will allow for more rational and safe drug administration protocols.

Lipoprotein metabolism

The pathways of cellular synthesis, assembly, and secretion of lipoproteins followed by their subsequent intravascular metabolism and cellular uptake provide an efficient system for the transport of exogenous and endogenous lipids. The present report reviews the pathways of normal lipoprotein metabolism and the roles played by specific apoproteins, transfer proteins, enzymes, and cellular receptors in facilitating the transport of lipids in plasma, as well as in the regulation of cellular cholesterol homeostasis.

Oxygen, antioxidants and brain dysfunction

Brain is a logical target of free radical damage, considering the large lipid content of myelin sheaths and the high rate of brain oxidative metabolism. Thus, the hypothesis that free radicals may be involved in the pathogenesis of certain CNS diseases has gained increasing popularity in recent years. In CNS ischemia-reperfusion injury, the role of free radicals appears to be well established, however, involvement of other factors, such as excitatory amino acids and prostaglandins, may also contribute to the production of neuronal necrosis following ischemia. Liberation of free iron appears to play a crucial role in the generation of reactive oxygen species in posttraumatic epilepsy. Although there is no direct evidence to indicate free radical involvement in the pathogenesis of Alzheimer's disease, brain trauma with release of iron, amyloid angiopathy and disturbances in blood-brain barrier function all appear to contribute to the development of ischemic episodes with free radical generation and neuronal degeneration. In Parkinson's disease, the substantia nigra appears to be under oxidative stress as evidenced by the findings of increased lipid peroxidation, reduced GSH levels, high concentration of iron and free radical generation via autocatalytic mechanisms within neuromelanin-containing catecholaminergic neurons. Regardless of the initial insult, a cascade of events involving both reactive oxygen radicals and mitochondrial metabolism is likely to contribute to cell injury.

Fatty acid degradation in plant peroxisomes: function and biosynthesis of the enzymes involved

In plants, the fatty acid oxidation enzyme apparatus is exclusively located within glyoxysomes or peroxisomes. Following the formation of the CoA-ester, the machinery for the degradation of endogenous fatty acids consists of acyl-CoA oxidase, D-3-hydroxyacyl-CoA hydrolyase, 2,3-enoyl-CoA isomerase, isoenzymes of the multifunctional protein and thiolase. The multiple location of particular enzyme activities on different species of protein is discussed in detail. In cucumber cotyledons, the multifunctional protein exhibits a C-terminal targeting signal, -PRM like other glyoxysomal or leaf peroxisomal proteins. In contrast, proteolytic modification takes place at the N-terminus of thiolase and malate dehydrogenase. Thus, distinct mechanisms are envisaged to take place during the transfer of the cytosolic precursor into glyoxysomes prior to the intra-organellar assembly of the mature enzyme.

Some computational models at the cellular level

A number of viewpoints on how a cell can be modelled are discussed in this paper in light of the ability it has to process information. The paper begins with a very brief summary of four general types of computation: sequential, parallel, distributed, and emergent. These form the general framework from which a number of comparisons are made. Several metaphors are introduced to enable reflections to be made about cellular computational properties. The most important metaphor, namely the cell as a machine, is discussed, and then a number of other ideas are introduced that complement much current thinking in this area. The idea of networks or circuits in the cell is then developed, as this provides a means of describing the mechanisms within a machine. Following on from this, three further metaphors are applied in order to overcome certain limitations in current machine thinking, cell-as-society, cell-as-text, and cell-as-field.

[Parametric resonance as a possible mechanism of action of superlow concentrations of biologically active substances at the cellular and subcellular levels]

At extra-low concentrations of biologically active substances (BAS) the limiting stage of processes determining their action at cell and sub-sell levels is BAS diffusion to the cell surface. According to proposed parametric resonance model the BAS activity extreme values are to be observed when the reciprocal values of collision frequency between BAS molecules and cell surface coincide (by order of magnitude) with the characteristic times of conformational relaxation of certain macromolecular structures responsible of the studied process. The calculation results do not contradict the experimental data.

A perspective on the biotechnological potential of extremophiles

It is well recognized that many environments considered by man to be extreme are colonized by microorganisms which are specifically adapted to these ecological niches. A diverse range of bacteria, cyanobacteria, algae and yeasts have been isolated from such habitats and it is now widely accepted that these microorganisms provide a valuable resource not only for exploitation in novel biotechnological processes but also as models for investigating how biomolecules are stabilized when subjected to extreme conditions. This short review summarizes our current state of knowledge of this unique group of microorganisms and their enzymes, and attempts to identify their future biotechnological potential.

Characteristics of putrescine uptake by human brush border membrane vesicles

Both putrescine and the polyamines spermidine and spermine are essential factors for growth and differentiation in all cells of higher eucaryotes. In principle, increased requirements of polyamines in mucosal cells either can be met by de novo-synthesis or by increasing the uptake from lumen (brush border membrane) or bloodstream (basolateral membrane). We therefore evaluated putrescine uptake in intestinal mucosal cells by using human brush border membrane vesicles (BBMV). Intravesicular uptake of putrescine was shown by osmoplots. This process was not saturable over a substrate range from 1 to 80 microM. Putrescine transport was also found to be independent of temperature (Q10 = 1.23). No differences in putrescine uptake rates were found in the presence or absence of Na+, and there was no evidence for any dependence of putrescine uptake from other cations. Our data indicate that putrescine uptake by human intestinal brush border membrane vesicles occurs by passive diffusion. It is concluded that a formerly described saturable and carrier mediated uptake in isolated intestinal mucosal cells from different species is probably influenced by active transport across the basolateral membranes. Therefore, further studies with isolated basolateral membranes are advocated.

Protein oxidation and aging

A number of systems that generate oxygen free radicals catalyze the oxidative modification of proteins. Such modifications mark enzymes for degradation by cytosolic neutral alkaline proteases. Protein oxidation contributes to the pool of damaged enzymes, which increases in size during aging and in various pathological states. The age-related increase in amounts of oxidized protein may reflect the age-dependent accumulation of unrepaired DNA damage that, in a random manner, affects the concentrations or activities of numerous factors that govern the rates of protein oxidation and the degradation of oxidized protein.

Application of ultrasound to biotechnology: an overview

Application of ultrasound to biotechnology is relatively new, but several processes that take place in the presence of cells or enzymes are activated by ultrasonic waves. High intensity ultrasonic waves break the cells and denaturize the enzymes. Low intensity ultrasonic waves can modify cellular metabolism or improve the mass transfer of reagents and products through the boundary layer or through the cellular wall and membrane. In the case of enzymes, the increase in the mass transfer rate of the reagents to the active site seems to be the most important factor. Immobilized enzymes are more resistant to thermal deactivation produced by ultrasound than native enzymes. Reverse micelles can be used to carry out synthesis using enzymes. Several applications of ultrasound to the biotechnology are discussed.

The seed germination model of enzyme catalysis

The activity of enzymes and other biological macromolecules is often sensitively dependent on physiochemical context. Seed germination provides an analogy that helps to elicit the control and information processing capabilities of enzymatic networks. Like a seed, the enzyme takes a particular action (complexes with a specific substrate and catalyzes a specific reaction) when a specific set of milieu influences is satisfied. The context sensitivity, specificity and speed are enormously enhanced by the parallelism inherent in the electronic wave function (i.e. by the superposition of electronic states). This parallelism is converted to speedup through electronic-conformational interactions. The quantum speedup effect allows biological 'switches' to have qualitatively greater pattern recognition capabilities than electronic switches. Consequently the information processing and control capabilities of biomolecular systems exceed the capabilities obtainable from classical models and exceed the intuitive expectations that have developed through the study of such models.

Regulation of enzyme activity in the cell: effect of enzyme concentration

The rapid development in our understanding of the regulation of enzyme activity makes it a high priority to ascertain whether the behavior of purified enzymes reflects their functional characteristics in vivo. Enzyme concentration is usually the most significant difference between routine in vitro assays and in vivo conditions, as it is well known that many intracellular enzymes are present in vivo at much higher concentrations than used in vitro. Various procedures are suitable for kinetic analysis at physiological concentrations of enzyme. Those more frequently used have been cell permeabilization, the utilization of purified enzymes at concentrations close to the in vivo range, and the addition of polyethylene glycol to increase the local protein concentration. In this review we briefly summarize observations on enzymes reported to exhibit concentration-dependent activity. The effect of enzyme concentration has been most thoroughly investigated in the case of phosphofructokinase. These studies may provide insight into the regulation of this important enzyme in the cell. The implications of both homologous and heterologous protein-protein interactions for the effect of enzyme concentration and their roles in the control of enzyme activity in vivo are also discussed.

A quantitative evaluation of the effect of enzyme complexes on the glycolytic rate in vivo: mathematical modeling of the glycolytic complex

The cellular distribution of free and bound glycolytic enzymes in vivo was estimated by means of a model based on previously determined association constants for individual binding interactions and in vivo protein concentrations. The calculations revealed that a significant proportion of the enzymes would be either associated with F-actin, or bound in binary enzyme-enzyme complexes in vivo. An analysis of the relative concentration, and relative activity, of F-actin-bound enzymes suggested that a complete glycolytic complex, composed of all enzymatic steps from phosphofructokinase (PFK) to lactate dehydrogenase (LDH) does not exist. This was indicated by a very low concentration of F-actin-associated phosphoglycerate kinase (PGK) and by a very low activity of F-actin bound aldolase and PGK; this model showed that aldolase and PGK would be absent from any F-actin bound complex. An analysis of soluble enzyme-enzyme associations indicated that formation of binary enzyme complexes may lead to an increased overall flux through glyceraldehyde 3-phosphate dehydrogenase and LDH, but would serve to decrease flux through PFK and aldolase. A 1.4-fold activation of PFK, which occurs when the soluble enzyme binds to F-actin, suggested that reversible binding of PFK to F-actin may represent a novel cellular mechanism for controlling glycolytic flux during periods of increased metabolic demand by controlling the key regulatory enzyme of glycolysis.