Characterization of the stabilizing effect of point mutations of pyruvate oxidase from Lactobacillus plantarum: protection of the native state by modulating coenzyme binding and subunit interaction.

Point mutations in the gene of pyruvate oxidase from Lactobacillus plantarum, with proline residue 178 changed to serine, serine 188 to asparagine, and alanine 458 to valine, as well as a combination of the three single point mutations, lead to a significant functional stabilization of the protein. The enzyme is a tetrameric flavoprotein with tightly bound cofactors, FAD, TPP, and divalent metal ions. Thus, stabilization may be achieved either at the level of tertiary or quaternary interactions, or by enhanced cofactor binding. In order to discriminate between these alternatives, unfolding, dissociation, and cofactor binding of the mutant proteins were analyzed. The point mutations do not affect the secondary and tertiary structure, as determined by circular dichroism and protein fluorescence. Similarly, the amino acid substitutions neither modulate the enzymatic properties of the mutant proteins nor do they stabilize the structural stability of the apoenzymes. This holds true for both the local and the global structure with unfolding transitions around 2.5 M and 5 M urea, respectively. On the other hand, deactivation of the holoenzyme (by urea or temperature) is significantly decreased. The most important stabilizing effect is caused by the Ala-Val exchange in the C-terminal domain of the molecule. Its contribution is close to the value observed for the triple mutant, which exhibits maximum stability, with a shift in the thermal transition of ca. 10 degrees C. The effects of the point mutations on FAD binding and subunit association are interconnected. Because FAD binding is linked to oligomerization, the stability of the mutant apoenzyme-FAD complexes is increased. Accordingly, mutants with maximum apparent FAD binding exhibit maximum stability. Analysis of the quaternary structure of the mutant enzymes in the absence and in the presence of coenzymes gives clear evidence that both improved ligand binding and subunit interactions contribute to the observed thermal stabilization.     

How protein stability and new functions trade off

Numerous studies have noted that the evolution of new enzymatic specificities is accompanied by loss of the protein's thermodynamic stability (DeltaDeltaG), thus suggesting a tradeoff between the acquisition of new enzymatic functions and stability. However, since most mutations are destabilizing (DeltaDeltaG>0), one should ask how destabilizing mutations that confer new or altered enzymatic functions relative to all other mutations are. We applied DeltaDeltaG computations by FoldX to analyze the effects of 548 mutations that arose from the directed evolution of 22 different enzymes. The stability effects, location, and type of function-altering mutations were compared to DeltaDeltaG changes arising from all possible point mutations in the same enzymes. We found that mutations that modulate enzymatic functions are mostly destabilizing (average DeltaDeltaG = +0.9 kcal/mol), and are almost as destabilizing as the "average" mutation in these enzymes (+1.3 kcal/mol). Although their stability effects are not as dramatic as in key catalytic residues, mutations that modify the substrate binding pockets, and thus mediate new enzymatic specificities, place a larger stability burden than surface mutations that underline neutral, non-adaptive evolutionary changes. How are the destabilizing effects of functional mutations balanced to enable adaptation? Our analysis also indicated that many mutations that appear in directed evolution variants with no obvious role in the new function exert stabilizing effects that may compensate for the destabilizing effects of the crucial function-altering mutations. Thus, the evolution of new enzymatic activities, both in nature and in the laboratory, is dependent on the compensatory, stabilizing effect of apparently "silent" mutations in regions of the protein that are irrelevant to its function.     

Effects of acclimation temperature on enzymatic capacities and mitochondrial membranes from the body wall of the earthworm Lumbricus terrestris

Many ectotherms respond to low temperature by adjusting capacities of enzymes from energy metabolism, restructuring membrane phospholipids and modulating membrane fluidity. Although much is known about the temperature biology of earthworms, it is not known to what extent earthworms employ compensatory changes in enzymatic capacities and membrane physical properties after exposure to low temperature. We examined activities of enzymes from glycolysis and central oxidative pathways as well as fluidity and phospholipid fatty acid composition of mitochondrial membranes prepared from the body wall of the temperate oligochaete Lumbricus terrestris after a one month acclimation to 5 degrees and 15 degrees C. No compensation occurs in central pathways of oxidative metabolism since activities of cytochrome-c oxidase and citrate synthase, when measured at a common temperature, are similar for 5 degrees C and 15 degrees C-acclimated animals. In contrast, activity of pyruvate kinase is elevated 1.3-fold after acclimation to 5 degrees C. Mitochondrial membranes display inverse compensation with respect to temperature (membranes from 5 degrees C animals are more ordered than membranes from 15 degrees C animals). Our results, in combination with earlier reports, indicate that routine metabolism in L. terrestris may be maintained at reduced temperatures with little or no change in enzymatic capacities and inverse compensation of mitochondrial membranes.     

Micellar enzymology

Experimental approaches to modelling the enzymatic function of biological membranes are discussed. Emphasis is given to pseudohomogeneous systems such as proteolipid complexes and enzymes in organic solvents; the latter are solubilized with phospholipids or synthetic surfactants. Methods for producing and studying such micellar systems are considered. The key research problems of micellar enzymology are formulated and its relation to enzyme membranology is discussed. Finally, the new potentialities are noted of applied enzymology (biotechnology) offered by application of a colloidal solution of water in organic solvents as a microheterogeneous medium for enzymatic reactions.     

Studies on the interaction of propranolol with erythrocyte membranes.

The interaction of propranolol with erythrocyte membranes at concentrations stabilizing intact erythrocytes against hypotonic hemolysis produced corresponding perturbations in membrane protein and particularly membrane phospholipid components as monitored by increases in the reactivity of membrane amino and sulfhydryl groups towards trinitrobenzenesulfonic acid and 5,5'-dithio-bis(2-nitro-benzoic acid), respectively. Membrane-propranolol interactions were also analyzed in terms of alterations produced in the kinetic properties of membrane enzymes. These experiments provided evidence that propranolol-induced perturbations were sufficiently generalized as to influence the activity of enzymatic processes associated with both inner and outer membrane surfaces. Configurational changes in membrane phospholipids were implicated in these effects of propranolol, which included alterations in functionally significant membrane-cation interactions, It is suggested that the findings described here may provide a basis for understanding molecular aspects of membrane stabilization in other systems.     

Selectionism and neutralism in molecular evolution

Charles Darwin proposed that evolution occurs primarily by natural selection, but this view has been controversial from the beginning. Two of the major opposing views have been mutationism and neutralism. Early molecular studies suggested that most amino acid substitutions in proteins are neutral or nearly neutral and the functional change of proteins occurs by a few key amino acid substitutions. This suggestion generated an intense controversy over selectionism and neutralism. This controversy is partially caused by Kimura's definition of neutrality, which was too strict (|2Ns|< or =1). If we define neutral mutations as the mutations that do not change the function of gene products appreciably, many controversies disappear because slightly deleterious and slightly advantageous mutations are engulfed by neutral mutations. The ratio of the rate of nonsynonymous nucleotide substitution to that of synonymous substitution is a useful quantity to study positive Darwinian selection operating at highly variable genetic loci, but it does not necessarily detect adaptively important codons. Previously, multigene families were thought to evolve following the model of concerted evolution, but new evidence indicates that most of them evolve by a birth-and-death process of duplicate genes. It is now clear that most phenotypic characters or genetic systems such as the adaptive immune system in vertebrates are controlled by the interaction of a number of multigene families, which are often evolutionarily related and are subject to birth-and-death evolution. Therefore, it is important to study the mechanisms of gene family interaction for understanding phenotypic evolution. Because gene duplication occurs more or less at random, phenotypic evolution contains some fortuitous elements, though the environmental factors also play an important role. The randomness of phenotypic evolution is qualitatively different from allele frequency changes by random genetic drift. However, there is some similarity between phenotypic and molecular evolution with respect to functional or environmental constraints and evolutionary rate. It appears that mutation (including gene duplication and other DNA changes) is the driving force of evolution at both the genic and the phenotypic levels.     

Extreme Entropy-Enthalpy Compensation in a Drug-Resistant Variant of HIV-1 Protease

The development of HIV-1 protease inhibitors has been the historic paradigm of rational structure-based drug design, where structural and thermodynamic analyses have assisted in the discovery of novel inhibitors. While the total enthalpy and entropy change upon binding determine the affinity, often the thermodynamics are considered in terms of inhibitor properties only. In the current study, profound changes are observed in the binding thermodynamics of a drug-resistant variant compared to wild-type HIV-1 protease, irrespective of the inhibitor bound. This variant (Flap+) has a combination of flap and active site mutations and exhibits extremely large entropy-enthalpy compensation compared to wild-type protease, 5-15 kcal/mol, while losing only 1-3 kcal/mol in total binding free energy for any of six FDA-approved inhibitors. Although entropy-enthalpy compensation has been previously observed for a variety of systems, never have changes of this magnitude been reported. The co-crystal structures of Flap+ protease with four of the inhibitors were determined and compared with complexes of both the wild-type protease and another drug-resistant variant that does not exhibit this energetic compensation. Structural changes conserved across the Flap+ complexes, which are more pronounced for the flaps covering the active site, likely contribute to the thermodynamic compensation. The finding that drug-resistant mutations can profoundly modulate the relative thermodynamic properties of a therapeutic target independent of the inhibitor presents a new challenge for rational drug design.     

Studies on the interaction of propranolol with erythrocyte membranes

The interaction of propranolol with erythrocyte membranes at concentrations stabilizing intact erythrocytes against hypotonic hemolysis produced corresponding perturbations in membrane protein and particularly membrane phospholipid components as monitored by increases in the reactivity of membrane amino and sulfhydryl groups towards trinitrobenzenesulfonic acid and 5,5′-dithio-bis-(2-nitro-benzoic acid), respectively. Membrane-propranolol interactions were also analyzed in terms of alterations produced in the kinetic properties of membrane enzymes. These experiments provided evidence that propranolol-induced perturbations were sufficiently generalized as to influence the activity of enzymatic processes associated with both inner and outer membrane surfaces. Configurational changes in membrane phospholipids were implicated in these effects of propranolol, which included alterations in functionally significant membrane-cation interactions. It is suggested that the findings described here may provide a basis for understanding molecular aspects of membrane stabilization in other systems.     

Stimulation of bioprocesses by ultrasound

Ultrasound (US) has become a ubiquitous technological process in a large variety of scientific disciplines. However, little information exists on the use of ultrasound to enhance biological processes and/or processing and consequently this paper provides an overview of work reported to date on this topic. This review provides a brief introduction to ultrasound and the history of ultrasound as applied to bioprocesses. This is followed by a discussion of the influence of US on discrete enzyme systems, enzymes used in bioremediation, microbial fermentations and enzymatic hydrolysis of biopolymers. Augmentation of anaerobic digestion by US is then considered along with enhancement of enzymes in food science and technology. The use of ultrasonically stimulated enzymes in synthesis is then considered and other relevant miscellaneous topics are described. It is concluded that the precise mechanism of action of US in bio-processing remains to be elucidated though a variety of plausible suggestions are made.     

The role of biotransformation in dietary (anti)carcinogenesis.

The fact that dietary compounds influence the susceptibility of human beings to cancer, is widely accepted. One of the possible mechanisms that is responsible for these (anti)carcinogenic effects is that dietary constituents may modulate biotransformation enzymes, thereby affecting the (anti)carcinogenic potential of other compounds. This ambiguous theme is the basis for the present paper. The possible effects of enzymatic bioactivation and detoxification of dietary constituents are discussed using two representative examples of phase I and phase II biotransformation enzymes i.e., cytochrome P450 and glutathione S-transferase. Furthermore, the impact of genetic polymorphisms of these two enzyme systems is considered. Although it is very difficult on the basis of the enzyme inducing or inhibiting properties of dietary compounds, especially to characterize them as anticarcinogenic, for certain constituents it is acknowledged that they have anticarcinogenic properties. As such, this provides for an important mechanistic substantiation of the established cancer chemopreventive effect of a diet rich in fruits and vegetables.     

Directed evolution of beta -glucosidase A from Paenibacillus polymyxa to thermal resistance

The beta-glucosidase encoded by the bglA gene from Paenibacillus polymyxa has a half-life time of 15 min at 35 degrees C and no detectable activity at 55 degrees C. We have isolated random mutations that enhance the thermoresistance of the enzyme. Following a directed evolution strategy, we have combined some of the isolated mutations to obtain a beta-glucosidase with a half-life of 12 min at 65 degrees C, in the range of resistance of thermophilic enzymes. No significant alteration of the kinetic parameters of the enzyme was observed. One of the mutants isolated in the screening for thermoresistant beta-glucosidase had the same resistance to denaturation as the wild type. This mutation caused the accumulation of enzyme in E. coli, probably due to its lower turnover. The structural changes responsible for the properties of the mutant enzymes have been analyzed. The putative causes increasing thermoresistance are as follows: the formation of an extra salt bridge, the replacement of an Asn residue exposed to the solvent, stabilization of the hydrophobic core, and stabilization of the quaternary structure of the protein.     

SER-HIS-ASP catalytic triad in model non-aqueous solvent environment: a computational study

Emerging new properties and applications of enzymes in organic solvents and ionic liquids are unabating. By applying a combined Quantum Mechanics/Continuum Mechanics computation on a prototypical catalytic triad serine-histidine-aspartate (SER-HIS-ASP) interacting with ethanol or acetonitrile molecules, the major difference between protic and aprotic solvents in effecting transition-state stabilization has been analyzed. Moderately polar aprotic solvent acetonitrile is predicted to be unable to stabilize the transition state in replacing the role of the oxyanion-hole environment, whereas protic ethanol solvent molecules of similar polarity to acetonitrile are adequate in re-gaining the enzymatic activities.     

Effect of mutagenesis at serine 653 of Arabidopsis thaliana acetohydroxyacid synthase on the sensitivity to imidazolinone and sulfonylurea herbicides.

Resistance to sulfonylurea and imidazolinone herbicides can occur by mutations in acetohydroxyacid synthase (EC 4.1.3.18). Changing serine 653 to asparagine is known to cause insensitivity to imidazolinones but not to sulfonylureas. Here, S-653 of the Arabidopsis thaliana enzyme was mutated to alanine, threonine and phenylalanine. The purified mutated enzymes resemble wild-type in their enzymatic properties. The threonine and phenylalanine mutants are imidazolinone-resistant and the latter is also slightly sulfonylurea-resistant. The alanine mutant remains sensitive to both herbicides. The results suggest that the beta-hydroxyl group is not required for imidazolinone binding and that the size of the side-chain determines resistance.     

Interactions in enzymatic reactions

The paper deals with interactions of substances via an enzymatic reaction (Bull. Math. Biophysics,25, 141–154, 1963). The substances are the activators, inhibitors and/or substrates of the reaction. Due to the bimolecularity of the processes in the reaction, the quantitative relation between the steady state amount of complexes and the amounts of the substances assumes a typical form. In multiple enzymatic reactions this form is more complicated, though basically similar. Because the substances may influence the steady state amounts of the complexes in opposite directions, the compensation and blocking effects are the properties of enzymatic reactions. The substances with the same direction of influence may potentiate each other. In the enzymatic reaction here considered, the potentiation is always non-negative.     

Brachyurins--serine collagenolytic enzymes from crabs

The properties of brachyurins, proteolytic enzymes belonging to a new subfamily of chymotrypsin-like proteases, are considered. These enzymes, found in various species of crustacean, exhibit mixed substrate specificity and a marked collagenolytic activity. The enzymatic and physicochemical properties of brachyurins I and their primary and spatial structures are discussed in detail. A separate chapter is devoted to the preparations of collagenases from the hepatopancreas of king crab: their action on the damaged skin and use in medicine.     

Brachyurins, Serine Collagenolytic Enzymes from Crabs

The properties of brachyurins, proteolytic enzymes belonging to a new subfamily of chymotrypsin-like proteases, are considered. These enzymes, found in various species of crustacean, exhibit mixed substrate specificity and a marked collagenolytic activity. The enzymatic and physicochemical properties of brachyurins I and their primary and spatial structures are discussed in detail. A separate chapter is devoted to the preparations of collagenases from the hepatopancreas of king crab: their action on the damaged skin and use in medicine.     

Stability and repair of DNA in hyperthermophilic Archaea

Evolutionary and physiological considerations argue that study of hyperthermophilic archaea should reveal new molecular aspects of DNA stabilization and repair. So far, these unusual prokaryotes have yielded a number of genes and enzymatic activities consistent with known mechanisms of excision repair, photo-reversal, and trans-lesion synthesis. However, other DNA enzymes of hyperthermophilic archaea show novel biochemical properties which may be related to DNA stability or repair at extremely high temperature but which remain difficult to evaluate rigorously in vivo. Perhaps the most striking feature of the hyperthermophilic archaea is that all of them whose genomes have been sequenced lack key genes of both the nucleotide excision repair and DNA mismatch repair pathways, which are otherwise highly conserved in biology. Although the growth properties of these micro-organisms hinder experimentation, there is evidence that some systems of excision repair and mutation avoidance operate in Sulfolobus spp. It will therefore be of strategic significance in the next few years to formulate and test hypotheses in Sulfolobus spp. and other hyperthermophilic archaea regarding mechanisms and gene products involved in the repair of UV photoproducts and DNA mismatches.     

Redesigning protein pKa values

The ability to re-engineer enzymatic pH-activity profiles is of importance for industrial applications of enzymes. We theoretically explore the feasibility of re-engineering enzymatic pH-activity profiles by changing active site pK(a) values using point mutations. We calculate the maximum achievable DeltapK(a) values for 141 target titratable groups in seven enzymes by introducing conservative net-charge altering point mutations. We examine the importance of the number of mutations introduced, their distance from the target titratable group, and the characteristics of the target group itself. The results show that multiple mutations at 10A can change pK(a) values up to two units, but that the introduction of a requirement to keep other pK(a) values constant reduces the magnitude of the achievable DeltapK(a). The algorithm presented shows a good correlation with existing experimental data and is available for download and via a web server at http://enzyme.ucd.ie/pKD.