Charge balance in the alpha-hydroxyacid dehydrogenase vacuole: an acid test

The proposal that the active site vacuole of NAD(+)-S-lactate dehydrogenase is unable to accommodate any imbalance in electrostatic charge was tested by genetically manipulating the cDNA coding for human muscle lactate dehydrogenase to make a protein with an aspartic acid introduced at position 140 instead of the wild-type asparagine. The Asn 140-Asp mutant enzyme has the same kcat as the wild type (Asn 140) at low pH (4.5), and at higher pH the Km for pyruvate increases 10-fold for each unit increase in pH up to pH 9. We conclude that the anion of Asp 140 is completely inactive and that it binds pyruvate with a Km that is over 1,000 times that of the Km of the neutral, protonated aspartic-140. Experimental results and molecular modeling studies indicate the pKa of the active site histidine-195 in the enzyme-NADH complex is raised to greater than 10 by the presence of the anion at position 140. Energy minimization and molecular dynamics studies over 36 ps suggest that the anion at position 140 promotes the opening of and the entry of mobile solvent beneath the polypeptide loop (98-110), which normally seals off the internal active site vacuole from external bulk solvent.

Duck liver 'malic' enzyme. Expression in Escherichia coli and characterization of the wild-type enzyme and site-directed mutants

A cDNA for duck liver 'malic' enzyme (EC 1.1.1.40) was subcloned into pUC-8, and the active enzyme was expressed in Escherichia coli TG-2 cells as a fusion protein including a 15-residue N-terminal leader from beta-galactosidase coded by the lacZ' gene. C99S and R70Q mutants of the enzyme were generated by the M13 mismatch technique. The recombinant enzymes were purified to near homogeneity by a simple two-step procedure and characterized relative to the enzyme isolated from duck liver. The natural duck enzyme has a subunit molecular mass of approx. 65 kDa, and the following kinetic parameters for oxidative decarboxylation of L-malate at pH 7.0: Km NADP+ (4.6 microM); Km L-malate (73 microM); kcat (160 s-1); Ka (2.4 microM) and Ka' (270 microM), dissociation constants of Mn2+ at 'tight' (activating) and 'weak' metal sites; and substrate inhibition (51% of kcat. at 8 mM-L-malate). Properties of the E. coli-derived recombinant wild-type enzyme are indistinguishable from those of the natural duck enzyme. Kinetic parameters of the R70Q mutant are relatively unaltered, indicating that Arg-70 is not required for the reaction. The C99S mutant has unchanged Km for NADP+ and parameters for the 'weak' sites (i.e. inhibition by L-malate, Ka'); however, kcat. decreased 3-fold and Km for L-malate and Ka each increased 4-fold, resulting in a catalytic efficiency [kcat./(Km NADP+ x Km L-malate x Ka)] equal to 3.7% of the natural duck enzyme. These results suggest that the positioning of Cys-99 in the sequence is important for proper binding of L-malate and bivalent metal ions.

Successful targeting of the mouse cystic fibrosis transmembrane conductance regulator gene in embryonal stem cells

We wish to construct a mouse model for the human inherited disease cystic fibrosis. We describe here the successful targeting in embryonal stem cells of the murine homologue (Cftr) of the cystic fibrosis transmembrane conductance regulator gene, as the first critical step towards this end. The targeting event precisely disrupts exon 10, the site of the major mutation in patients with cystic fibrosis. The targeted cells are pluripotent and competent to form chimaeras.

Binding of a chaperonin to the folding intermediates of lactate dehydrogenase

When Bacillus stearothermophilus LDH dimer is incubated with increasing concentrations of the denaturant guanidinium chloride, three distinct unfolded states of the molecule are observed at equilibrium [Smith, C. J., et al. (1991) Biochemistry 30, 1028-1036]. The kinetics of LDH refolding are consistent with an unbranched progression through these states. The Escherichia coli chaperonin, GroEL, binds with high affinity to the completely denatured form and more weakly to the earliest folding intermediate, thus retarding the refolding process. A later structurally defined folding intermediate, corresponding to a molten globule form, is not bound by GroEL; neither is the inactive monomer. The complex between GroEL and denatured LDH is destabilized by the binding of magnesium/ATP (Mg/ATP) or by the nonhydrolyzable analogue adenylyl imidodiphosphate (AMP-PNP). From our initial kinetic data, we propose that GroEL exists in two interconvertible forms, one of which is stabilized by the binding of Mg/ATP but associates weakly with the unfolded protein. The other is destabilized by Mg/ATP and associates strongly with unfolded LDH. The relevance of these findings to the role of GroEL in vivo is discussed.

EcoRV restriction endonuclease binds all DNA sequences with equal affinity

In the presence of MgCl2, the EcoRV restriction endonuclease cleaves its recognition sequence on DNA at least a million times more readily than any other sequence. In this study, the binding of the EcoRV restriction enzyme to DNA was examined in the absence of Mg2+. With each DNA fragment tested, several DNA-protein complexes were detected by electrophoresis through polyacrylamide. No differences were observed between isogenic DNA molecules that either contained or lacked the EcoRV recognition site. The number of complexes with each fragment varied with the length of the DNA. Three complexes were formed with a DNA molecule of 55 base pairs, corresponding to the DNA bound to 1, 2, or 3 molecules of the protein, while greater than 15 complexes were formed with a DNA of 381 base pairs. A new method was developed to analyze the binding of a protein to multiple sites on DNA. The method showed that the EcoRV enzyme binds to all DNA sequences, including the EcoRV recognition site, with the same equilibrium constant, though two molecules of the protein bind preferentially to adjacent sites on the DNA in a cooperative fashion. All of the complexes with a substrate that contained the EcoRV site dissociated upon addition of competitor DNA, but when the competitor was mixed with MgCl2, a fraction of the substrate was cleaved at the EcoRV site. The fraction cleaved was due mainly to the translocation of the enzyme from nonspecific sites on the DNA to the specific site.

Design and synthesis of new enzymes based on the lactate dehydrogenase framework

Analysis of the mechanism and structure of lactate dehydrogenases is summarized in a map of the catalytic pathway. Chemical probes, single tryptophan residues inserted at specific sites and a crystal structure reveal slow movements of the protein framework that discriminate between closely related small substrates. Only small and correctly charged substrates allow the protein to engulf the substrate in an internal vacuole that is isolated from solvent protons, in which water is frozen and hydride transfer is rapid. The closed vacuole is very sensitive to the size and charge of the substrate and provides discrimination between small substrates that otherwise have too few functional groups to be distinguished at a solvated protein surface. This model was tested against its ability to successfully predict the design and synthesis of new enzymes such as L-hydroxyisocaproate dehydrogenase and fully active malate dehydrogenase. Solvent friction limits the rate of forming the vacuole and thus the maximum rate of catalysis.

Creation of a large genomic deletion at the T-cell antigen receptor beta-subunit locus in mouse embryonic stem cells by gene targeting

Recently it has become possible to introduce predesigned mutations into a given gene in the mouse germ line by homologous recombination in embryonic stem cells. The mutations are usually introduced by inserting the neomycin phosphotransferase gene into an exon of a particular gene. Here we describe an extension of this method that can result in at least a 15-kilobase-long deletion. The deletion created in the present work encompasses one of the two diversity gene segments of the mouse T-cell receptor beta-subunit locus, 10 out of the 12 joining gene segments, and both constant gene segments. This strategy is a valuable alternative to sequential targeting of multiple genes forming a gene cluster, could simplify the construction of plasmids to be used for targeting, and could be the solution for inactivating small genes that have eluded conventional targeting approaches.

Detection and characterization of intermediates in the folding of large proteins by the use of genetically inserted tryptophan probes

L-Lactate dehydrogenase from Bacillus stearothermophilus was rebuilt by using site-directed mutagenesis to produce an enzymically active, tryptophan-less enzyme by replacing all the wild-type tryptophans (80, 150, and 203) by tyrosines. Nine single tryptophan-containing active enzymes were constructed from this enzyme by genetically replacing one of the tyrosines 36, 85, 147, 190, 203, 237, 248, 279, or 285 by tryptophan. The equilibrium and the time-resolved tryptophan fluorescence intensity and anisotropy were used to report unfolding events in guanidine hydrochloride (GHCl) monitored from these nine defined positions. Three structural transitions, half complete at 0.55, 1.7, and 2.8 M GHCl, were identified and defined four folding intermediates, I (native), II (expanded monomer 1), III (expanded monomer 2), and IV (random coil), stable at 0, 1, 2.2, and 4 M GHCl, respectively. Intermediate II is a globular monomer. All the probed alpha-helices and most of the beta-structure was intact. There was an increase in the rate but not the extent of the mobilities of six of the probed tryptophan side chains, indicating loss of tertiary structure. Circular dichroism (CD) showed all the secondary structure to be intact. Intermediate III is monomeric and still globular, but the tryptophan anisotropy indicated an increase mobility at positions 36, 85, 190, 203, 279, and 285. Helix alpha-B is further disrupted but helices alpha-1F, alpha-2G, and alpha 3G were still rigid. CD showed half the secondary structure to be still intact. Intermediate IV is a random coil in which all tryptophans have complete rotational freedom and the helix CD signal is lost.(ABSTRACT TRUNCATED AT 250 WORDS)

Designs for a broad substrate specificity keto acid dehydrogenase

Variations have been made to the structure of the nicotinamide adenine dinucleotide (NAD) dependent L-lactate dehydrogenase from Bacillus stearothermophilus at regions of the enzyme that we believe determine specificity toward different alpha-hydroxy acids (RCHOHCOO-, R = CH3, C2H5, etc.). Two regions of LDH that border the active site (but are not involved in the catalytic reaction) were altered in order to accommodate substrates with hydrophobic side chains larger than that of the naturally preferred substrate, pyruvate (R = CH3). The mutations 102-105GlnLysPro----MetValSer and 236-237AlaAla----GlyGly were made to increase the tolerance for large hydrophobic substrate side chains. The triple and double mutants alone gave little improvement for branched-chain-substituted pyruvates. The five changes together produced a broader substrate specificity alpha-hydroxy acid dehydrogenase, with a 55-fold improved kcat for alpha-ketoisocaproate to a value about 1/14 that of the native enzyme for pyruvate. Rational protein engineering enabled coupled changes in enzyme structure to be obtained with greater probability of success than random mutagenesis.

Expression of the copy DNA for human A4 and B4 L-lactate dehydrogenases in Escherichia coli

The human LDH-A and LDH-B cDNAs, containing the coding regions for the L-lactate dehydrogenase A4 (M) and B4 (H) polypeptides respectively have been cloned into Escherichia coli to place the cDNAs under the control of hybrid E. coli/Bacillus stearothermophilus transcriptional and translational signals. Human A4- and B4-isoenzymes are produced in E. coli cells harbouring the expression plasmids pHLDHA22 and pHLDHB10 at levels of 6.5 and 1.5% of the soluble protein of the cell, respectively. The tac promoter of these vectors was not induced by isopropyl beta-D-thiogalactopyranoside. The A4 and B4 human isoenzymes synthesized in E. coli were purified to homogeneity and show the same properties as isoenzymes isolated from human tissue. The amino acid sequences of 12 N-terminal residues of the human isoenzymes synthesized in E. coli were determined to be identical to those deduced from the DNA sequence of the cloned cDNAs except that the N-terminal methionine was absent from both. However, in contrast to LDH made in human cells, acetylation of the N-terminal alanine does not take place in E. coli cells.

The E2 protein of human papillomavirus type 16. Over-expression and purification of an active transcriptional regulator

The E2 open reading frame of human papillomavirus type 16 was inserted into the Escherichia coli vector pKK223-3, and expressed to greater than 15% of total cellular protein when induced with isopropyl beta-D-thiogalactopyranoside. The highest expressing clone was grown in bulk and the E2 protein purified to homogeneity by the following procedure: (a) isolation of the insoluble protein fraction; (b) extraction with urea; (c) quaternary amino-ethyl-Sepharose ion-exchange chromatography and (d) renaturation and chromatography on dextran sulphate. That the purified protein was fully functionally active was confirmed by its specific DNA-binding properties and its ability to activate gene transcription by over two orders of magnitude in an in vivo assay.

External morphology of the antennae of Damalinia ovis (Phthiraptera: Trichodectidae)

The antennae of adult Damalinia ovis, the sheep louse, were studied using light and scanning electron microscopy. Sensory structures are located on all three antennal segments with the predominant sensilla type being tactile. Nine different types of sensilla are described on the basis of external appearance. One of the sensilla, designated a "pit organ" because of its unusual shape, has not been described previously. A pair of these sensilla are present on each antenna, and their function is unknown. A group of 11 sensilla on the tip of each antenna contains olfactory and chemosensory pegs, and a possible thermohygroreceptor. The antennae are sexually dimorphic, the male having more tactile sensilla, two well-developed terminal hooks, and a different cuticular architecture on the posterior surface of antennal segment 1.

A single amino acid substitution in lactate dehydrogenase improves the catalytic efficiency with an alternative coenzyme

Using site-directed mutagenesis, the NADH-linked lactate dehydrogenase from Bacillus stearothermophilus has been specifically altered at a single residue to shift the coenzyme specificity towards NADPH. The single change is at position 53 in the amino acid sequence where a conserved aspartate has been replaced by a serine. This substitution was made to reduce steric hindrance on binding of the extra phosphate group of NADPH and to remove the negative charge of the aspartate group. The resultant mutant enzyme is 20 times more catalytically efficient than the wild-type enzyme with NADPH.

The control of Nezara viridula L. with introduced egg parasitoids in Australia. A review of a 'landmark' example of classical biological control

The history of Nezara viridula egg parasitoid introductions into Australia is critically reviewed. Using largely unpublished file material information is presented on the source of parasitoids, specific identification of parasitoids, numbers of parasitoids reared and released, and establishment and effects in the field. At least four species of egg parasitoids, in three genera, have been introduced and liberated into Australia since biological control efforts were first begun in 1933. There are records of 11 introductions involving Trissolcus basalis (Wollaston) (Egypt 1933; West Indies 1952-53; South Africa 1980; Brazil 1980; U.S.A. 1979-8 l), Trissolcus mitsukurii (Ashmead) (Japan l962), Ooencyrtus submetallicus (Howard) (West Indies 1952-53), and Telenomus chloropus (Thomson) (Japan 1962; Japan via U.S.A. 1980). Doubt is cast on the specific status of introductions from Italy (1956) and Pakistan (1 961), which are recorded in the literature as T, basalis. Evidence is presented that there is currently not enough information available to determine the specific classifications of these importations. Three programs in which Australian field populations of Trissolcus were bred and released elsewhere in Australia are also recorded. Post-release evaluation of introduced N. viridula egg parasitoids in Australia is reviewed. It is proposed that there is only circumstantial evidence to support the claim that N. viridula is under 'good' biological control by T. basalis in Australia. Areas of investigation that are of the most significance to current workers in N. viridula biological control are highlighted in the discussion.

From analysis to synthesis: new ligand binding sites on the lactate dehydrogenase framework. Part II

In Part I of this article (published in the March issue of TIBS1), substrate-binding and catalysis in lactate dehydrogenase were examined by genetic modification of the protein structure and analysis of the functional consequences. In Part II, the conclusions are used in the design and synthesis of two modified forms of the enzyme; one in which the substrate specificity is shifted to produce a more effective malate dehydrogenase than that isolated from the host organism and one which no longer requires its allosteric activator (fructose 1,6-bisphosphate).

From analysis to synthesis: new ligand binding sites on the lactate dehydrogenase framework. Part I

In Part I of this article, the naturally evolved protein framework of lactate dehydrogenase is investigated by genetically introduced modifications which reveal the structural basis of its catalytic and substrate-binding properties. In Part II (to be published in the April issue of TIBS), this analytical information is exploited in the design of two modified forms of the enzyme; one which is specific for a new substrate and one which lacks allosteric regulation.

Inaccurate calculation of drug output from nebulisers

A multistage liquid impinger was used to collect the nebulised cloud from three separate nebulisers. The output of sodium cromoglycate collected was determined by a spectrophotometric assay. Estimating drug output purely from weight loss during nebulisation resulted in a considerable overestimate compared with direct assay of the drug output from the nebulised cloud. During nebulisation, weight loss from the nebuliser occurs in the form of particle formation and also by evaporation. By only weighing the nebuliser chamber before and after nebulisation, weight loss due to evaporation is not taken into account and this is the cause of the overestimation of drug output by this method.

Germ line transmission and expression of a corrected HPRT gene produced by gene targeting in embryonic stem cells

The deletion mutation in the HPRT-deficient mouse embryonic stem (ES) cell line E14TG2a has been corrected by gene targeting. The presence of plasmid sequences in the correcting vector DNA did not affect the frequency of correction. We have characterized three different HPRT gene structures in correctants. Cells from one corrected clone have been introduced into mouse blastocysts, and germ line transmission of the ES cell-derived corrected gene has been achieved. The corrected gene has the same pattern of expression as the wild-type gene, with the characteristic elevated level of expression in brain tissue. Hence, we have demonstrated the feasibility of introducing targeted modifications into the mouse germ line by homologous recombination in ES cells.

A specific, highly active malate dehydrogenase by redesign of a lactate dehydrogenase framework

Three variations to the structure of the nicotinamide adenine dinucleotide (NAD)-dependent L-lactate dehydrogenase from Bacillus stearothermophilus were made to try to change the substrate specificity from lactate to malate: Asp197----Asn, Thr246----Gly, and Gln102----Arg). Each modification shifts the specificity from lactate to malate, although only the last (Gln102----Arg) provides an effective and highly specific catalyst for the new substrate. This synthetic enzyme has a ratio of catalytic rate (kcat) to Michaelis constant (Km) for oxaloacetate of 4.2 x 10(6)M-1 s-1, equal to that of native lactate dehydrogenase for its natural substrate, pyruvate, and a maximum velocity (250 s-1), which is double that reported for a natural malate dehydrogenase from B. stearothermophilus.

An investigation of the contribution made by the carboxylate group of an active site histidine-aspartate couple to binding and catalysis in lactate dehydrogenase

The influence of aspartate-168 on the proton-donating and -accepting properties of histidine-195 (the active site acid/base catalyst in lactate dehydrogenase) was evaluated by use of site-directed mutagenesis to change the residue to asparagine and to alanine. Despite the fact that asparagine could form a hydrogen bond to histidine while alanine could not, the two mutant enzymes have closely similar catalytic and ligand-binding properties. Both bind pyruvate and its analogue (oxamate) 200 times more weakly than the wild-type enzyme but show little disruption in their binding of lactate and its unreactive analogue, trifluorolactate. Neither mutation alters the binding of coenzymes (NADH and NAD+) or the pK of the histidine-195 residue in the enzyme-coenzyme complex. We conclude that a strong histidine-aspartate interaction is only formed when both coenzyme and substrate are bound. Deletion of the negative charge of aspartate shifts the equilibrium between enzyme-NADH-pyruvate (protonated histidine) and enzyme-NAD+-lactate (unprotonated histidine) toward the latter. In contrast to the wild-type enzyme, the rate of catalysis in both directions in the mutants is limited by a slow hydride ion transfer step.

The use of genetically engineered tryptophan to identify the movement of a domain of B. stearothermophilus lactate dehydrogenase with the process which limits the steady-state turnover of the enzyme

A general technique for monitoring the intramolecular motion of a protein is described. Genetic engineering is used to replace all the natural tryptophan residues with tyrosine. A single tryptophan residue is then inserted at a specific site within the protein where motion is then detected from the fluorescence characteristics of this fluorophore. This technique has been used in B. stearothermophilus lactate dehydrogenase mutant (W80Y, W150Y, W203Y, G106W) to correlate the slow closure of a surface loop of polypeptide (residues 98-110) with the maximum catalytic velocity of the enzyme.

The engineering of a more thermally stable lactate dehydrogenase by reduction of the area of a water-accessible hydrophobic surface

A site-directed mutant of Bacillus stearothermophilus lactate dehydrogenase (lactate:NAD+ oxidoreductase, EC 1.1.1.27) has been engineered in which the conserved hydrophobic residue isoleucine-250 has been replaced by the more hydrophilic residue asparagine. This isoleucine forms a large part of a water-accessible, hydrophobic surface in the active site of the apo-enzyme which is covered by the B-face of the nicotinamide ring when coenzymes are bound. Reduction in the area of this hydrophobic surface results in the mutant tetramer being more thermally stable than the wild-type enzyme.

Rational construction of a 2-hydroxyacid dehydrogenase with new substrate specificity

Using site-directed mutagenesis on the lactate dehydrogenase gene from Bacillus stearothermophilus, three amino acid substitutions have been made at sites in the enzyme which we suggest in part determine specificity toward different hydroxyacids (R-CHOH-COOH). To change the preferred substrates from the pyruvate/lactate pair (R = -CH3) to the oxaloacetate/malate pair (R = -CH2-COO-), the volume of the active site was increased (thr 246----gly), an acid was neutralized (asp-197----asn) and a base was introduced (gln-102 - greater than arg). The wild type enzyme has a catalytic specificity for pyruvate over oxaloacetate of 1000 whereas the triple mutant has a specificity for oxaloacetate over pyruvate of 500. Despite the severity and extent of these active site alterations, the malate dehydrogenase so produced retains a reasonably fast catalytic rate constant (20 s-1 for oxaloacetate reduction) and is still allosterically controlled by fructose-1,6-bisphosphate.