Biomedical subjects

J R Knowles

Publications and source records attributed to J R Knowles.

At least 91 records · Page 5Linked to original sources

PubMed1985

Phosphoenolpyruvate synthetase and pyruvate, orthophosphate dikinase: stereochemical consequences at both the beta-phospho and gamma-phospho groups of ATP.

[(R)-16O,17O,18O]Phosphoenolpyruvate and adenosine 5'-O-[(gamma S)-beta gamma-17O,gamma-17O,18O](3-thiotriphosphate) have been synthesized and used to determine the stereochemical course of the several displacements at phosphorus catalyzed by phosphoenolpyruvate synthetase and by pyruvate, orthophosphate dikinase, two enzymes that catalyze the formation of phosphoenolpyruvate from pyruvate and ATP. The catalytic mechanisms for each of these enzymes are believed to involve both phospho- and pyrophospho-enzyme intermediates. The stereochemical results are entirely in accord with these pathways: the beta-phospho group of ATP suffers overall retention of configuration that is presumably the consequence of two displacements with inversion, and the gamma-phospho group of ATP gamma S suffers inversion of configuration that is most probably the consequence of a single displacement at this center.

Adenosine Triphosphate↗

PubMed1985

Active site of triosephosphate isomerase: in vitro mutagenesis and characterization of an altered enzyme.

We have replaced the glutamic acid-165 at the active site of chicken triosephosphate isomerase with an aspartic acid residue using site-directed mutagenesis. Expression of the mutant protein in a strain of Escherichia coli that lacks the bacterial isomerase results in a complementation phenotype that is intermediate between strains that have no isomerase and strains that produce either the wild-type chicken enzyme or the native E. coli isomerase. The value of kcat for the purified mutant enzyme when glyceraldehyde 3-phosphate is the substrate is 1/1500th that of the wild-type enzyme, and the Km is decreased by a factor of 3.6. With dihydroxyacetone phosphate as substrate, the kcat value is 1/240th that of the wild-type enzyme, and Km is 2 times higher. The value of Ki for a competitive inhibitor, phosphoglycolate, is the same for the mutant and wild-type enzymes, at 2 X 10(-5) M. By treating the enzyme-catalyzed isomerization as a simple three step process and assuming that substrate binding is diffusion limited, it is evident that the mutation of glutamic acid-165 to aspartic acid principally affects the free energy of the transition state(s) for the catalytic reaction itself.

Animals↗

PubMed1984

Penicillanic acid sulfone: nature of irreversible inactivation of RTEM beta-lactamase from Escherichia coli.

When penicillanic acid sulfone in large molar excess is incubated with the RTEM beta-lactamase, the enzyme becomes inactivated irreversibly. From studies of the consequential spectroscopic changes, from the use of specifically tritiated penicillanic acid sulfone, and from comparison by isoelectric focusing of the enzyme after inactivation by the sulfone and by clavulanic acid, the inactivated enzyme appears to be cross-linked by a beta-aminoacrylate fragment deriving from C-5, C-6, and C-7 of the original beta-lactam. Model studies on the behavior of alcoholic solutions of penicillanic acid sulfone in the presence of amines are entirely consistent with this interpretation.

Chemical Phenomena↗

PubMed1984

6-(Methoxymethylene)penicillanic acid: inactivator of RTEM beta-lactamase from Escherichia coli.

The Z and E isomers of 6-(methoxymethylene)-penicillanic acid have been synthesized, and their interaction with the RTEM beta-lactamase has been studied. The Z isomer is an inhibitor and an inactivator of the enzyme, and there is some similarity between its behavior and that of other mechanism-based inactivators such as clavulanic acid and the penam sulfones. Kinetic analysis of the interaction of the enzyme with the Z isomer has allowed a detailed evaluation of the factors that are important in the design of anti-beta-lactamase agents. In contrast to the Z compound, the E isomer of 6-(methoxymethylene)penicillanic acid is not a substrate, an inhibitor, or an inactivator of the enzyme.

Binding, Competitive↗

PubMed1984

3-Deoxy-D-arabino-heptulosonic acid 7-phosphate: chemical synthesis and isolation from Escherichia coli auxotrophs.

A new chemical synthesis of 3-deoxy-D-arabino-heptulosonic acid 7-phosphate is described and contrasted to isolation of the same molecule from the growth medium of several different auxotrophic strains of Escherichia coli. The higher yielding chemical synthesis begins with 2-deoxyglucose while the less time-intensive biological approach proceeds directly from glucose. Growth and accumulation aspects of whole cell biological synthesis are discussed along with various aspects of the biological purification protocol. Both approaches can be utilized to produce substantial quantities of methyl (methyl 3-deoxy-D-arabino-heptulopyranosid)onate, a key intermediate for semisynthetic 3-deoxy-D-arabino-heptulosonic acid 7-phosphate and a number of its derivatives.

Deoxyglucose↗

PubMed1984

Dehydroquinate synthase from Escherichia coli: purification, cloning, and construction of overproducers of the enzyme.

Dehydroquinate synthase has been purified 9000-fold from Escherichia coli K-12 (strain MM294). The synthase is encoded by the aroB gene, which is carried by plasmid pLC29-47 from the Carbon-Clarke library. Construction of an appropriate host bearing pLC29-47 results in a strain that produces 20 times more enzyme than strain MM294. Subcloning of the aroB gene behind a tac promoter results in E. coli transformants that produce 1000 times more enzyme than MM294: the synthase constitutes 5% of the soluble protein of the cell. A laborious isolation from 50 g of wild-type E. coli cells yields 80 micrograms of impure enzyme, whereas 50 g of cells containing the subcloned gene yields 150 mg of homogeneous enzyme in a two-column purification. Dehydroquinate synthase is a monomeric protein of Mr 40 000-44 000. The chromosomal enzyme from E. coli K-12, the cloned enzyme encoded by the plasmid pLC29-47, and the subcloned inducible enzyme encoded by pJB14 all comigrate on polyacrylamide gel electrophoresis under denaturing conditions.

Chromatography, Gel↗

PubMed1984

The role of the beta-lactamase signal sequence in the secretion of proteins by Escherichia coli.

A derivative of pBR322 has been constructed that contains both a unique EcoRI restriction site right at the beginning of the signal codons of the beta-lactamase (bla) gene and a unique BstEII site just at the end of the bla signal codons. Although the signal peptide encoded by the new plasmid differs from the wild type (pBR322) by 2 amino acid residues (Ser 2 to Arg 2 and Ala 23 to Gly 23), the synthesis, transport, and processing of the beta-lactamase remain unchanged in Escherichia coli. Two deletion mutants, in which the bla signal codons have been almost completely excised, have also been constructed. Bacteria containing either of these plasmids produce, but do not secrete, an active beta-lactamase. Last, the bla signal codons have been precisely joined to the cDNA version of the triose phosphate isomerase (tpi) gene from chicken. Expression of this fusion gene in E. coli gives a hybrid protein that is neither secreted into the periplasm nor proteolytically processed. This result supports the view that there are characteristics of the mature protein that are necessary for the secretion across the inner membrane of E. coli.

Amino Acid Sequence↗

PubMed1984

Stereochemical course of phospho group transfer by human prostatic acid phosphatase.

The stereochemical course of the phospho transfer catalyzed by homogeneous human prostatic acid phosphatase was investigated using 31P nuclear magnetic resonance spectroscopy. Transphosphorylation from phenyl-(R)-[15O, 17O, 18O]phosphate to (S)-propane-1,2-diol occurs with overall retention of configuration at phosphorus. This stereochemical result is consistent with the interpretation that the hydrolysis of substrates by this enzyme proceeds by way of a covalent phosphoenzyme intermediate. Conditions for optimizing phospho transfer by this and related acid phosphatases have also been explored.

Acid Phosphatase↗

PubMed1984

Correlation of the effect of beta-lactamase inhibitors on the beta-lactamase in growing cultures of gram-negative bacteria with their effect on the isolated beta-lactamase.

The effectiveness of clavulanic acid, sulbactam, quinacillin sulfone, and the carbapenems MM13902 and MM4550 as inhibitors of TEM-2 beta-lactamase in growing cultures of gram-negative bacteria has been studied. Each of these beta-lactams inhibited the enzyme in intact cells, and the nature of the inhibition correlated with studies on the purified enzyme. The potency of these compounds as inhibitors of the beta-lactamase in vivo can be correlated with the amounts hydrolyzed by the purified enzyme under saturating conditions during the inhibition of the enzyme in vitro.

Ampicillin↗

PubMed1983

Secondary tritium isotope effects as probes of the enzymic and nonenzymic conversion of chorismate to prephenate.

To obtain information about the degree of concert of both the nonenzymic and the enzyme-catalyzed rearrangement of chorismate to prephenate, we have determined the secondary tritium isotope effects at the bond-making position (C-9) and the bond-breaking position (C-5) of chorismate. The isotope effects were determined by the competitive method, using either [5-3H,7-14C )chorismate or [9-3H,7-14C]chorismate as the substrate. In the nonenzymic reaction (pH 7.5, 60 degrees C), KH/kT is 1.149 +/- 0.012 for bond breaking (C-9) and 0.992 +/- 0.012 for bond making (C-5). This indicates an asymmetric transition state in which the new bond is hardly, if at all, formed, while the bond between C-5 and oxygen is substantially broken. In the enzymic reaction (pH 7.5, 30 degrees C), the values of kH/kT in both positions are unity within experimental error. It is most likely that the isotope effects are suppressed in the enzymic process and that the rate-limiting transition state occurs before the rearrangement itself. The kinetically significant transition state presumably involves either the binding step of the small equilibrium proportion of the axial conformer of the substrate or an isomerization of enzyme-bound chorismate from the more stable conformer in which the carboxyvinyloxy group is equatorial to that in which this group is axial. Rearrangement would then proceed relatively rapidly from the higher energy axial conformer.

3-Phosphoshikimate 1-Carboxyvinyltransferase↗

PubMed1983

Polarization of substrate carbonyl groups by yeast aldolase: investigation by Fourier transform infrared spectroscopy.

The infrared spectrum of the complex of D-fructose 1,6-bisphosphate bound to yeast aldolase displays three spectral features between 1700 and 1800 cm-1. One of these (at 1730 cm-1) corresponds to the carbonyl group of enzyme-bound D-fructose 1,6-bisphosphate and/or dihydroxyacetone phosphate. The frequency of this band, which is unaffected by the removal of the intrinsic zinc ion from the enzyme, demonstrates that this carbonyl group is not significantly polarized when the substrate binds to the enzyme. In contrast, the spectral band assigned to the carbonyl group of enzyme-bound D-glyceraldehyde 3-phosphate (at 1706 cm-1) appears at a frequency 24 cm-1 lower than when this substrate is in aqueous solution. This shift indicates considerable polarization of the carbonyl group when D-glyceraldehyde 3-phosphate is bound at the active site. The third spectral feature (at 1748 cm-1), which is observed only in the presence of potassium ion, probably corresponds to an enzymic carboxyl group in a nonpolar environment.

Chemical Phenomena↗

PubMed1983

Role of mono- and divalent metal cations in the catalysis by yeast aldolase.

The rate of deuterium exchange between [1-(S)-2H]dihydroxyacetone 3-phosphate and the solvent catalyzed by native and metal-substituted yeast aldolases has been measured. In the presence of 0.1 M potassium acetate at 15 degrees C, pH 7.3, the deuterium exchange reaction catalyzed by native yeast aldolase has a kcat of 95 s-1. In contrast to the 7-fold activity enhancement by 0.1 M potassium ion (relative to 0.1 M sodium ion) of the cleavage of D-fructose 1,6-bisphosphate catalyzed by native yeast aldolase, a negligible (1.1-fold) activation by 0.1 M potassium ion is observed in the rate of dedeuteration of [1(S)-2H]dihydroxyacetone 3-phosphate. The order of reactivity of the yeast metalloaldolases in the deuterium exchange roughly parallels that seen in the fructose bisphosphate cleavage reaction. These findings suggest that the carbonyl groups of enzyme-bound D-fructose 1,6-bisphosphate and dihydroxyacetone phosphate are both polarized by the active site divalent metal cation. A mechanistic formulation consistent with the results of this and the previous paper is presented.

Deuterium↗

PubMed1982

The stereochemical course at phosphorus of the reaction catalyzed by phosphoenolpyruvate carboxylase.

[(S)-16O,17O]Thiophosphoenolpyruvate has been used as a substrate in H218O for the reaction catalyzed by phosphoenolpyruvate carboxylase, and the absolute configuration of the product, inorganic [16O,17O,18O]thiophosphate, has been determined. The reaction proceeds with inversion of configuration at phosphorus, thus ruling out the cyclic mechanism that has been proposed for this enzyme. The stereochemical result is consistent with a stepwise mechanism involving the intermediate formation of carboxyphosphate.

Carboxy-Lyases↗

PubMed1982

Pyruvate kinase: is the mechanism of phospho transfer associative or dissociative?

To test for the possibility that pyruvate kinase proceeds via a dissociative path, we have investigated whether the complex enzyme . ADP . metaphosphate is transiently formed from the complex enzyme . ATP. It is shown that when highly purified pyruvate kinase is used, the rate of positional oxygen isotope exchange in ATP (beta, gamma bridge and beta nonbridge) is about 10(4) times slower in the absence of the cosubstrate pyruvate than it is in the presence of pyruvate. Further, the rate of racemization of the gamma-phospho group of [gamma (S)-16O,17O,18O]-ATP is undetectable, being at least 30 times slower even than the rate of positional isotope exchange. These tests thus provide no evidence that pyruvate kinase follows a dissociative mechanism. Indeed, it is argued that the available data are more consistent with an associative path. Evidence is presented that the single, associative, transition state is symmetrical, in which bond making and bond breaking processes are rather precisely balanced.

Adenosine Diphosphate↗

PubMed1982

Ribulose-1,5-bisphosphate carboxylase: enzyme-catalyzed appearance of solvent tritium at carbon 3 of ribulose 1,5-bisphosphate reisolated after partial reaction.

When ribulose 1,5-bisphosphate is allowed to react with carbon dioxide in tritiated water in the carboxylation reaction catalyzed by ribulose-1,5-bisphosphate carboxylase from Rhodospirillum rubrum, the ribulose 1,5-bisphosphate reisolated after partial reaction is found to be labeled. The specific radioactivity of the remaining substrate pool rises during the course of the reaction. Experiments in deuterium oxide show that the isotopic label resides on carbon 3. Earlier failures to detect this exchange process probably derive from the use of enzyme that was, in the absence of carbon dioxide, inactive. The present results provide direct evidence for the intermediacy of the enediol between C-2 and C-3 of ribulose 1,5-bisphosphate and show that the enolization step is at least partially rate limiting in the overall carboxylase reaction. The specific radioactivity of the product 3-phospho-D-glycerate remains constant throughout the course of the reaction at about one-sixth that of the solvent. This strengthens the argument against the involvement of "sticky" protons in the reaction.

Carbon↗

PubMed1982

Ribulose-1,5-bisphosphate carboxylase: fate of the tritium label in [3]3H]ribulose 1,5-bisphosphate during the enzyme-catalyzed reaction.

The reaction of [3-3H]ribulose 1,5-bisphosphate and CO2 with ribulose-1,5-bisphosphate carboxylase has been investigated in order to provide information about the early steps of the enzyme-catalyzed reaction. The specific radioactivity of ribulose 1,5-bisphosphate reisolated after partial reaction rises as the reaction proceeds, demonstrating that the isotopic discrimination (which results in the preferential consumption of unlabeled substrate) is more important than the equilibration of the hydrogen on C-3 with solvent protons. These data confirm the existence of the enediol intermediate and set limits on the range of permissible free-energy levels that there is a rather fine balance among the three critical transition states for this reaction (those of enolization, condensation of the enediol with CO2, and solvent exchange of the C-3 proton).

Carbon Dioxide↗

PubMed1982

Ribulose-1,5-bisphosphate carboxylase: primary deuterium kinetic isotope effect using [3-2H]ribulose 1,5-bisphosphate.

The primary deuterium kinetic isotope effect for the reaction of [3-2H]ribulose 1,5-bisphosphate with CO2 in the reaction catalyzed by ribulose-1,5-bisphosphate carboxylase has been determined. By use of highly purified substrates containing less than 0.13% of the C-3 epimer xylulose 1,5-bisphosphate (this material is known to be a potent competitive inhibitor), the kinetic isotope effect has been shown to be 1.2 +/- 0.2 (Vmax) and 1.3 +/- 0.3 (Vmax/Km). These values are clearly too small to be intrinsic isotope effects for the rate-limiting removal of the C-3 proton from ribulose 1,5-bisphosphate. The results confirm the conclusions from the tritium experiments reported in the previous two papers and emphasize the fine balance between the forward and reverse reactions of the enediol intermediate.

Carbon Dioxide↗

PubMed1982

Stereochemical course of the reactions catalyzed by the bacterial phosphoenolpyruvate:glucose phosphotransferase system.

The overall stereochemical course of the reactions leading to the phosphorylation of methyl alpha-D-glucopyranoside by the glucose-specific enzyme II (enzyme IIGlc) of the Escherichia coli phosphotransferase system has been investigated. With [(R)-16O,17O,18O]phosphoenolpyruvate as the phosphoryl donor and in the presence of enzyme I, HPr, and enzyme IIIGlc of the phosphotransferase system, membranes from E. coli containing enzyme IIGlc catalyzed the formation of methyl alpha-D-glucopyranoside 6-phosphate with overall inversion of the configuration at phosphorus (with respect to phosphoenolpyruvate). It has previously been shown that sequential covalent transfer of the phosphoryl group of phosphoenolpyruvate to enzyme I, to HPr, and to enzyme IIIGlc occurs before the final transfer from phospho-enzyme IIIGlc to the sugar, catalyzed by enzyme IIGlc. Because overall inversion of the configuration of the chiral phospho group of phosphoenolpyruvate implies an odd number of transfer steps, the phospho group has been transferred at least five times, and transfer from phospho-enzyme IIIGlc to the sugar must occur in two steps (or a multiple thereof). On the basis that no membrane protein other than enzyme IIGlc is directly involved in the final phospho transfer steps, our results imply that a covalent phospho-enzyme IIGlc is an intermediate during transport and phosphorylation of glucose by the E. coli phosphotransferase system.

Biological Transport↗