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J R Knowles

Publications and source records attributed to J R Knowles.

At least 127 records · Page 7Linked to original sources
PubMed1980

Direct observation of substrate distortion by triosephosphate isomerase using Fourier transform infrared spectroscopy.

The infrared spectrum of dihydroxyacetone phosphate bound to triosephosphate isomerase has been measured. There are two carbonyl bands corresponding to the bound substrate, with an intensity ratio of about 3:1. Relative to the carbonyl absorption of dihydroxyacetone phosphate in free solution, the major band is shifted by 19 cm-1 to 1713 cm-1, providing direct evidence of enzyme-induced distortion of the substrate. This strain is probably attributable to an enzymic electrophile that polarizes the carbonyl group of the substrate and thereby promotes catalysis.

Animals↗
PubMed1980

Stereochemical course of a phosphokinase using a chiral [18O]phosphorothioate. Comparison with the transfer of a chiral [16O,17O,18O]phosphoryl group.

Synthetic adenosine 5'-O-[3-18O,3-thio]triphosphate having the R configuration at the gamma-phosphorus has been used as a substrate in the reaction catalyzed by glycerol kinase. The product sn-glycerol 3-[18O]phosphorothioate has been isolated, and the configuration at phosphorus has been determined by ring closure to the two diastereoisomeric cyclic 2,3-phosphorothioates of sn-glycerol and analysis of the 18O content of each diastereoisomer. The structural identity of these diastereoisomers has been determined by correlation with one of the corresponding diastereoisomers of the cyclic 2,3-phosphorothioate of D-glycerate, whose crystal structure is reported here. From these experiments it is evident that glyc:rol kinase catalyzes the transfer of a thiophosphoryl group with inversion of the configuration at phosphorus, in gratifying agreement with the result from the transfer of a chiral [16O,17O,18O]phosphoryl group [Blättler, W. A., & Knowles, J. R. (1979) J. Am. Chem. Soc. 101, 510].

Adenosine Triphosphate↗
PubMed1979

Stereochemical course of phosphokinases. The use of adenosine [gamma-(S)-16O,17O,18O]triphosphate and the mechanistic consequences for the reactions catalyzed by glycerol kinase, hexokinase, pyruvate kinase, and acetate kinase.

We report the synthesis of adenosine [gamma-(S)-16O,17O,18O]triphosphate, an isotopically labeled species of ATP that is chiral at the gamma-phosphoryl group, the configuration of which has been confirmed by independent stereochemical analysis. This molecule has been used as a substrate in the reactions catalyzed by glycerol kinase and by acetate kinase. The resulting samples of isotopically labeled sn-glycerol 3-phosphate and of acetyl phosphate have been used as substrates in the alkaline phosphatase mediated transfer of the chiral phosphoryl groups to (S)-propane-1,2-diol, whence the configuration at phosphorus has been determined [Abbott, S. J., Jones, S. R., Weinman, S. A., & Knowles, J. R. (1978) J. Am. Chem. Soc. 100, 2558]. It is shown that glycerol kinase and acetate kinase (and, by virtue of an earlier correlation, pyruvate kinase and hexokinase) proceed by pathways that result in inversion of the configuration at phosphorus. The sterochemical approach provides an access to the otherwise cryptic events that are involved in phosphoryl-group transfer within the ternary complexes of these kinases and their substrates.

Acetate Kinase↗
PubMed1978

Retention of the oxygens at C-2 and C-3 of D-ribulose 1,5-bisphosphate in the reaction catalyzed by ribulose-1,5-bisphosphate carboxylase.

Ribulose-1,5-bisphosphate carboxylase catalyzes the conversion of D ribulose 1,5-bisphosphate and CO2 to 3-phospho-D-glycerate, with retention of the oxygen atoms at both C-2 and C-3 of the substrate. This observation is consistent with mechanistic pathways involving an enediol intermediate and eliminates suggested mechanisms that involve covalent intermediates between the enzyme and ribulose 1,5-bisphosphate in which the substrate oxygen at C-2 or C-3 is compulsorily lost.

Carboxy-Lyases↗
PubMed1978

Photoaffinity inhibition of dipeptide transport in Escherichia coli.

A dipeptide containing a nitrene precursor, glycyl-4-azido-2-nitro-L-phenylalanine, has been synthesized. This compound is a photoaffinity inhibitor of dipeptide transport in E. coli. In the dark, the dipeptide is a reversible inhibitor of glycylglycine uptake by live E. coli W cells. The 14C-labeled compound is a substrate for the transport system, with a Km of 7 micrometer and V max of 5 x 10(3) molecules cell-1 s-1 (compare 9 micrometer and 1 x 10(4) molecules cell-1 s-1, respectively, for the transport of glycylglycine under the same conditions). When intact E. coli cells are photolyzed at approximately 350 nm in the presence of the photolabile dipeptide, their ability to transport either glycylglycine or unphotolyzed glycyl-4-azido-2-nitro-L-phenylalanine is irreversibly inhibited, but their ability to transport arginine is unaffected. The presence of glycylglycine in the medium during photolysis protects the cells against the light-dependent inactivation of dipeptide transport.

Affinity Labels↗
PubMed1978

Critical ionization states in the reaction catalyzed by triosephosphate isomerase.

To allow the detailed interpretation of the pH dependences of the steady-state parameters for the reaction catalyzed by triosephosphate isomerase, three kinds of experiments have been performed. First, the value of kcat/Km for enzyme-catalyzed isomerization of the phosphonate analogue of D-glyceraldehyde 3-phosphate (2-hydroxy-4-phosphonobutyraldehyde) has been shown to titrate with an apparent pKa of 7.5, which is close to the phosphonate's second ionization constant. Secondly, the sulfate ester analogue of dihydroxyacetone phosphate (dihydroxyacetone sulfate), which exists only as a monoanion over the pH range of interest, has been shown not to bind detectably to the enzyme. Thirdly, an isotopic discrimination experiment at pH 5.2 has been compared with a similar investigation at pH 7.6. The results together demonstrate that both enzyme and substrate ionizations control the reaction rate in the pH range 5 to 8.

Animals↗
PubMed1978

Photogenerated reagents for membrane labeling. 1. Phenylnitrene formed within the lipid bilayer.

Phenylnitrene generated photochemically from phenyl azide that is bound to artificial phospholipid vesicles labels the fatty acid chains of the lipids in low yield. The labeling yield varies from approximately 3.3% with soybean lecithin (which is highly unsaturated) to approximately 0.25% with dimyristoyllecithin (which is completely saturated). Labeling is largely eliminated by reduced glutathione in the aqueous phase. Nitrenes are evidently unsatisfactory reagents for the labeling either of lipids or by analogy of the hydrophobic portions of membrane proteins. This is mainly because the long lifetimes and electrophilic character of nitrenes will lead to the preferential labeling of extrinsic membrane components. Phenyl azide itself is further compromised as a lipophilic reagent by its rather low partition coefficient into lipid bilayers, as measured by equilibrium dialysis.

Azides↗
PubMed1978

Photogenerated reagents for membrane labeling. 2. Phenylcarbene and adamantylidene formed within the lipid bilayer.

Phenylcarbene and adamantylidene have been generated photochemically from the corresponding diazirines within lipid bilayers. Reasonable yields of labeled fatty acid side chains have been observed. The products have been characterized by gas chromatography-mass spectrometry and derive both from the insertion of the carbene into carbon-hydrogen bonds of saturated fatty acids and from the addition of the carbene to the carbon-carbon double bonds of unsaturated fatty acids. In contrast to the results found using phenylnitrene, the lipid labeling by carbene is not reduced by the water-soluble scavenger glutath ione. Carbenes generated from diazirines are evidently superior reagents for the photolabeling of lipids and should be useful for identifying the intrinsic hydrophobic sections of membrane proteins.

Adamantane↗
PubMed1978

Kinetic studies on the inactivation of Escherichia coli RTEM beta-lactamase by clavulanic acid.

The kinetic details of the irreversible inactivation of the Escherichia coli RTEM beta-lactamase by clavulanic acid have been elucidated. Clavulanate is destroyed by the enzyme and simultaneously inhibits it by producing two catalytically inactive forms. One of these is transiently stable and decomposes to free enzyme (k = 3.8 X 10(-3) S-1), while the other corresponds to an irreversibly inactivated form. The transient complex is formed from the Michaelis complex at a rate (k approximately 3 X 10(-2) S-1) which is some threefold faster than the rate of formation of the irreversibly inactivated complex. The transient complex is, therefore, the principle enzyme form present after short time periods. In the presence of excess clavulanate, however, all the enzyme accumulates into the irreversibly inactivated form. The number of clavulanate turnovers that occur prior to complete enzyme inactivation is 115.

Anti-Bacterial Agents↗
PubMed1978

Chemical studies on the inactivation of Escherichia coli RTEM beta-lactamase by clavulanic acid.

Incubation of clavulanic acid with the beta-lactamase from Escherichia coli RTEM leads to enzyme-catalyzed depletion of clavulanic acid, to transient inhibition, and to irreversible inactivation of the enzyme. Both the transiently inhibited and the irreversibly inactivated species show a marked increase in the absorbance at 281 nm that is proportional to the decrease in enzyme activity. Hydroxylamine treatment of irreversibly inactivated enzyme restores about one-third of the catalytic activity, with a concomitant decrease in absorbance at 281 nm. Polyacrylamide isoelectric focusing of the irreversibly inactivated enzyme shows three bands of approximately equal intensity, different from native enzyme. Upon hydroxylamine treatment, one of the three bands disappears and now focuses identically with native enzyme. It is evident that the irreversible inactivation of enzyme by an excess of clavulanic acid generates three products, one of which can be reactivated by hydroxylamine.

Escherichia coli↗
PubMed1978

Adenosine 5'-O-([gamma-18O]gamma-thio)triphosphate chiral at the gamma-phosphorus: stereochemical consequences of reactions catalyzed by pyruvate kinase, glycerol kinase, and hexokinase.

The 2-[18O]phosphorothioate of D-glycerate, chiral at phosphorus, was prepared. The chiral phosphoryl group was transferred enzymically to ADP [by using enolase and pyruvate kinase (ATP:pyruvate 2-O-phosphotransferase; EC 2.7.1.40)] resulting in the synthesis of adenosine 5'-O-([gamma-18O],gamma-thio)triphosphate. This labeled ATP was used as a thiophosphoryl group donor in the reactions catalyzed by glycerol kinase (ATP:glycerol 3-phosphotransferase; EC 2.7.1.30) and by hexokinase (ATP:D-hexose 6-phosphotransferase; EC 2.7.1.1). The product from the latter (glucose 6-phosphorothioate) was converted enzymically into glycerol phosphorothioate. Determination of the relative configurations and diastereoisomeric purities of the samples of glycerol phosphorothioate demonstrates that all three phosphokinases (pyruvate kinase, glycerol kinase, and hexokinase) transfer the thiophosphoryl group with complete stereospecificity, and further shows that these reactions follow an identical stereochemical course.

Adenosine Triphosphate↗
PubMed1977

Affinity chromatography of aminoacyl-transfer ribonucleic acid synthetases. Small organic ligands.

The usefulness of affinity chromatography for the purification of aminoacyl-tRNA synthetases was explored by using column ligands derived from the corresponding amino acid and aminoalkyladenylate, a non-labile analogue of the aminoacyladenylate reaction intermediate. Four modes of attachment of the aminoalkyladenylate to Sepharose were studied. The interaction between amino acid derivatives and the corresponding aminoacyl-tRNA synthetases is too weak to allow their use as ligands for affinity chromatography. Attachment of the aminoalkyladenylate via the alpha-nitrogen atom of the amino acid or via C-8 of the nucleotide abolishes synthetase binding, and immobilization via the oxidized ribose ring is only marginally useful. However, attachment of the aminoalkyladenylate to the matrix via N-6 of the nucleotide allows strong and specific synthetase binding, and the use of such columns permits the isolation of homogeneous synthetase from crude mixtures. The effect of non-specific adsorption and the utility of pre-columns and of specific substrate elution are investigated and discussed.

Adenosine Monophosphate↗
PubMed1977

Affinity chromatography of aminoacyl-transfer ribonucleic acid synthetases. Cognate transfer ribonucleic acid as a ligand.

The use of tRNA affinity columns for the purification of aminoacyl-tRNA synthetases was investigated. A purification method for valyl-tRNA synthetase from Bacillus stearothermophilus is described that uses two affinity columns, one containing the pure cognate tRNA, and the other containing all tRNA species except the cognate tRNA. A method for the rapid preparation of the two columns was developed, which does not require prior isolation of cognate tRNA but makes use of the ability of the target synthetase to select its cognate tRNA. The usefulness of tRNA columns is compared with that of affinity columns derived from the aminoalkyladenylate reported in the preceding paper [Clarke & Knowles (1977) Biochem J. 167, 405-417].

Acylation↗
PubMed1977

Phosphoglycerate mutase from wheat germ: studies with isotopically labeled 3-phospho-D-glycerates showing that the catalyzed reaction is intramolecular. Appendix: phosphoglycerate mutase from wheat germ: isolation, crystallization, and properties.

The isomerization of 3-phospho-D-glycerate and 2-phospho-D-glycerate catalyzed by the cofactor-independent phosphoglycerate mutase from wheat germ (the isolation and crystallization of which is described in the Appendix) has been shown to be intramolecular by two methods. Mass-spectrometric analysis of the products from the isomerization of a mixture of 3-phospho-D-[2(-2)H]glycerate and 3-[18O]phospho-D-glycerate shows that there is no exchange of labeled phosphoryl group between carbon skeletons in the mutase-catalyzed reaction. Analysis of the products from the isomerization of a mixture of 3-phospho-D-[2(-2)H]glycerate and 3-[32p]phospho-D-glycerate by a method involving the kinetic discrimination between 2(-2)H and 2(-1)H species using the enolase isotope effect similarly shows that the wheat germ phosphoglycerate mutase mediates an intramolecular transfer of the phosphoryl group.

Adenosine Triphosphate↗