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R B Dunlap

Publications and source records attributed to R B Dunlap.

At least 55 records · Page 3Linked to original sources
PubMed1986

Evidence for the existence of covalent nucleotide-thymidylate synthase complexes, identification of site of attachment, and enhancement by folates.

The formation of covalent binary complexes of thymidylate synthase and its nucleotide substrate dUMP, product dTMP, and inhibitor, 5-fluorodeoxyuridylate (FdUMP) was investigated using the trichloroacetic acid precipitation method. It was observed that, in addition to FdUMP, both dUMP and dTMP were capable of covalent interactions with the enzyme in the absence of added folates. The presence of folate, dihydrofolate, or tetrahydrofolate (H4folate) was found to produce substantial enhancements in the covalent binding of both FdUMP and dUMP to the enzyme with H4folate being the most effective agent. Further, covalent binary complexes of the enzyme with the three radiolabeled nucleotides were isolated by trichloroacetic acid precipitation and subjected to CNBr cleavage. The active-site CNBr peptide was isolated by reverse phase high performance liquid chromatography, and the first five N-terminal amino acid residues were sequenced by the dansyl-Edman procedure. Each active site peptide obtained from the covalent binary complexes as well as that from the covalent inhibitory ternary complex formed from enzyme, FdUMP, and 5,10-methylene-H4folate exhibited an identical sequence of Ala-Leu-Pro-Pro-(X)-, and the 5th amino acid was found to be associated with radiolabeled nucleotide ligand. Dansyl-Edman sequence analysis of the active site CNBr peptide, derived from enzyme which had been treated with iodoacetic acid, gave a sequence of Ala-Leu-Pro-Pro-CmCys (where CmCys is carboxymethylcysteine), thus confirming the fact that the fifth residue from the N terminus is Cys-198. In all the cases, the active site Cys-198 residue was found to be covalently linked to the nucleotides. These results provide unequivocal proof that the covalent binary complexes of enzyme with dUMP and dTMP predicted in the catalytic reaction mechanism actually exist.

Deoxyuracil Nucleotides↗
PubMed1986

Synthesis and characterization of a selenium-containing substrate of alpha-chymotrypsin. Selenium-77 nuclear magnetic resonance observation of an acyl-alpha-chymotrypsin intermediate.

The selenium-containing ester p-nitrophenyl (phenylselenyl)acetate, C6H5SeCH2C(O)-OC6H4-p-(NO2), has been synthesized, characterized as a substrate for alpha-chymotrypsin (k2/KM = 15.2 X 10(3) M-1 s-1, KMapp = 5.16 X 10(-6) M, pH 7.77, 33% CH3CN, 25 degrees C), and shown to be an active-site titrant for the enzyme. A synthesis of the selenium-77 enriched p-nitrophenyl (phenylselenyl)acetate in 53% yield from 94.4% elemental selenium-77, followed by its reaction with alpha-chymotrypsin (pH 5.0, 0-3 degrees C), permitted the observation of the (phenylselenyl)acetyl-alpha-chymotrypsin reaction intermediate by selenium-77 NMR spectroscopy. This acyl-enzyme species had a chemical shift of 275.1 ppm relative to dimethyl selenide. Accompanying this resonance was a lower intensity, pH-dependent resonance that is assigned to (phenylselenyl)acetate on the basis of a pH titration of the model compound. Deacylation in the presence of hydrazine sulfate produced a resonance at 332.3 ppm in addition to the 302.2 ppm resonance of (phenylselenyl)acetate at pH 7.85. Denaturation of the acyl-enzyme resulted in a shift of the 275.1 ppm resonance to 334.6 ppm at pH 4.90, in good agreement with the selenium-77 chemical shift of the model compound, methyl (phenylselenyl)acetate, in CDCl3 (333.3 ppm). The large shielding observed for the native acyl-enzyme in comparison to the denatured species can be attributed to a resonance-perturbed ester linkage and/or steric compression at a nonbonding orbital of the selenium nucleus.

Animals↗
PubMed1986

Crystallization and crystallographic data for new forms of thymidylate synthase from Lactobacillus casei.

Several new crystal forms of thymidylate synthase (5,10-methlenetetrahydrofolate:dUMP C-methyltransferase; EC 2.1.1.45) were obtained by controlled pH change. In the crystals the dimeric molecule has a 2-fold symmetry axis coinciding with crystallographic symmetry. The crystals scatter to at least 2.7 A resolution in the synchrotron X-ray beam and appear to be suitable for high-resolution X-ray diffraction analysis. The crystals were successfully derivatized and preliminary results are reported for the covalent inhibitory ternary complex of thymidylate synthase, 5-fluoro-2'-deoxyuridylate and 5,10-methylenetetrahydrofolate.

Crystallography↗
PubMed1986

Trapping and partial characterization of an adduct postulated to be the covalent catalytic ternary complex of thymidylate synthase.

The proposed mechanism of action of thymidylate synthase envisages the formation of a covalent ternary complex of the enzyme with the substrate dUMP and the cofactor 5,10-methylenetetrahydrofolate (CH2H4folate). The proposed structure of this adduct has been based by analogy on that of the covalent inhibitory ternary complex thymidylate synthase-FdUMP-CH2H4folate. Our recent success in using the protein precipitant trichloroacetic acid to trap the latter complex and covalent binary complexes of the enzyme with FdUMP, dUMP, and dTMP led to the use of this technique in attempts to trap the transient putative covalent catalytic ternary complex. Experiments performed with [2-14C]dUMP and [3',5',7,9-3H]CH2H4folate show that both the substrate and the cofactor remained bound to the protein after precipitation with trichloroacetic acid. The trapped putative covalent catalytic complex was subjected to CNBr fragmentation, and the resulting peptides were fractionated by reverse-phase high-pressure liquid chromatography. The isolated active site peptide was shown to retain the two ligands and was further characterized by a limited sequence analysis using the dansyl Edman procedure. The inhibitory ternary complex, which was formed with [14C]FdUMP and [3H]CH2H4folate, served as a control. The active site peptide isolated from the CNBr-treated inhibitory ternary complex was also subjected to sequence analysis. The two peptides exhibited identical sequences for the first four residues from the N-terminus, Ala-Leu-Pro-Pro, and the fifth amino acid residue was found to be associated with the labeled nucleotides and the cofactor.(ABSTRACT TRUNCATED AT 250 WORDS)

Carbon Radioisotopes↗
PubMed1985

A nitrocellulose-filter assay for the binary complex of 5-fluorodeoxyuridylate and Lactobacillus casei thymidylate synthetase.

The interaction of 5-fluorodeoxyuridylate (FdUMP) with thymidylate synthetase to form a binary complex has been widely reported, yet previous attempts to detect this complex by nitrocellulose filtration have failed. In contrast, a nitrocellulose-filter-binding assay utilizing [6-3H]FdUMP which measures the interaction of the enzyme with the nucleotide is reported. Extensive washing of the nitrocellulose-filtered complex between FdUMP and the enzyme resulted in no loss of bound ligand. Following denaturation with trichloroacetic acid, intact complex was detected by nitrocellulose filtration. No binding was observed between 5-fluorodeoxyuridine and the enzyme or between FdUMP and the N-ethylmaleimide-modified enzyme. As measured by the nitrocellulose filtration method, at least a 600-fold excess of FdUMP to enzyme was required to achieve saturation. The stoichiometry of FdUMP bound to the enzyme detected at saturation was 0.5-0.6 for native samples. When identical samples were subjected to denaturation prior to filtration, the stoichiometry of nucleotide binding was 0.3-0.4.

Chemical Phenomena↗
PubMed1984

Isolation of the covalent binary complex of 5-fluorodeoxyuridylate and thymidylate synthetase by trichloroacetic acid precipitation.

Strong chemical evidence for the existence of a covalent binary complex between 5-fluorodeoxyuridylate and thymidylate synthetase was provided by the isolation of the complex by trichloroacetic acid precipitation. This result together with that of a control experiment with N-ethymaleimide inactivated thymidylate synthetase demonstrated that only nucleotide covalently bound to the protein survived repeated washings of the precipitate. Under the conditions used, a maximum binding stoichiometry of about 0.9 was obtained for the covalent binary complex, Kd = 1.1 X 10(-5) M. Also, a binding ratio of 1.7 was obtained for the methylenetetrahydrofolate-5-fluorodeoxyuridylate-thymidylate synthetase ternary complex.

Deoxyuracil Nucleotides↗
PubMed1984

Preparation of (-)-5,6,7,8-tetrahydrofolate using immobilized dihydrofolate reductase.

Dihydrofolate reductase from methotrexate-resistant Lactobacillus casei was immobilized on carbodiimide-activated CH-Sepharose. The immobilized enzyme was utilized in the synthesis of (-)-5,6,7,8-tetrahydrofolate from dihydrofolate and NADPH in a batchwise reaction system. The products of the reaction, (-)-tetrahydrofolate and NADP+, were separated on a Sephadex G-10 column equilibrated with 50 mM NH4HCO3 containing beta-mercaptoethanol and ethanol. The tetrahydrofolate was then characterized by ultraviolet and circular dichroic spectra and its reactivity as a cofactor in the thymidylate synthetase reaction.

Bacterial Proteins↗
PubMed1983

Correction for light absorption in fluorescence studies of protein-ligand interactions.

It is shown that absorption of the excitation light can lead to substantial systematic errors in fluorescence measurements of equilibrium constants for formation of protein-ligand complexes. The assumptions about the optical arrangement of the fluorescence spectrometer involved in the calculation of the correction of this absorption are discussed. A general semiempirical correction procedure which can be used for (calculated) absorbance values as high as 5 is described. The importance of choosing the excitation wavelength so as to minimize the necessity for these corrections is emphasized.

Ligands↗
PubMed1982

Carbon 13 nuclear magnetic resonance studies of Lactobacillus casei thymidylate synthetase containing biosynthetically incorporated [guanidino-13C]arginine.

Thymidylate synthetase, containing [guanidino-13C]arginine, was obtained from amethopterin-resistant Lactobacillus casei grown on a defined medium containing [guanidino-13C]arginine. Carbon 13 nuclear magnetic resonance spectroscopy was used to investigate the native enzyme and the response of 13C-enriched arginyl residues to binary and ternary complex formation and to chemical modification by 2,3-butanedione. Native enzyme exhibited four resonances (A, 158.3 ppm; B, 157.4 ppm; C, 156.9 ppm; and D, 156.1 ppm) in a chemical shift range of 2.2 ppm. The 12 arginyl residues per subunit of this enzyme were found in a 1:5:5:1 distribution in the four resonances. Carbon 13 NMR spectra revealed that of the four resonances, resonance C was most perturbed by binary and ternary complex formation. The ternary complex formed with [guanidino-13C]arginine-enriched enzyme, 5-fluoro-deoxyuridylate, and 5,10-methylenetetrahydrofolate exhibited two new resonances at 157.9 and 156.5 ppm. Carbon 13 NMR analysis of enzyme inactivated with butanedione yielded three new single-carbon resonances, one from resonance B and two from resonance C, demonstrating that three arginyl residues per subunit were derivatized. The results of the binary and ternary complex studies and the chemical modification experiment suggest that the active site arginyl residue is represented in resonance C of the native enzyme.

Arginine↗
PubMed1982

Demonstration of the feasibility of observing nuclear magnetic resonance signals of 77Se covalently attached to proteins.

Previous 77Se NMR relaxation time studies established the utility of 77Se NMR spectroscopy in studying low molecular weight (less than 500) selenium-containing molecules. Since the spin rotation and chemical shift anisotrophy mechanisms contributed significantly to the 77Se spin-lattice relaxation in these compounds, it was questionable as to whether the latter mechanism would be efficient enough to enable 77Se resonances to be observed in a reasonable period in high molecular weight selenobiomolecules. Thus, to address this problem, disulfide bonds of ribonuclease-A and lysozyme were reductively cleaved under denaturing conditions, and the resulting 7-8 sulfhydryl groups were treated with a new sulfhydryl group reagent containing selenium, 6,6'-diselenobis(3-nitrobenzoic acid), to give proteins containing covalently attached selenium in the form of selenenyl sulfides. The observation of high resolution 77Se NMR spectra of these proteins under denaturing conditions was accomplished. Five to six 77Se NMR resonances, which fell in a chemical shift range of 14-15 ppm, were observed for each protein and are compared to the chemical shifts of several model selenenyl sulfides derived from cysteine.

Dithionitrobenzoic Acid↗
PubMed1982

Modification of tyrosine residues in dihydrofolate reductase from Lactobacillus casei.

Dihydrofolate reductase from Lactobacillus casei was inactivated by reaction with tetranitromethane and 7-chloro-4-nitrobenzo-2-oxa-1,3-diazole. Loss of activity occurred with modification of four of the five tyrosine residues present in the enzyme. The presence of either substrate, NADPH or 7,8-dihydrofolate, as well as NADP and folate, provided extensive protection against inactivation, while NADH and tetrahydrofolate exhibited none. This protection from inactivation occurred on protection of two of the four susceptible tyrosines from modification. Nitration of the enzyme adversely affected its ability to bind substrates. Restoration of the pKa of the nitrated tyrosines by reduction of the nitro group to an amino group did not result in a regeneration of enzymatic activity. However, fluorotyrosine-containing enzyme, prepared by growing the bacterium in the presence of fluorotyrosine, exhibited specific activity identical to that of native enzyme over the pH range of 4.5-8. These results suggest that inactivation of dihydrofolate reductase by tyrosine modification occurs primarily due to a steric effect and that the active site tyrosines may participate in substrate binding.

4-Chloro-7-nitrobenzofurazan↗
PubMed1981

Light spectroscopic studies of the binary complex of Lactobacillus casei thymidylate synthetase and 5-fluoro-2'-deoxyuridylate.

In contrast to previous reports, fluorescence and ultraviolet difference spectroscopy are shown to reflect the interaction of the inhibitor, 5-fluoro-2'-deoxyuridylate, with thymidylate synthetase isolated from amethopterin-resistant Lactobacillus casei. Analysis of the quenching of protein fluorescence upon nucleotide binding yields a value of 2.1 X 10(5) M-1 for the association constant for binary complex formation. The ultraviolet difference spectrum for the nucleotide-enzyme complex exhibited a broad trough with the greatest loss of absorbance centered at 275 nm. Results of previous circular dichroic studies of nucleotide-enzyme binary complexes showed apparently parallel changes in ellipticity in the 267-269-nm and 290-nm regions, which were interpreted to reflect coordinated alteration in nucleotide and enzyme structure, respectively. When examined by difference circular dichroic spectroscopy, the nucleotide-enzyme interaction is accompanied by a substantial loss in ellipticity from 250 to 300 nm which is greatest at 280 nm. We interpret the results obtained from the three light spectroscopic techniques as indications of subtle alterations in the environments of certain tyrosine and tryptophan residues in the enzyme which are caused by the association of 5-fluoro-2'-deoxyuridylate with the enzyme.

Circular Dichroism↗
PubMed1981

Fluorine-19 nuclear magnetic resonance characterization of ternary complexes of folate derivatives, 5-fluorodeoxyuridylate and Lactobacillus.

Numerous biochemical techniques have been employed to characterize the covalent inhibitory ternary complex of thymidylate synthetase consisting of enzyme, 5-fluorodeoxyuridylate, and 5,10-methylenetetrahydrofolate. 19F NMR studies of this covalent ternary complex reveal a single, broad resonance centered at 12.7 ppm to higher shielding of free nucleotide, while the 5-fluorodexyuridylate-enzyme binary complex exhibits two resonances to higher shielding of free nucleotide, one at 1.4 ppm representing noncovalently bound ligand and the other at 34.5 ppm indicative of covalently bound 5,6-dihydro-5-fluorodeoxyuridylate. In order to follow the transformation of the latter binary complex to a ternary complex, we have employed 19F NMR to profile changes in the environment of the nucleotide which result from the interaction of folates with the coenzyme binding site. At low molar excesses of folates (5-fold), the effects observed in the 19F NMR spectrum fall into three major classes. (1) 5-Methyltetrahydrofolate exhibited a weak interaction with the binary complex. (2) Methotrexate and aminopterin, antifolate drugs, were observed to increase the exchange rate among the species detected in the 19F NMR spectrum of the binary complex. (3) Folate, dihydrofolate, and a series of tetrahydrofolate derivatives were found to shift the equilibrium of the binary complex toward the covalent 5,6-dihydro-5-fluorodeoxyuridylate-enzyme complex. With the latter folates the chemical shifts for the covalent species of these ternary complexes were found in the range of 35-40 ppm to higher shielding and are interpreted to reflect subtle differences in the strength and steric nature of the interaction of the folate ligand with the binary complex. These data illustrate that the latter folates promote the conversion of the enzyme-bound nucleotide to a species which would be poised to form the second covalent bond of the ternary complex, namely the linkage of the methylene group of the coenzyme with carbon 5 of the nucleotide.

Aminopterin↗