Pre-steady-state properties of bovine heart mitochondrial ATPase: a nucleotide-dependent H+ burst.

The transient kinetics of bovine heart mitochondrial ATPase (F1) depleted of loosely bound nucleotides were observed. The activation process which was shown as a lag time before steady-state hydrolysis observed previously (Clark et al. (1984) Arch. Biochem. Biophys. 233, 378-392) was preceded by a proton burst when F1 was stripped of its loose nucleotides. 5'-Adenylylimidodiphosphate (Ado PP[NH]P) or MgATP binding is shown to cause proton release. maximum proton release per F1 free of loosely bound nucleotides is observed with MgATP. Modification with NBD-CL of F1 that was nucleotide-depleted eliminated the proton burst, which suggests that the modified tyrosine (i.e., in the catalytic subunit) is directly involved in the release of protons.

Regulation of rat liver 4-hydroxy-2-ketoglutarate aldolase.

The possibility is examined that 4-hydroxy-2-ketoglutarate aldolase (4-hydroxy-2-ketoglutarate glyoxylatelyase, EC 4.1.3.16), the last step in hydroxyproline catabolism is regulated by intermediates of gluconeogenesis. Inhibition of isolated 4-hydoxy-2-ketoglutarate aldolase was examined using dual inhibition studies. It was found that the enzyme exhibits synergistic inhibition by oxaloacetate and pyruvate, but only when the substrate concentration is low. At substrate concentrations approaching saturation, the inhibition by the oxaloacetate and pyruvate becomes additive. These results are discussed in terms of possible control of the use of carbon from hydroxyproline breakdown in glucose production.

Histidine-49 is necessary for the pH-dependent transition between active and inactive states of the bovine F1-ATPase inhibitor protein.

The role of the histidyl residue at position 49 (H49) of the bovine mitochondrial F1-ATPase inhibitor protein (F1I) was examined by site-directed mutagenesis. Six amino acids (Q, E, K, V, L, and I) were substituted for H49 and the activities of the resulting inhibitor proteins were characterized with respect to pH. Each of the six mutations abolished the pH sensitivity which is characteristic of wild-type F1I. At pH 8.0 each of the mutations caused an increase in apparent maximum inhibition and a decrease in apparent Ki relative to wild type. At pH 6.7 the hydrophilic substitutions had little effect on apparent Ki, while the hydrophobic substitutions caused increases of 3.5- to 8.5-fold relative to wild type. The ratios of apparent Ki at pH 8.0 to apparent Ki at pH 6.7 were in the range of 0.5 to 1.6 for the mutants, whereas the wild-type value is 15.0. The mutations appear to shift the equilibrium between active and inactive conformations of F1I toward the active state. We find that H49 is required by F1I for sensitivity to pH and that it may facilitate the transition between active and inactive states of F1I. A possible role for H49 in the stabilization of the inactive state through participation in a multivalent complex with Zn2+ is also discussed.

An alternative mechanism for the nitrogen transfer reaction in asparagine synthetase.

In the absence of crystallographic data, the mechanism of nitrogen transfer from glutamine in asparagine synthetase (AS) remains under active investigation. Surprisingly, the glutamine-dependent AS from Escherichia coli (AsnB) appears to lack a conserved histidine residue, necessary for nitrogen transfer if the reaction proceeds by the accepted pathway in other glutamine amidotransferases, but retains the ability to synthesize asparagine. We propose an alternative mechanism for nitrogen transfer in AsnB which obviates the requirement for participation of histidine in this step. Our hypothesis may also be more generally applicable to other glutamine-dependent amidotransferases.

Immunoaffinity chromatography utilizing monoclonal antibodies. Factors which influence antigen-binding capacity.

Differences in antigen-binding capacity of a monoclonal antibody coupled to Sepharose under varying conditions were explored. The extent of cyanogen bromide activation, and the pH of the coupling reaction had a profound effect upon the rate of antibody coupling, but only small differences in antigen-binding capacity were observed if the antibody coupling reaction was terminated when 80-90% of the antibody was covalently coupled to Sepharose. However, if antibody was incubated with activated resin until 100% coupling was attained, the antigen-binding capacity of the resulting immunoadsorbent decreased significantly. Monoclonal antibody coupled to Sepharose via an N-hydroxysuccinimide ester linkage and approximately half the antigen-binding capacity of antibody coupled by CNBr activation. Concentrations of monoclonal antibodies as high as 13 mg/ml of packed resin could be used without noticeable steric hindrance.

Analysis of expressed sequence tags from Plasmodium falciparum.

An initiative was undertaken to sequence all genes of the human malaria parasite Plasmodium falciparum in an effort to gain a better understanding at the molecular level of the parasite that inflicts much suffering in the developing world. 550 random complimentary DNA clones were partially sequenced from the intraerythrocytic form of the parasite as one of the approaches to analyze the transcribed sequences of its genome. The sequences, after editing, generated 389 expressed sequence tag sites and over 105 kb of DNA sequences. About 32% of these clones showed significant homology with other genes in the database. These clones represent 340 new Plasmodium falciparum expressed sequence tags.

Current status of the Plasmodium falciparum genome project.

The Plasmodium falciparum Genome Project is a collaborative effort by many laboratories that will provide detailed molecular information about the parasite, which may be used for developing practical control measures. Initial goals are to prepare an electronically indexed clone bank containing partially sequenced clones representing up to 80% of the parasite's genes and to prepare an ordered set of overlapping clones spanning each of the parasite's 14 chromosomes. Currently, clones of genomic DNA, prepared as yeast artificial chromosomes, are arranged into contigs covering approximately 70% of the genome of parasite clone 3D7, gene sequence tags are available from more than contigs covering approximately 70% of the genome of parasite clone 3D7, gene sequence tags are available from more than 20% of the parasite's genes, and approximately 5% of the parasite's genes are tentatively identified from similarity searches of entries in the international sequence databases. A total of > 0.5 Mb of P. falciparum sequence tag data is available. The gene sequence tags are presently being used to complete YAC contig assembly and localize the cloned genes to positions on the physical map in preparation for sequencing the genome. Routes of access to project information and services are described.

Mapping the aspartic acid binding site of Escherichia coli asparagine synthetase B using substrate analogs.

Novel inhibitors of asparagine synthetase, that will lower circulating levels of blood asparagine, have considerable potential in developing new protocols for the treatment of acute lymphoblastic leukemia. We now report the indirect characterization of the aspartate binding site of Escherichia coli asparagine synthetase B (AS-B) using a number of stereochemically, and conformationally, defined aspartic acid analogs. Two compounds, prepared using novel reaction conditions for the stereospecific beta-functionalization of aspartic acid diesters, have been found to be competitive inhibitors with respect to aspartate in kinetic studies on AS-B. Chemical modification experiments employing [(fluorosulfonyl)benzoyl]adenosine (FSBA), an ATP analog, demonstrate that both inhibitors bind to the aspartate binding site of AS-B. Our results reveal that large steric alterations in the substrate are not tolerated by the enzyme, consistent with the failure of previous efforts to develop AS inhibitors using random screening approaches, and that all of the ionizable groups are placed in close proximity in the bound conformation of aspartate.

Comparison of glycine metabolism in mouse lymphoma cells either sensitive or resistant to L-asparaginase.

Previous work suggested a relationship between glycine metabolism and the effect of L-asparaginase upon tumor cells. Therefore, L5178Y (sensitive) or L5178Y/L-ASE (resistant) ascites lymphoma cells were incubated with 14C-labeled glyoxylate, glycine, serine, or asparagine, and the metabolism to other amino acids was measured by high performance liquid chromatography. Metabolic differences between the two cells lines were found. Under control conditions, the interconversion rate of glycine and serine via serine hydroxymethyltransferase (SHMT) was higher in sensitive than in resistant cells. The transformation rate of glyoxylate to serine was also higher in sensitive cells. These results may indicate a difference in the activity of SHMT. An alternate explanation would be that transport or diffusion of serine and glycine into sensitive cells is greater than into resistant cells. Several crucial metabolic differences were observed between the two cell types when L-asparaginase was added. A key difference is the decrease of glycine synthesis from glyoxylate observed in the sensitive cells compared to resistant cells which show no change. This suggests that asparagine is used for transamination of glyoxylate. Also, only sensitive cells appear to compensate for L-asparaginase-induced loss of glycine formation from glyoxylate by increasing glycine synthesis from serine. Alterations in sensitive tumor glycine metabolism may be an important function of L-asparaginase anticancer activity.

The effects of dietary amino acids on hepatic L-asparagine synthetase.

Rats were fed Roger's synthetic amino acid diets, complete or without asparagine, aspartate, or glutamate, for 2 weeks. Hepatic and serum amino acid content and hepatic asparagine synthetase were assayed before and after the test diets were administered. Special attention was paid to the multiple forms of asparagine synthetase present. Rats fed the test diet without asparagine exhibited high molecular weight (110,000) alpha-form and intermediate molecular weight (57,000) beta-form of asparagine synthetase. Rats fed the complete test diet and the test diet without asparatate exhibited only the beta-form of the enzyme. Rats fed the test diet without glutamate exhibited no enzyme activity. These data are related to the hepatic amino acid levels and to the role of asparagine and asparagine synthetase in amino acid homeostasis.

Methotrexate stimulation of asparagine synthetase activity in rat liver.

Methotrexate was found to stimulate asparagine synthetase activity in vivo by approximately six-fold in rat liver. The maximum effect of methotrexate on hepatic asparagine synthetase activity was observed sixteen hours after intraperitoneal injection of the drug. Cycloheximide, like methotrexate, is a protein synthesis inhibitor and was used to determine that asparagine synthetase activity was not preferentially stimulated under stress. As expected, hepatic asparagine synthetase activity falls markedly with the decreased protein synthesis caused by injection of cycloheximide. It is proposed that methotrexate inhibits serine-dependent glycine biosyn-thesis by decreasing the concentration of tetrahydrofolate for serine hydroxymethyltransferase. This leads to a stimulation of asparagine synthetase to provide nitrogen for asparagine-dependent glycine synthesis. This may provide an explanation of the observed chemotherapeutic synergism between asparaginase and methotrexate treatment.

Synthesis of gamma-monodentate and beta, gamma-bidentate CrITP. Isolation and characterization of the two chelation isomers and the individual diastereomers of beta, gamma-bidentate CrITP.

The two chelation isomers of CrITP, gamma-monodentate and beta, gamma-bidentate CrITP, as well as the diastereomers of beta, gamma-bidentate CrITP were synthesized, isolated, and characterized. Synthesis of these complexes was done using pH titration methods similar to that described by Cleland [W.W. Cleland, Methods Enzymol. 87, 159 (1982)], and separation of the two chelation isomers was accomplished with DEAE-sephadex A-25 using 0-0.3 N linear HCl gradient. Diastereomer separation (analytical and preparative scales) of beta, gamma-bidentate CrITP using reverse-phase high-performance liquid chromatography, and then analysis of the diastereomers with circular dichroism spectroscopy, shows four diastereomers that exist as two pairs of mirror-image isomers, similar to the four diastereomers of beta, gamma-bidentate CrATP as presented by Dunaway-Mariano and Cleland [D. Dunaway-Mariano and W.W. Cleland, Biochemistry 19, 1496 (1980)]. Reverse-phase high-performance liquid chromatography analysis of gamma-monodentate CrITP shows the presence of two major peaks, both of which convert to beta, gamma-bidentate CrITP upon incubation at pH 6.0 for 1 hr.

Kinetics of chromium nucleotide isomer interconversion.

The rates of chromium nucleotide isomer interconversion were studied as a function of pH, ionic strength, and temperature. Nucleotide isomers were separated using high voltage electrophoresis and gel filtration chromatography. The rate of conversion of monodentate adenosine 5'-monophosphate-chromium salt (CrADP) to the bidentate complex increased with increasing pH, temperature, and ionic strength. Optimal stability for CrADP complexes was found to be at pH 3.5 with a temperature of 4 degrees C. It was found that at pH values above 7.0, the chromium complexes rapidly decomposed even at 4 degrees C. It was found that the conversion of monodentate CrADP to binentate CrADP required the removal of one proton by the solvent. The activation energy for the conversion was found to be 7.3 kcal/mol at pH 6.5. The kinetics of the isomer interconversion are described in terms of possible conversion mechanisms.

Kinetic studies on the conformational isomerization reaction of the four diastereomers of beta,gamma-bidentate CrATP.

The rates of the conformational isomerization reaction of the diastereomers of beta,gamma-bidentate CrATP were studied as a function of pH, buffer concentration, ionic strength, and temperature. The progress of the reaction was monitored by quenching the reaction at various times, and then isolating the individual diastereomers and quantitating the percent of each. This was accomplished using the reverse-phase high-performance liquid chromatography separation technique developed in this laboratory [K. J. Gruys, and S. M. Schuster, Anal. Biochem. 125, 66-73 (1982)]. The rate constants for this isomerization were then determined by obtaining the best computer fit of the data to a reversible binary mechanism (i.e., A in equilibrium B) using interative descent methods. The reaction rate was shown to be dependent on pH, temperature, and ionic strength, but independent of buffer concentration. Keq. constants were independent of all variables except ionic strength. The results from this study are interpreted in terms of a reaction mechanism involving a preequilibrium ionization of the diastereomers followed by a rate-limiting interconversion process.

A new assay for L-asparagine synthetase.

A fast, relatively inexpensive method of measuring the enzymatic formation of L-asparagine from L-aspartate is presented. This radiochemical assay requires simple manipulations making it ideal for working with large numbers of samples, while maintaining high sensitivity and reproducibility. A mechanism similar to the enzymatic beta-decarboxylation of aspartate is utilized but in a nonenzymatic reaction. In the presence of pyridoxal and A13+ ions, the 14C of L-[4-14C]aspartate is decarboxylated while L-[4-14C]asparagine remains intact. This assay is shown to be suitable for measuring mammalian L-asparagine synthetase activity, while not requiring the isolation of assay enzymes.

Quantitation of immobilized proteins.

A method for the quantitative determination of immobilized proteins based on the binding and subsequent elution of Coomassie Blue R is presented. Also presented is a method for the immobilization of proteins in solution by entrapment in polyacrylamide. These entrapped proteins are then available for use in the assay method presented. Other analytical procedures can also be performed on the entrapped proteins, either alone or in combination with the protein quantitation. The dye binding and elution method presented provides a sensitive and, in most applications, rapid method for the quantitative detection of immobilized proteins. Rather than immobilization being an obstacle to the assay method, this approach utilizes the advantages of immobilization for the removal of excess reagents. Application of this approach to several types of immobilized protein are presented.

Effect of organic solvents on the beef heart mitochondrial adenosine triphosphatase.

The effect of organic solvents on the beef heart mitochondrial ATP-base-catalyzed ATP and ITP hydrolysis was examined. It was observed that numerous organic solvents stimulated ATP hydrolysis while ITP hydrolysis was inhibited. Methanol at 20% (v/v) was found to stimulate ATP hydrolysis by over 300%, while at the same methanol concentration ITP hydrolysis was inhibited approximately 50%. In the presence of 20% methanol, ATP hydrolysis exhibited linear plots of 1/[ATP] vs. 1/v, while in the absence of methanol negative cooperativity was observed. These data can be interpreted to imply that the catalytic and regulatory sites of the mitochondrial ATPase are being dissociated 20% methanol. The effect of methanol on the hydrolysis of ATP and ITP was examined as a function of pH. It was found that, at high pH in totally aqueous solutions, the hydrolysis of ATP and ITP was inhibited, while the presence of 20% methanol either caused the hydrolytic rate to peak and remain constant above pH 8 (with ATP as substrate) or caused the rate of hydrolysis to continue to increase above pH 8 (when ITP was the substrate). These data are interpreted to indicate that an acidic group in the active site may be ionizing, limiting the ATPase-catalyzed hydrolytic rate, and, with 20% methanol, this ionization was inhibited.

Purification and characterization of Saccharomyces cerevisiae DNA damage-responsive protein 48 (DDRP 48).

A yeast protein was purified from wild type Saccharomyces cerevisiae (S. cerevisiae) to near homogeneity using an ethanolamine affinity chromatography procedure. The N-terminal amino acid sequencing and the amino acid composition analyses identified this protein as the product of the second open reading frame of S. cerevisiae DNA Damage-responsive gene 48 (DDR48) (Treger, J.M., and McEntee, K. (1990) Mol. Cell. Biol. 10, 3174-3184) The first methionine residue encoded by the translation starting codon was not present in the mature protein which is designated as DDRP 48. DDRP 48 was found to be a negatively charged and highly hydrophilic glycoprotein. The glycosidase cleavage analyses suggested that DDRP 48 was mainly N-link-glycosylated. The apparent molecular mass of DDRP 48 was estimated to be approximately 65 kilodaltons. DDRP 48 was found able to hydrolyze ATP and GTP yielding PPi. The Km values for ATP and GTP are 0.29 mM and 0.58 mM, respectively. The Western blot analysis demonstrated that DDRP 48 was expressed to various concentrations in different S. cerevisiae strains. Increased DDRP 48 abundance was observed after yeast cells carrying the wild type RAD 52 gene were exposed to either ethylmethane sulfonate or heat shock treatments. After similar DNA-damaging treatments, however, no significant inductions of DDRP 48 were found in a rad 52 mutant strain. These observations are consistent with the predictions resulting from previous studies on transcriptional regulation of the DDR 48 gene (Maga, J.A., McClanahan, T.A., and McEntee, K. (1986) Mol. & Gen. Genet. 205, 276-284; McClanahan, T., and McEntee, K. (1986) Mol. Cell. Biol. 6, 90-96).