Transient kinetic approaches to enzyme mechanisms.
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Biochemistry↗
Biomedical subjects
G G Hammes
Publications and source records attributed to G G Hammes.
Membrane-protein structural mapping of chloroplast coupling factor in asolectin vesicles.
The spatial relationship of specific sites on chloroplast coupling factor, reconstituted in asolectin vesicles, to the bilayer surface has been studied with fluorescence methods. Fluorescence resonance energy transfer measurements have been used to map the distances of closest approach of the N,N'-dicyclohexylcarbodiimide-binding site and the disulfide on the gamma-polypeptide to the bilayer center. The dicyclohexylcarbodiimide site was labeled with N-cyclohexyl-N'-pyrenylcarbodiimide and the gamma-disulfide site with a coumarinyl derivative. The bilayer center was labeled with 25-[N-(7-nitro-2,1,3-benzoxadiazol-4-yl)-N-methylamino]-27-norc holesterol. The distances obtained, 15 and 43 A, respectively, were combined with previous measurements of the distance of closest approach between these sites and the membrane surface to estimate the perpendicular distances of the sites from the membrane surface. The depth of the dicyclohexylcarbodiimide site was also determined by studying the quenching of fluorescence by 5-, 7-, 12-, and 16-doxylstearic acids. The model developed suggests that the dicyclohexylcarbodiimide site is 6-10 A below the membrane surface and the gamma-disulfide is 16 A above the membrane surface. The distances measured are subject to a considerable uncertainty, but the proposed model provides a useful starting point for further structural studies.
Binding Sites↗
Rotational dynamics of chloroplast ATP synthase in phospholipid vesicles.
The rotational dynamics of the purified dicyclohexylcarbodiimide-sensitive H(+)-ATPase (DSA) reconstituted into phospholipid vesicles and of the DSA coreconstituted with the proton pump bacterio-rhodopsin were examined by using the technique of time-resolved phosphorescence emission anisotrophy. The phosphorescent probe erythrosin isothiocyanate was used to covalently label the gamma-polypeptide of DSA before reconstitution. Rotational correlation times were measured under a variety of conditions. The rotational correlation time was independent of the viscosity of the external medium but increased significantly as the microviscosity of the membrane increased. This indicates the rotational correlation times are a measure of the enzyme motion within the membrane. The activation energy associated with the rotational correlation time is 8-10 kcal/mol. At 4 degrees C, the correlation time, typically approximately 100-180 microseconds, was unaffected by the addition of substrates and the presence of a membrane pH gradient. Therefore, molecular rotation of the DSA does not appear to play an important role in enzyme catalysis or ion pumping.
Chloroplasts↗
The ATP binding site of the yeast plasma membrane proton-translocating ATPase.
Photoaffinity labeling of the active site of the yeast plasma membrane H(+)-ATPase has been studied with 2-azido-AMP and 2-azido-ATP. The ATPase activity of the enzyme decreases as the time of photolysis of the photoactive nucleotides in the presence of the enzyme increases. The covalent incorporation of [alpha-32P]2-azido-AMP into the enzyme and the inhibition of ATPase activity have comparable time courses. ATP protects the ATPase from incorporation of and photoinactivation by 2-azido-ATP or 2-azido-AMP. In the dark, 2-azido-ATP inhibits the ATPase at concentrations comparable to the apparent Michaelis constant for MgATP. After photolysis and proteolysis of the protein, three overlapping peptides labeled by the nucleotide analogues were purified by reversed-phase high performance liquid chromatography and sequenced. The peptides are derived from a region of the ATPase that is highly conserved in related cation pumps forming a phosphorylated intermediate during the catalytic cycle. Labeling with both nucleotide analogues occurs in peptides containing residues from aspartate 560 to lysine 566. The amino acids in this region conform to a consensus sequence for ATP binding derived from phosphofructokinase.
Adenosine Triphosphate↗
Cloning and expression of the yeast plasma membrane ATPase in Escherichia coli.
The yeast plasma membrane ATPase gene PMA1 was cloned into Escherichia coli using the high expression tac and T7 promoters. The gene product is toxic to the bacterial cell leading to very low expression levels and arrested growth of the host cell within minutes of induction. The expressed protein is immunologically cross-reactive with the yeast ATPase, comigrates with the original protein in sodium dodecyl sulfate-polyacrylamide gels, and is isolated in the E. coli membrane fraction. The partially purified protein exhibits ATPase activity.
Cell Membrane↗
Amino acid sequences of pyridoxal 5'-phosphate binding sites and fluorescence resonance energy transfer in chicken liver fatty acid synthase.
The amino acid sequences associated with pyridoxal 5'-phosphate binding sites in chicken liver fatty acid synthase have been determined: a site whose modification causes selective inhibition of the enoyl reductase activity and a site (site I) that is not associated with enzymatic activity. The amino acid sequences of peptides obtained by trypsin hydrolysis of the pyridoxamine 5'-phosphate labeled enzyme were determined. For the site associated with enoyl reductase activity, the sequence similarities between chicken and goose are extensive and include the sequence Ser-X-X-Lys, a characteristic structural feature of pyridoxamine enzymes. In addition, the spatial relationships between the pyridoxal 5'-phosphate binding sites and reductase site(s) have been studied with fluorescence resonance energy-transfer techniques. The distances between site I and the enoyl reductase and beta-ketoacyl reductase sites are greater than 50 and 41-44 A, respectively. The distance between the two reductase sites is greater than 49 A.
Amino Acid Sequence↗
Structural map of the dicyclohexylcarbodiimide site of chloroplast coupling factor determined by resonance energy transfer.
Fluorescence resonance energy-transfer measurements were made on the membrane-bound chloroplast coupling factor. The distances from the N,N'-dicyclohexylcarbodiimide-binding site on the membrane-bound portion of the enzyme (CF0) to the vesicle surface and to two sulfhydryl sites on the gamma-polypeptide were determined. The dicyclohexylcarbodiimide-binding site was labeled with the fluorescent species N-cyclohexyl-N'-pyrenylcarbodiimide. The vesicle surface was labeled with N-(7-nitro-2,1,3-benzoxadiazol-4-yl)phosphatidylethanolamine. Steady-state energy transfer between the fluorescent-labeled enzyme (energy donor) and varying concentrations of the ethanolamine derivative (energy acceptor) indicated that the distance of closest approach between the energy donor and the outer vesicle surface is 16-24 A. Two specific sites on the gamma-polypeptide were reacted with a coumarinylmaleimide derivative; one is a sulfhydryl that can be labeled only on the thylakoids under energized conditions (the "light" site), while the other is the disulfide site that regulates enzymatic activity. Energy-transfer measurements utilizing steady-state fluorescence and fluorescence lifetime methods indicated that the dicyclohexylcarbodiimide site is approximately 41 A from the light site and approximately 50 A from the gamma-disulfide site. These distances are used to extend the current structural model of the chloroplast coupling factor.
Carbodiimides↗
Topology of the yeast plasma membrane proton-translocating ATPase.
Four proteases have been used to assess the topology of the H+-ATPase from Saccharomyces cerevisiae reconstituted into phosphatidylserine vesicles. Limited proteolysis by trypsin and alpha-chymotrypsin inactivates the enzyme and produces stable, membrane-bound fragments. Sequence analyses of these peptides have located the peptide bonds hydrolyzed. The labile bonds are on opposite sides of a central hydrophilic domain containing consensus sequences for the site of phosphorylation and fluorescein isothiocyanate binding of several related ATPases. Limited proteolysis of the ATPase by elastase cuts approximately 50 amino acids from the C terminus, leaving the remaining membrane-bound fragments active. Proteolysis by carboxypeptidase Y in the presence and absence of detergent suggests that the C terminus is on the inside of the vesicle in this reconstitution. A model for the transmembrane arrangement of the polypeptide is proposed. In this model, the C terminus is on the inside of the vesicle, the N terminus is on the outside, the ATP binding region is on the outside, and the polypeptide passes through the membrane a minimum of five times.
Amino Acid Sequence↗
Molecular cloning and sequencing of chicken liver fatty acid synthase cDNA.
The complete amino acid sequence of chicken liver fatty acid synthase [acyl-CoA:malonyl-CoA C-acyltransferase (decarboxylating, oxoacyl- and enoyl-reducing, and thioester-hydrolyzing), EC 2.3.1.85] has been determined from the corresponding cDNA sequence. A 5.3-kilobase-pair (kbp) region of cDNA coding for chicken fatty acid synthase has been cloned and sequenced that is contiguous to the 2.3-kbp region previously sequenced [Yuan, Z., Liu, W. & Hammes, G.G. (1988) Proc. Natl. Acad. Sci. USA 85, 6328-6331]. The cDNA codes for the remaining 1677 amino acids of the previously unsequenced region of the protein. The amino acid sequence contains peptides known to be associated with the NADPH binding site of the enoylreductase active center, the acetyl/malonyltransacylase active site, the "waiting" site containing cysteine, and a pyridoxal 5'-phosphate binding site. Locations of the NADPH binding site of the beta-ketoacylreductase active site and of the dehydratase active site are proposed on the basis of protein sequence homologies to catalytic sites in other enzymes. The molecular weight of the complete polypeptide chain is 267,288. A linear functional map of the chicken fatty acid synthase derived from its primary sequence is presented.
Amino Acid Sequence↗
Homology analysis of the protein sequences of fatty acid synthases from chicken liver, rat mammary gland, and yeast.
Homology analyses of the protein sequences of chicken liver and rat mammary gland fatty acid synthases [acyl-CoA:malonyl-CoA C-acyltransferase (decarboxylating, oxoacyl- and enoyl-reducing and thioester hydrolyzing), EC 2.3.1.85] and yeast fatty acid synthase [fatty-acyl-CoA synthase; acyl-CoA:malonyl-CoA C-acyltransferase (decarboxylating, oxoacyl- and enoyl-reducing), EC 2.3.1.86] were carried out. The amino acid sequences of the chicken and rat enzymes are 67% identical. If conservative substitutions are allowed, 78% of the amino acids are matched. A region of low homologies exists between the functional domains, in particular around amino acid residues 1059-1264 of the chicken enzyme. Homologies between the active sites of chicken and rat and of chicken and yeast enzymes have been analyzed by an alignment method. A high degree of homology exists between the active sites of the chicken and rat enzymes. However, the chicken and yeast enzymes show a lower degree of homology. The NADPH-binding dinucleotide folds of the beta-ketoacyl reductase and the enoyl reductase sites were identified by comparison with a known consensus sequence for the NADP- and FAD-binding dinucleotide folds. The active sites of all of the enzymes are primarily in hydrophobic regions of the protein. This study suggests that the genes for the functional domains of fatty acid synthase were originally separated, and these genes were connected to each other by using different connecting nucleotide sequences in different species. An alternative explanation for the differences in rat and chicken is a common ancestry and mutations in the joining regions during evolution. A higher mutation rate in the joining regions than in the active site regions of the enzymes without loss of function might be expected.
Amino Acid Sequence↗
Studies of the phosphoenzyme intermediate of the yeast plasma membrane proton-translocating ATPase.
The yeast plasma membrane proton-pumping ATPase forms a phosphorylated intermediate during the hydrolysis of ATP. The fraction of enzyme phosphorylated during steady-state ATP hydrolysis was studied as a function of substrate concentration (MgATP), Mg2+ concentration, and pH. The dependence of the fraction of enzyme phosphorylated on the concentration of MgATP is sigmoidal, and the isotherms can be fit with parameters and mechanisms similar to those used to describe ATP hydrolysis. The isotherm is significantly more sigmoidal at pH 5.5 than at pH 6.0, with the limiting percentage (100.mol of phosphate/mol of enzyme) of enzyme phosphorylated being 70% and 6%, respectively, at the two pH values. The maxima in the steady-state rate of ATP hydrolysis occur at higher concentrations of Mg2+ and higher pH than the maxima in the fraction of enzyme phosphorylated. This suggests that the rate-determining step for ATP hydrolysis is different from that for enzyme phosphorylation and the hydrolysis of phosphoenzyme is enhanced by Mg2+ and high pH. The rate of phosphoenzyme formation was investigated with the quenched-flow method, but only a lower bound of 140 s-1 could be obtained for the rate constant at MgATP concentrations greater than 2.5 mM. Since the turnover number for ATP hydrolysis under similar conditions is 14 s-1, the rate-determining step in ATP hydrolysis occurs after enzyme phosphorylation.
Adenosine Triphosphate↗
Assessment of the number of nucleotide binding sites on chloroplast coupling factor 1 by the continuous variation method.
The method of continuous variation (Job plot analysis) and difference absorbance spectroscopy were used to investigate the binding of 2'(3')-(trinitrophenyl)-ADP and -ATP to chloroplast coupling factor 1 (CF1). Experiments performed at a low total concentration (30 microM) of nucleotide and enzyme binding sites (assuming three or four binding sites per CF1) could be interpreted in terms of approximately three nucleotide binding sites per CF1. At higher total concentrations (100 and 400 microM), the number of apparent binding sites increased to almost four. Computer-generated Job plots, using a protein-ligand complex formation scheme of n independent, nonequivalent binding sites, gave good fits to the experimental data at all concentrations when four binding sites were modeled. The dissociation constant of the fourth site was estimated to be approximately 20 microM. Additional nucleotide binding sites were not directly observed by this method and, if they exist, have very weak binding affinities (dissociation constants greater than approximately 1 mM).
Adenine Nucleotides↗
Correlation of enzymatic activities and aggregation state in chicken liver fatty acid synthase.
The relationships between the aggregation state and the enzymatic activities of chicken liver fatty acid synthase have been explored by monitoring the changes in light scattering, fluorescence, and the overall, beta-ketoacyl synthase, beta-ketoacyl reductase and enoyl reductase activities during dissociation and reassociation of the enzyme. The data obtained indicate that the enzyme dissociates at low temperature in both 0.1 M potassium phosphate (pH 7.0), 1 mM EDTA, and 5 mM Tris(hydroxymethyl)aminomethane, 35 mM glycine (pH 8.3) and 1 mM EDTA, but the extent of dissociation is less in the phosphate buffer. The assay conditions influence the assessment of the degree of dissociation and association: high temperatures, phosphate (high salt), NADPH and acetoacetyl-coenzyme A promote association of the monomeric enzyme, whereas dilution in the Tris-glycine buffer (low salt) and low temperature promote dissociation. Both the rate and extent of association and dissociation are altered by substrates. The monomeric enzyme does not possess beta-ketoacyl synthase and beta-ketoacyl reductase activities. Results obtained with the 1,3-dibromo-2-propanone cross-linked enzyme, which lacks beta-ketoacyl synthase activity, indicate that the NADPH-binding site of beta-ketoacyl reductase is disrupted at low ionic strength. In contrast, changes in ionic strength have little effect on the enoyl reductase activity. The dimer is stabilized by both electrostatic and hydrophobic interactions, with the former being of special importance for maintenance of the beta-ketoacyl reductase active site. site.
Animals↗
Amino acid sequences of substrate-binding sites in chicken liver fatty acid synthase.
The amino acid sequences of three essential regions of chicken liver fatty acid synthase have been determined: that around 4'-phosphopantetheine ("carrier" site), the substrate "loading" site containing serine, and a "waiting" site for the growing fatty acid containing cysteine. The amino acid sequence of the 4'-phosphopantetheine region was determined for the acetyl-, malonyl-, hydroxybutyryl-, and butyryl-enzyme with peptides obtained by hydrolysis of the enzyme with trypsin and Staphylococcus aureus (V8) protease. The sequence region around the essential serine was obtained for the acetyl- and malonyl-enzyme. The N-terminus of the tryptic peptide was blocked. However, the same sequence is obtained for the acetyl- and malonyl-peptide after S. aureus protease digestion, suggesting that the enzyme contains a single acyl transferase rather than two separate transacylases. The sequence around the cysteine was obtained by use of a radioactive iodoacetamide label. An unusual sequence of three serines adjacent to the cysteine was found. The strong similarities between peptides from different species for all three of the regions suggest that the multifunctional polypeptides from yeast and animals have evolved from the monofunctional enzymes of lower species.
Amino Acid Sequence↗
Function of tightly bound nucleotides on membrane-bound chloroplast coupling factor.
The kinetic behavior of tightly bound nucleotides on chloroplast coupling factor from spinach was determined under phosphorylating and nonphosphorylating conditions. Chloroplast coupling factor 1 (CF1) was labeled with tightly bound radioactive ADP and/or ATP at two specific sites and reconstituted with thylakoid membranes depleted of CF1 by treatment with NaBr. The initial incorporation and dissociation of ADP from one of the sites requires light but occurs at the same rate under phosphorylating and non-phosphorylating conditions. The initial rate is considerably slower than the rate of ATP synthesis, but nucleotide exchange is very rapid during steady-state ATP synthesis. A direct correspondence between this nucleotide binding site and a site on soluble CF1 that hydrolyzes ATP was demonstrated. A second site binds MgATP very tightly; the MgATP does not dissociate during ATP synthesis nor does its presence alter the rate of ATP synthesis. This is analogous to the behavior found for soluble CF1 during ATP hydrolysis. These results demonstrate that the tight-binding nucleotide sites on soluble CF1 and membrane-bound coupling factor are essentially identical in terms of binding properties and kinetic behavior during ATP hydrolysis and synthesis.
Adenosine Diphosphate↗
Characterization of three-subunit chloroplast coupling factor.
The delta- and epsilon-polypeptides were removed from chloroplast coupling factor 1 (CF1). The resulting enzyme, CF1(-delta, epsilon), is a stable active ATPase containing only alpha-, beta-, and gamma-polypeptides. The dependence of the steady-state kinetics of ATP hydrolysis catalyzed by CF1(-delta, epsilon) on the concentrations of ATP and ADP was found to be essentially the same as by activated CF1. Nucleotide binding studies with CF1(-delta, epsilon) revealed three binding sites: a nondissociable ADP site (site 1), a tight MgATP binding site (site 2), and a site that binds ADP and ATP with a dissociation constant in the micromolar range (site 3). Similar results have been obtained with CF1. For both CF1 and CF1(-delta, epsilon), the binding of MgATP at site 2 is tight only in the presence of Mg2+. Fluorescence resonance energy transfer was used to map distances between the gamma-sulfhydryl ("dark" site) and gamma-disulfide and between the gamma-sulfhydryl and the three nucleotide sites. These distances are within 5% of the corresponding distances on CF1. These results indicate that removal of the delta- and epsilon-polypeptides from CF1 does not cause significant changes in the structure, kinetics, and nucleotide binding sites of the enzyme.
Adenosine Diphosphate↗
Molecular cloning and sequencing of DNA complementary to chicken liver fatty acid synthase mRNA.
The cDNA corresponding to 4.18 kilobases (kb) of the mRNA of chicken liver fatty acid synthase has been cloned and sequenced. The cDNA corresponds to the 3' end of the mRNA and consists of a 1.87-kb noncoding tail and a 2.31-kb region encoding 769 amino acids of the C terminus of the enzyme. The thioesterase at the C terminus, preceded by the acyl carrier protein, can be identified from known amino acid sequences. However, the identity of the enzymes N terminal to the acyl carrier protein could not be ascertained. The partial amino acid sequence of the chicken liver fatty acid synthase shows greater than 70% similarity with the rat mammary gland enzyme.
Amino Acid Sequence↗
Rotation of nucleotide sites is not required for the enzymatic activity of chloroplast coupling factor 1.
New heterobifunctional photoaffinity cross-linking reagents, 6-maleimido-N-(4-benzoylphenyl)hexanamide, 12-maleimido-N-(4-benzoylphenyl)dodecanamide, and 12-[14C]maleimido-N-(4-benzoylphenyl)dodecanamide, were synthesized to investigate the mechanism of ATP hydrolysis by chloroplast coupling factor 1. These reagents react with sulfhydryl groups on the gamma-polypeptide. Subsequent photolysis cross-links the gamma-polypeptide covalently to alpha- and beta-polypeptides. The cross-linkers prevent major movements of the gamma-polypeptide with respect to the alpha- and beta-polypeptides but are sufficiently long to permit some flexibility in the enzyme structure. When approximately 50% of the gamma-polypeptide was cross-linked to alpha- and beta-polypeptides, a 7% loss in ATPase activity was observed for the longer cross-linker and a 12% loss for the shorter. These results indicate that large movements of alpha- and beta-polypeptides with respect to the gamma-polypeptide are not essential for catalysis. In particular, rotation of the polypeptide chains to create structurally equivalent sites during catalysis is not a required feature of the enzyme mechanism.
Binding Sites↗