Pseudo-enzymatic hydrolysis of 4-nitrophenyl acetate by human serum albumin: pH-dependence of rates of individual steps

Human serum albumin (HSA) displays esterase activity reflecting multiple irreversible chemical modifications rather than turnover. Here, kinetics of the pseudo-enzymatic hydrolysis of 4-nitrophenyl acetate (NphOAc) are reported. Under conditions where [HSA] ? 5×[NphOAc] and [NphOAc] ? 5×[HSA], the HSA-catalyzed hydrolysis of NphOAc is a first-order process for more than 95% of its course. From the dependence of the apparent rate constants k_app and k_obs on [HSA] and [NphOAc], respectively, values of K_s, k₊₂, and k₊₂/K_s were determined. Values of K_s, k₊₂, and k₊₂/K_s obtained at [HSA] ? 5×[NphOAc] and [NphOAc] ? 5×[HSA] are in good agreement, the deacylation step being rate limiting in catalysis. The pH-dependence of k₊₂/K_s, k₊₂, and K_s reflects the acidic pK_a shift of the Tyr411 catalytic residue from 9.0 ± 0.1 in the substrate-free HSA to 8.1 ± 0.1 in the HSA:NphOAc complex. Accordingly, diazepam inhibits competitively the HSA-catalyzed hydrolysis of NphOAc by binding to Tyr411.     

Lanthanum as a calcium-substituting ion for binding to sarcoplasmic reticulum ATPase

Ca2+ binding and internalization in sarcoplasmic reticulum ATPase can be investigated by the use of La3+ as a Ca2+ analog. Displacement kinetics of Ca2+ bound by La3+ in native vesicles is a slow biphasic process (k1 = 0.55 s-1 and k2 = 0.05 s-1) that is consistent with the existence of two Ca2+ binding populations whereas in leaky vesicles there appears to be a single population (k = 0.57 s-1). Rapid quench experiments demonstrate that Ca2+ internalization occurs with an initial burst (approximately 8 nmol/mg protein) associated with the presence of a phosphate-donor substrate in the reaction medium. While acid quenching for measurements of phosphoenzyme is instantaneous, La3+ quenching allows completion of one catalytic and transport cycle due to the slow La3+ exchange with Ca2+. This explains the apparent inconsistencies in the kinetics and stoichiometry of phosphoenzyme formation and Ca2+ internalization that are observed under certain experimental conditions.     

Irreversible inhibition of folate transport in Lactobacillus casei by covalent modification of the binding protein with carbodiimide-activated folate

Activated folate formed by reaction of folic acid and 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide irreversibly inhibits the folate transport system of Lactobacillus casei. Complete inhibition of both folate binding to the carrier protein and folate transport was achieved by pretreatment of the cells at low temperature (4 °C) and at neutral pH with 200 nm activated folate. Fifty percent inhibition of binding and transport occurred at 35 and 40 nm activated folate, respectively. Specificity was demonstrated by the fact that excess nonactivated folate added during the pretreatment step afforded complete protection of the binding protein against inhibition, and that activated folate had no effect on the binding or transport of thiamine. Rapid measurements at 4 °C were employed to show that, prior to the appearance of irreversible inhibition, activated folate (K_i = 15 nM) interacted reversibly with the binding site for folate (K_d = 0.8 nM). Cells treated with activated [³H]folate incorporated 1 mol of folate per mole of binding protein. Purification of the labeled protein followed by digestion with Pronase led to the isolation of a compound identified as ?-N-folyl lysine. The ?-amino group of a lysyl residue thus appears to be the nucleophilic group at the binding site that reacts with activated folate.     

Molybdenum(V) e.p.r. signals obtained from xanthine oxidase on reduction with aldehyde substrates and with 2-amino-4-hydroxy-6-formylpteridine.

2-Amino-4-hydroxy-6-formylpteridine, a known 'slow' substrate and inhibitor of xanthine oxidase, is unusual in that it gives rise under suitable conditions to all types of molybdenum(V) e.p.r. signals obtainable from the enzyme, namely Very Rapid, Rapid, Inhibited and Slow. The Very Rapid signal appears in a slightly modified form. The Inhibited signal, originally thought to be unique to reaction of methanol or of formaldehyde with xanthine oxidase, is now shown to be obtainable with several other aldehydes. These include, in addition to 2-amino-4-hydroxy-6-formylpteridine, acetaldehyde and glycoaldehyde. Parameters of the signals, obtained with the help of computer simulations, are presented. The appearance of Very Rapid and of Inhibited signals with these additional substrates may be of importance in elucidating the structure of the enzyme active centre. In agreement with previous work, the Very Rapid signal is attributed to an obligatory intermediate in turnover. On the other hand, the Inhibited signal is attributed to a side reaction, presumably inhibitory in nature, occurring during the catalytic process.     

ATP binding and hydrolysis-driven rate-determining events in the RFC-catalyzed PCNA clamp loading reaction

The multi-subunit replication factor C (RFC) complex loads circular proliferating cell nuclear antigen (PCNA) clamps onto DNA where they serve as mobile tethers for polymerases and coordinate the functions of many other DNA metabolic proteins. The clamp loading reaction is complex, involving multiple components (RFC, PCNA, DNA, and ATP) and events (minimally: PCNA opening/closing, DNA binding/release, and ATP binding/hydrolysis) that yield a topologically linked clamp·DNA product in less than a second. Here, we report pre-steady-state measurements of several steps in the reaction catalyzed by Saccharomyces cerevisiae RFC and present a comprehensive kinetic model based on global analysis of the data. Highlights of the reaction mechanism are that ATP binding to RFC initiates slow activation of the clamp loader, enabling it to open PCNA (at ~2 s(-1)) and bind primer-template DNA (ptDNA). Rapid binding of ptDNA leads to formation of the RFC·ATP·PCNA(open)·ptDNA complex, which catalyzes a burst of ATP hydrolysis. Another slow step in the reaction follows ATP hydrolysis and is associated with PCNA closure around ptDNA (8 s(-1)). Dissociation of PCNA·ptDNA from RFC leads to catalytic turnover. We propose that these early and late rate-determining events are intramolecular conformational changes in RFC and PCNA that control clamp opening and closure, and that ATP binding and hydrolysis switch RFC between conformations with high and low affinities, respectively, for open PCNA and ptDNA, and thus bookend the clamp loading reaction.     

Reconstitution of native Escherichia coli pyruvate oxidase from apoenzyme monomers and FAD

Pyruvate oxidase, a tetrameric enzyme consisting of 4 identical subunits, dissociates into apoenzyme monomers and free FAD when treated with acid ammonium sulfate in the presence of high concentrations of potassium bromide. Reconstitution of the native enzymatically active protein can be accomplished by incubating equimolar concentrations of apomonomers and FAD at pH 6.5. The kinetics of the reconstitution reaction have been measured by 1) enzyme activity assays, 2) spectrophotometric assays to measure FAD binding, and 3) high performance liquid chromatography analysis measuring the distribution of monomeric, dimeric, and tetrameric species during reconstitution. The kinetic analysis indicates that the second order reaction of apomonomers with FAD to form an initial monomer-FAD complex is fast. The rate-limiting step for enzymatic reactivation appears to be the folding of the polypeptide chain in the monomer-FAD complex to reconstitute the three-dimensional FAD binding site prior to subunit reassociation. The subsequent formation of native tetramers appears to proceed via an essentially irreversible dimer assembly pathway.     

Kinetic studies of 6-phosphogluconate dehydrogenase from sheep liver

The steady-state kinetics of the oxidative decarboxylation of 6-phosphogluconate catalysed by 6-phosphogluconate dehydrogenase from sheep liver in triethanolamine and phosphate buffers (pH 7.0) have been reinvestigated. In triethanolamine buffer the enzyme is inhibited by high NADP+ concentrations in the presence of low fixed concentrations of 6-phosphogluconate. Data are consistent with an asymmetric sequential mechanism in which NADP+ and 6-phosphogluconate bind randomly and product release is ordered. The pathway through the enzyme--6-phosphogluconate complex appears to be preferred in triethanolamine buffer. Pre-steady-state studies of the oxidative decarboxylation reaction at pH 6.0-8.0 show that hydride transfer is greater than 900 s-1. After the fast formation of NADPH in amounts equivalent to about half of the enzyme-active-centre concentration, the rate of NADPH formation is equal to the steady-state rate. Two possible interpretations are considered. Rapid fluorescence measurements of the displacement of NADPH from its complex with the enzyme at pH 6.0 and 7.0 indicate that the dissociation of NADPH is fast (greater than 800 s-1) and cannot be the rate-limiting step in oxidative decarboxylation. Coenzyme binding studies at equilibrium have been extended to include the determination of the dissociation constants for the binary complexes of enzyme with NADPH and NADP+ at pH 6.0-8.0 and the dissociation constant for NADPH in the ternary enzyme--6-phosphogluconate--NADPH complex in triethanolamine buffer, pH 7.0.     

Reactions of human liver peroxisomal alanine:glyoxylate aminotransferase with beta-chloro-L-alanine and L-cysteine: spectroscopic and kinetic analysis

In addition to the main transaminase reaction, the pyridoxal 5'-phosphate-dependent enzyme human liver peroxisomal alanine:glyoxylate aminotransferase (AGT) is able to catalyze the alpha,beta-elimination of beta-chloro-l-alanine with a catalytic efficiency similar to that of the physiological transaminase reaction with l-alanine. On the other hand, during the reaction of AGT with l-cysteine, changes in the coenzyme forms and analysis of the products reveal the occurrence of both beta-elimination and half-transamination of l-cysteine together with the pyruvate transamination. A mechanism in which a ketimine species is the common intermediate of half-transamination and beta-elimination of l-cysteine is proposed. l-cysteine partitions between these two reactions with a ratio of ~2.5. Rapid scanning stopped-flow and quench flow experiments permit the identification of reaction intermediates and the measurements of the kinetic parameters of l-cysteine half-transamination. The k(cat) of this reaction is 200- or 60-fold lower than that of l-alanine and l-serine, respectively. Conversely, l-cysteine binds to AGT with a binding affinity 30- and 200-fold higher than that of l-alanine and l-serine, respectively. This appears to be consistent with the calculated interaction energies of the l-cysteine, l-alanine and l-serine docked at the active site of AGT.     

High salt activation of recA protein ATPase in the absence of DNA

The recA protein of Escherichia coli is a DNA-dependent ATPase. In the absence of DNA, the rate of recA protein-promoted ATP hydrolysis drops 2000-fold, exhibiting an apparent kcat of approximately 0.015 min-1. This DNA-independent activity can be stimulated to levels approximating those observed with DNA by adding high concentrations (approximately 2M) of a wide variety of salts. The increase in ATP hydrolysis appears to require the minimal interaction of three to four ions with recA protein. The active species in ATP hydrolysis is an aggregate of recA protein. There appears to be little or no cooperativity with respect to ATP binding (Hill coefficient = 1.0). The salt-stimulated ATP hydrolysis reaction is dependent upon Mg2+ ions and is optimal between pH 7.0 and 8.0. In many respects, the high salt concentration appears to be functionally mimicking DNA in activating the recA protein ATPase.     

Rapid filtration analysis of nucleotide binding to Na,K-ATPase

Transient kinetic analysis of nucleotide binding to pig kidney Na,K-ATPase using a rapid filtration technique shows that the interaction between nucleotide and enzyme apparently follows simple first-order kinetics both for ATP in the absence of Mg(2+) and for ADP in the presence or absence of Mg(2+). Rapid filtration experiments with Na,K-ATPase membrane sheets may nevertheless suffer from a problem of accessibility for a fraction of the ATPase binding sites. Accordingly, we estimate from these data that for ATP binding in the absence of Mg(2+) and the presence of 35 mM Na(+) at pH 7.0 at 20 degrees C, the bimolecular binding rate constant k(on) is about 30 microM(-1) x s(-1) and the dissociation rate constant k(off) is about 8 s(-1). In the presence of 10 mM Mg(2+), the binding rate constant is the same as that in the absence of Mg(2+). For ADP or MgADP the binding rate constant is about 20 microM(-1) x s(-1) and the dissociation rate constant is about 12 s(-1). Results of rapid-mixing stopped-flow experiments with the fluorescent dye eosin are also consistent with a one-step mechanism of binding of eosin to the ATPase nucleotide site. The implication of these results is that nucleotide binding to Na,K-ATPase both in the absence and presence of Mg(2+) appears to be a single-step event, at least on the time scale accessible in these experiments.     

Characterization of steroid-binding macromolecules in small biological samples by a rapid minigel filtration method

A gel filtration method using small Sephadex G-200 columns has been developed for study of steroid-binding macromolecules. Rapid (2 hr) characterization of high affinity steroid-binding proteins is possible with this technique. It allows the study of a specific serum steroid binder such as sex steroid-binding globulin and permits its separation from the target tissue cytosolic estradiol receptor which was eluted as a single molety, both at low and high ionic strength. The technique provides an approach to the steroid receptor characterization presenting some advantages over the widely used density gradient centrifugation procedure. Due to the small amounts of binding proteins required, the method appears particularly well suited for the microanalysis of pathological material such as cancer tissue from humans.     

Inhibition of the soluble adenosine triphosphatase from mitochondria by adenylyl imidodiphosphate

1. Adenylyl imidodiphosphate is an inhibitor with high affinity for the soluble ATPase (adenosine triphosphatase) from mitochondria. 2. The reaction of the inhibitor with the ATPase is slow and estimates for the association and dissociation reaction rate constants are given. 3. The number of binding sites for the inhibitor appears to be doubled in the presence of 2,4-dinitrophenol. 4. Adenylyl imidodiphosphate is less effective as an inhibitor of the ATPase activity of this enzyme than of the inosine triphosphatase activity. It is also less effective on the ATPase of frozen-thawed or intact mitochondria and did not inhibit ADP-stimulated respiration by intact mitochondria.     

Resolution of Michaelis complex, acylation, and conformational change steps in the reactions of the serpin, plasminogen activator inhibitor-1, with tissue plasminogen activator and trypsin

Michaelis complex, acylation, and conformational change steps were resolved in the reactions of the serpin, plasminogen activator inhibitor-1 (PAI-1), with tissue plasminogen activator (tPA) and trypsin by comparing the reactions of active and Ser 195-inactivated enzymes with site-specific fluorescent-labeled PAI-1 derivatives that report these events. Anhydrotrypsin or S195A tPA-induced fluorescence changes in P1'-Cys and P9-Cys PAI-1 variants labeled with the fluorophore, NBD, indicative of a substrate-like interaction of the serpin reactive loop with the proteinase active-site, with the P1' label but not the P9 label perturbing the interactions by 10-60-fold. Rapid kinetic analyses of the labeled PAI-1-inactive enzyme interactions were consistent with a single-step reversible binding process involving no conformational change. Blocking of PAI-1 reactive loop-beta-sheet A interactions through mutation of the P14 Thr --> Arg or annealing a reactive center loop peptide into sheet A did not weaken the binding of the inactive enzymes, suggesting that loop-sheet interactions were unlikely to be induced by the binding. Only active trypsin and tPA induced the characteristic fluorescence changes in the labeled PAI-1 variants previously shown to report acylation and reactive loop-sheet A interactions during the PAI-1-proteinase reaction. Rapid kinetic analyses showed saturation of the reaction rate constant and, in the case of the P1'-labeled PAI-1 reaction, biphasic changes in fluorescence indicative of an intermediate resembling the noncovalent complex on the path to the covalent complex. Indistinguishable K(M) and k(lim) values of approximately 20 microM and 80-90 s(-1) for reaction of the two labeled PAI-1s with trypsin suggested that a diffusion-limited association of PAI-1 and trypsin and rate-limiting acylation step, insensitive to the effects of labeling, controlled covalent complex formation. By contrast, differing values of K(M) of 1.7 and 0.1 microM and of k(lim) of 17 and 2.6 s(-1) for tPA reactions with P1' and P9-labeled PAI-1s, respectively, suggested that tPA-PAI-1 exosite interactions, sensitive to the effects of labeling, promoted a rapid association of PAI-1 and tPA and reversible formation of an acyl-enzyme complex but impeded a rate-limiting burial of the reactive loop leading to trapping of the acyl-enzyme complex. Together, the results suggest a kinetic pathway for formation of the covalent complex between PAI-1 and proteinases involving the initial formation of a Michaelis-type noncovalent complex without significant conformational change, followed by reversible acylation and irreversible reactive loop conformational change steps that trap the proteinase in a covalent complex.     

Kinetic Studies of a (Na++ K++ Mg2+) ATPase in Sugar Beet Roots

Kinetic studies of a microsomal, dithiotreitol treated, homogenate from sugar beet roots led to the following conclusions about its ATPase activity: (1) MgATP in complex appears to be the primary substrate for the reaction. The reciprocal equilibrium constant for the binding to the enzyme is estimated to be approximately 0.2 × 10^?3M. (2) Free ATP acts as a competitive inhibitor of the MgATP. The binding constant is about twice as high as for MgATP. Consequently the enzyme has less affinity for ATP than for MgATP. (3) Free Mg²⁺ has little influence on the velocity, as the binding affinity of the enzyme for Mg²⁺ is almost negligible.     

Stopped-flow fluorescence kinetic studies of Glu-plasminogen. Conformational changes triggered by AH-site ligand binding

Binding of 6-aminohexanoic acid to the AH-site, a weak lysine binding site in Glu-plasminogen, alters the conformation of the molecule. The kinetics of the binding and the accompanying conformational change are investigated at pH 7.8, 25 degrees C. Changes of intrinsic protein fluorescence were measured as a function of time after rapid mixing in a stopped-flow apparatus. The results reflect a two-step reaction mechanism: Rapid association of Glu-plasminogen and 6-aminohexanoic acid (K1 = 44 mM) followed by the conformational change (k2 = 69 s-1 and k-2 = 3 s-1) with an overall dissociation constant Kd = 2.0 mM. Thus the conformational change is rather fast, t12 = 0.01 s. Its importance for the rates of Glu-plasminogen activation reactions is discussed.     

Synthesis of novel isoluminol probes and their use in rapid bacterial assays

Rapid assays for bacteria have been developed utilizing novel LysLysLys-isoluminol (14) and GluGlu-isoluminol (16) probes that have been derived from peptides which potentially mimic bacteriophage attachment protein binding regions. Compared to two conventional methods that are widely used, namely nucleic acid probes and polymerase chain reaction (PCR) assays, these types of probes may eventually have certain advantages, such as high sensitivity, and short preparation and assay time.     

A binding protein from rat nerve

Leucine has been found to bind competitively to a soluble protein (molecular weight 97,000 daltons) from rat sciatic nerve under certain experimental conditions to form a high molecular weight aggregate (MW greater than 302,000). Kinetic study showed that the equilibrium constant for leucine-binding is 1.33 X 10(4) l/m and the rate constants for binding and unbinding are k1 = 0.424 l/m/sec and k-1 = 3.18 X 10(5) sec-1 respectively. The binding reaction is accompanied by an endothermic enthalpy change of 5,000 cal/mole and the favorable equilibrium appears to be due to the large positive (35.3 eu) entropy of binding. L-Proline, thymidine, and succinic acid were also found to bind, non-competitively with leucine, to proteins in the same fraction. Binding of those compounds and leucine was enhanced by the presence of Mg2+. Rat muscle and plasma proteins did not significantly bind leucine under these experimental conditions. The presence of this binding protein in rat nerve suggests an additional mechanism in the metabolism and in the transport of amino acids for incorporation into a protein structure in nerve.     

Crowding effects on EcoRV kinetics and binding

The cytosol of the cell contains high concentrations of small and large macromolecules, but experimental data are often obtained in dilute solutions that do not reflect in vivo conditions. We have studied the crowding effect that large macromolecules have on EcoRV cleavage by adding high-molecular-weight Ficoll 70 to reaction solutions. Results indicate that Ficoll has surprisingly little effect on overall EcoRV reaction velocity because of offsetting increases in V(max) and K(m), and stronger nonspecific binding. The changes in measured parameters can largely be attributed to the excluded volume effects on reactant activities and the slowing of protein diffusion. Covolume reduction upon binding appears to reinforce nonspecific binding strength, and k(cat) appears to be slowed by stronger nonspecific binding, which slows product release. The data also suggest that effective Ficoll particle volume decreases as its concentration increases above a few weight percent, which may be due to Ficoll interpenetration or compression.     

Spectral properties of the higher oxidation states of prostaglandin H synthase

Prostaglandin H (PGH) synthase reacts with organic hydroperoxides and fatty acid hydroperoxides on a millisecond time scale to generate an intermediate that is spectrally similar to compound I of horseradish peroxidase. Compound I of PGH synthase is converted to compound II within 170 ms. Compound II decays to resting enzyme in a few seconds. Thus, the peroxidase reaction of PGH synthase appears to involve a cycle of native enzyme, compound I, and compound II, typical of heme-containing peroxidases. The Soret absorption maximum of compound I appears to occur at 412 nm but a small amount of compound II may be present. Soret maxima occur at 420, 433, and 419 for compound II, the ferrous enzyme, and the oxyferrous enzyme (compound III), respectively. Rapid scan analysis of the reaction of PGH synthase with arachidonic acid reveals the absorbance of compound II but no evidence for ferrous or oxyferrous enzyme.     

Nucleoside triphosphate specificity of tubulin

We have determined the binding affinity for binding of the four purine nucleoside triphosphates GTP, ITP, XTP, and ATP to E-site nucleotide- and nucleoside diphosphate kinase-depleted tubulin. The relative binding affinities are 3000 for GTP, 10 for ITP, 2 for XTP, and 1 for ATP. Thus, the 2-exocyclic amino group in GTP is important in determining the nucleotide specificity of tubulin and may interact with a hydrogen bond acceptor group in the protein. The 6-oxo group also makes a contribution to the high affinity for GTP. NMR ROESY experiments indicate that the four nucleotides have different average conformations in solution. ATP and XTP are characterized by a high anti conformation, ITP by a medium anti conformation, and GTP by a low anti conformation. Possibly, the preferred solution conformation contributes to the differences in affinities. When the tubulin E-site is saturated with nucleotide, there appears to be little difference in the ability of the four nucleotides to stimulate assembly. The critical protein concentration is essentially identical in reactions using the four nucleotides. All four of the nucleotides were hydrolyzed during the assembly reaction, and the NDPs were incorporated into the microtubule. We also examined the binding of two gamma-phosphoryl-modified GTP photoaffinity analogues, p(3)-1, 4-azidoanilido-GTP and p(3)-1,3-acetylanilido-GTP. These analogues are inhibitors of the assembly reaction and bind to tubulin with affinities that are 15- and 50-fold lower, respectively, than the affinty for GTP. The affinity of GTP is less sensitive to substitutions at the gamma-phosphoryl position that to changes in the purine ring.