Mathematical model of cell growth and phosphatase biosynthesis in Saccharomyces carlsbergensis under phosphate limitation.

The rate kinetics of growth and acid phosphate formation in the batch culture of Saccharomyces carlsbergensis LAM 1068 was studied under varying degrees of phosphate limitation. The mathematical model that was developed is concerned with the time lag for exponential growth, the biphasic growth on a substrate (glucose) and its product (ethanol), sustained growth on conservative phosphate, and the derepression of acid phosphatase. The numerical calculations using appropriate parametric constants successfully described the variation in the cell mass, glucose, ethanol, and inorganic phosphate concentrations, and the enzyme activity of acid phosphatase during aerobic growth of S. carlsbergensis under five different conditions of phosphate starvation. A simulation study revealed that the optimum initial phosphate concentration in the medium giving a high productivity of acid phosphatase was 2.0 mg phosphorus/g glucose liter.     

Transient binding patches: a plausible concept for drug binding

Dose–response curves for inhibitors (drugs) generally are analyzed by means of four-parameter fits, yielding IC₅₀, background, amplitude, and Hill coefficient. Hill coefficients ≠1 contradict 1:1 competition. If binding of substrates to proteins is a stepwise process where initial binding to initial locations (patches) leads to strong binding on defined sites, then drugs (non-endogenous inhibitors) may bind to those presumably larger patches and need not follow a 1:1 stoichiometry for specific inhibition. This concept was translated into three computable models and successfully fitted to 1,282 phosphatase dose–response curves. The models only required four parameters, namely, the equilibrium dissociation constant K _D(1) of the first inhibitor binding step, background, amplitude, and a compound interaction factor to quantify the interaction of inhibitors on those patches. Binding of one established inhibitor to the vaccinia virus VH1-related (VHR) phosphatase was directly measured with microcalorimetry, confirming multiple inhibitor binding with equilibrium constants obtained from corresponding inhibition curves.     

Acid phosphatase of HeLa cells: properties and regulation of lysosomal activity by serum.

Although the subcellular distribution profile of acid phosphatase in HeLa cells is typical of a lysosomal enzyme, different lysosomal (70–80%) and supernatant forms (20–30%) have been demonstrated by their differences in pH activity curves, substrate specificities, thermal stability, sensitivity to inhibitors, and kinetics. Enzymes of the lysosomal fraction displayed anomalous kinetics in the hydrolysis of p-nitrophenyl phosphate. The major lysosomal acid phosphatase activity appears to be associated with the membrane.The total acid phosphatase activity in the cell is controlled by the concentration of serum in the medium. The specific activity in the homogenates of cells grown in high serum concentration (30%) is about twice that of cells grown in low serum concentration (1%). This doubling of specific activity holds for the lysosomal enzyme (or enzymes), but little change occurs in the supernatant form (or forms). Two other lysosomal enzymes, β-glucuronidase and N-acetyl-β-d-hexosaminidase, do not increase in specific activity. The serum-dependent formation of acid phosphatase is sensitive to cycloheximide, actinomycin D, and cordycepin. Cycloheximide blocks the increase in enzymatic activity immediately, whereas cordycepin and actinomycin D have no effect for at least 8 h. These findings suggest that de novo protein synthesis is involved in the induction of lysosomal acid phosphatase by serum and that the mRNA for this enzyme is relatively stable.     

Time dependence of activation of muscle AMP-aminohydrolase by substrate and potassium ion

The kinetics of AMP-aminohydrolase, which under steady state conditions shows a typical sigmoid dependence of initial velocities versus substrate concentration, have been examined by rapid mixing methods. Using this technique it was observed that when substrate or substrate plus activator (K(+)) were mixed with enzyme, the rate of appearance of product markedly increased during the first few tenths of a second. The time course of this change in rate was taken to reflect the progress of activation by substrate or by K(+). On the other hand, addition of activator to enzyme prior to mixing with substrate gave process curves for the formation of product consistent with normal Michaelis-Menten behaviour.Under the conditions where the reaction was examined, the enzyme at time zero had less than 10% of the activity of the fully active enzyme. The time course for activation with K(+) followed a first order process with a rate constant of 10.6 sec(-1) at 20 degrees C. A simple mechanism consistent with the data and capable of explaining the sigmoid dependence of initial velocities versus substrate concentrations observed in steady state kinetics was proposed.     

Specific effects of ATP on the kinetics of reconstituted bovine heart cytochrome-c oxidase

Bovine heart cytochrome-c oxidase was reconstituted in liposomes and the kinetics of cytochrome c oxidation were measured by the polarographic and photometric method under uncoupled conditions in the presence of various polyvalent anions. In order to distinguish between specific and unspecific ionic effects of ATP, the photolabelling reagent 8-azido-ATP was applied. Covalently bound ATP at the enzyme complex caused the same increase of Km for cytochrome c as free ATP, if measured by the photometric assay. The increase of Km by photolabelling with 8-azido-ATP was completely prevented by ATP, but not by ADP. The data indicate the occurrence of a specific binding site for ATP at the cytosolic side of cytochrome-c oxidase, which, after binding of ATP, changes the kinetics of cytochrome c oxidation.     

Cooperative kinetics of human prostatic acid phosphatase

The steady-state kinetics of hydrolysis reaction catalysed by human prostatic acid phosphatase (PAP) by using 1-naphthyl phosphate, phenyl phosphate and phosphotyrosine as substrates has been studied at pH 5.5. The substrate binding curves were sigmoidal and Hill cooperation coefficient h was higher than 1 for each of the examined compounds. Thus, human prostatic acid phosphatase kinetics exhibits positive cooperativity towards the studied substrates. The extent of cooperativity was found to depend on the substrate used and on enzyme concentration. The highest cooperativity of PAP was observed for 1-naphthyl phosphate and the lowest for phosphotyrosine. When prostatic phosphatase concentration increased, Hill cooperation coefficient (h) and half saturation constant (K(0.5)) both grew, but the catalytic constant (k(cat)) remained constant, for each of the substrates studied. Ligand-induced association-dissociation equilibrium of the active oligomeric species (monomer-dimer-tetramer-oligomers) is suggested.     

Kinetics and mechanism of benzoylformate decarboxylase using 13C and solvent deuterium isotope effects on benzoylformate and benzoylformate analogues

Benzoylformate decarboxylase (benzoylformate carboxy-lyase, BFD; EC 4.1.1.7) from Pseudomonas putida is a thiamine pyrophosphate (TPP) dependent enzyme which converts benzoylformate to benzaldehyde and carbon dioxide. The kinetics and mechanism of the benzoylformate decarboxylase reaction were studied by solvent deuterium and 13C kinetic isotope effects with benzoylformate and a series of substituted benzoylformates (pCH3O, pCH3, pCl, and mF). The reaction was found to have two partially rate-determining steps: initial tetrahedral adduct formation (D2O sensitive) and decarboxylation (13C sensitive). Solvent deuterium and 13C isotope effects indicate that electron-withdrawing substituents (pCl and mF) reduce the rate dependence upon decarboxylation such that decreased 13(V/K) effects are observed. Conversely, electron-donating substituents increase the rate dependence upon decarboxylation such that a larger 13(V/K) is seen while the D2O effects on V and V/K are not dramatically different from those for benzoylformate. All of the data are consistent with substituent stabilization or destabilization of the carbanionic intermediate (or carbanion-like transition state) formed during decarboxylation. Additional information regarding the mechanism of the enzymic reaction was obtained from pH studies on the reaction of benzoylformate and the binding of competitive inhibitors. These studies suggest that two enzymic bases are required to be in the correct protonation state (one protonated and one unprotonated) for optimal binding of substrate (or inhibitors).     

Exosite binding tethers the macromolecular substrate to the prothrombinase complex and directs cleavage at two spatially distinct sites

The prothrombinase complex, composed of the proteinase, factor Xa, bound to factor Va on membranes, catalyzes thrombin formation by the specific and ordered proteolysis of prothrombin at Arg(323)-Ile(324), followed by cleavage at Arg(274)-Thr(275). We have used a fluorescent derivative of meizothrombin des fragment 1 (mIIaDeltaF1) as a substrate analog to assess the mechanism of substrate recognition in the second half-reaction of bovine prothrombin activation. Cleavage of mIIaDeltaF1 exhibits pseudo-first order kinetics regardless of the substrate concentration relative to K(m). This phenomenon arises from competitive product inhibition by thrombin, which binds to prothrombinase with exactly the same affinity as mIIaDeltaF1. As thrombin is known to bind to an exosite on prothrombinase, initial interactions at an exosite likely play a role in the enzyme-substrate interaction. Occupation of the active site of prothrombinase by a reversible inhibitor does not exclude the binding of mIIaDeltaF1 to the enzyme. Specific recognition of mIIaDeltaF1 is achieved through an initial bimolecular reaction with an enzymic exosite, followed by an active site docking step in an intramolecular reaction prior to bond cleavage. By alternate substrate studies, we have resolved the contributions of the individual binding steps to substrate affinity and catalysis. This pathway for substrate binding is identical to that previously determined with a substrate analog for the first half-reaction of prothrombin activation. We show that differences in the observed kinetic constants for the two cleavage reactions arise entirely from differences in the inferred equilibrium constant for the intramolecular binding step that permits elements surrounding the scissile bond to dock at the active site of prothrombinase. Therefore, substrate specificity is achieved by binding interactions with an enzymic exosite that tethers the protein substrate to prothrombinase and directs cleavage at two spatially distinct scissile bonds.     

Crystal structures of complexes of bacterial DD-peptidases with peptidoglycan-mimetic ligands: the substrate specificity puzzle

The X-ray crystal structures of covalent complexes of the Actinomadura R39 dd-peptidase and Escherichia coli penicillin-binding protein (PBP) 5 with β-lactams bearing peptidoglycan-mimetic side chains have been determined. The structure of the hydrolysis product of an analogous peptide bound noncovalently to the former enzyme has also been obtained. The R39 dd-peptidase structures reveal the presence of a specific binding site for the d-α-aminopimelyl side chain, characteristic of the stem peptide of Actinomadura R39. This binding site features a hydrophobic cleft for the pimelyl methylene groups and strong hydrogen bonding to the polar terminus. Both of these active site elements are provided by amino acid side chains from two separate domains of the protein. In contrast, no clear electron density corresponding to the terminus of the peptidoglycan-mimetic side chains is present when these β-lactams are covalently bound to PBP5. There is, therefore, no indication of a specific side-chain binding site in this enzyme. These results are in agreement with those from kinetics studies published earlier and support the general prediction made at the time of a direct correlation between kinetics and structural evidence. The essential high-molecular-mass PBPs have demonstrated, to date, no specific reactivity with peptidoglycan-mimetic peptide substrates and β-lactam inhibitors and, thus, probably do not possess a specific substrate-binding site of the type demonstrated here with the R39 dd-peptidase. This striking deficiency may represent a sophisticated defense mechanism against low-molecular-mass substrate-analogue inhibitors/antibiotics; its discovery should focus new inhibitor design.     

Isoforms of human cytochrome-c oxidase. Subunit composition and steady-state kinetic properties.

The subunit pattern and the steady-state kinetics of cytochrome-c oxidase from human heart, muscle, kidney and liver were investigated. Polyacrylamide gel electrophoresis of immunopurified cytochrome-c oxidase preparations suggest that isoforms of subunit VIa exist, which show differences in staining intensity and electrophoretic mobility. No differences in subunit pattern were observed between the other nucleus-encoded subunits of the various cytochrome-c oxidase preparations. Tissue homogenates, in which cytochrome-c oxidase was solubilised with laurylmaltoside, were directly used in the assays to study the cytochrome-c oxidase steady-state kinetics. Cytochrome-c oxidase concentrations were determined by immunopurification followed by separation and densitometric analysis of subunit IV. When studied in a medium of low ionic strength, the biphasic kinetics of the steady-state reaction between human ferrocytochrome c and the four human cytochrome-c oxidase preparations revealed large differences for the low-affinity TNmax (maximal turnover number) value, ranging from 77 s-1 for kidney to 273 s-1 for liver cytochrome-c oxidase at pH 7.4, I = 18 mM. It is proposed that the low-affinity kinetic phase reflects an internal electron-transfer step. For the steady-state reaction of human heart cytochrome-c oxidase with human cytochrome c, Km and TNmax values of 9 microM and 114 s-1 were found, respectively, at high ionic strength (I = 200 mM, pH 7.4). Only minor differences were observed in the steady-state activity of the various human cytochrome-c oxidases. The interaction between human cytochrome-c oxidase and human cytochrome-c proved to be highly specific. At high ionic strength, a large decrease in steady-state activity was observed when reduced horse, rat or bovine cytochrome c was used as substrate. Both the steady-state TNmax and Km parameters were strongly affected by the type of cytochrome c used. Our findings emphasize the importance of using human cytochrome c in kinetic assays performed with tissues from patients with a suspected cytochrome-c oxidase deficiency.     

New model for activation of yeast pyruvate decarboxylase by substrate consistent with the alternating sites mechanism: demonstration of the existence of two active forms of the enzyme

Pyruvate decarboxylase from yeast (YPDC, EC 4.1.1.1) exhibits a marked lag phase in the progress curves of product (acetaldehyde) formation. The currently accepted kinetic model for YPDC predicts that, only upon binding of substrate in a regulatory site, a slow activation step converts inactive enzyme into the active form. This allosteric behavior gives rise to sigmoidal steady-state kinetics. The E477Q active site variant of YPDC exhibited hyperbolic initial rate curves at low pH, not consistent with the model. Progress curves of product formation by this variant were S-shaped, consistent with the presence of three interconverting conformations with distinct steady-state rates. Surprisingly, wild-type YPDC at pH < or =5.0 also possessed S-shaped progress curves, with the conformation corresponding to the middle steady state being the most active one. Reexamination of the activation by substrate of wild-type YPDC in the pH range of 4.5-6.5 revealed two characteristic transitions at all pH values. The values of steady-state rates are functions of both pH and substrate concentration, affecting whether the progress curve appears "normal" or S-shaped with an inflection point. The substrate dependence of the apparent rate constants suggested that the first transition corresponded to substrate binding in an active site and a subsequent step responsible for conversion to an asymmetric conformation. Consequently, the second enzyme state may report on "unregulated" enzyme, since the regulatory site does not participate in its generation. This enzyme state utilizes the alternating sites mechanism, resulting in the hyperbolic substrate dependence of initial rate. The second transition corresponds to binding a substrate molecule in the regulatory site and subsequent minor conformational adjustments. The third enzyme state corresponds to the allosterically regulated conformation, previously referred to as activated enzyme. The pH dependence of the Hill coefficient suggests a random binding of pyruvate in a regulatory and an active site of wild-type YPDC. Addition of pyruvamide or acetaldehyde to YPDC results in the appearance of additional conformations of the enzyme.     

Enzyme synthesis in myxamoebae of the cellular slime mould Dictyostelium discoideum during growth in axenic culture

1. The specific activities of beta-N-acetylglucosaminidase, acid phosphatase, alpha-mannosidase, beta-glucosidase, UDP-glucose pyrophosphorylase and alkaline phosphatase have been determined in myxamoebae of the cellular slime mould Dictyostelium discoideum Ax-2 grown on different media and in different phases of the growth cycle. 2. Variations in enzymic composition occur with changes in growth medium and phase of the growth cycle. 3. The intracellular location of the enzymes studied has been determined. 4. Two enzymes, beta-N-acetylglucosaminidase and alpha-mannosidase, are not only synthesized preferentially as the myxamoebae enter the stationary phase of growth but they are also excreted. The excretion process appears to be specific, because other enzymes that occur in the same intracellular fraction are not excreted.     

Seminal plasma accelerates semen-derived enhancer of viral infection (SEVI) fibril formation by the prostatic acid phosphatase (PAP248-286) peptide

Amyloid fibrils contained in semen, known as SEVI, or semen-derived enhancer of viral infection, have been shown to increase the infectivity of HIV dramatically. However, previous work with these fibrils has suggested that extensive time and nonphysiologic levels of agitation are necessary to induce amyloid formation from the precursor peptide (a proteolytic cleavage product of prostatic acid phosphatase, PAP(248-286)). Here, we show that fibril formation by PAP(248-286) is accelerated dramatically in the presence of seminal plasma (SP) and that agitation is not required for fibrillization in this setting. Analysis of the effects of specific SP components on fibril formation by PAP(248-286) revealed that this effect is primarily due to the anionic buffer components of SP (notably inorganic phosphate and sodium bicarbonate). Divalent cations present in SP had little effect on the kinetics of fibril formation, but physiologic levels of Zn(2+) strongly protected SEVI fibrils from degradation by seminal proteases. Taken together, these data suggest that in the in vivo environment, PAP(248-286) is likely to form fibrils efficiently, thus providing an explanation for the presence of SEVI in human semen.     

A study of the role of histidine side-chains at the active centre of amylolytic enzymes

The role of histidine side-chains in reactions catalysed by porcine-pancreatic alpha-amylase, sweet-potato beta-amylase, and Aspergillus niger glucamylase has been studied by using diethyl pyrocarbonate, a specific protein reagent. Changes in the activity, binding affinity, and apparent kinetic parameters due to ethoxycarbonylation have been determined. For pancreas alpha-amylase, four of the eight histidine groups, for sweet-potato beta-amylase, six of the seven histidine groups, and for A. niger glucamylase, four of the six histidine groups were shown to be ethoxycarbonylated. Ethoxycarbonylation occurred as an apparent first-order reaction, with rate constants in the range 3.6–4.9 x 10^?2min^?1. Ethoxycarbonylation of the histidine group at the active centre rapidly inactivated alpha-amylase, whereas the other three groups are not located in the active centre, although activity and substrate binding are only slightly affected by their modification. For beta-amylase and glucamylase, only slight or no change in activity could be detected on ethoxycarbonylation, whereas significant changes were observed in the binding affinity.     

Kinetic model for the co-action of beta-amylase and debranching enzymes in the production of maltose

The kinetics of the hydrolysis of starch with beta-amylase and debranching enzymes was studied. The hydrolysis of the alpha-1, 6-glycoside bonds of the substrate by debranching enzymes does not create any new nonreducing ends, so debranching enzyme promotes the action of beta-amylase not by increasing the concentration of the substrate of beta-amylase but by increasing the linear linkage portion of the substrate. The introduction of an effective chain length function was used to formulate a kinetic model.     

A kinetic study of -acetohydroxy acid isomeroreductase from Salmonella typhimurium

The kinetic mechanism of α-acetohydroxy acid isomeroreductase from Salmonella typhimurium has been investigated by initial velocity kinetic and product inhibition studies. The results of the initial velocity studies are consistent with a sequential reaction. The product inhibition studies suggest an ordered reaction with NADPH and the acetohydroxy acid adding in that order, and dihydroxy acid release before NADP release.NADPH binding has been studied both by fluorimetric techniques and difference spectroscopy. From these investigations it has been calculated that 4 moles of NADPH bind per mole of enzyme; the first molecule of NADPH binds with a dissociation constant of 1.7 × 10^?6m, the subsequent 3 moles of NADPH bind with a constant of 6 × 10^?6m. Biphasic kinetics have been demonstrated at a wide range of NADPH concentrations. The occurrence of biphasic kinetics and two separate binding constants are discussed in terms of negative cooperativity.     

Kinetic study of the enzyme NADPH cytochrome-C (P-450) reductase: non-Michaelian behaviour

1. Contrary to what has been accepted until now, the enzyme exhibits non-Michaelian kinetics both against NADPH and against cytochrome-c as substrates; deviations were detected that have led to the proposition of a rate equation of minimum degree 2:2. 2. A general mechanism is proposed that includes, apart from the binding of the enzyme to NADPH, the formation of an enzyme-cytochrome-c complex, both routes leading to the formation of a ternary-complex NADPH-enzyme-acceptor. 3. From the latter, a series of intermediate steps finally leads to the release of the enzyme in conditions to start a new catalytic cycle. 4. Application of the King-Altman method to this mechanism yields a kinetic equation of degree 2:2 with respect to the cytochrome-c and NADPH, in accordance with our experimental results.     

Raw starch adsorption-desorption purification of a thermostable beta-amylase from Clostridium thermosulfurogenes

The beta-amylase from Clostridium thermosulfurogenes was readily adsorbed onto raw starch. The adsorbed beta-amylase was eluted from raw starch by using boiled soluble starch solution as an elutant. The soluble starch treated beta-amylase could not adsorb onto raw starch which indicates that the soluble and insoluble substrate binding sites of the beta-amylase may be the same. The beta-amylase was purified to homogeneity by raw starch adsorption-desorption techniques and octyl-Sepharose chromatography. It had a specific activity of 4188 units/mg protein. The insoluble substrate adsorption-desorption technique may be used for the purification of other enzymes.     

Cloning and nucleotide sequence of the gene coding for enzymatically active fragments of the Bacillus polymyxa beta-amylase.

The gene encoding beta-amylase was cloned from Bacillus polymyxa 72 into Escherichia coli HB101 by inserting HindIII-generated DNA fragments into the HindIII site of pBR322. The 4.8-kilobase insert was shown to direct the synthesis of beta-amylase. A 1.8-kilobase AccI-AccI fragment of the donor strain DNA was sufficient for the beta-amylase synthesis. Homologous DNA was found by Southern blot analysis to be present only in B. polymyxa 72 and not in other bacteria such as E. coli or B. subtilis. B. polymyxa, as well as E. coli harboring the cloned DNA, was found to produce enzymatically active fragments of beta-amylases (70,000, 56,000, or 58,000, and 42,000 daltons), which were detected in situ by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Nucleotide sequence analysis of the cloned 3.1-kilobase DNA revealed that it contains one open reading frame of 2,808 nucleotides without a translational stop codon. The deduced amino acid sequence for these 2,808 nucleotides encoding a secretory precursor of the beta-amylase protein is 936 amino acids including a signal peptide of 33 or 35 residues at its amino-terminal end. The existence of a beta-amylase of larger than 100,000 daltons, which was predicted on the basis of the results of nucleotide sequence analysis of the gene, was confirmed by examining culture supernatants after various cultivation periods. It existed only transiently during cultivation, but the multiform beta-amylases described above existed for a long time. The large beta-amylase (approximately 160,000 daltons) existed for longer in the presence of a protease inhibitor such as chymostatin, suggesting that proteolytic cleavage is the cause of the formation of multiform beta-amylases.     

Inactivation of o-diphenoloxidase in the pyrocatechol oxidation reaction

The inactivation kinetics of o-diphenoloxidase isolated from potato tubers was studied in the process of pyrocatechol oxidation. The enzyme when saturated with the substrate is inactivated with the inactivation rate constant kin = 0.5-1.0 min-1; kin depends on the initial concentration of pyrocatechol. The ultimate yield of the enzymic reaction product increases linearly with the initial concentration of the enzyme. Introduction of ethylene-diaminosulphate, a substance which condenses with o-quinones, does not increase the operation stability of o-diphenoloxidase. The data obtained evidence for inactivation of o-diphenoloxidase either at the level of the enzyme-substrate complex or due to bimolecular reaction with the substrate.