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At least 811 records · Page 45Linked to original sources

PubMed1999

Evidence for kinetic inhomogeneity in the curing of epoxy using the near-infrared multispectral imaging technique.

The kinetics of curing of an epoxy resin by amine was studied using a near-infrared (NIR) multispectral imaging spectrometer. This imaging spectrometer is capable of sensitively and rapidly recording NIR spectral images of a sample because it was constructed with an acousto-optic tunable filter and an InGaAs focal plane array NIR camera. The high sensitivity and fast scanning ability of the spectrometer make it suitable for kinetic determination of fast reactions. Additionally, it has features that conventional NIR spectrometers cannot offer, namely, its ability to provide kinetic information at different positions within a sample. Furthermore, the high spatial resolution and sensitivity of the InGaAs camera make it possible to determine the kinetics from data collected by a single pixel in the camera. The kinetics of curing of epoxy by amine, determined by this multispectral imaging instrument, show that the reaction rates within the sample are very inhomogeneous. Because of this kinetic inhomogeneity, differences in the degrees of cure at different positions within the sample can be as high as 37% when data from only a single pixel were used for calculation. The inhomogeneity was not be observed if an average of a large number of pixels were used.

Epoxy Compounds↗

PubMed2000

Protein redox potential measurements based on kinetic analysis with mediated continuous-flow column electrolytic spectroelectrochemical technique. Application to TTQ-containing methylamine dehydrogenase.

Kinetic determination of protein redox potentials with a mediated continuous-flow column electrolytic spectroelectrochemical technique (CFCESET) is described. In this method, the redox state of the mediator is completely regulated by the continuous-flow column electrolysis, and the homogeneous redox reaction between the mediator and a protein sample in the column is monitored spectroscopically at the downstream of the column. The protein/mediator reaction is in the pseudo-first-order kinetics, and then the rate equation is analytically solved. The kinetic analysis provides the protein redox potential as well as the homogeneous rate constant. In the kinetic measurements, equilibration of the system within the column is not required, which allows the use of increased kinds of mediators. This method was successfully applied to quinoprotein methylamine dehydrogenase containing tryptophan tryptophylquinone (TTQ) as a prosthetic group. The kinetic aspect is also valuable for the thermodynamic analysis with the mediated CFCESET. The half-life time of the kinetics can be utilized to optimize the system for the attainment of the equilibrated state within the column and can provide the assurance that the system is in equilibrium.

Electrochemistry↗

PubMed1995

Kinetics of inactivation of aminoacylase by 2-chloromercuri-4-nitrophenol: a new type of complexing inhibitor.

The kinetic theory of the substrate reaction during modification of enzyme activity previously described [Tsou (1988) Adv. Enzymol. 61, 381-436] has been applied to a study of the inactivation kinetics of aminoacylase by 2-chloromercuri-4-nitrophenol (MNP). The results indicate that the mechanism of reaction between MNP and aminoacylase is a special type of irreversible inhibition. The main features of this type of inhibitor are as follows: (i) the reaction kinetics of inhibitor with enzyme is a single exponential process; (ii) inhibition shows a noncompetitive, complexing behavior; (iii) the first inhibitor-enzyme complex, EI, still has some enzyme activity, and hence the plot of [P]infinity versus the reciprocal of inhibitor concentration gives a straight line with a positive intercept at the ordinate. On the basis of the kinetic equation of substrate reaction in the presence of the inhibitor, a plotting method has been developed for determining the inhibition kinetic constants. As an example, all reaction kinetic constants of aminoacylase with 2-chloromercuri-4-nitrophenol have been determined. The results of the present study suggest that the essential thiol group at the active site of aminoacylase may have a significant effect on the catalytic step but is not involved in substrate binding.

Amidohydrolases↗

PubMed1991

Electron transfer within xanthine oxidase: a solvent kinetic isotope effect study.

Solvent kinetic isotope effect studies of electron transfer within xanthine oxidase have been performed, using a stopped-flow pH-jump technique to perturb the distribution of reducing equivalents within partially reduced enzyme and follow the kinetics of reequilibration spectrophotometrically. It is found that the rate constant for electron transfer between the flavin and one of the iron-sulfur centers of the enzyme observed when the pH is jumped from 10 to 6 decreases from 173 to 25 s-1 on going from H2O to D2O, giving an observed solvent kinetic isotope effect of 6.9. An effect of comparable magnitude is observed for the pH jump in the opposite direction, the rate constant decreasing from 395 to 56 s-1. The solvent kinetic isotope effect on kobs is found to be directly proportional to the mole fraction of D2O in the reaction mix for the pH jump in each direction, consistent with the effect arising from a single exchangeable proton. Calculations of the microscopic rate constants for electron transfer between the flavin and the iron-sulfur center indicate that the intrinsic solvent kinetic isotope effect for electron transfer from the neutral flavin semiquinone to the iron-sulfur center designated Fe/S I is substantially greater than for electron transfer in the opposite direction and that the observed solvent kinetic isotope effect is a weighted averaged of the intrinsic isotope effects for the forward and reverse microscopic electron-transfer steps.(ABSTRACT TRUNCATED AT 250 WORDS)

Deuterium↗

PubMed1991

The two calcium ions initially bound to nonphosphorylated sarcoplasmic reticulum Ca(2+)-ATPase can no longer be kinetically distinguished when they dissociate from phosphorylated ATPase toward the lumen.

Using rapid filtration, we investigated the kinetics of release toward the lumen of sarcoplasmic reticulum vesicles of the two Ca2+ ions transported by the Ca(2+)-dependent ATPase of these vesicles. Release rates at 20 degrees C were measured by three methods, with vesicles previously made leaky with an ionophore. First, we measured the rate at which 45Ca2+ bound to ATPase approached its steady-state level after addition of ATP to the 45Ca(2+)-equilibrated ATPase. At pH 6 in the absence of potassium, the observed kinetics did not reveal any very fast phase of 45Ca2+ dissociation from phosphorylated ATPase. Second, we measured the kinetics of 45Ca2+ dissociation from phosphorylated ATPase in a "chase" experiment, by isotopic dilution of calcium under turnover conditions in the presence of potassium. We found that these kinetics were essentially monophasic. Moreover, when they were measured in the presence of a high concentration of calcium, designed to saturate the low-affinity calcium transport sites on the lumenal side of the ATPase, they only departed slightly from monophasic behavior, irrespective of the experimental pH (pH 6, 7, or 9). This small perturbation by high calcium concentrations of the observed dissociation kinetics was attributed to ADP-facilitated rapid exchange of 40Ca2+ for Mg2+ at the catalytic site of phosphorylated ATPase. The third method was based on the fact that phosphorylation-induced 45Ca2+ occlusion occurred faster than 45Ca2+ dissociation from nonphosphorylated ATPase: here, we measured the rate of 45Ca2+ internalization on addition to 45Ca(2+)-saturated ATPase of an unlabeled ATP-containing medium. This method allowed separate observation of the dissociation kinetics of each of the two 45Ca2+ ions bound to phosphorylated ATPase, after either one or the other had been labeled by a preliminary partial isotopic exchange in the non-phosphorylated state of the ATPase. We found that after ATP-induced phosphorylation, the two 45Ca2+ ions dissociated toward the lumenal medium with virtually identical rate constants; this was observed under different ionic and pH conditions and also in the presence of a high Ca2+ concentration. As a control, the same partial isotopic exchange procedure allowed us to confirm that, in contrast, when ATP was absent from the final dissociation medium, the two 45Ca2+ ions dissociated from nonphosphorylated ATPase toward the cytoplasmic medium at different rates, the one bound more deeply only dissociating after a lag period corresponding to dissociation of the superficial one.(ABSTRACT TRUNCATED AT 400 WORDS)

Adenosine Triphosphate↗

PubMed1992

Kinetics and mechanism of the folding of cytochrome c.

The reversible folding of cytochrome c in urea at pH 4.0 was investigated by repetitive pressure perturbation kinetics and by equilibrium spectroscopic methods. Two folding reactions were observed in the 1 ms to 10 s time range. The rates and amplitudes of these reactions depend on urea concentration in a complex manner, which is different for each process. The absorbance spectra of the kinetic amplitudes of the two reactions also differ from each other. A model with a three-state mechanism can quantitatively account for all of the kinetic and equilibrium data, and it enables us to determine the rate constants and volume changes of the two steps. If a rapid protonation step is added to the mechanism, the analysis can be extended to calculate the pH dependence of the rate and amplitude of the faster folding step. This pH dependence is in excellent agreement with previously published data [Tsong, T. Y. (1977) J. Biol. Chem. 252, 8778-8780]. Kinetic experiments in the 695-nm band show clearly that the axial ligand methionine-80 is involved in the slow folding process and the other axial ligand, histidine-18, is involved in the fast process. Additional experiments with a cyanogen bromide fragment of the protein, and fluorescence detection of the folding kinetics of the intact protein, support an interpretation of the model in terms of known structural elements of cytochrome c. This work provides new information about the mechanism of the folding of cytochrome c, resolves conflicts in earlier interpretations, and demonstrates the applicability of the repetitive pressure perturbation kinetics method to protein folding.

Animals↗

PubMed1992

Kinetic mechanism of the adenosine 3',5'-monophosphate dependent protein kinase catalytic subunit in the direction of magnesium adenosine 5'-diphosphate phosphorylation.

In order to define the overall kinetic mechanism of adenosine 3',5'-monophosphate dependent protein kinase catalytic subunit and also to elaborate the kinetic mechanism in the direction of peptide phosphorylation, we have determined its kinetic mechanism in the direction of MgADP phosphorylation. Studies of initial velocity as a function of uncomplexed Mg2+ (Mgf) in the absence and presence of dead-end inhibitors were used to define the kinetic mechanism. Data are consistent with the overall kinetic mechanism in the direction of MgADP phosphorylation being random with both the pathways allowed, i.e., the pathway in which MgADP binds to the enzyme prior to phosphorylated peptide and the pathway in which phosphorylated peptide binds to enzyme prior to MgADP. In addition, depending on the concentration of Mgf, one or the other pathway predominates. At low (0.5 mM) Mgf, the mechanism is steady-state ordered with the pathway in which phosphorylated peptide binds first being preferred; at high (10 mM) Mgf, the kinetic mechanism is equilibrium ordered, and the pathway in which MgADP binds first is preferred. This change in mechanism to equilibrium ordered at higher concentration of Mgf is due to an increase in affinity of the enzyme for MgADP and a decrease in affinity for the phosphorylated peptide. The Haldane relationship gives a Keq of 2 +/- 1 x 10(3) at pH 7.2, in agreement with the values obtained from 31P NMR (1.6 +/- 0.8 x 10(3)) and direct determination of reactant concentrations at equilibrium (3.5 +/- 0.6 x 10(3)).

Adenosine Diphosphate↗

PubMed1994

Kinetic mechanism of cytochrome c folding: involvement of the heme and its ligands.

The covalently attached heme and its axial ligands not only are essential for the structure and function of cytochrome c but they also play an important role in the folding process. Under typical denaturing conditions (concentrated guanidine hydrochloride or urea near pH 7), one of the axial ligands, His 18, remains bound to the oxidized heme iron, but the second ligand, Met 80, is replaced by a non-native histidine ligand (His 26 or His 33 in horse cytochrome c). Using quenched-flow and NMR methods, hydrogen exchange rates were measured for several individual amide protons in guanidine-denatured horse cytochrome c. The observation of a single highly protected (140-fold) backbone amide, that of His 18, suggests the presence of a persistent H-bond consistent with heme ligation of the His 18 side chain in the unfolded state. Heme absorbance changes induced by rapid acidification of oxidized cytochrome c in 4.5 M guanidine hydrochloride from pH 7.8 to 4.6 or below exhibit two kinetic phases with rates of 110 and 25 s-1, attributed to the dissociation of non-native histidine ligands from the heme in the unfolded state. The kinetics of folding from guanidine-denatured cytochrome c under a variety of initial and final conditions was investigated by stopped-flow methods, using tryptophan fluorescence as a conformational probe and Soret absorbance as a probe for the ligation state of the heme. A fast kinetic phase (80 s-1) accompanied by a major decrease in fluorescence and a minor absorbance change coincides with the formation of a partially folded intermediate with interacting chain termini detected in earlier pulsed NH exchange measurements [Roder, H., Elöve, G. A., & Englander, S. W. (1988) Nature 335, 700]. At neutral pH, an intermediate kinetic phase (1.8 s-1) accounts for 78% of the absorbance change and 47% of the fluorescence change. In contrast, the folding kinetics at pH 5 is dominated by the fast phase, and the amplitude of the intermediate phase is reduced to approximately 10%. The pH-dependent amplitude changes show titration behavior with an apparent pK of approximately 5.7, consistent with the protonation of a single histidine residue. The intermediate phase can also be suppressed by the addition of 20 mM imidazole. Since both of these conditions interfere with histidine ligation, the intermediate kinetic phase is attributed to the presence of a non-native histidine ligand (His 26 or His 33) that can become trapped in a partially folded intermediate.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗

PubMed1994

Kinetics of CheA autophosphorylation and dephosphorylation reactions.

The protein kinase CheA of Escherichia coli plays a central role in the signal transduction pathway controlling the swimming behavior of the cell in response to extracellular chemical gradients. CheA autophosphorylates at a rate controlled by the ligand binding state of chemotaxis receptor/transducer proteins. CheA directs the activities of CheY and CheB, effector proteins that become phosphorylated as a result of their interaction with phospho-CheA. In this study, we performed a detailed kinetic analysis of CheA's autophosphorylation reaction, and its dephosphorylation by ADP. Our kinetic data are consistent with a three-step mechanism for CheA autophosphorylation/dephosphorylation involving (i) substrate binding, (ii) phospho-transfer, and (iii) product release. We determined the dissociation constant for the kinetically defined CheA.ATP complex to be approximately 300 microM and the limiting rate constant for autophosphorylation to be approximately 0.026 s-1 at saturating ATP concentration. Our results indicate that the apparent dissociation constant of the phospho-CheA.ADP complex is approximately 42 microM and that the limiting rate constant for CheA dephosphorylation is approximately 0.028 s-1 at saturating ADP concentration. We corroborated the kinetically determined Kd values by performing independent ligand binding experiments. In addition, we found that the kinetics of trans-phosphorylation, involving mutant proteins CheA48HQ and CheA470GK, exhibited kinetic properties similar to those observed for autophosphorylation of wild-type CheA, although the limiting rate constant (0.008 s-1) was somewhat slower for this trans-phosphorylation reaction. These results will provide a framework for assessing the effects of various cheA mutations as well as for exploring the nature of CheA regulation by the chemotaxis receptor/transducer proteins.

Adenosine Diphosphate↗

PubMed1994

A kinetic mechanism for cleavage of precursor tRNA(Asp) catalyzed by the RNA component of Bacillus subtilis ribonuclease P.

A kinetic mechanism is presented for the cleavage of Bacillus subtilis precursor tRNA(Asp) catalyzed by the RNA component of B. subtilis ribonuclease P (RNase P) under optimal conditions (50 mM Tris Cl (pH 8.0), 100 mM MgCl2, and 800 mM NH4Cl, 37 degrees C). This kinetic mechanism was derived from measuring pre-steady-state, steady-state, single-turnover, and binding kinetics using a combination of quench-flow, gel filtration, and gel shift techniques. A minimal kinetic description involves the following: (1) binding of pre-tRNA(Asp) to RNase P RNA rapidly (6.3 x 10(6) M-1 s-1), but slower than the diffusion-controlled limit; (2) cleavage of the phosphodiester bond with a rate constant of 6 s-1; (3) dissociation of products in a kinetically preferred pathway, with the 5' RNA fragment dissociating first (> or = 0.2 s-1) followed by rate-limiting tRNA dissociation (0.02 s-1); and (4) formation of a second conformer of RNase P RNA during the catalytic cycle that is less stable and binds pre-tRNA(Asp) significantly more slowly (7 x 10(4) M-1 s-1). This scheme involves the isolation of individual steps in the reaction sequence, is consistent with steady-state data, and pinpoints the rate-determining step under a variety of conditions. This kinetic mechanism will facilitate a more accurate definition of the role of metals, pH, and the protein component in each step of the reaction and provide an essential background for understanding the influence of structural changes on the catalytic activity.

Bacillus subtilis↗

PubMed1986

Folding/unfolding kinetics of mutant forms of iso-1-cytochrome c with replacement of proline-71.

Proline-71, an evolutionally conserved residue that separates two short alpha-helical regions, is replaced by valine, threonine, or isoleucine in at least partially functional forms of iso-1-cytochrome c from Saccharomyces cerevisiae [Ernst, J. F., Hampsey, D. M., Stewart, J. W., Rackovsky, S., Goldstein, D., & Sherman, F. (1985) J. Biol. Chem. 260, 13225-13236]. To assign the effects of perturbations at position 71 to steps in the process of protein folding, the kinetic properties of the folding/unfolding reactions of normal protein and the three mutant forms are compared. At pH 6.0, 20 degrees C, fluorescence-detected folding/unfolding kinetics are monitored below, within, and above the equilibrium transition zone by using stopped-flow mixing to perform guanidine hydrochloride concentration jumps. Three kinetic phases are detected for each of the four proteins. The fastest of these phases (tau 3) differs in rate for the wild type and mutant proteins. The remaining kinetic phases (tau 1 and tau 2) have similar rates for all four proteins over the entire range of folding/unfolding conditions. The guanidine hydrochloride dependence of the relative amplitudes of the kinetic phases is complex and is sensitive to the nature of the substituent at position 71: each of the four proteins shows differences in the fraction of folding/unfolding associated with the two fastest rate processes. The results suggest that it is the location of the mutation in the primary structure rather than the nature of the substituent that determines which kinetic step (or steps) is changed in rate.(ABSTRACT TRUNCATED AT 250 WORDS)

Cytochrome c Group↗

PubMed1988

Kinetic mechanism of calcium binding to whiting parvalbumin.

Calcium binding to whiting parvalbumin induces large changes in the fluorescence, absorption, and circular dichroism spectra of the protein. The fluorescence emission maximum of the single tryptophan shifts from 325 to 348 nm upon the removal of calcium and decreases in intensity by 50%. All of the spectral changes are linear between 0 and 2 mol of calcium bound/mol of protein, which suggests that the only protein species present in significant concentration are PA0 and Pa-Ca2. The kinetics of calcium binding measured by stopped-flow fluorescence are accurately single exponential from 2 X 10(-7) to 2 X 10(-4) M free calcium. The kinetics of calcium dissociation show a pronounced lag and are best fit by two rate constants of 1.2 and 3.0 s-1. The minimal kinetic mechanism that adequately describes the rate and equilibrium data is a branched pathway mechanism in which the rate and equilibrium constants are markedly different for each pathway: (formula; see text) At [Ca] less than 2 microM the upper kinetic pathway of calcium binding predominates whereas at [Ca] greater than 2 microM calcium binding occurs predominantly by the lower kinetic pathway. Calcium dissociates primarily by the upper kinetic pathway.

Animals↗

PubMed1989

Uncoupling of oxidative phosphorylation: different effects of lipophilic weak acids and electrogenic ionophores on the kinetics of ATP synthesis.

Previous studies from this laboratory have shown that the kinetics of ATP synthesis by bovine heart submitochondrial particles (SMP) are modulated by the coupled rate of respiration between two extremes of Vmax and apparent Km's for ADP and Pi [Matsuno-Yagi, A., & Hatefi, Y. (1986) J. Biol. Chem. 261, 14031-14038; Hekman, C., Matsuno-Yagi, A., & Hatefi, Y. (1988) Biochemistry 27, 7559-7565]. Thus, with ADP as the variable substrate, ATP synthesis occurred with Vmax = 200 nmol of ATP min-1 (mg of protein)-1 at 30 degrees C and an apparent KmADP = 2-4 microM at low rates of respiration, and with Vmax = 11,000 nmol of ATP min-1 (mg of protein)-1 at 30 degrees C and an apparent KmADP = 120-160 microM at high rates of respiration. At intermediate respiration rates, it was necessary to introduce a third intermediate KmADP for best fit of the kinetic data, indicating that transition from one kinetic extreme to the other is not abrupt and involves intermediate kinetic states of the ATP synthase complexes. The present paper shows that uncouplers affect the kinetics of ATP synthesis by SMP in two ways. When used at moderate concentrations, electrogenic ionophores such as gramicidin D or valinomycin plus nigericin decreased the Vmax for ATP synthesis without changing the contributions of the low, intermediate, and high KmADP to the overall rate of ATP synthesis. By contrast, potent lipophilic weak acid uncouplers, such as FCCP, CCCP, S-13, and SF6847, decreased Vmax and converted the kinetics of ATP synthesis toward high KmADP.(ABSTRACT TRUNCATED AT 250 WORDS)

Acids↗

PubMed1989

Laser flash photolysis studies of the kinetics of reduction of spinach and Clostridium ferredoxins by a viologen analogue: electrostatically controlled nonproductive complex formation and differential reactivity among the iron-sulfur clusters.

We have studied the transient kinetics of electron transfer from a positively charged viologen analogue (propylene diquat), reduced by pulsed laser excitation of the deazariboflavin/EDTA system, to the net negatively charged ferredoxins from spinach and Clostridium pasteurianum. Spinach ferredoxin showed monophasic kinetics over the ionic strength range studied, consistent with the presence of only a single iron-sulfur center. Clostridium ferredoxin at low ionic strength showed biphasic kinetics, which indicates a differential reactivity of the two iron-sulfur centers of this molecule toward the electron donor. The kobsd values for the initial fast phase observed with Clostridium ferredoxin were ionic strength dependent, whereas the slow-phase kinetics were ionic strength independent. This correlates with the highly asymmetric charge distribution on the surface of the bacterial protein relative to the two iron-sulfur clusters. The kinetics corresponding to spinach ferredoxin reduction were also ionic strength dependent, and the results obtained with these kinetics and with the fast phase of the bacterial ferredoxin reduction were consistent with a mechanism involving electrostatically stabilized complex formation. For spinach ferredoxin, the second-order rate constant extrapolated to infinite ionic strength was 2-fold smaller, and the extrapolated limiting first-order rate constant was 10-fold smaller, than for Clostridium ferredoxin, indicating a smaller intrinsic reactivity of the spinach protein toward the electron donor. Differences in the rate constant values and the ionic strength dependencies with both ferredoxins are consistent with differences in cluster structure and environment and protein size and charge distribution. For both proteins, the total amount of ferredoxin reduced increased with the ionic strength.(ABSTRACT TRUNCATED AT 250 WORDS)

Clostridium↗

PubMed1990

Kinetics and mechanism of transfer of reduced and carboxymethylated apolipoprotein A-II between phospholipid vesicles.

The transfer of 14C-labeled, reduced and carboxymethylated human apolipoprotein A-II (RCM-AII) between small unilamellar vesicles (SUV) has been investigated. Ion-exchange chromatography was used for rapid separation of negatively charged egg phosphatidylcholine (PC)/dicetyl phosphate donor SUV containing bound 14C-labeled RCM-AII from neutral egg PC acceptor SUV present in 10-fold molar excess. The kinetics of 14C-labeled RCM-AII transfer in incubations of up to 12 h at 37 degrees C are consistent with the existence of fast, slow, and apparently "nontransferrable" pools of SUV-associated apolipoprotein; the transfers from these pools occur on the time scales of seconds or less, hours, and days/weeks, respectively. For donor SUV (0.15 mg of phospholipid/mL reaction mixture) containing about 15 RCM-AII molecules per vesicle, the sizes of the fast, slow, and nontransferrable pools are 13, 69, and 18%, respectively. The transfer of RCM-AII from the slow kinetic pool follows first-order kinetics, and the half-time (t 1/2) is about 3 h. The different kinetic pools of SUV-associated RCM-AII probably reflect apoprotein in different conformations of the SUV surface. Increasing the number of RCM-AII per donor SUV enlarges the size of the fast pool and increases the t 1/2 of transfer from the slow pool. In contrast, raising the incubation temperature reduces the t 1/2 of slow transfer. The t 1/2 of RCM-AII transfer from the slow kinetic pool is inversely proportional to the acceptor/donor SUV ratio which suggests that the transfer of apoprotein molecules in this kinetic pool is mediated by SUV collisions.(ABSTRACT TRUNCATED AT 250 WORDS)

Apolipoprotein A-II↗

PubMed1980

Kinetics of anticooperative binding of phenylalanyl-tRNAPhe and tRNAPhe to phenylalanyl-tRNA synthetase of Escherichia coli K10.

The kinetics of binding of Phe-tRNAPhe to phenylalanyl-tRNA synthetase were investigated by stopped-flow techniques employing 2-(p-toluidinyl)naphthalene-6-sulfonate as a reporter group. The kinetics were found to follow the concentration of Phe-tRNAPhe in terms of a saturation function. When added, tRNAPhe inhibited both the kinetics of association and the kinetics of dissociation. The kinetics of Phe-tRNAPhe binding have been analyzed to be a superposition of two reactions, the association to the phenylalanine-specific binding site and the association to the tRNA-specific binding site of the enzyme. The two modes are mutually exclusive. When tRNAPhe is added, the binding of Phe-tRNAPhe at the tRNA-specific site is suppressed by competitive inhibition. In binding to the tRNA-specific site, the unacylated tRNA affects the rates of association and dissociation of Phe-tRNAPhe binding at the Phe-specific site in terms of an antagonistic mechanism. The values of both rate constants are decreased depending on the degree of saturation of the enzyme with the unacylated tRNA before and after the association of Phe-tRNAPhe. A model is presented, and kinetic and equilibrium constants are determined.

Amino Acyl-tRNA Synthetases↗

PubMed1977

Kinetic properties of crystalline enzymes. Carboxypeptidase A.

Spectrochemical probes have demonstrated that the conformations of carboxypeptidase A differ in solution and in the crystalline state. Detailed kinetic studies of carboxypeptidase A crystals and solutions now show that the physical state of the enzyme is also a critical parameter that affects this enzyme's function. Thus, for all substrates examined, crystallization of the enzyme markedly reduces catalytic efficiency, kcat, from 20- to 1000-fold. In addition, substrate inhibition, apparent in solution for some di- and depsipeptides, is abolished with crystals, while longer substrates with normal kinetics in solution may exhibit activation with the crystals. The physical state of the enzyme also affects the mode of action of known modifiers of peptidase activity of the enzyme. In solution, addition of benzoylglycine or cinnamic acid markedly increases the rate of hydrolysis of CbzGly-Phe, but, with the crystalline enzyme, their addition hardly alters the activity. This is in accord with the weakening or absence of inhibitory enzyme-substrate binding modes. Kinetic studies on crystals were carried out over a range of enzyme concentrations, substrate concentrations, and crystal sizes, and in all instances the results are in good agreement with the theory developed by Katchalski for enzymes insolubilized by other means. Importantly, these kinetic parameters are determined under conditions which obviate artifacts due to diffusion limitation of substrates or products. The differences in the kinetic behavior of carboxypeptidase crystals, on the one hand, and of their solutions, on the other hand, bear importantly on efforts to interpret the function of the enzyme in structural terms. Hypothetical modes of substrate-enzyme interaction, generated by superimposing substrate models on the crystal structure of carboxypeptidase to stimulate kinetics in solution, have failed to detect all of these changes which affect inhibitory or activating binding modes.

Binding Sites↗

PubMed2002

Rapid kinetic studies of acetyl-CoA synthesis: evidence supporting the catalytic intermediacy of a paramagnetic NiFeC species in the autotrophic Wood-Ljungdahl pathway.

CO dehydrogenase/acetyl-CoA synthase (CODH/ACS), a key enzyme in the Wood-Ljungdahl pathway of anaerobic CO(2) fixation, is a bifunctional enzyme containing CODH, which catalyzes the reversible two-electron oxidation of CO to CO(2), and ACS, which catalyzes acetyl-CoA synthesis from CoA, CO, and a methylated corrinoid iron-sulfur protein (CFeSP). ACS contains an active site nickel iron-sulfur cluster that forms a paramagnetic adduct with CO, called the nickel iron carbon (NiFeC) species, which we have hypothesized to be a key intermediate in acetyl-CoA synthesis. This hypothesis has been controversial. Here we report the results of steady-state kinetic experiments; stopped-flow and rapid freeze-quench transient kinetic studies; and kinetic simulations that directly test this hypothesis. Our results show that formation of the NiFeC intermediate occurs at approximately the same rate as, and its decay occurs 6-fold faster than, the rate of acetyl-CoA synthesis. Kinetic simulations of the steady-state and transient kinetic results accommodate the NiFeC species in the mechanism and define the rate constants for the elementary steps in acetyl-CoA synthesis. The combined results strongly support the kinetic competence of the NiFeC species in the Wood-Ljungdahl pathway. The results also imply that the methylation of ACS occurs by attack of the Ni(1+) site in the NiFeC intermediate on the methyl group of the methylated CFeSP. Our results indicate that CO inhibits acetyl-CoA synthesis by inhibiting this methyl transfer reaction. Under noninhibitory CO concentrations (below 100 microM), formation of the NiFeC species is rate-limiting, while at higher inhibitory CO concentrations, methyl transfer to ACS becomes rate-limiting.

Acetate-CoA Ligase↗