Follow the protons: a low-barrier hydrogen bond unifies the mechanisms of the aspartic proteases

Seven proton transfers in five steps participate in a catalytic turnover of an aspartic protease. The Rosetta Stone for elucidating their role is a low-barrier hydrogen bond that holds the two aspartic carboxyls in a coplanar conformation. The proton of this bond shuttles between oxygens during chemical steps via hydrogen tunneling, unlike in previous proposals where it was transferred to substrate. After the release of products, both carboxyls are protonated and the bond is missing. Re-forming the bond is a significant step within a kinetic isomechanism. The bond also explains-at long last-the extremely low pK in pH profiles.

Uses of isotope effects in the study of enzymes

There have been few recent additions to the technical methods employed in the study of isotope effects, notable exceptions being the use of high pressure as an experimental variable and the measurement of heavy-atom isotope effects on maximal velocities using continuous-flow techniques. Most of the innovations are in the realm of new experimental designs that allow the asking of new questions. These designs include the use of isotope effects to: determine kinetic mechanisms, distinguish between changes in enzymatic activity and loss of active enzyme, distinguish between reactant-state origins and transition-state origins and quantify hydrogen tunneling, separate and quantify multiple origins of solvent isotope effects, distinguish between concerted and stepwise chemical mechanisms, characterize bond order changes in ligand binding, distinguish different pathways of inhibitor binding, and estimate intrinsic isotope effects.

Effect of pressure on deuterium isotope effects of formate dehydrogenase

High pressure causes biphasic effects on the oxidation of formate by yeast formate dehydrogenase as expressed on the kinetic parameter V/K, which measures substrate capture. Moderate pressure increases capture by accelerating hydride transfer. The transition state for hydride transfer has a smaller volume than the free formate plus the capturing form of enzyme, with DeltaV(double dagger) = -9.7 +/- 1.0 mL/mol. Pressures above 1.5 kbar decrease capture, reminiscent of effects on the conformational change associated with the binding of nicotinamide adenine dinucleotide (NAD(+)) to yeast alcohol dehydrogenase [Northrop, D. B., and Y. K. Cho (2000) Biochemistry 39, 2406-2412]. The collision complex, E-NAD(+), has a smaller volume than the more tightly bound reactant-state complex, E-NAD(+), with DeltaV = +83.4 +/- 5.2 mL/mol. A comparison of the effects of pressure on the oxidation of normal and deuteroformate shows that the entire isotope effect on hydride transfer, 2.73 +/- 0.20, arises solely from transition-state phenomena, as was also observed previously with yeast alcohol dehydrogense. In contrast, normal primary isotope effects arise solely from different zero-point energies in reactant states, and those that express hydrogen tunneling arise from a mixture of both reactant-state and transition-state phenomena. Moreover, pressure increases the primary intrinsic deuterium isotope effect, the opposite of what was observed with yeast alcohol dehydrogense. The lack of a decrease in the isotope effect is also contrary to empirical precedents from chemical reactions suspected of tunneling and to theoretical constructs of vibrationally enhanced tunneling in enzymatic reactions. Hence, this new experimental design penetrates transition states of enzymatic catalysis as never before, reveals the presence of phenomena foreign to chemical kinetics, and calls for explanations of how enzymes work beyond the tenants of physical organic chemistry.

Effects of high pressure on solvent isotope effects of yeast alcohol dehydrogenase

The effect of pressure on the capture of a substrate alcohol by yeast alcohol dehydrogenase is biphasic. Solvent isotope effects accompany both phases and are expressed differently at different pressures. These differences allow the extraction of an inverse intrinsic kinetic solvent isotope effect of 1.1 (i.e., (D(2(O)))V/K = 0.9) accompanying hydride transfer and an inverse equilibrium solvent isotope effect of 2.6 (i.e., (D(2(O)))K(s) = 0.4) accompanying the binding of nucleotide, NAD(+). The value of the kinetic effect is consistent with a reactant-state E-NAD(+)-Zn-OH(2) having a fractionation factor of phi approximately 0.5 for the zinc-bound water in conjunction with a transition-state proton exiting a low-barrier hydrogen bond with a fractionation factor between 0.6 and 0.9. The value of the equilibrium effect is consistent with restrictions of torsional motions of multiple hydrogens of the enzyme protein during the conformational change that accompanies the binding of NAD(+). The absence of significant commitments to catalysis accompanying the kinetic solvent isotope effect means that this portion of the proton transfer occurs in the same reactive step as hydride transfer in a concerted chemical mechanism. The success of this analysis suggests that future measurements of solvent isotope effects as a function of pressure, in the presence of moderate commitments to catalysis, may yield precise estimates of intrinsic solvent isotope effects that are not fully expressed on capture at atmospheric pressure.

Effect of pressure on deuterium isotope effects of yeast alcohol dehydrogenase: evidence for mechanical models of catalysis

Moderate pressure accelerates hydride transfer catalyzed by yeast alcohol dehydrogenase, indicative of a large negative volume of activation [Cho and Northrop (1999) Biochemistry 38, 7470-7475]. A comparison of the effects of pressure on the oxidation of normal versus dideuteriobenzyl alcohol generates a monophasic decrease in the intrinsic isotope effect; therefore, the volume of activation for the transition-state of deuteride transfer must be even more negative, by 10.4 mL/mol. This finding appears consistent with hydrogen tunneling previously proposed for this dehydrogenase [Cha, Y., Murray, C. J., and Klinman, J. P. (1989) Science 243, 1325-1330]. However, a global fit of the primary data shows that the entire isotope effect arises from a transition-state phenomenon, unlike normal isotope effects, which arise from different vibrational frequencies in reactant states, and tunneling isotope effects, which arise from a mixture of both states. Assuming the phenomenon is tunneling, the isotopic data are consistent with a Bell tunneling correction factor of Q(H) = 12 and an imaginary frequency of nu(H) = 1220 cm(-1), the first so calculated from experimental enzymatic data. This excessively large correction factor and the large difference in the isotopic activation volumes, plus the low isotope effects at extrapolated pressures, challenge traditional applications of physical organic chemistry and transition-state theory to enzymatic catalysis. They suggest instead that something other than transition-state stabilization or tunneling is responsible for the rate acceleration, something unique to the enzymatic transition state that does not occur in nonenzymatic reactions. Arguments for the vibrational model of coupled atomic motions and the fluctuating enzyme model of protein domain motion are put forward as possible interpretations.

Effects of pressure on the kinetics of capture by yeast alcohol dehydrogenase

High pressure causes biphasic effects on the oxidation of benzyl alcohol by yeast alcohol dehydrogenase as expressed in the kinetic parameter V/K which measures substrate capture. Moderate pressure increases the rate of capture of benzyl alcohol by activating the hydride transfer step. This means that the transition state for hydride transfer has a smaller volume than the free alcohol plus the capturing form of enzyme, with a DeltaV of -39 +/- 1 mL/mol, a value that is relatively large. This is the first physical property of an enzymatic transition state thus characterized, and it offers new possibilities for structure-activity analyses. Pressures of >1.5 kbar decrease the rate of capture of benzyl alcohol by favoring a conformation of the enzyme which binds nicotinamide adenine dinucleotide (NAD+) less tightly. This means that the ground state for tight binding, E-NAD+, has a larger volume than the collision complex, E-NAD+, with a DeltaV of 73 +/- 2 mL/mol. The equilibrium constant of the conformational change Keq is 75 +/- 13 at 1 atm. The effects of pressure on the capture of NAD+ have no activation phase because the conformational change is now being expressed kinetically instead of thermodynamically, together with but in opposition to hydride transfer, causing the effects to cancel. For yeast alcohol dehydrogenase, this conformational change had not been detected previously, but similar conformational changes have been found by spectroscopic means in other dehydrogenases, and some of them are also sensitive to pressure. The opposite signs for the volume change of tighter binding and hydride transfer run contrary to Pauling's hypothesis that substrates are bound more tightly in the transition state than in the Michaelian reactant state.

Rethinking fundamentals of enzyme action

Despite certain limitations, investigators continue to gainfully employ concepts rooted in steady-state kinetics in efforts to draw mechanistically relevant inferences about enzyme catalysis. By reconsidering steady-state enzyme kinetic behavior, this review develops ideas that allow one to arrive at the following new definitions: (a) V/K, the ratio of the maximal initial velocity divided by the Michaelis-Menten constant, is the apparent rate constant for the capture of substrate into enzyme complexes that are destined to yield product(s) at some later point in time; (b) the maximal velocity V is the apparent rate constant for the release of substrate from captured complexes in the form of free product(s); and (c) the Michaelis-Menten constant K is the ratio of the apparent rate constants for release and capture. The physiologic significance of V/K is also explored to illuminate aspects of antibiotic resistance, the concept of "perfection" in enzyme catalysis, and catalytic proficiency. The conceptual basis of congruent thermodynamic cycles is also considered in an attempt to achieve an unambiguous way for comparing an enzyme-catalyzed reaction with its uncatalyzed reference reaction. Such efforts promise a deeper understanding of the origins of catalytic power, as it relates to stabilization of the reactant ground state, stabilization of the transition state, and reciprocal stabilizations of ground and transition states.

Transpeptidation by porcine pepsin catalyzed by a noncovalent intermediate unique to its iso-mechanism

Porcine pepsin proteolysis of the hexapeptide Leu-Ser-p-nitro-Phe-Nle-Ala-Leu-OMe (where OMe = methoxy and Nle = norleucine) in the presence of dipeptide Leu-Leu synthesizes a new hexapeptide Leu-Ser-p-nitro-Phe-Leu-Leu. Contrary to transpeptidation kinetics of other proteases, which depend upon an acyl-enzyme intermediate, the time course for pepsin-catalyzed transpeptidation displays a distinct lag before reaching a steady-state reaction velocity. Moreover, this lag is coupled to burst kinetics for the formation of proteolytic products, Leu-Ser-p-nitro-Phe and Nle-Ala-Leu-OMe. The lag requires that free Leu-Ser-p-nitro-Phe accumulate in the reaction medium during the lag phase and subsequently rebind for transpeptidation. Consistent with this dissociative kinetic mechanism are normal solvent isotope effects on formation of the proteolytic products Leu-Ser-p-nitro-Phe (vH/vD = 2.2 +/- 0.2) and Nle-Ala-Leu-OMe (vH/vD = 1.8 +/- 0.1) as opposed to an inverse effect on the formation of the transpeptidation product Leu-Ser-p-nitro-Phe-Leu-Leu (vH/vD = 0.40 +/- 0.09). Because proteolysis is slower in D2O but transpeptidation is faster, the isotopically sensitive step must occur after release of both products of proteolysis, which precludes putative acyl-enzyme covalent intermediates. Isotopically enhanced transpeptidation is a new type of isotope effect but one that is consistent with the Uni Bi iso-mechanism previously postulated on the basis of solvent isotope effects on Vmax but not on Vmax/Km (Rebholz, K. L., and Northrop, D. B. (1991) Biochem. Biophys Res. Commun. 179, 65-69) and confirmed by solvent isotope effects on the onset of inhibition by pepstatin (Cho, Y.-K., Rebholz, K. L., and Northrop, D. B. (1994) Biochemistry 33, 9637-9642). As a new biochemical mechanism for peptide bond synthesis that has a potential for applications in biotechnology, it is here proposed that the energy necessary to drive peptide synthesis from free peptides comes from the sizable free energy drop associated with rehydration of the active site of pepsin in 55 M water.

Kinetics of enzymes with isomechanisms: britton induced transport catalyzed by bovine carbonic anhydrase II, measured by rapid-flow mass spectrometry

Induced transport of 13CO2 to H13CO3- by bovine carbonic anhydrase II in the presence of excess H12CO3- at pH 6.35 causes a temporary decrease in the concentration of 13CO2 from 0.169 to 0.092 +/- 0.003 mM, measured in less than half a second with a new rapid-flow, membrane-inlet mass spectrometer. From this perturbation, a value of 83 +/- 0.3 M-1 is calculated for the alpha term in Eq. [26] of H. G. Britton (Biochem. J. 133, 255-261, 1973). Combining alpha with the K(m) for bicarbonate (32 +/- 1 mM) and Eqs. [7] and [21] of K. L. Rebholz and D. B. Northrop (Methods Enzymol, 249, 211-240, 1995) yields a ratio of less than 0.57 +/- 0.04 for the apparent rate constants representing the isomerization segment and chemical conversion segment, respectively, of the enzyme-catalyzed dehydration of bicarbonate. These results provide proof positive for the previously inferred (but unproven despite universal acceptance) isomechanism for the carbonic anhydrases. Moreover, the data and new equations quantify the proposed internal proton transfer to be 64 +/- 4% rate-limiting for the bovine type II isoenzyme, a value similar to but more precise than estimates based upon solvent isotope effects and product inhibition kinetics.

Kinetics of enzymes with iso-mechanisms: solvent isotope effects

Kinetic isotope effects on enzymatic reactions which employ general acid or general base catalytic mechanisms may arise during reprotonations of free enzyme. These effects reveal kinetically significant isomerizations of the free enzyme, or iso-mechanisms. The effects are expressed kinetically at high concentrations of substrate, on Vmax or Kcat, but only thermodynamically at low substrate, on Vmax/K(m). The effects are also expressed on the noncompetitive inhibition constant of product inhibition, Kiip, because this parameter is dependent upon the steady-state concentration of the product form of free enzyme. A normal isotope effect on isomerization will decrease Vmax and Kiip, but not necessarily to the same degree. Which is greater will depend upon how rate-limiting the isomerization is to a complete turnover. Together they are related to the full effect on isomerization, DKiso, by their product: DKiso = DVmax DKiip. Moreover, precisely how rate-limiting the isomerization is to a turnover can be shown to be numerically equal to (DVmax - 1)/(DKiipDVmax - 1), which surprisingly, holds whether there are other isotope effects present or not. The new relationships applied to published data on bovine carbonic anhydrase II reveal an intrinsic solvent isotope effect of DK = 9 +/- 4, and an iso step that is less than 80% rate-limiting. Applied to porcine pepsin, a significant DV is accompanied by excessive standard error on DKiip, precluding the calculation of a definitive intrinsic solvent isotope effect.

Beyond enzyme kinetics: direct determination of mechanisms by stopped-flow mass spectrometry

The development of soft ionization techniques has made mass spectrometry an efficient and essential tool for the determinations of the primary structures of peptides and proteins. Recently the technique has been extended at an explosive rate to noncovalent structures as well as dynamics of protein-protein interactions. We propose here that interfacing mass spectrometry with a stopped-flow mixing device and applying these new techniques of soft ionization to enzymes undergoing catalysis will provide direct access to enzyme mechanisms, both kinetic mechanisms (which describe the comings and goings of substrates, products, and inhibitors) and chemical mechanisms (which describe the order of breaking and making chemical bonds). Transient-state measurements will provide the order of reaction events; steady-state measurements will provide the distribution and therefore the relative energy level of enzyme forms participating in those events; combining transient-state and steady-state measurements is therefore expected to provide sufficient information to construct a free energy diagram of the enzyme-catalyzed reaction.

Solvent isotope effects on the onset of inhibition of porcine pepsin by pepstatin

Pepstatin is a slow and tight-binding inhibitor of pepsin. Preincubating enzyme and inhibitor in H2O and in D2O in the absence of substrate generates an inverse solvent isotope effect of Dk = 0.69 +/- 0.06 on the apparent first-order rate constant for the decay in enzymatic activity. Proton inventory analysis of the inverse isotope effect suggests a single transition-state proton with a fractionation factor of 1.41 +/- 0.05. In contrast, combining enzyme with inhibitor and substrate (Leu-Ser-p-nitro-Phe-Nle-Ala-Leu-OMe) simultaneously along with observing the decay in enzymatic activity during catalytic turnovers generates a normal solvent isotope effect of Dk = 1.25 +/- 0.09. Proton inventory analysis of the normal isotope effect suggests a single reactant-state proton with a fractionation factor of 1.46 +/- 0.03. These two experimental designs are often considered equivalent, but the differences in isotopic data require that the pathway for onset of pepstatin inhibition in the absence of substrate must be different from the pathway in the presence of substrate. In the former, the inhibitor can only bind to free enzyme; in the latter, the inhibitor is hindered from binding to free enzyme because of competition with substrate but can bind to intermediate forms of enzyme generated during catalytic turnovers, downstream from enzyme-product complexes.

Kinetics of enzymes with iso-mechanisms: dead-end inhibition of fumarase and carbonic anhydrase II

Isomerization of free enzyme can be detected in kinetic patterns of dead-end inhibition because competitive substrate analogs yield noncompetitive inhibition versus product in reverse reaction kinetics. The ratio of slope and intercept inhibition constants allows a quantitative estimation of the relative kinetic significance of the isomerization to a catalytic turnover. Applying this kinetic analysis theoretically to inhibition data for bovine carbonic anhydrase II by anions [Y. Pocker and T. L. Deits (1982) J. Am. Chem. Soc. 104, 2424] provides an estimate of 43 +/- 13% for how rate-limiting the isomerization segment is at pH 6.6. Applying the analysis experimentally to porcine heart fumarase provides a competitive pattern of inhibition by trans-aconitate versus fumarate with Ki(s) = 2.0 +/- 0.5 mM, together with a non-competitive pattern versus malate, with Ki(s) = 0.8 +/- 0.1 mM and Kii = 2.3 +/- 0.4 mM. Assuming that the isomerization segment of fumarase is the reprotonation of an active site carboxyl and imidazole with pK1 = 5.53 and pK2 = 7.78 [Blanchard and Cleland (1980) Biochemistry 19, 4506], an apparent rate constant for the isomerization segment of fumarate hydration is estimated as 95 +/- 22 s-1, compared to 42 +/- 13 s-1 for the chemical segment and 29 +/- 0.7 s-1 for a complete turnover. In contrast, the values are 17000 +/- 5200, 82 +/- 25, and 82 +/- 3 s-1, respectively, for malate dehydration. Hence, the isomerization segment is 30 +/- 7% rate-limiting during fumarate hydration but less than 1% during malate dehydration.

Kinetics of enzymes with iso-mechanisms: analysis and display of progress curves

Isomerizations of free enzyme can be detected in progress curves as a deviation from linearity when plotted according to the linear transformation of integrated rate equations of Foster and Niemann. Iso-mechanisms can also be detected as a second inhibition constant when sets of progress curves are fitted by nonlinear regression to the integrated form of appropriate rate equations. The latter is extremely sensitive and can detect the presence of the additional inhibition constant from relationships between progress curves, even when a deviation from linearity is not apparent within individual plots using the graphical method. Both methods can detect iso-mechanisms from data that do not express oversaturation kinetics.

Kinetics of enzymes with iso-mechanisms: analysis of product inhibition

Isomerizations of free enzyme can be detected in kinetic patterns of product inhibition when the isomerization is partially rate-limiting. The kinetic pattern is non-competitive, owing to binding of substrate and product to different forms of free enzyme. This adds an additional term to the rate equation, sometimes represented as KSP. Several kineticists have noted that, as the rate of isomerization becomes high in relation to catalytic turnover, the intercept effect will become small, KSP will approach infinity, and the pattern will look competitive. Britton [(1973) Biochem. J. 133, 255-261] asserted that KSP will also approach infinity when the rate of isomerization becomes low. This second assertion is incorrect and can be traced to the particular model and graphical representation used to examine KSP as a function of relative rate constants. The function portrayed as a parabola with two roots for KSP is, instead, a straight line with one root. The algebraic condition justifying the second root obtains in the limit of zero in the rate of reaction and thus is not experimentally relevant, and the appearance of competitive inhibition, based on KSP alone, is not valid. Using a more general model, new equations are derived and presented which provide direct calculations of the apparent rate constants for free enzyme isomerizations from product-inhibition data when the equilibrium of the isomerization is near 1, and useful limits for the rate constants when greater than or less than 1.

Slow step after bond-breaking by porcine pepsin identified using solvent deuterium isotope effects

The relatively fast artificial substrate Leu-Ser-rho-nitro-Phe-Nle-Ala-Leu-OMe generates a solvent isotope effect of 1.51 +/- 0.02 only on the maximal velocity of peptide hydrolysis catalyzed by porcine pepsin (EC 3.4.23.1). The absence of an isotope effect on V/K places the isotopically-sensitive step after peptide bond cleavage and the release of the first product. Reprotonation of the active site aspartic carboxyls is proposed as the most likely interpretation of this observation. Structural and kinetic similarities between pepsin and other aspartic proteinases, including the therapeutically important targets HIV protease and renin, suggest a similar slow reprotonation step after catalysis. This mechanistic feature has important implications regarding inhibitor design; if most of the enzymes are present in a product-release form during steady-state turnover, then perhaps inhibitors should be designed as product analogs instead of substrate analogs.

Quantitative analysis of absorption spectra and application to the characterization of ligand binding curves

The spectrum of a chromophore may change as a result of perturbations in its environment. The spectral changes resulting from the perturbation are often followed by measurements at just one or two wavelengths but it is usually no more difficult to collect entire spectra. The problem comes in analysing the data from such a series of spectra. In this paper we will suggest a simple procedure in which the spectrum observed under any particular set of conditions may be considered to consist of the sum of two distinct spectral forms. The method, which is free of any assumptions regarding the quantitative relationship between the perturbation and the extent of spectral change, defines any given spectrum in terms of an apparent molar fraction of the contributing spectral forms. The variation of this apparent molar fraction provides information from which a quantitative relationship can be developed to describe the dependence of the spectral change on the perturbant. The method is illustrated using the model system of phenol red protonation and is applied to the characterization of the binding of azide ions to cobalt-substituted carbonic anhydrase.

Substrate specificities and structure-activity relationships for the nucleotidylation of antibiotics catalyzed by aminoglycoside nucleotidyltransferase 2''-I

Aminoglycoside nucleotidyltransferase 2''-I (formerly gentamicin adenylyltransferase) conveys antibiotic resistance to Gram-negative bacteria by transfer of AMP to the 2''-hydroxyl group of 4,6-substituted deoxystreptamine-containing aminoglycosides. The kinetics constants of thirteen aminoglycoside antibiotics and the magnesium chelates of eight nucleotide triphosphates were determined with purified enzyme. Eleven of the antibiotics exhibit substrate inhibition attributed to secondary binding of the aminoglycoside to an enzyme-AMP-aminoglycoside complex. Maximal velocities vary by only 4-fold, versus variation of values of Vmax/Km for the aminoglycosides of nearly 4000-fold, consistent with a Theorell-Chance kinetic mechanism as proposed for this enzyme [Gates, C. A., & Northrop, D. B. (1988) Biochemistry (second of three papers in this issue)] with the added specification that the binding of aminoglycosides is in rapid equilibrium. Under these conditions, Vmax/Km becomes kcat/Kd, where kcat is the net rate constant for catalysis (but not turnover) and Kd is the dissociation constant of aminoglycosides from a complex with enzyme and nucleotide. Values of kcat fall closely together into three distinct sets, with the 3',4'-dideoxygentamicins greater than gentamicins greater than kanamycins. These sets reflect unusual structure-activity correlations which are specific for catalysis but have nothing to do with the maximal velocity of this enzyme.(ABSTRACT TRUNCATED AT 250 WORDS)

Alternative substrate and inhibition kinetics of aminoglycoside nucleotidyltransferase 2''-I in support of a Theorell-Chance kinetic mechanism

Aminoglycoside nucleotidyltransferase 2''-I conveys multiple antibiotic resistance to Gram-negative bacteria because the enzyme adenylylates a broad range of aminoglycoside antibiotics as substrates [Gates, C. A., & Northrop, D. B. (1988) Biochemistry (preceding paper in this issue)]. The enzyme also catalyzes the transfer of a variety of nucleotides [Van Pelt, J. E., & Northrop, D. B. (1984) Arch. Biochem. Biophys. 230, 250-263]. This doubly broad substrate specificity makes it an excellent candidate for application of the alternative substrate diagnostic [Radika, K., & Northrop, D. B. (1984) Anal. Biochem. 141, 413-417] as a means to determine its kinetic mechanism. The kinetic patterns presented here are composed of one set of intersecting lines and one coincident line and are consistent with a Theorell-Chance kinetic mechanism in which nucleotide binding precedes aminoglycosides, pyrophosphate is released prior to the nucleotidylated aminoglycoside (Q), and turnover is controlled by the rate-limiting release of the final product. Substrate inhibition by tobramycin (B) is partial and uncompetitive versus Mg-ATP, indicating that B binds to the EQ complex, but not in the usual dead-end fashion common to an ordered sequential release of products; instead, Q may escape from the abortive EQB complex at a finite rate. Dead-end inhibition by neomycin C (I) is also partial and uncompetitive versus Mg-ATP but is slope-linear, intercept-hyperbolic, partial noncompetitive versus gentamicin A; both kinetic patterns signify the formation of a partial abortive EQI complex.(ABSTRACT TRUNCATED AT 250 WORDS)

Determination of the rate-limiting segment of aminoglycoside nucleotidyltransferase 2''-I by pH and viscosity-dependent kinetics

Aminoglycoside nucleotidyltransferase 2''-I follows a Theorell-Chance kinetic mechanism in which turnover is controlled by the rate-limiting release of the final product (Q), a nucleotidylated aminoglycoside [Gates, C. A., & Northrop, D. B. (1988) Biochemistry (second of three papers in this issue)]. The effects of viscosity on the kinetic constants of netilmicin, gentamicin C1, and sisomicin aminoglycoside substrates are as follows: no change in the substrate inhibition constants of all three antibiotics, a small but significant and highly unusual increase in Vmax/Km for netilmicin but large, normal decreases for gentamicin C1 and sisomicin, and marked decreases in the maximal velocities for all three. The lack of effect on substrate inhibition provides essential control experiments, signifying that glycerol does not interfere with binding of aminoglycosides to EQ and that the steady-state distribution of EQ does not increase as the release of Q is slowed by a viscosogen. The decrease in the Vmax/Km of better substrates indicates dominance by a diffusion-controlled component in the catalytic segment, attributed to the release of pyrophosphate. The presence of an increase in the Vmax/Km of the poor substrate, however, is inexplicable in terms of either single or multiple diffusion-controlled steps. Instead, it is here attributed to an equilibrium between conformers of the enzyme-nucleotide complex in which glycerol favors the conformation necessary for binding of aminoglycosides. The decrease in Vmax is consistent with the diffusion-controlled release of the final product determining enzymatic turnover.(ABSTRACT TRUNCATED AT 250 WORDS)

Kinetic distinction between rapid-equilibrium random and abortive ordered enzymatic mechanisms using alternative substrates or kinetic isotope effects

Alternative substrates, such as those isotopically-labeled, which differ in their rate constants of catalysis but not in their rate constants of binding, generate identical values of V/Ka in ordered kinetic mechanisms of bireactant enzymes. This is shown to be true even for the rapid-equilibrium ordered mechanism in which an abortive complex between free enzyme and the second substrate is formed. In contrast, rapid-equilibrium random mechanisms have non-identical values for V/Ka. Consequently, the effect of alternative substrates or isotope effects on V/Ka provides a means to distinguish between these nearly identical kinetic mechanisms.

Preparation and storage of isotopically labeled reduced nicotinamide adenine dinucleotide

A method for obtaining highly purified NADH in a dry, solid, and stable form is described. The method involves improvements of the ion-exchange and reversed-phase chromatographic procedures of C. J. Newton and S. M. Faynor, and D. B. Northrop (Anal. Biochem., 1983, 132, 50-53). The necessary time to prepare pure NADH has been reduced to a few hours. The final product, obtained by drying the nucleotide from absolute ethanol, shows no detectable decomposition either during the drying procedure or during storage under nitrogen gas at -20 degrees C for several months. Using dry product prepared from fixed volumes of ethanolic solution, standardized solutions of known amounts of the highly purified and stored NADH can be obtained in a few seconds.

The kinetic mechanism of kanamycin acetyltransferase derived from the use of alternative antibiotics and coenzymes

Kinetic data for the 6'-aminoglycoside-modifying enzyme, AAC(6')-4, also named kanamycin acetyltransferase, have been collected for six aminoglycoside antibiotics (amikacin, gentamicin C1a, kanamycin A, neomycin B, sisomicin, and tobramycin) and three coenzymes (acetyl-CoA, n-propionyl-CoA, and n-butyryl-CoA). The initial velocity pattern using acetyl-CoA favors a ping-pong kinetic mechanism (Kia = -0.34 +/- 0.34 microM), but the pattern using n-propionyl-CoA supports a sequential one (Kia = 2.7 +/- 0.8 microM). Kinetic analyses using alternative substrates confirm the sequential mechanism and, moreover, clearly identify a random order of addition of antibiotic and coenzyme because V/K values of antibiotics varied 40-fold as the identity of the coenzyme was changed and V/K values of coenzyme varied 13-fold as the identity of the antibiotic was changed. One or both sets of values would have remained unchanged if the mechanism were either ordered sequential or ping-pong. Combining these results with structure-activity data which argue for a rapid rate of release of substrates and products relative to the rate of enzymatic turnover (Radika, K., and Northrop, D. B. (1984) Biochemistry 25, in press) establishes the kinetic mechanism as rapid equilibrium random sequential.

Substrate specificities and structure-activity relationships for acylation of antibiotics catalyzed by kanamycin acetyltransferase

Antibiotic resistance caused by the presence of the plasmid pMH67 is mediated by the aminoglycoside acetyltransferase AAC(6')-4, also known as kanamycin acetyltransferase. Bacteria harboring the plasmid are resistant to the kanomycins plus a broad range of other deoxystreptamine-containing aminoglycosides but not to the gentamicins XK62-2 and C1 which are substituted at the 6'-position. Substrate specificity studies on the purified enzyme, however, now show that the enzyme acetylates an even broader range of aminoglycosides, including the gentamicins XK62-2 and C1. The enzyme also accepts several acyl-CoA esters, which differ in nucleotide as well as in acyl chain length. Application of the method of analysis of structure-activity data developed earlier for gentamicin acetyltransferase [Williams, J. W., & Northrop, D. B. (1978) J. Biol. Chem. 253, 5908-5914] to the kinetic data obtained for AAC(6')-4 shows that the turnover of the acylation reaction is limited by catalysis and not by the rate of release of either the acetylated antibiotic or CoA. Most structural changes in aminoglycosides cause changes in rates of release, and only drastic changes, near the 6'-amino group, affect catalysis. The structural requirements on aminoglycosides for enzymatic activity run parallel to the structural requirements for antibacterial activity.

Purification of two forms of kanamycin acetyltransferase from Escherichia coli

Kanamycin acetyltransferase acylates aminoglycoside antibiotics using acetyl-CoA, and thereby conveys bacterial resistance to several clinically important antibiotics, notably amikacin. The enzyme was quantitatively and reproducibly released from Escherichia coli W677 harboring plasmid pMH67 by a modified osmotic shock procedure (bacterial cells are incubated overnight in sucrose and again without sucrose before onset of osmotic shock). The enzyme was purified by dye-ligand chromatography on Affi-Gel Blue in addition to antibiotic affinity chromatography on neomycin-Sepharose-4B. The activity did not increase with subsequent chromatography on ion-exchange, hydrophobic, or molecular-exclusion gels. However, both dye-ligand and molecular-exclusion chromatography, as well as disc-gel electrophoresis, separated the purified enzyme equally into two active protein fractions. Based on the more active of the two forms, the purification was 112-fold with a specific activity of 1.9 IU/mg. The less-active form has an unusual absorbance spectrum, with a maximum near 255 nm, which cannot be explained by the amino acid composition. Chromatography of this form alone regenerated both forms, suggesting that the enzyme is noncovalently conjugated to an uncharged chromophore, such as a lipid. The purified enzyme has a very sharp pH optimum at 5.5 with a plateau on the alkaline side, but is most stable between pH 8.5 and 9.5. Data from electrophoresis in the presence of sodium dodecyl sulfate and gel-filtration on Ultrogel AcA 44 are consistent with a tetrameric protein of 60-70,000 Da.

Correlation of antibiotic resistance with Vmax/Km ratio of enzymatic modification of aminoglycosides by kanamycin acetyltransferase

Kinetic data for the antibiotic-modifying enzyme kanamycin acetyltransferase AAC(6')-IV have been determined for five aminoglycoside antibiotics (amikacin, gentamicin C1a, kanamycin A, sisomicin, and tobramycin) and compared with close-interval determinations of the minimal inhibitory concentrations of the same antibiotics against Escherichia coli W677 harboring the resistance plasmid pMH67. These minimal inhibitory concentrations for the resistant bacteria varied from 80 to 800 micrograms/ml. Of the kinetic parameters Vmax, Km, and Vmax/Km ratio only Vmax/Km ratio had a linear correlation with minimal inhibitory concentrations (r = +0.818) at pH 7.8, where all antibiotics produced substrate inhibition, but not at pH 6.0, where they did not. The correlation with only Vmax/Km ratio has implications regarding the expression of resistance within the dynamics of the bacterial cell (i.e., antibiotic uptake versus modification), whereas substrate inhibition presents an opportunity to search for new chemotherapeutic agents which will combat resistance directly.

Purification and properties of gentamicin nucleotidyltransferase from Escherichia coli: nucleotide specificity, pH optimum, and the separation of two electrophoretic variants

Gentamicin nucleotidyltransferase, AAD 2", catalyzes the transfer of a nucleotide to many aminoglycoside antibiotics, which are the drugs of choice in the treatment of gram-negative bacterial infections. The transfer is accompanied by the production of pyrophosphate, which is coupled to three other enzymes so that an increase in absorbance at 340 nm of NADPH can be monitored continuously as a quantitative assay of activity. A purification method was developed for this enzyme using all common principles of protein purification. These include selection of a desirable source of enzyme (choice of plasmid pMY 10), maximizing cellular yield of enzyme (controlled and monitored growth of Escherichia coli pMY 10/W677), selective extraction of protein (modified osmotic shock), removal of nucleic acids (precipitation with streptomycin sulfate), concentration of protein (precipitation with ammonium sulfate), removal of low-molecular-weight impurities (chromatography on Bio-Gel P-2), separation of proteins on the basis of charge (ion-exchange chromatography on DEAE-Bio-Gel A), separation of proteins according to a biospecific property (affinity chromatography on gentamicin-Affi-Gel), and separation of proteins according to size (gel filtration on Ultrogel AcA 54). Purification to near-homogeneity revealed the presence of two related forms of enzyme. The first had a specific activity of 0.134 units/mg, bound rapidly and tightly to gentamicin-Affi-Gel, eluted as a function of ionic strength from Ultrogel, and migrated faster during electrophoresis in both the presence and absence of sodium dodecyl sulfate. It has an isoelectric point of 5.7 +/- 0.2 and consists of a single polypeptide of 32,500 Da. Kinetic characterization showed a pH optimum of 9.5 and Michaelis constants of 2.76 +/- 0.35 microM for tobramycin, 404 +/- 28 microM for Mg-ATP, 2008 +/- 260 microM for Mg-CTP, 30 +/- 3 microM for Mg-dATP and Mg-dGTP, and 90 +/- 7 microM for Mg-dCTP and Mg-dTTP. The second form had a specific activity of 0.274 unit/mg. It also bound tightly to gentamicin-Affi-gel but the onset of binding was time dependent. This form migrated slower during polyacrylamide gel electrophoresis in both the presence and absence of sodium dodecyl sulfate. It has an isoelectric point of 6.0 +/- 0.2 and consists of a single polypeptide of 31,500 Da. The exact relationship between the two forms has not been elucidated. It is probable that they have a recent common ancestor or are the same polypeptide because the amino acid compositions and polypeptide chain lengths are essentially identical.(ABSTRACT TRUNCATED AT 400 WORDS)

Fitting enzyme-kinetic data to V/K

Kinetic data from enzyme-catalyzed reactions have been analyzed traditionally in terms of the Michaelis-Menten equation, which assumes that the maximal velocity (V) and the Michaelis constant (K) are the primary kinetic constants. But what is needed from most kinetic studies today is V/K. A new form of the equation is proposed which assumes that V and V/K are the primary kinetic constants: v = (V . S . V/K)/(V + S . V/K). Computer fittings of both experimental and simulated velocity data to both equations give results favoring the new equation.

Purification of reduced nicotinamide adenine dinucleotide by ion-exchange and high-performance liquid chromatography

Combining ion-exchange (AG MP-1) and reversed-phase (C-18) partition chromatography accomplishes a higher degree of purification of NADH than either method can provide alone. Final elution in 95% ethanol, dehydration with anhydrous sodium sulfate, and storage in dry 1,2-propanediol over molecular sieves prevents hydrolysis of the purified dinucleotide.

Minimal kinetic mechanism and general equation for deuterium isotope effects on enzymic reactions: uncertainty in detecting a rate-limiting step

A general equation is proposed for representing the kinetic functions which govern the expression of an isotope effect on the maximal velocity of an enzyme-catalyzed reaction. The origin and form of the functions are illustrated by examining a series of enzymatic mechanisms of progressively increasing complexity. The number of functions similarly increase, reaching a limit of three, with differing thermodynamic and kinetic properties. Further expansion of mechanisms causes an orderly and predictable algebraic expansion of each function, making it possible to write out, by simple inspection, the kinetic equation describing an isotope effect expressed on the maximal velocity for any enzymatic mechanism in which the isotope perturbs a single reactive step. The functions are interactive and allow for the possibility that an isotope effect on Vmax may be independent of the rate of a second, isotopically insensitive step, be it infinitely fast or slow. This allowance leads to an uncertainty of the ability of an isotope effect to detect a rate-limiting step, and the unequal distribution of kinetic and thermodynamic properties among three functions leads to an inadequacy of the singular concept of a rate-limiting step to serve as a basis for interpreting isotope effects on enzyme-catalyzed reactions. A minimal mechanism for consideration of isotope effects is proposed in order to embrace all three functions. It consists of a single catalytic step which is isotopically sensitive and reversible, two reversible precatalytic steps, and one reversible postcatalytic step, plus steps for binding and release of substrates and products.

Kinetic isotope effects in cytochrome P-450-catalyzed oxidation reactions. Intermolecular and intramolecular deuterium isotope effects during the N-demethylation of N,N-dimethylphentermine

Two N,N-dimethylphentermine (N,N-dimethyl-2-amino-2-methyl-3-phenylpropane) substrates differing in deuterium substitution have been used to determine the intermolecular and intramolecular isotope effects associated with the cytochrome P-450-dependent N-demethylation of this substrate. No intermolecular isotope effect was observed in Vmax or Vmax/Km when the reaction rates for this substrate were compared to those for the substrate in which both N-methyl groups contained deuterium. In contrast, identical isotope effects of 1.6 to 2.0 were observed in both Vmax and Vmax/Km when this reaction was studied with a substrate in which only one of the two N-methyl groups was substituted with deuterium. Furthermore, both the intermolecular and intramolecular isotope effects were independent of the cytochrome P-450/NADPH-cytochrome P-450 reductase mole ratio. From these data, it is concluded that: 1) the carbon-hydrogen bond cleavage step does not contribute significantly to Vmax; 2) the contribution of the carbon-hydrogen bond cleavage step to Vmax is not detectably increased through changes in the cytochrome P-450/NADPH-cytochrome P-450 reductase mole ratio; 3) the N-methyl groups are free to exchange at the enzyme active site. The basis for these conclusions is the proposal of a new kinetic model for interpretation of intramolecular isotope effects which shows that intramolecular isotope effects are not necessarily equal to intrinsic isotope effects and, in fact, may be much smaller.

Synthesis of a tight-binding, multisubstrate analog inhibitor of gentamicin acetyltransferase I

Gentamicin acetyltransferase I will catalyze acyl transfer from chloroacetylcoenzyme A to form 3-N-chloroacetylgentamicin. This product can be linked to coenzyme A to form a multisubstrate analog by nucleophilic displacement of the chlorine by the sulfur of coenzyme A. The analog can be purified by selective binding to cationic and anionic ion exchange resins. Kinetic analysis of a time-dependent onset and reversal of inhibition of gentamicin acetyltransferase I by the purified multisubstrate analog yields an inhibition constant of 5 approximately 20 x 10(-10) M. The inhibitor does not potentiate antibiotic activity against resistant Escherichia coli. Nevertheless, the effectiveness of the tight-binding between the enzyme and the multisubstrate analog demonstrates that inhibitors of resistance can be designed and prepared by specific enzymatic synthesis.

Spectrophotometric assay for amikacin using purified kanamycin acetyltransferase

A rapid spectrophotometric assay has been developed for measuring the concentrations of amikacin and related antibiotics in serum. The assay uses a purified enzyme from R-factor E. coli which acetylates amikacin with the production of coenzyme A, the latter in turn being reacted with a sulfhydryl reagent to produce stoichiometric amounts of a sensitive chromophore, that is measured in the visible spectrum. The system complements an earlier assay for gentamicin-related antibiotics thereby facilitating the rapid measurement of the concentrations of all clinically important aminoglycosides in serum.

Kinetic mechanisms of gentamicin acetyltransferase I. Antibiotic-dependent shift from rapid to nonrapid equilibrium random mechanisms

Initial velocity, product, dead-end, and substrate inhibition studies are described for gentamicin acetyltransferase I in the forward reaction. Initial velocity patterns were linear with tobramycin (Km acetyl-CoA = 1.7 micron, Km tobramycin = 1.6 micron), concave upward with sisomicin (V/K.Et = 1.7 X 10(7) M-1 s-1, indicative of nonrapid equilibrium conditions), and showed partial uncompetitive substrate inhibition with gentamicin C1a (Km acetyl-CoA = 1.3 micron, Km gentamicin C1a = 0.12 micron, KI = 6.5 micron). Product inhibition by CoA and acetyltobramycin consists of two competitive and two noncompetitive patterns. Dead-end inhibition by butyryl-CoA and neomycin consists of two competitive and two uncompetitive patterns. However, the uncompetitive pattern between neomycin and acetyl-CoA became noncompetitive when sisomicin rather than tobramycin was the nonvaried substrate. These results are consistent with a Random BiBi mechanism with synergism between binding sites which is nonrapid equilibrium with gentamicin C1a and sisomicin and rapid equilibrium with poor substrates such as tobramycin. The substrate inhibition by gentamicin C1a arises from a reduction in the rate of product (CoA) release which is partially rate-determining under nonrapid equilibrium conditions.

Purification and properties of gentamicin acetyltransferase I

Gentamicin acetyltransferase I is induced 13-fold in R factor resistant Escherichia coli by high concentrations (1 mg/ml) of gentamicin in the growth medium. The enzyme is maximally released from bacteria by osmotic shock in late-log phase, unlike previously studied periplasmic enzymes. Streptomycin sulfate and ammonium sulfate precipitations of shockate followed by affinity and ion-exchange chromatography recover 51% of the induced enzyme with a 360-fold increase in purity (12% of 4400-fold, uninduced). The purified enzyme appears homogeneous by six criteria, the first aminoglycoside inactivating enzyme so purified. Sodium dodecyl sulfate electrophoresis, amino acid analysis, and sedimentation analyses indicate a tetrameric protein of 63000 molecular weight. The protein does not contain tryptophan. Kinetic analyses yield apparent values of: Vmax = 3.4 +/- 0.2 mumol per min mg at pH 8 (optimum), Km (acetyl-CoA) = 3.9 +/- 0.2 muM, Km (gentamicin Cla) = 0.3 +/- 0.08 muM, KI (gentamicin substrate inhibition) = 160 +/- 29 muM. The activity of the enzyme is stable to a variety of conditions, including lyophilization and prolonged storage, and can be monitored by two convenient spectrophotometric assays.

A spectrophotometric assay for gentamicin

A rapid and accurate spectrophotometric assay has been developed for the determination of blood werum levels of gentamicin and related antibiotics. The assay uses a purified enzyme from Escherichia coli JR88/C600 that acetylates gentamicin with the production of coenzyme A, linked to a chemical reaction with a sulfhydryl reagent to produce stoichiometric amounts of a sensitive chromophore, monitored in the visible spectrum. The system provides advantages of speed, cost, convenience, accuracy, and enzyme stability to the desirable characteristics encountered with previous enzymatic methods.