The identification of chemical intermediates in enzyme catalysis by the rapid quench-flow technique.

Traditionally, enzyme transient kinetics have been studied by the stopped-flow and rapid quench-flow (QF) methods. Whereas stopped-flow is the more convenient, it suffers from two weaknesses: optically silent systems cannot be studied, and when there is a signal it cannot always be assigned to a particular step in the reaction pathway. QF is a chemical sampling method; reaction mixtures are aged for a few milliseconds or longer, 'stopped' by a quenching agent and the product or the intermediate is measured by a specific analytical method. Here we show that by exploiting the array of current analytical methods and different quenching agents, the QF method is a key technique for identifying, and for characterising kinetically, intermediates in enzyme reaction pathways and for determining the order by which bonds are formed or cleaved by enzymes acting on polymer substrates such as DNA.

Kinetics of structure and activity changes during the allosteric transition of aspartate transcarbamylase.

For the first time, the structural change associated with an allosteric transition has been monitored by X-ray solution scattering. The kinetics of the quaternary structure change of aspartate transcarbamylase were first slowed by using acetyl phosphate instead of carbamyl phosphate, and by the presence of 10% or 30% ethylene glycol. At 6.5 degrees C, the quaternary structure change was found to have a time constant of about 11 seconds. This appears to be larger than that obtained for the switching of homotropic co-operativity, measured by chemical quench under the same conditions.

Alteration of the ATP hydrolysis and actin binding properties of thrombin-cut myosin subfragment 1.

We have characterized various structural and enzymatic properties of the (68K-30K)-S-1 derivative obtained by thrombic cleavage [Chaussepied, P., Mornet, D., Audemard, E., Derancourt, J., & Kassab, R. (1986) Biochemistry (preceding paper in this issue)]. The far-ultraviolet CD spectra and thiol reactivity measurements indicated an unchanged overall polypeptide conformation of the enzyme whereas the CD spectra in the near-ultraviolet region suggested a local change in the environments of phenylalanine side chains; the latter finding was rationalized by considering the existence of about five of these amino acids in the vicinity of the cleavage sites. When the binding of Mg2+-ATP and Mg2+-ADP to the derivative was assessed by CD spectroscopy, distinct spectra were obtained with the two nucleotides as with native subfragment 1 (S-1), but some spectral features were unique to the nicked S-1. Stern-Volmer fluorescence quenching studies using acrylamide and the analogues 1,N6-ethenoadenosine 5'-triphosphate and 1,N6-ethenoadenosine 5'-diphosphate indicated that the complexes formed with the modified S-1 have a solute quencher accessibility close to that observed for the complexes with the normal S-1. However, in contrast to the parent enzyme, the thrombin-cut S-1 was unable to bind irreversibly Mg2+-ATP, nor did it form a stable Mg2+-ADP-sodium vanadate complex or achieve the entrapping of Mg2+-ADP after cross-linking of SH1 and SH2 with N,N'-p-phenylenedimaleimide. Additionally, the amplitude of the Pi burst was very low, indicating that the inactivation of the proteolyzed S-1 was linked to the suppression of the hydrolysis step in the ATPase cycle.(ABSTRACT TRUNCATED AT 250 WORDS)

Transient kinetics of adenosine 5'-triphosphate hydrolysis by covalently cross-linked actomyosin complex in water and 40% ethylene glycol by the rapid flow quench method.

The initial steps of the ATPase of covalently cross-linked actomyosin subfragment 1 (acto-SF-1) were studied by the rapid flow quench method, and the results obtained were compared with those with reversible (i.e., non-cross-linked) acto-SF-1 and SF-1 under identical conditions. Cross-linked acto-SF-1 plus [gamma-32P]ATP reaction mixture milliseconds old was quenched either in a large excess of unlabeled ATP (ATP chase) or in acid (Pi burst). The conditions were pH 8 and 15 degrees C at 5 mM or 0.15 M KCl and with or without 40% ethylene glycol. In 40% ethylene glycol (5 mM KCl), as with SF-1 and reversible acto-SF-1, the ATP chase was used to titrate active sites and to study the kinetics of ATP binding. Unlike those with SF-1 or reversible acto-SF-1, saturation kinetics were not obtained. The second-order rate constant for ATP binding was 3.1 X 10(6) M-1 s-1 for cross-linked acto-SF-1, 1.8 X 10(6) M-1 s-1 for reversible acto-SF-1, and 2 X 10(6) M-1 s-1 for SF-1. In Pi burst experiments, a transient phase could not be discerned. Because of a high kcat, cross-linked acto-SF-1 was difficult to study in aqueous solution, but at 5 mM KCl, the ATP chase and Pi burst curves were similar to those obtained in 40% ethylene glycol. At 0.15 M KCl the ATP chase curve was difficult to interpret (small amplitude), and there was a small Pi burst.(ABSTRACT TRUNCATED AT 250 WORDS)

Kinetics of the allosteric transition of aspartate transcarbamylase. Chemical quench studies.

Using a chemical quench device, the rate of synthesis of carbamyl aspartate from the substrates aspartate and carbamyl phosphate was followed as a function of the time between mixing the enzyme with substrates and quenching with trichloroacetic acid. This function, which is linear at long times, shows (at 4 degrees C) a transient lag phase of product of roughly 10 ms. However, when the catalytic subunit (in which the enzymatic activity is desensitized) is used instead of the enzyme, the lag disappears. Therefore the lag seems to be associated with the control functions of the enzyme, i.e. to represent the allosteric transition involved in substrate-substrate (homotropic) co-operativity. Thus the relaxation time for the activation process is roughly 10 ms. The implications of these results are examined.

Transient kinetics of the binding of ATP to actomyosin subfragment 1: evidence that the dissociation of actomyosin subfragment 1 by ATP leads to a new conformation of subfragment 1.

The initial steps by which ATP dissociates and binds to actomyosin subfragment 1 (acto-SF-1) were studied. Two techniques were used: stopped-flow (for acto-SF-1 dissociation kinetics) and rapid-flow quench with ATP chase quenching (for ATP binding kinetics). The experiments were carried out in 40% ethylene glycol-5 mM KCI, pH 8, at 15 degrees C. Under these conditions, the binding of SF-1 to actin remains very tight. As with SF-1, the ATP chase technique could be used, first, to titrate active sites and, second, to study the kinetics of ATP binding to acto-SF-1. The kinetic constants obtained were compared with those of SF-1 alone and with the acto-SF-1 dissociation kinetics under identical conditions. The kinetics of the acto-SF-1 dissociation did not vary with the actin to SF-1 ratio, but the ATP binding kinetics did, and a maximum value was reached at a mole ratio of 2.5. At high ATP (100 microM), kdiss = 300 s-1, which compares with 49 s-1 and 13 s-1 for the ATP binding kinetics for acto-SF-1 (actin to SF-1 = 1:1) and SF-1, respectively. As with SF-1, the ATP binding to acto-SF-1 follows a hyperbolic law with the ATP concentration. This suggests a rapid equilibrium (K) followed by an essentially irreversible step (k).(ABSTRACT TRUNCATED AT 250 WORDS)

Cryoenzymic studies on myosin subfragment 1: perturbation of an enzyme reaction by temperature and solvent.

The effects of temperature and solvent on myosin subfragment 1 ATPase have been studied. Under all of the conditions used the data could be fitted to the Bagshaw - Trentham pathway: (formula; see text) Ethylene glycol (40%) was used as the cryosolvent ; this makes K1 and k+2 measurable and allows for temperature studies over an extensive temperature range (+35 to -20 degrees C) and thus to reasonably accurate thermodynamic parameters. The following techniques were used: ATP chase (for K1 and k+2); Pi burst (k+2 or k+3 + k-3); single-turnover Pi burst [k0 = k +4K3 /(1 + K3)] absorption stopped flow (k+2 or k+3 + k-3); steady state (k+6 or k0). Myosin provides examples of causes for nonlinear Arrhenius and van't Hoff plots. A temperature-induced structural change is exemplified by a "jump" in an Arrhenius plot of k+2 and "breaks" in van't Hoff plots of K1 and K3. A change in rate-limiting step is illustrated from stopped-flow experiments ( kobsd approximately k+2 at low and approximately k+3 + k-3 at high temperatures) and steady-state experiments (kcat approximately k+6 at low and approximately k0 at high temperatures). A third cause is illustrated by k0: an Arrhenius plot of k0 is nonlinear since there is a break in K3. These studies illustrate the use of temperature perturbation as a way of revealing reaction intermediates and of defining the conditions required for the isolation of a particular intermediate.(ABSTRACT TRUNCATED AT 250 WORDS)

A jump in an Arrhenius plot can be the consequence of a phase transition. The binding of ATP to myosin subfragment 1.

The temperature dependence of the kinetics of the binding of ATP to myosin subfragment-1 was studied by an ATP chase technique in a rapid-flow-quench apparatus: (formula; see text) A temperature range of 30 degrees C to -15 degrees C was obtained with ethylene glycol as antifreeze. The Arrhenius plot of k2 is discontinuous with a jump at 12 degrees C. Above the jump delta H+ = 9.5 kcal/mol, below delta H+ = 28.5 kcal/mol. Few such Arrhenius plots are recorded in the literature but they are predicted from theory. Thus, we explain our results as a phase change of the subfragment 1-ATP system at 12 degrees C. This is in agreement with certain structural studies.

Evidence for the two-step binding of ATP to myosin subfragment 1 by the rapid-flow-quench method.

1. The initial steps on the myosin ATPase (EC 3.6.1.3) pathway are taken to be: (formula; see text) A two-step binding for ATP is assumed, but the evidence for it is unconvincing; because of the rapidity of the process unambiguous values for K1 and K2 are not available. 2. We investigated the myosin mechanism by the chemical flow-quench technique. Reaction mixtures containing [gamma-32P]ATP plus myosin subfragment 1 were quenched in unlabelled ATP (ATP chase) or acid (Pi burst). 3. We show that the ATP-chase method can lead directly to unambiguous values for K1 and k+2. 4. The binding process was slowed down by 40% ethylene glycol. It was studied as a function of the ATP concentration. A limiting plateau resulted, showing a two-step binding for ATP, and values for K1 and k+2 were obtained. 5. K1 and k+2 are rather sensitive to the experimental conditions. Ethylene glycol and lowering of the pH decrease both constants, but an increase in KCl concentration increases them. This suggests that the binding of ATP to myosin is of an electrostatic nature. 6. The Pi-burst method can lead directly to k+3 + k-3, but under certain conditions the kinetics are governed by K1 and k+2. This uncertainty of the interpretation of Pi-burst experiments is discussed.

A flow-quench apparatus for cryoenzymic studies. Application to the creatine kinase reaction.

The flow-quench method was adapted to sub-zero conditions. Two apparatus were constructed: a rapid flow-quench apparatus (which take samples in the 5--300-ms time range) and a time delay flow-quench apparatus (0.5 s and longer). The apparatus were constructed so that the reagents are only in contact with chemically inert materials : glass, poly(tetrafluoroethylene) and poly(trifluorochloroethylene). The modified flow-quench apparatus were used to study the initial formation of creatine phosphate by creatine kinase at -15 degrees C in the time range 5 ms to 10 s. As at +4 degrees C [Travers, F., Barman, T. E. and Bertrand, R. (1979) Eur. J. Biochem. 100, 149--155], the time course of product formation was complex and consisted of three phase: a lag phase, a burst phase and the steady-state phase. The apparatus were also used to test chemically for reaction intermediates involving labile phosphate and phospho-enzyme complexes on the creatine kinase reaction pathway at -15 degrees C. Since neither type of intermediate could be detected down to 5 ms, this enzyme probably proceeds via a direct in-line type of mechanism.

Cryoenzymic studies on the transition-state analog complex creatine kinase . ADPMg . nitrate . creatine.

Concomitant with the formation of the transition state analog complex creatine kinase . ADPMg . nitrate . creatine [Milner-White, E. J. and Watts, D. C. (1971) Biochem. J. 122, 727--740] there results a large difference spectrum. The shape of the spectrum was characteristic of tryptophan exposure. The kinetics of formation and final amplitude of the spectrum were studied at -15 degrees C using a stopped-flow apparatus. The results obtained allowed for a plausible reaction pathway for nitrate fixation: the ordered addition of nitrate and creatine to the binary enzyme-ADPMg complex, a slow protein isomerization and the final addition of a molecule each of nitrate and creatine. The kinetic parameters for the formation of the transition state analog complex were compared with those already known for the overall reaction obtained under the same conditions [Barman, T. E., Brun, A. and Travers, F. (1980) Dur. J. Biochem. 110, 397--403]. This comparison revealed a striking analogy between the two processes. This suggests that the conformation of creatine kinase in the analog complex is very similar to that in the transition state complex on the catalytic pathway.

Transient-phase studies on the creatine kinase reaction. The analysis of a reaction pathway with three intermediates.

1. The initial formation of creatine phosphate by creatine kinase was studied in the millisecond range and the effect of temperature on the transient and steady-state phases exploited. 2. At 25 degrees C and 35 degrees C there was no transient phase. This is in agreement with the results of Gutfreund [Engelborghs, Y., Marsh, A., and Gutfreund, H. (1975) Biochem. J. 151, 47--50]. 3. At 4 degrees C the time course of creatine phosphate formation was complex and consisted of three transient phases: a lag phase, a burst phase and a steady-state phase. Based on this result a reaction scheme for creatine kinase which includes three intermediates was proposed. Despite the completeness of the time course, the extraction of estimates for the rate constants was difficult and computer simulation and iterative methods had to be resorted to. 4. Attempts were made to provide evidence for the complex enzyme.ADP.metaphosphate.creatine on the creatine kinase reaction pathway [cf. Milner-White, E.J. and Watts, D.C. (1971) Biochem. J. 122, 727--740]. Under the conditions used these attempts were unsuccessful at times down to 2.5 ms, at 4 degrees C or 35 degrees C.

Transient-phase studies on the arginine kinase reaction.

1. The initial formation of arginine phosphate by arginine kinase was studied in the time range 2.8--50 ms by the quenched-flow method. 2. A transient burst phase of product formation was obtained, the amplitude of which was temperature-dependent. At 35 degrees C it was 0.64 mol arginine phosphate/mol arginine kinase and at 12 degrees C, 0.25 mol/mol. 3. These results show that for the reaction pathway of arginine kinase the rate-limiting step follows the formation of arginine phosphate on the enzyme. This is in contrast to the creatine kinase reaction where no transient phase was observed [Engelborghs, Y., Marsh, A. & Gutfreund, H. (1975) Biochem. J. 151, 47--50]. 4. The rate-limiting step on the arginine kinase reaction pathway is only slightly affected by temperature: the change in Kcat with temperature is due to a change of an equilibrium constant pertaining to at least two previous steps.

The chemistry of the reaction of 2-hydroxy-5-nitrobenzyl bromide with his-32 of alpha-lactalbumin.

His-32 of bovine or human alpha-lactalbumin reacts with the tryptophan reagent 2-hydroxy-5-nitrobenzyl bromide at pH 7. The reaction depends on the native conformation of the alpha-lactalbumin molecule and it is restricted to position 1 of the imidazole nucleus. The synthesis and characterization of 1-(2-hydroxy-5-nitrobenzyl)-histidine, 3-(2-hydroxy-5-nitrobenzyl)-histidine and 1,3-bis(2-hydroxy-5-nitrobenzyl)-histidine are described.

On the reactivities of the tryptophan residues of human alpha-lactalbumin to 2-hydroxy-5-nitrobenzyl bromide.

The reaction of human alpha-lactalbumin with the tryptophan reagent 2-hydroxy-5-nitrobenzyl bromide has been studied. This protein has 3 tryptophan residues (Trp-60, Trp-104 and Trp-118) all of which are accessible to the reagent at pH 2.7 or 7. Trp-60 of human alpha-lactalbumin is much more reactive than Trp-60 of bovine alpha-lactalbumin (Barman, T. E. (1972) Biochim. Biophys. Acta 257, 297-313). As with bovine alpha-lactalbumin, at pH 2.7, 2-hydroxy-5-nitrobenzyl bromide is specific for tryptophan but at pH 7 His-32 also reacts. When treated with the tryptophan reagent, both alpha-lactalbumins lose their specifier protein activities in the lactose synthase (UDPgalactose:D-glucose 4-beta-galactosyltransferase, EC 2.4.1.22) reaction.