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D R Trentham

Publications and source records attributed to D R Trentham.

At least 91 records · Page 5Linked to original sources
PubMed1975

Energy changes during the formation and interconversion of enzyme-substrate complexes.

The rate constants and equilibrium constants of the individual steps of several enzyme reactions may be determined by the application of rapid reaction methods and isotope techniques. This makes it possible to complement the formalism of the Haldane relation with details of the reaction mechanism. It has been shown that, in several enzyme reactions, steps involving chemical catalysis are fast and have small free-energy changes compared with those of the substrate binding and product dissociation processes. Data are presented in this paper for three enzyme reactions for which different methods have been used to elucidate the kinetic parameters of the elementary steps. For cardiac lactate dehydrogenase (EC 1.1.1.27), absorption and fluorescence spectroscopy have been used to distinguish the step involved in the chemical process from those involved in the formation of the substrate complex and the release of the product. The rate of interconversion between enzyme-bound substrates and products is fast compared with other steps and the equilibrium constant for the process is near unity. Consequently, the difference of standard free energy changes for the formation of the two ternary complexes correspons approximately to the overall free-energy change of the hydrogen transfer reaction. Isotope kinetic techniques can be used to study the reactions of triosephosphate isomerase (EC 5.3.1.1). With this enzyme, the interconversion of enzyme-bound substrate into product is comparable in rate to product dissociation. The reactions of myosin subfragment 1 with ATP, studied by fluorescence spectroscopy and chemical quenching, follow a similar pattern in that the equilibrium constant of the chemical step in which water reacts with protein-bound ATP is 9. In this case, however, there is a remarkably large free-energy change associated with a first-order process involved in the binding of ATP. The possible significance of these results to energy transduction in muscle contraction as well as in the biosynthesis of ATP is discussed.

Adenosine Triphosphatases↗
PubMed1975

Transient kinetic and isotopic tracer studies of the myosin adenosine triphosphatase reaction.

From transient kinetic studies of the Mg2+-dependent adenosine triphosphatase of myosin subfragment 1, prepared from rabbit skeletal muscle, a seven-step mechanism has been proposed. Features of this mechanism include two-step processes for ATP and ADP binding in which the binary complex isomerizes in addition to a rapid nucleotide association step. In the case of ATP a large negative standard free energy change is associated with the isomerization. An overall rate-limiting isomerization of the myosin-product complex prior to product release has been identified. Studies on the mechanism of cleavage of ATP bound to the active site indicate the process is readily reversible and can account for the observation that more than one oxygen of the product phosphate arises from water. This proposal has been substantiated by the finding that the oxygen atoms of the gamma-phosphoryl group of bound ATP also undergo extensive exchange with water.

Adenosine Diphosphate↗
PubMed1975

Oxygen exchange in the gamma-phosphoryl group of protein-bound ATP during Mg2+-dependent adenosine triphosphatase activity of myosin.

When ATP binds to myosin in the presence of Mg2+ there follows a rapid cleavage reaction to yield a myosin-product complex whose breakdown is rate-limiting in the overall adenosine triphosphatase reaction at 21 degrees and pH 8.0. Recent kinetic studies on this system have led to the proposal that the cleavage of ATP bound to myosin is reversible. This conclusion is based in part on the observation that when ATP is mixed with an excess of myosin active sites a small amount of tightly bound ATP exists whose life-time coincides with that of the myosin-product complex and implies these two species are in equilibrium during their decay. Previous oxygen exchange studies have shown that phosphate released as free product contains more than one oxygen atom from water. A rapid equilibration between myosin-bound ATP and a myosin-products complex can account for the extra water oxygen incorporation of the product phosphate. Such a model requires that the gamma-phosphoryl group of the bound ATP also exchanges its oxygen atoms with water. Results presented in this paper show that protein-bound ATP labeled in the three terminal oxygen atoms of the gamma-phosphoryl group with 18O exchanges about 75% of its label within 2 s of binding to the active site of myosin. This result provides chemical evidence for a model in which bound ATP undergoes a reversible reaction with water. Incomplete exchange may arise from kinetic and/or structural restraints on the mechanism and plausible models are discussed.

Adenosine Triphosphatases↗
PubMed1974

The characterization of myosin-product complexes and of product-release steps during the magnesium ion-dependent adenosine triphosphatase reaction.

Evidence is presented that the myosin subfragment-1-ADP complex, generated by the addition of Mg(2+) and ADP to subfragment 1, is an intermediate within the myosin Mg(2+)-dependent adenosine triphosphatase (ATPase) turnover cycle. The existence of this species as a steady-state intermediate at pH8 and 5 degrees C is demonstrated by fluorescence measurements, but its concentration becomes too low to measure at 21 degrees C. This arises because there is a marked temperature-dependence on the rate of the process controlling ADP dissociation from subfragment 1 (rate=1.4s(-1) at 21 degrees C, 0.07s(-1) at 5 degrees C). In the ATPase pathway this reaction is in series with a relatively temperature-insensitive process, namely an isomerization of the subfragment-1-product complex (rate=0.055s(-1) at 21 degrees C, 0.036s(-1) at 5 degrees C). By means of studies on the P(i) inhibition of nucleotide-association rates, a myosin subfragment-1-P(i) complex was characterized with a dissociation equilibrium constant of 1.5mm. P(i) appears to bind more weakly to the myosin subfragment-1-ADP complex. The studies indicate that P(i) dissociates from subfragment 1 at a rate greater than 40s(-1), and substantiates the existence of a myosin-product isomerization before product release in the elementary processes of the Mg(2+)-dependent ATPase. In this ATPase mechanism Mg(2+) associates as a complex with ATP and is released as a complex with ADP. In 0.1m-KCl at pH8 1.0mol of H(+) is released/mol of subfragment 1 concomitant with the myosin-product isomerization or P(i) dissociation, and 0.23 mol of H(+) is released/mol of subfragment when ATP binds to the protein, but 0.23 mol of H(+) is taken up again from the medium when ADP dissociates. Within experimental sensitivity no H(+) is released into the medium in the step involving ATP cleavage.

Adenosine Diphosphate↗
PubMed1974

The magnesium ion-dependent adenosine triphosphatase of myosin. Two-step processes of adenosine triphosphate association and adenosine diphosphate dissociation.

The kinetics of protein-fluorescence change when rabbit skeletal myosin subfragment 1 is mixed with ATP or adenosine 5'-(3-thiotriphosphate) in the presence of Mg(2+) are incompatible with a simple bimolecular association process. A substrate-induced conformation change with DeltaG(0)<-24kJ.mol(-1) (i.e. DeltaG(0) could be more negative) at pH8 and 21 degrees C is proposed as the additional step in the binding of ATP. The postulated binding mechanism is M+ATPright harpoon over left harpoonM.ATPright harpoon over left harpoonM*.ATP, where the association constant for the first step, K(1), is 4.5x10(3)m(-1) at I 0.14m and the rate of isomerization is 400s(-1). In the presence of Mg(2+), ADP binds in a similar fashion to ATP, the rate of the conformation change also being 400s(-1), but with DeltaG(0) for that process being -14kJ.mol(-1). The effect of increasing ionic strength is to decrease K(1), the kinetics of the conformation change being essentially unaltered. Alternative schemes involving a two-step binding process for ATP to subfragment 1 are possible. These are not excluded by the experimental results, although they are perhaps less likely because they imply uncharacteristically slow bimolecular association rate constants.

Adenosine Diphosphate↗
PubMed1974

Kinetic studies on oxidized nicotinamide--adenine dinucleotide-facilitated reactions of D-glyceraldehyde 3-phosphate dehydrogenase.

The kinetics of the acylation of d-glyceraldehyde 3-phosphate dehydrogenase from pig muscle by 1,3-diphosphoglycerate in the presence of NAD(+) has been analysed by using the relaxation temperature-jump method. At pH7.2 and 8 degrees C the rate of acylation of the NAD(+)-bound (or holo-) enzyme was 3.3x10(5)m(-1).s(-1) and the rate of phosphorolysis, the reverse reaction, was 7.5x10(3)m(-1).s(-1). After a temperature-jump perturbation the equilibrium of NAD(+) binding to the acyl-enzyme was re-established more rapidly than that of the acylation. The rate of phosphorolysis of the apoacylenzyme from sturgeon muscle and of aldehyde release from the d-glyceraldehyde 3-phosphate-apoenzyme complex were </=40m(-1).s(-1) and </=12s(-1) respectively at pH8.0 and 22 degrees C, which means that both processes are too slow to contribute significantly to the reaction pathway of the reversible NAD(+)-linked oxidative phosphorylation of d-glyceraldehyde 3-phosphate. Phosphorolysis of both acyl-apoenzyme and acyl-holoenzyme was first-order in P(i) up to 100mm-P(i) and more. PO(4) (3-) could be the reactive species of the phosphorolysis of the acyl-holoenzyme, in which case phosphorolysis is a diffusion-controlled reaction, although other kinetically indistinguishable rate equations for the reaction are possible.

Acylation↗
PubMed1973

The reversibility of adenosine triphosphate cleavage by myosin.

For the simplest kinetic model the reverse rate constants (k(-1) and k(-2)) associated with ATP binding and cleavage on purified heavy meromyosin and heavy meromyosin subfragment 1 from rabbit skeletal muscle in the presence of 5mm-MgCl(2), 50mm-KCl and 20mm-Tris-HCl buffer at pH8.0 and 22 degrees C are: k(-1)<0.02s(-1) and k(-1)=16s(-1). Apparently, higher values of k(-1) and k(-2) are found with less-purified protein preparations. The values of k(-1) and k(-2) satisfy conditions required by previous (18)O-incorporation studies of H(2) (18)O into the P(i) moiety on ATP hydrolysis and suggest that the cleavage step does involve hydrolysis of ATP or formation of an adduct between ATP and water. The equilibrium constant for the cleavage step at the myosin active site is 9. If the cycle of events during muscle contraction is described by the model proposed by Lymn & Taylor (1971), the fact that there is only a small negative standard free-energy change for the cleavage step is advantageous for efficient chemical to mechanical energy exchange during muscle contraction.

Adenosine Triphosphatases↗
PubMed1973

Kinetic studies of the acylation of pig muscle D-glyceraldehyde 3-phosphate dehydrogenase by 1,3-diphosphoglycerate and of proton uptake and release in the overall enzyme mechanism.

In the presence of NAD(+) the acylation by 1,3-diphosphoglycerate of the four active sites of pig muscle d-glyceraldehyde 3-phosphate dehydrogenase can be monitored at 365nm by the disappearance of the absorption band present in the binary complex of NAD(+) and the enzyme. A non-specific salt effect decreased the acylation rate 25-fold when the ionic strength was increased from 0.10 to 1.0. This caused acylation to be the rate-limiting process in the enzyme-catalysed reductive dephosphorylation of 1,3-diphosphoglycerate at high ionic strength at pH8. The salt effect permitted investigation of the acylation over a wide range of conditions. Variation of pH from 5.4 to 8.6 produced at most a two-fold change in the acylation rate. One proton was taken up per site acylated at pH8.0. By using a chromophoric H(+) indicator the rate of proton uptake could be monitored during the acylation and was also almost invariant in the pH range 5.5-8.5. Transient kinetic studies of the overall enzyme-catalysed reaction indicated that acylation was the process involving proton uptake at pH8.0. The enzyme mechanism is discussed in the light of these results.

Acylation↗
PubMed1972

Elementary processes of the magnesium ion-dependent adenosine triphosphatase activity of heavy meromyosin. A transient kinetic approach to the study of kinases and adenosine triphosphatases and a colorimetric inorganic phosphate assay in situ.

Transient kinetic studies of Mg(2+)-dependent heavy-meromyosin ATPase (adenosine triphosphatase) were done by monitoring the release of both ADP and P(i) into the reaction medium by using linked assay systems. The release of P(i) was monitored by its quantitative transfer to ADP, with concomitant reduction of NAD(+) in the presence of d-glyceraldehyde 3-phosphate, d-glyceraldehyde 3-phosphate dehydrogenase and phosphoglycerate kinase. The dissociation rates of the products, ADP and P(i), from heavy meromyosin were shown to be faster than the rate-controlling process, which occurs after the initial bond cleavage of ATP. The chromophoric ATP analogue, 6-mercapto-9-beta-d-ribofuranosylpurine 5'-triphosphate (thioATP) was used as a substrate and spectral changes associated with a single turnover of heavy meromyosin could be assigned to elementary processes of the mechanism. It was shown that the dissociation rate of thioADP was not the rate-controlling process of the thioATPase, whose catalytic-centre activity was 7.6 times that of the ATPase at pH8. The dissociation rate of ADP from heavy meromyosin was measured by using thioATP as displacing agent and was found to be 2.3s(-1), which is about 50 times the catalytic-centre activity of the ATPase at pH8. Transient kinetic studies with chromophoric adenosine phosphate analogues have general application for kinases and ATPases both in characterizing the chemical states of the intermediates and in delineating the elementary processes of the enzyme mechanism.

Adenosine Diphosphate↗
PubMed1971

Reactions of D-glyceraldehyde 3-phosphate dehydrogenase facilitated by oxidized nicotinamide-adenine dinucleotide.

Transient kinetic methods have been used to study the influence of NAD(+) on the rate of elementary processes of the reversible oxidative phosphorylation of d-glyceraldehyde 3-phosphate catalysed by d-glyceraldehyde 3-phosphate dehydrogenase. In the pH range 5-8 NAD(+) is bound to the enzyme during the following elementary processes of the mechanism: phosphorolysis of the acyl-enzyme, its formation from 1,3-diphosphoglycerate and the enzyme and the formation and breakdown of the glyceraldehyde 3-phosphate-enzyme complex. The rates of these four elementary processes only equal or exceed the turnover rate of the enzyme when NAD(+) is bound and are as much as 10(4) times the rates in the absence of NAD(+). Autocatalysis of the reductive dephosphorylation of 1,3-diphosphoglycerate occurs when glyceraldehyde 3-phosphate release is rate determining because NAD(+) is a reaction product. An important feature of the enzyme mechanism is that the negative-free-energy change of a chemical reaction, acyl-enzyme formation, is linked in a simple way to the positive-free-energy change of a dissociation reaction, NAD(+) release.

Animals↗
PubMed1971

Rate-determining processes and the number of simultaneously active sties of D-glyceraldehyde 3-phosphate dehydrogenase.

Transient kinetic studies of the reversible oxidative phosphorylation of d-glyceraldehyde 3-phosphate catalysed by d-glyceraldehyde 3-phosphate dehydrogenase show that all four sites of the tetrameric lobster enzyme are simultaneously active, apparently with equal reactivity. The rate-determining step of the oxidative phosphorylation is NADH release at high pH and phosphorolysis of the acyl-enzyme at low pH. For the reverse reaction the rate-determining step is a process associated with NADH binding, probably a conformation change, at high pH and d-glyceraldehyde 3-phosphate release at low pH. NADH has previously been shown to be a competitive inhibitor of the enzyme with respect to d-glyceraldehyde 3-phosphate and vice versa. This is consistent with the mechanism deduced from transient experiments given the additional proviso that 1-arseno-3-phosphoglycerate has a half-life of about 1min or longer at pH7. The dissociation constants of d-glyceraldehyde 3-phosphate and 1,3-diphosphoglycerate to the NAD(+)-bound enzyme are too large to measure but are nevertheless consistent with the low K(m) values of these substrates.

Binding Sites↗
PubMed1971

Reactions of D-glyceraldehyde 3-phosphate dehydrogenase with chromophoric thiol reagents.

The kinetics of the reaction of d-glyceraldehyde 3-phosphate dehydrogenase with 5,5'-dithiobis-(2-nitrobenzoic acid) show that NAD(+) dissociates from the enzyme before the reaction. In contrast 2-chloromercuri-4-nitrophenol reacts with the holoenzyme without prior dissociation of NAD(+). These studies and observations on the dissociation constant of NAD(+) to the lobster enzyme show that NAD(+) must dissociate from sites modified by substrates during the reductive dephosphorylation of 1,3-diphosphoglycerate. All four sites per tetramer of the apoenzyme are acylated by 1,3-diphosphoglycerate. Hydrolysis of the acyl-enzyme occurs at a significant rate even in the absence of NAD(+), which may explain previous estimates that only two sites per tetramer can readily be acylated.

Animals↗
PubMed1969

The active chemical state of D-glyceraldehyde 3-phosphate in its reactions with D-glyceraldehyde 3-phosphate dehydrogenase, aldolase and triose phosphate isomerase.

Glyceraldehyde 3-phosphate exists as the geminal diol and the free aldehyde in the molar ratio 29:1 in aqueous solution. The rate constant of the conversion of diol into aldehyde is 8.7x10(-2)sec.(-1) in the pH range 7.3-8.6 at 20 degrees . The free aldehyde is the substrate for d-glyceraldehyde 3-phosphate dehydrogenase. Over a wide concentration range of enzyme the rate of conversion of diol into aldehyde is the rate-limiting process in the catalytic oxidation of d-glyceraldehyde 3-phosphate by NAD(+). Aldolase and triose phosphate isomerase both liberate d-glyceraldehyde 3-phosphate as the aldehyde. This suggests that the relatively slow diol-aldehyde interconversion does not restrict the rate of glycolysis.

Chemical Phenomena↗
PubMed1969

A substate-induced conformation change in the reaction of alkaline phosphatase from Escherichia coli.

1. Benzyl phosphonates were prepared and their potentialities as chromophoric reagents for the exploration of the substrate-binding site of Escherichia coli alkaline phosphatase were investigated. 4-Nitrobenzylphosphonate is a competitive inhibitor of the enzyme. 2-Hydroxy-5-nitrobenzylphosphonate changes its spectrum on binding to the enzyme. This spectral change is reversed when the phosphonate is displaced from the enzyme by substrate. 2. The kinetics of the reaction of 2-hydroxy-5-nitrophenylphosphonate were studied by the stopped-flow and the temperature-jump techniques. It was found that the combination of the phosphonate with the enzyme occurred in two successive and reversible steps: enzyme-phosphonate complex-formation followed by rearrangement of the complex. The spectral change is associated with the rearrangement. At pH8 in 1m-sodium chloride at 22 degrees the rate constant is 167sec.(-1) for the rearrangement of the initially formed binary complex and is 18sec.(-1) for the reverse process. 3. It has previously been proposed that the reactions of phosphatase with its substrates include a distinct step between enzyme-substrate combination and chemical catalysis. The rate constant involved could be predicted but not measured from experiments with substrates. The value for the rate constant measured from the rate of the enzyme-phosphonate rearrangement is in excellent agreement with the predicted value. A model for the reaction mechanism is proposed that includes a conformation change in response to phosphate ester binding before phosphate transfer from substrate to enzyme.

Alkaline Phosphatase↗
PubMed1969

A new class of chromophoric organomercurials and their reactions with D-glyceraldehyde 3-phosphate dehydrogenase.

THE SYNTHESES OF THE FOLLOWING ORGANOMERCURIALS ARE DESCRIBED: 2-chloromercuri-4-nitrophenol, 2-chloromercuri-4,6-dinitrophenol, 4-chloromercuri-2-nitrophenol and 2,6-dichloromercuri-4-nitrophenol. All four organomercurials show large spectral changes in the visible spectrum when thiols displace a more weakly bound ligand such as EDTA from the mercury atom. These spectral changes are primarily associated with pK perturbation of the nitrophenols. The mercurials are therefore chromophoric probes for thiol groups in proteins and other thiols of biological interest. The enzyme d-glyceraldehyde 3-phosphate dehydrogenase from lobster muscle is used as a model system in which the properties of the organomercurials may be illustrated. In particular it is shown how d-glyceraldehyde 3-phosphate dehydrogenase carboxymethylated at the active site may be mercurated at a specific site. This mercurial derivative may be crystallized and shown to be isomorphous with the parent enzyme. The mercurials also act as ;reporter groups' by monitoring phosphate or pyrophosphate binding to the enzyme. The mercurials may also be used to estimate cations by an EDTA displacement method.

Chemical Phenomena↗
PubMed1968

The kinetics of the reaction of nitrophenyl phosphates with alkaline phosphatase from Escherichia coli.

1. The steady-state rate of hydrolysis of 2,4-dinitrophenyl phosphate catalysed by Escherichia coli phosphatase is identical with that of 4-nitrophenyl phosphate over the pH range 5.5-8.5. 2. The increase in the rate of the enzyme-catalysed decomposition of nitrophenyl phosphates in the presence of tris at pH8.1 and 5.9 is consistent with the hypothesis that tris increases the rate of decomposition of a phosphoryl-enzyme intermediate. At pH8.1 the rate of decomposition of the phosphoryl-enzyme is approximately twice as fast as the rate of its formation, whereas at pH5.9 the rate of formation of the phosphoryl-enzyme is considerably faster than its decomposition. 3. Pre-steady-state measurements of the initial transient of the liberation of 2,4-dinitrophenol during the reaction of the enzyme with 2,4-dinitrophenyl phosphate confirmed the above pH-dependence of the ratio of the rates of phosphorylation and dephosphorylation of the enzyme. At optimum pH (above pH8), when the phosphorylation of the enzyme by the substrate is rate-determining, this step must be controlled by a rearrangement of the enzyme or enzyme-substrate complex.

Alkaline Phosphatase↗