Regulatory behavior of monomeric enzymes. 2. A wheat-germ hexokinase as a mnemonical enzyme

Investigation of sugar binding kinetics of the E. coli sugar/H+ symporter XylE using solid supported membrane-based electrophysiology

Bacterial transporters are difficult to study using conventional electrophysiology because of their low transport rates and the small size of bacterial cells. Here, we applied solid-supported membrane–based electrophysiology to derive kinetic parameters of sugar translocation by the Escherichia coli xylose permease (XylE), including functionally relevant mutants. Many aspects of the fucose permease (FucP) and lactose permease (LacY) have also been investigated, which allow for more comprehensive conclusions regarding the mechanism of sugar translocation by transporters of the major facilitator superfamily. In all three of these symporters, we observed sugar binding and transport in real time to determine K_M, V_max, K_D, and k_obs values for different sugar substrates. K_D and k_obs values were attainable because of a conserved sugar-induced electrogenic conformational transition within these transporters. We also analyzed interactions between the residues in the available X-ray sugar/H⁺ symporter structures obtained with different bound sugars. We found that different sugars induce different conformational states, possibly correlating with different charge displacements in the electrophysiological assay upon sugar binding. Finally, we found that mutations in XylE altered the kinetics of glucose binding and transport, as Q175 and L297 are necessary for uncoupling H⁺ and d-glucose translocation. Based on the rates for the electrogenic conformational transition upon sugar binding (>300 s⁻¹) and for sugar translocation (2 s⁻¹ − 30 s⁻¹ for different substrates), we propose a multiple-step mechanism and postulate an energy profile for sugar translocation. We also suggest a mechanism by which d-glucose can act as an inhibitor for XylE.

Hysteresis and positive cooperativity as possible regulatory mechanisms of Trypanosoma cruzi hexokinase activity

In Trypanosoma cruzi, the causal agent of Chagas disease, the first six or seven steps of glycolysis are compartmentalized in glycosomes, which are authentic but specialized peroxisomes. Hexokinase (HK), the first enzyme in the glycolytic pathway, has been an important research object, particularly as a potential drug target. Here we present the results of a specific kinetics study of the native HK from T. cruzi epimastigotes; a sigmoidal behavior was apparent when the velocity of the reaction was determined as a function of the concentration of its substrates, glucose and ATP. This behavior was only observed at low enzyme concentration, while at high concentration classical Michaelis-Menten kinetics was displayed. The progress curve of the enzyme's activity displays a lag phase of which the length is dependent on the protein concentration, suggesting that HK is a hysteretic enzyme. The hysteretic behavior may be attributed to slow changes in the conformation of T. cruzi HK as a response to variations of glucose and ATP concentrations in the glycosomal matrix. Variations in HK's substrate concentrations within the glycosomes may be due to variations in the trypanosome's environment. The hysteretic and cooperative behavior of the enzyme may be a form of regulation by which the parasite can more readily adapt to these environmental changes, occurring within each of its hosts, or during the early phase of transition to a new host.

Conformational transition pathway in the activation process of allosteric glucokinase

Glucokinase (GK) is a glycolytic enzyme that plays an important role in regulating blood glucose level, thus acting as a potentially attractive target for drug discovery in the treatment of diabetes of the young type 2 and persistent hyperinsulinemic hypoglycemia of infancy. To characterize the activation mechanism of GK from the super-open state (inactive state) to the closed state (active state), a series of conventional molecular dynamics (MD) and targeted MD (TMD) simulations were performed on this enzyme. Conventional MD simulation showed a specific conformational ensemble of GK when the enzyme is inactive. Seven TMD simulations depicted a reliably conformational transition pathway of GK from the inactive state to the active state, and the components important to the conformational change of GK were identified by analyzing the detailed structures of the TMD trajectories. In combination with the inactivation process, our findings showed that the whole conformational pathway for the activation-inactivation-activation of GK is a one-direction circulation, and the active state is less stable than the inactive state in the circulation. Additionally, glucose was demonstrated to gradually modulate its binding pose with the help of residues in the large domain and connecting region of GK during the activation process. Furthermore, the obtained energy barriers were used to explain the preexisting equilibrium and the slow binding kinetic process of the substrate by GK. The simulated results are in accordance with the recent findings from the mutagenesis experiments and kinetic analyses. Our observations reveal a complicated conformational process in the allosteric protein, resulting in new knowledge about the delicate mechanisms for allosteric biological macromolecules that will be useful in drug design for targeting allosteric proteins.

Cooperativity in monomeric enzymes with single ligand-binding sites

Cooperativity is widespread in biology. It empowers a variety of regulatory mechanisms and impacts both the kinetic and thermodynamic properties of macromolecular systems. Traditionally, cooperativity is viewed as requiring the participation of multiple, spatially distinct binding sites that communicate via ligand-induced structural rearrangements; however, cooperativity requires neither multiple ligand binding events nor multimeric assemblies. An underappreciated manifestation of cooperativity has been observed in the non-Michaelis-Menten kinetic response of certain monomeric enzymes that possess only a single ligand-binding site. In this review, we present an overview of kinetic cooperativity in monomeric enzymes. We discuss the primary mechanisms postulated to give rise to monomeric cooperativity and highlight modern experimental methods that could offer new insights into the nature of this phenomenon. We conclude with an updated list of single subunit enzymes that are suspected of displaying cooperativity, and a discussion of the biological significance of this unique kinetic response.

Fluorescence measurements of nucleotide association with the Na(+)/K(+)-ATPase

The Na(+)/K(+)-ATPase, a membrane-associated ion pump, uses energy from the hydrolysis of ATP to pump 3 Na(+) ions out of and 2 K(+) into cells. The dependence of ATP hydrolysis on ATP concentration was measured using a fluorescence coupled-enzyme assay. The dependence on concentration of nucleotide association with the ATPase was examined using ADP and ATP-induced quenching of the fluorescence of ATPase labeled with Cy3-maleimide (Cy3-ATPase) or Alexa Fluor 546 carboxylic acid, succinimidyl ester (AF-ATPase). The kinetics of ATP hydrolysis in the presence of Na(+) and K(+) exhibited negative cooperativity with a Hill coefficient (n(H)) of 0.66 and a half-maximal concentration (K(0.5)) of 61 microM; in the absence of K(+), n(H) was 0.58 and K(0.5) was 13 microM. Nucleotide-induced fluorescence quenching exhibited negative cooperativity with an n(H) of 0.3-0.5. These results suggest that negative cooperativity observed in ATP hydrolysis is attributable to negative cooperativity in nucleotide association to the ATPase. Interaction between AF-ATPase and ATP labeled with Alexa Fluor 647 (AF-ATP) showed significant Förster resonance energy transfer (FRET). These results indicate that the ATPase exists as oligoprotomeric complexes in this preparation, and that this aggregation has significant effects on enzyme function.

Glucose modulation of glucokinase activation by small molecules

Small molecule activators of glucokinase (GK) were used in kinetic and equilibrium binding studies to probe the biochemical basis for their allosteric effects. These small molecules decreased the glucose K 0.5 ( approximately 1 mM vs approximately 8 mM) and the glucose cooperativity (Hill coefficient of 1.2 vs 1.7) and lowered the k cat to various degrees (62-95% of the control activity). These activators relieved GK's inhibition from glucokinase regulatory protein (GKRP) in a glucose-dependent manner and activated GK to the same extent as control reactions in the absence of GKRP. In equilibrium binding studies, the intrinsic glucose affinity to the activator-bound enzyme was determined and demonstrated a 700-fold increase relative to the apoenzyme. This is consistent with a reduction in apparent glucose K D and the steady-state parameter K 0.5 as a result of enzyme equilibrium shifting to the activator-bound form. The binding of small molecules to GK was dependent on glucose, consistent with the structural evidence for an allosteric binding site which is present in the glucose-induced, active enzyme form of GK and absent in the inactive apoenzyme [Kamata et al. (2004) Structure 12, 429-438]. A mechanistic model that brings together the kinetic and structural data is proposed which allows qualitative and quantitative analysis of the glucose-dependent GK regulation by small molecules. The regulation of GK activation by glucose may have an important implication for the discovery and design of GK activators as potential antidiabetic agents.

Thermodynamic analysis of the emergence of new regulatory properties in a phosphoribulokinase-glyceraldehyde 3-phosphate dehydrogenase complex

Glyceraldehyde 3-phosphate dehydrogenase and phosphoribulokinase exist as stable enzymes and as part of a complex in Chlamydomonas reinhardtii. We show here that phosphoribulokinase exerts an imprinting on glyceraldehyde 3-phosphate dehydrogenase, which affects its catalysis by decreasing the energy barrier of the reactions with NADH or NADPH by 3.8 +/- 0.5 and 1.3 +/- 0.3 kJ.mol(-1). Phosphoribulokinase and glyceraldehyde 3-phosphate dehydrogenase within the complex are regulated by NADP(H) but not by NAD(H). The activities of the metastable phosphoribulokinase and glyceraldehyde 3-phosphate dehydrogenase released from the complex preincubated with NADP(H) are different from those of the metastable enzymes released from the untreated complex. NADP(H) increases phosphoribulokinase and NADPH-glyceraldehyde 3-phosphate dehydrogenase activities with a (~)K(0.5 (NADP)) of 0.68 +/- 0.16 mm and a (~)K(0.5 (NADPH)) of 2.93 +/- 0.87 mm and decreases NADH-dependent activity. 1 mm NADP increases the energy barrier of the NADH-glyceraldehyde 3-phosphate dehydrogenase-dependent reaction by 1.8 +/- 0.2 kJ.mol(-1) and decreases that of the reactions catalyzed by phosphoribulokinase and NADPH-glyceraldehyde 3-phosphate dehydrogenase by 3 +/- 0.2 and 1.2 +/- 0.3 kJ.mol(-1), respectively. These cofactors have no effect on the independent stable enzymes. Therefore, protein-protein interactions may give rise to new regulatory properties.

Balanced branching in transcription termination

The theory of stochastic transcription termination based on free-energy competition [von Hippel, P. H. & Yager, T. D. (1992) Science 255, 809-812 and von Hippel, P. H. & Yager, T. D. (1991) Proc. Natl. Acad. Sci. USA 88, 2307-2311] requires two or more reaction rates to be delicately balanced over a wide range of physical conditions. A large body of work on glasses and large molecules suggests that this balancing should be impossible in such a large system in the absence of a new organizing principle of matter. We review the experimental literature of termination and find no evidence for such a principle, but do find many troubling inconsistencies, most notably, anomalous memory effects. These effects suggest that termination has a deterministic component and may conceivably not be stochastic at all. We find that a key experiment by Wilson and von Hippel [Wilson, K. S. & von Hippel, P. H. (1994) J. Mol. Biol. 244, 36-51] thought to demonstrate stochastic termination was an incorrectly analyzed regulatory effect of Mg(2+) binding.

Binding energy and the information content of some elementary biological processes

Protein interactions within a multimolecular complex can result in information and energy transfer between proteins. This can lead in turn to the emergence of novel functions of some proteins of the complex. Various examples of this situation can be found in the scientific literature. This is probably the case for prion protein, chloroplast phosphoribulokinase bound to glyceraldehyde phosphate dehydrogenase, Ras system, and pancreatic lipase bound to biomembranes, to cite but a few. Any enzyme reaction, or enzyme reaction network, carries Shannon entropy and information. On contrary to genome entropy, the entropy of enzyme reactions and metabolic sequences is sensitive to 'external' signals, such as substrate, effector and proton concentrations. Complex structural organization of the cell is associated with a higher entropy content, and one can calculate the gain of entropy and information due to integration and complexity. One may conclude from this brief analysis that the informational content of a living cell is much larger than that of its genome.

Allosteric activation of Arabidopsis threonine synthase by S-adenosylmethionine

Plant threonine synthase, in contrast to its bacterial counterpart, is strongly stimulated by S-adenosylmethionine via a noncovalent interaction [Giovanelli et al. (1984) Plant. Physiol. 76, 285-292]. The mechanism of activation remained, however, largely unknown. To further characterize this unusual role for S-adenosylmethionine, the Arabidopsis thaliana threonine synthase was overexpressed in Escherichia coli, purified to homogeneity, and then used for kinetic and enzyme-bound pyridoxal 5'-phosphate fluorescence equilibrium-binding experiments. We observed that the activating effect of S-adenosylmethionine results from an 8-fold increase in the rate of catalysis and from a 25-fold decrease in the Km value for the O-phosphohomoserine substrate. The data can be well fitted by a kinetic model assuming binding of two S-adenosylmethionine molecules on the native enzyme. We suggest that the dramatic modifications of the enzyme kinetic properties originate most presumably from an allosteric and cooperative transition induced by S-adenosylmethionine. This transition occurs at a much faster rate in the presence of the substrate than in its absence.

Information transfer in multienzyme complexes--1. Thermodynamics of conformational constraints and memory effects in the bienzyme glyceraldehyde-3-phosphate-dehydrogenase-phosphoribulokinase complex of Chlamydomonas reinhardtii chloroplasts

Oxidized phosphoribulokinase is almost inactive in its isolated state but becomes active when associated with glyceraldehyde-3-phosphate dehydrogenase. There is therefore an information transfer that takes place between these two enzymes. However, when the complex dissociates, free oxidized phosphoribulokinase is even more active than when it is associated with glyceraldehyde-3-phosphate dehydrogenase. This means that glyceraldehyde-3-phosphate dehydrogenase exerts an imprinting effect upon phosphoribulokinase which persists for a while after the parting of the two proteins. Various methods derived from statistical thermodynamics can be used to estimate the fraction of energy transferred from glyceraldehyde-3-phosphate dehydrogenase to phosphoribulokinase and which alters the kinetic parameters of the latter enzyme. In the complex, the decrease of the free energy associated with the binding of ribulose 5-phosphate is larger than that of ATP. This implies that the mutual association of the two enzymes facilitates the binding of the former substrate but is without effect on that of the latter. The main effect exerted by the association of the two enzymes is to decrease by about 10 kJ/mol the height of the energy barrier of the catalytic process. Phosphoribulokinase keeps an imprinting effect exerted by glyceraldehyde-3-phosphate dehydrogenase after the parting of the two enzymes. Part of the energy transferred from one protein to the other is used to decrease slightly the apparent binding free energy of the two substrates of phosphoribulokinase by about 1.5 kJ/mol. Whereas the previous association of the two enzymes does not significantly alter substrate binding to phosphoribulokinase, it greatly affects catalysis and decreases by about 16 kJ/mol the height of the energy barrier pertaining to this step. Therefore, within multienzyme complexes, information and energy can be transferred between proteins. Statistical thermodynamics offers the possibility of estimating how this energy is used to alter the various kinetic parameters of the reaction.

Characterization of H. parasuis periplasmic nucleotide pyrophosphatase as a potential target enzyme for inhibition of growth

The periplasmic nucleotide pyrophosphatase from Haemophilus parasuis was purified 750-fold to electrophoretic homogeneity through salt fractionation and ion-exchange and affinity chromatography. The purified enzyme was monomeric with an apparent M(r) of 70,000 and catalyzed the hydrolysis of the pyrophosphate bond of NAD to yield NMN and AMP as products. The enzyme exhibited negative cooperativity in the hydrolysis of a number of pyridine dinucleotides and structurally-related pyrophosphate compounds as indicated by biphasic double-reciprocal plots and Hill coefficients of 0.5. The kinetic parameters, K(m) and Vm, determined titrimetrically and analyzed through computer programs, were used to compare the relative effectiveness of dinucleotides containing nitrogen bases other than nicotinamide or adenine to that of NAD. Effective substrate-competitive inhibition of the pyrophosphatase was observed with purine and pyrimidine nucleoside diphosphates in the low micromolar concentration range. Although less effective, N1-alkylnicotinamide chlorides also inhibited competitively with respect to the substrate, NAD. In addition to being an effective inhibitor of the purified enzyme, adenosine diphosphate also inhibited growth of H. parasuis at a low micromolar concentration. This inhibition of growth correlates well with inhibition of the periplasmic pyrophosphatase which is supported by the fact that adenosine diphosphate does not effectively inhibit growth when the pyrophosphatase is by-passed by growth on nicotinamide mononucleotide. These observations are all consistent with the periplasmic nucleotide pyrophosphatase being essential for the growth of the organism on NAD and therefore, a very important enzyme with respect to the pathogenesis of the organism. 3-Aminopyridine mononucleotide, which also inhibited growth of H. parasuis at a low micromolar concentration, did not effectively inhibit the purified pyrophosphatase and a different target enzyme needs to be considered to explain growth inhibition by this derivative.

Isomerization of the free enzyme versus induced fit: effects of steps involving induced fit that bypass enzyme isomerization on flux ratios and countertransport

In a single-substrate-single-product enzyme reaction, "counter transport', which indicates that the ratio of the forward to the reverse fluxes is less than that expected from the Independence Relationship, is regarded as strong evidence for the free enzyme existing in two states, one of which combines with the substrate and the other with the product, with a slow isomerization between the two conditions. To account for positive and negative co-operativity, found with some enzymes, additional induced-fit reactions bypassing at least part of the isomerization have been proposed. The effects of such additional steps have been examined, using two models: in one, (a), the enzyme passes through an intermediate state during its isomerization, and both substrate and product may react with this state to give rise to the binary complexes; in the other, (b), the substrate may react with the enzyme as soon as the product is released and similarly with the reverse reaction, the isomerization thereby being bypassed completely. In the presence of such additional steps, the following can be concluded. (i) The data should be analysed in terms of the flux ratios, rather than observation of the amount of countertransport. (ii) The additional bypassing steps markedly change the pattern of dependence of the flux ratio on substrate and product concentrations. At high substrate and product concentrations, the ratio remains very dependent on how far the reaction is from equilibrium, and the kinetics are asymmetric. (iii) The mechanism causing the flux ratio to be less than that given by the Independence Relationship differs from that previously described, in that, at least in part, it arises from a 1:1 exchange between substrate and product. (iv) Despite this novel mechanism, there must be two states of the enzyme, combining respectively with substrate and product, and these must not be in rapid exchange. Thus countertransport remains very strong evidence for the existence of two such states. It is no longer a requirement that the enzyme states should be linked by an isomerization step. (v) Under no conditions can the flux ratio exceed that given by the Independence Relationship. (vi) Under unusual conditions the isomerization of the enzyme in model (b) may be undetectable by steady-state kinetics. (vii) Measurements of the coefficients in the flux ratio equations enable limits to be set to certain ratios of the rate constants. In addition to these conclusions, methods are described for (viii) analysing flux ratio data for the presence of induced fit steps and (ix) determining flux ratios from induced transport curves. The derivation of steady state-velocity equations show that: (x) both models may give rise to positive and negative 'co-operativity' and sigmoid substrate-velocity curves, but that, under conditions giving rise to sigmoid curves, the deviation of the flux ratio from that required by the Independence Relationship may be difficult to demonstrate because of the asymmetry of the system. Under all conditions the fluxes at equilibrium should obey hyperbolic kinetics.

Catalysis of reduction of carbohydrate 2-oxoaldehydes (osones) by mammalian aldose reductase and aldehyde reductase

In mammalian tissues, carbohydrate 2-oxoaldehydes, or 'osones', formed by cleavage of carbohydrate residues from glycated proteins, cause damage to cells and tissues by cross-linking of proteins. In the substrate specificity study reported here, we show that several osones are relatively good substrates for the reduced, unactivated form of aldose reductase (EC 1.1.1.21) from human and pig muscle, and aldehyde reductase (EC 1.1.1.2) from pig kidney, enzymes that have been well characterised both structurally and mechanistically. Since these enzymes are relatively ubiquitous, they may serve to protect a large number of tissues from damage, by catalysing the reduction of locally-produced osones. Reduction of all substrates by aldehyde reductase obeyed Michaelis-Menten kinetics. In contrast, a Hill constant of about 0.5 was obtained for aldose reductase-catalysed reduction of each of the carbohydrate 2-oxoaldehydes, and for several other substrates that were examined. Although this deviation from Michaelis-Menten kinetics has been ascribed to the presence of two forms of the enzyme, activated and unactivated, our results suggest that it is a characteristic of the unactivated form.

The reaction of cephalosporins with penicillin-binding protein 1b gamma from Escherichia coli

The kinetics of the reaction of purified penicillin-binding protein 1b gamma from Escherichia coli with cephalosporins suggest that the enzyme exists in two kinetically distinct conformations that are in slow equilibrium. One of these forms can effect rapid hydrolysis of some beta-lactams and it is only through its deactivation by conversion to the slower reacting form that complete inhibition can be achieved. With some cephalosporins and with penicillins having simple aromatic side-chains the reaction was slower and did not exhibit the same kinetic behaviour. This could be attributed to the rate of reaction being similar to the rate of conformation change and thus sets an upper limit on the isomerization rate.

Dissociation of enzyme oligomers: a mechanism for allosteric regulation

Most enzymes exist as oligomers or polymers, and a significant subset of these (perhaps 15% of all enzymes) can reversibly dissociate and reassociate in response to an effector ligand. Such a change in subunit assembly usually is accompanied by a change in enzyme activity, providing a mechanism for regulation. Two models are described for a physical mechanism, leading to a change in activity: (1) catalytic activity depends on subunit conformation, which is modulated by subunit dissociation; and (2) catalytic or regulatory sites are located at subunit interfaces and are disrupted by subunit dissociation. Examples of such enzymes show that both catalytic sites and regulatory sites occur at the junction of 2 subunits. In addition, for 9 enzymes, kinetic studies supported the existence of a separate regulatory site with significantly different affinity for the binding of either a substrate or a product of that enzyme. Over 40 dissociating enzymes are described from 3 major metabolic areas: carbohydrate metabolism, nucleotide metabolism, and amino acid metabolism. Important variables that influence enzyme dissociation include: enzyme concentration, ligand concentration, other cellular proteins, pH, and temperature. All these variables can be readily manipulated in vitro, but normally only the first two are physiological variables. Seven of these enzymes are most active as the dissociated monomer, the others as oligomers, emphasizing the importance of a regulated equilibrium between 2 or more conformational states. Experiments to test whether enzyme dissociation occurs in vivo showed this to be the case in 6 out of 7 studies, with 4 different enzymes.

Regulation of hepatocyte adenylate cyclase by amylin and CGRP: a single receptor displaying apparent negative cooperatively towards CGRP and simple saturation kinetics for amylin, a requirement for phosphodiesterase inhibition to observe elevated hepatocyte cyclic AMP levels and the phosphorylation of Gi-2

Challenge of intact hepatocytes with amylin only succeeded in elevating intracellular cyclic AMP levels and activating phosphorylase in the presence of the cAMP phosphodiesterase inhibitor IBMX. Both amylin and CGRP similarly activated adenylate cyclase, around 5-fold, although approximately 400-fold higher levels of amylin were required to elicit half maximal activation. Amylin activated adenylate cyclase though apparently simple Michaelien kinetics whereas CGRP elicited activation by kinetics indicative of apparent negative co-operativity. Use of the antagonist CGPP(8-37) showed that both CGRP and amylin activated hepatocyte adenylate cyclase through a common receptor by a mnemonical mechanism where it was proposed that the receptor co-existed in interconvertible high and low affinity states for CGRP. It is suggested that this model may serve as a paradigm for G-protein linked receptors in general. Amylin failed to both stimulate inositol phospholipid metabolism in hepatocytes and to elicit the desensitization of glucagon-stimulated adenylate cyclase. Amylin did, however, elicit the phosphorylation of the inhibitory guanine nucleotide regulatory protein Gi-2 in hepatocytes and prevented the action of insulin in reducing the level of phosphorylation of this G-protein.

The kinetics of non-stoichiometric bursts of beta-lactam hydrolysis catalysed by class C beta-lactamases

Class C beta-lactamases from Pseudomonas aeruginosa and several species of the Enterobacteriaceae have been observed to undergo a rapid burst in hydrolysis of beta-lactam antibiotics before relaxation to a steady-state rate of hydrolysis. The amplitude of the burst corresponds to the hydrolysis of between 1 and 10,000 mol of the substrate per mol of enzyme. The decay of the rate of hydrolysis in the burst phase comprises two exponential reactions, which indicates that there are three different reactive states of the enzymes. Examination of the kinetics of acylation by slowly reacting beta-lactams suggests that there are three forms of the free enzyme in slow equilibrium. Thus it would appear that the burst kinetics exhibited by class C enzymes can be attributed to redistribution of the enzyme between different conformations induced by the reaction with substrate.

A mnemonical or negative-co-operativity model for the activation of adenylate cyclase by a common G-protein-coupled calcitonin-gene-related neuropeptide (CGRP)/amylin receptor

Both amylin and calcitonin-gene-related neuropeptide (CGRP) activated adenylate cyclase activity in hepatocyte membranes around 5-fold in a dose-dependent fashion, with EC50 values of 120 +/- 14 and 0.3 +/- 0.14 nM respectively. Whereas amylin exhibited normal activation kinetics (Hill coefficient, h approximately 1), CGRP showed kinetics indicative of either multiple sites/receptor species having different affinities for this ligand or a single receptor species exhibiting apparent negative co-operativity (h approximately 0.21). The CGRP antagonist CGRP-(8-37)-peptide inhibited adenylate cyclase stimulated by EC50 concentrations of either amylin or CGRP. Inhibition by CGRP-(8-37) was selective in that markedly lower concentrations were required to block the action of amylin (IC50 = 3 +/- 1 nM) compared with that of CGRP itself (IC50 = 120 +/- 11 nM). Dose-effect data for inhibition of CGRP action by CGRP-(8-37) showed normal saturation kinetics (h approximately 1), whereas CGRP-(8-37) inhibited amylin-stimulated adenylate cyclase activity in a fashion which was indicative of either multiple sites or apparent negative co-operativity (h approximately 0.24). Observed changes in the kinetics of inhibition by CGRP-(8-37) of CGRP, but not amylin-stimulated adenylate cyclase, at concentrations of agonists below their EC50 values militated against a model of two distinct populations of non-interacting receptors each able to bind both amylin and CGRP. A kinetic model is proposed whereby a single receptor, capable of being activated by both CGRP and amylin, obeys either a mnemonical kinetic mechanism or one of negative co-operativity with respect to CGRP but not to amylin. The relative merits of these two models are discussed together with a proposal suggesting that the activation of adenylate cyclase by various G-protein-linked receptors may be described by a mnemonical model mechanism.

Testing and characterizing enzymes and membrane-bound carrier proteins acting on amphipathic ligands in the presence of bilayer membrane material and soluble binding protein. Application to the uptake of oleate into isolated cells

1. A multiphasic modelling approach [Heirwegh, Meuwissen, Vermeir & De Smedt (1988) Biochem. J. 254, 101-108] is applied to systems containing poorly water-soluble amphipathic reactants, membrane material, soluble binding protein and acceptor protein (enzyme or membrane-bound carrier protein). 2. The field of application is constrained by the assumptions (i) that the amount of acceptor-bound substrate is small compared with the total amount and (ii) that all preceding chemical reactions and steps of mass transport are rapid compared with the chemical change monitored. 3. Initial-rate formulae for systems in which an acceptor interacts with unbound or protein-bound ligand are given. The saturation curves are near-hyperbolic or sigmoidal, depending both (i) on the form of ligand (unbound or protein-bound) acted upon by the acceptor and (ii) on whether the assays are performed at constant concentration of soluble binding protein Cp or at constant substrate/binding-site molar ratio RS. 4. Several diagnostic features permit unequivocal distinction between acceptor action on unbound or protein-bound substrate. In the former case, saturation curves, run at the same constant concentration of one of several binding proteins of increasing binding affinity, will show progressively increasing inhibition, the shape changing from near-hyperbolic at Km' less than K1' to sigmoidal at Km' greater than K1'.Km' is the effective Michaelis constant of the acceptor and K1' the effective dissociation constant of the binding sites of the soluble protein (for the sites with the higher binding affinity, if several classes of binding site are present on the protein). Alternatively, the maximum velocity obtained at constant RS less than or equal to 1 should increase hyperbolically with RS/(1-RS) for a binding protein with a single class of binding site. The formula that applies when the binding protein contains two classes of independent binding site is also available. When the acceptor acts on protein-bound ligand, the maximum velocity obtained at constant binding-protein concentration, Cp, increases hyperbolically with Cp. 5. Application of these and additional criteria to initial-rate data on the uptake of oleate into isolated cells supports a mechanism of carrier-mediated uptake of the unbound ligand and allows one to clarify some observations that hitherto had been poorly explained. 6. The influence of soluble binding protein on the reaction and substrate specificities of ligand/acceptor interaction is also discussed. 7. In its present state, data treatment for 'double binding-protein systems' generally requires separate determination of the binding parameters of the soluble binding protein.(ABSTRACT TRUNCATED AT 400 WORDS)

Non-michaelian behavior of 5 alpha-reductase in human prostate

An in-depth analysis of the kinetics of 5 alpha-reductase in human prostatic tissue gave findings inconsistent with the claim that the enzyme is michaelian. In both hyperplastic and malignant tissue, the time-course of the conversion of testosterone (T) into dihydrotestosterone (DHT) was non-linear under conditions ensuring less than 15% conversion of substrate and cofactor. An initial rapid phase of conversion was followed by a long steady-state phase. This time-dependent change in conversion rate was not due to enzyme denaturation, fast inhibition by substrate or product effects. It resulted from a true slow transient kinetic process induced in the reactive enzyme by the substrates. Under our experimental conditions at pH 5.5, 5 alpha-reductase appeared to undergo a conformational change from an initially highly reactive form to a less reactive form. Since this "hysteretic" behavior was correlated with apparently negative cooperativity in enzyme kinetics, we postulate that, as previously described for other key metabolic enzymes, regulation of 5 alpha-reductase activity in the prostate depends on the molecular flexibility of the enzyme and on changes in the cooperativity of different enzyme forms over time. This original non-michaelian behavior may explain the conflicting kinetics reported so far in the literature for this enzyme. The clinical implications of 5 alpha-reductase hysteresis and its involvement in the damping of DHT production within the prostate are discussed.

Enzymes as biosensors. 1. Enzyme memory and sensing chemical signals

When a free enzyme exists under different conformations that 'slowly' isomerize during the conversion of a substrate into a product, the corresponding 'slow' relaxation component may interfere with the steady-state component. The apparent steady-state rate that may be measured under these conditions is called the meta-steady-state rate for it refers to the existence of metastable states of the enzyme during the reaction. By contrast to the real steady-state rate, the meta-steady-state rate is dependent upon the initial state of the enzyme, that is on the respective concentrations of the free enzyme forms. The simplest model that may display this type of behaviour is the mnemonical model. For a fixed concentration of the last product of the reaction sequence the meta-steady state is different depending on that concentration being reached by an increase or a decrease of a previous concentration. This means that the meta-steady-state rate describes a hysteresis loop as the product concentration is increased and decreased. Owing to the existence of metastable states, the enzyme system behaves as a biosensor that is able to detect both a concentration and the direction of a concentration change. The existence of the hysteresis loop of the meta-steady-state rate implies that the two free enzyme forms display hysteresis as well. A chemical potential, called the sensing potential, is specifically associated with the 'perception' of the direction of the thermodynamic force generated by the decrease or the increase of the concentration of the ligand that binds to one of the enzyme conformations. The sensing potential of the enzyme conformer that does not bind the product increases and reaches a plateau as the chemical potential of that product is raised. Alternatively the sensing potential of the other conformer vanishes at low and high chemical potentials of the product and is significant for intermediate chemical potentials. Enzymes that display very slow conformation changes may thus be viewed as elementary sensor devices.

Viscoelastic models for enzymes with multiple conformational states

In this article we represent an enzyme capable of exhibiting more than one conformational state as a viscoelastic unit embedded in a fluid medium. We show how this viscoelastic unit is thermally activated to make transitions between equilibrium states, and propose this model as a mesoscopic representation for transitions between conformational states of an enzyme. In this representation, kinetic constants for transitions between conformations are given explicitly in terms of interactions between the enzyme and the medium. Two applications of this model are discussed: mnemonic enzymes, and co-operative enzymes exhibiting half-of-the-sites reactivity.

Kinetics of hexokinase D ('glucokinase') with inosine triphosphate as phosphate donor. Loss of kinetic co-operativity with respect to glucose

When ATP, the normal phosphate donor for hexokinase D ('glucokinase'), is replaced by ITP, the positive co-operativity with respect to glucose disappears. This may be rationalized in relation to kinetic models for hexokinase D co-operativity, which assume that with the normal substrates the chemical reaction and subsequent release of products occur so rapidly that binding of substrates cannot approach equilibrium and is therefore not constrained by the thermodynamic requirement that the Hill coefficient for substrate binding cannot exceed the number of binding sites. ITP is a much poorer substrate than ATP, however: its Km value at high glucose concentrations is 24 times the value for ATP, whereas the value of the limiting rate V is decreased about 8-fold. Consequently it is no longer possible for the ternary complex to be converted into products rapidly enough to generate kinetic co-operativity. The negative co-operativity with respect to glucose observed in 2H2O with ATP as phosphate donor also disappears when ITP is used instead of ATP.

Co-operativity in monomeric enzymes

It has been known for at least 20 years that monomeric enzymes can in principle show kinetic behaviour similar in appearance to the binding of ligands to oligomeric proteins in which there are co-operative interactions between multiple binding sites. However, the initial lack of experimental examples of kinetic co-operativity suggested that in nature co-operativity always arose from interactions between binding sites. Now, however, several examples are known, most of which cannot be explained in terms of multiple binding sites on one polypeptide chain. All current theoretical models for monomeric co-operativity postulate that it arises from the presence in the mechanism of parallel pathways for substrate binding that are slow compared with the possible rate of the catalytic reaction. Rapid removal of the intermediates produced in the slow steps prevents them from approaching equilibrium and allows the appearance of kinetic properties that would not be possible in systems at equilibrium.

Mechanistic origin of the sigmoidal rate behaviour of rat liver hexokinase D ('glucokinase')

Two recent proposals to account for the kinetic co-operativity of hexokinase D ('glucokinase') from rat liver are examined. A model in which the deviations from Michaelis-Menten kinetics result from a random order of binding of the substrates [Pettersson (1986) Biochem. J. 233, 347-350] accounts satisfactorily for the behaviour as a function of glucose concentrations, but it also predicts observable substrate inhibition by MgATP, which is in fact not observed. An alternative proposal in which the deviations arise from recycling of an enzyme-MgADP complex [Pettersson (1986) Eur. J. Biochem. 154, 167-170] also accounts satisfactorily for some of the data, but the required enzyme-MgADP complex could not be detected in isotope-exchange measurements. Thus the mnemonical mechanism proposed originally [Storer & Cornish-Bowden (1977) Biochem. J. 165, 61-69], which explains the deviations in terms of a relatively slow interconversion between two forms of free enzyme, remains the most parsimonious explanation of the behavior of hexokinase D.

Kinetic implications of the occurrence of several relaxations in the conformational transition of mnemonical enzymes

If the conformational transition involved in enzyme memory occurs in several elementary steps, the time constant of the overall 'slow' relaxation is mostly determined by the individual values of the rate constants pertaining to the overall transconformation. The extent of kinetic co-operativity of the enzyme reaction, however, is mostly controlled by the degree of reversibility of the elementary steps of the conformational transition. There is then no simple relation between the time scale of the 'slow' transition and the extent of kinetic co-operativity of the enzyme reaction. A slow transition of about 10(-3) s-1 is therefore perfectly compatible with a strong positive or negative co-operativity and in particular with the negative co-operativity observed with wheat germ hexokinase LI. The relationship that has been established recently [Pettersson, G. (1986) Eur. J. Biochem. 154, 167-170] between the 'slow' enzyme relaxation and the extent of kinetic co-operativity holds only in the specific case where the transconformation occurs in one step. Owing to the possible occurrence of a multistep conformation change, the lack of this relationship means nothing as to the validity, or the invalidity, of the concept of mnemonical transition. More informative than the time scale of the 'slow' transition is its dependence with respect to glucose and glucose 6-phosphate, which both react with the enzyme. The effect of reaction products on the modulation of kinetic co-operativity is also of cardinal importance in the diagnosis of enzyme memory. Since an alternative model has been recently proposed by Pettersson (cited above) to explain the mechanistic origin of kinetic co-operativity of monomeric enzymes, the effect of products on the kinetic co-operativity predicted by this alternative model has been studied theoretically, in order to determine whether it is consistent with the experimental results obtained with wheat germ hexokinase LI. This analysis shows that the predictions of this model are in total disagreement with both the predictions of the mnemonical model and the experimental results obtained with wheat germ hexokinase LI, as well as with other enzymes. This alternative model cannot therefore be considered as a sensible explanation of the mechanistic origin of co-operativity of monomeric enzymes. It is therefore concluded that the mnemonical model which rests on numerous experimental results, obtained by different research groups, on different enzymes is the simplest and most likely explanation of the kinetic subtleties displayed by some monomeric enzymes, and in particular wheat germ hexokinase LI.

Mnemonic aspects of Escherichia coli DNA polymerase I. Interaction with one template influences the next interaction with another template

When Escherichia coli DNA polymerase I (Pol I) replicates a homopolymer, the excision/polymerization (exo/pol) ratio varies with enzyme and initiator concentration. The study of this effect in the case of poly(dA).oligo(dT) replication led us to propose a mnemonic model for Pol I, in which the 3' to 5' excision activity warms up when the enzyme is actively polymerizing, and cools down when it dissociates from the template. The model predicts that the exo/pol ratio must increase with processivity length and initiator concentration and decrease with enzyme concentration. It predicts also that contact of the enzyme with one template alters its excision efficiency towards another template. The exo/pol ratio and processivities of Pol I and its Klenow fragment were studied on four templates: poly(dA).(dT)10, poly(dT).(dA)10, poly(dC).(dG)10 and poly(dI).(dC)10. We show that the Klenow fragment is usually much less processive than Pol I and when this is the case it has a much lower exo/pol ratio. At equal processivity, the exo/pol ratios are nearly equal. Furthermore, many factors that influence processivity length (e.g. manganese versus magnesium, inorganic pyrophosphate, ionic strength) influence the exo/pol ratio in the same direction. The study of deaminated poly(dC) replication, where we followed incorporation and excision of both G and A residues, allowed us to assign the origin of the dNMP variations to changes in the 3' to 5' proof-reading activity of Pol I. Similarly, the lower dNMP turnover of the Klenow fragment observed with deaminated poly(dC) was specifically assigned to a decreased 3' to 5' exonuclease activity. The exo/pol ratio generally increased with initiator and decreased with enzyme concentration, in agreement with the model, except for poly(dI).oligo(dC), where it decreased with initiator concentration. However, by terminating chain elongation with dideoxy CTP, we showed directly that, even in this system, excision is relatively inefficient at the beginning of synthesis. Interaction of Pol I with poly(dA).(dT) or with poly(dC).(dG) modifies its exo/pol characteristics in the replication of poly(dI).(dC) and poly(dA).(dT), respectively. The Klenow enzyme is not sensitive to such influences and this correlates with its reduced processivity on the influencing templates. Our results reveal the existence of differences between Pol I and its Klenow fragment that are more profound than has been thought previously.(ABSTRACT TRUNCATED AT 400 WORDS)

Fine tuning of ribosomal accuracy

If the rate constant for peptide bond formation were high just after an amino acid incorporation and occasionally switched to a lower value afterwards, then the ribosome could compensate for tRNA imbalance specifically at hungry codons. A rigorous analysis of the scheme proves its effectiveness. For instance, a 10-fold reduction in cognate tRNA concentration may increase the error rate by only a factor of two.

Mechanistic origin of the kinetic cooperativity of hexokinase type L1 from wheat germ

A theoretical analysis is presented which shows that initial velocity data for hexokinase L1 catalysis of glucose phosphorylation by MgATP cannot be reconciled with the observed rate of the 'mnemonical' conformational transition which has been proposed to account for the kinetic cooperativity of the enzyme. The basic kinetic properties of hexokinase L1 and other allegedly 'mnemonical' enzymes appear to be fully consistent with an ordered ternary-complex mechanism in which the leading substrate participates in abortive-complex formation. It is concluded that, so far, no enzyme displaying kinetic cooperativity has been convincingly demonstrated to operate by a 'mnemonical' type of reaction mechanism.

Kinetic co-operativity of monomeric mnemonical enzymes. The significance of the kinetic Hill coefficient

The expression of the kinetic Hill coefficient for a two-substrate, two-product mnemonical enzyme has been derived. Its relation with the gamma coefficient, that is the slope of the reciprocal plots for 1/[A]----O, has been established. The variation of this Hill coefficient, as a function of the second substrate and product concentrations, has been studied theoretically. Whereas the gamma coefficient does not vary as a function of the substrate and first product concentrations, the kinetic Hill coefficient does. If the enzyme is positively co-operative, the Hill coefficient increases upon increasing the second substrate concentration and decreases if the first product concentration is increased. The converse is expected to occur if the enzyme displays a negative co-operativity. The last product may either reverse a positive co-operativity into a negative one or, alternatively, strengthen an already negative co-operativity. The co-operativity generated by the mnemonical model has been compared to the kinetic behaviour of a random model. These two models have been shown to be discriminated on the basis of the departure they show with respect to the Michaelis-Menten behaviour. These theoretical considerations have been applied to previously published data, obtained with wheat germ hexokinase LI. This monomeric enzyme has a negative co-operativity with respect to the preferred substrate, glucose. The Hill coefficient decreases with MgATP concentration, increases with MgADP concentration and decreases with glucose-6-phosphate concentration. This is exactly what is to be expected on the basis of the above theory of kinetic co-operativity.

Effect of glycerol on glucokinase activity: loss of cooperative behavior with respect to glucose

Glucose phosphorylation catalyzed by rat liver glucokinase measured at saturating concentrations of MgATP2- shows a cooperative response with respect to glucose in the concentration range 0.25-5 mM with a Hill coefficient of 1.6. In this range of glucose concentrations, the degree of cooperativity was dependent on the presence of glycerol in the assay mixture, and it decreased progressively and disappeared completely as the glycerol concentration reached about 20% (v/v) glycerol. If attention was confined to concentrations above 5 mM, no cooperativity could be detected either in the absence or in the presence of glycerol. The limiting velocity of the glucokinase reaction (measured at saturating concentrations of glucose and MgATP2-), and the half-saturation concentration for glucose and MgATP2- were all decreased by about 50-60% as the glycerol concentration was raised from zero to 30% (v/v). The presence of glycerol had no effect on the qualitative inhibition patterns of MgADP2-, glucose 6-phosphate, or N-acetylglucosamine, and only slight effects on the quantitative half-saturation values and inhibition constants. All of these effects caused by glycerol were fully reversible by decreasing the concentration of glycerol by dilution. Simulation studies based on the "mnemonical" model of glucokinase action proposed earlier [A. C. Storer and A. Cornish-Bowden (1977) Biochem. J. 165, 61-69] show that the effects of glycerol on glucokinase-catalyzed glucose phosphorylation can simply be explained assuming the glycerol favors the existence of the conformation of the enzyme with a higher affinity for glucose and thus supports the model.

Solvent isotope effects on the glucokinase reaction. Negative co-operativity and a large inverse isotope effect in 2H2O

The solvent isotope effects on the reaction catalysed by rat-liver glucokinase have been studied. At low concentrations of glucose and high concentrations of MgATP2- there is an inverse solvent isotope effect of 3.5. At high glucose concentrations there is a normal solvent isotope effect of 1.3. In 1H2O there is positive co-operativity with respect to glucose [ Storer , A.C. and Cornish - Bowden , A. (1976) Biochem. J. 159, 7-14], but this is changed to negative co-operativity in 2H2O. The half-saturation points for both glucose and MgATP2- are decreased in 2H2O compared with those in 1H2O. Explanations of these effects in terms of the mnemonical model proposed by Storer and Cornish - Bowden [Biochem. J. 65, 61-69 (1977)] were considered in computer simulation. Two interpretations could account for the results, either a decrease in the rate of interconversion of the two forms of free enzyme postulated in the model, or an increase in the affinity for glucose of the enzyme form with the lower affinity in 1H2O. The results of a proton-inventory analysis were consistent with either of these interpretations. The solvent isotope effects thus provide additional evidence for the mnemonical model as an explanation of glucokinase co-operativity.

A memory effect in DNA replication

A study of the polymerization/excision ratio in the replication of poly(dA), primed with oligo(dT), was carried out with E. coli DNA polymerase I, at various primer and enzyme concentrations. The variations in this ratio suggest that 1) the DNA polymerase is able to switch between two states of low and high exonuclease activities and 2) after dissociating from the template, the DNA polymerase drifts towards the low exonuclease state. The recovery of the high exonuclease state would require several successive incorporations.

Hysteretic behaviour of citrate synthase. Alternating sites during the catalytic cycle

Chemically and stereochemically pure (3S)-citryl-CoA was prepared enzymically and used as a substrate for citrate synthase to investigate the previously determined unexpectedly low rate of hydrolysis of the (3RS)-substrate. The unnatural R-diastereomer of this mixture is not inhibitory. At low enzyme concentrations the rate of citryl-CoA hydrolysis was linear until the reaction went near to completion; the hydrolysis approached Michaelis-Menten kinetics at high enzyme concentrations. In between these concentration extremes a biphasic rate dependence was detectable, where a fast initial phase lasting a few seconds was followed by a slow steady-state phase. Citrate synthase was characterized as a hysteretic enzyme existing in two interconvertible forms, which were designated according to their functions as hydrolase E and ligase E'. The hysteretic behaviour originates in the cleavage of citryl-CoA to acetyl-CoA and oxaloacetate. This reaction occurs on the ligase form E', which represents a trap for enzyme form E, the hydrolase. The conclusions given above are strengthened by the ordinary hydrolysis kinetics of (2S)-malyl-CoA, a substrate that is not subject to cleavage of the C-C bond on the synthase. The results satisfy the kinetic criterion for citryl-CoA being an intermediate of the physiological synthase reaction and, therefore, establish the oscillation of the synthase between hydrolase and ligase states during the catalytic cycle. A disorganization of these oscillations can be achieved by limited tryptic proteolysis of the synthase.

The comparative isozymology of vertebrate hexokinases

1. Multiple hexokinase isozymes have been found in most vertebrates. Since each isozyme displays distinctive structural, kinetic and regulatory characteristics, the system qualifies as a useful probe for studies on molecular evolution. 2. At least seven types of chromatographic patterns of liver hexokinases have been observed in mammals. In contrast, each Class of lower vertebrates present only two or three distinct profiles. 3. Aves and higher Reptiles do not have the same hexokinase isozymes as other vertebrates. The nature of the differences is poorly understood. 4. Ontogenetic changes of liver hexokinase profiles are quite different in rat, chick and frog. 5. Structural comparisons of three vertebrate hexokinases having a molecular weight of approximately 100,000 suggest that those isozymes originated from a pre-vertebrate ancestor through gene duplication followed by fusion and further duplication events. Another hexokinase (the so-called glucokinase), with half the molecular weight, may have arisen either as the result of subsequent even splitting of the fused gene or, less probably, by divergence from a duplicated gene before the fusion event.

Purification and properties of the insulin-stimulated cyclic AMP phosphodiesterase from rat liver plasma membranes

The peripheral high-affinity cyclic AMP phosphodiesterase from rat liver plasma membranes was purified to apparent homogeneity. The procedure used involved the initial purification of liver plasma membranes and the solubilization of the enzyme by using a high-ionic-strength medium. This was followed by chromatography of the enzyme on DEAE-cellulose, Affi-Gel Blue, a novel affinity column and Sephadex G-100. A 9500-fold purification of the enzyme with a 24% yield was achieved by this procedure. The purified enzyme was apparently monomeric (Mr 52000) as it exhibited identical molecular weights on analysis by gel filtration, sedimentation and sodium dodecyl sulphate/polyacrylamide-gel electrophoresis. It is suggested that the non-Michaelis kinetics exhibited by the enzyme are due to it obeying a mnemonical mechanism, where it displays Km 0.7 micrometer, Vmax. 9.1 units/mg of protein and Hill coefficient (h) 0.62. Cyclic GMP acts as a poor substrate for the enzyme, with Km 120 micrometer and Vmax. 0.4 unit/mg of protein, and also as an inhibitor of the enzyme, with I50 (concentration giving 50% inhibition) 150 micrometer when assayed at 0.4 micrometer-cyclic AMP. Inhibition by 5'-AMP is unlikely to be of physiological importance, as it is only a weak inhibitor of the enzyme (I50 47 mM assayed at 0.4 micrometer-cyclic AMP).