pH-induced co-operative effects in hysteretic enzymes. 2. pH-induced co-operative effects in a cell-wall beta-glucosyltransferase

A beta-glucosyltransferase, extracted and purified from the cell walls of isolated soybean cells, displays hysteretic behaviour. The enzyme is monomeric and has a negative co-operative between pH 5.5 and 7.5. Below and above these pH values, the enzyme follows, or approaches, classical Michaelis-Menten kinetics. The free enzyme and the enzyme-glucose complex exhibit, upon pH jumps, conformational transitions which may be followed by monitoring the fluorescence of enzyme-bound toluidinylnaphthalene sulfonate. Taken together these results are consistent with the model of pH-induced co-operativity described in the preceding paper in this journal. This special type of co-operativity relies on a change of the pK value of a strategic ionizable group located outside the active site in a region (or a domain) of the protein which undergoes the conformational transition. The result that at 'low' and 'high' pH values, the enzyme follows or approaches Michaelis-Menten kinetics is explained by assuming that the conformational changes do not affect the active site.     

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.     

Generalized microscopic reversibility, kinetic co-operativity of enzymes and evolution.

Generalized microscopic reversibility implies that the apparent rate of any catalytic process in a complex mechanism is paralleled by substrate desorption in such a way that this ratio is held constant within the reaction mechanism [Whitehead (1976) Biochem. J. 159, 449--456]. The physical and evolutionary significances of this concept, for both polymeric and monomeric enzymes, are discussed. For polymeric enzymes, generalized microscopic reversibility of necessity occurs if, within the same reaction sequence, the substrate stabilizes one type of conformation of the active site only. Generalized microscopic reversibility suppresses the kinetic co-operativity of the slow transition model [Ainslie, Shill & Neet (1972) J. Biol. Chem. 247, 7088--7096]. This situation is obtained if the free-energy difference between the corresponding transition states of the two enzyme forms is held constant along the reaction co-ordinate. This situation implies that the 'extra costs' of energy (required to pass each energy barrier) that are not covered by the corresponding binding energies of the transition states vary in a similar way along the two reaction co-ordinates. The regulatory behaviour of monomeric enzymes is discussed in the light of the concept of 'catalytic perfection' proposed by Albery & Knowles [(1976) Biochemistry 15, 5631--5640]. These authors claim that an enzyme will be catalytically 'perfect' when its catalytic efficiency is maximum. If this situation occurs for a monomeric enzyme obeying either the slow transition or the mnemonical model, it can be shown that the kinetic co-operativity disappears. In other words, kinetic co-operativity of a monomeric enzyme is 'paid for' at the expense of catalytic efficiency, and the monomeric enzyme cannot be simultaneously co-operative and catalytically very efficient. This is precisely what has been found experimentally in a number of cases.     

Self-organization and dynamics of an open futile cycle

The dynamic behaviour of an open futile cycle composed of two enzymes has been investigated in the vicinity of a steady-state. A necessary condition required for damped or sustained oscillations of the system is that enzyme E₂, which controls recycling of the substrate S₂, be inhibited by an excess of this substrate. In order for the system to be neutrally stable and therefore to exhibit sustained oscillations, it is not necessary for antagonist enzyme E₁ to be activated by its product S₂. If it is enzyme E₁ which is inhibited by an excess of its substrate S₁, the system has a saddle point. Other conditions for stability or instability of the system have been determined. If the enzyme E₁, which is not inhibited by the substrate, exhibits a slow conformational transition of the mnemonical type, this transition dramatically alters the stability behavior of the system. If the mnemonical enzyme E₁ were exhibiting a positive kinetic co-operativity, decreasing the rate of the conformational transition of the mnemonical enzyme will increase the stability of the whole system and will tend to damp the oscillations in the vicinity of the steady-state. If conversely the mnemonical enzyme E₁ were exhibiting a negative kinetic co-operativity, decreasing the rate of the enzyme conformational transition will decrease the stability of the system and will tend to create or amplify oscillations of the system taken as a whole. If these results may be extended to more complex metabolic cycles, involving more than two enzymes, it may be tentatively considered that positive co-operativity associated with slow transition has emerged in the course of evolution in order to limit temporal instabilities of metabolic cycles. Alternatively one may speculate that the “biological function” of negative co-operativity is to create or amplify these temporal instabilities.     

Ionic control of immobilized enzymes. Kinetics of acid phosphatase bound to plant cell walls.

When an enzyme is bound to an insoluble polyelectrolyte it may acquire novel kinetic properties generated by Donnan effects. It the enzyme is homogeneously distributed within the matrix, a variation of the electrostatic partition coefficient, when substrate concentration is varied, mimics either positive or negative co-operativity. This type of non-hyperbolic behaviour may be distinguished from true co-operativity by an analysis of the Hill plots. If the enzyme is heterogeneously distributed within the polyelectrolyte matrix, an apparent negative co-operativity occurs, even if the electrostatic partition coefficient does not vary when substrate concentration is varied in the bulk phase. If the partition coefficient varies, mixed positive and negative co-operativities may occur. All these effects must be suppressed by raising the ionic strength in the bulk phase. Attraction of cations by fixed negative charges of the polyanionic matrix may be associated with a significant decrease of the local pH. The magnitude of this effect is controlled by the pK of the fixed charges groups of the Donnan phase. The local pH cannot be much lower than the value of this pK. This effect may be considered as a regulatory device of the local pH. Acid phosphatase of sycamore (Acer pseudoplatanus) cell walls is a monomeric enzyme that displays classical Michaelis-Menten kinetics in free solution. However, when bound to small cell-wall fragments or to intact cells, it has an apparent negative co-operativity at low ionic strength. Moreover a slight increase of ionic strength apparently activates the bound enzymes and tends to suppress the apparent co-operativity. At I0.1, or higher, the bound enzyme has a kinetic behavior indistinguishable from that of the purified enzyme in free solution. These results are interpreted in the light of the Donnan theory. Owing to the repulsion of the substrate by the negative charges of cell-wall polygalacturonates, the local substrate concentration in the vicinity of the bound enzyme is smaller than the corresponding concentration in bulk solution. The kinetic results obtained are consistent with the view that there exist at least three populations of bound enzyme with different ionic environments: a first population with enzyme molecules not submitted to electrostatic effects, and two other populations with molecules differently submitted to these effects. The theory allows one to estimate the proportions of enzyme belonging to these populations, as well as the local pH values and the partition coefficients within the cell walls.     

Subunit coupling and kinetic co-operativity of polymeric enzymes. Amplification, attenuation and inversion effects

The principles of structural kinetics, as applied to dimeric enzymes, allow us to understand how the strength of subunit coupling controls both substrate-binding co-operativity, under equilibrium conditions, and kinetic co-operativity, under steady state conditions. When subunits are loosely coupled, positive substrate-binding co-operativity may result in either an inhibition by excess substrate or a positive kinetic co-operativity. Alternatively, negative substrate-binding co-operativity is of necessity accompanied by negative kinetic co-operativity. Whereas the extent of negative kinetic co-operativity is attenuated with respect to the corresponding substrate-binding co-operativity, the positive kinetic co-operativity is amplified with respect to that of the substrate-binding co-operativity. Strong kinetic co-operativity cannot be generated by a loose coupling of subunits. If subunit is propagated to the other, the dimeric enzyme may display apparently surprising co-operativity effects. If the strain of the active sites generated by subunit coupling is relieved in the non-liganded and fully-liganded states, both substrate-binding co-operativity and kinetic co-operativity cannot be negative. If the strain of the active sites however, is not relieved in these states, negative substrate-binding co-operativity is accompanied by either a positive or a negative co-operativity. The possible occurrence of a reversal of kinetic co-operativity, with respect to substrate-binding co-operativity, is the direct consequence of quaternary constraints in the dimeric enzyme. Moreover, tight coupling between subunits may generate a positive kinetic co-operativity which is not associated with any substrate-binding co-operativity. In other words a dimeric enzyme may well bind the substrate in a non co-operative fashion and display a positive kinetic co-operativity generated by the strain of the active sites.     

Zn2+ regulation of ornithine transcarbamoylase. II. Metal binding site

Two types of conformational changes are mediated in Escherichia coli ornithine transcarbamoylase by the metal ion zinc. Upon binding of zinc in rapid equilibrium, the enzyme undergoes an allosteric transition. In the absence of substrates, the zinc-bound enzyme further undergoes a slow isomerization with a concomitant activity loss. Three metal ions are tightly complexed in the isomerized enzyme as determined by gel chromatography and atomic absorption spectroscopy. Since the enzyme is a trimer composed of identical subunits, one zinc ion is bound per enzyme monomer. With the application of site-directed mutagenesis, the cysteinyl residue at position 273 of the enzyme has been identified as a metal ligand. When this residue is replaced by an alanine, zinc is no longer a tight-binding inhibitor and does not promote isomerization. The alteration in the action of zinc on the mutant enzyme is attributed to a reduced metal affinity. The mutant enzyme, when saturated by the metal, displays an intrinsic allostery unchanged from that of the wild-type; an identical Hill coefficient of 1.5 is found for zinc binding to the Ala273 and wild-type enzymes. Cys273 is also a binding site of L-ornithine. At pH 8.5, the Ala273 enzyme binds the substrate analog L-norvaline ten times more weakly and exhibits a kcat/Kmorn that is 27 times less than that of the wild-type enzyme. This finding supports our earlier interpretation that the zinc-induced ornithine co-operativity of ornithine transcarbamoylase is caused by direct competition between L-ornithine and the metal for the same site. As controls, each of the remaining three cysteinyl residues of the bacterial ornithine transcarbamoylase has also been replaced with alanine. These sulfhydryl groups are found not to be related to zinc complexation, ornithine binding or enzyme allostery.     

Negative co-operativity in glutamate dehydrogenase. Involvement of the 2-position in glutamate in the induction of conformational changes.

The 2-position substituent on substrates or substrate analogues for glutamate dehydrogenase is shown to be intimately involved in the induction of conformational changes between subunits in the hexamer by coenzyme. These conformational changes are associated with the negative co-operativity exhibited by this enzyme. 2-Oxoglutarate and L-2-hydroxyglutarate induce indications of co-operativity similar to those induced by the substrate of oxidative deamination, glutamate, in kinetic studies. Glutarate (2-position CH2) does not. A comparison of the effects of L-2-hydroxyglutarate and D-2-hydroxyglutarate or D-glutamate indicates that the 2-position substituent must be in the L-configuration for these conformational changes to be triggered. In addition, glutarate and L-glutamate in ternary enzyme-NAD(P)H-substrate complexes induce very different coenzyme fluorescence properties, showing that glutamate induces a different conformation of the enzyme-coenzyme complex from that induced by glutarate. Although glutamate and glutarate both tighten the binding of reduced coenzyme to the active site, the effect is much greater with glutamate, and the binding is described by two dissociation constants when glutamate is present. The data suggest that the two carboxy groups on the substrate are required to allow synergistic binding of coenzyme and substrate to the active site, but that interactions between the 2-position on the substrate and the enzyme trigger the conformational changes that result in subunit-subunit interactions and in the catalytic co-operativity exhibited by this enzyme.     

A model for the allosteric regulation of pH-sensitive enzymes.

1. In an enzyme that has two independent binding sites for a ligand, any inhibitor that binds solely to the free enzyme will give rise to positive co-operativity. 2. A model is considered for the allosteric control of enzymes by effectors in which their effects are mediated by ligand-induced perturbations of the ionization constants of a group or groups involved in the binding of substrate to the active site. 3. The model described offers a plausible explanation for the observation that the sigmoidal initial-rate curves reported for some regulatory enzymes are not expressed at all pH values where the enzyme is catalytically active.     

Conformational changes of glyceraldehyde-3-phosphate dehydrogenase induced by the binding of NAD. A unified model for positive and negative cooperativity.

The fluorescence of the natural coenzyme, NADH, is used to monitor the environment of the nicotinamide moiety at the active centre of rabbit muscle glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12). Changes of the fluorescence quantum yield and polarization of a small amount of NADH, totally bound by an excess of enzyme, show that at half-saturation of the oligomer with NAD a conformational change is induced which affects the active centre regions of the remaining subunits. This conformational transition is not effected by adenosine diphosphoribose, suggesting that the binding of the nicotinamide moiety of NAD to two subunits is essential for the change of tertiary structure of the remaining subunits that causes the observed changes of the fluorescence properties of the ADH "tracer probe". It is suggested that this conformational transition of the oligomer is responsible for the major decrease of affinity for NAD which occurs at half-saturation, and possibly for the activation by NAD+ of the reductive dephosphorylation reaction catalysed by the enzyme. It is also suggested, by analogy with haemoglobin, that the molecular basis of the negative cooperativity may be the creation of additional intersubunit bonds during the binding of the first two NAD molecules to the tetramer, and a change from a "relaxed" quaternary structure to a "tense" structure at half-saturation.     

The 'slow' pH-induced conformational transition of chloroplast fructose 1,6-bisphosphatase and the control of the Calvin cycle

A slow conformation change of chloroplastic reduced fructose bisphosphatase is detected upon raising the pH from 7 to 8 or upon lowering the pH from 8 to 7. These conformation changes are fully reversible. In the time scale investigated these processes occur in one step. Their time constants and their amplitudes have been determined and analyzed as a function of proton concentration. The results obtained are consistent with the view that upon ionization or protonation of a strategic ionizable group the protein undergoes a 'slow' conformational transition that may be followed by conventional fluorescence techniques. Since illumination brings about a pH rise of chloroplastic stroma from 7 to 8, the above results suggest that light activation of fructose bisphosphatase is at least in part due to a slow conformation change of this enzyme.     

A dynamical model for a co-operative enzyme.

Proteins partially immersed in the hydrophobic portion of a lipid bilayer interact by means of London-van der Waals non-bonding dispersion forces. Moreover, in certain organelles, enzymes are structured in a lattice or ordered matrix. These conditions may facilitate the establishment of long-range correlations between proteins. We studied the dynamical properties of a model for an enzyme endowed with a highly co-operative conformational transition between two reactive states. Two cases were considered, a closed system and an open system. In the closed system for different degrees of interaction among the proteins, it was found that for a substrate concentration greater than a certain threshold an abrupt change of enzymatic activity occurs. This biphasic behavior has been observed in the enzymatic activity of crystalline mitochondrial aspartate aminotransferase and for some other crystalline enzymes. In the analysis of the open system, for a specific input rate of the substrate, two different dynamics were found depending on the selected degree of interaction. For a certain value of a parameter phi, representing the degree of interaction among the reacting units, three steady states co-exist. This multiplicity confers excitable properties to the model. For larger values of phi, limit cycle type solutions were obtained. Thus, a sustained oscillatory product formation of the enzymatic reaction is observed. These results are compared with experimental observations of enzyme extracts detected by NMR.     

Letter: Kinetic negative co-operativity in the allosteric model of Monod, Wyman and Changeux

The co-operativity of homotropic interactions between substrate molecules in oligomeric enzymes is analyzed in the frame of the concerted transition theory of Monod et al. (1965). A discussion of the Hill coefficient n_H allows determination of the conditions for negative co-operativity (n_H < 1). This phenonomenon, usually taken as indicative of a sequential mechanism (Koshland et al., 1966), can be accounted for by the concerted model when the enzyme represents a K-V or V system, i.e. when the two protomer conformational states postulated in the theory differ in their catalytic activity. However, only negative co-operativity for catalysis can be explained by the concerted model, not negative co-operativity of binding.     

State and reactivity of tryptophyl residues in two bacterial proteases from Sorangium sp.

The state and reactivity of tryptophyl residues in two proteolytic enzymes from Sorangium sp. were investigated by means of the following methods: spectrophotometric oxidation of tryptophans with N-bromosuccinimide, 2-hydroxy-5-nitrobenzyl bromide, and H2O2 in dioxane, optical rotatory dispersion, ultraviolet difference spectrophotometry, solvent perturbation and viscosity measurements. Out of two tryptophyl residues/molecule of alpha-lytic protease, one appears to be completely buried, while the other seems to be exposed. None of these two residues seem to be responsible for the activity of the enzyme. The beta-lytic protease undergoes an irreversible conformational transition between pH 5.0 and 3.5. Out of total four tryptophyl residues/molecule, only one is fully exposed at neutral pH. The other three are gradually exposed in the pH transition region. The degree of exposure and the dimensions of "cavities" shielding tryptophyl residues were estimated. The tryptophyl residues of of beta-lytic protease do not seem to participate in substrate binding or the active site; they are rather one of the determinants of the conformational state of the enzyme.     

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.     

Studies of glutamate dehydrogenase. Regulation of glutamate dehydrogenase from Candida utilis by a pH and temperature-dependent conformational transition.

Glutamate dehydrogenase from Candida utilis undergoes a reversible conformational transition between an active and an inactive state at low pH AND low temperature. This conformational transition can also be followed by fluorescence measurements. The temperature-dependent equilibrium between the active and the inactive state is characterized by a transition temperature of 10.7 degrees C and a delta H value of 148 kcal/mol (620 kJ/mol). The temperature dependence of the enzymic activity above 15 degrees C yields an activation energy of 15 kcal/mol (63 kJ/mol), a larger value than that for the beef liver enzyme (9 kcal/mol; 38 kJ/mol). In contrast to the yeast enzyme the Arrhenius plot is linear and, therefore, the beef liver enzyme is not transformed into an inactive conformation at low temperatures. Sedimentation analysis shows that the inactivation of the Candida utilis enzyme is not caused by change in the quaternary structure. The pH dependence of the conformational transition at low pH measured by fluorescence change is characterized by a pK value of 7.01 for the enzyme in the absence and of 6.89 for the enzyme in the presence of 2-oxoglutarate with a Hill coefficient of 3.4 in both cases. Similar results are found when the pH dependence of the enzymic activity is analyzed. With the beef liver enzyme the same pK value is obtained but with a Hill coefficient of 1 indicating cooperativity only in the case of the Candida utilis enzyme. The best fit of the pH dependence of the rate constants of the fluorescence changes was obtained with pK values of 7.45 and 6.45 for the active and the inactive state respectively. In this model the lowest time constant which is obtained at the pH of the equilibrium was found to be 0.05 s-1. Preincubation experiments with the substrate 2-oxoglutarate but not with the coenzyme shift the equilibrium to the active conformation. The coenzyme obviously reduces the rate constant of the conformational transition. The sedimentation coefficient (SO20, w) and the molecular weight were found to be 11.0 S and 276 000, respectively. The enzyme molecule is built up by six polypeptide chains each having a molecular weight of 47 000.     

Catalytic efficiency, kinetic co-operativity of oligomeric enzymes and evolution

The catalytic performance of an enzyme, whether it is monomeric or oligomeric, depends on extra costs of energy in passing from the initial ground state to the various transition states, along the reaction co-ordinate. The improvement, during evolution, of the catalytic performance of individual subunits implies that three structural requirements are met in the course of an enzyme reaction: the unstrained enzyme subunits exist in the ground states under two conformations, one corresponding to the non-liganded state and the other to the liganded state; the inter-subunit strain is relieved in the various transition states; the subunits bound to the various transition states S not equal to, X not equal to and P not equal to have the same conformation. These structural requirements are precisely those which have been used to derive structural rate equations for polymeric enzymes. When subunits are loosely coupled, their arrangement controls the various rate constants, but not the extra costs of energy required to reach the various transition states. Moreover, one cannot expect the rate curve to display any sigmoidicity under these conditions. If subunits are tightly coupled and if the strained non-liganded and half-liganded states are destabilized with respect to the corresponding unstrained states, that is if they contain more conformational energy, the oligomeric enzyme is more catalytically efficient than the ideally isolated subunits. Moreover, if the available conformational energy of the half-liganded state is more than twice that of the non-liganded state, kinetic co-operativity is positive and the rate curve is sigmoidal. It is therefore the extent of inter-subunit strain in the half-liganded state which controls the appearance of sigmoidal kinetic behaviour. If subunits are tightly coupled but if inter-subunit strain is relieved in both the non-liganded and fully-liganded states, the half-liganded state controls both the catalytic efficiency of the enzyme and the sigmoidicity of the rate curve. Sigmoidicity and high catalytic efficiency are to be observed when this half-liganded state is destabilized relative to the corresponding unstrained state.(ABSTRACT TRUNCATED AT 400 WORDS)     

An aspartate transcarbamylase lacking catalytic subunit interactions. Study of conformational changes by ultraviolet absorbance and circular dichroism spectroscopy.

A modified form of aspartate transcarbamylase is synthesized by Escherichia coli in the presence of 2-thiouracil which does not exhibit homotropic cooperative interactions between active sites yet retains heterotropic cooperative interactions due to nucleotide binding. The conformational changes induced in the modified enzyme by the binding of different ligands (substrates, substrate analogs, a transition state analog, and nucleotide effectors) were studied using ultraviolet absorbance and circular dichroism difference spectroscopy. Comparison of the results for the modified enzyme and its isolated subunits to those for the native enzyme and its isolated subunits showed that the conformational changes detected by these methods are qualitatively similar in the two enzymes. Comparison of the absorbance difference spectra due to the binding of a transition substrate analog to the intact native or modified enzymes to the corresponding results for the isolated subunits suggested that ligand binding causes an increased exposure to solvent of certain tyrosyl and phenylalanyl residues in the intact enzymes but not in the isolated subunits. This result is consistent with a diminution of subunit contacts due to substrate binding in the course of homotropic interactions in the native enzyme. Such conformational changes, though perhaps necessary for homotropic cooperativity, are not sufficient to cause homotropic cooperativity since the modified enzyme gave identical perturbations. Interactions of the transition state analog, N-(phosphonacetyl)-L-aspartate, with the modified enzyme were studied. Enzyme kinetic data obtained at low aspartate concentrations showed that this transition state analog does not stimulate activity, but rather exhibits the inhibition predicted for the total absence of homotropic cooperative interactions in the modified enzyme. Spectrophotometric titrations of the number of catalytic sites with the transition state analog showed that the modified enzyme and its isolated subunits possess, respectively, four and two high affinity sites for the inhibitor instead of six and three observed in the case of the normal enzyme and its isolated catalytic subunits. These results are correlated with the lower specific enzymatic activities of the modified enzyme and its catalytic subunits compared to the normal corresponding enzymatic species.     

Conformational selection and induced changes along the catalytic cycle of Escherichia coli dihydrofolate reductase

Protein function often involves changes between different conformations. Central questions are how these conformational changes are coupled to the binding or catalytic processes during which they occur, and how they affect the catalytic rates of enzymes. An important model system is the enzyme dihydrofolate reductase (DHFR) from Escherichia coli, which exhibits characteristic conformational changes of the active‐site loop during the catalytic step and during unbinding of the product. In this article, we present a general kinetic framework that can be used (1) to identify the ordering of events in the coupling of conformational changes, binding, and catalysis and (2) to determine the rates of the substeps of coupled processes from a combined analysis of nuclear magnetic resonance R₂ relaxation dispersion experiments and traditional enzyme kinetics measurements. We apply this framework to E. coli DHFR and find that the conformational change during product unbinding follows a conformational‐selection mechanism, that is, the conformational change occurs predominantly prior to unbinding. The conformational change during the catalytic step, in contrast, is an induced change, that is, the change occurs after the chemical reaction. We propose that the reason for these conformational changes, which are absent in human and other vertebrate DHFRs, is robustness of the catalytic rate against large pH variations and changes to substrate/product concentrations in E. coli. Proteins 2012;. © 2012 Wiley Periodicals, Inc.     

Role of histidines in the binding of violaxanthin de-epoxidase to the thylakoid membrane as studied by site-directed mutagenesis

Regulation of violaxanthin de-epoxidase (VDE) involves a conformational change at low lumenal pH, followed by binding of the enzyme to the thylakoid membrane. The role of histidine residues in this process was studied by release of unbound enzyme from thylakoids upon sonication, on a pH scale from 4.7 to 7.1. The co-operativity for binding of spinach VDE (four histidines) to the membrane was found to be 3.8, with respect to protons, and had an inflexion point at pH 6.6, whereas VDE from wheat (three histidines) showed a co-operativity of 2.9 and had an inflexion point at pH 6.2. Mutant forms of VDE were constructed and probed for their binding to the outside of thylakoid membranes. With one or two histidines substituted for alanine or arginine, a lower co-operativity (1.6–2.3) was found, compared with the wild type. Based on these findings, and that the pKa value for histidine is within the range where the VDE binding takes place, we propose that protonation of the histidine residues at low pH induces the conformational change of VDE, and hence indirectly regulates binding of the enzyme to the thylakoid membrane.