Thermodynamics of heterotropic interactions. The glutamate dehydrogenase . NADPH . glutamate complex

Detecting "silent" allosteric coupling

Using isothermal calorimetry (ITC), we have found one case where a well-characterized allosteric activator showed no sign of allostery in its ΔG° of binding to successive sites on multiple subunits and another case where successive binding showed no ΔG° binding allostery but did show large entropy-compensated flip-flopping enthalpy changes. This behavior, which we have termed "isoergonic cooperativity" and others have referred to as "silent coupling" is quite simply explained by basic linkage theory when reactions are considered beyond the ΔG° level. Thus, direct calorimetric determination of all thermodynamic parameters including ΔH°, ΔS°, ΔG°, ΔC (p)°, and d(ΔC (p)°/dt) provides a more informative depiction of a ligand binding event and its consequences than does the mere measurement of ΔG° alone. We further discuss the benefits and limitations of methods that have previously been used to study silent coupling. In particular, ITC is free of the numerous pitfalls inherent in the application of van't Hoff and Årrhenius plots to allosteric phenomena. Aside from having a 30-fold advantage in precision, ITC is capable of measuring changes in enthalpy directly at five more levels of mathematical differentiation than are available to van't Hoff type approaches.

Studying the allosteric energy cycle by isothermal titration calorimetry

Isothermal titration calorimetry (ITC) is a powerful biophysical technique which allows a complete thermodynamic characterization of protein interactions with other molecules. The possibility of dissecting the Gibbs energy of interaction into its enthalpic and entropic contributions, as well as the detailed additional information experimentally accessible on the intermolecular interactions (stoichiometry, cooperativity, heat capacity changes, and coupled equilibria), make ITC a suitable technique for studying allosteric interactions in proteins. Two experimental methodologies for the characterization of allosteric heterotropic ligand interactions by ITC are described in this chapter, illustrated with two proteins with markedly different structural and functional features: a photosynthetic electron transfer protein and a drug target viral protease.

Allostery: an illustrated definition for the 'second secret of life'

Although allosteric regulation is the 'second secret of life', the molecular mechanisms that give rise to allostery currently elude understanding. In my opinion, experimental progress is hampered by a commonly used but misleading definition of allostery as protein structural changes that are elicited by the binding of a single ligand. Allostery is more strictly defined in functional terms as a comparison of how one ligand binds in the absence, versus the presence, of a second ligand. Therefore, as each of the two binding events involves two protein complexes, a study of allostery must consider four complexes and not just two. Such a comparison can distinguish allosteric from non-allosteric protein changes, the importance of which is frequently overlooked. When a study of all four complexes is not feasible, an alternative, albeit limited, strategy can identify subsets of allosteric-specific changes.

Enzymatic reaction sequences as coupled multiple traces on a multidimensional landscape

We propose that an enzyme-catalyzed reaction is best described by a large, three-dimensional potential energy surface, defined by the number of enzyme conformers in one dimension, the number of reaction steps as the second and Gibbs free energy as the third. Aside from accommodating experimental observations that do not fit current mechanistic paradigms, such a surface enables multiple intersecting reaction pathways, pathway funneling, ligand binding energy transduction and kinetic coupling between alternative reaction pathways. The landscape also confers flexibility, enabling an enzyme to seek out an optimal pathway for any reaction conditions that might occur. Thus, coupled pathways enable relatively minor differences in experimental conditions to result in abrupt phenomenological changes in the observed behavior of the reaction.

Exact analysis of heterotropic interactions in proteins: Characterization of cooperative ligand binding by isothermal titration calorimetry

Intramolecular interaction networks in proteins are responsible for heterotropic ligand binding cooperativity, a biologically important, widespread phenomenon in nature (e.g., signaling transduction cascades, enzymatic cofactors, enzymatic allosteric activators or inhibitors, gene transcription, or repression). The cooperative binding of two (or more) different ligands to a macromolecule is the underlying principle. To date, heterotropic effects have been studied mainly kinetically in enzymatic systems. Until now, approximate approaches have been employed for studying equilibrium heterotropic ligand binding effects, except in two special cases in which an exact analysis was developed: independent binding (no cooperativity) and competitive binding (maximal negative cooperativity). The exact analysis and methodology for characterizing ligand binding cooperativity interactions in the general case (any degree of cooperativity) using isothermal titration calorimetry are presented in this work. Intramolecular interaction pathways within the allosteric macromolecule can be identified and characterized using this methodology. As an example, the thermodynamic characterization of the binding interaction between ferredoxin-NADP+ reductase and its three substrates, NADP+, ferredoxin, and flavodoxin, as well as the characterization of their binding cooperativity interaction, is presented.

Mechanistic interpretation of tryptophan fluorescence quenching in the time courses of glutamate dehydrogenase catalyzed reactions

We have related the ratios of the protein fluorescence quenching and nucleotide absorbance time courses for the glutamate dehydrogenase catalyzed oxidative deamination of L-glutamate to identify the occurrence and sequential location of a previously demonstrated charge-transfer intermediate. Static studies showed the major portion of the fluorescence quenching signal to be due to radiationless singlet energy transfer from tryptophan to reduced coenzyme chromophores and that conformational changes contribute little to this signal. The ratio approach applied to the transient time courses shows correspondingly that, over most of the time range, the fluorescence quenching signal provides a quantitative measure of the sum of all posthydride transfer species. However, it also indicates the very early occurrence of a species of anomalous optical properties for the reaction catalyzed by the Clostridium symbiosum enzyme as well as that from bovine liver. Transient-state kinetic isotope effect time courses of both the fluorescence and the absorbance signals confirm that this species must be the prehydride charge-transfer complex in both enzyme reactions. Kinetic analysis of alpha-deuterio- and alpha-protio-L-glutamate reaction time courses proves the kinetic competence of the assignments. These results also demonstrate that the intramolecular transfer of a proton from the alpha-amino group of the substrate to an immediately adjacent aspartate carboxylate group on the enzyme is an obligatory initial event in the reactions catalyzed by both enzyme species, even though the occurrence of protein release from a critical lysine residue to the solvent occurs at different phases in those two reactions. The abnormally low intrinsic KIE required to simulate both the alpha-deuterio-L-glutamate reaction and its protio counterpart implies that the transition state of the hydride transfer step must be highly asymmetric.

A difference in the sequence of steps in the reactions catalyzed by two closely homologous forms of glutamate dehydrogenase

Glutamate dehydrogenase from beef liver (bl GDH) and the corresponding enzyme from Clostridium symbiosum (cs GDH) each catalyze the same sequence of chemical events in the oxidative deamination of L-glutamate. This catalysis involves interactions between at least six conserved functional groups, each of which appears to occupy the same geometric position with respect to the substrate molecule in both enzyme--coenzyme--L-glutamate reactive ternary complexes. In both cases steady-state V/K pH profiles indicate the requirement for the transfer to the solvent of a single proton from the same abnormal lysine for L-glutamate to bind and react; the pK of that lysine is the same for both enzymes. Here we report studies of the proton traffic between enzyme and solvent using direct pH-stat back-titration and indicator dye measurements on dead-end inhibitor ternary complexes, simultaneous transient-state time courses of proton and product, and transient-state kinetic isotope studies on both enzymes. We find that in the cs GDH catalyzed reaction the single proton is released only after the hydride transfer step whereas in the bl GDH reaction this proton release occurs prior to the hydride transfer step, despite the fact that the substrate molecule undergoes the same sequence of chemical events in both reactions. Interpreting these results in the context of the X-ray crystallographic structures of cs GDH and its NAD binary complex and of thermodynamic studies of bl GDH and its complexes, we conclude that the difference in the relative times of proton release in the two enzyme-catalyzed reactions must be ascribed to a difference in the sequence of active site cleft-opening and -closing events in the two identical reaction sequences. We suggest a possible biological significance to this unusual method of modulating a common reaction to suit differing metabolic roles.

Characterization of specific interactions of coenzymes, regulatory nucleotides and cibacron blue with nucleotide binding domains of enzymes by analytical affinity chromatography

The dissociation constant for the complex of rhodanese and Cibacron Blue, determined by analytical affinity chromatography using rhodanese immobilized on controlled-pore glass (CPG) beads (200 nm pore diameter) and aminohexyl-Cibacron Blue, was 44 microM which agreed well with the kinetic inhibition constant, suggesting that the dye binds at or near the active site of this enzyme. Formation of a binary complex of the dye and lactate dehydrogenase (LDH) was also characterized by direct chromatography of LDH on CPG/immobilized Cibacron Blue (KD = 0.29 microM). The binary complex formed between LDH and NADH was characterized by analytical affinity chromatography using both CPG/immobilized LDH and immobilized Cibacron Blue. Since the dye competes with NADH in binding to the active site of LDH, competitive elution chromatography using the immobilized dye allows determination of the dissociation constant of the soluble LDH.NADH complex. Agreement between the dissociation constants determined by direct chromatography of NADH on immobilized LDH (KD = 1.4 microM) and that determined for the soluble complex (KD = 2.4 microM) indicates that immobilization of LDH did not affect the interaction. Formation of various binary, ternary and quaternary complexes of bovine liver glutamate dehydrogenase (GDH) with glutamate, NADPH, NADH, and ADP was also investigated using immobilized GDH. This approach allows characterization of the enzyme/ligand interactions without the complicating effect of enzyme self-association. The affinity for NADPH is considerably greater in the ternary complex (including glutamate) as compared to the binary complex (0.38 microM vs 22 microM); however, occupancy of the regulatory site by ADP greatly reduces the affinity in both complexes (6.4 microM and 43 microM, respectively).(ABSTRACT TRUNCATED AT 250 WORDS)

NADPH binding induced proton ionization as a cause of nonlinear heat capacity changes in glutamate dehydrogenase

Functional group interactions involved in the formation of the glutamate dehydrogenase-NADPH binary complex have been studied by three independent but complementary approaches: the pH dependence of the overall dissociation constant measured by an improved differential spectroscopic technique; the pH dependence of the enthalpy of complex formation measured by flow calorimetry; and the pH dependence of the number of protons released to, or taken up from, the solvent in the complex formation reaction, measured by titration. We conclude that the coenzyme binds to the enzyme through three distinguishable interactions: a pH-independent process involving the binding of the reduced nicotinamide ring; a relatively weak "proton-stabilizing" process, occurring at low pH involving the shift at a pK of 6.3 in the free enzyme to 7.0 in the enzyme-NADPH complex; and a stronger "proton-destabilizing" process, occurring at a higher pH involving a shift of a pK of 8.5 in the enzyme down to 6.9 in the enzyme-NADPH complex. The proton ionization of the free enzyme involved in this third interaction exhibits some unusual thermodynamic parameters, having delta Go = +11.5 +/- 0.1 kcal mol-1, delta Ho = +19 +/- 1 kcal mol-1, and delta So = +23 eu. We show here that this proton ionization step is directly related to and indeed constitutes the "implicit" shift in enzyme macrostates which we have shown to be responsible for the existence of large highly nonlinear delta Cpo effects in the formation of this complex [Fisher, H. F., Colen, A. H., & Medary, R. T. (1981) Nature (London) 292, 271-272].

pH-dependent thermodynamic parameters of the glutamate dehydrogenase-alpha-ketoglutarate-NADPH complex

The enthalpy of formation of the reactive bovine glutamate dehydrogenase-alpha-ketoglutarate-NADPH complex has been measured as a function of pH, at two temperatures and in two buffer systems having different enthalpies of ionization. The results demonstrate the existence of an extensive two-way traffic of protons between the buffer and the complex itself. While the pattern in a single buffer is too complex to resolve within the experimental limitations imposed by the system, we develop a theory which shows that the difference in delta H0H+ between buffers of different enthalpies of ionization has a simpler, more easily resolvable form. From such a relationship we show that in the process of binding of a molecule of NADPH to the enzyme-alpha-ketoglutarate complex, a proton has been shifted from the buffer to the complex and that this is due to the shift of the pK of an ionized group on the enzyme to a much higher value when the complex is formed. The delta Cp of formation of the complex is -450 cal . deg.-1 . M-1, and is pH independent. Implications of these results for the interpretation of enthalpies of enzyme-complex formation obtained at a single pH, and at one temperature, with one buffer system are mentioned. The complexity of the pattern of the dependence of delta H0, taken together with the magnitudes of the individual features of these dependencies, suggest that a number of large pK shifts occur when the enzyme-NADPH-alpha-ketoglutarate complex is formed. It is quite probable that these shifts represent a sizeable fraction of the machinery of the catalytic mechanism.