Slow ligand-induced transitions in the allosteric phosphofructokinase from Escherichia coli

Conformational adaptation in drug-target interactions and residence time

Although drug-target interactions are commonly illustrated in terms of structurally static binding and dissociation events, such descriptions are inadequate to explain the impact of conformational dynamics on these processes. For high-affinity interactions, both the association and dissociation of drug molecules to and from their targets are often controlled by conformational changes of the target. Conformational adaptation can greatly influence the residence time of a drug on its target (i.e., the lifetime of the binary drug-target complex); long residence time can lead to sustained pharmacology and may also mitigate off-target toxicity. In this perspective, the kinetics of drug-target association and dissociation reactions are explored, with particular emphasis on the impact of conformational adaptation on drug-target residence time.

Rapid pyrophosphate release from transcriptional elongation complexes appears to be coupled to a nucleotide-induced conformational change in E. coli core polymerase

In the nucleotide addition cycle, pyrophosphate is generated upon incorporation of each nucleotide. Rapid release of pyrophosphate is essential for facile transcription elongation. Stopped-flow kinetic studies involving alterations in the intrinsic protein fluorescence of the core polymerase upon the binding of pyrophosphate to well-defined elongation complexes (ECs) indicate that the intrinsic off-rate of pyrophosphate (k=5.7-8.1 s(-1)) is too slow to account for the rapid rate of nucleotide incorporation that occurs during processive transcription elongation. Stopped-flow kinetic studies on UTP binding followed by UMP incorporation into an EC as monitored by alterations in the intrinsic protein fluorescence of the core polymerase resulted in a set of first-order rate constants that varied in a hyperbolic manner as a function of UTP concentration. This is consistent with a binding step (K(UTP)=17±6 μM) followed by a conformational change (k=623±54 s(-1)) in the core polymerase. In comparable studies on ATP binding and AMP incorporation into an EC, the data were also consistent with a binding step (K(ATP)=44±6 μM) followed by a conformational change (k=411±51 s(-1)) in the core polymerase. In stopped-flow kinetic studies with α,β-methyleneadenosine 5' triphosphate, which can bind to the EC but cannot lead to nucleotide incorporation, the analysis of the hyperbolic dependence of the observed first-order rate constant on α,β-methyleneadenosine 5' triphosphate concentration yielded a value of 20±13 μM for the apparent dissociation constant and a value of 221±36 s(-1) for the first-order rate constant for the associated conformational change in the core polymerase. This indicates that the conformational change in the core polymerase precedes chemistry. In conjunction with previously reported results on the increase in the rate of pyrophosphate release in the presence of the next cognate nucleotide for incorporation, the data are consistent with a model in which rapid pyrophosphate release is coupled to a conformational change in the core polymerase that precedes chemistry and that occurs upon the binding of the next cognate nucleotide for incorporation.

A pre-steady state analysis of ligand binding to human glucokinase: evidence for a preexisting equilibrium

Cooperativity with glucose is a key feature of human glucokinase (GK), allowing its crucial role as a glucose sensor in hepatic and pancreatic cells. We studied the changes in enzyme intrinsic tryptophan fluorescence induced by binding of different ligands to this monomeric enzyme using stopped-flow and equilibrium binding methods. Glucose binding data under pre-steady state conditions suggest that the free enzyme in solution is in a preexisting equilibrium between at least two conformers (super-open and open) which differ in their affinity for glucose (Kd* = 0.17 +/- 0.02 mM and Kd = 73 +/- 18 mM). Increasing the glucose concentration changes the ratio of the two conformers, thus yielding an apparent Kd of 3 mM (different from a Km of 7-10 mM). The rates of conformational transitions of free and GK complexed with sugar are slow and during catalysis are most likely affected by ATP binding, phosphate transfer, and product release steps to allow the kcat to be 60 s-1. The ATP analogue PNP-AMP binds to free GK (super-open) and GK-glucose (open) complexes with comparable affinities (Kd = 0.23 +/- 0.02 and 0.19 +/- 0.08 mM, respectively). However, cooperativity with PNP-AMP observed under equilibrium binding conditions in the presence of glucose (Hill slope of 1.6) is indicative of further complex tightening to the closed conformation. Another physiological modulator (inhibitor), palmitoyl-CoA, binds to GK with similar characteristics, suggesting that conformational changes induced upon ligand binding are not restricted by an active site ligand. In conclusion, our data support control of GK activity and Km through the ratio of distinct conformers (super-open, open, and closed) through either substrate or other ligand binding and/or dissociation.

Pre-steady state quantification of the allosteric influence of Escherichia coli phosphofructokinase

Stopped-flow kinetics was utilized to determine how allosteric activators and inhibitors of wild-type Escherichia coli phosphofructokinase influenced the kinetic rate and equilibrium constants of the binding of substrate fructose 6-phosphate. Monitoring pre-steady state fluorescence intensity emission changes upon an addition of a ligand to the enzyme was possible by a unique tryptophan per subunit of the enzyme. Binding of fructose 6-phosphate to the enzyme displayed a two-step process, with a fast complex formation step followed by a relatively slower isomerization step. Systematic addition of fructose 6-phosphate to phosphofructokinase in the absence and presence of several fixed concentrations of phosphoenolpyruvate indicated that the inhibitor binds to the enzyme concurrently with the substrate, forming a ternary complex and inducing a conformational change, rather than a displacement of the equilibrium as predicted by the classical two-state model (Monod, J., Wyman, J., and Changeux, J. P. (1965) J. Mol. Biol. 12, 88-118). The activator, MgADP, also altered the affinity of fructose 6-phosphate to the enzyme by forming a ternary complex. Furthermore, both phosphoenolpyruvate and MgADP act by influencing the fast complex formation step while leaving the slower enzyme isomerization step essentially unchanged.

Analysis of rapid, large-scale protein quaternary structural changes: time-resolved X-ray solution scattering of Nudaurelia capensis omega virus (NomegaV) maturation

Time-resolved small-angle X-ray scattering (TR-SAXS) was used to study the kinetics of a large conformational change that occurs during the maturation of an icosahedral virus. Virus-like particles (VLPs) of the T=4 non-enveloped RNA virus Nudaurelia capensis omega virus (NomegaV) were shown to undergo a large pH-dependent conformational change. Electron cryo-microscopy (cryoEM) and X-ray solution scattering were used to show that the precursor VLP (procapsid) was 16 % larger in diameter than the resulting capsid, which was shown by the cryoEM study to closely resemble the infectious mature virion. The procapsid form of the VLPs was observed at pH 7.5 and was converted to the capsid form at pH 5.0. Static SAXS measurements of the VLPs in solutions ranging between these pH values determined that the half-titration point of the transition was pH 6.0. Time-resolved SAXS experiments were performed on VLP solutions by initiating a pH change from 7.5 to 5.0 using a stopped-flow device, and the time-scale of the conformational change occurred in the subsecond range. Using a less drastic pH change (lowering the pH to 5.8 or 5.5), the conformational change occurred more slowly, on the subminute or minute time-scale, with the detection of a fast-forming intermediate in the transition. Further characterization using static SAXS measurements showed that the conformational change was initially reversible but became irreversible after autoproteolytic maturation was about 15 % complete. In addition to characterizing the large quaternary conformational change, we have been able for the first time to demonstrate that it takes place on the subsecond time-scale, a regime comparable to that observed in other multisubunit assemblies.

Kinetic characterization of a T-state of Ascaris suum phosphofructokinase with heterotropic negative cooperativity by ATP eliminated

The affinity analogue, 2',3'-dialdehyde ATP has been used to chemically modify the ATP-inhibitory site of Ascaris suum phosphofructokinase, thereby locking the enzyme into a less active T-state. This enzyme form has a maximum velocity that is 10% that of the native enzyme in the direction of fructose 6-phosphate (F6P) phosphorylation. The enzyme displays sigmoid saturation for the substrate fructose 6-phosphate (S0.5 (F6P) = 19 mM and nH = 2.2) at pH 6.8 and a hyperbolic saturation curve for MgATP with a Km identical to that for the native enzyme. The allosteric effectors, fructose 2,6-bisphosphate and AMP, do not affect the S0.5 for F6P but produce a slight (1.5- and 2-fold, respectively) V-type activation with Ka values (effector concentration required for half-maximal activation) of 0.40 and 0.24 mM, respectively. Their activating effects are additive and not synergistic. The kinetic mechanism for the modified enzyme is steady-state-ordered with MgATP as the first substrate and MgADP as the last product to be released from the enzyme surface. The decrease in V and V/K values for the reactants likely results from a decrease in the equilibrium constant for the isomerization of the E:MgATP binary complex, thus favoring an unisomerized form. The V and V/KF6P are pH dependent with similar pK values of about 7 on the acid side and 9.8 on the basic side. The microenvironment of the active site appears to be affected minimally as evidenced by the similarity of the pK values for the groups involved in the binding site for F6P in the modified and native enzymes.

The enzyme activity allosteric regulation model based on the composite nature of catalytic and regulatory sites concept

A new kinetic model of enzymatic catalysis is proposed, which postulates that enzyme solutions are equilibrium systems of oligomers differing in the number of subunits and in the mode of their assembly. It is suggested that the catalytic and regulatory sites of allosteric enzymes are of composite nature and appear as a result of subunits joining. Two possible joining modes are postulated at each oligomerization step. Catalytic site may arise on oligomer formed only by one of these modes. Effector acts by fastening together components of certain oligomeric form and increases the life time of this form. It leads to a shift of oligomer equilibrium and increases a proportion of effector-binding oligomers. Effectors-activators bind the oligomers carrying composite catalytic sites and effectors-inhibitors bind the oligomers, which do not carry active catalytic sites. Thus, catalytic activity control in such system is explained by effector-induced changes of a catalytic sites number, but not of a catalytic site activity caused by changes of subunit's tertiary structure. The postulates of the model do not contradict available experimental data and lead to a new type of general rate equation, which allows to describe and understand the specific kinetic behavior of allosteric enzymes as well as Michaelis type enzymes. All known rate equations of allosteric The equation was tested by modeling the kinetics of human erythrocyte phosphofructokinase. It enabled to reproduce quantitatively the 66 kinetic curves experimentally obtained for this enzyme under different reaction conditions.

Transient kinetic analysis of adenosine 5'-triphosphate binding-induced conformational changes in the allosteric chaperonin GroEL

GroEL with an intrinsic fluorescent probe was generated by introducing the mutation Phe44 --> Trp. Different concentrations of ATP were rapidly mixed with GroEL containing this mutation, and the time-resolved change in fluorescence emission, upon excitation at 280 nm, was followed. Three kinetic phases were observed: a fast phase with a large amplitude and two slower phases with small amplitudes. The phases were assigned by (i) determining their dependence on ATP concentration; (ii) measuring their sensitivity to the mutation Arg197 --> Ala, which decreases cooperativity in ATP binding; and (iii) by carrying out mixing experiments of GroEL also with ADP, ATPgammaS, and ATP without K+. The apparent rate constant corresponding to the fast phase displays a bi-sigmoidal dependence on ATP concentration with Hill coefficients that are strikingly similar to those determined in steady-state experiments. This phase, which reflects ATP-induced conformational changes, is sensitive to the mutation Arg197 --> Ala in a manner that parallels steady-state experiments. The rate of conformational change in the presence of ATP is >100 sec-1, which is fast relative to most protein folding rates, whereas in the absence of ATP it is approximately 0.7 s-1. The second phase reflects the transition from an ATP-bound state of GroEL to an ADP-bound state. The third phase, with the smallest amplitude, reflects release of residual contaminants. The results in this study are found to be consistent with the nested model for cooperativity in ATP binding by GroEL [Yifrach, O., and Horovitz, A. (1995) Biochemistry 34, 5303-5308].

Allosteric activation increases the maximum velocity of E. coli phosphofructokinase

Several mutations that cause a decrease of 25 to 65% of the catalytic activity, were introduced at different positions in the phosphofructokinase from Escherichia coli, and the influence of the allosteric activator GDP on these mutants was measured. In the case of the wild-type enzyme, GDP converts the highly cooperative saturation towards fructose-6-phosphate into a hyperbolic saturation with almost no change in the maximum velocity. The mutants Glu148 --> Leu, Leu178 --> Val and Leu178 --> Trp are still cooperative for fructose-6-phosphate, and their cooperativity is also abolished or markedly decreased by GDP. In addition, GDP acts on these mutants as an activator of maximum velocity, and increases their catalytic rate constants by 35 to 65% depending on the mutation. The Leu178 --> Val mutant is even as active as the wild-type enzyme in the presence of GDP. The Thr125 --> Ser mutation decreases the maximum velocity by 60% and also suppresses the cooperativity towards fructose-6-phosphate. Accordingly, the only effect of GDP on the Thr125 --> Ser mutant is on its maximum velocity and not on its affinity for fructose-6-phosphate. However, the maximum velocity of this mutant is not increased by GDP but reduced by 33%. These results show that GDP affects the maximum velocity of these mutants and suggest that the activation by GDP of the wild-type enzyme measured by steady-state kinetics could be partially due to an increase of the maximum velocity, and not exclusively to an increase of the affinity for fructose-6-phosphate.