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Activation of p53 DNA binding activity by point mutation.

The p53 tumor suppressor protein can adopt both latent, non-DNA binding and active, DNA binding forms, and p53 activity is thought to be regulated in cells, at least in part, through a conformational shift which leads to sequence specific DNA binding. In vitro, this allosteric regulation of DNA binding by p53 has been shown to be mediated through the C-terminus of the protein. We show here that although deletion of the C-terminal 16 amino acids of p53 did not activate DNA binding, deletion of a further eight amino acids resulted in constitutive activation of DNA binding activity. Simultaneous mutation of the three lysine residues within these eight amino acids also resulted in constitutive DNA binding activity, although this was reduced when only two of these lysines were altered. The deletion or point mutants of p53 showing constitutive DNA binding activity did not display clear evidence of DNA binding site specificity, although some binding site preference was seen with the point mutants. Each of the constitutively active p53 mutants retained transcriptional activity and induced both cell cycle arrest and apoptosis in transiently transfected cells at rates comparable with the wild type protein.

Allosteric Regulation↗

[Preservation of the allosteric properties of the protein receptor for acetylcholine in detergent solution without addition of lipids].

Solubilization by Na cholate of acetylcholine receptor-rich membrane fragments from Torpedo marmorata, followed by exchange of NA cholate by the neutral detergent "Tween 80" yields the receptor protein in its 9 S soluble light form; under these conditions, without adding lipids, the receptor protein conserves its characteristic binding properties for the fluorescent agonist Dns-C6-Cho as followed by fast kinetic techniques, and the allosteric regulation by non-competitive blockers.

Allosteric Regulation↗

[Effect of lactate and glycolytic intermediates on muscle creatine kinase].

Inhibition of rabbit muscle creatine kinase by lactate, glucose-6-phosphate and PEP occurs immediately and depends on the concentration of the effectors and enzyme properties. Desensitization of creatine kinase to these effectors is described. Partial desensitization to G-6-P and lactate occurs after the enzyme preincubation with dithiothreitol. A complete loss of sensitivity to lactate and a significant loss of sensitivity to G-6-P and PEP occurs after the enzyme storage at -15 degrees during several weeks. The data obtained support our previously made assumption on the allosteric regulation of the MM isoenzyme of creatine kinase.

Allosteric Regulation↗

Regulation of the raffinose permease of Escherichia coli by the glucose-specific enzyme IIA of the phosphoenolpyruvate:sugar phosphotransferase system.

In enteric bacteria, chromosomally encoded permeases specific for lactose, maltose, and melibiose are allosterically regulated by the glucose-specific enzyme IIA of the phosphotransferase system. We here demonstrate that the plasmid-encoded raffinose permease of enteric bacteria is similarly subject to this type of inhibition.

Allosteric Regulation↗

Cooperative binding of the sugar substrates and allosteric regulatory protein (enzyme IIIGlc of the phosphotransferase system) to the lactose and melibiose permeases in Escherichia coli and Salmonella typhimurium.

An Escherichia coli strain which overproduces the lactose permease was used to investigate the mechanism of allosteric regulation of this permease and those specific for melibiose, glycerol, and maltose by the phosphoenolpyruvate-sugar phosphotransferase system (PTS). Thio-beta-digalactoside, a high affinity substrate of the lactose permease, released the glycerol and maltose permeases from inhibition by methyl-alpha-d-glucoside. Resumption of glycerol uptake occurred immediately upon addition of the galactoside. The effect was not observed in a strain which lacked or contained normal levels of the lactose permease, but growth of wild-type E. coli in the presence of isopropyl-beta-thiogalactoside plus cyclic AMP resulted in enhanced synthesis of the lactose permease so that galactosides relieved inhibition of glycerol uptake. Thiodigalactoside also relieved the inhibition of glycerol uptake caused by the presence of other PTS substrates such as fructose, mannitol, glucose, 2-deoxyglucose, and 5-thioglucose. Inhibition of adenylate cyclase activity by methyl-alpha-glucoside was also relieved by thiodigalactoside in E. coli T52RT provided that the lactose permease protein was induced to high levels. Cooperative binding of sugar and enzyme III(Glc) to the melibiose permease in Salmonella typhimurium was demonstrated, but no cooperativity was noted with the glycerol and maltose permeases. These results are consistent with a mechanism of PTS-mediated regulation of the lactose and melibiose permeases involving a fixed number of allosteric regulatory proteins (enzyme III(Glc)) which may be titrated by the increased number of substrate-activated permease proteins. This work suggests that the cooperativity in the binding of sugar substrate and enzyme III(Glc) to the permease, demonstrated previously in in vitro experiments, has mechanistic significance in vivo. It substantiates the conclusion that PTS-mediated regulation of non-PTS permease activities involves direct allosteric interaction between the permeases and enzyme III(Glc), the postulated regulatory protein of the PTS.

Adenylyl Cyclase Inhibitors↗

Mutual inhibition of the dimerized Na/Ca-K exchanger in rod photoreceptors.

In the dark, rod photoreceptors sustain a continuous influx of Na and Ca ions through the cGMP-gated channels of the rod outer segments (ROS). Whereas Na ions are extruded in the inner segment by the Na-pump, Ca ions are extruded already in the ROS by Na/Ca-K exchange. Our previous findings indicate that in the ROS plasma membrane, exchanger and channel form a complex of two exchangers associated per channel. Here, we report evidence of a novel regulatory mechanism of the dimerized exchanger, based on the following findings: (1), thiol-specific cross-linking with dimaleimides resulted in an increase of the Na/Ca-K exchange activity which correlated with the size of the cross-linking reagent, i.e., with increasing separation of the monomers in a dimerized exchanger; (2), partial proteolysis of the exchanger also increased the exchange rate by about a factor of two; (3), disintegration of the channel-exchanger complex by solubilization of the ROS membranes and preparation of proteoliposomes resulted in a twofold enhancement of the exchange rate; however (4), partial proteolysis of proteoliposomes, in which the exchanger molecules exist as monomers, did not result in any enhancement of the exchange rate. These findings suggest an inhibitory protein domain at the contact site of the dimerized exchanger. The physiological implication of this inference will be discussed in terms of a potential allosteric regulation of the exchanger in the channel-exchanger complex.

Allosteric Regulation↗

Conformational equilibrium of an enzyme catalytic site in the allosteric transition.

The dynamic equilibrium of a catalytic site between active and inactive conformations, the missing link between the structure and function of allosteric enzymes, was identified using protein engineering and NMR techniques. Kinetic analyses of the wild-type and three mutants of Thermus L-lactate dehydrogenase established that the allosteric property of the enzyme is associated with a concerted transition between the high-affinity (R) and low-affinity (T) states. By introducing mutations, we prepared an enzyme in which the R and T states were balanced. The conformation of the enzyme-bound coenzyme, NAD+, which interacts directly with the substrate, was analyzed using NMR spectroscopy. NAD+ bound to the mutant enzyme was in a conformational mixture of the active and inactive forms, while NAD+ took on predominantly one of the two forms when it was bound to the other enzymes we had analyzed. We interpret this to mean that the catalytic site is in equilibrium between the two conformations. The ratio of the conformers of each enzyme agreed with the [T]/[R] ratio as determined by kinetic analyses. Therefore, it is the identified conformational equilibrium of the catalytic site that governs the allosteric regulation of the enzyme activity.

Allosteric Regulation↗

[Prostaglandin E2 as a lipophilic allosteric modulator of the Na pump].

Curves of inhibition of rat brain Na, K-ATPase and K-pNPPase by prostaglandin E2 (PGE2) showed a sigmoidal shape with nH for PGE2 of 1.4 +/- 0.1 and 1.3 +/- 0.1, respectively. The desensitization of the enzymes with 0.25 M urea (4 degrees, 15 min) caused a loss of their cooperative interaction with PGE2. 2.0 mM PGE2 shifts the temperature break in the Arrhenius plots for the ATPase from 19.8 degrees to 23 degrees and simultaneously increased the Ea below the break by 9.5 kcal/mol. After treatment of the ATPase with phospholipase A2 PGE2 showed no cooperative interaction with the enzyme. Modulation of membrane enzymes by means of the surrounding lipid phasic state appears to be the general mechanism of their indirect allosteric regulation.

4-Nitrophenylphosphatase↗

Tyrosine 315 determines optimal recruitment of ZAP-70 to the T cell antigen receptor.

Recruitment of ZAP-70 protein tyrosine kinase to the T cell antigen receptor (TCR) is mediated by the binding of the SH2 domains of this enzyme to phosphorylated ITAM motifs in the CD3 and TCRzeta subunits. We have previously shown that the efficiency of both positive and negative thymocyte selection was decreased in knock-in mice expressing ZAP-70 mutated at Tyr315 (ZAP-70-Y315F), a residue laying in the interdomain B of this protein. Surprisingly, in these cells the amount of phosphorylated TCRzeta chain co-precipitating with ZAP-70-Y315F was significantly reduced compared to control mice. We report now that the binding affinity of ZAP-70-Y315F to phosphorylated ITAM is reduced as compared to the wild-type protein, whereas the intrinsic catalytic activity is untouched. Consequently, phosphorylated ITAM appear to be more accessible to protein tyrosine phosphatases (PTP) and can be readily dephosphorylated. We provide evidence suggesting that the defective ITAM binding induced by Tyr315 mutation is independent of the putative role of this residue as a binding site for Vav-1. Finally, we found that the extracellular signal-regulated kinase pathway is impaired in ZAP-70-Y315F-expressing mice. Collectively, these results demonstrate that Tyr315 has an unsuspected structural role in ZAP-70 and may allosterically regulate the function of the nearby SH2 domains.

Allosteric Regulation↗

Changes in the modulations of kinetics and allosteric properties of muscle phosphofructokinase of young and old rats.

In vitro studies on various modulations in kinetics and allosteric properties of muscle phosphofructokinase (EC 2.7.1.11) were undertaken, using purified enzyme from young (25-weeks) and old (100-weeks) albino rats. In comparison to normal K0.5 values for fructose-6-phosphate, increase in this value in response to ATP and citrate inhibition, decrease in K0.5 due to AMP activation and extent of ATP inhibition with increase in pH, were observed to be decreased more markedly with the enzyme of old than with that of young rats. Extent of citrate inhibition, reversals of ATP and citrate effects in response to AMP activation, and synergism of citrate and ATP inhibitions were also seen to be decreased considerably with muscle PFK of old in comparison to that of young rats. Such age-related changes in muscle PFK suggest the alterations in allosteric regulation of this enzyme during aging of the animal.

Aging↗

The solution structure of the bacterial HSP70 chaperone protein domain DnaK(393-507) in complex with the peptide NRLLLTG.

The Hsp70 family of molecular chaperones participates in a number of cellular processes, including binding to nascent polypeptide chains and assistance in protein (re)folding and degradation. We present the solution structure of the substrate binding domain (residues 393-507) of the Escherichia coli Hsp70, DnaK, that is bound to the peptide NRLLLTG and compare it to the crystal structure of DnaK(389-607) bound to the same peptide. The construct discussed here does not contain the alpha-helical domain that characterizes earlier published peptide-bound structures of the Hsp70s. It is established that removing the alpha-helical domain in its entirety does not affect the primary interactions or structure of the DnaK(393-507) in complex with the peptide NRLLLTG. In particular, the arch that protects the substrate-binding cleft is also formed in the absence of the helical lid. 15N-relaxation measurements show that the peptide-bound form of DnaK(393-507) is relatively rigid. As compared to the peptide-free state, the peptide-bound state of the domain shows distinct, widespread, and contiguous differences in structure extending toward areas previously defined as important to the allosteric regulation of the Hsp70 chaperones.

Allosteric Regulation↗

New perspectives on the storage and organization of muscle glycogen.

Due to its large mass, skeletal muscle contains the largest depot of stored carbohydrate in the body in the form of muscle glycogen. Readily visualized by the electron microscope, glycogen granules appear as bead-like structures localized to specific subcellular locales. Each glycogen granule is a functional unit, not only containing carbohydrate, but also enzymes and other proteins needed for its metabolism. These proteins are not static, but rather associate and dissociate depending on the carbohydrate balance in the muscle. This review examines glycogen-associated proteins, their interactions, and roles in regulating glycogen metabolism. While certain enzymes such as glycogen synthase and glycogen phosphorylase have been extensively studied, other proteins such as the glycogen initiating and targeting proteins are just beginning to be understood. Two metabolically distinct forms of glycogen, pro- and marcoglycogen have been identified that vary in their carbohydrate complement per molecule and have different sensitivities to glycogen synthesis and degradation. Glycogen regulation takes place not only by allosteric regulation of enzymes, but also due to other factors such as subcellular location, granule size, and association with various glycogen-related proteins.

1,4-alpha-Glucan Branching Enzyme↗

Kinetic pathway for the slow to fast transition of thrombin. Evidence of linked ligand binding at structurally distinct domains.

The kinetic pathway for the Na+-induced slow --> fast transition of thrombin was characterized. The slow form was shown to consist of two conformers in a 3:1 ratio (ES2:ES1) at 5 degrees C, pH 7.4, Gamma/2 0.3. ES2 binds Na+ 3 orders of magnitude faster than does ES1. The small molecule active site-directed inhibitor L-371,912, and the exosite I binding ligand hirugen, like Na+, bind selectively to ES2 and induce the slow --> fast conversion of thrombin. The slow --> fast transition is limited by the rate of conversion of ES1 to ES2 (k approximately 28 s-1 at 5 degrees C). Replacement of Arg-221a or Lys-224 at the Na+ binding site with Ala appears to selectively alter the slow form and reduce the apparent affinity of the mutants for Na+ and L-371,912. This replacement, however, has little effect on the affinity for the inhibitor in the presence of saturating concentrations of Na+. The kinetically linked ligand binding at the Na+ binding site, exosite I, and the active site of thrombin characterized in the present study indicates the basis for the plasticity of this important enzyme, and suggests the possibility that the substrate specificity and, therefore, the procoagulant and anticoagulant activities of thrombin may be subject to allosteric regulation by as yet unidentified physiologically important effectors.

Allosteric Regulation↗

Structural analysis of porcine brain nitric oxide synthase reveals a role for tetrahydrobiopterin and L-arginine in the formation of an SDS-resistant dimer.

Nitric oxide synthases (NOSs), which catalyze the formation of the ubiquitous biological messenger molecule nitric oxide, represent unique cytochrome P-450s, containing reductase and mono-oxygenase domains within one polypeptide and requiring tetrahydrobiopterin as cofactor. To investigate whether tetrahydrobiopterin functions as an allosteric effector of NOS, we have analyzed the effect of the pteridine on the conformation of neuronal NOS purified from porcine brain by means of circular dichroism, velocity sedimentation, dynamic light scattering and SDS-polyacrylamide gel electrophoresis. We report for the first time the secondary structure of NOS, showing that the neuronal isozyme contains 30% alpha-helix, 14% antiparallel beta-sheet, 7% parallel beta-sheet, 19% turns and 31% other structures. The secondary structure of neuronal NOS was neither modulated nor stabilized by tetrahydrobiopterin, and the pteridine did not affect the quaternary structure of the protein, which appears to be an elongated homodimer with an axial ratio of approximately 20/1 under native conditions. Low temperature SDS-polyacrylamide gel electrophoresis revealed that tetrahydrobiopterin and L-arginine synergistically convert neuronal NOS into an exceptionally stable, non-covalently linked homodimer surviving in 2% SDS and 5% 2-mercaptoethanol. Ligand-induced formation of an SDS-resistant dimer is unprecedented and suggests a novel role for tetrahydrobiopterin and L-arginine in the allosteric regulation of protein subunit interactions.

Allosteric Regulation↗

PPP1R6, a novel member of the family of glycogen-targetting subunits of protein phosphatase 1.

A complementary DNA encoding a novel human protein phosphatase 1 (PP1) glycogen-targetting subunit of molecular mass 33 kDa has been sequenced. PPP1R6 is 31% identical to the glycogen-targetting subunit (G(L)) of PP1 from rat liver, 28% identical to the N-terminal region of the glycogen-targetting subunit (G(M)) from human skeletal muscle and 27% identical to glycogen-targetting subunit PPP1R5. Unlike human PPP1R5 and its murine homologue PTG, whose mRNAs are most abundant in skeletal muscle, heart and liver, PPP1R6 is present at similar levels in a wide variety of tissues. The PPP1R6 is associated with glycogen in muscle but is not subject to the same modes of covalent and allosteric regulation as G(M) and G(L).

Allosteric Regulation↗

Conversion of non-allosteric pyruvate kinase isozyme into an allosteric enzyme by a single amino acid substitution.

Pyruvate kinase M1, a non-allosteric isozyme, was converted into an allosteric enzyme by replacement of an amino acid in the intersubunit contact. The substitution of Ala-398 with Arg resulted in the pronounced allosteric enzyme. The Hill coefficient and the substrate concentration giving one-half of Vmax for the mutant with respect to phosphoenolpyruvate were 2.7 and 0.41 mM, respectively, whereas those values for the wild type were 1.0 and 0.049 mM. This mutation, however, gave rise to only minor effects on the apparent values of Km for ADP and on Vmax. Furthermore, in contrast to the wild-type enzyme, the mutant was activated by fructose 1, 6-bisphosphate. The Hill coefficient of the mutant was no longer increased by the allosteric inhibitor, L-phenylalanine, indicating that the equilibrium for the unligated enzyme is largely shifted toward the T-state. These results suggest that Ala-398 is one of the most critical residues allowing the enzyme to prefer the R-state and that allosteric regulation of pyruvate kinase involves amino acid residues in the intersubunit contact.

Allosteric Regulation↗

Cooperativity in cytochrome P450 3A4: linkages in substrate binding, spin state, uncoupling, and product formation.

Understanding the detailed metabolic mechanisms of membrane-associated cytochromes P450 is often hampered by heterogeneity, ill-defined oligomeric state of the enzyme, and variation in the stoichiometry of the functional P450.reductase complexes in various reconstituted systems. Here, we describe the detailed characterization of a functionally homogeneous 1:1 complex of cytochrome P450 3A4 (CYP3A4) and cytochrome P450 reductase solubilized via self-assembly in a nanoscale phospholipid bilayer. CYP3A4 in this complex showed a nearly complete conversion from the low- to high-spin state when saturated with testosterone (TS) and no noticeable modulation due to the presence of cytochrome P450 reductase. Global analysis of equilibrium substrate binding and steady-state NADPH consumption kinetics provided precise resolution of the fractional contributions to turnover of CYP3A4 intermediates with one, two, or three TS molecules bound. The first binding event accelerates NADPH consumption but does not result in significant product formation due to essentially complete uncoupling. Binding of the second substrate molecule is critically important for catalysis, as the product formation rate reaches a maximum value with two TS molecules bound, whereas the third binding event significantly improves the coupling efficiency of redox equivalent usage with no further increase in product formation rate. The resolution of the fractional contributions of binding intermediates of CYP3A4 into experimentally observed overall spin shift and the rates of steady-state NADPH oxidation and product formation provide new detailed insight into the mechanisms of cooperativity and allosteric regulation in this human cytochrome P450.

Allosteric Regulation↗

Structures of bovine glutamate dehydrogenase complexes elucidate the mechanism of purine regulation.

Glutamate dehydrogenase is found in all organisms and catalyses the oxidative deamination of l-glutamate to 2-oxoglutarate. However, only animal GDH utilizes both NAD(H) or NADP(H) with comparable efficacy and exhibits a complex pattern of allosteric inhibition by a wide variety of small molecules. The major allosteric inhibitors are GTP and NADH and the two main allosteric activators are ADP and NAD(+). The structures presented here have refined and modified the previous structural model of allosteric regulation inferred from the original boGDH.NADH.GLU.GTP complex. The boGDH.NAD(+).alpha-KG complex structure clearly demonstrates that the second coenzyme-binding site lies directly under the "pivot helix" of the NAD(+) binding domain. In this complex, phosphates are observed to occupy the inhibitory GTP site and may be responsible for the previously observed structural stabilization by polyanions. The boGDH.NADPH.GLU.GTP complex shows the location of the additional phosphate on the active site coenzyme molecule and the GTP molecule bound to the GTP inhibitory site. As expected, since NADPH does not bind well to the second coenzyme site, no evidence of a bound molecule is observed at the second coenzyme site under the pivot helix. Therefore, these results suggest that the inhibitory GTP site is as previously identified. However, ADP, NAD(+), and NADH all bind under the pivot helix, but a second GTP molecule does not. Kinetic analysis of a hyperinsulinism/hyperammonemia mutant strongly suggests that ATP can inhibit the reaction by binding to the GTP site. Finally, the fact that NADH, NAD(+), and ADP all bind to the same site requires a re-analysis of the previous models for NADH inhibition.

Adenosine Diphosphate↗