A shift of dynamic equilibrium between the KIT active and inactive states causes drug resistance

Tyrosine phosphorylation, a highly regulated post-translational modification, is carried out by the enzyme tyrosine kinase (TK). TKs are important mediators in signaling cascades, facilitating diverse biological processes in response to stimuli. TKs may acquire mutations leading to malignancy and are viable targets for anti-cancer drugs. Mast/stem cell growth factor receptor KIT is a TK involved in cell differentiation, whose dysregulation leads to various types of cancer, including gastrointestinal stromal tumors, leukemia, and melanoma. KIT can be targeted by a range of inhibitors that predominantly bind to the inactive state of the enzyme. A mutation Y823D in the activation loop of KIT is known to be responsible for the loss of sensitivity to some drugs in metastatic tumors. We used all-atom molecular dynamics simulations to study the impact of Y823D on the KIT conformation and dynamics and compared it to the effect of phosphorylation of Y823. We simulated in total 6.4 μs of wild-type, mutant and phosphorylated KIT in the active- and inactive-state conformations. We found that Y823D affects the protein dynamics differently: in the active state, the mutation increases the protein stability, whereas in the inactive state it induces local destabilization, thus shifting the dynamic equilibrium towards the active state, altering the communication between distant regulatory regions. The observed dynamics of the Y823D mutant is similar to the dynamics of KIT phosphorylated at position Y823, thus we hypothesize that this mutation mimics a constitutively active kinase, which is not responsive to inhibitors that bind its inactive conformation.     

Control of metabolic interconversion of isocitrate dehydrogenase between the catalytically active and inactive forms in Escherichia coli

The enzymic interconversion of Escherichia coli isocitrate dehydrogenase (ICDH) between the catalytically active and inactive forms is mediated through the activities of ICDH-kinase/phosphatase in response to changes in the metabolic environment. In this study, the use of mutant strains devoid of isocitrate lyase ( aceA:: Tn10 ) and pyruvate dehydrogenase activities revealed that the signal which triggers the reversible inactivation of ICDH in vivo is not directly related to acetate itself, but rather to the need to maintain high intracellular levels of isocitrate and free co-enzyme A. The use of these mutants also revealed, rather unexpectedly, that acetate grown cells contain more ICDH protein than those grown with other carbon sources and that the catalytic activity of ICDH kinase/phosphatase is in excess of cellular demands. Furthermore, this study also revealed the presence of a 50-kDa (±2 kDa) acetate-specific polypeptide, the identity of which has yet to be established.     

Conformations of the active and inactive states of opsin

The signaling state metarhodopsin II of the visual pigment rhodopsin decays to the apoprotein opsin and all-trans retinal, which are then regenerated to rhodopsin by the visual cycle. Opsin is known to have at neutral pH only a small residual constitutive activity toward its G protein transducin, which is thought to play a considerable role in light adaptation (bleaching desensitization). In this study we show with Fourier-transform infrared spectroscopy that after metarhodopsin II decay, opsin exists in two conformational states that are in a pH-dependent equilibrium at 30 degrees C with a pK of 4.1 in the presence of hydroxylamine scavenging the endogenous all-trans retinal. Despite the lack of the native agonist in its binding pocket, the low pH opsin conformation is very similar to that of metarhodopsin II and is likewise stabilized by peptides derived from rhodopsin's cognate G protein, transducin. The high pH form, on the other hand, has some conformational similarity to the inactive metarhodopsin I state. We therefore conclude that the opsin apoprotein displays intrinsic conformational states that are merely modulated by bound all-trans retinal.     

Interaction between the mitochondrial ATP synthetase and ATPase inhibitor protein. Active/inactive slow pH-dependent transitions of the inhibitor protein

The rate of mitochondrial ATPase inactivation by the naturally occurring inhibitor protein in the presence of saturating ATP and Mg2+ at pH 8.0 depends hyperbolically on the amount of inhibitor added; the upper limit of an apparent first-order constant for the inactivation process is 1.0(-1) at 25 degrees C. A dramatic difference in the inactivation rate is observed when the protein inhibitor is added to the same assay system from either acidic (pH 4.8) or alkaline (pH 8.2) solutions. The slow reversible transition of the inhibitor from its rapidly reacting 'acidic' form to the slow reacting 'alkaline' form occurs when the solution of the protein inhibitor is subjected to a pH-jump from 4.8 to 8.2 (t1/2 approximately 30s at 25 degrees C). The pH-profile of the inhibitor active/inactive equilibrium suggests that a group with pKa approximately 6.5 is involved in the transition. Treatment of the inhibitor protein with a histidine-specific reagent (e.g. diethyl pyrocarbonate) abolishes its inactivating effect on the ATPase activity. It is concluded that the protonation/deprotonation of the inhibitor protein followed by its slow conformational changes is the rate-limiting step in the inhibitor-ATP synthetase interaction.     

Inhibition of interconversion of ribosomes between forms active and inactive in 30 S subunit functions by aminoglycoside antibiotics

Antibiotics of the aminoglycoside group interfere with the reversible interconversions of 70 S ribosomes between forms active and inactive in the binding of aminoacyl-tRNA. Both inactivation and reactivation are strongly inhibited by streptomycin and neomycin. Activation is also weakly inhibited by kanamycin and inactivation is inhibited by kasugamycin.     

Catalytic activity of NADH-ubiquinone oxidoreductase (complex I) in intact mitochondria. evidence for the slow active/inactive transition

The mammalian purified dispersed NADH-ubiquinone oxidoreductase (Complex I) and the enzyme in inside-out submitochondrial particles are known to be the slowly equilibrating mixture of the active and de-activated forms (Vinogradov, A. D. (1998) Biochim. Biophys. Acta 1364, 169-185). We report here the phenomenon of slow active/de-active transition in intact mitochondria where the enzyme is located within its natural environment being exposed to numerous mitochondrial matrix proteins. A simple procedure for permeabilization of intact mitochondria by channel-forming antibiotic alamethicin was worked out for the "in situ" assay of Complex I activity. Alamethicin-treated mitochondria catalyzed the rotenone-sensitive NADH-quinone reductase reaction with exogenousely added NADH and quinone-acceptor at the rates expected if the enzyme active sites would be freely accessible for the substrates. The matrix proteins were retained in alamethicin-treated mitochondria as judged by their high rotenone-sensitive malate-cytochrome c reductase activity in the presence of added NAD(+). The sensitivity of Complex I to N-ethylmaleimide and to the presence of Mg(2+) was used as the diagnostic tools to detect the presence of the de-activated enzyme. The NADH-quinone reductase activity of alamethicin-treated mitochondria was sensitive to neither N-ethylmaleimide nor Mg(2+). After exposure to elevated temperature (37 degrees C, the conditions known to induce de-activation of Complex I) the enzyme activity became sensitive to the sulfhydryl reagent and/or Mg(2+). The sensitivity to both inhibitors disappeared after brief exposure of the thermally de-activated mitochondria with malate/glutamate, NAD(+), and cytochrome c (the conditions known for the turnover-induced reactivation of the enzyme). We conclude that the slow active/de-active Complex I transition is a characteristic feature of the enzyme in intact mitochondria and discuss its possible physiological significance.     

Reaction of (Na-K)ATPase with 7-chloro-4-nitrobenzo-2-oxa-1,3-diazole: evidence for an essential tyrosine at the active site.

The reaction of 7-chloro-4-nitrobenzo-2-oxa-1,3-diazole [NBD-Cl] with purified eel electrophax Na+ and K+ stimulated adenosine triphosphatase [(Na-K)ATPase] has been monitored by changes in the (Na-K)ATPase activity, the K+ stimulated p-nitrophenyl phosphatase [PNPase] activity, and the protein ultraviolet absorption spectrum. The NBD-Cl reacts with two tyrosine residues per mol of enzyme (approximately 6-7 nmol/mg of protein), as judged by changes in protein absorption spectra and incorporation of [14C]NBD-Cl. The modified tyrosine groups are located on the Mr = 95 000 polypeptide chain and react at different rates. Only one tyrosine modification is necessary for complete inhibition of (Na-K)ATPase activity, although both must be modified for complete inhibition of PNPase activity. Reversal of these modifications by 2-mercaptoethanol restores 65% of both activities. Na+ increases the rate of tyrosine modification, K+ decreases the rate, and ATP affords the more reactive tyrosine group complete protection. NBD-Cl modification of approximately 6-7 nmol of tyrosine groups/mg of protein results in a large decrease in ATP affinity as judged by equilibrium binding. These results are compared with similar results obtained from NBD-Cl modification of the coupling factors of oxidative phosphorylation and photophosphorylation. A model is presented suggesting an asymmetric arrangement of two 95 000 polypeptide chains with a single tyrosine residue at the ATP site.     

Na-K activated ATPase and the release of acetylcholine and noradrenaline

1. It has been shown that different experimental conditions known to inhibit Na-K-activated ATPase, and enzyme present in the neuronal membranes, are able to promote transmitter release (ACh, NA, etc.) from different tissues, simply by making the membrane leaky. 2. Under physiological conditions, Ca entering the cell transiently inhibits membrane ATPase, resulting in a transient change in membrane permeability and a subsequent release of transmitter. 3. When membrane ATPase inhibitor was used one part of the release proved to be Ca-independent. This finding indicates that the voltage and Ca-dependent link of transmitter release can be by-passed by direct membrane ATPase inhibitors (ouabain). 4. Neurochemical and electrophysiological evidence was obtained on mouse diaphragm that most of the released ACh is cytoplasmic and Na-K ATPase inhibition is responsible for its release. 5. The stimulation of membrane ATPase (by switching off K and its readmission) results in an inhibition of both ACh and noradrenaline release evoked by axonal stimulation. 6. It is suggested that, in those cases where the varicose axon terminals do not make synaptic contact, the transmitter released from the cytoplasmic pool contributes to the transmission, since during diffusion (sometimes few thousand nm) transmitter of different origins becomes mixed up.     

Catalysis by Glomerella cingulata cutinase requires conformational cycling between the active and inactive states of its catalytic triad

Cutinase belongs to a group of enzymes that catalyze the hydrolysis of esters and triglycerides. Structural studies on the enzyme from Fusarium solani have revealed the presence of a classic catalytic triad that has been implicated in the enzyme's mechanism. We have solved the crystal structure of Glomerella cingulata cutinase in the absence and in the presence of the inhibitors E600 (diethyl p-nitrophenyl phosphate) and PETFP (3-phenethylthio-1,1,1-trifluoropropan-2-one) to resolutions between 2.6 and 1.9 Å. Analysis of these structures reveals that the catalytic triad (Ser136, Asp191, and His204) adopts an unusual configuration with the putative essential histidine His204 swung out of the active site into a position where it is unable to participate in catalysis, with the imidazole ring 11 Å away from its expected position. Solution-state NMR experiments are consistent with the disrupted configuration of the triad observed crystallographically. H204N, a site-directed mutant, was shown to be catalytically inactive, confirming the importance of this residue in the enzyme mechanism. These findings suggest that, during its catalytic cycle, cutinase undergoes a significant conformational rearrangement converting the loop bearing the histidine from an inactive conformation, in which the histidine of the triad is solvent exposed, to an active conformation, in which the triad assumes a classic configuration.     

(Na-K)ATPase activity along the nephrons in normal and adrenalectomized rats measured by quantitative cytochemistry

A cytochemical method was used to measure total, ouabain insensitive and specific (Na-K)ATPase activities along the rat nephron. Enzyme activity was expressed as per cent of mean integrated extinction with reference to a calibrated filter. The lowest mean values of total, ouabain-insensitive, and (Na-K)ATPase activities were found in the proximal convoluted tubule (PCT). In the distal convoluted tubule (DCT), total and ouabain-insensitive activities (77.8 per cent and 45.8 per cent, respectively) were significantly higher than in the medullary thick ascending limb (MAL) (66.0 per cent and 24.6 per cent, respectively). Mean values of (Na-K)ATPase activity were significantly lower in DCT than in MAL (32.0 per cent and 41.3 per cent, respectively). Using Lineweaver-Burk plots, the KM ATP value for total ATPase activity was found to be 2.33, 1.79, and 3.63 mM in DCT, MAL, and PCT respectively. Maximal velocity was lower in PCT than in MAL and DCT. For (Na-K)ATPase, the smallest KM value was found in MAL (0.95 mM) and was 2.73 and 5.71 mM in DCT and PCT respectively. Maximal velocity was the highest in MAL (49.3 per cent), lower in DCT (36.1 per cent) and least in PCT (22.5 per cent). ATPase was measured in the MAL and DCT from rats fed a normal (N-Na+) or a high (Hi-Na+) sodium diet, and from Hi-Na+ rats one week after adrenalectomy (ADX). In the MAL, (Na-K)ATPase tended to be higher in Hi-Na+ than in rats, but was significantly lower in ADX than in Hi-Na+.(ABSTRACT TRUNCATED AT 250 WORDS)     

Hysteretic properties of soluble F1 ATPase from Escherichia coli. Evidence for a slow transition between two conformational states of the enzyme.

The soluble Escherichia coli coupling factor, EC F₁ ATPase, was incubated at several temperatures ranging from ?10 to 37 °C before measuring enzyme activity at 10 °C. Under these conditions, the specific activity strongly depends on the preincubation temperature and it appears that ATPase can be reversibly switched from a stable low-activity state to a stable high-activity state. Sedimentation experiments ruled out the possibility that this change of state was due to cold dissociation of the major subunits. Preincubation at several concentrations of protein showed that the change of state corresponded to a monomolecular reaction scheme. The curve of specific activity versus temperature is sigmoidal, and the horizontal asymptote observed at low temperature is different from zero. Analysis of the stability of both states of the enzyme did not agree with the possibility that the low-activity state is an early intermediate of the process of cold inactivation. Experiments with enzyme missing the inhibitory subunit, ?, showed that this subunit is not needed for the conversion from the high-activity state to the low-activity state. The ΔH values for the change of state were calculated.     

Interconversion of two distinct states of active CF0-CF1 (chloroplast ATPase complex) in chloroplasts

Chloroplast ATPase complex is activated by illumination in the presence or absence of dithiothreitol. ATPase complex which has been activated without dithiothreitol catalyzes ATP hydrolysis which is insensitive to stimulation by NH4Cl and is highly sensitive to medium pH. Addition of dithiothreitol during illumination results in an increase in the stimulating effect of NH4Cl on ATP hydrolysis and a decrease in pH sensitivity of ATP hydrolysis. With increasing time in the dark, the ability of NH4Cl to stimulate ATP hydrolysis decreases and the effect of pH on the ATP hydrolysis increases. The onset of resistance to NH4Cl stimulation and the increase in sensitivity to pH are accelerated by ADP and the acceleration is inhibited by Pi. ATP hydrolysis restores NH4Cl sensitivity and renders the activity more resistant to pH. These results suggest that active chloroplast ATPase complex converts its state reversibly from the NH4Cl-insensitive and highly pH-sensitive one to the NH4Cl-sensitive and relatively pH-insensitive one. The conversion from the former to the latter requires both sulfhydryl compound and energy.