Regulation through phosphorylation/dephosphorylation cascade systems

Folding and Stability of Ankyrin Repeats Control Biological Protein Function

Ankyrin repeat proteins are found in all three kingdoms of life. Fundamentally, these proteins are involved in protein-protein interaction in order to activate or suppress biological processes. The basic architecture of these proteins comprises repeating modules forming elongated structures. Due to the lack of long-range interactions, a graded stability among the repeats is the generic properties of this protein family determining both protein folding and biological function. Protein folding intermediates were frequently found to be key for the biological functions of repeat proteins. In this review, we discuss most recent findings addressing this close relation for ankyrin repeat proteins including DARPins, Notch receptor ankyrin repeat domain, IκBα inhibitor of NFκB, and CDK inhibitor p19^INK4d. The role of local folding and unfolding and gradual stability of individual repeats will be discussed during protein folding, protein-protein interactions, and post-translational modifications. The conformational changes of these repeats function as molecular switches for biological regulation, a versatile property for modern drug discovery.

In vitro and in vivo phosphorylation of the Cav2.3 voltage-gated R-type calcium channel

During the recording of whole cell currents from stably transfected HEK-293 cells, the decline of currents carried by the recombinant human Cav2.3+β3 channel subunits is related to adenosine triphosphate (ATP) depletion after rupture of the cells. It reduces the number of functional channels and leads to a progressive shift of voltage-dependent gating to more negative potentials (Neumaier F., et al., 2018). Both effects can be counteracted by hydrolysable ATP, whose protective action is almost completely prevented by inhibition of serine/threonine but not tyrosine or lipid kinases. These findings indicate that ATP promotes phosphorylation of either the channel or an associated protein, whereas dephosphorylation during cell dialysis results in run-down. Protein phosphorylation is required for Cav2.3 channel function and could directly influence the normal features of current carried by these channels. Therefore, results from in vitro and in vivo phosphorylation of Cav2.3 are summarized to come closer to a functional analysis of structural variations in Cav2.3 splice variants.

Quantitative analysis of global phosphorylation changes with high-resolution tandem mass spectrometry and stable isotopic labeling

Quantitative measurement of specific protein phosphorylation sites is a primary interest of biologists, as site-specific phosphorylation information provides insights into cell signaling networks and cellular dynamics at a system level. Over the last decade, selective phosphopeptide enrichment methods including IMAC and metal oxides (TiO₂ and ZrO₂) have been developed and greatly facilitate large scale phosphoproteome analysis of various cells, tissues and living organisms, in combination with modern mass spectrometers featuring high mass accuracy and high mass resolution. Various quantification strategies have been applied to detecting relative changes in expression of proteins, peptides, and specific modifications between samples. The combination of mass spectrometry-based phosphoproteome analysis with quantification strategies provides a straightforward and unbiased method to identify and quantify site-specific phosphorylation. We describe common strategies for mass spectrometric analysis of stable isotope labeled samples, as well as two widely applied phosphopeptide enrichment methods based on IMAC(NTA-Fe³⁺) and metal oxide (ZrO₂). Instrumental configurations for on-line LC-tandem mass spectrometric analysis and parameters of conventional bioinformatic analysis of large data sets are also considered for confident identification, localization, and reliable quantification of site-specific phosphorylation.

Reversible adenylylation of glutamine synthetase is dynamically counterbalanced during steady-state growth of Escherichia coli

Glutamine synthetase (GS) is the central enzyme for nitrogen assimilation in Escherichia coli and is subject to reversible adenylylation (inactivation) by a bifunctional GS adenylyltransferase/adenylyl-removing enzyme (ATase). In vitro, both of the opposing activities of ATase are regulated by small effectors, most notably glutamine and 2-oxoglutarate. In vivo, adenylyltransferase (AT) activity is critical for growth adaptation when cells are shifted from nitrogen-limiting to nitrogen-excess conditions and a rapid decrease of GS activity by adenylylation is needed. Here, we show that the adenylyl-removing (AR) activity of ATase is required to counterbalance its AT activity during steady-state growth under both nitrogen-excess and nitrogen-limiting conditions. This conclusion was established by studying AR(-)/AT(+) mutants, which surprisingly displayed steady-state growth defects in nitrogen-excess conditions due to excessive GS adenylylation. Moreover, GS was abnormally adenylylated in the AR(-) mutants even under nitrogen-limiting conditions, whereas there was little GS adenylylation in wild-type strains. Despite the importance of AR activity, we establish that AT activity is significantly regulated in vivo, mainly by the cellular glutamine concentration. There is good general agreement between quantitative estimates of AT regulation in vivo and results derived from previous in vitro studies except at very low AT activities. We propose additional mechanisms for the low AT activities in vivo. The results suggest that dynamic counterbalance by reversible covalent modification may be a general strategy for controlling the activity of enzymes such as GS, whose physiological output allows adaptation to environmental fluctuations.

Noise and critical phenomena in biochemical signaling cycles at small molecule numbers

Biochemical reaction networks in living cells usually involve reversible covalent modification of signaling molecules, such as protein phosphorylation. Under conditions of small molecule numbers, as is frequently the case in living cells, mass-action theory fails to describe the dynamics of such systems. Instead, the biochemical reactions must be treated as stochastic processes that intrinsically generate concentration fluctuations of the chemicals. We investigate the stochastic reaction kinetics of covalent modification cycles (CMCs) by analytical modeling and numerically exact Monte Carlo simulation of the temporally fluctuating concentration. Depending on the parameter regime, we find for the probability density of the concentration qualitatively distinct classes of distribution functions including power-law distributions with a fractional and tunable exponent. These findings challenge the traditional view of biochemical control networks as deterministic computational systems and suggest that CMCs in cells can function as versatile and tunable noise generators.

Expressions for the fractional modification in different monocyclic enzyme cascade systems: analysis of their validity tested by numerical integration

This paper presents the derivation, under a minimal set of assumptions, of a general expression for the steady-state fractional modification of an interconvertible protein involved in four different schemes of monocyclic enzyme cascade systems. From this general expression we derive, as particular cases, other, simpler expressions by applying additional assumptions and which have, therefore, a smaller range of validity. Some of these particular expressions coincide with those already obtained in previous contributions on individualised analyses. We discuss the relationships between the kinetic parameters and the concentrations needed for the fulfilment of the additional assumptions. The goodness of the analysis was tested by reference to the shape in the steady-state of the simulated time progress curves obtained by numerical integration.

Effect of binding in cyclic phosphorylation-dephosphorylation process and in energy transformation

The effects of binding on the phosphorylation-dephosphorylation cycle (PDPC) - one of the key components of the signal transduction processes - is analyzed based on a mathematical model. The model shows that binding of proteins, forming a complex, diminishes the ultrasensitivity of the PDPC to the differences in activity between kinase and phosphatase in the cycle. It is also found that signal amplification depends upon the strength of the binding affinity of the protein (phosphorylated or dephosphorylated) to other proteins . It is also observed that the amplification of signal is not only dependent on phosphorylation potential but also on binding properties and resulting adjustments in binding energies.

Kinetic models of phosphorylation cycles: A systematic approach using the rapid-equilibrium approximation for protein–protein interactions

Activation-inactivation cycles of signalling proteins and transcription factors catalysed by kinases and phosphatases are a core component of cellular signal transduction. We present a systematic kinetic analysis of a phosphorylation cycle that starts from the description of elementary protein-protein interaction and catalytic steps. A rapid-equilibrium approximation for protein interactions is used to reduce the set of parameters. The resulting description consists of a kinetic equation for the phosphorylation of the target and a set of conservation conditions for kinase and phosphatase. Generally no explicit rate laws exist for the two enzymes; linear or Michaelis-Menten rate equations can be obtained in special cases. Key parameters that determine the stimulus-response curve and the response time of the cycle are the concentrations of kinase and phosphatase relative to the target protein and the affinities of the two enzymes for the different phosphorylation states of the target. Characterizing the response curve by the global response coefficient, we obtain a phase diagram that shows the existence of three kinds of behaviours: graded, ultrasensitive, and a previously undescribed biphasic response. Two kinds of competition effect turn out to shape the behaviour: (1) the degree of product inhibition of each enzyme, and (2) the competition between kinase and phosphatase to bind the target protein, as determined by their relative target affinities. The approach outlined here may be useful also for analysing more complex systems, including multiple phosphorylation and kinase cascades.

Quantification of the glycogen cascade system: the ultrasensitive responses of liver glycogen synthase and muscle phosphorylase are due to distinctive regulatory designs

Background

Signaling pathways include intricate networks of reversible covalent modification cycles. Such multicyclic enzyme cascades amplify the input stimulus, cause integration of multiple signals and exhibit sensitive output responses. Regulation of glycogen synthase and phosphorylase by reversible covalent modification cycles exemplifies signal transduction by enzyme cascades. Although this system for regulating glycogen synthesis and breakdown appears similar in all tissues, subtle differences have been identified. For example, phosphatase-1, a dephosphorylating enzyme of the system, is regulated quite differently in muscle and liver. Do these small differences in regulatory architecture affect the overall performance of the glycogen cascade in a specific tissue? We address this question by analyzing the regulatory structure of the glycogen cascade system in liver and muscle cells at steady state.

Results

The glycogen cascade system in liver and muscle cells was analyzed at steady state and the results were compared with literature data. We found that the cascade system exhibits highly sensitive switch-like responses to changes in cyclic AMP concentration and the outputs are surprisingly different in the two tissues. In muscle, glycogen phosphorylase is more sensitive than glycogen synthase to cyclic AMP, while the opposite is observed in liver. Furthermore, when the liver undergoes a transition from starved to fed-state, the futile cycle of simultaneous glycogen synthesis and degradation switches to reciprocal regulation. Under such a transition, different proportions of active glycogen synthase and phosphorylase can coexist due to the varying inhibition of glycogen-synthase phosphatase by active phosphorylase.

Conclusion

The highly sensitive responses of glycogen synthase in liver and phosphorylase in muscle to primary stimuli can be attributed to distinctive regulatory designs in the glycogen cascade system. The different sensitivities of these two enzymes may exemplify the adaptive strategies employed by liver and muscle cells to meet specific cellular demands.

Glutaredoxin: role in reversible protein s-glutathionylation and regulation of redox signal transduction and protein translocation

Reversible posttranslational modifications on specific amino acid residues can efficiently regulate protein functions. O-Phosphorylation is the prototype and analogue to the rapidly emerging mechanism of regulation known as S-glutathionylation. The latter is being recognized as a potentially widespread form of modulation of the activities of redox-sensitive thiol proteins, especially those involved in signal transduction pathways and translocation. The abundance of reduced glutathione in cells and the ready conversion of sulfenic acids and S-nitroso derivatives to S-glutathione mixed disulfides support the notion that reversible S-glutathionylation is likely to be the preponderant mode of redox signal transduction. The glutaredoxin enzyme has served as a focal point and important tool for evolution of this regulatory mechanism because of its characterization as a specific and efficient catalyst of protein-SSG de-glutathionylation (akin to phosphatases). Identification of specific mechanisms and enzyme(s) that catalyze formation of protein-SSG intermediates, however, is largely unknown and represents a prime objective for furthering understanding of this evolving mechanism of cellular regulation. Several proteomic approaches, including the use of cysteine-reactive fluorescent and radiolabel probes, have been developed to detect arrays of proteins whose cysteine residues are modified in response to oxidants, thus identifying them as potential interconvertible proteins to be regulated by redox signaling (glutathionylation). Specific criteria were used to evaluate current data on cellular regulation via S-glutathionylation. Among many proteins under consideration, actin, protein tyrosine phosphatase-1B, and Ras stand out as the best current examples for establishing this regulatory mechanism.

Thermodynamic and kinetic analysis of sensitivity amplification in biological signal transduction

Based on a thermodynamic analysis of the kinetic model for the protein phosphorylation-dephosphorylation cycle, we study the ATP (or GTP) energy utilization of this ubiquitous biological signal transduction process. It is shown that the free energy from hydrolysis inside cells, DeltaG (phosphorylation potential), controls the amplification and sensitivity of the switch-like cellular module; the response coefficient of the sensitivity amplification approaches the optimal 1 and the Hill coefficient increases with increasing DeltaG. We discover that zero-order ultrasensitivity is mathematically equivalent to allosteric cooperativity. Furthermore, we show that the high amplification in ultrasensitivity is mechanistically related to the proofreading kinetics for protein biosynthesis. Both utilize multiple kinetic cycles in time to gain temporal cooperativity, in contrast to allosteric cooperativity that utilizes multiple subunits in a protein.

Twenty-four hour exposure to prostaglandin downregulates prostanoid receptor binding but does not alter PGE(2)-mediated sensitization of rat sensory neurons

Although the tissue levels of prostaglandins are elevated for a relatively long period during injury or inflammation, few studies have been performed to assess the effects of prolonged prostaglandin exposure on receptor binding and activity in sensory neurons. Consequently, we examined whether unilateral inflammation or a 24 h exposure to prostaglandin E2 (PGE2) altered binding of this prostanoid in spinal cord tissue or in isolated sensory neurons, respectively. To assess functional changes in EP receptors, we also examined PGE2-induced cAMP production and the prostanoid-mediated augmentation of substance P release from isolated sensory neurons after acute and 24 h pretreatment with PGE2. Injection of complete Freund's adjuvant into the hindpaw decreased binding of PGE2 in ipsilateral, but not contralateral dorsal spinal cord 24 h after injection. This decrease in Bmax was blocked by administration of intrathecal ketorolac (10 nmol/microl/h) for 24 h prior to and throughout the period of inflammation, suggesting that the inflammation-induced decrease in binding is dependent on prostaglandin synthesis. In an analogous manner, treating sensory neurons grown in culture with 1 microM PGE2 for 24 h decreased [3H]-PGE2 binding by approximately 50% without altering binding affinity. Exposing neuronal cultures to 1 microM PGE2 for 24 h also reduced, but did not abolish the ability of the prostanoid to increase the production of cAMP. This treatment, however, did not significantly alter the ability of PGE2 to augment the evoked release of immunoreactive substance P from sensory neurons. These results demonstrate that under conditions that significantly downregulate PGE2 binding, sensory neurons are still capable of maintaining PGE2-mediated sensitization.

Analysis of protein homeostatic regulatory mechanisms in perturbed environments at steady state

Nine different protein homeostatic regulatory mechanisms were analysed for their ability to maintain a generic protein P within a specified range of a set-point steady-state concentration while perturbed by external processes that altered the rates at which P was produced and/or consumed. Steady state regulatory effectiveness was defined by the area within a rectangular region of "perturbation space", where axes correspond to rates of positive and negative perturbations. The size of this region differed in accordance with the regulatory elements composing the homeostatic mechanism. Such elements included basic negative feedback control of transcription (in which P, at some high concentration relative to its set-point value, binds to the gene G that encodes it, thereby inhibiting transcription), multiple sequential binding of a feedback effector (two P's bind sequentially to G), and dimerization of a feedback effector (a P(2) dimer binds to G). Two homeostatic mechanisms included a cascade structure, one with and one without translational feedback control. Another mechanism included feedback control of P degradation. Finally, two mechanisms illustrated the limits of regulatory systems. One lacked all regulatory elements (and included only an invariant rate of P synthesis and degradation) while the other assumed perfect (Boolean) regulation, in which transcription is completely inhibited at [P]>[P](sp) and is fully active at [P]<[P](sp). All of the systems evaluated are known, but the analytical expressions developed here allow quantitative comparisons between them. These expressions were evaluated at values typical of the average protein in Escherichia coli. A method for building regulatory networks by linking semi-independent regulatory modules is discussed.

Magnetic field perturbations as a tool for controlling enzyme-regulated and oscillatory biochemical reactions

The feasibility of magnetic field perturbations as a tool for controlling enzyme-regulated and oscillatory biochemical reactions is studied. Our approach is based on recent experimental results that revealed magnetic field effects on the in vitro activity of enzyme systems in accordance with the radical pair mechanism. A minimum model consisting of two coupled enzyme-regulated reactions is discussed that combines, in a self-consistent manner, magnetic field-sensitive enzyme kinetics with non-linear dynamical principles. Furthermore, a simple detector mechanism is described that is capable of responding to an oscillatory input. Results reveal that moderate-strength magnetic fields (B=1-100 mT) may effectively alter the dynamics of the system. In particular, a response behavior is observed that depends on: (1) the combination of static and time-varying magnetic fields; (2) the field amplitude; and (3) the field frequency in a non-linear fashion. The specific response behavior is critically determined by the biochemical boundary conditions as defined by the kinetic properties of the system. We propose an experimental implementation of the results based on the oscillatory peroxidase-oxidase reaction controlled by the enzyme horseradish peroxidase.

Characterization of the mechanism of regulation of Ca2+/ calmodulin-dependent protein kinase I by calmodulin and by Ca2+/calmodulin-dependent protein kinase kinase

Ca2+/calmodulin-dependent protein kinase I (CaMKI) is maintained in an autoinhibited state by the interaction of a COOH-terminal helix-loop-helix (Ile286-Met316) regulatory domain with the catalytic core. Activation of the enzyme by calmodulin (CaM) also allows CaMKI to be phosphorylated and activated by a second enzyme, CaMK kinase (CaMKK). To more thoroughly characterize the regulation of CaMKI by CaM and its interrelationship with phosphorylation by CaMKK, we have carried out a detailed structure-function analysis using recombinant wild-type (WT) and mutant forms of CaMKI and CaMKK. CaMKI-WT, in the absence of CaM, or CaMKI-299 and CaMKI-298 were autoinhibited and could not be phosphorylated by CaMKK-433 (a truncated constitutively active form of CaMKK). Removal of Phe298 (CaMK-297) generated a constitutively active form of CaMKI that was also phosphorylated by CaMKK-433. CaMKI-WT was essentially inactive in the absence of CaM (K0.5 for activation by CaM approximately 30 nM). Mutation of Ile294 and Phe298 to alanine (CaMKI-2A) resulted in measurable basal enzyme activity. Additional mutation of Ile286 and Val290 to alanine (CaMKI-4A) increased this basal activity. Mutation of Trp303 (CaMKI-W303S) resulted in a large increase in the K0.5 for CaM ( approximately 100 microM), supporting a role for this residue as an initial target for CaM. Mutation of Phe307 (CaMKI-F307A) resulted in increased basal enzyme activity, supporting a role for this residue in autoinhibition of CaMKI. Together these studies demonstrate the critical role of specific amino acids in the autoinhibition of CaMKI and also in its activation by CaM and phosphorylation by CaMKK.

Endogenous protein phosphorylation and protein kinase activity in winged bean

In winged bean (Psophocarpus tetragonolobus) protein kinases (E.C. 2.7.1.37) were found in all tissues studied. There was a significant increase in kinase activity during seed development, with a concomitant enhancement in the phosphorylation of a number of polypeptides; this was reversed in germinating seed cotyledons. Protein phosphorylation was apparently correlated with the increase in the protein content of the developing seed and the growing axis. At least three distinct autophosphorylating proteins could be distinguished in the developing seeds after SDS-PAGE, indicating the presence of different types of protein kinases in winged bean.

Protein molecules as computational elements in living cells

Many proteins in living cells appear to have as their primary function the transfer and processing of information, rather than the chemical transformation of metabolic intermediates or the building of cellular structures. Such proteins are functionally linked through allosteric or other mechanisms into biochemical 'circuits' that perform a variety of simple computational tasks including amplification, integration and information storage.

Purification and characterization of a high-molecular-weight protein induced in rat serum during the development of cardiac hypertrophy

A relatively high-molecular-weight polypeptide was found in rat serum within 6 h after aortic constriction in experimental animals. This polypeptide persists for about 7 days of the postoperative period and disappears at later stage of hypertrophy (40%). Further, fractionation and purification of this protein through DEAE-Sepharose and gel filtration chromatography have revealed that this protein is a single polypeptide and its relative molecular weight is 135 kDa. Immunoprecipitation and immunofluorescence microscopic analysis have indicated the presence of the above polypeptide in the nuclear fraction of heart cells. Studies on phosphorylation in vitro have revealed that this protein is a phosphoprotein. DNase I sensitivity and hybridization using a muscle specific gene probe have indicated the involvement of this protein in template associated changes in heart nuclei. Further the possibility of this protein being synthesized by heart cells indicates that this protein could traverse back and forth between heart cells and the extracellular fluid, suggesting an autocrine/paracrine role for this protein during the development of cardiac hypertrophy.

Covalent modification of proteins as a threshold mechanism in development

Thresholds are a central but somewhat neglected aspect of cellular processes in development. An analysis has been made of the conditions in which different thresholds can be generated in the covalent modification of a number of target proteins when the concentration of an effector is continuously increased. It is assumed that the effector, which could represent a morphogen, activates, for example, kinases that phosphorylate the proteins. Thresholds are found when the modifying enzymes are saturated by their protein substrates, i.e. in conditions of zero-order ultrasensitivity (Goldbeter, A. & Koshland, D. E. 1981. An amplified sensitivity arising from covalent modification in biological systems. Proc. natn. Acad. Sci. U.S.A. 78, 6840-6844). Sequential thresholds can be generated when the kinase/phosphatase pairs differ either in the ratio of maximum modification rates or in the affinity of the effector for each kinase.

Insulin and glucose regulation of glycogen synthase in rat calvarial osteoblastlike cells

Insulin has been shown to stimulate collagen, noncollagen protein and nucleic acid synthesis in bone cells in vitro. However, the effects of insulin on intermediary carbohydrate metabolism in osteoblasts, and in particular on the key regulatory enzyme glycogen synthase, have not been directly examined. Accordingly, we developed a microassay for glycogen synthase (GS) to examine insulin and glucose regulation of this enzyme in cultured osteoblastlike cells. In osteoblast-enriched rat calvarial bone explants incubated for 24 hours in 5 mM glucose, insulin (0.1-100 nM) produced a dose-related stimulation of GSa (glucose-6-phosphate independent GS activity). The insulin-stimulated increase in GSa ranged from a 30% increase in the presence of 0.1 nM insulin to a 163% increase produced by 100 nM insulin, both significant at P less than 0.01. In contrast, GSb (glucose-6-phosphate dependent GS activity) was significantly increased only at a supraphysiologic insulin concentration (100 nM). The GS activity ratio (GSa/GSb) increased with insulin concentration from 0.1-100 nM. Basal values for GSa and GSb activity did not differ between explants incubated in 5mM or 15 mM glucose for 24 hours. However, incubation in the presence of 15 mM glucose blunted the insulin-stimulated increase in GSa activity, with 100 nM insulin producing only a 75% increase in GSa activity. In contrast, maximal insulin-stimulated GSb levels were not affected by high glucose medium. In explants incubated in glucose-free medium, basal GSa activity was significantly greater than in the presence of glucose.(ABSTRACT TRUNCATED AT 250 WORDS)

Application of 19F nuclear magnetic resonance to examine covalent modification reactions of tyrosyl derivatives: a study of calcineurin catalysis

The hydrolysis of fluorotyrosine phosphate by the calmodulin-activated phosphatase calcineurin has been monitored by 19F nuclear magnetic resonance spectroscopy. Previous work had established that the 19F nuclear magnetic resonance shift of the fluorine nucleus was altered after the phosphorylation of the phenolic hydroxyl group (B. Martin, C.J. Pallen, J.H. Wang, and D.J. Graves (1985) J. Biol. Chem. 260, 14592-14597). The disappearance of substrate and the appearance of product can be measured simultaneously with this approach. Application of the integrated form of the Michaelis-Menten equation yields estimates of the kinetic parameter, KM, close to the values obtained by initial rate kinetics. The velocity term, VM, was also evaluated to be approximately the same value. Calcineurin was determined not to be inactivated over the time period of the reaction. The results demonstrate that 19F nuclear magnetic resonance spectroscopy can be applied to the examination of enzyme-catalyzed reactions.

Cyclic phosphorylation/dephosphorylation cascade in bovine brain coated vesicles

Coated vesicles are involved in transport of membrane proteins between several intracellular membrane-bound compartments. These vesicles possess a specific 50-kDa protein which is phosphorylated and dephosphorylated by a coated-vesicle-specific kinase and phosphatase. We studied this phosphorylation/dephosphorylation cascade system and show that the phosphorylation level of the 50-kDa protein is governed by the ATP/ADP ratio.

Biochemical markers of aging

It is the purpose of this report to identify possible metabolic deficiencies that might serve as biochemical markers of aging. It is proposed that the multiplicity of physical and physiological changes associated with aging could be most readily explained by alterations in the regulation and/or the activities of enzymes that occupy central positions in metabolism. Specifically, a search for metabolic markers of aging might include efforts to determine if there are age-related changes in the following enzymes or enzyme systems: (a) allosteric enzymes that catalyze reactions in highly branched metabolic pathways; (b) enzymes that catalyze opposing reactions between metabolites that are common intermediates in biosynthetic and biodegradative pathways (reactions which in the absence of final control would lead to futile substrate cycling); (c) enzymes that catalyze bimolecular reactions in which one member of a coenzyme pair is a cosubstrate (e.g., reactions involving NAD+ or NADH); (d) enzymes that are regulated by phosphorylation/dephosphorylation cycles; and (e) G-protein-dependent enzyme systems. It is also emphasized that changes in the concentrations and ratios of coenzyme substrate pairs (e.g., [NAD]/[NADH], [CoA]/[acyl CoA]) and the energy charge ratio [ATP] + 0.5 [ADP]/[ATP] + [ADP] + [AMP] may signal deviations from normal metabolism and therefore might be reliable markers of aging. In addition, because of their critical roles in metabolism, changes in the concentration of GTP, GDP and the second messengers, c-AMP, c-GMP should be monitored. Finally, it is noted that the accumulation of the altered forms of some enzymes which occurs during aging reflects imbalance between posttranslational modification of the enzymes and the degradation of the altered enzyme forms. The biological mechanisms involved and the genetic implications are discussed.

Vasodilator-stimulated protein phosphorylation in platelets is mediated by cAMP- and cGMP-dependent protein kinases

Vasodilators such as sodium nitroprusside, nitroglycerin and various prostaglandins are capable of inhibiting platelet aggregation associated with an increase of either cGMP or cAMP. In our studies with intact platelets, prostaglandin E1 and sodium nitroprusside stimulated the phosphorylation of several proteins which could be distinguished from proteins known to be phosphorylated by a calmodulin-regulated protein kinase or by protein kinase C. Prostaglandin E1 (10 microM) or dibutyryl cAMP (2 mM) stimulated the phosphorylation of proteins with apparent relative molecular masses, Mr, of 240,000, 68,000, 50,000, and 22,000 in intact platelets. These proteins were also phosphorylated in response to low concentrations (1-2 microM) of cAMP in a particulate fraction of platelets. In intact platelets, sodium nitroprusside (100 microM) and the 8-bromo derivative of cGMP (2 mM) increased the phosphorylation of one protein of Mr 50,000 which was also phosphorylated in response to low concentrations (1-2 microM) of cGMP in platelet membranes. An additional protein (Mr 24,000) appeared to be phosphorylated to a lesser degree in intact platelets by prostaglandin E1 and sodium nitroprusside. Since the phosphorylation of the protein of Mr 50,000 was stimulated both in intact platelets by cyclic-nucleotide-elevating agents and cyclic nucleotide analogs, as well as in platelet membranes by cyclic nucleotides, this phosphoprotein was analyzed by limited proteolysis, tryptic fingerprinting and phosphoamino acid analysis. These experiments indicated that the 50-kDa proteins phosphorylated by sodium nitroprusside and prostaglandin E1 were identical, and that the peptide of the 50-kDa protein phosphorylated by both agents was also the same as the peptide derived from the 50-kDa protein phosphorylated in platelet membranes by cGMP- and cAMP-dependent protein kinases, respectively. Regulation of protein phosphorylation mediated by cAMP- and cGMP-dependent protein kinases may be the molecular mechanism by which those vasodilators, capable of increasing either cAMP or cGMP, inhibit platelet aggregation.

Bistability and irreversible transitions in a simple substrate cycle

The dynamic properties of a simple substrate cycle involving two antagonist enzymes are investigated. One of these enzymes exhibits a non-linearity through inhibition by excess substrate. Depending either on the interconverted substrate pool concentration or the maximal activity of the non-inhibited enzyme, monostability, bistability and irreversible transitions may occur. A reversible bistable cycle is shown to present interesting features for regulatory purposes as it can respond to external (and/or internal) modulations in two different ways: A buffering effect by efficient stabilization of the steady-states, or, an increase in sensitivity by switching the system from one regime to the opposite one. The plausible biochemical and biological implications of irreversible transitions are discussed and emphasized in terms of "metabolic transitions".

Conformational responses of an arachidonate- and U46619-binding haemoprotein in relation to platelet activation

Antibodies were raised, in rabbits, against an arachidonate- and U46619-binding protein purified from calf platelets. Spectral measurements and immunodiffusion experiments were employed to follow conformational responses of the protein in relation to platelet activation. Upon treatment with the platelet agonists, arachidonate and PGH2, as well as the common haem ligands, imidazole and CN-, the purified protein had its Soret band red-shifted, with hypochromicity, but the protein saturated with the agonists, not with the haem ligands, showed altered antigenic properties in immunodiffusion experiments. In an analogous manner activation of gel-filtered calf platelets with high concentrations of ADP and A23187, as well as by cold, had Soret bands of extracts of sonicated platelets red-shifted, with hypochromicity; concomitantly, antigenically different conformations of the protein appeared in Triton X-100 extracts of the activated platelets. A protein immunologically related to the platelet protein was detected in Triton X-100 extracts of calf neutrophils. It is suggested that conformational changes of the protein induced by arachidonate or prostaglandin endoperoxides or H2O2 formed in different compartments during platelet activation by different stimuli may be a biochemical mechanism of stimulus-response coupling and that similar mechanisms might operate in other cell types.

Reversible regulation of the nitrogenase iron protein from Rhodospirillum rubrum by ADP-ribosylation in vitro

Nitrogenase activity in the photosynthetic bacterium Rhodospirillum rubrum is reversibly regulated by interconversion of the Fe protein between a modified and an unmodified form. Since the discovery of the activation process in 1976, investigators have been unable to demonstrate the inactivation (modification) reaction in vitro. In this study, NAD-dependent modification and concomitant inactivation of the Fe protein were demonstrated in crude extracts of R. rubrum. Activation of the in vitro-modified Fe protein by activating enzyme and structural similarity between the in vivo and in vitro modifications are presented as evidence that the in vitro modification is the physiologically relevant ADP-ribosylation reaction. Using a partially purified preparation, we showed that the inactivating enzyme activity is stimulated by divalent metal ions and ADP, that O2-denatured Fe protein will not serve as a substrate, and that dithionite inhibits the modification reaction.

Phosphorylation sites and inactivation of branched-chain alpha-ketoacid dehydrogenase isolated from rat heart, bovine kidney, and rabbit liver, kidney, heart, brain, and skeletal muscle

Branched-chain alpha-ketoacid dehydrogenase complex was isolated from rat heart, bovine kidney, and rabbit liver, heart, kidney, brain, and skeletal muscle. Phosphorylation to approximately 1 mol Pi/mol alpha-subunit of the alpha-ketoacid decarboxylase component was linearly associated with 90-95% inactivation. The complex from some tissues (i.e., from rabbit kidney and heart, and rat heart) showed 30-40% more phosphate incorporation for an additional 5-10% inactivation. Reverse-phase HPLC analysis of tryptic digests of 32P-labeled complexes from all of the above tissues revealed two major (peaks 1 and 2) and one minor (peak 3) phosphopeptide which represent phosphorylation sites 1, 2, and a combination of 1 and 2, respectively. These phosphopeptides, numbered according to the order of elution from reverse-phase HPLC, had the same elution time regardless of the tissue or animal source of the complex. The amino acid sequence of site 1 from rabbit heart branched-chain alpha-ketoacid dehydrogenase was Ile-Gly-His-His-Ser(P)-Thr-Ser-Asp-Asp-Ser-Ser-Ala-Tyr-Arg. Regardless of the source of the complex, both sites were almost equally phosphorylated until total phosphorylation was approximately 1 mol Pi/mol of alpha-subunit and the rate of inactivation was correlated with the rate of total, site 1, or site 2 phosphorylation. Phosphorylation beyond this amount was associated with greater site 2 than site 1 phosphorylation. alpha-Chloroisocaproate, a potent inhibitor of branched-chain alpha-ketoacid dehydrogenase kinase activity, greatly reduced total phosphorylation and inactivation; however, phosphorylation of site 2 was almost abolished and inactivation was directly correlated with phosphorylation of site 1. Thus, the complex isolated from different tissues and mammals had an apparent conservation of amino acid sequence adjacent to the phosphorylation sites. Both sites were phosphorylated to a similar extent temporally although site 1 phosphorylation was directly responsible for inactivation.

Immunological characterization of phosphoprotein phosphatases

Phosphoprotein phosphatases regulate the biological activities of proteins through their involvement in cyclic phosphorylation/dephosphorylation cascades. A variety of multimeric phosphatases have been isolated and grouped into several classes, termed type 1 and types 2A, 2B, and 2C. To elucidate the relationship between the different phosphoprotein phosphatases, highly purified enzymes from soil amoebae, turkey gizzards, bovine heart and brain, and rabbit skeletal muscle and reticulocytes were tested for immunological antigenic relatedness. Two heterologous antibody preparations were employed for this purpose. One was made against an Acanthamoeba type 2A phosphatase and the other was made to bovine brain phosphatase type 2B (calcineurin, holoenzyme). Specific subunit cross-reactivity was examined by protein blot ("Western") analysis. The antibody to the type 2A phosphatase reacted with the catalytic subunits of every type 2 enzyme tested, including both the catalytic and Ca2+-binding subunits of the Ca2+/calmodulin-dependent type 2B phosphatase (calcineurin), bovine cardiac type 2A phosphatase, and turkey gizzard smooth muscle phosphatase-1 (type 2A1). It did not react with any type 1 phosphatase (catalytic subunit or ATP-Mg-dependent). The antigenic relatedness of calcineurin and the bovine cardiac type 2A phosphatase (Mr 38,000) was demonstrated further by protein blot analysis showing that the anti-calcineurin antibody cross-reacted with both enzymes. The mutual cross-reactivity poses an intriguing problem because these enzymes are so different in their molecular structures and modes of regulation. The degree of evolutionary conservation exhibited by the antigenic cross-reactivity of the type 2 enzymes from a broad range of species and tissues suggests a strong selective pressure on maintaining one or more features of these important regulatory enzymes.