Nucleotide-dependent Processes Research Articles

Single Molecule FRET - A Multi-Environment Ruler for Determining Structure and Dynamics

Studies of multi-domain proteins and multi-protein machines necessitate a deeper understanding of dynamic structure and transient conformations. Therefore, conventional structure determination methods need to be integrated into dynamic detection approaches. We developed a hybrid method that integrates x-ray structure information into self-consistent distance networks based on single-molecule Förster resonance energy transfer (FRET) [1,2]. By analyzing time-correlated distance distributions globally, we can separate real protein dynamics and fluctuations from modelling uncertainties, and ultimately generate time-correlated structural ensembles. On top of that, we reveal correlated small- and large-scale intra-molecular fluctuations from time-resolved, color- and polarization-sensitive fluorescence measurements. We applied our approach to the heat shock protein Hsp90. The chaperone activates large sets of signal transduction proteins often assisted by co-chaperones [3]. These conformation- and nucleotide-dependent processes are not yet comprehensively understood. Our approach resembled the x-ray structure of Hsp90's closed conformation with an RMSD of 2.8 Å. Beyond that, we resolved the previously unknown dynamic open structure of this multidomain protein. The large-scale fluctuations on the lower millisecond timescale might be the basis of a general regulation mechanism. Finally, I want to show how FRET can be orthogonally integrated into cross-disciplinary platforms such as a microfluidics [4] and others, enabling the simultaneous detection of dynamic structure and low-affinity interactions. [1] Hellenkamp B, Wortmann P, Kandzia F, Zacharias M, Hugel T. Multidomain structure and correlated dynamics determined by self-consistent FRET networks. Nature Methods 14(2), 174-180 (2017) [2] Hellenkamp B, Schmid S et al. Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study Nature Methods 15, 669-676 (2018) [3] Taipale, M et al. Quantitative Analysis of Hsp90-Client Interactions Reveals Principles of Substrate Recognition. Cell 140(5), 987-1001 (2012) [4] Hellenkamp B, Thurn J, Stadlmeier M, Hugel T., submitted

The Immunosuppressant Mycophenolic Acid Alters Nucleotide and Lipid Metabolism in an Intestinal Cell Model

The study objective was to elucidate the molecular mechanisms underlying the negative effects of mycophenolic acid (MPA) on human intestinal cells. Effects of MPA exposure and guanosine supplementation on nucleotide concentrations in LS180 cells were assessed using liquid chromatography-mass spectrometry. Proteomics analysis was carried out using stable isotope labeling by amino acids in cell culture combined with gel-based liquid chromatography-mass spectrometry and lipidome analysis using 1H nuclear magnetic resonance spectroscopy. Despite supplementation, depletion of guanosine nucleotides (p < 0.001 at 24 and 72 h; 5, 100, and 250 μM MPA) and upregulation of uridine and cytidine nucleotides (p < 0.001 at 24 h; 5 μM MPA) occurred after exposure to MPA. MPA significantly altered 35 proteins mainly related to nucleotide-dependent processes and lipid metabolism. Cross-reference with previous studies of MPA-associated protein changes widely corroborated these results, but showed differences that may be model- and/or method-dependent. MPA exposure increased intracellular concentrations of fatty acids, cholesterol, and phosphatidylcholine (p < 0.01 at 72 h; 100 μM MPA) which corresponded to the changes in lipid-metabolizing proteins. MPA affected intracellular nucleotide levels, nucleotide-dependent processes, expression of structural proteins, fatty acid and lipid metabolism in LS180 cells. These changes may compromise intestinal membrane integrity and contribute to gastrointestinal toxicity.

Nucleotide dependent processes in the thylakoid lumen of higher plant chloroplast

In this study, the putative anion transporter 1 (ANTR1) from Arabidopsis thaliana was shown to be localized to the chloroplast thylakoid membrane by Western blotting with two different peptide-specific antibodies. ANTR1 is homologous to the type I of mammalian Na+-dependent inorganic phosphate (Pi) transporters. The function of ANTR1 as a Na+-dependent Pi transporter was demonstrated by heterologous expression and uptake of radioactive Pi into Escherichia coli cells. The expression of ANTR1 conferred increased growth rates to the transformed cells and stimulated Pi uptake in a pH- and Na+-dependent manner as compared with the control cells. Among various tested effectors, Pi was the preferred substrate. Although it competed with the uptake of Pi, glutamate was not transported by ANTR1 into E. coli. In relation to its function as a Pi transporter, several physiological roles for ANTR1 in the thylakoid membrane are proposed, such as export of Pi produced during nucleotide metabolism in the thylakoid lumen back to the chloroplast stroma and balance of the trans-thylakoid H+ electrochemical gradient storage.

The Tail Domain of Myosin Va Modulates Actin Binding to One Head

Calcium activates full-length myosin Va steady-state enzymatic activity and favors the transition from a compact, folded "off" state to an extended "on" state. However, little is known of how a head-tail interaction alters the individual actin and nucleotide binding rate and equilibrium constants of the ATPase cycle. We measured the effect of calcium on nucleotide and actin filament binding to full-length myosin Va purified from chick brains. Both heads of nucleotide-free myosin Va bind actin strongly, independent of calcium. In the absence of calcium, bound ADP weakens the affinity of one head for actin filaments at equilibrium and upon initial encounter. The addition of calcium allows both heads of myosin Va.ADP to bind actin strongly. Calcium accelerates ADP binding to actomyosin independent of the tail but minimally affects ATP binding. Although 18O exchange and product release measurements favor a mechanism in which actin-activated Pi release from myosin Va is very rapid, independent of calcium and the tail domain, both heads do not bind actin strongly during steady-state cycling, as assayed by pyrene actin fluorescence. In the absence of calcium, inclusion of ADP favors formation of a long lived myosin Va.ADP state that releases ADP slowly, even after mixing with actin. Our results suggest that calcium activates myosin Va by allowing both heads to interact with actin and exchange bound nucleotide and indicate that regulation of actin binding by the tail is a nucleotide-dependent process favored by linked conformational changes of the motor domain.

Multiple evidence for nucleotide metabolism in the chloroplast thylakoid lumen.

The apparatus of photosynthetic energy conversion in chloroplasts is quite well characterized with respect to structure and function. Light-driven electron transport in the thylakoid membrane is coupled to synthesis of ATP, used to drive energy-dependent metabolic processes in the stroma and the outer surface of the thylakoid membrane. The role of the inner (luminal) compartment of the thylakoids has, however, remained largely unknown although recent proteomic analyses have revealed the presence of up to 80 different proteins. Further, there are no reports concerning the presence of nucleotides in the thylakoid lumen. Here, we bring three lines of experimental evidence for nucleotide-dependent processes in this chloroplast compartment. (i) The thylakoid lumen contains a protein of 17.2 kDa, catalyzing the transfer of the gamma-phosphate group from ATP to GDP, proposed to correspond to the nucleoside diphosphate kinase III. (ii) The 33-kDa subunit of photosystem II, bound to the luminal side of the thylakoid membrane and associated with the water-splitting process, can bind GTP. (iii) The thylakoid membrane contains a nucleotide transport system that is suggested to be associated with a 36.5-kDa nucleotide-binding protein. Our results imply, against current dogmas, that the thylakoid lumen contains nucleotides, thereby providing unexpected aspects on this chloroplast compartment from a metabolic and regulatory perspective and expanding its functional significance beyond a pure bioenergetic function.

Annexins as Neuroprotective Agents in the Central Nervous System

In the past ten years, experimental observations have accumulated that annexins, forming a family of homologous Ca2+- and membrane-binding proteins and represented in mammalian tissues by 12 subfamilies, are expressed in the central nervous system (CNS). Here, they exhibit multiple functions, including the role of neuroprotective agents. It was found that annexins may be related to some CNS pathologies and disorders. In addition, in vitro, they were found to bind neurotransmitter precursors and nucleotides. The nucleotide-binding properties of annexins included GTP-induced calcium channel activity. These properties suggest that some annexin isoforms may play the role of a coupling factor between calcium homeostasis and cellular metabolism in neurons and neuroendocrine cells, especially in light of the observation that annexins participate in nucleotide-dependent processes, such as vesicular transport in neurotransmitter release, and they also interact with nucleotide-binding proteins in brain.

Postsynaptic application of a cAMP analogue reverses long-term potentiation in hippocampal CA1 pyramidal neurons.

The molecular mechanisms that underlie the maintenance of long-term potentiation (LTP) remain unclear. We have examined the influence of postsynaptic cAMP-dependent processes on LTP maintenance in CA1 hippocampal cells. After LTP induction, drugs affecting cAMP-dependent processes were perfused into the cell through a patch pipette. A cAMP analogue, Rp-cAMPS (4 mM), dramatically decreased the amplitude of potentiated synaptic responses. The amplitude of responses in the control pathway was also decreased but to a lesser extent, indicating a specific effect on the potentiation process. This specific effect was not due to the larger amplitude of potentiated responses, was not use-dependent and, unlike other factors that affect LTP maintenance, did not depend on the delay (2, 10, or 25 min) of drug application after LTP induction. Lower concentrations of Rp-cAMPS (1.0 and 0.4 mM) also produced an inhibitory effect but reduced the LTP and control pathways comparably. One possible action of Rp-cAMPS is competitive inhibition of protein kinase A (PKA). Surprisingly, a potent and noncompetitive PKA inhibitor, regulatory type II subunit of PKA, produced only a weak depression of potentiated and control responses indicating there must be other targets for Rp-cAMPS. Moreover, Sp-8-OH-cAMPS, which is an activator of PKA, and Rp-8-OH-cAMPS, which is a weak inhibitor of PKA, both produced effects similar to those of Rp-cAMPS. We conclude that there are postsynaptic cyclic nucleotide-dependent processes that can specifically alter the mechanisms that maintain LTP and that are not primarily dependent on PKA.

Pseudechetoxin: a peptide blocker of cyclic nucleotide-gated ion channels.

Ion channels activated by the binding of cyclic nucleotides first were discovered in retinal rods where they generate the cell's response to light. In other systems, however, it has been difficult to unambiguously determine whether cyclic nucleotide-dependent processes are mediated by protein kinases, their classical effector enzymes, or cyclic nucleotide-gated (CNG) ion channels. Part of this difficulty has been caused by the lack of specific pharmacological tools. Here we report the purification from the venom of the Australian King Brown snake of a peptide toxin that inhibits current through CNG channels. This toxin, which we have named Pseudechetoxin (PsTx), was purified by cation exchange and RP-HPLC and has a molecular mass of about 24 kDa. When applied to the extracellular face of membrane patches containing the alpha-subunit of the rat olfactory CNG channel, PsTx blocked the cGMP-dependent current with a Ki of 5 nM. Block was independent of voltage and required only a single molecule of toxin. PsTx also blocked CNG channels containing the bovine rod alpha-subunit with high affinity (100 nM), but it was less effective on the heteromeric version of the rod channel (Ki approximately 3 microM). We have obtained N-terminal and partial internal sequence data and the amino acid composition of PsTx. These data indicate that PsTx is a basic protein that exhibits some homology with helothermine, a toxin isolated from the venom of the Mexican beaded lizard. PsTx promises to be a valuable pharmacological tool for studies on the structure and physiology of CNG channels.

Conformationally variable Rab protein surface regions mapped by limited proteolysis and homology modelling.

Tryptic proteolysis of the small GTPases Rab4 and Rab5 is a multi-step, nucleotide-dependent process. Using N-terminal peptide sequencing, matrix-assisted laser desorption ionization-time-of-flight MS and molecular modelling, we identified the three initial sites of proteolysis in Rab5 as Arg-4, Arg-81 and Arg-197. Arg-4 and Arg-81 lie within regions previously implicated in Rab5 endocytic function, and Arg-197 lies in a region involved in membrane targeting. Topologically, Arg-81 lies within the conformationally variable Switch II region shown to be important for protein-protein interactions of other GTPases. Homology modelling studies on Rab5 indicate that the Arg-81 side chain is buried in the Rab5 GTP conformation, but is solvent-accessible in the GDP conformation, explaining the dependence of proteolysis on nucleotides. Peptide mapping of Rab4 was performed to take advantage of additional scissile bonds within Switch II to determine more precisely the limits of the nucleotide-dependent protease-accessible region. The Rab4 cleavage sites corresponded to Arg-81 and Pro-87 of Rab5, and taken together with the finding that Rab5 was not cleaved at Arg-91 this analysis defines an eight-residue surface-exposed conformationally variable region lying in the centre of Switch II. A sequence comparison of Rab proteins shows these eight residues to have a loosely conserved motif that we term Switch II(v) for its relative variability. C-terminal to Switch II(v) is a highly conserved Rab-specific YYRGA motif that we term Switch II(c) for its constant sequence. N-terminal to Switch II(v) is a sequence-invariant G-domain involved in nucleotide binding and hydrolysis. We propose that the Rab Switch II(v) region imparts specificity to nucleotide-dependent protein-protein interactions.

The effect of inhibitors of free radical generating-enzymes on low-density lipoprotein oxidation by macrophages

Oxidised low-density lipoprotein (LDL) produced by the action of arterial cells, including macrophages, has been implicated in atherosclerosis. We have investigated the effect of inhibitors of various cellular free-radical generating enzymes on macrophage-mediated LDL oxidation. Xanthine oxidase and nitric oxide synthase are not responsible for LDL modification by resident mouse peritoneal macrophages. Eicosatetraynoic acid, a lipoxygenase inhibitor, produced a dose-dependent irreversible inhibition of macrophage modification of LDL, but at concentrations rather close to those toxic to the cells. Diphenyl and diphenylene iodonium, NADPH oxidase and mitochondrial electron transport inhibitors, inhibited macrophage oxidation of LDL, at concentrations that were not obviously toxic. This suggests that NAPDH oxidase, or some other flavin nucleotide-dependent process, may be involved in LDL oxidation by macrophages. Wortmannin and thiopropionic acid dilauryl ester did not inhibit LDL oxidation, suggesting that inhibition of NADPH oxidase may not be the means by which the iodonium compounds inhibit LDL oxidation. Macrophages from C3H/HeJ mice, which lack receptors for lipopolysaccharide, modified LDL normally, suggesting that the inadvertent priming of resident macrophages by traces of lipopolysaccharide bound to LDL was not involved in LDL oxidation.

Adrenergic stimulation of sea urchin sperm cells.

The noradrenergic agonists norepinephrine and isoproterenol elicit greater stimulatory swimming responses in sea urchin spermatozoa than epinephrine. The beta-blocker atenolol induces an even greater motile rate, while the alpha-blocker phentolamine has only a moderate effect, it also causes a minimal reduction in the sperm cells' response to atenolol. Caffeine increases the motility but to a lesser degree than 8-Br-cAMP. In drug interaction assays, both caffeine and 8-Br-cAMP depress the adrenergic effects. Agents that affect access of calcium to the flagellar apparatus (verapamil and trifluoperazine) depress the motility below the level of the controls when incubated separately with the sperm suspensions and counteract the stimulation due to atenolol. Adrenergic modulation of sperm motility thus appears to be both a calcium-dependent and a cyclic nucleotide-dependent process.

Calcitonin gene-related peptide stimulates adenylate cyclase activation via a guanine nucleotide-dependent process in rat liver plasma membranes.

To evaluate the functional relationship between the liver calcitonin gene-related peptide (CGRP) receptor and guanine nucleotide-binding proteins, we investigated the effects of nucleotides not only on adenylate cyclase activation by CGRP, but also on 125I-[Tyr0]rat CGRP binding to rat liver plasma membranes. In the presence of GTP, rat CGRP stimulated adenylate cyclase activity in a dose-dependent manner in rat liver plasma membranes, and this effect was reduced in the absence of GTP. Salmon calcitonin also enhanced adenylate cyclase activation in the presence of GTP, but only in higher concentrations. On the other hand, guanine nucleotides not only decreased 125I-[Tyr0]rat CGRP binding to rat liver plasma membranes, but also accelerated the dissociation of label binding, and the removal of Mg2+ from incubation medium attenuated this inhibitory action of GTP on 125I-[Tyr0]rat CGRP binding to membranes. Scatchard analysis of the data revealed that the reduction of 125I-[Tyr0]rat CGRP binding by GTP was due to the decrease in binding affinity without a significant change in binding capacity. These findings lead us to conclude that binding of CGRP to its receptors activates adenylate cyclase in rat liver plasma membranes via a guanine nucleotide-dependent process, suggesting the involvement of guanine nucleotide-binding stimulatory protein in the action of CGRP.

Guanine nucleotide effects on catecholamine secretion from digitonin-permeabilized adrenal chromaffin cells.

The nonhydrolyzable GTP analogue guanosine 5'-(beta, gamma-imido)triphosphate (GMP-PNP) produced an ATP-dependent but Ca2+-independent stimulation of [3H]norepinephrine release from permeabilized chromaffin cells. This stimulation of secretion was 25-35% of the secretion induced by 10 microM Ca2+. A similar Ca2+-independent stimulation was produced by other non-hydrolyzable GTP analogues. No effect was seen with a variety of other nucleotides, including GTP. The GMP-PNP effect was specifically inhibited by low concentrations of guanine nucleotides. Addition of cAMP did not mimic the Ca2+-independent GMP-PNP effect, but did slightly enhance Ca2+-dependent secretion. Pretreatment with pertussis toxin had no effect on Ca2+-dependent secretion or on the GMP-PNP effect. There was no detectable diglyceride or inositol phosphate produced during GMP-PNP treatment, and addition of diglyceride and inositol trisphosphate did not induce secretion. Guanosine 5'-(beta-thio)diphosphate (GDP-beta-S), in addition to its ability to inhibit the GMP-PNP effect, partially inhibited Ca2+-dependent secretion. At 10 microM free Ca2+, the effects of GMP-PNP and Ca2+ were nonadditive. In fact, secretion in the presence of both GMP-PNP and 10 microM Ca2+ was slightly less than secretion due to Ca2+ alone. These data suggest that a guanine nucleotide-dependent process interacts in some way with one or more components of the normal Ca2+-dependent secretory pathway. However, it may not be an intrinsic part of the mechanism underlying Ca2+-dependent secretion.

New photoactivatable cyclic nucleotides produce intracellular jumps in cyclic AMP and cyclic GMP concentrations.

The cyclic nucleotides cyclic AMP and cyclic GMP are important intracellular messengers mediating the responses to neurotransmitters and neurohormones and regulating cellular function over a wide range of time scales. Despite the widespread acceptance of this second messenger mechanism in many systems, much remains unknown about their mechanism of action, except that such events are associated with increases or decreases in intracellular cyclic nucleotides. Quantitative descriptions of cyclic nucleotide-dependent processes are hampered by the absence of a means by which intracellular cyclic nucleotide concentrations can be accurately controlled. We have now designed, synthesized and characterized new, substituted photolabile cyclic nucleotide analogues, the 4,5-dimethoxy-2-nitrobenzyl esters of cyclic AMP and cyclic GMP (Fig. 1), which are physiologically inert before irradiation and which liberate free cyclic AMP or cyclic GMP on absorption of a photon. The thermal properties and photolysis rates and efficiencies of light-induced release of cyclic nucleotides from these analogues are more favourable than for the simple o-nitrobenzyl derivatives used previously. These molecules should permit intracellular "concentration jumps' of cyclic AMP or cyclic GMP to be produced in cells under physiological investigation with spatial and temporal resolution unmatched by conventional techniques.

Evolutionary aspects of the biological action of cyclic nucleotides

This paper describes the wide variety of functions of cyclic nucleotides in living organisms. Modifications in cyclic AMP function during the process of evolution from primitive unicellular organisms to highly organized multicellular systems are considered. Studies with a synchronous eukaryotic cell culture permit us to estimate changes in the cyclic nucleotide content throughout the cell cycle as well as in the activity of the enzymes related to cyclic nucleotides and their metabolism. The antimitogenic role of cyclic nucleotides during the period prior to mitosis is elucidated, and the cyclic nucleotide-dependent processes, in particular phosphorylation of nuclear proteins, are shown to be characteristic only of early stages of the cell cycle. Other studies on the role and significance of cyclic nucleotides in systems of multiple biological mediators are reviewed.

Enterotoxins of escherichia coli and epilepsy

Evidence exists that cyclic nucleotides play an important role in the stabilisation of developing synapses during the early postnatal period, and later on participate in the generation of the slow excitatory and inhibitory postsynaptic potentials. It is postulated that enterotoxins of Escherichia coli, due to their long-lasting and specific action on cyclic nucleotide-dependent processes, provide a unique mechanism for selective impairment of synaptogenesis in the abscence of cell loss. Therefore it seems possible that early enteritis, when caused by certain pathogenic strains of Escherichia coli, might be an aetiological factor in the genesis of idiopathic epilepsy.