Detection of ATP-binding to growth factors

ATP binding to Nerve Growth Factor (NGF) and pro-Nerve Growth Factor (proNGF): an endogenous molecular switch modulating neurotrophins activity

ATP has recently been reconsidered as a molecule with functional properties which go beyond its recognized role of the energetic driver of the cell. ATP has been described as an allosteric modulator as well as a biological hydrotrope with anti-aggregation properties in the crowded cellular environment. The role of ATP as a modulator of the homeostasis of the neurotrophins (NTs), a growth factor protein family whose most known member is the nerve growth factor (NGF), has been investigated. The modulation of NTs by small endogenous ligands is still a scarcely described area, with few papers reporting on the topic, and very few reports on the molecular determinants of these interactions. However, a detailed atomistic description of the NTs interaction landscape is of urgent need, aiming at the identification of novel molecules as potential therapeutics and considering the wide range of potential pharmacological applications for NGF and its family members. This mini-review will focus on the unique cartography casting the interactions of the endogenous ligand ATP, in the interaction with NGF as well as with its precursor proNGF. These interactions revealed interesting features of the ATP binding and distinct differences in the binding mode between the highly structured mature NGF and its precursor, proNGF, which is characterized by an intrinsically unstructured domain. The overview on the recent available data will be presented, together with the future perspectives on the field.

Small Endogenous Ligands Modulation of Nerve Growth Factor Bioactivity: A Structural Biology Overview

Experiments with cell cultures and animal models have provided solid support for the assumption that Nerve Growth Factor (NGF) plays a key role in the regulation of neuronal cell survival and death. Recently, endogenous ligands have been proposed as physiological modulators of NGF biological activity as part of this regulatory cascade. However, the structural and mechanistic determinants for NGF bioactivity remain to be elucidated. We recently unveiled, by an integrated structural biology approach, the ATP binding sites of NGF and investigated the effects on TrkA and p75^NTR receptors binding. These results pinpoint ATP as a genuine endogenous modulator of NGF signaling, paving the way to the characterization of not-yet-identified chemical diverse endogenous biological active small molecules as novel modulators of NGF. The present review aims at providing an overview of the currently available 3D structures of NGF in complex with different small endogenous ligands, featuring the molecular footprints of the small molecules binding. This knowledge is essential for further understanding the functional role of small endogenous ligands in the modulation of neurotrophins signaling in physiological and pathological conditions and for better exploiting the therapeutic potentialities of NGF.

Endogenous modulators of neurotrophin signaling: Landscape of the transient ATP-NGF interactions

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High-resolution solution NMR structure of rhNGF has been determined.

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Quinary interactions characterize ATP binding to rhNGF.

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SPR, ITC and STD-NMR reveal ATP binding to rhNGF with mM affinity.

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NMR and MD analysis pinpoint to the presence of two binding sites of ATP on rhNGF.

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Stoichiometry of ATP-Mg²⁺ or Zn²⁺-rhNGF mixtures affects K_D affinity to TrkA/p75^NTR.

The Nerve Growth Factor (NGF) neurotrophin acts in the maintenance and growth of neuronal populations. Despite the detailed knowledge of NGF’s role in neuron physiology, the structural and mechanistic determinants of NGF bioactivity modulated by essential endogenous ligands are still lacking. We present the results of an integrated structural and advanced computational approach to characterize the extracellular ATP-NGF interaction. We mapped by NMR the interacting surface and ATP orientation on NGF and revealed the functional role of this interaction in the binding to TrkA and p75^NTR receptors by SPR. The role of divalent ions was explored in conjunction with ATP. Our results pinpoint ATP as a likely transient molecular modulator of NGF signaling, in health and disease states.

Applying mass spectrometry to study non-covalent biomolecule complexes

Non-covalent interactions are essential for the structural organization of biomacromolecules and play an important role in molecular recognition processes, such as the interactions between proteins, glycans, lipids, DNA, and RNA. Mass spectrometry (MS) is a powerful tool for studying of non-covalent interactions, due to the low sample consumption, high sensitivity, and label-free nature. Nowadays, native-ESI MS is heavily used in studies of non-covalent interactions and to understand the architecture of biomolecular complexes. However, MALDI-MS is also becoming increasingly useful. It is challenging to detect the intact complex without fragmentation when analyzing non-covalent interactions with MALDI-MS. There are two methodological approaches to do so. In the first approach, different experimental and instrumental parameters are fine-tuned in order to find conditions under which the complex is stable, such as applying non-acidic matrices and collecting first-shot spectra. In the second approach, the interacting species are "artificially" stabilized by chemical crosslinking. Both approaches are capable of studying non-covalently bound biomolecules even in quite challenging systems, such as membrane protein complexes. Herein, we review and compare native-ESI and MALDI MS for the study of non-covalent interactions.

Neural Stem Cells Rescue Cognitive and Motor Dysfunction in a Transgenic Model of Dementia with Lewy Bodies through a BDNF-Dependent Mechanism

Accumulation of α-synuclein (α-syn) into insoluble aggregates occurs in several related disorders collectively referred to as synucleinopathies. To date, studies have used neural stem cells (NSCs) to examine questions about α-syn propagation, but have overlooked the therapeutic potential of NSC transplantation to modulate cognition in disorders such as dementia with Lewy bodies or Parkinson’s disease dementia. Here, we show that striatal transplantation of NSCs into aged α-syn transgenic mice significantly improves performance in multiple cognitive and motor domains. This recovery is associated with NSC expression of brain-derived neurotrophic factor (BDNF), which restores depleted levels and modulates dopaminergic and glutamatergic systems. Most importantly, transplantation of BDNF-depleted NSCs fails to improve behavior, whereas AAV-mediated BDNF delivery mimics the benefits of NSC transplantation, supporting a critical role for this neurotrophin in functional improvement. Thus, NSC transplantation could offer a promising approach to treat the understudied yet devastating cognitive components of many synucleinopathies.

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α-Synuclein mice exhibit significant DLB/PDD-associated cognitive and motor deficits

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Striatal NSC transplantation dramatically improves cognitive and motor function

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BDNF is necessary for NSC-mediated behavioral improvements

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NSC-BDNF promotes recovery by regulating dopaminergic and glutamatergic systems

Foscarnet reduces FGF2-induced proliferation of human umbilical vein endothelial cells and has antineoplastic activity against human anaplastic thyroid carcinoma cells

In contrast to many reports dealing with inhibitors of growth factor receptors like VEGF or FGFR, only few reports of low molecular weight inhibitors, which are directed against growth factors itself, are known. Here, foscarnet, an antiviral drug which inhibits several viral DNA polymerases by mimic pyrophosphate of nucleotides, was identified to interact with fibroblast growth factor 2 and stabilize the growth factor against tryptic digestion similar like the non-nitrogen containing bisphosphonates clodronate and etidronate that we have reported just recently as inhibitors of FGF-induced cell proliferation. Foscarnet competes with ATP against the binding on fibroblast growth factor 2 at the heparin/ATP-binding domain. This indicates binding of foscarnet at the heparin-binding domain of FGF2. This interaction of foscarnet with fibroblast growth factor 2 reduces FGF2-induced proliferation of human umbilical vein endothelial cells and intracellular signaling via ERK1/2 kinases in this cell line. Additionally, foscarnet reduces in a dose-dependent manner proliferation of CAL-62 cells that belong to anaplastic thyroid carcinoma, a rare but lethal type of thyroid cancer that expresses FGF2.

Nerve growth factor and brain-derived neurotrophic factor but not granulocyte colony-stimulating factor, nimodipine and dizocilpine, require ATP for neuroprotective activity after oxygen-glucose deprivation of primary neurons

In previous work, we have demonstrated by radiolabeling, mass spectrometry and site-directed mutagenesis that nerve growth factor (NGF) as well as brain-derived neurotrophic factor (BDNF) and fibroblast growth factor 2 (FGF2) are capable of ATP-binding and that this binding appears to be essential for their neuroprotective activity. In this study, we attempted to shed some light on the question whether ATP is a general prerequisite for neuroprotection. Therefore, we used the non-ATP-binding granulocyte colony-stimulating factor (GCSF), the calcium antagonist nimodipine and the NMDA antagonist dizocilpine to find out whether they need ATP for neuroprotection comparable to NGF and BDNF. However, ATP was not necessary for the neuroprotective effects of GCSF, nimodipine and dizocilpine on primary cultures of rat cortical neurons damaged by oxygen-glucose deprivation whereas neuroprotection was demonstrable for NGF and BDNF only when ATP was present in the culture medium at a concentration higher than ca. 0.4nmol/l. In circular dichroism studies ATP caused changes of the secondary structure of NGF but not of GCSF. Taken together, we suggest that ATP is not a general prerequisite for neuroprotectivity but some growth factors like NGF and BDNF can stimulate their receptors only if they have bound ATP.

ATP-NGF-complex, but not NGF, is the neuroprotective ligand

We have shown previously that nerve growth factor (NGF) requires only low nanomolar ATP concentrations in the cell culture medium to protect cortical rat neurons (CRN) from cellular damage induced by staurosporine (STS). We have also demonstrated before that NGF and other growth factors form stable non-covalent complexes with ATP. Here we demonstrated that 8N(1)ATP-NGF, but not NGF, protected CRN against damage. The photo-reactive ATP derivative 8N(3)ATP was incubated with NGF and was trapped in its position by UV irradiation forming a covalent bond. The cross-link with a molar ratio of 1:1 (8N(1)ATP:NGF) was confirmed by mass spectrometry. Circular dichroism experiments revealed that 8N(1)ATP altered the secondary structure of NGF in the same way as ATP did. Covalently bound 8N(1)ATP-NGF was shown to be stable in the presence of the ATP-hydrolyzing enzyme alkaline phosphatase while the non-covalent ATP-NGF-complex dissociated with the removal of free ATP from the solution. 8N(1)ATP-NGF protected CRN against damage by STS independently of free ATP in the culture medium. These results suggest that the ATP-NGF-complex, but not NGF, is the active ligand.

Binding of ATP to vascular endothelial growth factor isoform VEGF-A165 is essential for inducing proliferation of human umbilical vein endothelial cells

BACKGROUND

ATP binding is essential for the bioactivity of several growth factors including nerve growth factor, fibroblast growth factor-2 and brain-derived neurotrophic factor. Vascular endothelial growth factor isoform 165 (VEGF-A(165)) induces the proliferation of human umbilical vein endothelial cells, however a dependence on ATP-binding is currently unknown. The aim of the present study was to determine if ATP binding is essential for the bioactivity of VEGF-A(165).

RESULTS

We found evidence that ATP binding to VEGF-A(165) induced a conformational change in the secondary structure of the growth factor. This binding appears to be significant at the biological level, as we found evidence that nanomolar levels of ATP (4-8 nm) are required for the VEGF-A(165)-induced proliferation of human umbilical vein endothelial cells. At these levels, purinergic signaling by ATP via P2 receptors can be excluded. Addition of alkaline phosphate to cell culture lowered the ATP concentration in the cell culture medium to 1.8 nM and inhibited cell proliferation.

CONCLUSIONS

We propose that proliferation of endothelial cells is induced by a VEGF-A(165)-ATP complex, rather than VEGF-A(165) alone.

Interaction of ATP with fibroblast growth factor 2: biochemical characterization and consequence for growth factor stability

Background

Fibroblast growth factor 2, a well-characterized heparin-binding growth factor, is involved in many biological processes like embryogenesis, cell proliferation and angiogenesis. However, this growth factor is very unstable and shows rapid degradation in aqueous solution. Beside the well-known stabilization of FGF2 by heparin or heparan sulphate, the recently discovered binding to ATP also shows a stabilizing and protective effect on this growth factor.

Results

Here we determined the dissociation constant of ATP on FGF2 by equilibrium microdialysis (K_D: 59.8 μM) and analyzed the impact of this binding on secondary structure by CD-spectroscopy. ATP-binding to FGF2 significantly changed the secondary structure of this growth factor with a shift to random coil structure elements. We also analyzed the influence of this binding on the stability of FGF2 in aqueous solution over a period of 2 h. While the amount of untreated FGF2 is reduced drastically over this period of time, ATP-binding reduces the degradation considerably.

Conclusions

Taken together, our data suggest an important role of ATP in FGF2-stabilization beside the well known-role of heparin and heparan sulphate.

ATP-dependent stabilization and protection of fibroblast growth factor 2

Fibroblast growth factor 2 (FGF2) plays a pivotal role in cell proliferation, angiogenesis and neuroprotection. Several clinical trials using this growth factor in bone regeneration, wound healing and cardioprotection are initiated but the inadequate stability of FGF2 after application is one major problem. Binding of ATP to FGF2 and other growth factors has been demonstrated recently. Here we report that ATP, other nucleoside triphosphates and sodium triphosphate protect FGF2 from trypsin, plasmin and neutrophile elastase digestion in vitro. A molar ratio of 2:1 (ligand/FGF2) is sufficient for these protective effects. ADP shows only little, AMP no stabilizing effect on FGF2 indicating that the number of phosphate residues is important. Protection of FGF2 by ATP can be abolished by the addition of alkaline phosphatase hydrolyzing free and FGF2-bound ATP. The mutant FGF2 (K128A/R129A/K134A/K144A) with strongly reduced ATP-binding capacity revealed no detectable protease resistance after incubation with ATP. Furthermore, a stabilizing effect of ATP on FGF2 could also be demonstrated in cell culture experiments. ATP bound to FGF2 increased FGF2-dependent human umbilical vein endothelial cells proliferation when the growth factor was treated with neutrophile elastase or heat. For the first time these data demonstrate protection of FGF2 by bound ATP, other nucleoside triphosphates or sodium triphosphate from rapid protease digestion. Our data provide new evidence that nucleoside triphosphates are capable of protecting FGF2 and favours such stabilization for various, especially medical applications.

Binding of ATP to nerve growth factor: characterization and relevance for bioactivity

Growth factors and their mechanisms of action have been studied extensively. However, it remained widely unrecognized that binding of ATP to growth factors is a prerequisite for their bioactivity. Here we demonstrated the binding of ATP to nerve growth factor (NGF) as well as its relevance for neuroprotection. By using mass spectrometry-based methodology we identified one or two molecules of ATP as being bound to NGF. To test neuroprotective activity of NGF we used primary cultures of rat cortical neurons damaged by staurosporine. ATP was indispensable for the neuroprotective effect of NGF. When the ATP concentration in the culture medium was reduced below approximately 2 nM by adding alkaline phosphatase (AP) or ATPase the neuroprotective activity of NGF was abolished. Site-directed mutagenesis within the heparin-binding domain (HBD) of NGF abolished ATP-binding and the neuroprotective effect. Thus, NGF has to bind ATP to be capable of protecting neurons.

Fibroblast growth factor 2 requires complex formation with ATP for neuroprotective activity

The neurotrophic and neuroprotective activity of fibroblast growth factor (FGF2) is well documented. In this study, we attempted to demonstrate that binding of ATP to FGF2 is essential for its neuroprotective effect. Incubation of primary cultures of rat embryonic (E18) cortical neurons with alkaline phosphatase decreased the ATP concentration in the culture medium from about 8 to 0.3 nM measured luminometrically. Reduction of ATP concentration below 1 nM abolished the neuroprotective effect of FGF2. However, when the more stable nucleotide triphosphate gammaS-ATP was used which could not be cleaved by alkaline phosphatase, FGF2 still protected the cultured cortical neurons against damage. In control experiments alkaline phosphatase alone did not influence neuroprotection. In addition, also ATPase and apyrase were used as ATP cleaving enzymes. Added to the culture medium, both enzymes were capable of decreasing ATP below the critical level of approximately 1 nM, and the neuroprotective activity of FGF2 was abolished. Thus, our results demonstrate for the first time that the FGF2/ATP complex but not FGF2 alone mediates neuroprotection.

Mass spectrometry of protein-ligand complexes: enhanced gas-phase stability of ribonuclease-nucleotide complexes

Noncovalent protein-ligand complexes are readily detected by electrospray ionization mass spectrometry (ESI-MS). Ligand binding stoichiometry can be determined easily by the ESI-MS method. The ability to detect noncovalent protein-ligand complexes depends, however, on the stability of the complexes in the gas-phase environment. Solution binding affinities may or may not be accurate predictors of their stability in vacuo. Complexes composed of cytidine nucleotides bound to ribonuclease A (RNase A) and ribonuclease S (RNase S) were detected by ESI-MS and were further analyzed by MS/MS. RNase A and RNase S share similar structures and biological activity. Subtilisin-cleavage of RNase A yields an S-peptide and an S-protein; the S-peptide and S-protein interact through hydrophobic interactions with a solution binding constant in the nanomolar range to generate an active RNase S. Cytidine nucleotides bind to the ribonucleases through electrostatic interactions with a solution binding constant in the micromolar range. Collisionally activated dissociation (CAD) of the 1:1 RNase A-CDP and CTP complexes yields cleavage of the covalent phosphate bonds of the nucleotide ligands, releasing CMP from the complex. CAD of the RNase S-CDP and CTP complexes dissociates the S-peptide from the remaining S-protein/nucleotide complex; further dissociation of the S-protein/nucleotide complex fragments a covalent phosphate bond of the nucleotide with subsequent release of CMP. Despite a solution binding constant favoring the S-protein/S-peptide complex, CDP/CTP remains electrostatically bound to the S-protein in the gas-phase dissociation experiment. This study highlights the intrinsic stability of electrostatic interactions in the gas phase and the significant differences in solution and gas-phase stabilities of noncovalent complexes that can result.

Investigation of non-covalent complexes of glutathione with common amino acids by electrospray ionization mass spectrometry

AIM

To study the non-covalent interaction between glutathione and common amino acids.

METHODS

A stoichiometry of glutathione and common amino acids were mixed to reach the equilibrium, and then the mixed solution was investigated by electrospray ionization mass spectrometry (ESI-MS). The binding of the complexes was further examined by collision-induced dissociation (CID) in a tandem mass spectrometer as well as UV spectroscopy. To avoid distinct ionization efficiency discrepancy and signal suppression in the ESI-MS measurements, the interaction between glutathione (GSH) and glutamate (Glu) was quantitatively evaluated. The total concentrations and series of m/z of peak intensities for glutathione and amino acids could be achieved, respectively. Due to the existence of some oligomeric species arising from glutathione or amino acids, an improved calculation formula was proposed to calculate the dissociation constants of glutathione binding to amino acids.

RESULTS

The ESI mass spectra revealed that glutathione could interact easily with Met, Phe, Tyr, Ser, or Ile to form non-covalent complexes. The binding of the complexes was further confirmed by CID experiments in a tandem mass spectrometer as well as UV spectroscopy. Moreover, an improved calculation formula was successfully applied to determine the dissociation constants of glutathione binding to Glu, His, or Gln. Finally, a possible formation mechanism for the complexes of glutathione with amino acids was proposed.

CONCLUSION

The reduced polypeptide gamma-glutathione can interact with each of 8 common amino acids, including Glu, His, and Gln to form non-covalent complexes with different affinity.

ATP-binding on fibroblast growth factor 2 partially overlaps with the heparin-binding domain

Fibroblast growth factor 2 (FGF2), an intensively studied heparin-binding cytokine, is an important modulator of cell growth and differentiation under both physiological and pathophysiological conditions. It has been shown recently that ATP binds to FGF2 and that this binding is crucial for its biological function. In this study we demonstrated that divalent cations were not necessary for binding of ATP to FGF2, but it could be demonstrated that heparin blocked the labelling of FGF2 with ATP indicating an involvement of the heparin-binding domain (aa 128-144) in ATP-binding. FGF2, bound to Heparin Sepharose, could be eluted with ATP and GTP, but not with cAMP, AMP or ADP. Successive mutation of positively charged amino acid residues located in the heparin-binding domain drastically reduced the signal intensity of [gamma-(32)P]ATP labelled FGF2 indicating that this domain is not only important for heparin binding to FGF2 but also for ATP-binding.