Structural characterization of the self-association of the death domain of p75(NTR.)

Natural Products for Neurodegeneration: Regulating Neurotrophic Signals

Neurodegenerative disorders (NDs) are heterogeneous groups of ailments typically characterized by progressive damage of the nervous system. Several drugs are used to treat NDs but they have only symptomatic benefits with various side effects. Numerous researches have been performed to prove the advantages of phytochemicals for the treatment of NDs. Furthermore, phytochemicals such as polyphenols might play a pivotal role in rescue from neurodegeneration due to their various effects as anti-inflammatory, antioxidative, and antiamyloidogenic agents by controlling apoptotic factors, neurotrophic factors (NTFs), free radical scavenging system, and mitochondrial stress. On the other hand, neurotrophins (NTs) including nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), NT4/5, and NT3 might have a crucial neuroprotective role, and their diminution triggers the development of the NDs. Polyphenols can interfere directly with intracellular signaling molecules to alter brain activity. Several natural products also improve the biosynthesis of endogenous genes encoding antiapoptotic Bcl-2 as well as NTFs such as glial cell and brain-derived NTFs. Various epidemiological studies have demonstrated that the initiation of these genes could play an essential role in the neuroprotective function of dietary compounds. Hence, targeting NTs might represent a promising approach for the management of NDs. In this review, we focus on the natural product-mediated neurotrophic signal-modulating cascades, which are involved in the neuroprotective effects.

Revising the mechanism of p75NTR activation: intrinsically monomeric state of death domains invokes the "helper" hypothesis

The neurotrophin receptor p75NTR plays crucial roles in neuron development and regulates important neuronal processes like degeneration, apoptosis and cell survival. At the same time the detailed mechanism of signal transduction is unclear. One of the main hypotheses known as the snail-tong mechanism assumes that in the inactive state, the death domains interact with each other and in response to ligand binding there is a conformational change leading to their exposure. Here, we show that neither rat nor human p75NTR death domains homodimerize in solution. Moreover, there is no interaction between the death domains in a more native context: the dimerization of transmembrane domains in liposomes and the presence of activating mutation in extracellular juxtamembrane region do not lead to intracellular domain interaction. These findings suggest that the activation mechanism of p75NTR should be revised. Thus, we propose a novel model of p75NTR functioning based on interaction with "helper" protein.

Death domain of p75 neurotrophin receptor: a structural perspective on an intracellular signalling hub

The death domain (DD) is a globular protein motif with a signature feature of an all-helical Greek-key motif. It is a primary mediator of a variety of biological activities, including apoptosis, cell survival and cytoskeletal changes, which are related to many neurodegenerative diseases, neurotrauma, and cancers. DDs exist in a wide range of signalling proteins including p75 neurotrophin receptor (p75^NTR ), a member of the tumour necrosis factor receptor superfamily. The specific signalling mediated by p75^NTR in a given cell depends on the type of ligand engaging the extracellular domain and the recruitment of cytosolic interactors to the intracellular domain, especially the DD, of the receptor. In solution, the p75^NTR -DDs mainly form a symmetric non-covalent homodimer. In response to extracellular signals, conformational changes in the p75^NTR extracellular domain (ECD) propagate to the p75^NTR -DD through the disulfide-bonded transmembrane domain (TMD) and destabilize the p75^NTR -DD homodimer, leading to protomer separation and exposure of binding sites on the DD surface. In this review, we focus on recent advances in the study of the structural mechanism of p75^NTR -DD signalling through recruitment of diverse intracellular interactors for the regulation and control of diverse functional outputs.

Structural Characterization of the p75 Neurotrophin Receptor: A Stranger in the TNFR Superfamily

Although p75 neurotrophin receptor (p75^NTR) was the founding member of the tumor necrosis factor (TNF) receptor superfamily (TNFRSF), it is an atypical TNFRSF protein. p75^NTR like TNF-R1 and Fas-R contain an extracellular domain with four cysteine-rich domains (CRD) and a death domain (DD) in the intracellular region. While TNFRSF proteins are activated by trimeric TNFSF ligands, p75^NTR forms dimers activated by dimeric neurotrophins that are structurally unrelated to TNFSF proteins. In addition, although p75^NTR shares with other members the interaction with the TNF receptor-associated factors to activate the NF-κB and cell death pathways, p75^NTR does not interact with the DD-containing proteins FADD, TRADD, or MyD88. By contrast, the DD of p75^NTR is able to recruit several protein interactors via a full catalog of DD interactions not described before in the TNFRSF. p75-DD forms homotypic symmetrical DD-DD complexes with itself and with the related p45-DD; forms heterotypic DD-CARD interactions with the RIP2-CARD domain, and forms a new interaction between a DD and RhoGDI. All these features, in addition to its promiscuous interactions with several ligands and coreceptors, its processing by α- and γ-secretases, the dimeric nature of its transmembrane domain and its "special" juxtamembrane region, make p75^NTR a truly stranger in the TNFR superfamily. In this chapter, I will summarize the known structural aspects of p75^NTR and I will analyze from a structural point of view, the similitudes and differences between p75^NTR and the other members of the TNFRSF.

NMR Dynamics of Transmembrane and Intracellular Domains of p75NTR in Lipid-Protein Nanodiscs

P75NTR is a type I integral membrane protein that plays a key role in neurotrophin signaling. However, structural data for the receptor in various functional states are sparse and controversial. In this work, we studied the spatial structure and mobility of the transmembrane and intracellular parts of p75NTR, incorporated into lipid-protein nanodiscs of various sizes and compositions, by solution NMR spectroscopy. Our data reveal a high level of flexibility and disorder in the juxtamembrane chopper domain of p75NTR, which results in the motions of the receptor death domain being uncoupled from the motions of the transmembrane helix. Moreover, none of the intracellular domains of p75NTR demonstrated a propensity to interact with the membrane or to self-associate under the experimental conditions. The obtained data are discussed in the context of the receptor activation mechanism.

Structural basis of death domain signaling in the p75 neurotrophin receptor

Death domains (DDs) mediate assembly of oligomeric complexes for activation of downstream signaling pathways through incompletely understood mechanisms. Here we report structures of complexes formed by the DD of p75 neurotrophin receptor (p75^NTR) with RhoGDI, for activation of the RhoA pathway, with caspase recruitment domain (CARD) of RIP2 kinase, for activation of the NF-kB pathway, and with itself, revealing how DD dimerization controls access of intracellular effectors to the receptor. RIP2 CARD and RhoGDI bind to p75^NTR DD at partially overlapping epitopes with over 100-fold difference in affinity, revealing the mechanism by which RIP2 recruitment displaces RhoGDI upon ligand binding. The p75^NTR DD forms non-covalent, low-affinity symmetric dimers in solution. The dimer interface overlaps with RIP2 CARD but not RhoGDI binding sites, supporting a model of receptor activation triggered by separation of DDs. These structures reveal how competitive protein-protein interactions orchestrate the hierarchical activation of downstream pathways in non-catalytic receptors.

DOI:http://dx.doi.org/10.7554/eLife.11692.001

Cells have proteins called receptors on their surface that can bind to specific molecules on the outside of the cell. Typically, this binding activates the receptor and the activated receptor then triggers some biochemical changes inside the cell. For many receptors, the portion of the receptor inside the cell is essentially an enzyme that can trigger a biochemical change by itself. Some receptors, however, lack any enzymatic activity, and it is often unclear how these ‘non-catalytic receptors’ trigger changes inside a cell.

A protein called p75 neurotrophin receptor (or p75^NTR for short) is a non-catalytic receptor that is expressed when neurons are injured and its activity leads to the death of the neurons and related cells. Inhibiting this non-catalytic receptor is an attractive strategy for limiting the damage caused by diseases of the nervous system. However, the molecular mechanisms behind the activity of p75^NTR are not well understood.

Previous biochemical studies set out to answer the question of how p75^NTR engages with components of the signaling machinery inside the cell, and found several components that interact with this receptor. Now, Lin et al. have tried to gain a more detailed understanding of those interactions at a molecular level. This involved solving the three-dimensional structures of three protein complexes that involve part of p75^NTR (called the “death domain”) and one of two signaling components (called RhoGDI and RIP2).

Two of the protein complexes showed that RIP2 and RhoGDI bind to the receptor’s death domain at partially overlapping sites, although RIP2 binds about 100 times more strongly than RhoGDI.A third protein complex showed an interaction between two copies of the death domain, which involves a surface of the receptor that overlaps with RIP2’s, but not RhoGDI’s, binding site.

These structures, together with the results of other experiments, allowed Lin et al. to propose a model that could explain how p75^NTR is activated. First, the two death domains must be separated. Next, RIP2 is recruited to the receptor, and outcompetes and displaces RhoGDI. This change in protein-protein interactions switches the receptor’s signaling from one pathway to the other. Now that these structures are available, they can be used in future experiments to design specific changes in the receptor that would allow researchers to dissect its different activities.

DOI:http://dx.doi.org/10.7554/eLife.11692.002

Myelin-associated glycoprotein modulates apoptosis of motoneurons during early postnatal development via NgR/p75(NTR) receptor-mediated activation of RhoA signaling pathways

Myelin-associated glycoprotein (MAG) is a minor constituent of nervous system myelin, selectively expressed on the periaxonal myelin wrap. By engaging multiple axonal receptors, including Nogo-receptors (NgRs), MAG exerts a nurturing and protective effect the axons it ensheaths. Pharmacological activation of NgRs has a modulatory role on p75^NTR-dependent postnatal apoptosis of motoneurons (MNs). However, it is not clear whether this reflects a physiological role of NgRs in MN development. NgRs are part of a multimeric receptor complex, which includes p75^NTR, Lingo-1 and gangliosides. Upon ligand binding, this multimeric complex activates RhoA/ROCK signaling in a p75^NTR-dependent manner. The aim of this study was to analyze a possible modulatory role of MAG on MN apoptosis during postnatal development. A time course study showed that Mag-null mice suffer a loss of MNs during the first postnatal week. Also, these mice exhibited increased susceptibility in an animal model of p75^NTR-dependent MN apoptosis induced by nerve-crush injury, which was prevented by treatment with a soluble form of MAG (MAG-Fc). The protective role of MAG was confirmed in in vitro models of p75^NTR-dependent MN apoptosis using the MN1 cell line and primary cultures. Lentiviral expression of shRNA sequences targeting NgRs on these cells abolished protection by MAG-Fc. Analysis of RhoA activity using a FRET-based RhoA biosensor showed that MAG-Fc activates RhoA. Pharmacological inhibition of p75^NTR/RhoA/ROCK pathway, or overexpression of a p75^NTR mutant unable to activate RhoA, completely blocked MAG-Fc protection against apoptosis. The role of RhoA/ROCK signaling was further confirmed in the nerve-crush model, where pretreatment with ROCK inhibitor Y-27632 blocked the pro-survival effect of MAG-Fc. These findings identify a new protective role of MAG as a modulator of apoptosis of MNs during postnatal development by a mechanism involving the p75^NTR/RhoA/ROCK signaling pathway. Also, our results highlight the relevance of the nurture/protective effects of myelin on neurons.

Heterodimerization of p45-p75 modulates p75 signaling: structural basis and mechanism of action

The formation of a p45-p75 heterodimer overrides p75’s inhibition of nerve regeneration by stopping p75 homodimers from forming and creating a complex with the Nogo receptor.

The p75 neurotrophin receptor, a member of the tumor necrosis factor receptor superfamily, is required as a co-receptor for the Nogo receptor (NgR) to mediate the activity of myelin-associated inhibitors such as Nogo, MAG, and OMgp. p45/NRH2/PLAIDD is a p75 homologue and contains a death domain (DD). Here we report that p45 markedly interferes with the function of p75 as a co-receptor for NgR. P45 forms heterodimers with p75 and thereby blocks RhoA activation and inhibition of neurite outgrowth induced by myelin-associated inhibitors. p45 binds p75 through both its transmembrane (TM) domain and DD. To understand the underlying mechanisms, we have determined the three-dimensional NMR solution structure of the intracellular domain of p45 and characterized its interaction with p75. We have identified the residues involved in such interaction by NMR and co-immunoprecipitation. The DD of p45 binds the DD of p75 by electrostatic interactions. In addition, previous reports suggested that Cys257 in the p75 TM domain is required for signaling. We found that the interaction of the cysteine 58 of p45 with the cysteine 257 of p75 within the TM domain is necessary for p45–p75 heterodimerization. These results suggest a mechanism involving both the TM domain and the DD of p45 to regulate p75-mediated signaling.

Injuries to the brain and spinal cord often result in paralysis due to the fact that the injured nerves cannot regrow to reach their normal targets and carry out their functions. At the injury sites, there are proteins released from the damaged myelin that bind the Nogo receptor (NgR) on the nerve and inhibit its regeneration. The NgR needs to form a complex with the p75 neurotrophin receptor in order to mediate this inhibitory signal. Here we found that p45, a homologue of p75, can also bind to p75 and block its inhibitory activity when overexpressed. To perform its function, p75 needs to dimerize through both its transmembrane and intracellular domains, facilitating the recruitment of several proteins. Our structural and functional studies show that p45 binds specifically to conserved regions in the p75 transmembrane and the intracellular domain and that this blocks p75 dimerization along with its downstream signaling. Thus, this study demonstrates that altering the oligomerization of p75 is a good strategy to override p75's inhibitory effects on nerve regeneration, and it opens the door for the design of specific p75 inhibitors for therapeutic applications.

Structural features of the Nogo receptor signaling complexes at the neuron/myelin interface

Upon spinal cord injury, the central nervous system axons are unable to regenerate, partially due to the repulsive action of myelin inhibitors, such as the myelin-associated glycoprotein (MAG), Nogo-A and the oligodendrocyte myelin glycoprotein (OMgp). These inhibitors bind and signal through a single receptor/co-receptor complex that comprises of NgR1/LINGO-1 and either p75 or TROY, triggering intracellular downstream signaling that impedes the re-growth of axons. Structure-function analysis of myelin inhibitors and their neuronal receptors, particularly the NgRs, have provided novel information regarding the molecular details of the inhibitor/receptor/co-receptor interactions. Structural and biochemical studies have revealed the architecture of many of these proteins and identified the molecular regions important for assembly of the inhibitory signaling complexes. It was also recently shown that gangliosides, such as GT1b, mediate receptor/co-receptor binding. In this review, we highlight these studies and summarize our current understanding of the multi-protein cell-surface complexes mediating inhibitory signaling events at the neuron/myelin interface.