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 (p75NTR) 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 p75NTR 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 p75NTR 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.

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Structural and functional elucidation of NF-κB signaling by the p75 neurotrophin receptor through recruitment of TRADD

10.1101/2021.02.07.430167 ◽

2021 ◽

Author(s):

Ning Zhang ◽

Lilian Kisiswa ◽

Ajeena Ramanujan ◽

Zhen Li ◽

Eunice Weiling Sim ◽

...

Keyword(s):

Intracellular Signaling ◽

Adaptor Protein ◽

Adaptor Proteins ◽

Neurotrophin Receptor ◽

Structural Basis ◽

P75 Neurotrophin Receptor ◽

Death Domain ◽

Structural Mechanism ◽

Downstream Signaling ◽

Developing Neurons

Abstractp75 neurotrophin receptor (p75NTR) is a critical mediator of neuronal death and tissue remodeling and has been implicated in various neurodegenerative diseases. The death domain (DD) of p75NTR is an intracellular signaling hub and has been shown to interact with diverse adaptor proteins. However, the structural mechanism and physiological relevance of the adaptor protein TRADD in neuronal p75NTR signaling remain poorly understood. Here we report an NMR structure of the complex between p75NTR-DD and TRADD-DD and elucidate the structural basis of specific DD recognition in the p75NTR/TRADD signaling pathway. Furthermore, we identify spatiotemporal overlap of p75NTR and TRADD expression in developing cerebellar granule neurons (CGNs) at early postnatal stages and reveal the functional role of TRADD recruitment to p75NTR in the regulation of canonical NF-κB signaling and cell survival in CGNs. Our results provide a new structural framework for understanding how the recruitment of TRADD to p75NTR through DD interactions creates a membrane-proximal platform to propagate downstream signaling in developing neurons.

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Decision letter: Structural basis of death domain signaling in the p75 neurotrophin receptor

10.7554/elife.11692.022 ◽

2015 ◽

Keyword(s):

Neurotrophin Receptor ◽

Structural Basis ◽

P75 Neurotrophin Receptor ◽

Death Domain

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Faculty Opinions recommendation of Structural basis of death domain signaling in the p75 neurotrophin receptor.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.726000533.793512774 ◽

2016 ◽

Author(s):

Mark Bothwell

Keyword(s):

Neurotrophin Receptor ◽

Structural Basis ◽

P75 Neurotrophin Receptor ◽

Death Domain

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Author response: Structural basis of death domain signaling in the p75 neurotrophin receptor

10.7554/elife.11692.023 ◽

2015 ◽

Author(s):

Zhi Lin ◽

Jason Y Tann ◽

Eddy TH Goh ◽

Claire Kelly ◽

Kim Buay Lim ◽

...

Keyword(s):

Author Response ◽

Neurotrophin Receptor ◽

Structural Basis ◽

P75 Neurotrophin Receptor ◽

Death Domain

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Selection of a Peptide Ligand to the p75 Neurotrophin Receptor Death Domain and Determination of Its Binding Sites by NMR

Biochemical and Biophysical Research Communications ◽

10.1006/bbrc.1999.0101 ◽

1999 ◽

Vol 255 (1) ◽

pp. 104-109 ◽

Cited By ~ 13

Author(s):

Leopold L. Ilag ◽

Christine Rottenberger ◽

Edvards Liepinsh ◽

Günter Wellnhofer ◽

Fritz Rudert ◽

...

Keyword(s):

Binding Sites ◽

Neurotrophin Receptor ◽

Peptide Ligand ◽

P75 Neurotrophin Receptor ◽

Death Domain ◽

Selection Of

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Structural basis of O-GlcNAc recognition by mammalian 14-3-3 proteins

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1722437115 ◽

2018 ◽

Vol 115 (23) ◽

pp. 5956-5961 ◽

Cited By ~ 15

Author(s):

Clifford A. Toleman ◽

Maria A. Schumacher ◽

Seok-Ho Yu ◽

Wenjie Zeng ◽

Nathan J. Cox ◽

...

Keyword(s):

Signaling Pathways ◽

Protein Interactions ◽

Posttranslational Modification ◽

Structural Basis ◽

Biological Processes ◽

Protein Protein Interactions ◽

Downstream Signaling ◽

Biochemical Effects ◽

Signaling Mechanisms ◽

Human Proteins

O-GlcNAc is an intracellular posttranslational modification that governs myriad cell biological processes and is dysregulated in human diseases. Despite this broad pathophysiological significance, the biochemical effects of most O-GlcNAcylation events remain uncharacterized. One prevalent hypothesis is that O-GlcNAc moieties may be recognized by “reader” proteins to effect downstream signaling. However, no general O-GlcNAc readers have been identified, leaving a considerable gap in the field. To elucidate O-GlcNAc signaling mechanisms, we devised a biochemical screen for candidate O-GlcNAc reader proteins. We identified several human proteins, including 14-3-3 isoforms, that bind O-GlcNAc directly and selectively. We demonstrate that 14-3-3 proteins bind O-GlcNAc moieties in human cells, and we present the structures of 14-3-3β/α and γ bound to glycopeptides, providing biophysical insights into O-GlcNAc-mediated protein–protein interactions. Because 14-3-3 proteins also bind to phospho-serine and phospho-threonine, they may integrate information from O-GlcNAc and O-phosphate signaling pathways to regulate numerous physiological functions.

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NMR for the design of functional mimetics of protein-protein interactions: one key is in the building of bridges

Biochemistry and Cell Biology ◽

10.1139/o98-046 ◽

1998 ◽

Vol 76 (2-3) ◽

pp. 177-188 ◽

Cited By ~ 18

Author(s):

Jianxing Song ◽

Feng Ni

Keyword(s):

Protein Interactions ◽

Binding Sites ◽

Experimental Approach ◽

Structural Information ◽

Peptide Ligands ◽

Protein Protein Interactions ◽

Binding Residues ◽

Related Proteins ◽

Binding Inhibitors

Using the design of bivalent and bridge-binding inhibitors of thrombin as an example, we review an NMR-based experimental approach for the design of functional mimetics of protein-protein interactions. The strategy includes: (i) identification of binding residues in peptide ligands by differential resonance perturbation, (ii) determination of protein-bound structures of peptide ligands by use of transferred NOEs, (iii) minimization of larger protein and peptide ligands on the basis of NMR structural information, and (iv) linkage of two weakly binding mimetics to produce an inhibitor with enhanced affinity and specificity. This approach can be especially effective for the design of potent and selective functional mimetics of protein-protein interactions because it is less likely that the surfaces of two related proteins or enzymes share two identical binding sites or regions.Key words: NMR, protein-protein interactions, functional mimetics, bridge-binding inhibitors, thrombin.

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Elucidating the druggable interface of protein−protein interactions using fragment docking and coevolutionary analysis

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1615932113 ◽

2016 ◽

Vol 113 (50) ◽

pp. E8051-E8058 ◽

Cited By ~ 36

Author(s):

Fang Bai ◽

Faruck Morcos ◽

Ryan R. Cheng ◽

Hualiang Jiang ◽

José N. Onuchic

Keyword(s):

Drug Design ◽

Protein Interactions ◽

Binding Sites ◽

Hot Spots ◽

Therapeutic Agents ◽

Molecular Probes ◽

Therapeutic Drug ◽

Protein Protein Interactions ◽

Protein Surface ◽

Fragment Docking

Protein−protein interactions play a central role in cellular function. Improving the understanding of complex formation has many practical applications, including the rational design of new therapeutic agents and the mechanisms governing signal transduction networks. The generally large, flat, and relatively featureless binding sites of protein complexes pose many challenges for drug design. Fragment docking and direct coupling analysis are used in an integrated computational method to estimate druggable protein−protein interfaces. (i) This method explores the binding of fragment-sized molecular probes on the protein surface using a molecular docking-based screen. (ii) The energetically favorable binding sites of the probes, called hot spots, are spatially clustered to map out candidate binding sites on the protein surface. (iii) A coevolution-based interface interaction score is used to discriminate between different candidate binding sites, yielding potential interfacial targets for therapeutic drug design. This approach is validated for important, well-studied disease-related proteins with known pharmaceutical targets, and also identifies targets that have yet to be studied. Moreover, therapeutic agents are proposed by chemically connecting the fragments that are strongly bound to the hot spots.

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