NAMPT translocates to the nucleus following interaction with GAPDH to sustain NAD synthesis
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Orbitrap Fusion Lumos
ORGANISM(S): Mus Musculus (ncbitaxon:10090)
SUBMITTER: 
Armando Genazzani
PROVIDER: MSV000084426 | MassIVE | Mon Oct 07 03:19:00 BST 2019
REPOSITORIES: MassIVE
Similar Datasets
Project description:Chemical cross-linking coupled with mass spectrometry has emerged as a powerful strategy which enables global profiling of protein interactome with direct interaction interfaces in complex biological systems. The alkyne-tagged enrichable cross-linkers are preferred to improve the coverage of low-abundance cross-linked peptides, combined with click chemistry for biotin conjugation to allow the cross-linked peptides enrichment. Herein, together with in vivo chemical cross-linking by alkyne-tagged cross-linker, we explored the click chemistry-based enrichment approaches on protein and peptide level with three cleavable click chemistry ligands, respectively. By comparison, the approach of protein-based click chemistry conjugation with acid-cleavable tag was demonstrated to permit the most cross-linked peptides identification. The advancement of this strategy enhanced the proteome-wide cross-linking analysis, constructing a 5,518 protein-protein interactions network among 1,871 proteins with wide abundance distribution in cell. Therefore, all these results demonstrated a guideline value of our work for efficient cross-linked peptides enrichment, thus facilitated the in-depth profiling of protein interactome for functional analysis.
2022-07-15 | PXD035355 | JPOST Repository
Project description:Analysis of the structure of the MTA1 complex using chemical cross-linking mass spectrometry
2022-11-30 | PXD038459 |
Project description:Pull-down of poly(A)-mRNA cross linked proteins using two cross-linking methods (conventional cross-linking and PAR-cross-linking) to identify all mRNA-binding proteins (GO:0003729). The provided data is quantitative proteomic data for comparison of cross-linking and control samples.
2012-08-14 | E-MTAB-869 | biostudies-arrayexpress
Project description:Mass spectrometry analysis in combination with the site-specific chemical cross-linking has emerged as a powerful method in study of three-dimensional structure of protein complex and in mapping of protein-protein interactions (PPIs). Even though in vitro cross-linking experiments have been widely applied to investigate the specific interactions of a bait protein and its targets, the measurement of in vivo protein tertiary structure and PPIs has been problematic and strenuous due to the dynamic nature of the biological systems and a lower number of cross-linked peptides that can be isolated via MudPIT (Multidimensional Protein Identification Technology) for mass spectrometry analysis. Using Arabidopsis thaliana as a model multicellular eukaryotic organism, we have attempted to develop an improved in vivo chemical cross-linking and mass spectrometry (or IPXL-MS) workflow, which aims at optimizing the in vivo cross-linking conditions, establishing of a MudPIT procedure for enrichment of cross-linked peptides, and developing an integrated software program to identify the in planta chemical cross-linked peptides, by which three pairs of in vivo cross-linked peptides of high-confidence has been identified twice from two independent biological replicates. This work has demarked a beginning of alternative proteomic approach in study of in vivo protein tertiary structure and PPIs in higher plants. This in vivo cross-linking approach may be applied into other model multicellular organisms, such as mouse, for molecular systems biological research.
2016-06-28 | PXD003658 | Pride
Project description:Chemical cross-linking coupled with mass spectrometry has emerged as a powerful strategy which enables global profiling of protein interactome with direct interaction interfaces in complex biological systems. The alkyne-tagged enrichable cross-linkers are preferred to improve the coverage of low-abundance cross-linked peptides, combined with click chemistry for biotin conjugation to allow the cross-linked peptides enrichment. However, a systematic evaluation on the efficiency of click approaches (protein-based or peptide-based) and diverse cleavable click chemistry ligands (acid, reduction, photo) for cross-linked peptides enrichment and release is lacking. Herein, together with in vivo chemical cross-linking by alkyne-tagged cross-linker, we explored the click chemistry-based enrichment approaches on protein and peptide level with three cleavable click chemistry ligands, respectively. By comparison, the approach of protein-based click chemistry conjugation with acid-cleavable tag was demonstrated to permit the most cross-linked peptides identification. The advancement of this strategy enhanced the proteome-wide cross-linking analysis, constructing a 5,518 protein-protein interactions network among 1,871 proteins with wide abundance distribution in cell. Therefore, all these results demonstrated a guideline value of our work for efficient cross-linked peptides enrichment, thus facilitated the in-depth profiling of protein interactome for functional analysis.
2022-07-14 | PXD035317 | JPOST Repository
Project description:Cross-linking mass spectrometry of the sheep Sec61-TRAP complex
| MSV000090438 | MassIVE
Project description:Cross-linking MS data from the yeast Mediator complex. Cross-linking was performed using either BS3 or 1:1 mix of d0:d12 DSS. Includes unfractionated, SEC enriched, high pH reverse phase fractionated, DDA and inclusion list generated files.
2015-08-13 | MSV000079237 | MassIVE
Project description:we used cross-linking mass spectrometry to determine the molecular architecture of the Dam1 complex alone and bound to microtubules. Our data provide a map of the subunit arrangement of the Dam1 complex. Analysis of the Dam1 complex assembled around microtubules reveals that the Spc34 and Ask1 subunits are likely involved in self -assembly whereas the Duo1 and Dam1 subunits both interact with microtubules. We also demonstrate that the C termini of Dam1 and Duo1 provide the microtubule binding properties to the Dam1 complex. Our data provides key information on the organization of the Dam1 complex around microtubules.
2016-03-01 | PXD003678 | Pride
Project description:Raw data of cross linking sites mapping of TMEM175-LAMP1 complex.
2023-04-10 | MSV000091672 | MassIVE
Project description:In response to starvation, cells undergo a metabolic shift to ensure their survival by shutting down protein synthesis and activating catabolic processes, including autophagy, to degrade proteins and recycle nutrients. These processes, however, do require protein synthesis. We asked how this fundamental conflict is resolved. Upon starvation, cells activate the Integrated Stress Response (ISR) and inhibit mammalian target of rapamycin complex 1 (mTORC1). The ISR inhibits protein translation through the phosphorylation of the alpha subunit of eukaryotic translation initiation factor 2 (eIF2), whereas mTORC1 inhibition induces activation of the transcription factors TFEB/TFE3. We discovered that PPP1R15A (aka GADD34), a member of the protein phosphatase 1 complex (PP1) is a direct and early target of TFEB. GADD34 recruits PP1 to dephosphorylate eIF2 and thus fine-tunes protein synthesis to enable translation of the transcriptional program induced by starvation leading to a sustained autophagic flux.
2020-09-30 | PXD016149 | Pride