Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Boyce 4023 GlcNac Mapping Project

ABSTRACT: Bottom up proteomic analysis of gigaxonin to characterize GlcNac PTMs sites

INSTRUMENT(S): Orbitrap Fusion ETD

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: Erik Soderblom

LAB HEAD: Michael Boyce

PROVIDER: PXD012488 | Pride | 2019-12-12

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ID37834.dat	Other
	ID37834.raw	Raw
	ID39968.dat	Other
	ID39968.raw	Raw

Items per page:

1 - 4 of 4

Publications

Gigaxonin glycosylation regulates intermediate filament turnover and may impact giant axonal neuropathy etiology or treatment

Chen Po-Han PH Hu Jimin J Wu Jianli J Huynh Duc T DT Smith Timothy J TJ Pan Samuel S Bisnett Brittany J BJ Smith Alexander B AB Lu Annie A Condon Brett M BM Chi Jen-Tsan JT Boyce Michael M

JCI insight 20191126 1

Gigaxonin (also known as KLHL16) is an E3 ligase adaptor protein that promotes the ubiquitination and degradation of intermediate filament (IF) proteins. Mutations in human gigaxonin cause the fatal neurodegenerative disease giant axonal neuropathy (GAN), in which IF proteins accumulate and aggregate in axons throughout the nervous system, impairing neuronal function and viability. Despite this pathophysiological significance, the upstream regulation and downstream effects of normal and aberrant ...[more]

PMID: 31944090

Similar Datasets

Yildirim 4398 Nup153 Interactome

Project description:Identify Nup153 interacting proteins in Co-IP coupled with LC-MS/MS

2021-03-10 | PXD015441 | Pride

Global PhosphoTyrosinylated Protein Profile of Cell-Matrix Adhesion Complexes of Trabecular Meshwork Cells

Project description:Identification of Tyrosine phosphorylated proteins in the ECM enriched fraction isolated from Human TM cells. Bottom up LC-MS/MS analysis of pY antibody enriched peptides from mouse ECM.

2020-06-02 | PXD015377 | Pride

Structural and functional fine mapping of cysteines in mammalian glutaredoxin reveal a hierarchy of susceptibility to oxidative inactivation

Project description:Protein-S-glutathionylation (PSSG) is a post-translational modification involving the conjugation of glutathione to reactive protein thiols, which can modulate the activity and structure of key cellular proteins. Glutaredoxins (GLRX) are oxidoreductases that regulate this process by performing the reversible deglutathionylation reaction. Mammalian GLRX only requires the N-terminal cysteine in the thioredoxin domain to carry out deglutathionylation. However, GLRX has five cysteines that are potentially vulnerable to oxidative modification, and oxidation of GLRX itself has been reported in close association with aggregation and loss of activity. Further, the specific cysteines within GLRX that are vulnerable to oxidative modification and their relative reactivities with oxidants remain unknown. Herein, we utilized various molecular modeling approaches coupled with site-directed mutagenesis of each cysteine both individually and in combination to address how the five cysteines present in GLRX influence the enzyme’s biological activity and susceptibility to dimerization and inactivation. We report that mutation of cysteine 26 (C26) to serine of murine GLRX1 confers a higher rate of deglutathionylation. We further demonstrate that C8 and C83 are targets for PSSG in vitro while C79 is less vulnerable due to steric hindrance. Hydrogen peroxide also caused inactivation of GLRX that was only protected against with mutation of C8 or C83. Both experimental and modeling evidence indicates C8 contributes to dimer formation. Lastly, combinatorial mutation of C8, C26, and C83 results in increased biological activity and resistance to aggregation and oxidative inactivation. Overall, these results from our corroborated experimental and computational studies have valuable implications for the use of GLRX as a therapeutic in settings of dysregulated protein glutathionylation.

2023-10-24 | PXD026486 | Pride

Developing In Vivo Cross-linking Mass Spectrometry (XL-MS) to Decipher Protein Interaction Landscapes at the Proteome Scale

Project description:We have developed a new and robust in vivo cross-linking mass spectrometry (XL-MS) that utilizes a multifunctional MS-cleavable cross-linker to enable the efficient capture, enrichment, and identification of in vivo cross-linked peptides at the whole proteome scale.

2021-07-30 | PXD012788 | Pride

Profiling primary and secondary targets of ARF7 and ARF19 in Arabidopsis thaliana roots

Project description:Arabidopsis thaliana AF7/ARF19 double knockout with ARF7 reintroduced under its own promotor with a glucocorticoid receptor added were treated with Auxin, Dexamethazone and cycloheximide to determine primary and secondary ARF7 auxin sensitive downstream targets

2015-04-01 | E-MTAB-3451 | biostudies-arrayexpress

An 8-Mercaptoquinoline Motif Enriches Minichromosome Maintenance Complex Components as Significant Metalloprotein Targets in Live Cells

Project description:Affinity-based probes are valuable tools for detecting binding interactions between small molecules and proteins in complex biological environments. Metalloproteins are a class of therapeutically significant biomolecules which bind metal ions as part of key structural or catalytic domains and are compelling targets for study. However, there is currently a limited range of chemical tools suitable for profiling the metalloproteome. Here, we describe the preparation and application of a novel, photoactivatable affinity based probe for detection of a subset of previously challenging to engage metalloproteins. The probe, bearing an 8 mercaptoquinoline metal chelator, was anticipated to engage several zinc metalloproteins, including the 26S proteasome subunit Rpn11. Upon translation of the labelling experiment to mammalian cell lysates, proteomic analysis revealed that several metalloproteins were competitively enriched. An 8-mercaptoquinoline diazirine probe was found to effectively enrich multiple components of the minichromosome maintenance complex, a zinc metalloprotein assembly with helicase activity essential to DNA replication.

2024-06-28 | PXD052663 | Pride

Gene expression profiles for genetically engineered human hepatoma HepG2/8F_HS cells with or without heat treatment, cultured as monolayer or spheroids

Project description:We developed genetically engineered HepG2/8F_HS cells, in which eight liver-enriched transcription factor (LETF) genes—hepatocyte nuclear factor (HNF)-1α, HNF-1β, HNF-3β, HNF-4α, HNF-6, CCAAT/enhancer binding protein (C/EBP)-α, C/EBP-β and C/EBP-γ— under the control of TRE/PCMVmin promoter were introduced into a previously developed human hepatoma cell line (HepG2-HSP). The heat-inducible synthetic promoter system was introduced into HepG2 cells and tetracycline-responsive transactivator (tTA) and enhanced green fluorescent protein (EGFP) were expressed via positive feedback of tTA transcription in response to heat treatment. HepG2/8F_HS cells can induce high liver functions by heat treatment via overexpression of LETF genes.

2022-04-04 | E-MTAB-11486 | biostudies-arrayexpress

A novel integrated extraction protocol for multi-omic studies in heavily degraded samples

Project description:The combination of multi-omic techniques, e.g. genomics, transcriptomics, proteomics, metabolomics and epigenomics has revolutionised studies in medical research. These are employed to support biomarker discovery, better understand molecular pathways and identify novel drug targets. Despite concerted efforts in integrating omic datasets, there is an absence for the integration of all four biomolecules in a single extraction protocol. Here, we demonstrate for the first time a novel, minimally destructive integrated protocol for the simultaneous extraction of artificially degraded DNA, proteins, lipids and metabolites from pig brain samples. We used an MTBE-based approach to separate lipids and metabolites, followed by subsequent isolation of DNA and proteins. We have validated this protocol against standalone extraction protocols and show comparable or higher yield of all four biomolecules. This integrated protocol is key towards facilitating preservation of irreplaceable samples while promoting downstream analyses and successful data integration by removing bias from univariate dataset noise and varied distribution characteristics. Keywords: deg

2024-08-09 | PXD047606 | Pride

Targeting mitochondrial reactive oxygen species alleviates allergic airway disease in a mouse model of obese allergic asthma

Project description:Obesity is associated with severe, difficult to control asthma, and increased airway oxidative stress. Mitochondrial reactive oxygen species (mROS) are an important source of oxidative stress leading us to hypothesize that targeting mROS in obese allergic asthma might be an effective treatment strategy. Using a mouse model of house dust mite (HDM) induced allergic airway disease in mice fed a low- (LFD) or high-fat diet (HFD), and the mitochondrial antioxidant MitoQuinone (MitoQ); we investigated the effects of obesity and mROS on airway inflammation, remodelling and airway hyperreactivity (AHR). HDM induces airway inflammation, remodelling and hyperreactivity in both lean and obese mice. Obese allergic mice showed increased lung tissue eotaxin levels, airway tissue eosinophilia and AHR when compared to lean allergic mice. MitoQ reduced markers of airway inflammation, remodelling and hyperreactivity in both lean and obese allergic mice, and tissue eosinophilia in obeseHDM mice. mROS regulates cell signalling by protein oxidation of multiple downstream targets: MitoQ reduced HDM-induced cysteine-sulfenylation of several proteins including those involved in the unfolded protein response (UPR). In summary, mROS mediates the development of allergic airway disease and hence MitoQ might be effective for the treatment for asthma, and specific features of obese asthma.

2023-06-02 | PXD029715 | Pride

Ablation or Inhibition of Protein Disulfide Isomerase A3 (PDIA3) in Aberrant Club Cells Attenuates Osteopontin (SPP1) Production and Pulmonary Fibrosis

Project description:Rationale: The role of club cells in the pathology of Idiopathic Pulmonary Fibrosis IPF is not well understood. PDIA3, an endoplasmic reticulum (ER) based redox chaperone catalyzes the cysteine disulfide bonds (-S-S-) in various fibrosis-related proteins; however, mechanisms of action of PDIA3 in pulmonary fibrosis is not fully elucidated. Objectives: To examine the role of club cells and PDIA3 in the pathogenesis of pulmonary fibrosis (PF) and therapeutic potential of inhibition of PDIA3 in PF. Methods: The impact of PDIA3 and aberrant club cells in PF was studied by retrospective analysis of human transcriptome data from LGRC, and specific deletion and inhibition of PDIA3 in club cells and blocking Osteopontin (SPP1) downstream of PDIA3 in mice. Measurements and Main Results: The PDIA3 along with club cell secretory protein (SCGB1A1 or CCSP) signatures are upregulated in IPF compared to control patients, and PDIA3 increases correlate with a decrease in lung function in IPF patients. The Bleomycin (BLM) model of PF showed increases in aberrant CCSP and PDIA3 positive cells in the lung parenchyma. Ablation of Pdia3, specifically in CCSP cells, decreases CCSP cells along with PF in mice. The therapeutic administration of a PDI inhibitor LOC14 reversed the BLM-induced CCSP cells and PF in mice. The proteomic screen of the PDIA3 partners revealed SPP1 as a major interactor in PF. Blocking SPP1 attenuated the development of PF in mice. Conclusions: Collectively, this study demonstrates a new relationship of club cells, with PDIA3, SPP1, and a putative pathological function of club cells in pulmonary fibrosis.

2021-11-11 | PXD021715 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data