Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Substrates of the ATR kinase - Phosphoproteomics

ABSTRACT: Identification and validation of substrates of the ATR kinase by quantitative phosphoproteomics

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: Frederic Lamoliatte

LAB HEAD: John Rouse

PROVIDER: PXD041250 | Pride | 2024-01-15

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20230102_UniprotSwissProt_Human_CanoIso.fasta	Fasta
	20230220_FL_Rathan_JR_D01_10uL.raw	Raw
	20230220_FL_Rathan_JR_D02_10uL.raw	Raw
	20230220_FL_Rathan_JR_D03_10uL.raw	Raw
	20230220_FL_Rathan_JR_D04_10uL.raw	Raw

Items per page:

1 - 5 of 14

Similar Datasets

Nuclear substrates of the CDKL5 kinase - Phosphoproteomics

Project description:Identification of nuclear substrates of the CDKL5 kinase by quantitative phosphoproteomics

2020-12-10 | PXD022916 | Pride

NRBP1 pseudokinase binds to and activates the WNK pathway in response to osmotic stress - Figure 5B / 6A

Project description:Please refer to the manuscript for a detailed description.

2025-07-21 | PXD062619 | Pride

E3 activity-based proteomic profiling of HEK293 cells treated with ATPgammaS

Project description:RNF213 is novel transthiolating E3 ligase that is activated by ATP. To determine whether cellular RNF213 is activated by elevated ATP levels, we electroplated an E3 activity-based probe into HEK293 cells stably expressing RNF213 in a knockout background. DIA analysis was performed in cells that were coelectroporated with the poorly hydrolysable ATP analog, ATPgS, or buffer control.

2025-04-25 | PXD063291 | Pride

NRBP1 pseudokinase binds to and activates the WNK pathway in response to osmotic stress - Figure 1D/S1C

Project description:Please refer to the manuscript for a detailed description.

2025-07-21 | PXD062616 | Pride

Direct ionic stress sensing and mitigation by the transcription factor NFAT5

Project description:Homeostatic control of intracellular ionic strength is essential for protein, organelle and genome function, yet mechanisms that sense and enable adaptation to ionic stress remain poorly understood in animals. We find that the transcription factor NFAT5 directly senses solution ionic strength using a C-terminal intrinsically disordered region. Both in intact cells and in a purified system, NFAT5 forms dynamic, reversible biomolecular condensates in response to increasing ionic strength. This self-associative property, conserved from insects to mammals, allows NFAT5 to accumulate in the nucleus and activate genes that restore cellular ion content. Mutations that reduce condensation or those that promote aggregation both reduce NFAT5 activity, highlighting the importance of optimally tuned associative interactions. To investigate the composition of NFAT5 condensates in response to hypertonic stress, proteins in close proximity of NFAT5 were identified using a variant of NFAT5 fused to TurboID as bait. Hypertonic stress increases NFAT5 proximity to protein complexes belonging to the GO gene sets of “transcription coactivator activity” and “positive regulation of DNA templated transcription initiation.” Closer inspection revealed that the association between NFAT5 and two transcriptional co-activators (the mediator complex and BRD4) and RNAPII itself increased in response to hypertonic stress.

2025-04-17 | PXD052591 | Pride

Light-controlled affinity purification of protein complexes

Project description:Methods to affinity purify proteins are widely used in protein research. One important application is to identify interacting proteins of an affinity-purified protein of interest (POI) by mass spectrometry. Here, we developed an optogenetics-derived and light-controlled affinity purification method based on the light-regulated reversible protein interaction between phytochrome B (PhyB) and its phytochrome interacting factor 6 (PIF6). We engineered a truncated variant of PIF6 comprising only 22 amino acids that can be genetically fused to the POI as an affinity tag. Thereby the POI can be purified with PhyB-functionalized resin material using 660 nm light for binding and washing and 740 nm light for elution. As proof-of-concept, we expressed PIF-tagged variants of the tyrosine kinase ZAP70 in ZAP70-deficient Jurkat T cells, purified ZAP70 and associating proteins using our light-controlled system and identified the interaction partners by mass spectrometry

2019-03-18 | PXD012156 | Pride

S. cerevisiae subjected to prolonged heat stress of 37 ºC

Project description:Differential proteome composition of wild-type yeast cells (S. cerevisiae BY4741) grown at 30 ºC or 37 ºC was studied using SILAC based quantitative proteomics.

2015-04-23 | PXD001864 | Pride

Phosphoproteomic study of TOR inhibition in Chlamydomonas reinhardtii

Project description:For further details, please refer to the publication.

2018-09-11 | PXD007221 | Pride

Cryo-slicing BN-MS of rat brain mitochondrial proteins

Project description:Blue-native gel electrophoresis (BN) is a powerful method for protein separation. Combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS) it enables large-scale identification of protein complexes and their subunits. Current BN-MS approaches, however, are limited in size resolution, comprehensiveness and quantification. Here, we present a new methodology combining defined sub-mm slicing of BN gels by a cryo-microtome with high-performance LC-MS/MS and label-free quantification of proteins. Application of this cryo-slicing BN-MS approach (csBN-MS) to mitochondria from brain demonstrated a high degree of comprehensiveness, quantification accuracy and size resolution. The technique provided abundance-mass profiles for 743 mitochondrial proteins including all canonical subunits of the oxidative respiratory chain assembled into 13 distinct (super)complexes. Moreover, the data revealed COX7R as a constitutive subunit of distinct supercomplexes and identified novel assemblies of porins and TOM proteins. Together, csBN-MS enables quantitative profiling of complexomes with resolution close to the limits of native gel electrophoresis.

2015-12-01 | PXD002681 | Pride

Generative Deep Learning Pipeline Yields Potent Gram-negative Antibiotics

Project description:The escalating crisis of multiresistant bacteria demands the rapid discovery of novel antibiotics that transcend the limitations imposed by the biased chemical space of current libraries. To address this challenge, we introduce an innovative deep learning-driven pipeline for de novo antibiotic design. This unique approach leverages a chemical language model, trained on a diverse chemical space encompassing drug-like molecules and natural products, coupled with transfer learning on diverse antibiotic scaffolds to efficiently generate structurally unprecedented antibiotic candidates. Through the use of predictive modeling and expert curation, we prioritized and synthesized the most promising and readily available candidates. Notably, our efforts culminated in a lead candidate demonstrating potent activity against methicillin-resistant Staphylococcus aureus. Iterative refinement through automated synthesis of 40 derivatives yielded a suite of active compounds, including 30 with activity against S. aureus and 17 against Escherichia coli. Among these, lead compound D8 exhibited remarkable submicromolar and single-digit micromolar potency against the aforementioned pathogens, respectively. Mechanistic investigations point to the generation of radical species as its primary mode of action. This work showcases the power of our innovative deep learning framework to significantly accelerate and expand the horizons of antibiotic drug discovery.

2025-10-06 | PXD066005 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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