Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

HeLa cell protein interactome of polyamine affinity-based probes.

ABSTRACT: HeLa cells were incubated with affinity-based probes designed as synthetic analogs of endogenous metabolites: putrescine, spermidine, and spermine, while a monoamine compound served as a control. Probe-protein interactions were captured in situ using UV-induced crosslinking. After cell lysis, biorthogonal ligation and affinity purification of the probe-conjugated proteins were carried out. These proteins were digested with trypsin, and the resulting peptides were labeled with TMT. Proteins that showed enrichment in samples treated with polyamine probes, compared to those treated with the monoamine control, were identified as polyamine-binding proteins.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Hela Cell

SUBMITTER: Remigiusz Serwa

LAB HEAD: Remigiusz A. Serwa

PROVIDER: PXD058706 | Pride | 2025-09-22

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	RS51B_powt_z_RS1.raw	Raw
	RS51B_powt_z_RS1_reinj.raw	Raw
	checksum.txt	Txt
	txt.zip	Other

Items per page:

1 - 4 of 4

Similar Datasets

Temporal control of acute protein aggregate turnover by UBE3C and NRF1-dependent proteasomal pathways

Project description:A hallmark of neurodegenerative diseases such as Parkinson’s Disease is the progressive loss of proteostasis, leading to the conversion of misfolded proteins into aggregates and subsequent cytotoxicity. To combat this toxicity, cells have evolved degradation pathways (ubiquitin-proteasome system and autophagy) that detect and degrade misfolded proteins. Here, we find that aggregation burden dictates the activation of proteasome-dependent quality control pathways. Initial misfolded proteins, enriched in oligomers, utilize UBE3C-dependent proteasomal degradation, while higher aggregation levels, enriched in larger insoluble structures, activate the NRF1 transcription factor to increase proteasome subunit transcription, and subsequent degradation capacity of cells. The role of UBE3C and NRF1 in aggregation clearance may provide therapeutic targets aimed to preventing neurodegenerative disease.

2024-10-09 | PXD055227 | Pride

Chemoproteomics Reveals Chemical Diversity and Dynamics of 4-Oxo-2-nonenal Modifications in Cells

Project description:4-Oxo-2-nonenal (ONE) derived from lipid peroxidation modifies nucleophiles and transduces redox signaling by its reactions with proteins. However, the molecular interactions between ONE and complex proteomes and their dynamics in situ remain largely unknown. Here we de-scribe a quantitative chemoproteomic analysis of protein adduction by ONE in cells, in which the cellular target profile of ONE is mimicked by its alkynyl surrogate. The analysis reveals four types of ONE-derived modifications in cells, including ketoamide and Schiff-base adducts to lysine, Michael adducts to cysteine, and a novel pyrrole adducts to cysteine. ONE-derived adducts co-localize and crosstalk with many histone marks and redox sensitive sites. All four types of modifications derived from ONE can be reversed site-specifically in cells. In summary, our study provides much-needed mechanistic insights into the cellular signaling and potential toxicities associated with this important lipid derived electrophile.

2022-02-24 | PXD006680 | Pride

Targeting Ras-, Rho-, and Rab-Family GTPases via a Conserved Cryptic Pocket

Project description:The family of Ras-like GTPases consists of over 150 different members, regulated by an even larger number of guanine exchange factors (GEFs) and GTPase-activating proteins (GAPs) which comprise cellular switch networks that govern cell motility, growth, polarity, protein trafficking, and gene expression. Efforts to develop selective small molecule probes and drugs for these proteins have been hampered by the high affinity of GTP and lack of allosteric regulatory sites. This paradigm was recently challenged by the discovery of a cryptic allosteric pocket in the Switch II region of K-Ras. Here we ask if similar pockets are present in GTPases beyond K-Ras. We systematically surveyed members of the Ras-, Rho-, and Rab-family of GTPases and found that many GTPases exhibit targetable Switch II pockets. Notable differences in the composition and conservation of key residues offer potential for the development of optimized inhibitors for many members of this previously undruggable family.

2025-05-07 | PXD054414 | Pride

A small-molecule inhibitor targeting AKR1C1 suppresses cell proliferation and metastasis in non-small cell lung cancer

Project description:Non-small cell lung cancer (NSCLC) is one of the leading causes of cancer-related deaths, characterized by highly invasion and metastasis. Aldo-keto reductase family 1 member C1 (AKR1C1) plays an important role in cancer cell proliferation and metastasis and has gained attention as an anticancer drug target. Here we report that the natural sesquiterpene lactone alantolactone (ALA) was shown to bind directly to AKR1C1 through the Proteome Integral Solubility Alteration (PISA) analysis, a label-free target identification approach based on thermal proteome profiling.

2022-05-20 | PXD031082 | Pride

Protein interactions with HA-tagged cytoplasmic dynein-2 DATASET2

Project description:To identify those proteins interacting with the cytoplasmic dynein-2 using mammalian cell lines stably expressing HA-tagged intermediate chain subunits, WDR34 (DYNC2I2) or WDR60 (DYNC2I1).

2023-01-24 | PXD031152 | Pride

The Proteomics landscape of human aorta and mice aorta

Project description:NOTCH1 mutation and deficiency is etiologically associated to aortopathy combined with bicuspid aortic valve malformation; currently no medication is available for its treatment. Therefore, in this study, our focus turns to seeking the key downstream target genes and pharmacotherapeutic possibilities for NOTCH1 deficient aortopathy.

2024-12-10 | PXD044019 | Pride

Pharmacological Targeting of Casein Kinase 1δ Suppresses Oncogenic NRAS-Driven Melanoma

Project description:Activating mutations in NRAS account for 15-20% of melanoma, yet effective anti-NRAS therapies are still lacking. In this study, we unveil the casein kinase 1δ (CK1δ) as an uncharacterized regulator of oncogenic NRAS mutations, specifically Q61R and Q61K, which are the most prevalent NRAS mutations in melanoma. The genetic ablation or pharmacological inhibition of CK1δ markedly destabilizes NRAS mutants and suppresses their oncogenic functions. Moreover, we identify USP46 as a bona fide deubiquitinase of NRAS mutants. Mechanistically, CK1δ directly phosphorylates USP46 and activates its deubiquitinase activity towards NRAS mutants, thus promoting oncogenic NRAS-driven melanocyte malignant transformation and melanoma progression in vitro and in vivo. Our findings underscore the significance of the CK1δ-USP46 axis in stabilizing oncogenic NRAS mutants and provide preclinical evidence that targeting this axis holds promise as a therapeutic strategy for human melanoma harboring NRAS mutations.

2024-09-19 | PXD051431 | Pride

Proteins identified by LC-MS/MS analysis to associate with RecJ4-StrepII (vs. empty vector).

Project description:RecJ4 association with RecJ3, RNase J and Cdc48A investigated by pullingown strep tagged-RecJ4 with its partner proteins

2023-06-22 | PXD019933 | Pride

RNase J, RecJ3, RNase J, RecJ3, Cdc48a and Cas7 co-purify with RecJ4-StrepII in the presence of γATP. and Cas7 co-purify with RecJ4-StrepII in the presence of γATP.

Project description:detecting core complex formation for RecJ3/4 and RNase J form a core complex.

2023-06-22 | PXD019932 | Pride

Proteins associated with Cdc48A identified by LC-MS\MS data

Project description:His6-Cdc48a and associated proteins purified from H. volcanii. A) SDS- PAGE of proteins purified by Ni2+ -chromatography. H. volcanii carrying empty vector control (H1209-pJAM202c, lane 1) and ectopically expressing His6-Cdc48a (H1209- pJAM1409, lane 2). Red bars indicate regions of gel excised. B) Proteins identified in gel slices by LC-MS/MS analysis. Criteria for protein inclusion: FDR < 0.01%, normalized total spectra minus control > 50, protein threshold > 99% and 2 peptide minimum. Based on spectral counting, Cdc48a and DUF111 were most abundant in regions (a) and (b), respectively, as indicated. DHS1, deoxyhypusine synthase. DUF111, Cdc48a gene neighbor of unknown function. TnaA, tryptophanase; Rps3, ribosomal protein S3; n.d., not detected.

2023-06-22 | PXD019906 | Pride