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TranscriptomicsDifferential production of Type I IFN determines the reciprocal levels of IL-10 and proinflammatory cytokines produced by C57BL/6 and BALB/c macrophages
Pattern recognition receptors (PRR) detect microbial products and induce cytokines which shape the immunological response. Interleukin-12 (IL-12), tumor necrosis factor alpha (TNF-α) and IL-1β are proinflammatory cytokines which can be essential for resistance against infection, but if produced at...
ORGANISM(S): Mus musculus 
2016-09-07 | E-GEOD-79809 | biostudies-arrayexpress
ProteomicsGlobal Proteolysis During Starvation Governs Proteome Remodeling and a Survival-Regrowth Trade-off in Bacteria
Starving bacteria must synthesize stress proteins to survive, but how protein synthesis persists in the absence of nutrient influx is unclear. We show that, in Escherichia coli, carbon starvation triggers large-scale proteome remodeling, with global proteolysis supplying both the amino acids (AAs) a...
ORGANISM(S): Escherichia coli 
2026-09-30 | PXD060434 | Pride
Quantitative biology Bacteria Starvation Degradation Proteolysis 
ProteomicsThe Escherichia coli replication initiator DnaA is titrated on the chromosome
DNA replication initiation is orchestrated in bacteria by the replication initiator DnaA. Two models for regulation of DnaA activity in Escherichia coli have been proposed: the switch between an active and inactive form and the titration of DnaA on the chromosome. Although proposed decades ago, expe...
ORGANISM(S): Escherichia coli 
2025-07-28 | PXD064841 | Pride
Titration model Single-particle tracking photoactivatable localisation microscopy Switch model Dnaa protein Oric Dnaa boxes chromosome binding Data Replication initiator 
ProteomicsEstablishment of titration-based control of DNA replication in Escherichia coli
Escherichia coli couples the initiation of DNA replication with cell size by modulating the activity of the replication initiator protein DnaA. The activity of DnaA is regulated both by its interconversion between an active and inactive form and by its titration on chromosomal binding sites. Whereas...
ORGANISM(S): Escherichia coli 
2026-09-10 | PXD075568 | Pride
Hyper-replicative stress Dnaa-atp/dnaa-adp switch Replication forks Dnaa boxes Dnaa Titration-based control of dna replication 
UnknownAchieving Effective Multimodal Imaging with Rare-Earth Ion-Doped CaF2 Nanoparticles.
Not available
S-EPMC9024546 | biostudies-literature
ProteomicsEnzyme expression kinetics by Escherichia coli during transition from rich to minimal media depends on proteome reserves
Bacterial fitness depends on adaptability to changing environments. In rich growth medium, which is replete with amino acids, Escherichia coli primarily expresses protein synthesis machineries, which comprise ~40% of cellular proteins and are required for rapid growth. Upon transition to minimal med...
ORGANISM(S): Escherichia coli 
2023-02-06 | PXD035278 | Pride
Proteomics Amino acid biosynthesis Growth transition Ribosome biogenesis Coarse-grained theory 
Proteomicsselective protein O-glcNAcylation in cells by a proximity-directed O-GlcNAc transferase
O-Linked N-acetylglucosamine (O-GlcNAc) is a monosaccharide that plays an essential role in cellular signaling throughout the nucleocytoplasmic proteome of eukaryotic cells. Yet, the study of post-translational modifications like O-GlcNAc has been limited by the lack of strategies to induce O-GlcNA...
ORGANISM(S): Homo sapiens (Human) 
2021-09-08 | PXD016041 | Pride
Ogt Glycoproteomics Nanobody O-glcnac 
ProteomicsA cleavable chelation-assisted biotin probe enables the discovery of a celecoxib binding site on prostaglandin E synthase
The coxibs are a subset of non-steroidal anti-inflammatory drugs (NSAIDs) that selectively target cyclooxygenase-2 (COX-2) to inhibit prostaglandin signaling and reduce inflammation. However, only celecoxib remains in use, necessitating exploration of broader mechanisms of the coxibs. Here, we rep...
ORGANISM(S): Homo sapiens (Human) 
2024-01-04 | PXD014299 | Pride
Human 
ProteomicsA binding site hotspot map of the FKBP12–rapamycin–FRB ternary complex by photo-affinity labeling and mass spectrometry-based proteomics
Structural characterization of small molecule binding site hotspots within the global proteome is uniquely enabled by photo-affinity labeling (PAL) coupled with chemical enrichment and unbiased analysis by mass spectrometry (MS). MS-based binding site hotspot maps provide structural resolution of in...
ORGANISM(S): Homo sapiens (Human) 
2019-07-17 | PXD014319 | Pride
Photo-affinity labeling Structural protemics 
ProteomicsA binding site hotspot map of the FKBP12–rapamycin–FRB ternary complex by photo-affinity labeling and mass spectrometry-based proteomics
PRIDE > Archive > PXD013420 Project PXD013420 Download Project Files Summary Title A binding site hotspot map of the FKBP12–rapamycin–FRB ternary complex by photo-affinity labeling and mass spectrometry-based proteomics Description Structural characterization of small molecule binding site hotspo...
ORGANISM(S): Homo sapiens (Human) 
2024-01-04 | PXD014283 | Pride
Photo-affinity labeling Structural proteomics 
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