Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

PTMs in yeast complexes - We investigate the roles of natively present PTMs on stability of interactions in three large and essential yeast Saccharomyces cerevisiae complexes: exosome, RNA polymerase II and 26S proteasome.

ABSTRACT: We investigate the roles of natively present PTMs on stability of interactions in three large and essential yeast Saccharomyces cerevisiae complexes: exosome, RNA polymerase II and 26S proteasome.

INSTRUMENT(S): 4800 Proteomics Analyzer

ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: Piero Giansanti

LAB HEAD: Albert J. R. Heck

PROVIDER: PXD008324 | Pride | 2018-09-13

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	TT1_120612_PG_Exosome_Chymo_1_recal_371_445.wiff	Wiff
	TT1_120612_PG_Exosome_Chymo_1_recal_371_445.wiff.mtd	Wiff
	TT1_120612_PG_Exosome_Chymo_1_recal_371_445.wiff.scan	Wiff
	TT1_120612_PG_Exosome_Chymo_2_recal_371_445.wiff	Wiff
	TT1_120612_PG_Exosome_Chymo_2_recal_371_445.wiff.mtd	Wiff

Items per page:

1 - 5 of 275

Similar Datasets

Enabling Photoactivated Cross-linking Mass Spectrometric Analysis of Protein Complexes by Novel MS-cleavable Cross-linkers

Project description:Cross-linking mass spectrometry (XL-MS) is a powerful tool for studying protein-protein interactions and elucidating architectures of protein complexes. While residue-specific XL-MS studies have been very successful, accessibility of interaction regions non-targetable by specific chemistries remain difficult. Photochemistry has shown great potential in capturing those regions due to nonspecific reactivity, but low yields and high complexities of photocross-linked products have hindered their identification, limiting current studies predominantly to single proteins. Here, we describe the development of three novel MS-cleavable heterobifunctional cross-linkers, namely SDASO (Succinimidyl diazirine sulfoxide), to enable fast and accurate identification of photocross-linked peptides by MSn. The MSn-based workflow allowed SDASO XL-MS analysis of the yeast 26S proteasome, demonstrating the feasibility of photocross-linking of large protein complexes for the first time. Comparative analyses have revealed that SDASO cross-linking is robust and captures interactions complementary to residue-specific reagents, providing the foundation for future applications of photocross-linking in complex XL-MS studies.

2021-05-07 | PXD022690 | Pride

26S proteasome is conserved, therapeutically relevant mediator of mutant p53 gain-of-function in cancer

Project description:Mutant p53 proteins, resulting form frequent TP53 tumor suppressor missense mutations, possess gain-of-function activities and are among the most widespread and robust oncoproteins in human tumors. They are potentially important but understudied therapeutic targets. No studies to date have distinguished common, therapeutically relevant mutant p53 gain-of-function effects, from effects specific to different mutant variants and cell backgrounds. Here we identify 26S proteasome machinery as the common downstream effector controlled by mutant p53s in Triple Negative Breast Cancer (TNBC - aggressive carcinomas with TP53 as the most frequently mutated locus) and conserved in other human cancers. We have identified this pathway using a combination of single-model, multi-method vertical analysis (whole cell proteome, RNA sequencing an ChIP sequencing) and multi-cell line, horizontal analysis of transcriptiomes. We found that different missense mutant p53s regardless of the cell background transcriptionaly activate whole 26S proteasome machinery. Proteasome activity is significantly increased in p53 mutant versus wild-type or knockdown/null status - in cellular and mouse models as well as in human breast tumors. Increased proteasome activity leads to inhibition of tumor suppressive pathways. The control of mutant p53 over proteasome transcription and activity results in the increased resistance to proteasome inhibitors. By combining the mutant p53 targeting agents and proteasome inhibitor we were able to overcome the “bounce-back” proteasome inhibitor resistance mechanism in mutant p53 bearing TNBC cells and xenografts in vivo.

2016-05-03 | PXD001673 | Pride

26S proteasome crosslinking mass spectrometry data for mi-filter

Project description:In this project we are describing a novel mono- and intralink filter (mi-filter) that is applicable to any kind of crosslinking data and workflow. It stipulates that only proteins for which at least one monolink or intra-protein crosslink has been identified within a given dataset are considered for an inter-protein cross-link and therefore participate in a PPI. We show that this simple and intuitive filter has a dramatic effect on all types of crosslinking-data ranging from single protein complexes, over medium-complexity affinity enrichments to proteome-wide settings and significantly improves false-discovery rates for inter-protein links in all types of XL-MS data.

2022-12-14 | PXD031215 | Pride

Ubiquitin remenants identification following in vitro assay of 20S and 26S proteasome using naked and ubiquitined cyclin

Project description:A systematic and comparative study of the proteolysis products generated by purified human 26S and 20S proteasome following the in vitro cleavage of non-modified (naked), mono-ubiquitinated and poly-ubiquitinated cyclin B.

2021-11-02 | PXD028912 | Pride

Proteasome degradation of synthetic ubiquitinated globin

Project description:Analysis of the peptides resulting from proteasome-mediated degradation of K48-linked tetra ubiquitin conjugated to alpha globin

2021-08-24 | PXD004456 | Pride

Endogenous anti-tumorigenic nitro-fatty acids are a novel type of direct and potent inhibitor of the 26S proteasome

Project description:Nitro-fatty acids (NFAs) are endogenous lipid mediators causing a broad spectrum of anti-inflammatory effects by covalent modification of key proteins within inflammatory signaling pathways. Their potential as anti-tumorigenic therapeutics has recently been demonstrated in animal models of solid tumors. Herein, we evaluated the anti-tumorigenic effects of NFAs in colon carcinoma cells and other solid and leukemic tumor cell lines. NFAs inhibited the ubiquitin–proteasome system (UPS) by directly targeting the 26S proteasome, leading to polyubiquitination and inhibition of the proteasomal activities. Suppression of the UPS induced the unfolded protein response, resulting in tumor cell death. The NFA-mediated effects were rather strong, highly specific, largely irreversible, and represent a mechanistically new mode of action for UPS suppression. The present study extends the knowledge on the biological actions of NFAs as possible endogenous tumor-suppressive factors. Furthermore, NFAs might be lead structures for the design of a novel class of direct proteasome inhibitors.

2024-03-26 | PXD041458 | Pride

Secretome of Granulicatella adiacens

Project description:This project investigated the proteins secreted into extracellular medium by the oral bacterium G. adiacens.

2019-04-09 | PXD013000 | Pride

Kinetic principles of chemical cross-link formation for protein-protein interactions

Project description:Proteins play a central role in most biological processes within the cell and deciphering how they interact is key to understand their function. Cross-linking coupled to mass spectrometry is an essential tool for elucidating protein-protein interactions. Despite its importance, we still know surprisingly little about the principles that underlie the process of chemical cross-link formation itself and how it is influenced by different physicochemical factors. To understand the molecular details of cross-link formation, we have set-up a comprehensive kinetic model and carried out simulations of protein cross-linking on large protein complexes. We dissect the contribution on the cross-link yield of parameters such as amino acid reactivity, cross-linker concentration, and hydrolysis rate. Our model can compute cross-link formation based solely on the structure of a protein complex, thereby enabling realistic predictions for a diverse set of systems. We quantitatively show how cross-links and mono-links are in direct competition and how the hydrolysis rate and abundance of cross-linker and proteins directly influence their relative formation. We show how cross-links and mono-links exist in a “all-against-all” competition due to their simultaneous formation, resulting in a non-intuitive network of interdependence. We show that this interdependence is locally confined and mainly limited to direct neighbors or residues in direct vicinity. These results enable us to identify the optimal cross-linker concentration at which the maximal number of cross-links are formed. Taken together, our study establishes a comprehensive kinetic model to quantitatively describe cross-link formation for protein-protein interactions.

2024-10-10 | PXD053500 | Pride

Arabidopsis cell LC-MSMS - Proteomics analysis reveals a highly heterogeneous proteasome composition and the post-translational regulation of peptidase activity under pathogen signaling in plants

Project description:26S proteasome was affinity-purified with anti-FLAG beads and separated by 2-DE method. Each spot was cut and digested by Trypsin enzyme, which finaly applied for LC-MS/MS nalysis using a LTQ-Orbitrap XL (Thermo Scientific). The obtained spectra were compared against 35,386 sequences in The Arabidopsis Information Resource 10 (TAIR10; http://www.arabidopsis.org/) using the MASCOT server (version 2.4; Matrix Science) with the following search parameters: threshold set-off at 0.05 in the ion-score cut-off; protein identification cut-off set to two assigned spectra per predicted protein; peptide tolerance at 10 ppm; MS/MS tolerance at +/- 0.5 Da; peptide charge of 2+ or 3+; trypsin as the enzyme and allowing up to one missed cleavage; carboxymethylation on cysteines as a fixed modification and oxidation on methionine as a variable modification.

2014-07-28 | PXD000417 | Pride

Proteomics of the periodontal pathogen Prevotella intermedia secretome in biofilm and planktonic lifestyles

Project description:Protein secretion into extracellular space is an important virulence mechanism both among Gram negative and Gram-positive bacteria. Prevotella intermedia, an important species associated with periodontitis, is known to be resistant to several antibiotics. Since P. intermedia is a part of normal oral microbiota, its complete elimination is not possible. Despite the remarkable clinical significance P. intermedia has, little is known about the molecular basis for its virulence. The aim of this study was to characterize the secretome of P. intermedia in biofilm and planktonic life mode. Proteins in the secretome preparations were identified by nanoLC-ESI-MS/MS. The biofilm secretome showed 109 proteins while the planktonic secretome showed 136 proteins. The biofilm and the planktonic secretomes contained 17 and 33 signal-peptide bearing proteins, 13 and 18 lipoproteins, respectively. Proteins with predicted virulence potential were 39 in biofilm and 44 in planktonic secretomes, respectively. Gene ontology analysis revealed that the biofilm secretome displayed a markedly higher percent proteins compared to planktonic secretome in terms of cellular amino acid metabolic process, nitrogen compound metabolic process, protein binding and methyltransferase and kinase activities. In conclusion, this study revealed differences in the protein profiles of P. intermedia biofilm and planktonic secretomes. This may set a basis for asking further questions into molecular mechanisms how this species exerts its virulence potential in the oral cavity.

2022-05-19 | PXD029419 | 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