Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomic discovery of chemical probes that perturb protein complexes in human cells

ABSTRACT: Proteomic discovery of chemical probes that perturb protein complexes in human cells

PROVIDER: PRJNA909188 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR22544216.fastq.gz	Fastqsanger.gz
	SRR22544217.fastq.gz	Fastqsanger.gz
	SRR22544218.fastq.gz	Fastqsanger.gz
	SRR22544219.fastq.gz	Fastqsanger.gz
	SRR22544220.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 16

Similar Datasets

Proteomic discovery of chemical probes that perturb protein complexes in human cells II

Project description:Proteomic discovery of chemical probes that perturb protein complexes in human cells II

| PRJNA911743 | ENA

Proteomic discovery of chemical probes that perturb protein complexes in human cells

Project description:Most proteins in the human proteome lack chemical probes, and several large-scale and generalizable small-molecule binding assays have been introduced to address this problem. How compounds discovered in such “binding-first” assays affect protein function, nonetheless, often remains unclear. Here, we describe a “function first” proteomic strategy that uses size exclusion chromatography (SEC) to assess the global impact of electrophilic compounds on protein complexes in human cells. Integrating the SEC data with cysteine-directed activity-based profiling identifies changes in protein-protein interactions that are caused by site-specific liganding events, including the stereoselective engagement of cysteines in PSME1 and SF3B1 that disassemble the PA28 proteasome regulatory complex and remodel the spliceosome, respectively. Our findings thus show how multidimensional proteomic analysis of focused libraries of electrophilic compounds can expedite the discovery of chemical probes with site-specific functional effects on protein complexes in human cells. In this experiment, we probed the RNA-binding profile of DDX42 by eCLIP via an endogenously introduced HA-tag in the context of various SF3B1 ligands.

2023-04-13 | GSE220185 | GEO

Proteomic discovery of chemical probes that perturb protein complexes in human cells II

2023-04-13 | GSE220845 | GEO

Proteomic discovery of chemical probes that perturb protein complexes in human cells

Project description:Most proteins in the human proteome lack chemical probes, and several large-scale and generalizable small-molecule binding assays have been introduced to address this problem. How compounds discovered in such “binding-first” assays affect protein function, nonetheless, often remains unclear. Here, we describe a “function-first” proteomic strategy that uses size exclusion chromatography (SEC) to assess the global impact of electrophilic compounds on protein complexes in human cells. Integrating the SEC data with cysteine-directed activity-based protein profiling identifies changes in protein-protein interactions that are caused by site-specific liganding events, including the stereoselective engagement of cysteines in PSME1 and SF3B1 that disrupt the PA28 proteasome regulatory complex and stabilize a dynamic state of the spliceosome, respectively. Our findings thus show how multidimensional proteomic analysis of focused libraries of electrophilic compounds can expedite the discovery of chemical probes with site-specific functional effects on protein complexes in human cells.

2023-04-20 | PXD029655 | Pride

Pseudouridine-chemical probes-Nanopore direct RNA sequencing

Project description:Pseudouridine-chemical probes-Nanopore direct RNA sequencing

| PRJEB51316 | ENA

Global proteomic characterization of photosystem II complexes from Synechocystis 6803

Project description:In this study, we undertook a global proteomics analysis of isolated PSII complexes, comparing protein profiles of HT3 (C-terminal hexahistidine tagged CP47 protein) to those of deltaPsbV HT3, deltaPsbP HT3, and deltaPsbQ HT3. The sensitivity of these techniques allowed for identification of not only stoichiometric components of active PSII complexes, but also for the identification of proteins that are transiently associated with PSII throughout its lifecycle, such as assembly, repair, or degradation partners. From the results, we identified an operon of unknown function which contains binding domains for photosynthetic cofactors and which we have named the cofactor integration operon (cio). Upon deletion of the operon, photosynthetic capacity is decreased, indicating a function in PSII-mediated activity. Keywords: proteomic, photosystem II, cyanobacteria

2008-08-18 | GSE9577 | GEO

Investigating peptide-Coenzyme A-conjugates as chemical probes for proteomic profiling of N-terminal and lysine acetyltransferases

Project description:Acetyl groups are transferred from Acetyl-Coenzyme A (Ac-CoA) to protein N-termini and lysine side chains by N-terminal acetyltransferases (NATs) and lysine acetyltransferases (KATs), respectively. Building on lysine-CoA conjugates as KAT probes, we have synthesized peptide probes with CoA conjugated to N-terminal alanine (α-Ala-CoA), proline (α-Pro-CoA) or tri-glutamic acid (α-3Glu-CoA) units for interactome profiling of NAT complexes. These probes recruited catalytic and auxiliary subunits of the major NAT complexes from cell lysates specifically. The α-Ala-CoA probe was more specific in recruiting NAT catalytic and auxiliary subunits when compared to a lysine CoA-conjugate which bound only a subset of endogenous KATs. Interactome profiling with the α-Pro-CoA probe showed reduced NAT recruitment in favor of metabolic CoA binding proteins, while α-3Glu-CoA steered the interactome towards NAA80 and NatB. These findings agreed with the inherent substrate specificities of the target proteins and showed that N-terminal CoA-conjugated peptides are versatile probes for NAT complex profiling in lysates of physiological and pathological backgrounds.

2022-05-02 | PXD032957 | JPOST Repository

Function-first proteomic strategies for chemical probe discovery in human cells

Project description:Function-first proteomic strategies for chemical probe discovery in human cells

| PRJNA768835 | ENA

Systematic discovery of endogenous human ribonucleoprotein complexes

Project description:An exploration of human protein complexes in the presence and absence of RNA reveals endogenous ribonucleoprotein complexes

2019-09-19 | GSE137651 | GEO

Systematic discovery of endogenous human ribonucleoprotein complexes

Project description:Systematic discovery of endogenous human ribonucleoprotein complexes

| PRJNA566149 | ENA