Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Modular DNA origami compartments for the engineering of a protein unfolding and degradation pathway

ABSTRACT: Within the cell, chemical reactions are often confined and organized through a modular architecture. In this project, a cell-free nanoscale model of the proteasome was analyzed that exploits this compartmentalization principle to perform regulated protein unfolding and degradation. To this end, the protein unfolding machine p97 and the protease chymotrypsin were encapsulated in different DNA nanocompartments, and the sequential unfolding and proteolytic degradation of a model substrate, I3mEos were monitored at different time points via LC-MS/MS-based proteomics using LFQ quantification.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Farnusch Kaschani

LAB HEAD: Farnusch Kaschani

PROVIDER: PXD050816 | Pride | 2024-07-25

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ACE_0842.fasta	Fasta
	ACE_0842_JH01.raw	Raw
	ACE_0842_JH02.raw	Raw
	ACE_0842_JH03.raw	Raw
	ACE_0842_JH04.raw	Raw

Items per page:

1 - 5 of 68

Similar Datasets

Analysis of peptides formed by an extended semisynthetic protease nanomachine

Project description:Within the cell, chemical reactions are often confined and organized through a modular architecture. In this project, a cell-free nanoscale model was analyzed that exploits this compartmentalization principle to perform regulated protein unfolding and degradation. To this end, protein degradation products resulting from degradation by the protease chymotrypsin, which was encapsulated in a DNA nanocompartment, were identified and quantified using an LFQ algorithm.

2024-07-25 | PXD045825 | Pride

Unfolding the inactive X chromosome

Project description:Unfolding the inactive X chromosome

| PRJNA478454 | ENA

Epigenetic regulation by dynamic RNA G-quadruplex folding and unfolding (DMS-Seq)

Project description:Whether RNA G-quadruplexes (rG4) form extensively in vivo and what roles they play remain actively debated. Among their proposed functions is recognition of Polycomb repressive complex 2 (PRC2), but how the interaction results in epigenetic regulation is not understood. Here we demonstrate that rG4s form dynamically during ES cell differentiation and require ATRX’s helicase function to unwind competing secondary structures. Mutating ATRX causes rG4 depletion on a transcriptome-wide basis and dramatically increases gene expression. We identify and mutate rG4s within Xist RNA and mechanistically separate PRC2’s recruitment versus catalysis. Surprisingly, although rG4s recruit PRC2, unfolding the rG4 structure causes PRC2 hyperactivation, entrapment of PRC2 in the S1 chromosomal compartment, and loss of gene silencing. Thus, we link dynamic rG4 folding and unfolding to PRC2 recruitment, trans-compartmental Xist migration, regulated activation of PRC2, and whole-chromosome gene silencing.

2024-05-17 | GSE219079 | GEO

Epigenetic regulation by dynamic RNA G-quadruplex folding and unfolding (ChIP-Seq)

2024-05-17 | GSE219082 | GEO

Epigenetic regulation by dynamic RNA G-quadruplex folding and unfolding (RNA-Seq)

2024-05-17 | GSE219081 | GEO

Epigenetic regulation by dynamic RNA G-quadruplex folding and unfolding (CHART-Seq)

2024-05-17 | GSE219080 | GEO

Surveyance of apparent proteome unfolding curves via thiol labelling

Project description:Census of apparent proteome unfolding curves following urea denaturation in cell lysate using thiol reactivity probe tetraphenylethene maleimide (TPE-MI).

2022-05-19 | PXD022640 | Pride

Visualization of the Cdc48 AAA+ ATPase protein unfolding pathway: Substrate Identification

Project description:The Cdc48 AAA+ ATPase is an abundant and essential enzyme that unfolds substrates in multiple protein quality control pathways. The enzyme includes two conserved AAA+ ATPase cassettes, D1 and D2, that assemble as hexameric rings with D1 stacked above D2. Here, we report an ensemble of structures of Cdc48 affinity purified from lysate in complex with the adaptor Shp1 in the act of unfolding substrate. Our analysis reveals a continuum of structural snapshots that spans the entire translocation cycle. These data reveal new elements of Shp1-Cdc48 binding and support a “hand-over-hand” mechanism in which the sequential movement of individual subunits is closely coordinated. D1 hydrolyzes ATP and disengages from substrate prior to D2, while D2 rebinds ATP and re-engages with substrate prior to D1, thereby explaining the dominant role played by D2 in substrate translocation/unfolding.

2024-10-17 | PXD048280 | Pride

Surveyance of apparent proteome unfolding curves via thiol labelling under HSP70 inhibition

Project description:Census of apparent proteome unfolding curves following urea denaturation in cell lysate derived from control of VER155008-treated N2a cells using thiol reactivity probe tetraphenylethene maleimide (TPE-MI).

2022-05-20 | PXD030567 | Pride

Transcription forms and remodels supercoiling domains unfolding large scale chromatin structures

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-02-17 | E-GEOD-43451 | biostudies-arrayexpress