PXD030869

PXD030869 is an original dataset announced via ProteomeXchange.

Title	A Proteome-Wide Map of Chaperone-Assisted Protein Refolding in a Cytosol-like Milieu
Description	The journey by which proteins navigate their energy landscapes to their native structures is complex, involving (and sometimes requiring) many cellular factors and processes operating in partnership with a given polypeptide chain’s intrinsic energy landscape. The cytosolic environment and its complement of chaperones play critical roles in granting proteins safe passage to their native states; however, the complexity of this medium has generally precluded biophysical techniques from interrogating protein folding under cellular-like conditions for single proteins, let alone entire proteomes. Here, we develop a limited-proteolysis mass spectrometry approach paired within an isotope-labeling strategy to globally monitor the structures of refolding E. coli proteins in the cytosolic medium and with the chaperones, GroEL/ES (Hsp60) and DnaK/DnaJ/GrpE (Hsp70/40). GroEL can refold the majority (85%) of the E. coli proteins for which we have data, and is particularly important for restoring acidic proteins and proteins with high molecular weight, trends that come to light because our assay measures the structural outcome of the refolding process itself, rather than indirect measures like binding or aggregation. For the most part, DnaK and GroEL refold a similar set of proteins, supporting the view that despite their vastly different structures, these two chaperones both unfold misfolded states, as one mechanism in common. Finally, we identify a cohort of proteins that are intransigent to being refolded with either chaperone. The data support a model in which chaperone-nonrefolders have evolved to fold efficiently once and only once, co-translationally, and remain kinetically trapped in their native conformations.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:55:05.864.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Stephen Fried
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2022-01-10 04:10:12	ID requested
1	2022-11-23 14:50:05	announced
⏵ 2	2023-11-14 08:55:06	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

submitter keyword: Protein Refolding, Chaperone Refolding, GroEl/ES Folding, Proteomics

Stephen Fried
contact affiliation	Johns Hopkins University, Chemistry Department, Fried Lab, USA
contact email	sdfried@jhu.edu
lab head
Stephen Fried
contact affiliation	Johns Hopkins University
contact email	sdfried@jhu.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD030869
     1. Label: PRIDE project
     2. Name: A Proteome-Wide Map of Chaperone-Assisted Protein Refolding in a Cytosol-like Milieu