PXD037995-2

PXD037995 is an original dataset announced via ProteomeXchange.

Title	Folding stabilities of ribosome-bound nascent polypeptides probed by mass spectrometry
Description	The folding of most proteins occurs during the course of their translation while their tRNA-bound C-termini are embedded in the ribosome. How the close proximity of nascent proteins to the ribosome influences their folding thermodynamics remains poorly understood. Here, we have developed a mass spectrometry-based approach for determining the stabilities of nascent polypeptide chains using methionine oxidation as a folding probe. This approach enables quantitative measurements sub-global folding stabilities of ribosome nascent chains (RNCs) within complex protein mixtures and extracts. To validate the methodology, we analyzed the folding thermodynamics of three model proteins (DHFR, CheY and DinB) in soluble and ribosome-bound states. The data indicated that the ribosome can significantly alter the stability of nascent polypeptides. Ribosome-induced stability modulations were highly variable among different folding domains and were dependent on localized charge distributions within nascent polypeptides. The results implicated electrostatic interactions between the ribosome surface and nascent polypeptides as the cause of ribosome-induced stability modulations. The study establishes a robust proteomic methodology for analyzing localized stabilities within ribosome-bound nascent polypeptides and sheds light on how the ribosome influences the thermodynamics of protein folding.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_06:41:28.358.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ruiyue Tan
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	monohydroxylated residue; formylated residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2022-11-07 09:27:57	ID requested
1	2023-08-08 18:15:35	announced
⏵ 2	2023-11-14 06:41:28	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

submitter keyword: Protein stability

Co-translational protein folding

Ribosome

Translation

Proteomics

Mass spectrometry (MS)

Methionine oxidation

Sina Ghaemmaghami
contact affiliation	Ghaemmaghami lab, biology department, University of Rochester
contact email	sina.ghaemmaghami@rochester.edu
lab head
Ruiyue Tan
contact affiliation	University of Rochester
contact email	rtan12@ur.rochester.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD037995
     1. Label: PRIDE project
     2. Name: Folding stabilities of ribosome-bound nascent polypeptides probed by mass spectrometry