PXD049463-1

PXD049463 is an original dataset announced via ProteomeXchange.

Title	HDX-MS finds that partial unfolding with sequential domain activation controls condensation of a cellular stress marker
Description	Poly(A)-binding protein (Pab1), a canonical stress granule marker, condenses upon heat shock or starvation, promoting adaptation, The molecular basis of condensation has remained elusive due to a dearth of techniques to probe structure directly in condensates. Here we apply hydrogendeuterium exchange/mass spectrometry (HDX-MS) to investigate the molecular mechanism of Pab1’s condensation. We find that Pab1’s four RNA recognition motifs (RRMs) undergo different levels of partial unfolding upon condensation, and the changes are similar for thermal and pH stresses. Although structural heterogeneity is observed, the ability of MS to describe individual subpopulations allows us to identify which regions become partially unfolded and contribute to the condensate’s interaction network. Our data yield a clear molecular picture of Pab1’s stresstriggered condensation, which we term sequential activation, wherein each RRM becomes activated at a temperature where it partially unfolds and associates with other likewise activated RRMs to form the condensate. This model thus implies that sequential activation is dictated by the underlying free energy surface, an effect we refer to as thermodynamic specificity. Our study represents a methodological advance for elucidating the interactions that drive biomolecular condensation that we anticipate will be widely applicable. Furthermore, our findings demonstrate how condensation can use thermodynamic specificity to perform an acute response to multiple stresses, a potentially general mechanism for stress-responsive proteins.
HostingRepository	PRIDE
AnnounceDate	2024-03-22
AnnouncementXML	Submission_2024-03-21_18:30:23.931.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ruofan Chen
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2024-02-18 05:13:56	ID requested
⏵ 1	2024-03-21 18:30:24	announced

10.1073/PNAS.2321606121;

submitter keyword: hydrogen exchange, cellular stress response, mass spectrometry, Pab1,Liquid-liquid phase separation

Tobin R.
contact affiliation	Department of Biochemistry and Molecular Biology, University of Chicago
contact email	trsosnic@uchicago.edu
lab head
Ruofan Chen
contact affiliation	University of Chicago
contact email	ruofanchen0@gmail.com
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/03/PXD049463

PRIDE project URI

• PRIDE
  1. PXD049463
     1. Label: PRIDE project
     2. Name: HDX-MS finds that partial unfolding with sequential domain activation controls condensation of a cellular stress marker